diff options
501 files changed, 3604 insertions, 1879 deletions
diff --git a/app-admin/eselect/ChangeLog b/app-admin/eselect/ChangeLog index 47d1515ce..79d1aacfc 100644 --- a/app-admin/eselect/ChangeLog +++ b/app-admin/eselect/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/app-admin/eselect/ChangeLog,v 1.179 2011/01/22 21:38:52 ulm Exp $ +*eselect-1.4.4-r102 (06 Jun 2015) + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> +eselect-1.4.4-r102.ebuild, + -eselect-1.4.4-r100.ebuild, -eselect-1.4.4-r101.ebuild, + -files/eselect-1.4.2-alternatives.patch, + files/eselect-1.4.4-alternatives.patch: + app-admin/eselect: Add latest patch + *eselect-1.4.4-r101 (24 May 2015) 24 May 2015; Justin Lecher <jlec@gentoo.org> +eselect-1.4.4-r101.ebuild, diff --git a/app-admin/eselect/eselect-1.4.4-r100.ebuild b/app-admin/eselect/eselect-1.4.4-r100.ebuild deleted file mode 100644 index 8001cf173..000000000 --- a/app-admin/eselect/eselect-1.4.4-r100.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools eutils bash-completion-r1 - -DESCRIPTION="Gentoo's multi-purpose configuration and management tool" -HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" -SRC_URI="http://dev.gentoo.org/~ulm/eselect/${P}.tar.xz" - -LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-3.0 )" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="doc emacs vim-syntax" - -RDEPEND="sys-apps/sed - || ( - sys-apps/coreutils - sys-freebsd/freebsd-bin - app-misc/realpath - )" -DEPEND="${RDEPEND} - app-arch/xz-utils - doc? ( dev-python/docutils )" -RDEPEND="!app-admin/eselect-news - ${RDEPEND} - sys-apps/file - sys-libs/ncurses" - -PDEPEND="emacs? ( app-emacs/eselect-mode ) - vim-syntax? ( app-vim/eselect-syntax )" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-1.4.2-alternatives.patch - AT_M4DIR="." eautoreconf -} - -src_compile() { - emake - use doc && emake html -} - -src_install() { - emake DESTDIR="${D}" install - newbashcomp misc/${PN}.bashcomp ${PN} - dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt - use doc && dohtml *.html doc/* - - # needed by news module - keepdir /var/lib/gentoo/news - if ! use prefix; then - fowners root:portage /var/lib/gentoo/news - fperms g+w /var/lib/gentoo/news - fi - - # band aid for prefix - if use prefix; then - cd "${ED}"/usr/share/eselect/libs || die - sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die - fi -} - -pkg_postinst() { - # fowners in src_install doesn't work for the portage group: - # merging changes the group back to root - if ! use prefix; then - chgrp portage "${EROOT}/var/lib/gentoo/news" \ - && chmod g+w "${EROOT}/var/lib/gentoo/news" - fi -} diff --git a/app-admin/eselect/eselect-1.4.4-r101.ebuild b/app-admin/eselect/eselect-1.4.4-r102.ebuild index 67b835c52..67b835c52 100644 --- a/app-admin/eselect/eselect-1.4.4-r101.ebuild +++ b/app-admin/eselect/eselect-1.4.4-r102.ebuild diff --git a/app-admin/eselect/files/eselect-1.4.2-alternatives.patch b/app-admin/eselect/files/eselect-1.4.2-alternatives.patch deleted file mode 100644 index 3f4a34bcf..000000000 --- a/app-admin/eselect/files/eselect-1.4.2-alternatives.patch +++ /dev/null @@ -1,616 +0,0 @@ -Index: bin/eselect.in -=================================================================== ---- bin/eselect.in (revision 863) -+++ bin/eselect.in (working copy) -@@ -22,10 +22,15 @@ - # Where are modules installed by default? - ESELECT_DEFAULT_MODULES_PATH="${ESELECT_DATA_PATH}/modules" - -+# Where are auto-generated modules placed? (e.g. from alternatives-2.eclass) -+ESELECT_AUTO_GENERATED_MODULES_PATH="${ESELECT_DEFAULT_MODULES_PATH}/auto" -+ - # Look in these places for modules --ESELECT_MODULES_PATH=( \ -- "${HOME}/.eselect/modules" \ -- "${ESELECT_DEFAULT_MODULES_PATH}" ) -+ESELECT_MODULES_PATH=( -+ "${HOME}/.eselect/modules" -+ "${ESELECT_DEFAULT_MODULES_PATH}" -+ "${ESELECT_AUTO_GENERATED_MODULES_PATH}" -+) - - # Look in this place for libraries - ESELECT_CORE_PATH="${ESELECT_DATA_PATH}/libs" ---- bin/Makefile.am.orig 2013-09-02 14:35:05.328684465 +0400 -+++ bin/Makefile.am 2013-09-02 14:49:50.895842067 +0400 -@@ -4,6 +4,7 @@ - dosed = @SED@ -e 's%\@BASH\@%$(BASH)%g' \ - -e 's%\@DATADIR\@%$(datadir)%g' \ - -e 's%\@EPREFIX\@%$(EPREFIX)%g' \ -+ -e 's%\@LIBEXECDIR\@%$(datadir)%g' \ - -e 's%\@VERSION\@%$(VERSION)$(EXTRAVERSION)%g' - - % : %.in -Index: libs/Makefile.am -=================================================================== ---- libs/Makefile.am (revision 863) -+++ libs/Makefile.am (working copy) -@@ -1,6 +1,7 @@ - eselectlibsdir = $(datadir)/$(PACKAGE_NAME)/libs/ - - eselectlibs_DATA = \ -+ alternatives.bash \ - config.bash \ - core.bash \ - default.eselect \ -@@ -14,6 +15,7 @@ - tests.bash - - EXTRA_DIST = \ -+ alternatives.bash.in \ - config.bash.in \ - core.bash.in \ - default.eselect.in \ -@@ -30,7 +32,8 @@ - -e 's%\@SED\@%@SED@%g' \ - -e 's%\@PORTAGEQ\@%@PORTAGEQ@%g' \ - -e 's%\@ENV_UPDATE\@%@ENV_UPDATE@%g' \ -- -e 's%\@CANONICALISE\@%@CANONICALISE@%g' -+ -e 's%\@CANONICALISE\@%@CANONICALISE@%g' \ -+ -e 's%\@sysconfdir\@%@sysconfdir@%g' - - %.bash : %.bash.in - @$(dosed) $< > $@ ---- libs/alternatives.bash.in.orig 1970-01-01 01:00:00.000000000 +0100 -+++ libs/alternatives.bash.in 2011-09-06 18:55:43.000000000 +0100 -@@ -0,0 +1,550 @@ -+# Copyright 2008 Mike Kelly -+# Copyright 2009 David Leverton -+# Copyright 2010 Bo Ørsted Andresen -+# 2010: Adapted to eselect Sebastien Fabbro (who doesn't like copyrights) -+# Distributed under the terms of the GNU General Public License v2 -+ -+inherit config output path-manipulation -+ -+ALTERNATIVESDIR_ROOTLESS="@sysconfdir@/env.d/alternatives" -+ALTERNATIVESDIR="${EROOT}${ALTERNATIVESDIR_ROOTLESS}" -+ -+get_current_provider() { -+ local dieprefix="Could not determine current provider for ${ALTERNATIVE}" -+ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then -+ local provider=$(readlink "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: readlink ${symlink} failed") -+ [[ ${provider} == */* ]] && die "${dieprefix}: malformed target for ${symlink}" -+ -+ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} || -+ ( -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} && ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ) ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} is not a directory" -+ fi -+ -+ echo "${provider}" -+ -+ elif [[ -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current is not a symlink" -+ fi -+} -+ -+compare_importance() { -+ local IFS=. -+ local a=( ${1} ) b=( ${2} ) -+ local -i i=0 -+ while (( i<${#a[@]} && i<${#b[@]} )); do -+ if (( a[i]<b[i] )); then -+ return 0 -+ elif (( a[i]>b[i] )); then -+ return 1 -+ fi -+ i+=1 -+ done -+ (( i<${#b[@]} )) -+} -+ -+sort_providers() { -+ local begin=${1:-0} -+ local count=${2:-${#providers[@]}} -+ [[ ${count} -le 1 ]] && return 0 -+ sort_providers ${begin} $((count/2)) -+ sort_providers $((begin+count/2)) $((count-count/2)) -+ local left=( "${providers[@]:begin:count/2}" ) -+ local right=( "${providers[@]:begin+count/2:count-count/2}" ) -+ local -i x i=0 j=0 -+ for (( x=begin; x<begin+count; ++x )); do -+ if (( j>=${#right[@]} )) || { (( i<${#left[@]} )) && compare_importance "${left[i]%%:*}" "${right[j]%%:*}"; }; then -+ providers[x]=${left[i++]} -+ else -+ providers[x]=${right[j++]} -+ fi -+ done -+} -+ -+get_providers() { -+ local p= importance providers=() -+ for p in "${ALTERNATIVESDIR}/${ALTERNATIVE}"/* ; do -+ [[ -d ${p} && ! -L ${p} ]] || continue -+ p=${p##*/} -+ -+ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") -+ importance=${importance:-0} -+ [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" -+ -+ providers+=( "${importance}:${p}" ) -+ done -+ -+ sort_providers -+ for (( p=${#providers[@]}-1 ; p>=0 ; --p )); do -+ echo "${providers[p]#*:}" -+ done -+} -+ -+### show action ### -+describe_show() { -+ echo "Show the current provider in use for ${ALTERNATIVE}" -+} -+ -+do_show() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local current="$(get_current_provider)" -+ if [[ -z "${current}" ]] ; then -+ echo "(none)" -+ return 2 -+ fi -+ echo "${current}" -+} -+ -+options_show() { -+ : -+} -+ -+### list action ### -+describe_list() { -+ echo "Lists all available providers for ${ALTERNATIVE}" -+} -+ -+do_list() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local n cur= providers=( $(get_providers) ) -+ write_list_start "Available providers for ${ALTERNATIVE}:" -+ -+ cur="$(get_current_provider)" -+ -+ if [[ -n "${providers[@]}" ]] ; then -+ for (( n = 0 ; n < ${#providers[@]} ; ++n )) ; do -+ [[ ${cur} == "${providers[${n}]}" ]] && \ -+ providers[${n}]="${providers[${n}]} $(highlight '*')" -+ done -+ write_numbered_list "${providers[@]}" -+ else -+ write_kv_list_entry "(none found)" "" -+ fi -+} -+ -+options_list() { -+ : -+} -+ -+### files action ### -+describe_files() { -+ echo "Lists symlinks provided by the currently selected provider" -+} -+ -+do_files() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local cur="$(get_current_provider)" p= -+ [[ -n "${cur}" ]] || die -q "No selected provider, hence no symlinks provided" -+ local dieprefix="Could not list symlinks provided for ${ALTERNATIVE}" -+ -+ local errors symlink rootsymlink -+ while read -r -d '' symlink; do -+ rootsymlink="${EROOT}${symlink}" -+ rootsymlink=${rootsymlink//+(\/)/\/} -+ echo "${rootsymlink}" -+ if [[ -L ${rootsymlink} ]]; then -+ if [[ ! -e ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} is dangling symlink" -+ errors=yes -+ fi -+ elif [[ -d ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} is a directory" -+ errors=yes -+ elif [[ -e ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} exists but is not a symlink" -+ errors=yes -+ else -+ write_error_msg "${rootsymlink} does not exist" -+ errors=yes -+ fi -+ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+} -+ -+options_files() { -+ : -+} -+ -+### set action ### -+ -+describe_set() { -+ echo "Sets a provider for ${ALTERNATIVE}" -+} -+ -+describe_set_parameters() { -+ echo "[ --force ] <provider>" -+} -+ -+describe_set_options() { -+ echo "--force : overwrite or remove existing non-symlink files (but not directories) if necessary" -+ echo "<provider> : the name of the provider to use or the index of the provider preceeded by a dash" -+} -+ -+do_set() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local force provider providers -+ if [[ ${1} == --force ]]; then -+ force=yes -+ shift -+ fi -+ -+ if [[ ${1} == -+([[:digit:]]) ]]; then -+ providers=( $(get_providers) ) -+ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" -+ provider=${providers[${1#-}-1]} -+ else -+ provider="${1}" -+ fi -+ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" -+ local dieprefix="Could not set provider ${provider} for alternative ${ALTERNATIVE}" -+ -+ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then -+ if is_number ${provider} ; then -+ providers=( $(get_providers) ) -+ [[ -n ${providers[${1#-}-1]} ]] && -+ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" -+ fi -+ die -q "The given provider (${provider}) does not exist" -+ fi -+ -+ local symlink newsymlinks=() oldsymlinks=() -+ -+ while read -r -d '' symlink; do -+ local nicesymlink=${symlink#.} -+ nicesymlink=${nicesymlink//+(\/)/\/} -+ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: bad symlink ${symlink}?" -+ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: bad symlink ${symlink}?" -+ -+ newsymlinks+=( "${nicesymlink}" ) -+ done < <( -+ cd "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || die "${dieprefix}: cd failed" -+ find . -type l -print0 | LC_ALL=C sort -r -u -z) -+ [[ ${#newsymlinks[@]} -gt 0 ]] || die "${dieprefix}: does not provide any symlinks?" -+ -+ if [[ -f ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then -+ while read -r -d '' symlink; do -+ local nicesymlink=${symlink//+(\/)/\/} -+ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" -+ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" -+ -+ oldsymlinks+=( "${nicesymlink}" ) -+ done < <(LC_ALL=C sort -r -u -z "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list") -+ [[ ${#oldsymlinks[@]} -gt 0 ]] || die "${dieprefix}: old provider ${oldcur} does not provide any symlinks?" -+ -+ elif [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list || -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list is not a file" -+ fi -+ -+ local pass errors= -+ for pass in check perform; do -+ local -i new_i=0 old_i=0 -+ while [[ -n ${newsymlinks[new_i]} || -n ${oldsymlinks[old_i]} ]]; do -+ -+ if ( LC_ALL=C; [[ ${newsymlinks[new_i]} < ${oldsymlinks[old_i]} ]] ); then -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${oldsymlinks[old_i]} ]]; then -+ : -+ elif [[ -d ${EROOT}${oldsymlinks[old_i]} ]]; then -+ write_error_msg "Can't remove ${EROOT}${oldsymlinks[old_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${oldsymlinks[old_i]} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Removing ${EROOT}${oldsymlinks[old_i]} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to remove ${EROOT}${oldsymlinks[old_i]}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ rm -f "${ROOT}${oldsymlinks[old_i]}" || die "${dieprefix}: rm failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ -+ old_i+=1 -+ -+ else -+ local target=${ALTERNATIVESDIR_ROOTLESS#/}/${ALTERNATIVE}/_current${newsymlinks[new_i]} dir=${newsymlinks[new_i]%/*} -+ while [[ -n ${dir} ]]; do -+ target=../${target} -+ dir=${dir%/*} -+ done -+ -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${newsymlinks[new_i]} ]]; then -+ : -+ elif [[ -d ${EROOT}${newsymlinks[new_i]} ]]; then -+ write_error_msg "Can't overwrite ${EROOT}${newsymlinks[new_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${newsymlinks[new_i]} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Overwriting ${EROOT}${newsymlinks[new_i]} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to overwrite ${EROOT}${newsymlinks[new_i]}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ mkdir -p "${EROOT}${newsymlinks[new_i]%/*}" || die "${dieprefix}: mkdir -p failed" -+ ln -snf "${target#/}" "${EROOT}${newsymlinks[new_i]}" || die "${dieprefix}: ln -snf failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ -+ [[ ${newsymlinks[new_i]} == ${oldsymlinks[old_i]} ]] && old_i+=1 -+ new_i+=1 -+ fi -+ done -+ -+ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" -+ done -+ -+ local oldcur="$(get_current_provider)" -+ ln -snf "${provider}" "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: ln -snf failed" -+ -+ : >"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: emptying/creating _current_list failed" -+ for symlink in "${newsymlinks[@]}"; do -+ echo -n -e "${symlink}\\0" >>"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: appending ${symlink} to _current_list failed" -+ done -+ return 0 -+} -+ -+_options_parameters() { -+ [[ -n ${2} && ${2} != --descriptions ]] && die -q "Unrecognised option ${2}" -+ local describe_func=describe_${1#options_}_options descriptions=${2} opt options oldifs=$IFS -+ if is_function ${describe_func}; then -+ IFS=$'\n' -+ options=( $(${describe_func}) ) -+ IFS=$oldifs -+ for opt in "${options[@]}"; do -+ [[ ${opt} == --* ]] || continue -+ if [[ -n ${descriptions} ]]; then -+ echo "${opt/ : /:}" -+ else -+ echo "${opt%% : *}" -+ fi -+ done -+ fi -+} -+ -+options_set() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+### update action ### -+ -+describe_update() { -+ echo "Set a default provider if no valid one currently exists" -+} -+ -+describe_update_parameters() { -+ echo "[--ignore] <provider>" -+} -+ -+describe_update_options() { -+ echo "--ignore : update to any valid provider EXCEPT the specified provider" -+ echo "<provider> : the name of the provider to use" -+} -+ -+do_update() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local p cur=$(get_current_provider) providers=( $(get_providers) ) ignore -+ if [[ "--ignore" == ${1} ]] ; then -+ # Try everything except setting the provider to the given -+ # one. So, if it isn't the given one, we end up doing -+ # nothing. Bug #128 -+ shift -+ ignore=${1} -+ fi -+ -+ if [[ ${cur} == ${1} && -z ${ignore} ]]; then -+ # if current provider was just updated, reselect it since it could have changed -+ do_set "${cur}" && return 0 -+ elif [[ -n ${cur} && ${cur} != ${ignore} ]] ; then -+ # verify existing provider's symlinks -+ local p= bad=0 -+ while read -r -d '' p ; do -+ [[ -L "${EROOT}${p}" && -e "${EROOT}${p}" ]] || (( bad++ )) -+ done < "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+ -+ [[ "${bad}" -eq 0 ]] && return 0 -+ # fix existing provider if possible -+ has "${cur}" "${providers[@]}" && do_set "${cur}" && return 0 -+ elif has "${1}" "${providers[@]}" && [[ -z ${ignore} ]] ; then -+ # switch to new provider if none was set before or it can't be fixed -+ do_set "${1}" && return 0 -+ fi -+ -+ # if no valid provider has been selected switch to first available, valid -+ # provider, sorted according to importance -+ for p in "${providers[@]}"; do -+ [[ ${ignore} != ${p} ]] && do_set "${p}" && return 0 -+ done -+ -+ # if a provider is set but no providers are available anymore cleanup -+ cur=$(get_current_provider) -+ if [[ -n ${cur} ]]; then -+ do_unset "${cur}" && return 2 -+ fi -+ # if no provider is set and none are available that are not ignored, return 2 for cleanup -+ [[ -z ${providers[@]} || ${providers[@]} == ${ignore} ]] && return 2 -+ -+ # we tried everything to select a valid provider, but failed -+ return 1 -+} -+ -+options_update() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+### unset action ### -+ -+describe_unset() { -+ echo "Unset any symlinks created for the current provider for ${ALTERNATIVE}." -+} -+ -+describe_unset_parameters() { -+ echo "[ --force ]" -+} -+ -+describe_unset_options() { -+ echo "--force : remove existing non-symlink files (but not directories) if necessary" -+} -+ -+do_unset() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local force= -+ if [[ ${1} == --force ]]; then -+ force=yes -+ shift -+ fi -+ -+ local cur="$(get_current_provider)" p= -+ [[ -n "${cur}" ]] || die -q "Nothing to unset" -+ local dieprefix="Could not unset provider for ${ALTERNATIVE}" -+ -+ local one=false symlink pass errors= -+ for pass in check perform; do -+ while read -r -d '' symlink; do -+ one=true -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${symlink} ]]; then -+ : -+ elif [[ -d ${EROOT}${symlink} ]]; then -+ write_error_msg "Can't remove ${EROOT}${symlink}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${symlink} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Removing ${EROOT}${symlink} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to remove ${EROOT}${symlink}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ rm -f "${EROOT}${symlink}" || die "${dieprefix}: rm failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+ -+ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" -+ done -+ -+ ${one} || die "${dieprefix}: does not provide any symlinks?" -+ -+ rm "${ALTERNATIVESDIR}/${ALTERNATIVE}"/{_current,_current_list} || die "${dieprefix}: rm failed" -+} -+ -+options_unset() { -+ _options_parameters $FUNCNAME "$@" -+ get_current_provider -+} -+ -+### script action ### -+ -+describe_script() { -+ echo "Output an evalable script fragment to set PATH, LD_LIBRARY_PATH and MANPATH to use the specified provider" -+} -+ -+describe_script_parameters() { -+ echo "[--sh | --csh] [<provider>]" -+} -+ -+describe_script_options() { -+ echo "--sh : use Bourne shell syntax (default)" -+ echo "--csh : use C shell syntax" -+ echo "<provider> : the provider to use or the index of the provider preceeded by a dash (if not specified, use the system default)" -+} -+ -+do_script() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local syntax=sh provider providers -+ if [[ ${1} == --sh ]]; then -+ shift -+ elif [[ ${1} == --csh ]]; then -+ syntax=csh -+ shift -+ fi -+ -+ if [[ ${1} == -+([[:digit:]]) ]]; then -+ providers=( $(get_providers) ) -+ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" -+ provider=${providers[${1#-}-1]} -+ else -+ provider="${1}" -+ fi -+ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" -+ -+ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then -+ if is_number ${provider} ; then -+ providers=( $(get_providers) ) -+ [[ -n ${providers[${1#-}-1]} ]] && -+ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" -+ fi -+ die -q "The given provider (${provider}) does not exist" -+ fi -+ -+ local variables=( PATH LD_LIBRARY_PATH MANPATH ) -+ [[ -n ${!default_*} ]] && local ${!default_*} -+ local default_LD_LIBRARY_PATH=$(grep '^[^#]' "${EROOT}"/etc/ld.so.conf | tr '\n' ':')/lib:/usr/lib -+ local default_MANPATH=$(MANPATH= man -C"${EROOT}"/etc/man.conf -w) -+ -+ local var IFS=: -+ for var in "${variables[@]}"; do -+ local defvar=default_${var} path paths=( ) -+ for path in ${!var}; do -+ [[ ${path} == ${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/* ]] && continue -+ [[ -n ${provider} && -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) -+ paths+=( "${path}" ) -+ done -+ -+ [[ -n ${provider} ]] && for path in ${!defvar}; do -+ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) -+ done -+ -+ local newval=${paths[*]} -+ if [[ ${newval} != ${!var} ]]; then -+ newval=${newval//\'/\'\\\'\'} -+ if [[ ${syntax} == sh ]]; then -+ echo "${var}='${newval}'; export ${var}" -+ else -+ echo "setenv ${var} '${newval}'" -+ fi -+ fi -+ done -+} -+ -+options_script() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/app-admin/eselect/files/eselect-1.4.4-alternatives.patch b/app-admin/eselect/files/eselect-1.4.4-alternatives.patch index 71c2e67da..b2b943274 100644 --- a/app-admin/eselect/files/eselect-1.4.4-alternatives.patch +++ b/app-admin/eselect/files/eselect-1.4.4-alternatives.patch @@ -226,10 +226,10 @@ index 027ef73..a5fe373 100644 @$(dosed) $< > $@ diff --git a/libs/alternatives-common.bash.in b/libs/alternatives-common.bash.in new file mode 100644 -index 0000000..99de48e +index 0000000..64d74df --- /dev/null +++ b/libs/alternatives-common.bash.in -@@ -0,0 +1,372 @@ +@@ -0,0 +1,488 @@ +# Copyright 2015 Gentoo Foundation +# Copyright 2008 Mike Kelly +# Copyright 2009, 2013 David Leverton @@ -238,7 +238,7 @@ index 0000000..99de48e + +inherit config output path-manipulation + -+ALTERNATIVESDIR_ROOTLESS="@sysconfdir@/env.d/alternatives" ++: "${ALTERNATIVESDIR_ROOTLESS:=@sysconfdir@/env.d/alternatives}" +ALTERNATIVESDIR="${EROOT%/}${ALTERNATIVESDIR_ROOTLESS}" + +get_current_provider() { @@ -298,7 +298,8 @@ index 0000000..99de48e + [[ -d ${p} && ! -L ${p} ]] || continue + p=${p##*/} + -+ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") ++ [[ -e "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance" ]] && ++ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") + importance=${importance:-0} + [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" + @@ -466,6 +467,117 @@ index 0000000..99de48e + return 0 +} + ++### add action ### ++alternatives_describe_add() { ++ echo "Add provider to selected alternative" ++} ++ ++alternatives_describe_add_parameters() { ++ echo "<provider> <importance> <source> <target> [<source> <target> [...]]" ++} ++ ++alternatives_describe_add_options() { ++ echo "<provider> : the name of the alternative provider" ++ echo "<importance> : interger value, representing the importance of the provider" ++ echo "<source> : source of the symlink" ++ echo "<target> : destination for the symlink" ++} ++ ++alternatives_do_add() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ (( $# >= 4 )) && (( ($#-2)%2 == 0)) || \ ++ die "exactly 3+N*2 arguments where N>=1 required" ++ local provider=${1} ++ local importance=${2} ++ shift 2 ++ local index src target ret=0 ++ local provider_dir="${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" ++ ++ # Creating base dir ++ if [[ ! -e "${provider_dir}" ]]; then ++ mkdir -p "${provider_dir}" || die "Failed to create ${provider_dir}" ++ elif [[ ! -d "${provider_dir}" ]]; then ++ die "${provider_dir} exists but is a file" ++ else ++ die "${provider_dir} already present. You need ot remove it before adding it again" ++ fi ++ ++ # Make sure importance is a signed integer ++ if [[ -n ${importance} ]] && ! [[ ${importance} =~ ^[0-9]+(\.[0-9]+)*$ ]]; then ++ die "Invalid importance (${importance}) detected" ++ else ++ # Setting importance ++ echo ${importance} > "${provider_dir}/_importance" ++ fi ++ ++ # Process source-target pairs ++ while (( $# >= 2 )); do ++ src=${1//+(\/)/\/}; target=${2//+(\/)/\/} ++ if [[ ${src} != /* ]]; then ++ die "Source path must be absolute, but got ${src}" ++ else ++ local reltarget= dir=${provider_dir}${src%/*} ++ while [[ -n ${dir} ]]; do ++ reltarget+=../ ++ dir=${dir%/*} ++ done ++ ++ reltarget=${reltarget%/} ++ [[ ${target} == /* ]] || reltarget+=${src%/*}/ ++ reltarget+=${target} ++ mkdir -p "${provider_dir}${src%/*}" || die "Failed to create ${provider_dir}${src%/*}" ++ ln -sf "${reltarget}" "${provider_dir}${src}" || die "Failed to create symlink" ++ # The -e test will fail if existing symlink points to non-existing target, ++ # so check for -L also. ++ # Say ${ED}/sbin/init exists and links to /bin/systemd (which doesn't exist yet). ++# if [[ -e ${ED}${src} || -L ${ED}${src} ]]; then ++# local fulltarget=${target} ++# [[ ${fulltarget} != /* ]] && fulltarget=${src%/*}/${fulltarget} ++# if [[ -e ${ED}${fulltarget} || -L ${ED}${fulltarget} ]]; then ++# die "${src} defined as provider for ${fulltarget}, but both already exist in \${ED}" ++# else ++# mv "${ED}${src}" "${ED}${fulltarget}" || die ++# fi ++# fi ++ fi ++ shift 2 ++ done ++} ++ ++alternatives_options_add() { ++ _options_parameters ${FUNCNAME#alternatives_} "$@" ++} ++ ++### remove action ### ++ ++alternatives_describe_remove() { ++ echo "Remove a provider for selected alternative" ++} ++ ++alternatives_describe_remove_parameters() { ++ echo "<provider>" ++} ++ ++alternatives_describe_remove_options() { ++ echo "<provider> : the name of the alternative provider to be removed" ++} ++ ++alternatives_do_remove() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ if [[ -d "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" ]]; then ++ rm -r "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || \ ++ die "Failed to remove '${provider}' for '${ALTERNATIVE}'" ++ else ++ einfo "'${provider}' is not a provider for '${ALTERNATIVE}'" ++ fi ++} ++ ++alternatives_options_remove() { ++ _options_parameters ${FUNCNAME#alternatives_} "$@" ++} ++ +### update action ### + +# available in both "eselect alternatives" and individual modules @@ -502,6 +614,10 @@ index 0000000..99de48e + [[ -n ${best} && -n ${1} && -z ${ignore} ]] && die -q "Cannot specify both --best and a provider" + + if [[ -n ${best} ]] ; then ++ # set best provider ++ : # fall through to "switch to first available" loop below ++ elif [[ $# == "0" ]] && [[ -z ${cur} ]]; then ++ # if nothing is specified + : # fall through to "switch to first available" loop below + elif [[ ${cur} == ${1} && -z ${ignore} ]]; then + # if current provider was just updated, reselect it since it could have changed @@ -541,13 +657,13 @@ index 0000000..99de48e + +alternatives_options_update() { + _options_parameters ${FUNCNAME#alternatives_} "$@" -+ if [[ -n ${ALTERNATIVE} ]]; then -+ get_providers -+ else -+ for alt in ${ALTERNATIVESDIR_ROOTLESS}/_*/*/_importance; do -+ echo ${alt} | cut -d/ -f5 -+ done | sort -u -+ fi ++ if [[ -n ${ALTERNATIVE} ]]; then ++ get_providers ++ else ++ for alt in ${ALTERNATIVESDIR_ROOTLESS}/_*/*/_importance; do ++ echo ${alt} | cut -d/ -f5 ++ done | sort -u ++ fi +} + +### unset action stub ### @@ -604,10 +720,10 @@ index 0000000..99de48e +# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/libs/alternatives.bash.in b/libs/alternatives.bash.in new file mode 100644 -index 0000000..c2512e1 +index 0000000..1b5a2b0 --- /dev/null +++ b/libs/alternatives.bash.in -@@ -0,0 +1,249 @@ +@@ -0,0 +1,293 @@ +# Copyright 2015 Gentoo Foundation +# Copyright 2008 Mike Kelly +# Copyright 2009, 2013 David Leverton @@ -726,6 +842,50 @@ index 0000000..c2512e1 + get_providers +} + ++### add action ### ++ ++describe_add() { ++ alternatives_describe_add ++} ++ ++describe_add_parameters() { ++ alternatives_describe_add_parameters ++} ++ ++describe_add_options() { ++ alternatives_describe_add_options ++} ++ ++do_add() { ++ alternatives_do_add ++ ++ # make sure we have something selected ++ eselect ${provider} show > /dev/null || eselect ${provider} update --best ++} ++ ++### remove action ### ++ ++describe_remove() { ++ alternatives_describe_remove ++} ++ ++describe_remove_parameters() { ++ alternatives_describe_remove_parameters ++} ++ ++describe_remove_options() { ++ alternatives_describe_remove_options ++} ++ ++do_remove() { ++ alternatives_do_remove ++ ++# if no provider is present, remove whole Alternative ++ if ! eselect ${provider} update --best > /dev/null; then ++ eselect alternatives remove ${ALTERNATIVE} ++ fi ++} ++ +### update action ### + +# all functions implemented in alternatives-common.bash as defined for @@ -803,7 +963,7 @@ index 0000000..c2512e1 + + local idx=${!} + if [[ ${idx} == +(-|+|[[:digit:]]) ]]; then -+ idx=${1#+(-|+)} ++ idx=${1#+(-|+)} + providers=( $(get_providers) ) + (( ${idx} <= ${#providers[@]} )) || die -q "The given provider with index (${idx}) does not exist" + provider=${providers[${idx}-1]} @@ -871,10 +1031,10 @@ index 73960c4..4da6465 100644 env.eselect \ diff --git a/modules/alternatives.eselect b/modules/alternatives.eselect new file mode 100644 -index 0000000..b1c219f +index 0000000..912bb3d --- /dev/null +++ b/modules/alternatives.eselect -@@ -0,0 +1,50 @@ +@@ -0,0 +1,165 @@ +# Copyright 2015 Gentoo Foundation +# Copyright 2008 Mike Kelly +# Copyright 2009, 2013 David Leverton @@ -896,11 +1056,11 @@ index 0000000..b1c219f + ENDOFTEXT +} + -+### update action ### -+ +# all functions implemented in alternatives-common.bash as defined for +# both "eselect alternatives" and individual modules + ++### update action ### ++ +describe_update() { + alternatives_describe_update +} @@ -925,6 +1085,121 @@ index 0000000..b1c219f + alternatives_options_update +} + ++### create action ### ++ ++describe_create() { ++ echo "Create a new alternative" ++} ++ ++describe_create_parameters() { ++ echo "<alternative>" ++} ++ ++describe_create_options() { ++ echo "<alternative> : the name of the alternative to create" ++} ++ ++do_create() { ++ [[ $# == 1 ]] || die "Need exactly one alternative name" ++ ++ local auto_dir="${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++ local auto_file="${auto_dir}/${1}.eselect" ++ ++ if [[ ! -e "${auto_file}" ]]; then ++ if [[ ! -e "${auto_dir}" ]]; then ++ mkdir -p "${auto_dir}" || die "Failed to create ${auto_dir}" ++ elif [[ ! -d "${auto_dir}" ]]; then ++ die "${auto_dir} exists but is a file" ++ fi ++ cat >> ${auto_file} <<- ENDOFTEXT ++ DESCRIPTION="${DESCRIPTION} for ${1}" ++ VERSION="${VERSION}" ++ MAINTAINER="${MAINTAINER}" ++ ESELECT_MODULE_GROUP="Alternatives" ++ ++ ALTERNATIVE="${1}" ++ ++ inherit alternatives ++ ENDOFTEXT ++ fi ++} ++ ++### delete action ### ++ ++describe_delete() { ++ echo "Delete an existing alternative" ++} ++ ++describe_delete_parameters() { ++ echo "<alternative>" ++} ++ ++describe_delete_options() { ++ echo "<alternative> : the name of the alternative to delete" ++} ++ ++do_delete() { ++ [[ $# == 1 ]] || die "Need exactly one alternative name" ++ ++ local auto_dir="${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++ local auto_file="${auto_dir}/${1}.eselect" ++ ++ if [[ -e "${auto_file}" ]]; then ++ rm "${auto_file}" || die "Failed to remove alternative: ${1}" ++ fi ++} ++ ++### add action ### ++ ++describe_add() { ++ alternatives_describe_add ++} ++ ++describe_add_parameters() { ++ echo "<alternative> $(alternatives_describe_add_parameters)" ++} ++ ++describe_add_options() { ++ echo "<alternative> : the name of the alternative to add a provider for" ++ alternatives_describe_add_options ++} ++ ++do_add() { ++ local ALTERNATIVE=$1 ++ shift ++ [[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'" ++ alternatives_do_add "$@" ++} ++ ++options_add() { ++ alternatives_options_add ++} ++ ++### remove action ### ++ ++describe_remove() { ++ alternatives_describe_remove ++} ++ ++describe_remove_parameters() { ++ echo "<alternative> $(alternatives_describe_remove_parameters)" ++} ++ ++describe_remove_options() { ++ echo "<alternative> : the name of the alternative to remove a provider from" ++ alternatives_describe_remove_options ++} ++ ++do_remove() { ++ local ALTERNATIVE=$1 ++ shift ++ [[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'" ++ alternatives_do_remove "$@" ++} ++ ++options_remove() { ++ alternatives_options_remove ++} diff --git a/modules/modules.eselect b/modules/modules.eselect index 038f630..eb73e16 100644 --- a/modules/modules.eselect diff --git a/app-benchmarks/btl/ChangeLog b/app-benchmarks/btl/ChangeLog index ea8c75791..978091101 100644 --- a/app-benchmarks/btl/ChangeLog +++ b/app-benchmarks/btl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for app-benchmarks/btl -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + app-benchmarks/btl: Add bitbucket to remote-id in metadata.xml + 14 Jun 2013; Justin Lecher <jlec@gentoo.org> btl-9999.ebuild, metadata.xml: Bump to EAPI=5 and drop KEYWORDS of live ebuilds diff --git a/app-benchmarks/btl/metadata.xml b/app-benchmarks/btl/metadata.xml index 51688ab86..3a7222f06 100644 --- a/app-benchmarks/btl/metadata.xml +++ b/app-benchmarks/btl/metadata.xml @@ -8,4 +8,7 @@ <description>Bench Template Library</description> </maintainer> <longdescription>This package contains a modified copy of the BTL.</longdescription> + <upstream> + <remote-id type="bitbucket">spiros/btl</remote-id> + </upstream> </pkgmetadata> diff --git a/app-vim/vim-gromacs/ChangeLog b/app-vim/vim-gromacs/ChangeLog index b9c719358..74853f725 100644 --- a/app-vim/vim-gromacs/ChangeLog +++ b/app-vim/vim-gromacs/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for app-vim/vim-gromacs -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + app-vim/vim-gromacs: Add github to remote-id in metadata.xml + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> vim-gromacs-9999.ebuild: removed empty line diff --git a/app-vim/vim-gromacs/metadata.xml b/app-vim/vim-gromacs/metadata.xml index 046c58b8a..de2225605 100644 --- a/app-vim/vim-gromacs/metadata.xml +++ b/app-vim/vim-gromacs/metadata.xml @@ -5,4 +5,7 @@ <longdescription lang="en"> VIM syntax plugin which provides syntax highlighting for the gromacs files. </longdescription> + <upstream> + <remote-id type="github">HubLot/vim-gromacs</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-cpp/icnc/ChangeLog b/dev-cpp/icnc/ChangeLog index 8de9e15ef..72d7f2105 100644 --- a/dev-cpp/icnc/ChangeLog +++ b/dev-cpp/icnc/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-cpp/icnc: Add github to remote-id in metadata.xml + 08 Feb 2015; Christoph Junghans <ottxor@gentoo.org> icnc-9999.ebuild: fix bug #539318 diff --git a/dev-cpp/icnc/metadata.xml b/dev-cpp/icnc/metadata.xml index 745b9e1ce..c3e80bdd7 100644 --- a/dev-cpp/icnc/metadata.xml +++ b/dev-cpp/icnc/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>ottxor@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <upstream> + <remote-id type="github">icnc/icnc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/gluegen/ChangeLog b/dev-java/gluegen/ChangeLog index 4982a6bbb..d23d7be03 100644 --- a/dev-java/gluegen/ChangeLog +++ b/dev-java/gluegen/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/gluegen: Add github to remote-id in metadata.xml + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> +files/2.2.4-dont-copy-jars.patch, +files/2.2.4-dont-strip.patch, +files/2.2.4-dont-test-archive.patch, gluegen-2.2.4.ebuild: diff --git a/dev-java/gluegen/metadata.xml b/dev-java/gluegen/metadata.xml index d29f3a9fd..d6bbcc249 100644 --- a/dev-java/gluegen/metadata.xml +++ b/dev-java/gluegen/metadata.xml @@ -13,4 +13,7 @@ on the IR before glue code emission. GlueGen is currently powerful enough to bind even low-level APIs such as the Java Native Interface (JNI) and the AWT Native Interface (JAWT) back up to the Java programming language. </longdescription> + <upstream> + <remote-id type="github">sgothel/gluegen</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/jeuclid-core/ChangeLog b/dev-java/jeuclid-core/ChangeLog index b61221d1d..5c2ebdcc5 100644 --- a/dev-java/jeuclid-core/ChangeLog +++ b/dev-java/jeuclid-core/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/jeuclid-core: Updating remote-id in metadata.xml + 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> jeuclid-core-3.1.8.ebuild, jeuclid-core-3.1.9-r1.ebuild: Move to EAPI=5 diff --git a/dev-java/jeuclid-core/metadata.xml b/dev-java/jeuclid-core/metadata.xml index f80c0f1ba..d023325b1 100644 --- a/dev-java/jeuclid-core/metadata.xml +++ b/dev-java/jeuclid-core/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> JEuclid is a complete MathML rendering solution, consisting of: * A MathViewer application * Command line converters from MathML to other formats @@ -12,4 +12,7 @@ This package contains the basic JEuclid rendering and document handling classes. </longdescription> + <upstream> + <remote-id type="sourceforge">jeuclid</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/jhealpix/ChangeLog b/dev-java/jhealpix/ChangeLog index b0d2ba520..a3c5e5de2 100644 --- a/dev-java/jhealpix/ChangeLog +++ b/dev-java/jhealpix/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-java/jhealpix -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/jhealpix: Updating remote-id in metadata.xml + *jhealpix-3.11 (16 Jun 2013) 16 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +jhealpix-3.11.ebuild, diff --git a/dev-java/jhealpix/metadata.xml b/dev-java/jhealpix/metadata.xml index 9bb9481d8..debe4d929 100644 --- a/dev-java/jhealpix/metadata.xml +++ b/dev-java/jhealpix/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. This package contains the Java framework. </longdescription> + <upstream> + <remote-id type="sourceforge">jhealpix</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/jogl/ChangeLog b/dev-java/jogl/ChangeLog index 84ec1abb4..411673c12 100644 --- a/dev-java/jogl/ChangeLog +++ b/dev-java/jogl/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/jogl: Add github to remote-id in metadata.xml + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> -files/disable-applet.diff, -files/jogl-2.2.4-notests.patch, jogl-2.2.4.ebuild: diff --git a/dev-java/jogl/metadata.xml b/dev-java/jogl/metadata.xml index 975a649d1..cb3e7c1dd 100644 --- a/dev-java/jogl/metadata.xml +++ b/dev-java/jogl/metadata.xml @@ -9,4 +9,7 @@ to provide hardware-supported 3D graphics to applications written in Java. <use> <flag name="cg">Enable NVidia Cg binding.</flag> </use> + <upstream> + <remote-id type="github">sgothel/jogl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-lang/conceptual/ChangeLog b/dev-lang/conceptual/ChangeLog index 429e81647..b1ab5942e 100644 --- a/dev-lang/conceptual/ChangeLog +++ b/dev-lang/conceptual/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-lang/conceptual: Updating remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> conceptual-1.4.ebuild, metadata.xml: dev-lang/conceptual: fix SLOT operators diff --git a/dev-lang/conceptual/metadata.xml b/dev-lang/conceptual/metadata.xml index cdf1b6724..35143c2de 100644 --- a/dev-lang/conceptual/metadata.xml +++ b/dev-lang/conceptual/metadata.xml @@ -8,4 +8,7 @@ <use> <flag name="gui">Build the Java base graphical interface</flag> </use> + <upstream> + <remote-id type="sourceforge">conceptual</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-lang/ispc/ChangeLog b/dev-lang/ispc/ChangeLog index 529d48d08..afec6c690 100644 --- a/dev-lang/ispc/ChangeLog +++ b/dev-lang/ispc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-lang/ispc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-lang/ispc: Add github to remote-id in metadata.xml + 25 Oct 2014; Christoph Junghans <ottxor@gentoo.org> ispc-9999.ebuild: sync with gx86 diff --git a/dev-lang/ispc/metadata.xml b/dev-lang/ispc/metadata.xml index 06c3d15a6..4663d3aa7 100644 --- a/dev-lang/ispc/metadata.xml +++ b/dev-lang/ispc/metadata.xml @@ -5,4 +5,7 @@ <email>ottxor@gentoo.org</email> <name>Christoph Junghans</name> </maintainer> + <upstream> + <remote-id type="github">ispc/ispc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-lang/terra/ChangeLog b/dev-lang/terra/ChangeLog index 32af2a21d..817b66bb0 100644 --- a/dev-lang/terra/ChangeLog +++ b/dev-lang/terra/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-lang/terra: Add github to remote-id in metadata.xml + *terra-2015.03.12 (24 Apr 2015) 24 Apr 2015; Christoph Junghans <ottxor@gentoo.org> +metadata.xml, diff --git a/dev-lang/terra/metadata.xml b/dev-lang/terra/metadata.xml index 745b9e1ce..2e41c46b1 100644 --- a/dev-lang/terra/metadata.xml +++ b/dev-lang/terra/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>ottxor@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <upstream> + <remote-id type="github">zdevito/terra</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/boost-compute/ChangeLog b/dev-libs/boost-compute/ChangeLog index eefb055eb..0b089ee71 100644 --- a/dev-libs/boost-compute/ChangeLog +++ b/dev-libs/boost-compute/ChangeLog @@ -1,10 +1,25 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> + boost-compute-9999.ebuild, metadata.xml: + dev-libs/boost-compute: Update HOMEPAGE, SRC_URI and github remote-id: project + was transfered on from kylelutz to boostorg + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/boost-compute: Add github to remote-id in metadata.xml + +*boost-compute-0.4-r1 (05 Jun 2015) + + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> + +boost-compute-0.4-r1.ebuild, +files/boost-compute-0.4-CMakeLists.patch, + -boost-compute-0.4.ebuild, boost-compute-9999.ebuild: + Fix BoostComputeConfig.cmake location + *boost-compute-9999 (01 Feb 2015) *boost-compute-0.4 (01 Feb 2015) 01 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, +boost-compute-9999.ebuild, +boost-compute-0.4.ebuild: Add Boost.Compute to overlay -
\ No newline at end of file + diff --git a/dev-libs/boost-compute/boost-compute-0.4.ebuild b/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild index 9782d2a2f..9782d2a2f 120000 --- a/dev-libs/boost-compute/boost-compute-0.4.ebuild +++ b/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild diff --git a/dev-libs/boost-compute/boost-compute-9999.ebuild b/dev-libs/boost-compute/boost-compute-9999.ebuild index 320fa9d85..aebd86d14 100644 --- a/dev-libs/boost-compute/boost-compute-9999.ebuild +++ b/dev-libs/boost-compute/boost-compute-9999.ebuild @@ -7,16 +7,16 @@ EAPI=5 inherit eutils cmake-utils DESCRIPTION="A header-only C++ Computing Library for OpenCL" -HOMEPAGE="https://github.com/kylelutz/compute" +HOMEPAGE="https://github.com/boostorg/compute" LICENSE="Boost-1.0" SLOT="0" if [[ ${PV} == "9999" ]] ; then - EGIT_REPO_URI="https://github.com/kylelutz/compute.git git://github.com/kylelutz/compute.git" + EGIT_REPO_URI="https://github.com/boostorg/compute.git git://github.com/boostorg/compute.git" inherit git-r3 KEYWORDS="" else - SRC_URI="https://github.com/kylelutz/compute/archive/v${PV}.tar.gz -> ${P}.tar.gz" + SRC_URI="https://github.com/boostorg/compute/archive/v${PV}.tar.gz -> ${P}.tar.gz" KEYWORDS="~amd64" S="${WORKDIR}/compute-${PV}" fi @@ -26,3 +26,7 @@ RDEPEND=" virtual/opencl " DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}"-0.4-CMakeLists.patch +) diff --git a/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch b/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch new file mode 100644 index 000000000..86d3a9e29 --- /dev/null +++ b/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch @@ -0,0 +1,14 @@ +Install the BoostComputeConfig to /usr/lib/cmake instead of /usr/share/cmake. + +Patch by Marius Brehler. +--- CMakeLists.txt ++++ CMakeLists.txt +@@ -81,7 +81,7 @@ configure_file( + # install cmake config file + install( + FILES ${BoostCompute_BINARY_DIR}/BoostComputeConfig.cmake +- DESTINATION share/cmake/BoostCompute ++ DESTINATION lib/cmake/BoostCompute + ) + + # install header files diff --git a/dev-libs/boost-compute/metadata.xml b/dev-libs/boost-compute/metadata.xml index ae0b30066..b93ef2986 100644 --- a/dev-libs/boost-compute/metadata.xml +++ b/dev-libs/boost-compute/metadata.xml @@ -12,4 +12,7 @@ and provides access to compute devices, contexts, command queues and memory buffers. </longdescription> + <upstream> + <remote-id type="github">boostorg/compute</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/boost/ChangeLog b/dev-libs/boost/ChangeLog index d0283a478..3c5bc03b4 100644 --- a/dev-libs/boost/ChangeLog +++ b/dev-libs/boost/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/boost: Updating remote-id in metadata.xml + 02 Apr 2015; Justin Lecher <jlec@gentoo.org> boost-1.56.0-r2.ebuild, metadata.xml: dev-libs/boost: Move to new CAT diff --git a/dev-libs/boost/metadata.xml b/dev-libs/boost/metadata.xml index 8e49be56d..3fc1693b8 100644 --- a/dev-libs/boost/metadata.xml +++ b/dev-libs/boost/metadata.xml @@ -35,4 +35,7 @@ over 200MB of extra disk space. </flag> </use> + <upstream> + <remote-id type="sourceforge">boost</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/libcuda/ChangeLog b/dev-libs/libcuda/ChangeLog index 74035e500..21a96bef5 100644 --- a/dev-libs/libcuda/ChangeLog +++ b/dev-libs/libcuda/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-libs/libcuda -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/libcuda: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> libcuda-9999.ebuild, metadata.xml: Punt base.eclass; add missing die; drop nneeded patches diff --git a/dev-libs/libcuda/metadata.xml b/dev-libs/libcuda/metadata.xml index f233055c0..f78356fd3 100644 --- a/dev-libs/libcuda/metadata.xml +++ b/dev-libs/libcuda/metadata.xml @@ -5,4 +5,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">shinpei0208/gdev</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/libgdev/ChangeLog b/dev-libs/libgdev/ChangeLog index bba9675f2..471e930e1 100644 --- a/dev-libs/libgdev/ChangeLog +++ b/dev-libs/libgdev/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-libs/libgdev -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/libgdev: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> libgdev-9999.ebuild, metadata.xml: Punt base.eclass; add missing die; drop nneeded patches diff --git a/dev-libs/libgdev/metadata.xml b/dev-libs/libgdev/metadata.xml index f233055c0..f78356fd3 100644 --- a/dev-libs/libgdev/metadata.xml +++ b/dev-libs/libgdev/metadata.xml @@ -5,4 +5,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">shinpei0208/gdev</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/utf8proc/ChangeLog b/dev-libs/utf8proc/ChangeLog index f822d346b..758f69e9a 100644 --- a/dev-libs/utf8proc/ChangeLog +++ b/dev-libs/utf8proc/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/utf8proc: Add github to remote-id in metadata.xml + +*utf8proc-1.2-r1 (25 May 2015) + + 25 May 2015; Justin Lecher <jlec@gentoo.org> +utf8proc-1.2-r1.ebuild, + -utf8proc-1.2.ebuild, files/utf8proc-1.2-buildflags.patch, metadata.xml: + dev-libs/utf8proc: Fix build process, https://github.com/gentoo- + science/sci/issues/427 + *utf8proc-1.2 (21 May 2015) 21 May 2015; Marius Brehler <marbre@linux.sungazer.de> diff --git a/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch b/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch index 4d583e417..de8847cdf 100644 --- a/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch +++ b/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch @@ -1,14 +1,40 @@ -Adjust build flags. Proted from 1.1.6. + Makefile | 9 +++++---- + 1 file changed, 5 insertions(+), 4 deletions(-) -Patch by Marius Brehler. ---- Makefile -+++ Makefile -@@ -6,7 +6,7 @@ AR=ar +diff --git a/Makefile b/Makefile +index aba2453..5fab07d 100644 +--- a/Makefile ++++ b/Makefile +@@ -6,8 +6,8 @@ AR=ar INSTALL=install # compiler settings -cflags = -O2 -std=c99 -pedantic -Wall -fpic -DUTF8PROC_EXPORTS $(CFLAGS) -+cflags = -std=c99 -pedantic -fpic -DUTF8PROC_EXPORTS $(CFLAGS) - cc = $(CC) $(cflags) +-cc = $(CC) $(cflags) ++CFLAGS ?= -O2 ++CFLAGS += -std=c99 -pedantic -Wall -fpic -DUTF8PROC_EXPORTS # shared-library version MAJOR.MINOR.PATCH ... this may be *different* + # from the utf8proc version number because it indicates ABI compatibility, +@@ -54,18 +54,19 @@ data/utf8proc_data.c.new: libutf8proc.$(SHLIB_EXT) data/data_generator.rb data/c + $(MAKE) -C data utf8proc_data.c.new + + utf8proc.o: utf8proc.h utf8proc.c utf8proc_data.c +- $(cc) -c -o utf8proc.o utf8proc.c ++ $(CC) $(CFLAGS) -c -o utf8proc.o utf8proc.c + + libutf8proc.a: utf8proc.o + rm -f libutf8proc.a + $(AR) rs libutf8proc.a utf8proc.o + + libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH): utf8proc.o +- $(cc) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o ++ $(CC) $(LDFLAGS) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o + chmod a-x $@ + + libutf8proc.so: libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) + ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@ ++ ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@.$(MAJOR) + + libutf8proc.$(MAJOR).dylib: utf8proc.o + $(cc) -dynamiclib -o $@ $^ -install_name $(libdir)/$@ -Wl,-compatibility_version -Wl,$(MAJOR) -Wl,-current_version -Wl,$(MAJOR).$(MINOR).$(PATCH) diff --git a/dev-libs/utf8proc/metadata.xml b/dev-libs/utf8proc/metadata.xml index f8fff5b6f..4d104ac19 100644 --- a/dev-libs/utf8proc/metadata.xml +++ b/dev-libs/utf8proc/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription> + <herd>sci</herd> + <longdescription> utf8proc is a library for processing UTF-8 encoded Unicode strings. Some features are Unicode normalization, stripping of default ignorable characters, case folding and detection of grapheme @@ -11,4 +11,7 @@ (U+2212) and “Hyphen-Minus” (U+002D, ASCII Minus) all into the ASCII minus sign, to make them equal for comparisons. </longdescription> + <upstream> + <remote-id type="github">JuliaLang/utf8proc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/utf8proc/utf8proc-1.2.ebuild b/dev-libs/utf8proc/utf8proc-1.2-r1.ebuild index 349806f39..e00835dec 100644 --- a/dev-libs/utf8proc/utf8proc-1.2.ebuild +++ b/dev-libs/utf8proc/utf8proc-1.2-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit eutils +inherit eutils toolchain-funcs DESCRIPTION="library for processing UTF-8 encoded Unicode strings" HOMEPAGE="http://www.public-software-group.org/utf8proc" @@ -20,12 +20,17 @@ src_prepare() { } src_compile() { - emake libutf8proc.so - use static-libs & emake libutf8proc.a + emake \ + libutf8proc.so \ + $(usex static-libs libutf8proc.a "") \ + CC=$(tc-getCC) \ + AR=$(tc-getAR) +# CFLAGS="${CFLAGS}" +# LDFLAGS="${LDFLAGS} -Wl,--soname,lib${PN}.${PV}" } src_install() { doheader utf8proc.h - dolib.so libutf8proc.so + dolib.so libutf8proc.so* use static-libs && dolib.a libutf8proc.a } diff --git a/dev-ml/gsl-ocaml/ChangeLog b/dev-ml/gsl-ocaml/ChangeLog index c724b6d0c..069753b13 100644 --- a/dev-ml/gsl-ocaml/ChangeLog +++ b/dev-ml/gsl-ocaml/ChangeLog @@ -1,10 +1,15 @@ # ChangeLog for dev-ml/gsl-ocaml -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> gsl-ocaml-1.10.2.ebuild: + dev-ml/gsl-ocaml: Bump EAPI=5 + + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-ml/gsl-ocaml: Add bitbucket to remote-id in metadata.xml + *gsl-ocaml-1.10.2 (11 Aug 2012) 11 Aug 2012; Guillaume Horel <guillaume.horel@gmail.com> +gsl-ocaml-1.10.2.ebuild, +metadata.xml: new package from #390583 - diff --git a/dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild b/dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild index 379d48fb7..c2568388d 100644 --- a/dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild +++ b/dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 OASIS_BUILD_DOCS=1 OASIS_BUILD_TESTS=1 @@ -21,7 +21,7 @@ IUSE="examples test" DEPEND=">=sci-libs/gsl-1.10" RDEPEND="${DEPEND}" -DOCS=( "CHANGES.txt" "README.md" "NOTES.md" "TODO.md" ) +DOCS=( CHANGES.txt README.md NOTES.md TODO.md ) src_prepare() { oasis_configure_opts="$(use_enable examples)" diff --git a/dev-ml/gsl-ocaml/metadata.xml b/dev-ml/gsl-ocaml/metadata.xml index f7b1637ca..8a2bb7bd7 100644 --- a/dev-ml/gsl-ocaml/metadata.xml +++ b/dev-ml/gsl-ocaml/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang='en'> + <herd>sci</herd> + <longdescription lang="en"> GSL interface for OCaml </longdescription> + <upstream> + <remote-id type="bitbucket">mmottl/gsl-ocaml</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild b/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild index 5149f7a46..c9e5d206a 100644 --- a/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild +++ b/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -20,7 +20,7 @@ RDEPEND=" sci-biology/bioperl sci-biology/ucsc-genome-browser[static-libs]" DEPEND="${RDEPEND} - virtual/perl-Module-Build" + dev-perl/Module-Build" SRC_TEST="do" diff --git a/dev-perl/Bio-BigFile/ChangeLog b/dev-perl/Bio-BigFile/ChangeLog index df9646dfc..4d69032ac 100644 --- a/dev-perl/Bio-BigFile/ChangeLog +++ b/dev-perl/Bio-BigFile/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for dev-perl/Bio-BigFile -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> Bio-BigFile-1.07.ebuild, + metadata.xml: + dev-perl/Bio-BigFile: Fix dependency problems due to recent mask of perl-core + packages + 18 Sep 2013; Justin Lecher <jlec@gentoo.org> -Bio-BigFile-1.06.ebuild, +Bio-BigFile-1.07.ebuild, metadata.xml: Version Bump, fix deps @@ -12,4 +17,3 @@ 09 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> Bio-BigFile-1.06.ebuild: initial ebuild, see bug #402835 - diff --git a/dev-perl/Bio-BigFile/metadata.xml b/dev-perl/Bio-BigFile/metadata.xml index 2bc893037..07b525505 100644 --- a/dev-perl/Bio-BigFile/metadata.xml +++ b/dev-perl/Bio-BigFile/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild index f18e1829f..e7e83d765 100644 --- a/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild +++ b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -18,6 +18,6 @@ IUSE="" RDEPEND="" DEPEND="${RDEPEND} dev-perl/DBD-Pg - virtual/perl-Module-Build" + dev-perl/Module-Build" SRC_TEST="do" diff --git a/dev-perl/Bio-DB-Das-Chado/ChangeLog b/dev-perl/Bio-DB-Das-Chado/ChangeLog index 02aefe01a..dd72b25b8 100644 --- a/dev-perl/Bio-DB-Das-Chado/ChangeLog +++ b/dev-perl/Bio-DB-Das-Chado/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for dev-perl/Bio-DB-Das-Chado -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> Bio-DB-Das-Chado-0.34.ebuild, + metadata.xml: + dev-perl/Bio-DB-Das-Chado: Fix dependency problems due to recent mask of perl- + core packages + 24 Sep 2014; Justin Lecher <jlec@gentoo.org> -Bio-DB-Das-Chado-0.32.ebuild, +Bio-DB-Das-Chado-0.34.ebuild, metadata.xml: Version Bump; Bump to EAPI=5 @@ -16,4 +21,3 @@ 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +Bio-DB-Das-Chado-0.32.ebuild, +metadata.xml: dev-perl/Bio-DB-Das-Chado: new package required by sci-biology/gbrowse - diff --git a/dev-perl/Bio-DB-Das-Chado/metadata.xml b/dev-perl/Bio-DB-Das-Chado/metadata.xml index 2bc893037..07b525505 100644 --- a/dev-perl/Bio-DB-Das-Chado/metadata.xml +++ b/dev-perl/Bio-DB-Das-Chado/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/dev-perl/opal-client/ChangeLog b/dev-perl/opal-client/ChangeLog index 16c477298..ff44246c3 100644 --- a/dev-perl/opal-client/ChangeLog +++ b/dev-perl/opal-client/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-perl/opal-client -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-perl/opal-client: Updating remote-id in metadata.xml + 01 Nov 2014; Justin Lecher <jlec@gentoo.org> opal-client-1.9.2.ebuild, metadata.xml: Bump to EAPI=5 @@ -18,4 +21,3 @@ 21 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml, +opal-client-1.9.3.ebuild: Initial checkin to sci - diff --git a/dev-perl/opal-client/metadata.xml b/dev-perl/opal-client/metadata.xml index 897aa2e6b..46dbd9940 100644 --- a/dev-perl/opal-client/metadata.xml +++ b/dev-perl/opal-client/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="sourceforge">opaltoolkit</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/RecSQL/ChangeLog b/dev-python/RecSQL/ChangeLog index ef054f357..e995523c0 100644 --- a/dev-python/RecSQL/ChangeLog +++ b/dev-python/RecSQL/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/RecSQL -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/RecSQL: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> RecSQL-9999.ebuild: Switch from git-2 to git-r3 diff --git a/dev-python/RecSQL/metadata.xml b/dev-python/RecSQL/metadata.xml index 098ac091a..ba2081c24 100644 --- a/dev-python/RecSQL/metadata.xml +++ b/dev-python/RecSQL/metadata.xml @@ -6,4 +6,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">orbeckst/RecSQL</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astlib/ChangeLog b/dev-python/astlib/ChangeLog index 992453036..2da13d24b 100644 --- a/dev-python/astlib/ChangeLog +++ b/dev-python/astlib/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/astlib -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/astlib: Updating remote-id in metadata.xml + *astlib-0.7.0 (29 Apr 2013) 29 Apr 2013; Sébastien Fabbro <bicatali@gentoo.org> +astlib-0.7.0.ebuild, diff --git a/dev-python/astlib/metadata.xml b/dev-python/astlib/metadata.xml index 306677cbb..b4d862f31 100644 --- a/dev-python/astlib/metadata.xml +++ b/dev-python/astlib/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> astLib is a set of Python modules that provides some tools for research astronomers. It can be used for simple plots, statistics, common calculations, coordinate conversions, and manipulating FITS @@ -12,4 +12,7 @@ In Gentoo, PyWCSTools is using the stock library instead of the bundled one. </longdescription> + <upstream> + <remote-id type="sourceforge">astlib</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy-helpers/ChangeLog b/dev-python/astropy-helpers/ChangeLog index 50e83351d..1e7733c0c 100644 --- a/dev-python/astropy-helpers/ChangeLog +++ b/dev-python/astropy-helpers/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/astropy-helpers: Add github to remote-id in metadata.xml + 16 Apr 2015; Justin Lecher <jlec@gentoo.org> -Manifest, -astropy-helpers-0.4.1.ebuild: dev-python/astropy-helpers: In CVS diff --git a/dev-python/astropy-helpers/metadata.xml b/dev-python/astropy-helpers/metadata.xml index bacda05a5..e449320c9 100644 --- a/dev-python/astropy-helpers/metadata.xml +++ b/dev-python/astropy-helpers/metadata.xml @@ -6,4 +6,8 @@ astropy-helpers is a collection of build tools used by astropy that may be used by other projects. </longdescription> + <upstream> + <remote-id type="pypi">astropy-helpers</remote-id> + <remote-id type="github">astropy/astropy-helpers</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astroquery/ChangeLog b/dev-python/astroquery/ChangeLog index 4d7161d23..f5aadb9b9 100644 --- a/dev-python/astroquery/ChangeLog +++ b/dev-python/astroquery/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/astroquery -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/astroquery: Add github to remote-id in metadata.xml + *astroquery-0.2 (22 Aug 2014) *astroquery-9999 (22 Aug 2014) diff --git a/dev-python/astroquery/metadata.xml b/dev-python/astroquery/metadata.xml index 7fe0b4555..ba28af97d 100644 --- a/dev-python/astroquery/metadata.xml +++ b/dev-python/astroquery/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Astroquery is a package containing a collection of tools to use online astronomical databases. It integrates with Astropy and aims to support many services with a uniform API. </longdescription> + <upstream> + <remote-id type="pypi">astroquery</remote-id> + <remote-id type="github">astropy/astroquery</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/brewer2mpl/ChangeLog b/dev-python/brewer2mpl/ChangeLog index a79da6e04..a806cec23 100644 --- a/dev-python/brewer2mpl/ChangeLog +++ b/dev-python/brewer2mpl/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/brewer2mpl: Add github to remote-id in metadata.xml + *brewer2mpl-9999 (04 Feb 2015) *brewer2mpl-1.4.1 (04 Feb 2015) diff --git a/dev-python/brewer2mpl/metadata.xml b/dev-python/brewer2mpl/metadata.xml index a37a47ac0..42e39bdf4 100644 --- a/dev-python/brewer2mpl/metadata.xml +++ b/dev-python/brewer2mpl/metadata.xml @@ -12,4 +12,8 @@ colors of all 165 colorbrewer2.org color maps. The color map data ships with brewer2mpl so no internet connection is required. </longdescription> + <upstream> + <remote-id type="pypi">brewer2mpl</remote-id> + <remote-id type="github">jiffyclub/brewer2mpl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ccdproc/ChangeLog b/dev-python/ccdproc/ChangeLog index bb3af4dd1..2852131eb 100644 --- a/dev-python/ccdproc/ChangeLog +++ b/dev-python/ccdproc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/ccdproc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ccdproc: Add github to remote-id in metadata.xml + *ccdproc-0.2.1 (18 Oct 2014) 18 Oct 2014; Joseph Jon Booker <joe@neoturbine.net> +ccdproc-0.2.1.ebuild, diff --git a/dev-python/ccdproc/metadata.xml b/dev-python/ccdproc/metadata.xml index 3cbb671a6..cdfbe201f 100644 --- a/dev-python/ccdproc/metadata.xml +++ b/dev-python/ccdproc/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> ccdproc is a AstroPy-affliated package for the basic reduction of CCD images. It provides a framework for accounting for error propagation and bad pixel tracking through the reduction steps. </longdescription> + <upstream> + <remote-id type="pypi">ccdproc</remote-id> + <remote-id type="github">astropy/ccdproc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/coards/metadata.xml b/dev-python/coards/metadata.xml index c95dbb8d2..a94fb6cc1 100644 --- a/dev-python/coards/metadata.xml +++ b/dev-python/coards/metadata.xml @@ -9,4 +9,7 @@ This module converts between a given COARDS time specification and a Python datetime object, which is much more useful. </longdescription> + <upstream> + <remote-id type="pypi">coards</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/dimensionful/ChangeLog b/dev-python/dimensionful/ChangeLog index e18714fad..647ffbeda 100644 --- a/dev-python/dimensionful/ChangeLog +++ b/dev-python/dimensionful/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/dimensionful -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/dimensionful: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> dimensionful-9999.ebuild: Switch from git-2 to git-r3 @@ -14,4 +17,3 @@ 19 Feb 2012; Kacper Kowalik <xarthisius@gentoo.org> +dimensionful-9999.ebuild, +metadata.xml: [dev-python/dimensionful] initial import, ebuild written by me - diff --git a/dev-python/dimensionful/metadata.xml b/dev-python/dimensionful/metadata.xml index ef58ee263..ecf6df5d9 100644 --- a/dev-python/dimensionful/metadata.xml +++ b/dev-python/dimensionful/metadata.xml @@ -5,4 +5,7 @@ <email>xarthisius@gentoo.org</email> <name>Kacper Kowalik</name> </maintainer> + <upstream> + <remote-id type="github">caseywstark/dimensionful</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/emcee/metadata.xml b/dev-python/emcee/metadata.xml index b4cb18f4a..726f85321 100644 --- a/dev-python/emcee/metadata.xml +++ b/dev-python/emcee/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> This provides a set of sparse matrix types for Python, with modules which implement: - Iterative methods for solving linear systems of equations @@ -13,4 +13,7 @@ standard sparse and dense matrix libraries (UMFPACK/AMD, SuperLU, BLAS/LAPACK) for maximum performance and robustness. </longdescription> + <upstream> + <remote-id type="pypi">emcee</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ffc/ChangeLog b/dev-python/ffc/ChangeLog index 37662b34f..07f0f2629 100644 --- a/dev-python/ffc/ChangeLog +++ b/dev-python/ffc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/ffc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ffc: Add bitbucket to remote-id in metadata.xml + 16 Jul 2014; Andrew Reisner <andrew@reisner.co> ffc-1.3.0.ebuild: fixed dependency issue diff --git a/dev-python/ffc/metadata.xml b/dev-python/ffc/metadata.xml index 34821f2af..893659eac 100644 --- a/dev-python/ffc/metadata.xml +++ b/dev-python/ffc/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> FFC works as a compiler for multilinear forms by generating code (C or C++) for the evaluation of a multilinear form given in mathematical notation. This new approach to form evaluation makes it possible to @@ -10,4 +10,7 @@ mathematical notation and the generated code is as efficient as hand-optimized code. </longdescription> + <upstream> + <remote-id type="bitbucket">fenics-project/ffc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ffnet/ChangeLog b/dev-python/ffnet/ChangeLog index 23434feb5..49cfe6fe9 100644 --- a/dev-python/ffnet/ChangeLog +++ b/dev-python/ffnet/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/ffnet -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ffnet: Updating remote-id in metadata.xml + 09 Apr 2014; Justin Lecher <jlec@gentoo.org> -ffnet-0.6.2.ebuild, +ffnet-0.7.1.ebuild, metadata.xml: Version Bump; fix distutils-r1 eclass usage @@ -28,4 +31,3 @@ 26 Jan 2010; Sébastien Fabbro <bicatali@gentoo.org> +ffnet-0.6.2.ebuild, +metadata.xml: Import. Ebuild submitted by Marek Wojciechowski bug #158038 - diff --git a/dev-python/ffnet/metadata.xml b/dev-python/ffnet/metadata.xml index 56358e20c..d5cbb7029 100644 --- a/dev-python/ffnet/metadata.xml +++ b/dev-python/ffnet/metadata.xml @@ -9,4 +9,7 @@ <use> <flag name="matplotlib">Use matplotlib for drawing</flag> </use> + <upstream> + <remote-id type="sourceforge">ffnet</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/fiat/ChangeLog b/dev-python/fiat/ChangeLog index 26d00d366..2c71ff6ce 100644 --- a/dev-python/fiat/ChangeLog +++ b/dev-python/fiat/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/fiat -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/fiat: Add bitbucket to remote-id in metadata.xml + 16 Jul 2014; Andrew Reisner <andrew@reisner.co> fiat-1.3.0.ebuild, fiat-1.4.0.ebuild: Added keyword diff --git a/dev-python/fiat/metadata.xml b/dev-python/fiat/metadata.xml index a67ae626b..b9c29fa54 100644 --- a/dev-python/fiat/metadata.xml +++ b/dev-python/fiat/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order @@ -12,4 +12,7 @@ supported on triangles and tetrahedra. Upcoming versions will also support Hermite and nonconforming elements. </longdescription> + <upstream> + <remote-id type="bitbucket">fenics-project/fiat</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/gammapy/ChangeLog b/dev-python/gammapy/ChangeLog index e94737626..bfb8bcf98 100644 --- a/dev-python/gammapy/ChangeLog +++ b/dev-python/gammapy/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/gammapy -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/gammapy: Add github to remote-id in metadata.xml + *gammapy-0.1 (28 Aug 2014) 28 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> +gammapy-0.1.ebuild, diff --git a/dev-python/gammapy/metadata.xml b/dev-python/gammapy/metadata.xml index 1370ffdb0..948014d9a 100644 --- a/dev-python/gammapy/metadata.xml +++ b/dev-python/gammapy/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Gammapy is a package for simulating and analysing gamma-ray sky data. It is currently designed to support users of telescopes such as Fermi, H.E.S.S, and CTA in primarily Galactic plane survey studies. </longdescription> + <upstream> + <remote-id type="pypi">gammapy</remote-id> + <remote-id type="github">gammapy/gammapy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/healpy/ChangeLog b/dev-python/healpy/ChangeLog index 5251a637c..3ae21e5a2 100644 --- a/dev-python/healpy/ChangeLog +++ b/dev-python/healpy/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/healpy -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/healpy: Add github to remote-id in metadata.xml + *healpy-1.7.4 (03 Mar 2014) 03 Mar 2014; Sébastien Fabbro <bicatali@gentoo.org> +healpy-1.7.4.ebuild, diff --git a/dev-python/healpy/metadata.xml b/dev-python/healpy/metadata.xml index bd104d9d7..6157d9af6 100644 --- a/dev-python/healpy/metadata.xml +++ b/dev-python/healpy/metadata.xml @@ -1,13 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang='en'> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Healpy provides a python package to manipulate healpix maps. It is based on the standard numeric and visualisation tools for Python, Numpy and matplotlib. </longdescription> -<upstream> - <remote-id type="pypi">healpy</remote-id> -</upstream> + <upstream> + <remote-id type="pypi">healpy</remote-id> + <remote-id type="github">healpy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/imageutils/ChangeLog b/dev-python/imageutils/ChangeLog index 133e25091..4f637ac60 100644 --- a/dev-python/imageutils/ChangeLog +++ b/dev-python/imageutils/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/imageutils -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/imageutils: Add github to remote-id in metadata.xml + *imageutils-9999 (08 Aug 2014) 08 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> +imageutils-9999.ebuild, diff --git a/dev-python/imageutils/metadata.xml b/dev-python/imageutils/metadata.xml index 281f12fe7..7eae1bb53 100644 --- a/dev-python/imageutils/metadata.xml +++ b/dev-python/imageutils/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> imageutils is a collection of image processing utilities that are generally useful to astronomers. These will likely become part of the core AstroPy package before the 1.0 release. </longdescription> + <upstream> + <remote-id type="pypi">imageutils</remote-id> + <remote-id type="github">astropy/imageutils</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/instant/ChangeLog b/dev-python/instant/ChangeLog index af28b7f08..722f6f1b9 100644 --- a/dev-python/instant/ChangeLog +++ b/dev-python/instant/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/instant -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/instant: Add bitbucket to remote-id in metadata.xml + *instant-1.3.0 (16 Jul 2014) *instant-1.4.0 (16 Jul 2014) diff --git a/dev-python/instant/metadata.xml b/dev-python/instant/metadata.xml index c446ffa73..37fa71c43 100644 --- a/dev-python/instant/metadata.xml +++ b/dev-python/instant/metadata.xml @@ -1,10 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> Instant is a Python module that allows for instant inlining of C and C++ code in Python. It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project (http://www.fenics.org) </longdescription> + <upstream> + <remote-id type="bitbucket">fenics-project/instant</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/matlab_wrapper/ChangeLog b/dev-python/matlab_wrapper/ChangeLog index 478753411..f396c02ff 100644 --- a/dev-python/matlab_wrapper/ChangeLog +++ b/dev-python/matlab_wrapper/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/matlab_wrapper: Add github to remote-id in metadata.xml + *matlab_wrapper-9999 (20 Jan 2015) *matlab_wrapper-0.9.6 (20 Jan 2015) diff --git a/dev-python/matlab_wrapper/metadata.xml b/dev-python/matlab_wrapper/metadata.xml index f24eccb56..4bdcc4c27 100644 --- a/dev-python/matlab_wrapper/metadata.xml +++ b/dev-python/matlab_wrapper/metadata.xml @@ -13,4 +13,8 @@ shell. MATLAB session is started in the background and appears as a regular Python module. </longdescription> + <upstream> + <remote-id type="pypi">matlab_wrapper</remote-id> + <remote-id type="github">mrkrd/matlab_wrapper</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/matplotlib2tikz/ChangeLog b/dev-python/matplotlib2tikz/ChangeLog new file mode 100644 index 000000000..0ee8f934f --- /dev/null +++ b/dev-python/matplotlib2tikz/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for dev-python/matplotlib2tikz +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/matplotlib2tikz: Add github to remote-id in metadata.xml + +*matplotlib2tikz-0.1.0 (31 May 2015) +*matplotlib2tikz-9999 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +matplotlib2tikz-0.1.0.ebuild, +matplotlib2tikz-9999.ebuild, +metadata.xml: + New ebuild written by me diff --git a/dev-python/matplotlib2tikz/Manifest b/dev-python/matplotlib2tikz/Manifest new file mode 100644 index 000000000..b3bc18006 --- /dev/null +++ b/dev-python/matplotlib2tikz/Manifest @@ -0,0 +1 @@ +DIST matplotlib2tikz-0.1.0.tar.gz 16369 SHA256 d1c07d8a7d5fcdba77509769f2a477a75562d6b87d1de9d50ea78ea0f1285acd SHA512 0ed25659afeeec279c0d97033b37357fa9c91d49f3547a789b1add9faa7285e73a4eec94c3cd70d1edfa7186cbad1d452256586ceb7066a8908ad2d3e73a274e WHIRLPOOL eabe83d14b1d0c362bc325e0a9b5612cd787098440df634fa4bbf828e6c5b7085ec78d00545ab9d2463e9251a3c1978b8edd866ea74ef4b1d58da251e82be0b3 diff --git a/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild b/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild new file mode 120000 index 000000000..49bc235a9 --- /dev/null +++ b/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild @@ -0,0 +1 @@ +matplotlib2tikz-9999.ebuild
\ No newline at end of file diff --git a/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild b/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild new file mode 100644 index 000000000..6af9d49d6 --- /dev/null +++ b/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} ) + +inherit distutils-r1 + +DESCRIPTION="Python script for converting matplotlib figures into native Pgfplots (TikZ) figures" +HOMEPAGE="https://github.com/nschloe/matplotlib2tikz" + +if [ ${PV} = "9999" ] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/nschloe/${PN}.git git://github.com/nschloe/${PN}.git" + KEYWORDS="" +else + SRC_URI="https://github.com/nschloe/matplotlib2tikz/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" +fi + +LICENSE="LGPL-3" +SLOT="0" +IUSE="" + +RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}] + dev-texlive/texlive-pictures" +DEPEND="${RDEPEND}" + #test? ( dev-python/pytest[${PYTHON_USEDEP}] )" diff --git a/dev-python/matplotlib2tikz/metadata.xml b/dev-python/matplotlib2tikz/metadata.xml new file mode 100644 index 000000000..112456f47 --- /dev/null +++ b/dev-python/matplotlib2tikz/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <maintainer> + <email>marbre@linux.sungazer.de</email> + <name>Marius Brehler</name> + </maintainer> + <upstream> + <remote-id type="github">nschloe/matplotlib2tikz</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/meshpy/ChangeLog b/dev-python/meshpy/ChangeLog index 1f223ae38..084d36c0a 100644 --- a/dev-python/meshpy/ChangeLog +++ b/dev-python/meshpy/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for dev-python/meshpy -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*meshpy-2014.1 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> +meshpy-2014.1.ebuild: + Version bump; Implement python_test() + *meshpy-2013.1.2 (14 Jun 2013) 14 Jun 2013; Justin Lecher <jlec@gentoo.org> -meshpy-0.91.2.ebuild, diff --git a/dev-python/meshpy/Manifest b/dev-python/meshpy/Manifest index 62fc27c21..607e920e1 100644 --- a/dev-python/meshpy/Manifest +++ b/dev-python/meshpy/Manifest @@ -1 +1,2 @@ DIST MeshPy-2013.1.2.tar.gz 1885753 SHA256 425ffa0f5a7dacfc1301bbb165ff78fbe6beacb0ab6c0a8dd581f565896c6762 SHA512 6004a609fc62ff44e5770a0d041da42eea1e185def5b1efca357d4cac3dcd34a7ccb5b0ca2d2f7fb4ba81bbc0251b8c998eb64bcff828f05cfc1a0a49385b9ae WHIRLPOOL 48266e5838c6a416622fc0cc804112af1331b9d74952030e225500f8f6426c4a9679088e8f3b06dbf26169128e33e2173bae73d198e20b5ffabd02c9e7762660 +DIST MeshPy-2014.1.tar.gz 1851120 SHA256 a090729c9b99360b2741099906361b2e9ba6373b97707817c9b81f66531380b6 SHA512 d8d7823df60250382577f67bb5ffd3b6523c84729c013220eaddccfa4b227839c2e0ffb285f87e752cf0dc5292eb1e5c693d04139d2fb33a05877e0b2b1bcecc WHIRLPOOL b84442d92933c5b5745c8a91ba4f65df80a1c94fd08668d8575c154de61ce0b67605f87b638341adb3f2b43ab8d2f6c82989e9d2bfcab177dabdf0119f07ab9b diff --git a/dev-python/meshpy/meshpy-2014.1.ebuild b/dev-python/meshpy/meshpy-2014.1.ebuild new file mode 100644 index 000000000..9727775af --- /dev/null +++ b/dev-python/meshpy/meshpy-2014.1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python{3_3,3_4} ) + +inherit distutils-r1 + +MY_PN="MeshPy" + +DESCRIPTION="Quality triangular and tetrahedral mesh generation for Python" +HOMEPAGE="http://mathema.tician.de/software/meshpy http://pypi.python.org/pypi/MeshPy" +SRC_URI="mirror://pypi/M/${MY_PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + dev-libs/boost[python,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pytools[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +S="${WORKDIR}/${MY_PN}-${PV}" + +python_prepare_all() { + sed 's: delay = 10: delay = 1:g' -i aksetup_helper.py || die + distutils-r1_python_prepare_all +} + +python_compile() { + mkdir "${BUILD_DIR}" || die + echo "BOOST_PYTHON_LIBNAME = [\'boost_${EPYTHON}-mt\']">> "${BUILD_DIR}"/siteconf.py + distutils-r1_python_compile +} + +python_test() { + py.test || die +} diff --git a/dev-python/meshpy/metadata.xml b/dev-python/meshpy/metadata.xml index 0c0b3caa3..5bd8e24f7 100644 --- a/dev-python/meshpy/metadata.xml +++ b/dev-python/meshpy/metadata.xml @@ -10,4 +10,7 @@ In order to generate these 2D and 3D meshes, MeshPy provides Python interfaces to two well-regarded mesh generators, Triangle by J. Shewchuk and TetGen by Hang Si. Both are included in the package in slightly modified versions. </longdescription> + <upstream> + <remote-id type="pypi">MeshPy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/montage-wrapper/metadata.xml b/dev-python/montage-wrapper/metadata.xml index 101fb4b35..5cfc153a9 100644 --- a/dev-python/montage-wrapper/metadata.xml +++ b/dev-python/montage-wrapper/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription> + <herd>sci-astronomy</herd> + <longdescription> This Astropy-affiliated package provides a python wrapper to the Montage Astronomical Image Mosaic Engine, including both functions to access individual Montage commands, and high-level functions to facilitate mosaicking and re-projecting. </longdescription> + <upstream> + <remote-id type="pypi">montage-wrapper</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/newrelic/ChangeLog b/dev-python/newrelic/ChangeLog index c2eb3a987..f904df843 100644 --- a/dev-python/newrelic/ChangeLog +++ b/dev-python/newrelic/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*newrelic-2.50.0.39 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +newrelic-2.50.0.39.ebuild: + Version bump + *newrelic-2.44.0.36 (03 Mar 2015) 03 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, diff --git a/dev-python/newrelic/Manifest b/dev-python/newrelic/Manifest index eb70f7c7d..d32de2b4f 100644 --- a/dev-python/newrelic/Manifest +++ b/dev-python/newrelic/Manifest @@ -1 +1,2 @@ DIST newrelic-2.44.0.36.tar.gz 656605 SHA256 373d3af3e9f0c233932ddcf024f978eed3bd6ceaee9563aedb65c029f7f9b2b7 SHA512 2e9b7b6afd74c562c82813d0245822a194e151abf1e32827915b83677db811032711418ae2bd0c26b3ea4727323ca53d538862957d8cd07f7f6a2ce26630a682 WHIRLPOOL a36537b56d9e18c5143149821120296e3aae53094d9038bc0f2e4ac175820f7d6600c84d8cf17199d7a53e6dc93ef2e41885f17f2ace7de87c97a3100200149d +DIST newrelic-2.50.0.39.tar.gz 662564 SHA256 fddd47a8d048e0c5f42eee511a8aaf35891c996d6c959553c7bec8b3ac74b3cb SHA512 935973b7897348113ab40ac4f1ea173cf31886057569a0384e4a26d96463220a43768a4dd88ac4e4a8a7db01ab4fe6fde7825860a7fbd62911ead5fc2e3f0774 WHIRLPOOL e2044913e7274703fe76368db84f2f670810653b08855e5ac067e8f009b42cb222bd8958c92a12401ac5a1630d2797f0ae77f832d85288941d56eb181efe1693 diff --git a/dev-python/newrelic/metadata.xml b/dev-python/newrelic/metadata.xml index b87287f06..d5e4ca843 100644 --- a/dev-python/newrelic/metadata.xml +++ b/dev-python/newrelic/metadata.xml @@ -6,4 +6,7 @@ Python agent for the New Relic web application performance monitoring service. </longdescription> + <upstream> + <remote-id type="pypi">newrelic</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/newrelic/newrelic-2.50.0.39.ebuild b/dev-python/newrelic/newrelic-2.50.0.39.ebuild new file mode 100644 index 000000000..92fd5f79a --- /dev/null +++ b/dev-python/newrelic/newrelic-2.50.0.39.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) + +inherit distutils-r1 + +MY_PN="newrelic" + +DESCRIPTION="New Relic Python Agent" +HOMEPAGE="http://newrelic.com/docs/python/new-relic-for-python" + +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +KEYWORDS="~amd64" + +LICENSE="newrelic" +SLOT="0" + +RDEPEND=" + || ( + dev-python/bottle[${PYTHON_USEDEP}] + dev-python/cherrypy[${PYTHON_USEDEP}] + dev-python/django[${PYTHON_USEDEP}] + dev-python/flask[${PYTHON_USEDEP}] + dev-python/pylons[${PYTHON_USEDEP}] + dev-python/pyramid[${PYTHON_USEDEP}] + )" + #|| ( + # dev-python/cython[${PYTHON_USEDEP}] + # virtual/pypy + # virtual/pypy3 + #)" +DEPEND="${RDEPEND}" + +src_install() { + default + dobin scripts/newrelic-admin +} diff --git a/dev-python/nvidia-ml-py/metadata.xml b/dev-python/nvidia-ml-py/metadata.xml index 75b9f4d16..07ccaa0d1 100644 --- a/dev-python/nvidia-ml-py/metadata.xml +++ b/dev-python/nvidia-ml-py/metadata.xml @@ -10,4 +10,7 @@ Provides a Python interface to GPU management and monitoring functions. This is a wrapper around the NVML library. </longdescription> + <upstream> + <remote-id type="pypi">nvidia-ml-py</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/omniorbpy/ChangeLog b/dev-python/omniorbpy/ChangeLog index 3c8f8cac9..97660aa5b 100644 --- a/dev-python/omniorbpy/ChangeLog +++ b/dev-python/omniorbpy/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/omniorbpy: Updating remote-id in metadata.xml + 08 Apr 2015; Justin Lecher <jlec@gentoo.org> omniorbpy-3.4.ebuild: dev-python/omniorbpy: Fix python dependency diff --git a/dev-python/omniorbpy/metadata.xml b/dev-python/omniorbpy/metadata.xml index 897aa2e6b..50d473bb3 100644 --- a/dev-python/omniorbpy/metadata.xml +++ b/dev-python/omniorbpy/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="sourceforge">omniorb</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/opal-client/ChangeLog b/dev-python/opal-client/ChangeLog index c75fb455c..9b6b8d455 100644 --- a/dev-python/opal-client/ChangeLog +++ b/dev-python/opal-client/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/opal-client -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/opal-client: Updating remote-id in metadata.xml + 15 Oct 2013; Justin Lecher <jlec@gentoo.org> opal-client-2.4.1.ebuild, metadata.xml: Add missing PYTHON_DEPS and PYTHON_REQUIRED_USE @@ -33,4 +36,3 @@ 21 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml, +opal-client-1.9.3.ebuild: Initial checkin to sci - diff --git a/dev-python/opal-client/metadata.xml b/dev-python/opal-client/metadata.xml index f17a827e3..a32846566 100644 --- a/dev-python/opal-client/metadata.xml +++ b/dev-python/opal-client/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">opaltoolkit</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/photutils/ChangeLog b/dev-python/photutils/ChangeLog index fe8069d96..2c0ec070b 100644 --- a/dev-python/photutils/ChangeLog +++ b/dev-python/photutils/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/photutils -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/photutils: Add github to remote-id in metadata.xml + *photutils-9999 (08 Aug 2014) 08 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> +metadata.xml, diff --git a/dev-python/photutils/metadata.xml b/dev-python/photutils/metadata.xml index 9f819f64b..7cb319709 100644 --- a/dev-python/photutils/metadata.xml +++ b/dev-python/photutils/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> photutils is a python package for determining photometric properties of sources in astronomical images. This includes source detection, centroid and shape parameters, and performing photometry. </longdescription> + <upstream> + <remote-id type="pypi">photutils</remote-id> + <remote-id type="github">astropy/photutils</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pickleshare/ChangeLog b/dev-python/pickleshare/ChangeLog new file mode 100644 index 000000000..bf4233eb4 --- /dev/null +++ b/dev-python/pickleshare/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for dev-python/pickleshare +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pickleshare: Add github to remote-id in metadata.xml + +*pickleshare-0.5 (31 May 2015) +*pickleshare-9999 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, + +pickleshare-0.5.ebuild, +pickleshare-9999.ebuild: + Initial ebuild (required for >dev-python/ipython-3.1.0) diff --git a/dev-python/pickleshare/Manifest b/dev-python/pickleshare/Manifest new file mode 100644 index 000000000..79e862d1c --- /dev/null +++ b/dev-python/pickleshare/Manifest @@ -0,0 +1 @@ +DIST pickleshare-0.5.tar.gz 4441 SHA256 c0be5745035d437dbf55a96f60b7712345b12423f7d0951bd7d8dc2141ca9286 SHA512 1021b76591b5b1d6c777e03c9544fea63602f719b786a2a2e73590f8e8275156fa69b336adf81a6e8abcaad2263eacd76ce4abf2ceff04126ff6b1ffd96cb4e3 WHIRLPOOL 07907feb8dab2dfbfc74e43d17cc076027ab450091a8dd4af197019c6c46e268eda1d5761ab22fc774e37090ab7d51212d82ba284d89018fbc0f52c38f235c62 diff --git a/dev-python/pickleshare/metadata.xml b/dev-python/pickleshare/metadata.xml new file mode 100644 index 000000000..ea703f9fd --- /dev/null +++ b/dev-python/pickleshare/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <longdescription> + Like shelve, a PickleShareDB object acts like a normal dictionary. + Unlike shelve, many processes can access the database + simultaneously. Changing a value in database is immediately visible + to other processes accessing the same database. + Concurrency is possible because the values are stored in separate + files. Hence the "database" is a directory where all files are + governed by PickleShare. + </longdescription> + <upstream> + <remote-id type="pypi">pickleshare</remote-id> + <remote-id type="github">pickleshare/pickleshare</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/pickleshare/pickleshare-0.5.ebuild b/dev-python/pickleshare/pickleshare-0.5.ebuild new file mode 120000 index 000000000..16ddbe44b --- /dev/null +++ b/dev-python/pickleshare/pickleshare-0.5.ebuild @@ -0,0 +1 @@ +pickleshare-9999.ebuild
\ No newline at end of file diff --git a/dev-python/pickleshare/pickleshare-9999.ebuild b/dev-python/pickleshare/pickleshare-9999.ebuild new file mode 100644 index 000000000..5c56ccb9c --- /dev/null +++ b/dev-python/pickleshare/pickleshare-9999.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python{3_3,3_4} ) + +inherit distutils-r1 + +DESCRIPTION="A small 'shelve' like datastore with concurrency support" +HOMEPAGE="https://github.com/pickleshare/pickleshare" + +if [ ${PV} == "9999" ] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git" +else + SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + KEYWORDS="~amd64" + # test_pickleshare.py is not included in the pickleshare-0.5 source + # we fetched from pipy + RESTRICT="test" +fi + +LICENSE="MIT" +SLOT="0" +IUSE="test" + +RDEPEND=" + dev-python/path-py[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +python_test() { + distutils_install_for_testing + cd "${TEST_DIR}"/lib || die + cp "${S}"/test_pickleshare.py "${TEST_DIR}"/lib/ || die + py.test || die +} diff --git a/dev-python/prettyplotlib/metadata.xml b/dev-python/prettyplotlib/metadata.xml index 123422a50..621e56cd1 100644 --- a/dev-python/prettyplotlib/metadata.xml +++ b/dev-python/prettyplotlib/metadata.xml @@ -9,4 +9,7 @@ Python matplotlib-enhancer library which painlessly creates beautiful default matplotlib plots. </longdescription> + <upstream> + <remote-id type="pypi">prettyplotlib</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ptyprocess/ChangeLog b/dev-python/ptyprocess/ChangeLog new file mode 100644 index 000000000..d67ba2736 --- /dev/null +++ b/dev-python/ptyprocess/ChangeLog @@ -0,0 +1,18 @@ +# ChangeLog for dev-python/ptyprocess +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ptyprocess: Add github to remote-id in metadata.xml + + 30 May 2015; Justin Lecher <jlec@gentoo.org> -Manifest, + -ptyprocess-0.5.ebuild, ptyprocess-9999.ebuild: + dev-python/ptyprocess: Add missing test funcion and drop ebuild which was + moved to tree + +*ptyprocess-0.5 (29 May 2015) +*ptyprocess-9999 (29 May 2015) + + 29 May 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, + +ptyprocess-0.5.ebuild, +ptyprocess-9999.ebuild: + Initial ebuild diff --git a/dev-python/ptyprocess/metadata.xml b/dev-python/ptyprocess/metadata.xml new file mode 100644 index 000000000..217a66929 --- /dev/null +++ b/dev-python/ptyprocess/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <upstream> + <remote-id type="github">pexpect/ptyprocess</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/ptyprocess/ptyprocess-9999.ebuild b/dev-python/ptyprocess/ptyprocess-9999.ebuild new file mode 100644 index 000000000..6d24550a5 --- /dev/null +++ b/dev-python/ptyprocess/ptyprocess-9999.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="Run a subprocess in a pseudo terminal" +HOMEPAGE="https://github.com/pexpect/ptyprocess" +SRC_URI="" +EGIT_REPO_URI="https://github.com/pexpect/${PN}.git git://github.com/pexpect/${PN}.git" + +LICENSE="ISC" +SLOT="0" +KEYWORDS="" +IUSE="test" + +DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +python_test() { + py.test --verbose --verbose || die +} diff --git a/dev-python/pyfftw/ChangeLog b/dev-python/pyfftw/ChangeLog index 3c19f1ea4..abebe1952 100644 --- a/dev-python/pyfftw/ChangeLog +++ b/dev-python/pyfftw/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 30 May 2015; Marius Brehler <marbre@linux.sungazer.de> pyfftw-9999.ebuild: + Implement python_test() + *pyfftw-9999 (04 Feb 2015) *pyfftw-0.9.2 (04 Feb 2015) diff --git a/dev-python/pyfftw/metadata.xml b/dev-python/pyfftw/metadata.xml index 07e8f0384..707eaf20d 100644 --- a/dev-python/pyfftw/metadata.xml +++ b/dev-python/pyfftw/metadata.xml @@ -10,4 +10,7 @@ A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms. </longdescription> + <upstream> + <remote-id type="pypi">pyFFTW</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyfftw/pyfftw-9999.ebuild b/dev-python/pyfftw/pyfftw-9999.ebuild index 962cf05fc..1d34389ff 100644 --- a/dev-python/pyfftw/pyfftw-9999.ebuild +++ b/dev-python/pyfftw/pyfftw-9999.ebuild @@ -23,6 +23,7 @@ fi LICENSE="BSD" SLOT="0" +IUSE="test" RDEPEND=" >=dev-python/numpy-1.8.0[${PYTHON_USEDEP}] @@ -30,3 +31,11 @@ RDEPEND=" >=dev-python/cython-0.19.1[${PYTHON_USEDEP}] " DEPEND="${RDEPEND}" + +python_test() { + distutils_install_for_testing + cd "${TEST_DIR}"/lib || die + cp "${S}"/setup.py "${TEST_DIR}"/lib/ || die + cp -r "${S}"/test "${TEST_DIR}"/lib/ || die + esetup.py test || die +} diff --git a/dev-python/pyhdf/ChangeLog b/dev-python/pyhdf/ChangeLog index 9a3683c2c..08370d422 100644 --- a/dev-python/pyhdf/ChangeLog +++ b/dev-python/pyhdf/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for dev-python/pyhdf -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pyhdf: Updating remote-id in metadata.xml + 14 Jun 2013; Justin Lecher <jlec@gentoo.org> pyhdf-0.8.3.ebuild, metadata.xml: Bump to EAPI=5 and distutils-r1.eclass - diff --git a/dev-python/pyhdf/metadata.xml b/dev-python/pyhdf/metadata.xml index 194e251e3..87469d49e 100644 --- a/dev-python/pyhdf/metadata.xml +++ b/dev-python/pyhdf/metadata.xml @@ -9,4 +9,7 @@ <use> <flag name="szip">Allow to use <pkg>sci-libs/szip</pkg> for SZIP compression method in SDsetcompress()</flag> </use> + <upstream> + <remote-id type="sourceforge">pysclint</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pynomo/ChangeLog b/dev-python/pynomo/ChangeLog index 5fc5c8b85..2116da469 100644 --- a/dev-python/pynomo/ChangeLog +++ b/dev-python/pynomo/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/pynomo -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pynomo: Updating remote-id in metadata.xml + *pynomo-0.2.2 (01 Jul 2014) 01 Jul 2014; Witold Pilat (fau) <witold.pilat@gmail.com> +metadata.xml, diff --git a/dev-python/pynomo/metadata.xml b/dev-python/pynomo/metadata.xml index f293a3afc..42183519d 100644 --- a/dev-python/pynomo/metadata.xml +++ b/dev-python/pynomo/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<maintainer> - <email>witold.pilat@gmail.com</email> -</maintainer> -<longdescription> + <maintainer> + <email>witold.pilat@gmail.com</email> + </maintainer> + <longdescription> Pynomo is a program to create (pdf) nomographs (nomograms) using Python interpreter. A nomograph (nomogram) is a graphical solution to an equation. </longdescription> + <upstream> + <remote-id type="sourceforge">pynomo</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pysolar/ChangeLog b/dev-python/pysolar/ChangeLog index a103d4a14..1c538ff17 100644 --- a/dev-python/pysolar/ChangeLog +++ b/dev-python/pysolar/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/pysolar -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pysolar: Add github to remote-id in metadata.xml + 23 Jul 2013; Sébastien Fabbro <bicatali@gentoo.org> -pysolar-0.4.4.ebuild, metadata.xml, pysolar-0.5.ebuild: dev-python/pysolar: Fixed syntax, removed old, keyword for prefix diff --git a/dev-python/pysolar/metadata.xml b/dev-python/pysolar/metadata.xml index 96827aac9..072ad7c77 100644 --- a/dev-python/pysolar/metadata.xml +++ b/dev-python/pysolar/metadata.xml @@ -1,15 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun. It includes code for extremely precise ephemeris calculations, and more. Pysolar can calculate the location of the sun or the shading percentage as a function of time for a row of 2-axis tracked panels. </longdescription> -<upstream> - <remote-id type="pypi">Pysolar</remote-id> -</upstream> + <upstream> + <remote-id type="pypi">Pysolar</remote-id> + <remote-id type="github">pingswept/pysolar</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pysparse/ChangeLog b/dev-python/pysparse/ChangeLog index 189c671d9..ee022f590 100644 --- a/dev-python/pysparse/ChangeLog +++ b/dev-python/pysparse/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/pysparse -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pysparse: Updating remote-id in metadata.xml + 06 May 2013; Justin Lecher <jlec@gentoo.org> pysparse-1.1.1-r1.ebuild: USe internal umfpack due to incompatibility with latest umfpack from tree @@ -28,4 +31,3 @@ +files/pysparse-1.1-setup.patch, +files/pysparse-1.1-superlu3.patch, +metadata.xml: Initial import - diff --git a/dev-python/pysparse/metadata.xml b/dev-python/pysparse/metadata.xml index 84d83504b..f5da15e04 100644 --- a/dev-python/pysparse/metadata.xml +++ b/dev-python/pysparse/metadata.xml @@ -13,4 +13,7 @@ standard sparse and dense matrix libraries (UMFPACK/AMD, SuperLU, BLAS/LAPACK) for maximum performance and robustness. </longdescription> + <upstream> + <remote-id type="sourceforge">pysparse</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/python-ivi/ChangeLog b/dev-python/python-ivi/ChangeLog index f299a0285..f0498551c 100644 --- a/dev-python/python-ivi/ChangeLog +++ b/dev-python/python-ivi/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/python-ivi: Add github to remote-id in metadata.xml + *python-ivi-9999 (23 Jan 2015) *python-ivi-0.14.9 (23 Jan 2015) diff --git a/dev-python/python-ivi/metadata.xml b/dev-python/python-ivi/metadata.xml index b4235335b..6c3444c18 100644 --- a/dev-python/python-ivi/metadata.xml +++ b/dev-python/python-ivi/metadata.xml @@ -12,4 +12,7 @@ use Python VXI-11, Python USBTMC, PyVISA, pySerial and linux-gpib to connect to instruments. </longdescription> -</pkgmetadata>
\ No newline at end of file + <upstream> + <remote-id type="github">python-ivi/python-ivi</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/python-vxi11/ChangeLog b/dev-python/python-vxi11/ChangeLog index e3ba7e6ef..8cbe4a547 100644 --- a/dev-python/python-vxi11/ChangeLog +++ b/dev-python/python-vxi11/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/python-vxi11: Add github to remote-id in metadata.xml + *python-vxi11-9999 (23 Jan 2015) *python-vxi11-0.7 (23 Jan 2015) diff --git a/dev-python/python-vxi11/metadata.xml b/dev-python/python-vxi11/metadata.xml index 05deeb066..d9174e52f 100644 --- a/dev-python/python-vxi11/metadata.xml +++ b/dev-python/python-vxi11/metadata.xml @@ -11,4 +11,7 @@ instrument control protocol. It is compatible with VXI-11, LXI instruments and VXI-11 to GPIB bridges (HP E2050A, etc.). </longdescription> -</pkgmetadata>
\ No newline at end of file + <upstream> + <remote-id type="github">python-ivi/python-vxi11</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/pythoncgns/metadata.xml b/dev-python/pythoncgns/metadata.xml index 897aa2e6b..83eff763e 100644 --- a/dev-python/pythoncgns/metadata.xml +++ b/dev-python/pythoncgns/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="pypi">CGNS</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/simplepam/ChangeLog b/dev-python/simplepam/ChangeLog index 1f3e6b271..c9e8f09cf 100644 --- a/dev-python/simplepam/ChangeLog +++ b/dev-python/simplepam/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/simplepam: Add github to remote-id in metadata.xml + *simplepam-0.1.5 (03 Mar 2015) *simplepam-9999 (03 Mar 2015) diff --git a/dev-python/simplepam/metadata.xml b/dev-python/simplepam/metadata.xml index 48fcc9381..04613906b 100644 --- a/dev-python/simplepam/metadata.xml +++ b/dev-python/simplepam/metadata.xml @@ -8,4 +8,8 @@ authenticate function that allows the caller to authenticate a given username / password against the PAM system. </longdescription> + <upstream> + <remote-id type="pypi">simplepam</remote-id> + <remote-id type="github">leonnnn/python3-simplepam</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/specutils/ChangeLog b/dev-python/specutils/ChangeLog index 6447cd6a1..53a0b768e 100644 --- a/dev-python/specutils/ChangeLog +++ b/dev-python/specutils/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/specutils -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/specutils: Add github to remote-id in metadata.xml + *specutils-9999 (08 Aug 2014) 08 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> +metadata.xml, diff --git a/dev-python/specutils/metadata.xml b/dev-python/specutils/metadata.xml index 91594d03b..e0d374f5d 100644 --- a/dev-python/specutils/metadata.xml +++ b/dev-python/specutils/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> specutils is a package to implement utilities and data structures to analyse astronomical spectra within python. It extends NDData from Astropy into a class with special handling of 1D spectra. </longdescription> + <upstream> + <remote-id type="pypi">specutils</remote-id> + <remote-id type="github">astropy/specutils</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ufl/ChangeLog b/dev-python/ufl/ChangeLog index 135766527..1685c46b3 100644 --- a/dev-python/ufl/ChangeLog +++ b/dev-python/ufl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/ufl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ufl: Add bitbucket to remote-id in metadata.xml + *ufl-1.3.0 (16 Jul 2014) *ufl-1.4.0 (16 Jul 2014) diff --git a/dev-python/ufl/metadata.xml b/dev-python/ufl/metadata.xml index c1c80201a..ddf216c08 100644 --- a/dev-python/ufl/metadata.xml +++ b/dev-python/ufl/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element @@ -12,4 +12,7 @@ <use> <flag name="scipy">Adds support for evaluating Bessel functions using <pkg>dev-python/scipy</pkg></flag> </use> + <upstream> + <remote-id type="bitbucket">fenics-project/ufl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/viper/ChangeLog b/dev-python/viper/ChangeLog index 036f6367f..85d81efb6 100644 --- a/dev-python/viper/ChangeLog +++ b/dev-python/viper/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/viper -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/viper: Updating remote-id in metadata.xml + *viper-1.0.1 (14 Jun 2013) 14 Jun 2013; Justin Lecher <jlec@gentoo.org> -viper-0.4.6.ebuild, @@ -13,4 +16,3 @@ 14 Dec 2010; Nico Schlömer <nico.schloemer@gmail.com> +viper-0.4.6.ebuild, +metadata.xml: Initial import. - diff --git a/dev-python/viper/metadata.xml b/dev-python/viper/metadata.xml index c1ca1a083..39623d309 100644 --- a/dev-python/viper/metadata.xml +++ b/dev-python/viper/metadata.xml @@ -1,10 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> Viper is a minimalistic scientific plotter and run-time visualization module. Viper has support for visualizing meshes and solutions in DOLFIN. </longdescription> + <upstream> + <remote-id type="launchpad">fenics-viper</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-tcltk/togl/ChangeLog b/dev-tcltk/togl/ChangeLog index 0a29a36dc..f66fddd99 100644 --- a/dev-tcltk/togl/ChangeLog +++ b/dev-tcltk/togl/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> togl-1.7-r1.ebuild: + dev-tcltk/togl: Add SLOT operator + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> togl-1.7-r1.ebuild: Bump to EAPI=5; Cleanup diff --git a/dev-tcltk/togl/metadata.xml b/dev-tcltk/togl/metadata.xml index b229aec85..987e72a0d 100644 --- a/dev-tcltk/togl/metadata.xml +++ b/dev-tcltk/togl/metadata.xml @@ -1,5 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> + <herd>sci</herd> + <upstream> + <remote-id type="sourceforge">togl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-tcltk/togl/togl-1.7-r1.ebuild b/dev-tcltk/togl/togl-1.7-r1.ebuild index 9d17cb0ce..891128af1 100644 --- a/dev-tcltk/togl/togl-1.7-r1.ebuild +++ b/dev-tcltk/togl/togl-1.7-r1.ebuild @@ -15,7 +15,8 @@ SLOT="1.7" KEYWORDS="~amd64 ~x86" IUSE="debug +threads" -RDEPEND="dev-lang/tk +RDEPEND=" + dev-lang/tk:0 virtual/opengl" DEPEND="${RDEPEND}" @@ -32,7 +33,7 @@ src_configure() { } src_install() { - emake DESTDIR="${D}" install + default rm "${D}"/usr/include/* || die insinto /usr/include/${PN}-${SLOT} doins togl*.h diff --git a/dev-tex/pythontex/ChangeLog b/dev-tex/pythontex/ChangeLog index a608dfc2f..7f6f08cce 100644 --- a/dev-tex/pythontex/ChangeLog +++ b/dev-tex/pythontex/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-tex/pythontex: Add github to remote-id in metadata.xml + *pythontex-0.14-r1 (12 May 2015) 12 May 2015; Justin Lecher <jlec@gentoo.org> +pythontex-0.14-r1.ebuild, diff --git a/dev-tex/pythontex/metadata.xml b/dev-tex/pythontex/metadata.xml index 1087ec907..f94d2c754 100644 --- a/dev-tex/pythontex/metadata.xml +++ b/dev-tex/pythontex/metadata.xml @@ -5,4 +5,7 @@ <use> <flag name="highlighting">PLEASE FIX MY DESCRIPTION</flag> </use> + <upstream> + <remote-id type="github">gpoore/pythontex</remote-id> + </upstream> </pkgmetadata> diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass index 5a7eb6cc2..4fcf67295 100644 --- a/eclass/alternatives-2.eclass +++ b/eclass/alternatives-2.eclass @@ -21,17 +21,17 @@ # sure you explicitly run alternatives-2_pkg_{postinst,prerm} where appropriate. case "${EAPI:-0}" in - 0|1|2|3) + 0|1|2|3|4) die "Unsupported EAPI=${EAPI:-0} (too old) for ${ECLASS}" ;; - 4|5) + 5) ;; *) die "Unsupported EAPI=${EAPI} (unknown) for ${ECLASS}" ;; esac -DEPEND=">=app-admin/eselect-1.4.4-r100" +DEPEND=">=app-admin/eselect-1.4.4-r102" RDEPEND="${DEPEND} !app-admin/eselect-blas !app-admin/eselect-cblas @@ -56,87 +56,12 @@ ALTERNATIVES_DIR="/etc/env.d/alternatives" alternatives_for() { debug-print-function ${FUNCNAME} "${@}" - (( $# >= 5 )) && (( ($#-3)%2 == 0)) || \ - die "${FUNCNAME} requires exactly 3+N*2 arguments where N>=1" - local alternative=${1} provider=${2} importance=${3} index src target ret=0 - shift 3 + dodir /etc/env.d/alternatives - # Make sure importance is a signed integer - if [[ -n ${importance} ]] && ! [[ ${importance} =~ ^[0-9]+(\.[0-9]+)*$ ]]; then - eerror "Invalid importance (${importance}) detected" - ((ret++)) - fi - - # Create alternative provider subdirectories under ALTERNATIVES_DIR if needed - [[ -d "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}" ]] || \ - dodir "${ALTERNATIVES_DIR}/${alternative}/${provider}" - - # Keep track of provided alternatives for use in pkg_{postinst,prerm}. - # Keep a mapping between importance and provided alternatives - # and make sure the former is set to only one value. - if ! has "${alternative}:${provider}" "${ALTERNATIVES_PROVIDED[@]}"; then - # Add new provider and set its importance - index=${#ALTERNATIVES_PROVIDED[@]} - ALTERNATIVES_PROVIDED+=( "${alternative}:${provider}" ) - ALTERNATIVES_IMPORTANCE[index]=${importance} - [[ -n ${importance} ]] && \ - echo "${importance}" > "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}/_importance" - else - # Set importance for existing provider - for ((index=0;index<${#ALTERNATIVES_PROVIDED[@]};index++)); do - if [[ ${alternative}:${provider} == ${ALTERNATIVES_PROVIDED[index]} ]]; then - if [[ -n ${ALTERNATIVES_IMPORTANCE[index]} ]]; then - if [[ -n ${importance} && ${ALTERNATIVES_IMPORTANCE[index]} != ${importance} ]]; then - eerror "Differing importance (${ALTERNATIVES_IMPORTANCE[index]} != ${importance}) detected" - ((ret++)) - fi - else - ALTERNATIVES_IMPORTANCE[index]=${importance} - [[ -n ${importance} ]] && \ - echo "${importance}" > "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}/_importance" - fi - fi - done - fi + ALTERNATIVESDIR_ROOTLESS="${ED}/etc/env.d/alternatives" \ + eselect alternatives add ${@} || die - # Process source-target pairs - while (( $# >= 2 )); do - src=${1//+(\/)/\/}; target=${2//+(\/)/\/} - if [[ ${src} != /* ]]; then - eerror "Source path must be absolute, but got ${src}" - ((ret++)) - - else - local reltarget= dir=${ALTERNATIVES_DIR}/${alternative}/${provider}${src%/*} - while [[ -n ${dir} ]]; do - reltarget+=../ - dir=${dir%/*} - done - - reltarget=${reltarget%/} - [[ ${target} == /* ]] || reltarget+=${src%/*}/ - reltarget+=${target} - dodir "${ALTERNATIVES_DIR}/${alternative}/${provider}${src%/*}" - dosym "${reltarget}" "${ALTERNATIVES_DIR}/${alternative}/${provider}${src}" - - # The -e test will fail if existing symlink points to non-existing target, - # so check for -L also. - # Say ${ED}/sbin/init exists and links to /bin/systemd (which doesn't exist yet). - if [[ -e ${ED}${src} || -L ${ED}${src} ]]; then - local fulltarget=${target} - [[ ${fulltarget} != /* ]] && fulltarget=${src%/*}/${fulltarget} - if [[ -e ${ED}${fulltarget} || -L ${ED}${fulltarget} ]]; then - die "${src} defined as provider for ${fulltarget}, but both already exist in \${ED}" - else - mv "${ED}${src}" "${ED}${fulltarget}" || die - fi - fi - fi - shift 2 - done - - # Stop if there were any errors - [[ ${ret} -eq 0 ]] || die "Errors detected for ${provider}, provided for ${alternative}" + ALTERNATIVES_CREATED+=( ${1} ) } # @FUNCTION: cleanup_old_alternatives_module @@ -151,7 +76,7 @@ cleanup_old_alternatives_module() { if [[ -f "${old_module}" && $(grep 'ALTERNATIVE=' "${old_module}" | cut -d '=' -f 2) == "${alt}" ]]; then local version="$(grep 'VERSION=' "${old_module}" | grep -o '[0-9.]\+')" if [[ "${version}" == "0.1" || "${version}" == "20080924" ]]; then - echo "rm ${old_module}" + einfo "rm ${old_module}" rm "${old_module}" || eerror "rm ${old_module} failed" fi fi @@ -168,30 +93,12 @@ cleanup_old_alternatives_module() { alternatives-2_pkg_postinst() { debug-print-function ${FUNCNAME} "${@}" - local a alt provider module_version="20150521" - local EAUTO="${EROOT%/}/usr/share/eselect/modules/auto" - - for a in "${ALTERNATIVES_PROVIDED[@]}"; do - alt="${a%:*}" - provider="${a#*:}" - if [[ ! -f "${EAUTO}/${alt}.eselect" \ - || "$(grep '^VERSION=' "${EAUTO}/${alt}.eselect" | grep -o '[0-9]\+')" \ - -ne "${module_version}" ]]; then - if [[ ! -d ${EAUTO} ]]; then - install -d "${EAUTO}" || eerror "Could not create eselect modules dir" - fi - einfo "Creating alternatives eselect module for ${alt}" - cat > "${EAUTO}/${alt}.eselect" <<- EOF - # This module was automatically generated by alternatives-2.eclass - DESCRIPTION="Alternatives for ${alt}" - VERSION="${module_version}" - MAINTAINER="eselect@gentoo.org" - ESELECT_MODULE_GROUP="Alternatives" - - ALTERNATIVE="${alt}" - - inherit alternatives - EOF + local alt + + for alt in ${ALTERNATIVES_CREATED[@]}; do + if ! eselect ${alt} show > /dev/null; then + einfo "Creating Alternative for ${alt}" + eselect alternatives create ${alt} fi # Set alternative provider if there is no valid provider selected @@ -211,25 +118,20 @@ alternatives-2_pkg_postinst() { alternatives-2_pkg_prerm() { debug-print-function ${FUNCNAME} "${@}" - local a alt provider ignore ret - local EAUTO="${EROOT%/}/usr/share/eselect/modules/auto" + local alt ret # If we are uninstalling, update alternatives to valid provider [[ -n ${REPLACED_BY_VERSION} ]] || ignore="--ignore" - for a in "${ALTERNATIVES_PROVIDED[@]}"; do - alt="${a%:*}" - provider="${a#*:}" + + for alt in ${ALTERNATIVES_CREATED[@]}; do eselect "${alt}" update ${ignore} "${provider}" - ret=$? - [[ -n ${REPLACED_BY_VERSION} ]] || \ - einfo "Removing ${provider} alternative module for ${alt}, current is $(eselect ${alt} show)" + case ${ret} in 0) : ;; 2) # This was last provider for the alternative, remove eselect module einfo "Cleaning up unused alternatives module for ${alt}" - rm "${EAUTO}/${alt}.eselect" || \ - eerror "rm ${EAUTO}/${alt}.eselect failed" + eselect alternatives delete "${alt}" || eerror "Failed to remove ${alt}" ;; *) eerror "eselect ${alt} update ${provider} returned ${ret}" diff --git a/profiles/categories b/profiles/categories index 34c941a6d..20ed0d65e 100644 --- a/profiles/categories +++ b/profiles/categories @@ -1,7 +1,6 @@ app-admin app-benchmarks app-doc -app-editors app-forensics app-portage app-text @@ -10,7 +9,6 @@ dev-cpp dev-java dev-lang dev-libs -dev-lua dev-ml dev-perl dev-python @@ -33,7 +31,6 @@ sci-mathematics sci-misc sci-physics sci-visualization -sys-apps sys-cluster sys-devel sys-infiniband diff --git a/sci-astronomy/chealpix/ChangeLog b/sci-astronomy/chealpix/ChangeLog index 538bc3f08..5934ac20f 100644 --- a/sci-astronomy/chealpix/ChangeLog +++ b/sci-astronomy/chealpix/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/chealpix -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-astronomy/chealpix: Updating remote-id in metadata.xml + *chealpix-3.11.2 (03 Feb 2014) 03 Feb 2014; Sébastien Fabbro <bicatali@gentoo.org> +chealpix-3.11.2.ebuild, diff --git a/sci-astronomy/chealpix/metadata.xml b/sci-astronomy/chealpix/metadata.xml index de81d6067..4a26a0dc1 100644 --- a/sci-astronomy/chealpix/metadata.xml +++ b/sci-astronomy/chealpix/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. This package contains the C library. </longdescription> + <upstream> + <remote-id type="sourceforge">healpix</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-astronomy/healpix_cxx/ChangeLog b/sci-astronomy/healpix_cxx/ChangeLog index 1e48b7415..72dc0ac7a 100644 --- a/sci-astronomy/healpix_cxx/ChangeLog +++ b/sci-astronomy/healpix_cxx/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/healpix_cxx -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-astronomy/healpix_cxx: Updating remote-id in metadata.xml + *healpix_cxx-3.11.2 (03 Feb 2014) 03 Feb 2014; Sébastien Fabbro <bicatali@gentoo.org> diff --git a/sci-astronomy/healpix_cxx/metadata.xml b/sci-astronomy/healpix_cxx/metadata.xml index 391b83cad..fee3b68d3 100644 --- a/sci-astronomy/healpix_cxx/metadata.xml +++ b/sci-astronomy/healpix_cxx/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. This package contains the C++ library and programs. </longdescription> + <upstream> + <remote-id type="sourceforge">healpix</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-astronomy/healpix_idl/ChangeLog b/sci-astronomy/healpix_idl/ChangeLog index e12f4a5bc..969ed48d4 100644 --- a/sci-astronomy/healpix_idl/ChangeLog +++ b/sci-astronomy/healpix_idl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/healpix_idl -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-astronomy/healpix_idl: Updating remote-id in metadata.xml + *healpix_idl-3.11 (16 Jun 2013) 16 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +healpix_idl-3.11.ebuild, diff --git a/sci-astronomy/healpix_idl/metadata.xml b/sci-astronomy/healpix_idl/metadata.xml index 020cd30c0..4f8d241a1 100644 --- a/sci-astronomy/healpix_idl/metadata.xml +++ b/sci-astronomy/healpix_idl/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. This package contains the IDL/GDL routines and plots. </longdescription> + <upstream> + <remote-id type="sourceforge">healpix_idl</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-astronomy/libthesky/ChangeLog b/sci-astronomy/libthesky/ChangeLog index 8252177ae..a274b210d 100644 --- a/sci-astronomy/libthesky/ChangeLog +++ b/sci-astronomy/libthesky/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-astronomy/libthesky: Updating remote-id in metadata.xml + 09 May 2015; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.3.2.ebuild, +metadata.xml: Moved ebuild to Science overlay @@ -52,4 +55,3 @@ 26 Aug 2013; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.0.1.ebuild, +metadata.xml: - diff --git a/sci-astronomy/libthesky/metadata.xml b/sci-astronomy/libthesky/metadata.xml index 2012f3ed4..b27321594 100644 --- a/sci-astronomy/libthesky/metadata.xml +++ b/sci-astronomy/libthesky/metadata.xml @@ -6,4 +6,7 @@ <email>AstroFloyd@gmail.com</email> <name>AstroFloyd</name> </maintainer> + <upstream> + <remote-id type="sourceforge">libthesky</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild new file mode 100644 index 000000000..b7e28666a --- /dev/null +++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +if [ "$PV" == "9999" ]; then + inherit git-r3 +fi + +DESCRIPTION="Asssemble contigs/scaffolds using related reference sequence" +HOMEPAGE="https://github.com/baoe/AlignGraph + http://bioinformatics.oxfordjournals.org/content/30/12/i319.long" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git" + KEYWORDS="" +else + SRC_URI="" + KEYWORDS="" +fi + +LICENSE="Artistic-2" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/blat + sci-biology/bowtie" + +# AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both +# need to be installed on the system. AlignGraph’s run time is currently 23–57 min +# per million aligned reads. In the performance tests of this study, the memory usage +# was 36–50 GB, and it stays <100 GB even for entire mammalian genomes. These requirements +# are more moderate than those of most de novo assemblers (Luo et al., 2012). + +# 8 threads are hardcoded. Currently users cannot make changes to this, since this is +# a moderate choice for either single CPU machines (overhead for parallelization would +# not be too large) or multiple CPU machines. Another reason is, the bottleneck for the +# runtime is usually from BLAT, no matter how many threads there are for Bowtie2. +src_compile(){ + cd AlignGraph || die + $(tc-getCXX) ${CXXFLAGS} -o AlignGraph AlignGraph.cpp -lpthread + cd ../Eval-AlignGraph || die + $(tc-getCXX) ${CXXFLAGS} -o Eval-AlignGraph Eval-AlignGraph.cpp -lpthread +} + +src_install(){ + dobin AlignGraph/AlignGraph Eval-AlignGraph/Eval-AlignGraph + dodoc README.md +} diff --git a/sci-biology/AlignGraph/ChangeLog b/sci-biology/AlignGraph/ChangeLog new file mode 100644 index 000000000..d1a50d2ba --- /dev/null +++ b/sci-biology/AlignGraph/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/AlignGraph +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/AlignGraph: Add github to remote-id in metadata.xml + +*AlignGraph-9999 (25 May 2015) + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +AlignGraph-9999.ebuild, +metadata.xml: + sci-biology/AlignGraph: new package diff --git a/sci-biology/AlignGraph/metadata.xml b/sci-biology/AlignGraph/metadata.xml new file mode 100644 index 000000000..91aa93dea --- /dev/null +++ b/sci-biology/AlignGraph/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">baoe/AlignGraph</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/BRANCH/ChangeLog b/sci-biology/BRANCH/ChangeLog index 03ab1fc78..73a69afe4 100644 --- a/sci-biology/BRANCH/ChangeLog +++ b/sci-biology/BRANCH/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/BRANCH: Add github to remote-id in metadata.xml + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> BRANCH-9999.ebuild: Move from git-2 to git-r3 eclass; add HOMEPAGE; be verbose during compilation; install docs @@ -11,4 +14,3 @@ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BRANCH-9999.ebuild, +metadata.xml: initial ebuild - diff --git a/sci-biology/BRANCH/metadata.xml b/sci-biology/BRANCH/metadata.xml index 2bc893037..a41257bf2 100644 --- a/sci-biology/BRANCH/metadata.xml +++ b/sci-biology/BRANCH/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">baoe/BRANCH</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/BlastToSam/ChangeLog b/sci-biology/BlastToSam/ChangeLog index 945f023ec..c90d4ecd1 100644 --- a/sci-biology/BlastToSam/ChangeLog +++ b/sci-biology/BlastToSam/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/BlastToSam: Add github to remote-id in metadata.xml + *BlastToSam-9999 (29 Apr 2015) 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/BlastToSam/metadata.xml b/sci-biology/BlastToSam/metadata.xml index 2bc893037..5be99c3d3 100644 --- a/sci-biology/BlastToSam/metadata.xml +++ b/sci-biology/BlastToSam/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">AstrorEnales/BlastToSam</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml index 2bc893037..d5d97aa75 100644 --- a/sci-biology/HTSeq/metadata.xml +++ b/sci-biology/HTSeq/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="pypi">HTSeq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/InterMine/ChangeLog b/sci-biology/InterMine/ChangeLog index 48beb17c4..a78e71a5f 100644 --- a/sci-biology/InterMine/ChangeLog +++ b/sci-biology/InterMine/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/InterMine: Add github to remote-id in metadata.xml + 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> InterMine-0.98.ebuild: Fix license, homepage and move from git-2 to git-r3 @@ -11,4 +14,3 @@ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +InterMine-0.98.ebuild, +metadata.xml: initial ebuild - diff --git a/sci-biology/InterMine/metadata.xml b/sci-biology/InterMine/metadata.xml index 2bc893037..b370f551e 100644 --- a/sci-biology/InterMine/metadata.xml +++ b/sci-biology/InterMine/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">intermine/intermine</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog index 6fd8f5c4c..4e2164c0b 100644 --- a/sci-biology/TransDecoder/ChangeLog +++ b/sci-biology/TransDecoder/ChangeLog @@ -1,7 +1,10 @@ -# ChangeLog for sci-biology/transdecoder +# ChangeLog for sci-biology/TransDecoder # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/TransDecoder: Add github to remote-id in metadata.xml + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> transdecoder-2.0.1.ebuild: sci-biology/transdecoder: more ebuild cleanup diff --git a/sci-biology/TransDecoder/metadata.xml b/sci-biology/TransDecoder/metadata.xml index 2bc893037..33de46b4c 100644 --- a/sci-biology/TransDecoder/metadata.xml +++ b/sci-biology/TransDecoder/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">TransDecoder/TransDecoder</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/Trinotate/ChangeLog b/sci-biology/Trinotate/ChangeLog index 4ef519a5f..86519b975 100644 --- a/sci-biology/Trinotate/ChangeLog +++ b/sci-biology/Trinotate/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> Trinotate-2.0.1.ebuild: + sci-biology/Trinotate: Fix whitespaces + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/Trinotate: Add github to remote-id in metadata.xml + *Trinotate-2.0.1 (30 Apr 2015) 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild index 8665fb403..0cf111604 100644 --- a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild +++ b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild @@ -35,8 +35,8 @@ RDEPEND="${DEPEND} # $HMMSEARCH_BINARY = "/path/to/hmmsearch2"; src_install(){ - perl_set_version - dobin Trinotate + perl_set_version + dobin Trinotate insinto /usr/share/"${PN}" doins -r admin java sample_data util TrinotateWeb insinto ${VENDOR_LIB}/${PN} diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml index 2bc893037..2fa34fe9c 100644 --- a/sci-biology/Trinotate/metadata.xml +++ b/sci-biology/Trinotate/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">Trinotate/Trinotate</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/aghermann/ChangeLog b/sci-biology/aghermann/ChangeLog index d2f653bbd..9936cbb51 100644 --- a/sci-biology/aghermann/ChangeLog +++ b/sci-biology/aghermann/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Andrei Zavada <johnhommer@gmail.com> aghermann-1.0.5.ebuild: + New upstream version. + 10 Apr 2015; Andrei Zavada <johnhommer@gmail.com> aghermann-1.0.4.ebuild: New upstream version. diff --git a/sci-biology/aghermann/Manifest b/sci-biology/aghermann/Manifest index 19798d8ec..5d580eaca 100644 --- a/sci-biology/aghermann/Manifest +++ b/sci-biology/aghermann/Manifest @@ -1,2 +1,3 @@ DIST aghermann-1.0.3.tar.xz 499492 SHA256 fa4d0543665d8e4767ff61e436ffee7249b1767e72bd4ef83e7d2a0eb03b66c0 SHA512 61b84aebfd0f22f7f831508652c8994dcd3861b354fc29022c7717b995f901200d541c491b7fd9328ccc9af7dd71779a5d8a3fc18e75fa78fc48b9ff98d72ee0 WHIRLPOOL 0f99b9d521d15fa513df905359db3f627376c83988c7b7a7bd1ad1617591acb25aa74941dc4e754443f4f879852258d65323580a2e0ae2c79024fc80c692af83 DIST aghermann-1.0.4.tar.xz 499872 SHA256 522a8c571c9e8aaecfb997f057a01298f804bff139c052d15b3347bdf2a58722 SHA512 ff891f71480ae25cce884bfea714c11eb0536cccfe4ade8c9b742d74db63dba6664e80d7f53272e95de1e04e1fdfb895ef278106a31a1d904e95cb062c4277c8 WHIRLPOOL fbfc6c3084b6d46f460b387cba521726b6fea4f4cacfd7907011507db66cc86700c7e36a1b6823d7a7fbd04d06986ec2e12654048544730765516265799af2f9 +DIST aghermann-1.0.5.tar.xz 500112 SHA256 a0c6ccd2e740f283559b92ee6fa7ff5c92699bae72cf10a7a7f6fb53e45a258e SHA512 3355664dfa59d81c110e5da4b883c09729fee440328b6c5b568f2b412d1ad3e09503832acfe4874a7b45f3330446bb2e3e144607e3af922c6ce2484162d6d4ab WHIRLPOOL ec8f5662345a9f67d59dfe7e80b8396eefcaba45e4be8ddd899e842ed35a617d92ea503d3380868f5e851a3b90d06018ecae6ad986bf015aee4f8aa14c89a211 diff --git a/sci-biology/aghermann/aghermann-1.0.5.ebuild b/sci-biology/aghermann/aghermann-1.0.5.ebuild new file mode 100644 index 000000000..8e4a8cae2 --- /dev/null +++ b/sci-biology/aghermann/aghermann-1.0.5.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="5" + +DESCRIPTION="A sleep-research experiment manager, EDF viewer & Achermann's Process S model runner" +HOMEPAGE="http://johnhommer.com/academic/code/aghermann" +SRC_URI="http://johnhommer.com/academic/code/aghermann/source/${P}.tar.xz" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/lua:* + dev-libs/libconfig + dev-libs/libunique:3 + media-libs/libsamplerate + sci-libs/fftw:3.0 + sci-libs/gsl + sci-libs/itpp + x11-libs/gtk+:3 + x11-libs/vte:2.91" + +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_configure() { + econf --bindir="${EPREFIX}"/bin +} diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog index 1a2a11d02..74d1a5dbf 100644 --- a/sci-biology/amos/ChangeLog +++ b/sci-biology/amos/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + amos-3.1.0-r2.ebuild, amos-9999.ebuild: + added dev-qt/qt3support:4 to DEPEND because 'scanelf -qn /usr/bin/hawkeye' + confirms libQt3Support.so is used (thanks to Davide Pesavento pesa@g.o) + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> amos-3.1.0-r2.ebuild, amos-9999.ebuild: sci-biology/amos: fixed installation of perl-related files diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild index fd81df623..0b777e2a2 100644 --- a/sci-biology/amos/amos-3.1.0-r2.ebuild +++ b/sci-biology/amos/amos-3.1.0-r2.ebuild @@ -22,7 +22,8 @@ IUSE="mpi qt4" DEPEND=" mpi? ( virtual/mpi ) dev-libs/boost - qt4? ( dev-qt/qtcore:4[qt3support] ) + qt4? ( dev-qt/qtcore:4[qt3support] + dev-qt/qt3support:4 ) sci-biology/blat sci-biology/jellyfish" RDEPEND="${DEPEND} diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild index c47a5b6f8..9ac9c4c2d 100644 --- a/sci-biology/amos/amos-9999.ebuild +++ b/sci-biology/amos/amos-9999.ebuild @@ -23,7 +23,8 @@ IUSE="mpi qt4" DEPEND=" mpi? ( virtual/mpi ) dev-libs/boost - qt4? ( dev-qt/qtcore:4[qt3support] ) + qt4? ( dev-qt/qtcore:4[qt3support] + dev-qt/qt3support:4 ) sci-biology/blat sci-biology/jellyfish" RDEPEND="${DEPEND} diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog index 7f9152a7a..1bf8c1aa9 100644 --- a/sci-biology/argo-bin/ChangeLog +++ b/sci-biology/argo-bin/ChangeLog @@ -1,7 +1,21 @@ # ChangeLog for sci-biology/argo-bin -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + argo-bin-1.0.31.ebuild, argo-bin-2.0.3.ebuild: + sci-biology/argo-bin: remove IUSE + +*argo-bin-2.0.3 (26 May 2015) + + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +argo-bin-2.0.3.ebuild, argo-bin-1.0.31.ebuild: + sci-biology/argo-bin: ebuild cleanup; version bump + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + argo-bin-1.0.31.ebuild: + sci-biology/argo-bin: redefine S variable so we can chdir to a WORKDIR (not + sure why the jar archive must be unpacked there at all ...) + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> argo-bin-1.0.31.ebuild: Cleaned ebuild - diff --git a/sci-biology/argo-bin/Manifest b/sci-biology/argo-bin/Manifest index 7cda4c55d..73550affb 100644 --- a/sci-biology/argo-bin/Manifest +++ b/sci-biology/argo-bin/Manifest @@ -1 +1,2 @@ -DIST argo.jar 26624770 SHA256 33ece2dba7ee5cc36f5aab99b3e7df2d641b261d86aacac00745e9d4a2e914cf +DIST argo.jar 26624770 SHA256 33ece2dba7ee5cc36f5aab99b3e7df2d641b261d86aacac00745e9d4a2e914cf SHA512 fc1aaa39453502054d402386d3551014d71a81a73593420fe5073a462b3f605e00e8b32e21e54a4f669a3f09a25e8946db17928c65c17beea26ec4316e91458d WHIRLPOOL a1a83d721f4273cee97ac04e9935c5254adf84f9187c5a7330339f71cad826cab3eb375105ba454835d5803de5d476615b6c497fb47af37536a1211d48a6b09e +DIST argo2.jar 27685069 SHA256 7ebcb16d7dcf85d1a7c8ef427f78a4cb6a48b9ff2a1814b6d4931cf4f9218002 SHA512 8a03cfe6016ffa2d661dbf04ce9fde6e5474fcf111336399c934c481a4c71758b3007a20f3af931725c9e2f5f2bf3bc0c1d131cdda6e57992c10a6c0854207a8 WHIRLPOOL c89249b732c6450eb69170f0d00950a854a613eba10aee53290f1bf50ac1888bcbd7a2902788e824125702e2002e80015d0b21fcbd89bd0593688c4878d981e4 diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild index 6a708d5c3..a59ae7a06 100644 --- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild +++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild @@ -1,24 +1,28 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit java-utils-2 toolchain-funcs DESCRIPTION="Visualization and manually annotating whole genomes" -HOMEPAGE="http://www.broadinstitute.org/annotation/argo/" +HOMEPAGE="http://www.broadinstitute.org/annotation/argo2 + http://www.broadinstitute.org/annotation/argo" SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar" -#SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz" +# +# Release Number: 1.0.31 +# Release Date: 2010-02-05 LICENSE="LGPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="java" +IUSE="" -DEPEND="" +DEPEND="!sci-biology/argo" RDEPEND="${DEPEND} - java? ( >=virtual/jre-1.4 )" + >=virtual/jre-1.5:*" +S="${WORKDIR}" src_install() { java-pkg_newjar "${DISTDIR}"/argo.jar argo.jar diff --git a/sci-biology/argo-bin/argo-bin-2.0.3.ebuild b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild new file mode 100644 index 000000000..8e475e6c3 --- /dev/null +++ b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-utils-2 toolchain-funcs + +DESCRIPTION="Visualization and manually annotating whole genomes" +HOMEPAGE="http://www.broadinstitute.org/annotation/argo2 + http://www.broadinstitute.org/annotation/argo" +SRC_URI="http://www.broadinstitute.org/annotation/argo2/releases/argo2.jar" +# +# Release Number: 3 +# Release Date: 2010-06-23 + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="!sci-biology/argo" +RDEPEND="${DEPEND} + >=virtual/jre-1.5:*" +S="${WORKDIR}" + +src_install() { + java-pkg_newjar "${DISTDIR}"/argo2.jar argo2.jar + java-pkg_dolauncher +} diff --git a/sci-biology/argo/ChangeLog b/sci-biology/argo/ChangeLog index 950f76d09..72a3d3cb9 100644 --- a/sci-biology/argo/ChangeLog +++ b/sci-biology/argo/ChangeLog @@ -2,5 +2,8 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> argo-1.0.24.ebuild: + sci-biology/argo: ebuild cleanup + 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> argo-1.0.24.ebuild: fix java depencies syntax diff --git a/sci-biology/argo/argo-1.0.24.ebuild b/sci-biology/argo/argo-1.0.24.ebuild index 00d3742d7..6e522b616 100644 --- a/sci-biology/argo/argo-1.0.24.ebuild +++ b/sci-biology/argo/argo-1.0.24.ebuild @@ -7,8 +7,12 @@ EAPI=5 inherit java-pkg-2 java-ant-2 java-utils-2 toolchain-funcs DESCRIPTION="Production tool for visualizing and manually annotating whole genomes" -HOMEPAGE="http://www.broadinstitute.org/annotation/argo/" +HOMEPAGE="http://www.broadinstitute.org/annotation/argo2 + http://www.broadinstitute.org/annotation/argo" SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz" +# +# cat workspace-2008-03-11/annotation/argo/version.txt +# Gebo-1.0.17-build-1313 LICENSE="LGPL-3" SLOT="0" @@ -16,6 +20,7 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND=" + !sci-biology/argo-bin >=virtual/jdk-1.5:* dev-java/ant-core" RDEPEND=">=virtual/jre-1.5:*" @@ -29,5 +34,7 @@ src_compile(){ src_install() { java-pkg_dojar annotation/dist/argo/argo.jar + #java-pkg_dolauncher --jar argo.jar java-pkg_dojar annotation/dist/argo/argo-applet-unproguarded.jar + #java-pkg_dolauncher --jar argo-applet-unproguarded.jar } diff --git a/sci-biology/artemis-bin/Manifest b/sci-biology/artemis-bin/Manifest index d9651ab45..3bd261d96 100644 --- a/sci-biology/artemis-bin/Manifest +++ b/sci-biology/artemis-bin/Manifest @@ -1,2 +1,4 @@ DIST artemis.pdf 1149449 SHA256 ab573b4ea7b895cb7d2a97e4d42a71938f1feda44e2da22fe5b079583ad87ba6 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb WHIRLPOOL a75266ae72075ea7547560a9046c1e0f813956b94a5c3d9af3cd08a579ed60af842c6ece94e6b1dfa5db1820094069edb7d88b4ee6256410ebced4310739d79f DIST artemis_compiled_v16.0.11.tar.gz 10722613 SHA256 0413c3f0deab4d813bc4f3af7aef8cca09ad2111b3497a0696c18a31857ffd4b SHA512 a0fb9f64b0fb869bde9fe2d1788ed938a16ea0bd75315abd93e65af89772fe9d4589b7e7813286c9b1d90f1f3133c16d9bc35ce78d1740c5631ca0e32633e421 WHIRLPOOL 0682bdfead9f95a17180816ed445226c128a804f8db3549c78627b510330694b60fd7ab0e419766bf08295f3a266eefd0dfd85c0d1244c80009b5aba0c29052a +DIST artemis_v16.0.11.jar 11292419 SHA256 f368714105646cfc31460cfcfb72b8b33490c7684ee5323d7dd181060039c80f SHA512 2fbd7c5ab12c2ca710906324eb5ee861d4821eaf923f630a800ce2b2de4e43c3971cf6c470140aa2654741ab79440a2039e8b9a17502ca955432d9ef311e9f84 WHIRLPOOL fc605625b536853ee7657b09bca93f04b9f1da67a093875bcfac0d4948f7daf020c26f0624b551aba36f21e87a7ee8b933e0e26c45a715ea2fe6cb9211d0f78f +DIST sartemis_v16.0.11.jar 11832144 SHA256 834ad0464405843904b173f38220f47867ec8eb779cb2c37d6de7ba585ef133c SHA512 6fd63ac81eed727816fe633cde3e9fab9eaf71a61c74aef4f82c8c4dc24efe93ce86494ebdf3fcb3d82e50aed5c277f383f67c1b7b68ae81cf872f2982bc1850 WHIRLPOOL 874ab57f11b011a222efd4b91278614941b096756faf0259b844453dfb082d99bae503faa2ffaeb6c4d56b4317b3bcc00a49f8b5b16d6c7cc02968b4911c503a diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild index d089c7fc0..3c0415906 100644 --- a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild +++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild @@ -10,22 +10,35 @@ MY_V="16" DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool" HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis" -SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz + ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_v"${PV}".jar + ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/sartemis_v"${PV}".jar ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf" - LICENSE="GPL-2" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" IUSE="" -DEPEND="sci-biology/samtools - sci-biology/BamView" +S="${WORKDIR}"/artemis + +DEPEND=" + !sci-biology/artemis + sci-biology/samtools" RDEPEND="${DEPEND} >=virtual/jre-1.6" src_install(){ - dodoc artemis.pdf + cp -p "${DISTDIR}"/artemis_v"${PV}".jar artemis.jar || die + java-pkg_dojar artemis.jar + cp -p "${DISTDIR}"/sartemis_v"${PV}".jar sartemis.jar || die + java-pkg_dojar sartemis.jar + dodoc "${DISTDIR}"/artemis.pdf README } -# do not know what is the diffeerence between artemis_compiled_v16.0.6.tar.gz, artemis_v16.0.6.jar and sartemis_v16.0.6.jar -# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.6/ +# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files +# artemis_v16.0.11.jar and sartemis_v16.0.11.jar +# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.11/ + +pkg_postinst(){ + einfo "For BAM file support please install sci-biology/BamView" +} diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog index 4bebaffc8..818f34c42 100644 --- a/sci-biology/artemis/ChangeLog +++ b/sci-biology/artemis/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 09 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild: + sci-biology/artemis: ebuild cleanup; officially there is not install and one + needs to keep the structure of the source tree and execute directly from + there; therefore the ebuild does not work yet + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild: sci-biology/artemis: fix SLOT operators diff --git a/sci-biology/artemis/Manifest b/sci-biology/artemis/Manifest new file mode 100644 index 000000000..1c027d782 --- /dev/null +++ b/sci-biology/artemis/Manifest @@ -0,0 +1 @@ +DIST artemis.pdf 1149449 SHA256 ab573b4ea7b895cb7d2a97e4d42a71938f1feda44e2da22fe5b079583ad87ba6 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb WHIRLPOOL a75266ae72075ea7547560a9046c1e0f813956b94a5c3d9af3cd08a579ed60af842c6ece94e6b1dfa5db1820094069edb7d88b4ee6256410ebced4310739d79f diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild index 630e392f3..8db550951 100644 --- a/sci-biology/artemis/artemis-9999.ebuild +++ b/sci-biology/artemis/artemis-9999.ebuild @@ -6,9 +6,9 @@ EAPI=5 inherit java-pkg-2 java-ant-2 git-r3 -DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool" +DESCRIPTION="DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool" HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis" -SRC_URI="" +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf" EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis" LICENSE="GPL-2" @@ -21,13 +21,41 @@ RDEPEND=" sci-biology/samtools >=virtual/jre-1.6:*" DEPEND="${RDEPEND} + !sci-biology/artemis-bin dev-java/ant-core - >=virtual/jdk-1.6:*" + >=virtual/jdk-1.6:* + dev-java/log4j + dev-java/jdbc-postgresql + dev-java/jakarta-regexp + dev-java/batik + dev-java/j2ssh + sci-biology/picard + dev-java/biojava" +# some more dependencies extracted from /usr/bin/act +# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar, +# # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html # http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial -# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf - # BamView is at http://bamview.sourceforge.net/ + +src_compile(){ + ant || die +} + +src_install(){ + dobin act act.command art dnaplotter gff2embl + java-pkg_dojar ant-build/artemis.jar + dodoc "${DISTDIR}"/artemis.pdf README +} + +# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files +# artemis_v16.0.11.jar and sartemis_v16.0.11.jar +# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.11/ + +pkg_postinst(){ + einfo "For BAM file support please install sci-biology/BamView" + einfo " from http://bamview.sourceforge.net" +} diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog index ae9f1c67b..d24d31d94 100644 --- a/sci-biology/augustus/ChangeLog +++ b/sci-biology/augustus/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $ +*augustus-3.1 (25 May 2015) + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +augustus-3.1.ebuild, -augustus-3.0.3.ebuild: + sci-biology/augustus: version bump + 16 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild: sci-biology/augustus: Switch RDEPEND - DEPEND diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest index 1a68ffa25..2de508495 100644 --- a/sci-biology/augustus/Manifest +++ b/sci-biology/augustus/Manifest @@ -1 +1 @@ -DIST augustus-3.0.3.tar.gz 81617475 SHA256 557364b86483c67ee11d05c074e12157ced7e4f4fe779889cd54c2c22579bf2d SHA512 8d573e800551aa8011e5663705b08a3ab4bc04acfb05041dd53738f40c8aec2ecb5794b9173a07f3ff0380413a9b6867f03cd3e7001b704eef2ebcab656452ab WHIRLPOOL d57dff333f0786b19278e971303a13d5d77c5e01d803c8e488505d6c1efa24068a0052ef5f7f9b8d1b5f9e954f0b9b64124a90acdc3896776ef23b01166920e7 +DIST augustus-3.1.tar.gz 75867488 SHA256 6db15a859537ccab8739e09c9c28f59c31dd9781e19d91f0d4489f60c7c15486 SHA512 7662b9610d8c1fa7311e3c94b698f0051d4ec885645f5def8df0a9c65a42bd11d2e538c640170716b5f6a4064ad52549be80be977724cd2d52d9623fcd85e061 WHIRLPOOL 9409cd8c6272a39b52c8338d7a59099c86ba4b106ab6227927ea8e0afc3016db3914cacacf8873d259483d73d10d143b3123780fe39591e5b54b91ccba161288 diff --git a/sci-biology/augustus/augustus-3.0.3.ebuild b/sci-biology/augustus/augustus-3.1.ebuild index d0fe711cf..d0fe711cf 100644 --- a/sci-biology/augustus/augustus-3.0.3.ebuild +++ b/sci-biology/augustus/augustus-3.1.ebuild diff --git a/sci-biology/bamtools/ChangeLog b/sci-biology/bamtools/ChangeLog index 8afcd01cf..54378eb20 100644 --- a/sci-biology/bamtools/ChangeLog +++ b/sci-biology/bamtools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/bamtools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bamtools: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild, metadata.xml: Switch from git-2 to git-r3 @@ -25,4 +28,3 @@ 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild: Moved from 'git' to 'git-2' - diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml index e304b1287..1bb8db887 100644 --- a/sci-biology/bamtools/metadata.xml +++ b/sci-biology/bamtools/metadata.xml @@ -7,4 +7,7 @@ <name>Martin Mokrejs</name> </maintainer> <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> + <upstream> + <remote-id type="github">pezmaster31/bamtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog index f8f7b58ac..a53d27c16 100644 --- a/sci-biology/bcftools/ChangeLog +++ b/sci-biology/bcftools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bcftools: Add github to remote-id in metadata.xml + *bcftools-1.2 (02 Mar 2015) 02 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml index 2bc893037..39c1d32fa 100644 --- a/sci-biology/bcftools/metadata.xml +++ b/sci-biology/bcftools/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">samtools/bcftools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog index a36ef570b..e72833e57 100644 --- a/sci-biology/bedtools/ChangeLog +++ b/sci-biology/bedtools/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> bedtools-2.22.1.ebuild: + sci-biology/bedtools: Bump to EAPI=5 + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bedtools: Add github to remote-id in metadata.xml + *bedtools-2.22.1 (14 Jan 2015) 14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/bedtools/bedtools-2.22.1.ebuild b/sci-biology/bedtools/bedtools-2.22.1.ebuild index df72ec7b3..97a20b3f7 100644 --- a/sci-biology/bedtools/bedtools-2.22.1.ebuild +++ b/sci-biology/bedtools/bedtools-2.22.1.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit flag-o-matic diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml index d841c4bcb..6edffa4a6 100644 --- a/sci-biology/bedtools/metadata.xml +++ b/sci-biology/bedtools/metadata.xml @@ -12,5 +12,6 @@ </longdescription> <upstream> <remote-id type="google-code">bedtools</remote-id> + <remote-id type="github">arq5x/bedtools2</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/biobambam/ChangeLog b/sci-biology/biobambam/ChangeLog new file mode 100644 index 000000000..79127ede4 --- /dev/null +++ b/sci-biology/biobambam/ChangeLog @@ -0,0 +1,6 @@ +# ChangeLog for sci-biology/biobambam +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/biobambam: Add github to remote-id in metadata.xml diff --git a/sci-biology/biobambam/metadata.xml b/sci-biology/biobambam/metadata.xml index 9dab65018..7f3371953 100644 --- a/sci-biology/biobambam/metadata.xml +++ b/sci-biology/biobambam/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-biology</herd> -<longdescription lang="en"> + <herd>sci-biology</herd> + <longdescription lang="en"> This package contains some tools for processing BAM files including bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name @@ -12,4 +12,7 @@ bamrecompress: reads BAM and writes BAM with a defined compression setting. This bamsort: reads BAM and writes BAM resorted by coordinates or query name bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name </longdescription> + <upstream> + <remote-id type="github">gt1/biobambam</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog index cbcd71882..97f68443b 100644 --- a/sci-biology/blue/ChangeLog +++ b/sci-biology/blue/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*blue-1.1.3 (26 May 2015) + + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.3.ebuild, + blue-1.1.2.ebuild: + sci-biology/blue: version bump, updated HOMEPAGE and SRC_URI + 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> blue-1.1.2.ebuild: improved comments based on email from upstream diff --git a/sci-biology/blue/Manifest b/sci-biology/blue/Manifest index eaacef198..91292c1f6 100644 --- a/sci-biology/blue/Manifest +++ b/sci-biology/blue/Manifest @@ -1,2 +1,6 @@ -DIST Correcting_reads_with_Blue.pdf 821286 SHA256 b20cf2524740a2fbacee6bf0dbb652c06a00a3a1b112d448114cebe900bc970d SHA512 73906f2844d89dbf7dcf6a163d8763b8995669871082abf362c4cc4fa8b21fa180cad0c4f024ea4d82a32a0fcda8d4e85a563d58cc7fd2b49dc63c09c88ef714 WHIRLPOOL 754b77f034f1df878f8b942f6985212a3da0f57576a6a5bbd06564591ac41c40396c147a91a2792ab226a7c30a23179e3118724f72ee289bd2133b61c14a2ec1 +DIST blue-1.1.2-Changes_for_Blue_1.1.2.pdf 310372 SHA256 c40a06a780223642152d30cf12c11b35af80c5778e2b584c490ded7acb962e36 SHA512 1f6d595018e880a9d10197816881fa88bbc1da9613fb83d0c3b77fe3ea22e614a9fc9783abfa7f649c242a4966a6929c53fcd1b845f98280d50c491b4cff8f73 WHIRLPOOL 7ead99964d95a3a6c77acde87c9b90e4d031838eb60e000f20c7e96f85e854b8118b57a0a69d4d927ece7e58fccfa322ce0b4eb9d7420f0bfb58f71b06ae7296 +DIST blue-1.1.2-Correcting_reads_with_Blue.pdf 560129 SHA256 4938a9e98851a8c13d96fd0ce3be15f97c00cb008751594884fa2f13bac9c561 SHA512 1341a7f3d4c77b3a3f8d66f57b4cc976930bf7d28219d77a3a91efde0bc76f08bf0159c98df3227a2484dc0fe7d40904dbbde74dc03b6c110649285314a07585 WHIRLPOOL e6089c2e895d7c693c2f2dd30ffe7c3911d9cc67f971e9da8551333f75b99a35927927a3cea728438de4310acc9da4ad99e51ec75ac49acd306a60b53b395f9d DIST blue-1.1.2.tar.gz 658544 SHA256 c038fa9fd76330cb70059cd47979327708368e2d6b6d7edae00825ba39dc23bd SHA512 933b2a8bb1e1f3fed241cff2eac9566d49d77c3f97b2f22f4a8194f3cdf25c09ae474b4d681ff65914d695598579fded6433f6a47ad06b78879c36d58402ea4b WHIRLPOOL 32c89ae39cfadab9beae038afd530cf85d8c8775a84bd5e2c29a2e67246d9b09d5c872492c1836dfab6fe20e9f59a1b0aaddc5dc051393030ccff39bb08fec8e +DIST blue-1.1.3-Changes_for_Blue_1.1.3.pdf 310372 SHA256 c40a06a780223642152d30cf12c11b35af80c5778e2b584c490ded7acb962e36 SHA512 1f6d595018e880a9d10197816881fa88bbc1da9613fb83d0c3b77fe3ea22e614a9fc9783abfa7f649c242a4966a6929c53fcd1b845f98280d50c491b4cff8f73 WHIRLPOOL 7ead99964d95a3a6c77acde87c9b90e4d031838eb60e000f20c7e96f85e854b8118b57a0a69d4d927ece7e58fccfa322ce0b4eb9d7420f0bfb58f71b06ae7296 +DIST blue-1.1.3-Correcting_reads_with_Blue.pdf 560129 SHA256 4938a9e98851a8c13d96fd0ce3be15f97c00cb008751594884fa2f13bac9c561 SHA512 1341a7f3d4c77b3a3f8d66f57b4cc976930bf7d28219d77a3a91efde0bc76f08bf0159c98df3227a2484dc0fe7d40904dbbde74dc03b6c110649285314a07585 WHIRLPOOL e6089c2e895d7c693c2f2dd30ffe7c3911d9cc67f971e9da8551333f75b99a35927927a3cea728438de4310acc9da4ad99e51ec75ac49acd306a60b53b395f9d +DIST blue-1.1.3.tar.gz 717341 SHA256 42c5b3a2156712e34d0537bcdc97aedf72ea0ab363527f1448e20969ebc4b355 SHA512 fc51965a063ced80304b3e59eb538742f6f4a2970d02cecc346aa8b15e961a242b6ce6cc3a847c8e4f478bee997ed5794f304d201554398130c1a16bceb84c30 WHIRLPOOL 087552bfd7f9e9b9be578519cdb31802cec82b140da80bdd30f9b0fe14cdaeea58b0277e33c6c3603201e293d463ec03631fa1395334e8f38f812ed97b6f04af diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild index 5b9ed96ae..945a35d12 100644 --- a/sci-biology/blue/blue-1.1.2.ebuild +++ b/sci-biology/blue/blue-1.1.2.ebuild @@ -5,11 +5,11 @@ EAPI=5 DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions" -HOMEPAGE="http://www.csiro.au/Outcomes/ICT-and-Services/Software/Blue.aspx" +HOMEPAGE="http://www.bioinformatics.csiro.au/blue" SRC_URI=" - http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx -> ${P}.tar.gz - http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Correcting_reads_with_Blue.ashx -> Correcting_reads_with_Blue.pdf" - + http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz + http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf + http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf" LICENSE="GPL-2+" SLOT="0" KEYWORDS="" @@ -29,6 +29,10 @@ src_compile(){ src_install(){ dobin Tessel.exe GenerateMerPairs.exe Blue.exe # one could install also the *.exe.so files for speedup into /usr/bin/ + + # The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made. + + # In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently? } # it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector diff --git a/sci-biology/blue/blue-1.1.3.ebuild b/sci-biology/blue/blue-1.1.3.ebuild new file mode 100644 index 000000000..945a35d12 --- /dev/null +++ b/sci-biology/blue/blue-1.1.3.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions" +HOMEPAGE="http://www.bioinformatics.csiro.au/blue" +SRC_URI=" + http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz + http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf + http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf" +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="dev-lang/mono" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/Linux + +src_compile(){ + Blue/compile.sh || die + Tessel/compile.sh || die + GenerateMerPairs/compile.sh || die +} + +src_install(){ + dobin Tessel.exe GenerateMerPairs.exe Blue.exe + # one could install also the *.exe.so files for speedup into /usr/bin/ + + # The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made. + + # In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently? +} + +# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index 4be1ee3aa..d2248db7b 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bowtie: Updating remote-id in metadata.xml + 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bowtie-1.1.1.ebuild, bowtie-2.2.3.ebuild, bowtie-2.2.5.ebuild: sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2) diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml index f17a827e3..e49341707 100644 --- a/sci-biology/bowtie/metadata.xml +++ b/sci-biology/bowtie/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">bowtie-bio</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bx-python/ChangeLog b/sci-biology/bx-python/ChangeLog index 87a323962..6c3346626 100644 --- a/sci-biology/bx-python/ChangeLog +++ b/sci-biology/bx-python/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bx-python: Add bitbucket to remote-id in metadata.xml + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> bx-python-0.7.2.ebuild, bx-python-9999.ebuild: sci-biology/bx-python: Streamline ebuild diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index b7551a6aa..1e685c91f 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -6,4 +6,8 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="pypi">bx-python</remote-id> + <remote-id type="bitbucket">james_taylor/bx-python</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/codonw/ChangeLog b/sci-biology/codonw/ChangeLog index 00b6629e0..4226f0e7e 100644 --- a/sci-biology/codonw/ChangeLog +++ b/sci-biology/codonw/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/codonw: Updating remote-id in metadata.xml + +*codonw-1.4.4-r2 (30 May 2015) + + 30 May 2015; Justin Lecher <jlec@gentoo.org> +codonw-1.4.4-r2.ebuild, + -codonw-1.4.4-r1.ebuild, metadata.xml: + sci-biology/codonw: Workaround file collision by appending PN to every + command, bug #344713, bug #550388 + 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> condow-1.4.4-r1.ebuild: Move to EAPI=5. @@ -14,4 +24,3 @@ 28 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package sci-biology/codonw, ebuild written by me - diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild index 85c0c5e9e..99c6994a7 100644 --- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild @@ -20,7 +20,8 @@ KEYWORDS="~amd64 ~x86" S=${WORKDIR}/codonW src_prepare() { - sed -e 's/$(CC) -c/& -DBSD/' \ + sed \ + -e 's/$(CC) -c/& -DBSD/' \ -e 's/$(CFLAGS) $(objects)/$(CFLAGS) $(LDFLAGS) $(objects)/' \ -i Makefile || die } @@ -30,10 +31,11 @@ src_compile() { } src_install() { - dobin codonw + local i + dobin ${PN} # woohoo watch out for collisions for i in rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc; do - dosym codonw /usr/bin/${i} + dosym codonw /usr/bin/${i}-${PN} done dodoc *.txt } diff --git a/sci-biology/codonw/metadata.xml b/sci-biology/codonw/metadata.xml index 3302123e5..1930fee10 100644 --- a/sci-biology/codonw/metadata.xml +++ b/sci-biology/codonw/metadata.xml @@ -1,9 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">codonw</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml index 2bc893037..21184a5d6 100644 --- a/sci-biology/cutadapt/metadata.xml +++ b/sci-biology/cutadapt/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="pypi">cutadapt</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/dcmstack/ChangeLog b/sci-biology/dcmstack/ChangeLog index 91a0d5d0f..6b8c0b1b5 100644 --- a/sci-biology/dcmstack/ChangeLog +++ b/sci-biology/dcmstack/ChangeLog @@ -2,22 +2,23 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ - 31 Mar 2015; <chymera@gentoo.org> dcmstack-9999.ebuild: + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: gentoo does not support python 2_6 - 31 Mar 2015; <chymera@gentoo.org> dcmstack-9999.ebuild: + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: corrected python compatibilities - 31 Mar 2015; <chymera@gentoo.org> dcmstack-9999.ebuild: + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: added python 3.3 compatibility - 31 Mar 2015; <chymera@gentoo.org> dcmstack-9999.ebuild: + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: removed unneeded bits, sorted eclasses - 31 Mar 2015; <chymera@gentoo.org> dcmstack-9999.ebuild: + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: updated deps *dcmstack-9999 (31 Mar 2015) - 31 Mar 2015; <chymera@gentoo.org> +dcmstack-9999.ebuild, +metadata.xml: + 31 Mar 2015; Horea Christian <h.chr@mail.ru> +dcmstack-9999.ebuild, + +metadata.xml: new package, initial draft diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog index f4e2dcd62..b3b197f41 100644 --- a/sci-biology/discrover/ChangeLog +++ b/sci-biology/discrover/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/discrover: Add github to remote-id in metadata.xml + *discrover-1.6.0 (18 Mar 2015) 18 Mar 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.6.0.ebuild, diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml index fb652d7be..85d16cfe7 100644 --- a/sci-biology/discrover/metadata.xml +++ b/sci-biology/discrover/metadata.xml @@ -22,4 +22,7 @@ Link to the standalone Rmathlib for statistical routines </flag> </use> + <upstream> + <remote-id type="github">maaskola/discrover</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/epga/ChangeLog b/sci-biology/epga/ChangeLog index 1e947a08e..225a25bf2 100644 --- a/sci-biology/epga/ChangeLog +++ b/sci-biology/epga/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/epga: Add github to remote-id in metadata.xml + 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> epga-9999.ebuild: Switch from git-2 to git-r3; Cleanup diff --git a/sci-biology/epga/metadata.xml b/sci-biology/epga/metadata.xml index 2bc893037..52749c688 100644 --- a/sci-biology/epga/metadata.xml +++ b/sci-biology/epga/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">bioinfomaticsCSU/EPGA</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/est2assembly/ChangeLog b/sci-biology/est2assembly/ChangeLog index 902484828..19a53e11b 100644 --- a/sci-biology/est2assembly/ChangeLog +++ b/sci-biology/est2assembly/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + est2assembly-1.08.ebuild: + fix S variable, use PV in URI + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> est2assembly-1.08.ebuild, est2assembly-9999.ebuild: Bump EAPI; drop KEYWORDS from live ebuild; fix deps diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild index dcbcfb5e8..e9878a7f3 100644 --- a/sci-biology/est2assembly/est2assembly-1.08.ebuild +++ b/sci-biology/est2assembly/est2assembly-1.08.ebuild @@ -6,7 +6,7 @@ EAPI=5 DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display" HOMEPAGE="http://code.google.com/p/est2assembly/" -SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_1.08.tar.gz" +SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_${PV}.tar.gz" LICENSE="GPL-3" SLOT="0" @@ -24,3 +24,5 @@ DEPEND=" sci-biology/emboss sci-biology/bioperl" RDEPEND="${DEPEND}" + +S="${WORKDIR}"/"${PN}" diff --git a/sci-biology/exonerate-gff3/ChangeLog b/sci-biology/exonerate-gff3/ChangeLog index a7873b87c..bde29ffde 100644 --- a/sci-biology/exonerate-gff3/ChangeLog +++ b/sci-biology/exonerate-gff3/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/exonerate-gff3: Add github to remote-id in metadata.xml + *exonerate-gff3-9999 (02 Apr 2015) 02 Apr 2015; Justin Lecher <jlec@gentoo.org> +exonerate-gff3-9999.ebuild, diff --git a/sci-biology/exonerate-gff3/metadata.xml b/sci-biology/exonerate-gff3/metadata.xml index 5205079c7..21e8763b3 100644 --- a/sci-biology/exonerate-gff3/metadata.xml +++ b/sci-biology/exonerate-gff3/metadata.xml @@ -9,4 +9,7 @@ <use> <flag name="utils">Unknown</flag> </use> + <upstream> + <remote-id type="github">hotdogee/exonerate-gff3</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog index b828a60ff..cd180e7ea 100644 --- a/sci-biology/fastqc/ChangeLog +++ b/sci-biology/fastqc/ChangeLog @@ -2,6 +2,21 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + fastqc-0.11.3.ebuild: + more comments on the external dependencies + + 10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + fastqc-0.11.3.ebuild: + add dependency on jhdf5; more ebuild cleanup + +*fastqc-0.11.3 (30 May 2015) + + 30 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +fastqc-0.11.3.ebuild, -fastqc-0.11.2.ebuild: + sci-biology/fastqc: version bump, added perl dependency, Apache ant-building + does not work still + 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +files/build.xml, fastqc-0.11.2.ebuild: added build.xml exported by author from Eclipse IDE (it doesn't work under ant diff --git a/sci-biology/fastqc/Manifest b/sci-biology/fastqc/Manifest index c8dd062ca..4e8207292 100644 --- a/sci-biology/fastqc/Manifest +++ b/sci-biology/fastqc/Manifest @@ -1 +1 @@ -DIST fastqc_v0.11.2_source.zip 996798 SHA256 efee48358830f5120b5a39311d5f50352b1476e89bf5ea4ad6ce1ab831ee7eee SHA512 c0443d7b8313b488090832c7697662d6fccbe8bddf42d7941bb8a3f50e55c104cfa06e2edbd0e04c5fc5de02eadd61830ceddf2c944228a1ce9479d846a750b3 WHIRLPOOL 2aeae03c18595a7a56b88f353b2490d7a826aa7130451e3fc05faf111c1aeea67f5ea617225cedc1d11172ee5c3f823b1f0793278ef5910b8bec00468de76ce9 +DIST fastqc_v0.11.3_source.zip 10073593 SHA256 b62b1aea957af9051b30d306183df239b095eac4f8d281478c372b25c61fe44d SHA512 bab27d6997ad6525b7804ba9a3a54eec1cdb835d548c2840ae882334902d12eea4bbff549370669176ade76633a5f1d7dc6f7ee865a25f1a41b525764660b471 WHIRLPOOL 843039e115aa0101e687ad9fe9b40d4e658e96f6dbebe87a9f4074c1f3ea46910f3dac1a3426ec329a194a542580ca16ce5d22c348500453ba357c27f15a7f06 diff --git a/sci-biology/fastqc/fastqc-0.11.2.ebuild b/sci-biology/fastqc/fastqc-0.11.2.ebuild deleted file mode 100644 index dadc2881d..000000000 --- a/sci-biology/fastqc/fastqc-0.11.2.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit java-pkg-2 eutils java-ant-2 - -DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" -HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" -SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="sci-biology/picard - >=virtual/jre-1.5:*" -RDEPEND="${DEPEND} - >=virtual/jdk-1.5:* - dev-java/ant-core" - -S="${WORKDIR}"/FastQC - -src_prepare(){ - cp "${FILESDIR}"/build.xml . || die -} - -src_install(){ - dobin fastqc run_fastqc.bat - dodoc README.txt RELEASE_NOTES.txt - - # TODO: need to compile java in uk/ac/babraham/FastQC/ - # and decide whether jbzip2-0.9.jar is a standard java lib or not - # ignore the sam-1.32.jar, that is likely library already in sci-biology/picard -} diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild new file mode 100644 index 000000000..7c8cb9e7b --- /dev/null +++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 eutils java-ant-2 + +DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" +HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" +SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/picard + sci-libs/jhdf5 + >=virtual/jre-1.5:*" +RDEPEND="${DEPEND} + dev-lang/perl + >=virtual/jdk-1.5:* + dev-java/ant-core" + +S="${WORKDIR}"/FastQC + +src_prepare(){ + cp "${FILESDIR}"/build.xml . || die +} + +src_compile(){ + ant || die +} + +src_install(){ + dobin fastqc run_fastqc.bat + dodoc README.txt RELEASE_NOTES.txt + + # There is no fastqc.jar. The output from the compilation is the set of + # .class files (a jar file is just a zip file full of .class files). All + # you need to copy out is the contents of the bin subdirectory, the rest of + # the download you can discard. + # + # jbzip2-0.9.jar comes from https://code.google.com/p/jbzip2 + # + # ignore the sam-1.103.jar and rely on /usr/share/picard/lib/sam.jar from sci-biology/picard + # The sam-1.103.jar library comes from + # http://sourceforge.net/projects/picard/files/sam-jdk/. Note that there is + # a newer version of this codebase at https://github.com/samtools/htsjdk but + # that FastQC is NOT yet compatible with the updated API (this will probably + # happen in a future release). This library is needed to read SAM/BAM + # format files. + # cisd-jhdf5.jar should be provided by sci-libs/jhdf5 +} diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog index f233c5472..931fa7947 100644 --- a/sci-biology/fastx_toolkit/ChangeLog +++ b/sci-biology/fastx_toolkit/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/fastx_toolkit -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/fastx_toolkit: Add github to remote-id in metadata.xml + *fastx_toolkit-0.0.14 (20 Jan 2014) 20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml index 897aa2e6b..bd98b5829 100644 --- a/sci-biology/fastx_toolkit/metadata.xml +++ b/sci-biology/fastx_toolkit/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="github">agordon/fastx_toolkit</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ffindex/ChangeLog b/sci-biology/ffindex/ChangeLog index a711d80ab..7dfb4b433 100644 --- a/sci-biology/ffindex/ChangeLog +++ b/sci-biology/ffindex/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/ffindex: Add github to remote-id in metadata.xml + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ffindex-0.9.9.3.ebuild: + sci-biology/ffindex: fix SRC_URI because TransDecoder which contains this + bundled thing has moved + *ffindex-0.9.9.3 (08 Jan 2015) 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/ffindex/Manifest b/sci-biology/ffindex/Manifest index 7f4aa956c..83f501c15 100644 --- a/sci-biology/ffindex/Manifest +++ b/sci-biology/ffindex/Manifest @@ -1 +1 @@ -DIST TransDecoder_r20140704.tar.gz 21189681 SHA256 fb53c9601c4ae9b3cd8e937f158ae3f15439115609bc7658effffa24af53517e SHA512 fa70e440c3f8b8d11da780858ff6433adf9065b126b29eb047983b17913e382c677a272881ee78be8e30867bbd447eb9bda71bd11abda5203d6a3abfb5316e90 WHIRLPOOL d603d06c8c1e84f3e721c0f5e43b2519766eaae1fc0456ece07ff43c13971706aecb24473813b7606ca885d2ef526648fc28f874200a53037b4aa6b291c4864d +DIST TransDecoder-2.0.1.tar.gz 9925281 SHA256 ce069da72c8a04e739f8c057af4f97187bf587d3f0d3db40465dfc2c89393e22 SHA512 fd12aeda089a12036e288e58eb0a3c3b9bb1f104f6821102d84ba6ddaec1a9dd32ec7937cd87129ff9814c7c8e26b6b98d27c6af8edd7ed6b5335c4878f649de WHIRLPOOL 61c6b7fe5684becdb28a3bccb113fea07889a2c4e6627e92cd27c1a90ca53f5a88504e048363a1322f1108dd6ebd5549c52aee9d438fbcfb2023390c79c126ec diff --git a/sci-biology/ffindex/ffindex-0.9.9.3.ebuild b/sci-biology/ffindex/ffindex-0.9.9.3.ebuild index 1a9a9a18f..c3ff78e5d 100644 --- a/sci-biology/ffindex/ffindex-0.9.9.3.ebuild +++ b/sci-biology/ffindex/ffindex-0.9.9.3.ebuild @@ -6,7 +6,8 @@ EAPI=5 DESCRIPTION="Simple index/database for huge amounts of small files" HOMEPAGE="http://pubshare.genzentrum.lmu.de/scientific_computing/software/ffindex" -SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz" +#SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz" +SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/TransDecoder.tar.gz -> TransDecoder-2.0.1.tar.gz" LICENSE="CC-BY-3.0" SLOT="0" diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml index 2bc893037..33de46b4c 100644 --- a/sci-biology/ffindex/metadata.xml +++ b/sci-biology/ffindex/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">TransDecoder/TransDecoder</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog index 8921fb7ac..be68896f6 100644 --- a/sci-biology/freebayes/ChangeLog +++ b/sci-biology/freebayes/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/freebayes: Add github to remote-id in metadata.xml + 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> freebayes-9999.ebuild: install also the vcftools binaries although it should be a separate package diff --git a/sci-biology/freebayes/metadata.xml b/sci-biology/freebayes/metadata.xml index 2bc893037..88b381109 100644 --- a/sci-biology/freebayes/metadata.xml +++ b/sci-biology/freebayes/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">ekg/freebayes</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog index f97b5dafc..086612dba 100644 --- a/sci-biology/fsl/ChangeLog +++ b/sci-biology/fsl/ChangeLog @@ -2,78 +2,81 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ - 09 Apr 2015; <chymera@gentoo.org> -files/fsl-5.0.4-fsldir_redux.patch: + 09 Apr 2015; Horea Christian <h.chr@mail.ru> + -files/fsl-5.0.4-fsldir_redux.patch: removed 5.0.4 redux patch - 07 Apr 2015; <chymera@gentoo.org> -fsl-5.0.4.ebuild, -fsl-5.0.5.ebuild: + 07 Apr 2015; Horea Christian <h.chr@mail.ru> -fsl-5.0.4.ebuild, + -fsl-5.0.5.ebuild: removed ebuilds with unavailable sources - 07 Apr 2015; <chymera@gentoo.org> fsl-5.0.6.ebuild: + 07 Apr 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: added new gentoo fsl-5.0.6 source location - 30 Mar 2015; <chymera@gentoo.org> +files/fsl-5.0.8-fsldir_redux.patch, - -files/fsl-5.0.8-redux.patch, fsl-5.0.8.ebuild: + 30 Mar 2015; Horea Christian <h.chr@mail.ru> + +files/fsl-5.0.8-fsldir_redux.patch, -files/fsl-5.0.8-redux.patch, + fsl-5.0.8.ebuild: implemented 5.0.8 fsldir redux patch - 30 Mar 2015; <chymera@gentoo.org> +files/fsl-5.0.8-redux.patch: + 30 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-redux.patch: 5.0.8 redux patch by François Bissey - 29 Mar 2015; <chymera@gentoo.org> fsl-5.0.8.ebuild: + 29 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: using the 5.0.8 headers patch - 29 Mar 2015; <chymera@gentoo.org> +files/fsl-5.0.8-headers.patch, + 29 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-headers.patch, files/fsl-5.0.4-headers.patch: reimplmented pathc fsl-5.0.4-headers - 28 Mar 2015; <chymera@gentoo.org> fsl-5.0.8.ebuild: + 28 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: ported changes from 5.0.6 regarding FSLDIR - 28 Mar 2015; <chymera@gentoo.org> files/fsl-5.0.4-headers.patch: + 28 Mar 2015; Horea Christian <h.chr@mail.ru> files/fsl-5.0.4-headers.patch: hunk implemented by upstream - 28 Mar 2015; <h.chr@mail.ru> fsl-5.0.8.ebuild: + 28 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: using new setup patch file for new ebuild - 28 Mar 2015; <h.chr@mail.ru> +files/fsl-5.0.8-setup.patch: + 28 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-setup.patch: new pathc by François Bissey - 25 Mar 2015; <h.chr@mail.ru> fsl-5.0.4.ebuild, fsl-5.0.5.ebuild, - fsl-5.0.8.ebuild: + 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.4.ebuild, + fsl-5.0.5.ebuild, fsl-5.0.8.ebuild: added licences to all versions - 25 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: added license for included gdchart - 25 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: set the correct licences - 11 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 11 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: installing fslversion - 11 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 11 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: sed-ing before installing - 10 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: changed grep wrapper - 10 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: reformatted tcl sed calls - 10 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: fixed tcl location according to instructions by kiwifb - 10 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: installing fsl.sh - 05 Mar 2015; <h.chr@mail.ru> fsl-5.0.6.ebuild: + 05 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: removing faulty check - 04 Mar 2015; <h.chr@mail.ru> files/99fsl: + 04 Mar 2015; Horea Christian <h.chr@mail.ru> files/99fsl: added FSLPATH *fsl-5.0.8 (20 Feb 2015) - 20 Feb 2015; <h.chr@mail.ru> +fsl-5.0.8.ebuild: + 20 Feb 2015; Horea Christian <h.chr@mail.ru> +fsl-5.0.8.ebuild: bumped version 18 Oct 2013; François Bissey <francois.bissey@canterbury.ac.nz> diff --git a/sci-biology/gffutils/ChangeLog b/sci-biology/gffutils/ChangeLog index 486a807cc..c61729349 100644 --- a/sci-biology/gffutils/ChangeLog +++ b/sci-biology/gffutils/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/gffutils: Add github to remote-id in metadata.xml + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> gffutils-0.8.3.ebuild: sci-biology/gffutils: Streamline ebuild diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml index b7551a6aa..32143ba08 100644 --- a/sci-biology/gffutils/metadata.xml +++ b/sci-biology/gffutils/metadata.xml @@ -6,4 +6,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="github">daler/gffutils</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/glean/ChangeLog b/sci-biology/glean/ChangeLog index c1783a3e5..f9faa5ac5 100644 --- a/sci-biology/glean/ChangeLog +++ b/sci-biology/glean/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> glean-1.0.1.ebuild: + sci-biology/glean: Fix dependency problems due to recent mask of perl-core + packages + *glean-1.0.1 (02 May 2015) 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +glean-1.0.1.ebuild, diff --git a/sci-biology/glean/glean-1.0.1.ebuild b/sci-biology/glean/glean-1.0.1.ebuild index 709c9f992..9f39cecbe 100644 --- a/sci-biology/glean/glean-1.0.1.ebuild +++ b/sci-biology/glean/glean-1.0.1.ebuild @@ -22,7 +22,7 @@ RDEPEND="${DEPEND} virtual/perl-Storable virtual/perl-Getopt-Long virtual/perl-Data-Dumper - virtual/perl-Module-Pluggable + dev-perl/Module-Pluggable dev-perl/Algorithm-Diff sci-biology/bioperl graphviz? ( dev-perl/GraphViz )" diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog index 20edbaead..243b3e9d4 100644 --- a/sci-biology/igv/ChangeLog +++ b/sci-biology/igv/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/igv: Add github to remote-id in metadata.xml + *igv-2.3.52 (11 May 2015) 11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml index fc7c76942..ddebe6007 100644 --- a/sci-biology/igv/metadata.xml +++ b/sci-biology/igv/metadata.xml @@ -6,4 +6,7 @@ <name>Andrey Kislyuk</name> </maintainer> <herd>sci-biology</herd> + <upstream> + <remote-id type="github">broadinstitute/IGV</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog index f67fb339a..dc085a65b 100644 --- a/sci-biology/khmer/ChangeLog +++ b/sci-biology/khmer/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/khmer -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/khmer: Add github to remote-id in metadata.xml + *khmer-1.0.1 (15 May 2014) 15 May 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild, diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml index 2bc893037..bfbb83e90 100644 --- a/sci-biology/khmer/metadata.xml +++ b/sci-biology/khmer/metadata.xml @@ -6,4 +6,8 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="pypi">khmer</remote-id> + <remote-id type="github">ged-lab/khmer</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/lighter/ChangeLog b/sci-biology/lighter/ChangeLog index a24b93614..aac7e6b24 100644 --- a/sci-biology/lighter/ChangeLog +++ b/sci-biology/lighter/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/lighter: Add github to remote-id in metadata.xml + *lighter-9999 (01 May 2015) 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/lighter/metadata.xml b/sci-biology/lighter/metadata.xml index 2bc893037..5a9ca59a9 100644 --- a/sci-biology/lighter/metadata.xml +++ b/sci-biology/lighter/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">mourisl/Lighter</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog index 2c85c80cd..8a60b082e 100644 --- a/sci-biology/manatee-igs/ChangeLog +++ b/sci-biology/manatee-igs/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/manatee-igs -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> manatee-igs-2.23.1.ebuild: + sci-biology/manatee-igs: Fix dependency problems due to recent mask of perl- + core packages + 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> manatee-igs-2.23.1.ebuild: Both versions of manatee have same license, so rename unify the license @@ -24,4 +28,3 @@ 08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +manatee-igs-2.23.1.ebuild, +metadata.xml: new package for prokaryotic genome annotation and editing - diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild index b858a9d5b..fb0fa9f2b 100644 --- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild +++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild @@ -1,13 +1,14 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema" HOMEPAGE="http://manatee.sourceforge.net/igs" -SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz - http://manatee.sourceforge.net/igs/docs/README_Linux.txt" +SRC_URI=" + http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz + http://manatee.sourceforge.net/igs/docs/README_Linux.txt" LICENSE="Artistic-Manatee" SLOT="0" @@ -15,35 +16,35 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND=" - >=dev-libs/expat-1.95.8 - >=media-libs/gd-2.0.34 - virtual/perl-CGI - dev-perl/Bio-DB-Das-Chado - dev-perl/DBI - dev-perl/DBD-mysql - dev-perl/XML-Parser - dev-perl/XML-Twig - dev-perl/XML-Simple - dev-perl/XML-Writer - dev-perl/HTML-Template - dev-perl/Tree-DAG_Node - virtual/perl-File-Spec - virtual/perl-Data-Dumper - dev-perl/GD - dev-perl/GDTextUtil - dev-perl/GDGraph - virtual/perl-Storable - dev-perl/Log-Log4perl - dev-perl/Log-Cabin - dev-perl/DateManip - dev-perl/IO-Tee - dev-perl/MLDBM - dev-perl/JSON - dev-perl/JSON-Any - sci-biology/bioperl" + >=dev-libs/expat-1.95.8 + >=media-libs/gd-2.0.34 + dev-perl/CGI + dev-perl/Bio-DB-Das-Chado + dev-perl/DBI + dev-perl/DBD-mysql + dev-perl/XML-Parser + dev-perl/XML-Twig + dev-perl/XML-Simple + dev-perl/XML-Writer + dev-perl/HTML-Template + dev-perl/Tree-DAG_Node + virtual/perl-File-Spec + virtual/perl-Data-Dumper + dev-perl/GD + dev-perl/GDTextUtil + dev-perl/GDGraph + virtual/perl-Storable + dev-perl/Log-Log4perl + dev-perl/Log-Cabin + dev-perl/DateManip + dev-perl/IO-Tee + dev-perl/MLDBM + dev-perl/JSON + dev-perl/JSON-Any + sci-biology/bioperl" RDEPEND="${DEPEND} - >=dev-db/mysql-5.0 - >=www-servers/apache-2.2" + >=dev-db/mysql-5.0 + >=www-servers/apache-2.2" S="${WORKDIR}"/manatee-"${PV}"_linux diff --git a/sci-biology/metaseq/ChangeLog b/sci-biology/metaseq/ChangeLog index a61a470db..058230ae6 100644 --- a/sci-biology/metaseq/ChangeLog +++ b/sci-biology/metaseq/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/metaseq: Add github to remote-id in metadata.xml + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> metaseq-0.5.3.ebuild: sci-biology/metaseq: Streamline ebuild diff --git a/sci-biology/metaseq/metadata.xml b/sci-biology/metaseq/metadata.xml index b7551a6aa..8174cbd9e 100644 --- a/sci-biology/metaseq/metadata.xml +++ b/sci-biology/metaseq/metadata.xml @@ -6,4 +6,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="github">daler/metaseq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/minced/ChangeLog b/sci-biology/minced/ChangeLog index f1317ddbc..8f2fcc345 100644 --- a/sci-biology/minced/ChangeLog +++ b/sci-biology/minced/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/minced: Add github to remote-id in metadata.xml + 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> minced-9999.ebuild: sci-biology/minced: fixed the launcher diff --git a/sci-biology/minced/metadata.xml b/sci-biology/minced/metadata.xml index 2bc893037..193c48204 100644 --- a/sci-biology/minced/metadata.xml +++ b/sci-biology/minced/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">ctSkennerton/minced/tree/master</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog new file mode 100644 index 000000000..8e61af53c --- /dev/null +++ b/sci-biology/mira/ChangeLog @@ -0,0 +1,133 @@ +# ChangeLog for sci-biology/mira +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.31 2015/04/07 14:33:30 jlec Exp $ + + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/mira: Updating remote-id in metadata.xml + + 25 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-4.0.2.ebuild, + +files/mira-4.0.2-cout.patch: + Build fix for newer gcc, #537564 + +*mira-4.0.2 (23 Jan 2015) + + 23 Jan 2015; Justin Lecher <jlec@gentoo.org> +mira-4.0.2.ebuild: + Version Bump, thanks Martin Mokrejš for the work + + 23 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-3.9.18.ebuild: + Add workaroung for m4 dir location, #536172 + + 14 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1.ebuild: + Drop old + + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> mira-3.9.18.ebuild: + Stable for x86, wrt bug #497218 + + 12 Jan 2014; Pacho Ramos <pacho@gentoo.org> mira-3.9.18.ebuild: + amd64 stable, bug #497218 + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild: + Punt base.eclass + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r1.ebuild, + -mira-3.4.0.2.ebuild: + Drop old + +*mira-3.9.18 (07 Jul 2013) + + 07 Jul 2013; Justin Lecher <jlec@gentoo.org> +mira-3.9.18.ebuild: + Version Bump; fixed compilation with dev-libs/boost-1.53.0 and some libtool + versions, #450322; thanks Martin Mokrejs for all his work + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*mira-3.4.0.2 (07 Nov 2012) + + 07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild, + mira-3.2.1-r1.ebuild, +mira-3.4.0.2.ebuild, + +files/mira-3.4.0.2-boost-1.50.patch: + Version Bump, #377807 + +*mira-3.2.1-r1 (07 Nov 2012) + + 07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild, + +mira-3.2.1-r1.ebuild, +files/mira-3.2.1-boost-1.50.patch: + Fix for boost >1.50, #425468 + + 08 Jul 2012; Justin Lecher <jlec@gentoo.org> -mira-3.0.5.ebuild, + -mira-3.2.0.ebuild: + Drop old + + 25 Jun 2012; Jeff Horelick <jdhore@gentoo.org> mira-3.2.1.ebuild: + marked x86 per bug 418439 + + 24 Jun 2012; Agostino Sarubbo <ago@gentoo.org> mira-3.2.1.ebuild: + Stable for amd64, wrt bug #418439 + + 23 Jun 2012; Kacper Kowalik <xarthisius.kk@gmail.com> mira-3.2.1.ebuild: + Don't install docs that are no longer there, thanks to David Abbott for the + patch + +*mira-3.2.1 (21 May 2011) + + 21 May 2011; Andrey Kislyuk <weaver@gentoo.org> +mira-3.2.1.ebuild: + Version bump and fix bug 367921 + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> mira-3.2.0.ebuild: + Stable on amd64 wrt bug #353568 + + 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> mira-3.2.0.ebuild: + x86 stable wrt bug #353568 + + 17 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.2.0.ebuild: + Remove doc USE flag and dependency, workaround for bug 340419 + +*mira-3.2.0 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.0.ebuild, + -mira-3.0.3.ebuild, +mira-3.2.0.ebuild: + Version bump, drop old + + 28 Jun 2010; Justin Lecher <jlec@gentoo.org> mira-3.0.0.ebuild, + mira-3.0.3.ebuild, mira-3.0.5.ebuild: + Prepared for prefix, #325929 + +*mira-3.0.5 (05 May 2010) + + 05 May 2010; Andrey Kislyuk <weaver@gentoo.org> +mira-3.0.5.ebuild: + Version bump + +*mira-3.0.3 (18 Mar 2010) + + 18 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.2.ebuild, + +mira-3.0.3.ebuild: + Hotfix from upstream + +*mira-3.0.2 (10 Mar 2010) + + 10 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.1.ebuild, + +mira-3.0.2.ebuild: + Hotfix from upstream + +*mira-3.0.1 (06 Mar 2010) + + 06 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> +mira-3.0.1.ebuild: + Version bump (bugfix release) + + 25 Feb 2010; Samuli Suominen <ssuominen@gentoo.org> mira-3.0.0.ebuild, + +files/mira-3.0.0-asneeded.patch: + Fix ax_lib_expat.m4 macro to not use LDFLAGS for passing libraries wrt + #305547 by Kacper Kowalik. + + 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild: + add eautoreconf + + 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild: + Install 3rd party files + +*mira-3.0.0 (02 Feb 2010) + + 02 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mira-3.0.0.ebuild: + New package, ebuild written by me diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest new file mode 100644 index 000000000..a095295dd --- /dev/null +++ b/sci-biology/mira/Manifest @@ -0,0 +1,2 @@ +DIST mira-4.9.5.tar.bz2 10444005 SHA256 07160f9847edcb5109fa9085109f73a18849473fc2afdcda1118faf3c5fc3d77 SHA512 f56bd9e1c6982b501534bc8c64fed0ed81f20505546d6e79b48cfed3d82780a43691e985f5be3910af55adf12a955dbf1901cb1da1f182636d5e1357d8129cf8 WHIRLPOOL be0abe4213ecbe40534bee65dba390ac3695d3763123ad93c4a32bbcded15aa2f99ef93304b8e4cdc65728f0859e2748ad828826919bf7e4fc6b8499bccbdf9c +DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2 diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch new file mode 100644 index 000000000..427192294 --- /dev/null +++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch @@ -0,0 +1,24 @@ + config/m4/ax_boost_regex.m4 | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4 +index 1ac06af..5b7be93 100644 +--- a/config/m4/ax_boost_regex.m4 ++++ b/config/m4/ax_boost_regex.m4 +@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX], + for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + if test "x$link_regex" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + fi diff --git a/sci-biology/mira/files/mira-4.9.5-cout.patch b/sci-biology/mira/files/mira-4.9.5-cout.patch new file mode 100644 index 000000000..14feb0284 --- /dev/null +++ b/sci-biology/mira/files/mira-4.9.5-cout.patch @@ -0,0 +1,16 @@ + src/progs/quirks.C | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/src/progs/quirks.C b/src/progs/quirks.C +index 47e5ee8..060b6f3 100644 +--- a/src/progs/quirks.C ++++ b/src/progs/quirks.C +@@ -25,6 +25,8 @@ + + #include <boost/filesystem.hpp> + ++#include <iostream> ++ + // make the "tcmalloc: large alloc" messages from TCMallom disappear + // by setting the reporting environment variable to a very large value + // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1 diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml new file mode 100644 index 000000000..a2c7c1a0a --- /dev/null +++ b/sci-biology/mira/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">mira-assembler</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild new file mode 100644 index 000000000..e643b5b79 --- /dev/null +++ b/sci-biology/mira/mira-4.9.5.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v 1.2 2015/01/25 17:04:35 jlec Exp $ + +EAPI=5 + +MIRA_3RDPARTY_PV="06-07-2012" +MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) + +inherit autotools eutils multilib + +DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" +HOMEPAGE="http://www.chevreux.org/projects_mira.html" +SRC_URI=" + http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2 + mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" +# http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 +# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 +# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" + +S="${WORKDIR}"/"${PN}"-"${MY_PV}" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc" + +CDEPEND=" + dev-libs/boost + dev-util/google-perftools" +DEPEND="${CDEPEND} + app-editors/vim-core + dev-libs/expat" +RDEPEND="${CDEPEND}" + +#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED +# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) +DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) + +# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1 +src_prepare() { + find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die + epatch \ + "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ + "${FILESDIR}"/${P}-cout.patch + + sed \ + -e "s:-O[23]::g" \ + -e "s:-funroll-loops::g" \ + -i configure.ac || die + + eautoreconf +} + +src_configure() { + econf \ + --with-boost="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-thread=boost_thread-mt +} + +#src_compile() { +# base_src_compile +# # TODO: resolve docbook incompatibility for building docs +# if use doc; then emake -C doc clean docs || die; fi +#} + +src_install() { + default + dodoc ${DOCS[@]} + + dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} + dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} +} + +pkg_postinst() { + einfo "Documentation is no longer built, you can find it at:" + einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" +} diff --git a/sci-biology/mrfast/ChangeLog b/sci-biology/mrfast/ChangeLog index f5dd75faf..d621fb810 100644 --- a/sci-biology/mrfast/ChangeLog +++ b/sci-biology/mrfast/ChangeLog @@ -1,9 +1,11 @@ # ChangeLog for sci-biology/mrfast -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/mrfast: Updating remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mrfast-2.1.0.3.ebuild, +mrfast-2.6.0.1.ebuild, -files/mrfast-2.1.0.3-disc_buffer_overflow.patch, metadata.xml: Version Bump; punt base.eclass - diff --git a/sci-biology/mrfast/metadata.xml b/sci-biology/mrfast/metadata.xml index fc7c76942..dec6e9f34 100644 --- a/sci-biology/mrfast/metadata.xml +++ b/sci-biology/mrfast/metadata.xml @@ -6,4 +6,7 @@ <name>Andrey Kislyuk</name> </maintainer> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">mrfast</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mrsfast/ChangeLog b/sci-biology/mrsfast/ChangeLog index b0aea7fdb..49579cc44 100644 --- a/sci-biology/mrsfast/ChangeLog +++ b/sci-biology/mrsfast/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for sci-biology/mrsfast -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/mrsfast: Updating remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mrsfast-2.3.0.2.ebuild, +mrsfast-2.6.0.4.ebuild, metadata.xml: Version Bump; punt base.eclass - diff --git a/sci-biology/mrsfast/metadata.xml b/sci-biology/mrsfast/metadata.xml index fc7c76942..1ad193e4c 100644 --- a/sci-biology/mrsfast/metadata.xml +++ b/sci-biology/mrsfast/metadata.xml @@ -6,4 +6,7 @@ <name>Andrey Kislyuk</name> </maintainer> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">mrsfast</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index ccef946ae..0267684f7 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 11 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/ncbi-tools++-12.0.0-bdb6.patch, ncbi-tools++-12.0.0.ebuild: + sci-biology/ncbi-tools++: added upstream patch to compile against sys- + libs/db-6.0.30 + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ncbi-tools++-12.0.0.ebuild: sci-biology/ncbi-tools++: re-added KEYWORDS diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch new file mode 100644 index 000000000..9589481d4 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch @@ -0,0 +1,114 @@ +Index: include/db/bdb/bdb_file.hpp +=================================================================== +--- include/db/bdb/bdb_file.hpp (revision 470126) ++++ include/db/bdb/bdb_file.hpp (working copy) +@@ -660,6 +660,9 @@ + void x_ConstructKeyBuf(); + void x_ConstructDataBuf(); + ++ static int x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, ++ size_t* locp); ++ + private: + auto_ptr<CBDB_BufferManager> m_KeyBuf; + auto_ptr<CBDB_BufferManager> m_DataBuf; +Index: src/db/bdb/bdb_blob.cpp +=================================================================== +--- src/db/bdb/bdb_blob.cpp (revision 470126) ++++ src/db/bdb/bdb_blob.cpp (working copy) +@@ -583,12 +583,31 @@ + return m_DBT_Data->size; + } + ++#if DB_VERSION_MAJOR >= 6 ++extern "C" { ++ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, ++ size_t*); ++ int BDB_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) ++ { return BDB_Uint4Compare(db, dbt1, dbt2); } ++ int BDB_ByteSwap_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, ++ size_t*) ++ { return BDB_ByteSwap_Uint4Compare(db, dbt1, dbt2); } ++} ++#endif ++ + void CBDB_LobFile::SetCmp(DB*) + { ++#if DB_VERSION_MAJOR >= 6 ++ BDB_CompareFunction_V6 func = BDB_Uint4Compare_V6; ++ if (IsByteSwapped()) { ++ func = BDB_ByteSwap_Uint4Compare_V6; ++ } ++#else + BDB_CompareFunction func = BDB_Uint4Compare; + if (IsByteSwapped()) { + func = BDB_ByteSwap_Uint4Compare; + } ++#endif + + _ASSERT(func); + int ret = m_DB->set_bt_compare(m_DB, func); +Index: src/db/bdb/bdb_file.cpp +=================================================================== +--- src/db/bdb/bdb_file.cpp (revision 470126) ++++ src/db/bdb/bdb_file.cpp (working copy) +@@ -1535,12 +1535,27 @@ + } + + ++#if DB_VERSION_MAJOR >= 6 ++int CBDB_File::x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) ++{ ++ const CBDB_BufferManager* key_buf ++ = static_cast<const CBDB_BufferManager*>(db->app_private); ++ _ASSERT(key_buf); ++ return (key_buf->GetCompareFunction())(db, dbt1, dbt2); ++} ++#endif ++ ++ + void CBDB_File::SetCmp(DB* db) + { + _ASSERT(m_DB_Type == eBtree); ++#if DB_VERSION_MAJOR >= 6 ++ int ret = db->set_bt_compare(db, x_CompareShim); ++#else + BDB_CompareFunction func = m_KeyBuf->GetCompareFunction(); + _ASSERT(func); + int ret = db->set_bt_compare(db, func); ++#endif + BDB_CHECK(ret, 0); + + if (m_PrefixCompress) { +@@ -2056,12 +2071,31 @@ + BindKey("id", &IdKey); + } + ++#if DB_VERSION_MAJOR >= 6 ++extern "C" { ++ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, ++ size_t*); ++ int BDB_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) ++ { return BDB_Int4Compare(db, dbt1, dbt2); } ++ int BDB_ByteSwap_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, ++ size_t*) ++ { return BDB_ByteSwap_Int4Compare(db, dbt1, dbt2); } ++} ++#endif ++ + void CBDB_IdFile::SetCmp(DB* /* db */) + { ++#if DB_VERSION_MAJOR >= 6 ++ BDB_CompareFunction_V6 func = BDB_Int4Compare_V6; ++ if (IsByteSwapped()) { ++ func = BDB_ByteSwap_Int4Compare_V6; ++ } ++#else + BDB_CompareFunction func = BDB_Int4Compare; + if (IsByteSwapped()) { + func = BDB_ByteSwap_Int4Compare; + } ++#endif + + _ASSERT(func); + int ret = m_DB->set_bt_compare(m_DB, func); diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index efe49f701..2948c7402 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -120,6 +120,7 @@ src_prepare() { "${FILESDIR}"/${P}-configure.patch "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch "${FILESDIR}"/${P}-fix-install.patch + "${FILESDIR}"/${P}-bdb6.patch ) # "${FILESDIR}"/${P}-as-needed.patch # "${FILESDIR}"/${P}-fix-creaders-linking.patch diff --git a/sci-biology/ngsview/ChangeLog b/sci-biology/ngsview/ChangeLog index 231f7fe5a..bdd09d059 100644 --- a/sci-biology/ngsview/ChangeLog +++ b/sci-biology/ngsview/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/ngsview: Updating remote-id in metadata.xml + + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/ngsview: Updating remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ngsview-0.91.ebuild: sci-biology/ngsview: fix SLOT operators diff --git a/sci-biology/ngsview/metadata.xml b/sci-biology/ngsview/metadata.xml index 2bc893037..11f9c4b13 100644 --- a/sci-biology/ngsview/metadata.xml +++ b/sci-biology/ngsview/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="sourceforge">ngsview</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/perlprimer/ChangeLog b/sci-biology/perlprimer/ChangeLog index 123306dd1..f3b587a57 100644 --- a/sci-biology/perlprimer/ChangeLog +++ b/sci-biology/perlprimer/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/perlprimer -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/perlprimer: Updating remote-id in metadata.xml + 10 Nov 2014; Justin Lecher <jlec@gentoo.org> -perlprimer-1.1.17.ebuild, +perlprimer-1.1.21.ebuild, metadata.xml: Bump to EAPI=5; Version Bump @@ -14,4 +17,3 @@ cleaned up ebuild Added ~x86 as requested in bug 231230 removed redundant database - diff --git a/sci-biology/perlprimer/metadata.xml b/sci-biology/perlprimer/metadata.xml index f17a827e3..4d85fe0a5 100644 --- a/sci-biology/perlprimer/metadata.xml +++ b/sci-biology/perlprimer/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">perlprimer</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/plinkseq/ChangeLog b/sci-biology/plinkseq/ChangeLog index ade061533..10c843e63 100644 --- a/sci-biology/plinkseq/ChangeLog +++ b/sci-biology/plinkseq/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + plinkseq-0.10.ebuild: + reported a file collision to upstream + *plinkseq-0.10 (10 May 2015) 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild b/sci-biology/plinkseq/plinkseq-0.10.ebuild index 153c161a2..22f917b10 100644 --- a/sci-biology/plinkseq/plinkseq-0.10.ebuild +++ b/sci-biology/plinkseq/plinkseq-0.10.ebuild @@ -27,5 +27,7 @@ src_prepare(){ src_install(){ cd build/execs || die + # TODO: avoid file collision with sci-biology/fsl + # https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm dobin gcol browser pseq behead mm smp tab2vcf mongoose pdas } diff --git a/sci-biology/prokka/ChangeLog b/sci-biology/prokka/ChangeLog index caef8bafa..a5e4045b3 100644 --- a/sci-biology/prokka/ChangeLog +++ b/sci-biology/prokka/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild: + sci-biology/prokka: require either of ncbi-tools++ or ncbi-blast+ + 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild: sci-biology/prokka: more DEPs recorded diff --git a/sci-biology/prokka/prokka-1.11.ebuild b/sci-biology/prokka/prokka-1.11.ebuild index c7a9d8181..9e0e86c7e 100644 --- a/sci-biology/prokka/prokka-1.11.ebuild +++ b/sci-biology/prokka/prokka-1.11.ebuild @@ -19,7 +19,7 @@ RDEPEND="${DEPEND} sys-process/parallel sci-biology/bioperl sci-biology/prodigal - sci-biology/ncbi-tools++ + sci-biology/ncbi-tools++ || ( sci-biology/ncbi-blast+ ) sci-biology/hmmer sci-biology/infernal sci-biology/exonerate diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog index d4cc4783b..2fb878ae1 100644 --- a/sci-biology/pybedtools/ChangeLog +++ b/sci-biology/pybedtools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/pybedtools: Add github to remote-id in metadata.xml + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> pybedtools-0.6.9.ebuild: sci-biology/pybedtools: Streamline ebuild diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml index b7551a6aa..3352804f1 100644 --- a/sci-biology/pybedtools/metadata.xml +++ b/sci-biology/pybedtools/metadata.xml @@ -6,4 +6,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="github">daler/pybedtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml index b7551a6aa..44913ccb4 100644 --- a/sci-biology/pyfaidx/metadata.xml +++ b/sci-biology/pyfaidx/metadata.xml @@ -6,4 +6,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="pypi">pyfaidx</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/rum/ChangeLog b/sci-biology/rum/ChangeLog index 3dd7b15fd..62ff2bf3c 100644 --- a/sci-biology/rum/ChangeLog +++ b/sci-biology/rum/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> rum-2.0.5.5.ebuild: + sci-biology/rum: Use perl virtuals, add missing die; use PN for tarball + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/rum: Add github to remote-id in metadata.xml + *rum-2.0.5.5 (18 Apr 2015) 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, diff --git a/sci-biology/rum/Manifest b/sci-biology/rum/Manifest index 5142af72a..7ef715410 100644 --- a/sci-biology/rum/Manifest +++ b/sci-biology/rum/Manifest @@ -1 +1 @@ -DIST v2.0.5_05.tar.gz 5420665 SHA256 077fdee93f70d3d7cec05ddac22f07b22759f22c1fb63f927769beed2cd0670c SHA512 7a6600e7d98fa4649a281b161eaaaa2fbfd337b7b26b0d054e23974aa555a383d476b5464183b259812330c4e00a36be44a5efe210950e2ad24ab867375cb9be WHIRLPOOL ebcd634341016a46c098bc4708f93b51fa46f79dd367162711a965d3167f734f640d55f8415062e513f776149f645de7933b7f681614f3b38c1a3ec1a35d2585 +DIST rum-2.0.5.5.tar.gz 5420665 SHA256 077fdee93f70d3d7cec05ddac22f07b22759f22c1fb63f927769beed2cd0670c SHA512 7a6600e7d98fa4649a281b161eaaaa2fbfd337b7b26b0d054e23974aa555a383d476b5464183b259812330c4e00a36be44a5efe210950e2ad24ab867375cb9be WHIRLPOOL ebcd634341016a46c098bc4708f93b51fa46f79dd367162711a965d3167f734f640d55f8415062e513f776149f645de7933b7f681614f3b38c1a3ec1a35d2585 diff --git a/sci-biology/rum/metadata.xml b/sci-biology/rum/metadata.xml index 2bc893037..e6b052fa8 100644 --- a/sci-biology/rum/metadata.xml +++ b/sci-biology/rum/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">itmat/rum/wiki</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/rum/rum-2.0.5.5.ebuild b/sci-biology/rum/rum-2.0.5.5.ebuild index c8fc01b93..3411f20f4 100644 --- a/sci-biology/rum/rum-2.0.5.5.ebuild +++ b/sci-biology/rum/rum-2.0.5.5.ebuild @@ -8,7 +8,7 @@ inherit perl-module eutils DESCRIPTION="RNA-Seq Unified Mapper (digital normalization)" HOMEPAGE="https://github.com/itmat/rum/wiki" -SRC_URI="https://github.com/itmat/rum/archive/v2.0.5_05.tar.gz" +SRC_URI="https://github.com/itmat/rum/archive/v2.0.5_05.tar.gz -> ${P}.tar.gz" # stable #EGIT_REPO_URI="https://github.com/PGFI/rum/tags" @@ -21,9 +21,9 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="dev-lang/perl - dev-perl/Log-Log4perl - perl-core/autodie" +DEPEND=" + dev-perl/Log-Log4perl + virtual/perl-autodie" RDEPEND="${DEPEND} sci-biology/seqclean sci-biology/blat @@ -33,8 +33,6 @@ RDEPEND="${DEPEND} S="${WORKDIR}/${PN}-2.0.5_05" src_install(){ - emake install - rm "${D}"/usr/lib64/perl5/vendor_perl/*/RUM/bowtie - rm "${D}"/usr/lib64/perl5/vendor_perl/*/RUM/blat - rm "${D}"/usr/lib64/perl5/vendor_perl/*/RUM/mdust + default + rm "${ED}"/usr/lib64/perl5/vendor_perl/*/RUM/{bowtie,blat,mdust} ]] die } diff --git a/sci-biology/sabre/ChangeLog b/sci-biology/sabre/ChangeLog index fb47d2375..a43393aaa 100644 --- a/sci-biology/sabre/ChangeLog +++ b/sci-biology/sabre/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/sabre: Add github to remote-id in metadata.xml + 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> sabre-9999.ebuild: Switch from git-2 to git-r3; Cleanup diff --git a/sci-biology/sabre/metadata.xml b/sci-biology/sabre/metadata.xml index 2bc893037..dfc808149 100644 --- a/sci-biology/sabre/metadata.xml +++ b/sci-biology/sabre/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">najoshi/sabre</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog index b897449ec..5b870c43c 100644 --- a/sci-biology/salmon/ChangeLog +++ b/sci-biology/salmon/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/salmon: Add github to remote-id in metadata.xml + 23 May 2015; Michael Schubert <mschu.dev@gmail.com> files/salmon-0.3.2-no-boost-static.patch: sci-biology/salmon: clean patch diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml index b7551a6aa..c72510b68 100644 --- a/sci-biology/salmon/metadata.xml +++ b/sci-biology/salmon/metadata.xml @@ -6,4 +6,7 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <upstream> + <remote-id type="github">COMBINE-lab/salmon</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog index 5e1efcee7..f5eaa814a 100644 --- a/sci-biology/samtools/ChangeLog +++ b/sci-biology/samtools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/samtools: Updating remote-id in metadata.xml + *samtools-1.0-r2 (11 May 2015) *samtools-1.1-r1 (11 May 2015) *samtools-1.2-r1 (11 May 2015) diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml index f17a827e3..74dc02bc9 100644 --- a/sci-biology/samtools/metadata.xml +++ b/sci-biology/samtools/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">samtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/scaffold_builder/ChangeLog b/sci-biology/scaffold_builder/ChangeLog index 5663f61d2..0db66bf40 100644 --- a/sci-biology/scaffold_builder/ChangeLog +++ b/sci-biology/scaffold_builder/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + scaffold_builder-20131122.ebuild: + sci-biology/scaffold_builder: set proper LICENSE to the one mentioned in the + http://www.scfbm.org/content/pdf/1751-0473-8-23.pdf article and also in the + COPYING.txt file in the distribution .zip file + + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + scaffold_builder-20131122.ebuild: + sci-biology/scaffold_builder: noted RDEPEND, added second HOMEPAGE + *scaffold_builder-20131122 (30 Jan 2015) 30 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild index dc14a4d91..40110cc89 100644 --- a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild +++ b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild @@ -7,19 +7,21 @@ EAPI=5 S="${WORKDIR}" DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly" -HOMEPAGE="http://sourceforge.net/projects/scaffold-b/" +HOMEPAGE="http://sourceforge.net/projects/scaffold-b + http://edwards.sdsu.edu/scaffold_builder" SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf" #http://www.scfbm.org/content/8/1/23 -LICENSE="CC-BY-2.0" +LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" IUSE="" DEPEND="" RDEPEND="${DEPEND} + sci-biology/mummer dev-lang/python" src_install(){ diff --git a/sci-biology/screed/ChangeLog b/sci-biology/screed/ChangeLog index 28c056131..66b9d3432 100644 --- a/sci-biology/screed/ChangeLog +++ b/sci-biology/screed/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/screed -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/screed: Add github to remote-id in metadata.xml + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> screed-0.7.1.ebuild: removed empty line diff --git a/sci-biology/screed/metadata.xml b/sci-biology/screed/metadata.xml index f17a827e3..a773552b0 100644 --- a/sci-biology/screed/metadata.xml +++ b/sci-biology/screed/metadata.xml @@ -2,4 +2,8 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="pypi">screed</remote-id> + <remote-id type="github">ged-lab/screed</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/scythe/ChangeLog b/sci-biology/scythe/ChangeLog index 679d1b148..d577319ad 100644 --- a/sci-biology/scythe/ChangeLog +++ b/sci-biology/scythe/ChangeLog @@ -1,10 +1,12 @@ # ChangeLog for sci-biology/scythe -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/scythe: Add github to remote-id in metadata.xml + *scythe-0.992 (24 Mar 2014) 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +scythe-0.992.ebuild, +metadata.xml: bundled Makefile forces -O3, wrong version number, but works - diff --git a/sci-biology/scythe/metadata.xml b/sci-biology/scythe/metadata.xml index 2bc893037..540814e51 100644 --- a/sci-biology/scythe/metadata.xml +++ b/sci-biology/scythe/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">vsbuffalo/scythe</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog index 1408f942d..af6716396 100644 --- a/sci-biology/sga/ChangeLog +++ b/sci-biology/sga/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/sga: Add github to remote-id in metadata.xml + 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> sga-9999.ebuild: Switch from git-2 to git-r3; Cleanup; Add missing die @@ -10,4 +13,3 @@ 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sga-9999.ebuild, +metadata.xml: new package; forces its own optimization flags but works fine - diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml index 4e873d87d..5ac32df20 100644 --- a/sci-biology/sga/metadata.xml +++ b/sci-biology/sga/metadata.xml @@ -6,7 +6,10 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<use> - <flag name='jemalloc'>Use <pkg>dev-libs/jemalloc</pkg></flag> -</use> + <use> + <flag name="jemalloc">Use <pkg>dev-libs/jemalloc</pkg></flag> + </use> + <upstream> + <remote-id type="github">jts/sga</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/sickle/ChangeLog b/sci-biology/sickle/ChangeLog index 4d539a201..060cfa220 100644 --- a/sci-biology/sickle/ChangeLog +++ b/sci-biology/sickle/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/sickle: Add github to remote-id in metadata.xml + *sickle-1.33 (09 Mar 2015) 09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sickle-1.33.ebuild, diff --git a/sci-biology/sickle/metadata.xml b/sci-biology/sickle/metadata.xml index 2bc893037..74adcee63 100644 --- a/sci-biology/sickle/metadata.xml +++ b/sci-biology/sickle/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">najoshi/sickle</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/spm/ChangeLog b/sci-biology/spm/ChangeLog index eea45ba5b..3ee22afe8 100644 --- a/sci-biology/spm/ChangeLog +++ b/sci-biology/spm/ChangeLog @@ -2,26 +2,28 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ - 11 Mar 2015; <chymera@gentoo.org> spm-12.ebuild: + 11 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: installing into octave M subdirectory - 10 Mar 2015; <chymera@gentoo.org> spm-12.ebuild: + 10 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: installing ALL the things - 04 Mar 2015; <chymera@gentoo.org> spm-12.ebuild: + 04 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: typo - 04 Mar 2015; <chymera@gentoo.org> spm-12.ebuild: + 04 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: fixed doins path *spm-12 (04 Mar 2015) - 04 Mar 2015; <chymera@gentoo.org> +spm-12.ebuild, spm-8.ebuild: + 04 Mar 2015; Horea Christian <h.chr@mail.ru> +spm-12.ebuild, + spm-8.ebuild: removed slots, added new version - 17 Feb 2015; <chymera@gentoo.org> -spm-8.ebuild.orig, spm-8.ebuild: + 17 Feb 2015; Horea Christian <h.chr@mail.ru> -spm-8.ebuild.orig, + spm-8.ebuild: added quotation marks, removed ori file - 17 Feb 2015; <chymera@gentoo.org> +metadata.xml, +spm-8.ebuild.orig, - spm-8.ebuild: + 17 Feb 2015; Horea Christian <h.chr@mail.ru> +metadata.xml, + +spm-8.ebuild.orig, spm-8.ebuild: added metadata diff --git a/sci-biology/swissknife/ChangeLog b/sci-biology/swissknife/ChangeLog index a71e1c1d3..ecb4b87ae 100644 --- a/sci-biology/swissknife/ChangeLog +++ b/sci-biology/swissknife/ChangeLog @@ -1,8 +1,11 @@ # ChangeLog for sci-biology/swissknife -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> swissknife-1.70.ebuild: + sci-biology/swissknife: Fix dependency problems due to recent mask of perl- + core packages + 24 Sep 2014; Justin Lecher <jlec@gentoo.org> -swissknife-1.67.ebuild, +swissknife-1.70.ebuild, metadata.xml: Version Bump; Bump to EAPI=5 - diff --git a/sci-biology/swissknife/swissknife-1.70.ebuild b/sci-biology/swissknife/swissknife-1.70.ebuild index 3955e7420..102865637 100644 --- a/sci-biology/swissknife/swissknife-1.70.ebuild +++ b/sci-biology/swissknife/swissknife-1.70.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -14,7 +14,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="virtual/perl-Module-Build" +DEPEND="dev-perl/Module-Build" RDEPEND="${DEPEND} >=dev-lang/perl-5.002:=" #dev-perl/Carp diff --git a/sci-biology/tgicl/ChangeLog b/sci-biology/tgicl/ChangeLog index 683f68c53..76e65851e 100644 --- a/sci-biology/tgicl/ChangeLog +++ b/sci-biology/tgicl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/tgicl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild: + sci-biology/tgicl: Fix dependency problems due to recent mask of perl-core + packages + 24 Sep 2014; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild, metadata.xml: Bump to EAPI=5 - diff --git a/sci-biology/tgicl/tgicl-2.1.ebuild b/sci-biology/tgicl/tgicl-2.1.ebuild index 0c920ea5d..67bb99d46 100644 --- a/sci-biology/tgicl/tgicl-2.1.ebuild +++ b/sci-biology/tgicl/tgicl-2.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND=" - virtual/perl-Module-Build + dev-perl/Module-Build sci-biology/cap3-bin sci-biology/ncbi-tools sci-biology/cdbfasta diff --git a/sci-biology/trim_galore/ChangeLog b/sci-biology/trim_galore/ChangeLog index e87a544f5..6cb3dfe21 100644 --- a/sci-biology/trim_galore/ChangeLog +++ b/sci-biology/trim_galore/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*trim_galore-0.4.0 (30 May 2015) + + 30 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +trim_galore-0.4.0.ebuild, -trim_galore-0.3.7.ebuild: + sci-biology/trim_galore: version bump; ajusted S variable to match current + upstream's packaging habit; still needs fastqc package to be finished + *trim_galore-0.3.7 (24 Feb 2015) 24 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/trim_galore/Manifest b/sci-biology/trim_galore/Manifest index 8cacc777c..3f46bbb6e 100644 --- a/sci-biology/trim_galore/Manifest +++ b/sci-biology/trim_galore/Manifest @@ -1 +1 @@ -DIST trim_galore_v0.3.7.zip 1719173 SHA256 f8adfab475452b9c1e9d0e94ffc7bfa2cd2ae6f6e0e7c0cf5c354d9a8fe66680 SHA512 ea79f80827596968f7826455da975b63afb690c1a94e6eac5c9c2c84f86eb47581286e31ef3850f0b29360300b3cbc7e30f107a4094197a48f231100749979ea WHIRLPOOL 2b1f74351afce1c25a925000b2b0aa1d3c50d6c2d5cf3b73abde8d3b49dc2cca3a264071583497e4ca9356b301035d4fb94d3161389aa2070b69c6647bb27cd4 +DIST trim_galore_v0.4.0.zip 1271343 SHA256 b7146c4a3c541910925ab4b490b754c467d4641bfd53e304884d837f95e859ba SHA512 71a742fe0f5d851f46bd21c3da2fdea5f6b048462179fb4784e49e7fd82fca51a521eda97f18844f6edbcf7e222189cef995c05d0433139b931dc8a351ce2924 WHIRLPOOL 40b40ff3032632083e7c2ce876eb116a05896b0500e981120b32acc93063499bc520aac4d7059fb6e8fa67ffdf0c5736f13717a3522dfa5e4099114b3a16d752 diff --git a/sci-biology/trim_galore/trim_galore-0.3.7.ebuild b/sci-biology/trim_galore/trim_galore-0.4.0.ebuild index 4a0c4bdce..f27f48a3e 100644 --- a/sci-biology/trim_galore/trim_galore-0.3.7.ebuild +++ b/sci-biology/trim_galore/trim_galore-0.4.0.ebuild @@ -6,8 +6,7 @@ EAPI=5 DESCRIPTION="Perl wrapper around Cutadapt and FastQC to adapter and quality trimming" HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore" -SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v"${PV}".zip" - +SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v${PV}.zip" LICENSE="GPL-3" SLOT="0" KEYWORDS="" @@ -20,7 +19,7 @@ RDEPEND=" sci-biology/fastqc ${DEPEND}" -S="${WORKDIR}"/trim_galore_zip +S="${WORKDIR}" src_install(){ dobin trim_galore diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog index f4ce466b7..c8d81e0c1 100644 --- a/sci-biology/trinityrnaseq/ChangeLog +++ b/sci-biology/trinityrnaseq/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> trinityrnaseq-2.0.6.ebuild: sci-biology/trinityrnaseq: added missing quotes diff --git a/sci-biology/trinityrnaseq/metadata.xml b/sci-biology/trinityrnaseq/metadata.xml index 2bc893037..5fa67e941 100644 --- a/sci-biology/trinityrnaseq/metadata.xml +++ b/sci-biology/trinityrnaseq/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog index 6299944b4..d52282e88 100644 --- a/sci-biology/wgs-assembler/ChangeLog +++ b/sci-biology/wgs-assembler/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*wgs-assembler-8.3_rc2 (25 May 2015) + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +wgs-assembler-8.3_rc2.ebuild, -wgs-assembler-8.3_rc1.ebuild: + version bump + *wgs-assembler-8.2 (18 Apr 2015) *wgs-assembler-8.3_rc1 (18 Apr 2015) diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest index c9e10da82..c8a83d2a4 100644 --- a/sci-biology/wgs-assembler/Manifest +++ b/sci-biology/wgs-assembler/Manifest @@ -1,2 +1,2 @@ DIST wgs-8.2.tar.bz2 21179974 SHA256 6ee026031928a27e9dde2343c174e9d027bfca84a2207309113a07f81888b88e SHA512 375baabf5df453f14d757c614771a15c32b2450beee82fae55b5db75c19a689a731e2e9653ee7acf835e82daa6ef7cc565ef0e40811ff742db1fc50142c1ec4b WHIRLPOOL 51d202acdbdc97268ceec235e9a8faf60a994cfbab8bc0b7151115fabdb893562ca5847a880b7b6bdd8d1857f40bef52d38754194bad807329af18ada6b40e4f -DIST wgs-8.3rc1.tar.bz2 24306354 SHA256 2e000d04273df2cc3ce2514beb812d5772b7127d469d088bb9293e522ae32096 SHA512 041ac1d62f4386333052ff15c7206ae504a045b2bf242603cde913eece5a84cee33bbe9223cb1b49c36af2afbf3472f429deeb4b00198fb8a72727fbbe6482db WHIRLPOOL 75450b75d6bc253dbe1909fc475c9270f7b04625f6c237ae514d554f02dba48fa59cf32148d49fadbe64ad311ddd891bcb810e9ee7589413649d088600a439ee +DIST wgs-8.3rc2.tar.bz2 24603412 SHA256 6ba1711ebe56629b670be87ae040ac948057474b3959666a88f0862c6a40f27b SHA512 10646ce59c3d557b744287b63f8f0ff494fd6919c61974389b9a3870a03b19067d58ba3f545afbc1e1dfda85cac76ea0e84474911442ae2097660cc6ea73fc44 WHIRLPOOL d3a5356839c6242b3deb2184963d7afd072c67d92590de8902cfeefd2fe564db3a0510677c9a9203a39be4bc4bf7861fbaf3ff9990e640b9965514b64b335ce1 diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild index 831af99ce..c9e564120 100644 --- a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild +++ b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $ -EAPI=4 +EAPI=5 PYTHON_DEPEND=2 @@ -59,20 +59,20 @@ src_install() { sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die - dobin kmer/${MY_S}/bin/* - insinto /usr/$(get_libdir)/${PN} - use static-libs && doins kmer/${MY_S}/lib/* + dobin kmer/"${MY_S}"/bin/* + insinto /usr/"$(get_libdir)/${PN}" + use static-libs && doins kmer/"${MY_S}"/lib/* - insinto /usr/include/${PN} - doins kmer/${MY_S}/include/* + insinto /usr/include/"${PN}" + doins kmer/"${MY_S}"/include/* - insinto /usr/share/${PN}/lib - doins -r ${MY_S}/bin/TIGR - rm -rf ${MY_S}/bin/TIGR || die - dobin ${MY_S}/bin/* - use static-libs && dolib.a ${MY_S}/lib/* + insinto /usr/share/"${PN}"/lib + doins -r "${MY_S}"/bin/TIGR + rm -rf "${MY_S}"/bin/TIGR || die + dobin "${MY_S}"/bin/* + use static-libs && dolib.a "${MY_S}"/lib/* dodoc README # avoid file collision - rm -f ${D}/usr/bin/jellyfish + rm -f "${D}"/usr/bin/jellyfish } diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild index 73518ed55..22a765bdd 100644 --- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild +++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild @@ -2,18 +2,17 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $ -EAPI=4 +EAPI=5 PYTHON_DEPEND=2 inherit eutils python toolchain-funcs -MY_PV="8.3rc1" +MY_PV="${PV/_}" # convert from _rc2 to rc2 DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG" HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" -#SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" -SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-8.3rc1.tar.bz2" +SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-${MY_PV}.tar.bz2" LICENSE="GPL-2" SLOT="0" @@ -62,20 +61,20 @@ src_install() { sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die - dobin kmer/${MY_S}/bin/* - insinto /usr/$(get_libdir)/${PN} - use static-libs && doins kmer/${MY_S}/lib/* + dobin kmer/"${MY_S}"/bin/* + insinto /usr/$(get_libdir)/"${PN}" + use static-libs && doins kmer/"${MY_S}"/lib/* - insinto /usr/include/${PN} - doins kmer/${MY_S}/include/* + insinto /usr/include/"${PN}" + doins kmer/"${MY_S}"/include/* insinto /usr/share/${PN}/lib - doins -r ${MY_S}/bin/TIGR - rm -rf ${MY_S}/bin/TIGR || die - dobin ${MY_S}/bin/* + doins -r "${MY_S}"/bin/TIGR + rm -rf "${MY_S}"/bin/TIGR || die + dobin "${MY_S}"/bin/* use static-libs && dolib.a ${MY_S}/lib/* dodoc README # avoid file collision - rm -f ${D}/usr/bin/jellyfish + rm -f "${D}"/usr/bin/jellyfish } diff --git a/sci-chemistry/GromacsWrapper/ChangeLog b/sci-chemistry/GromacsWrapper/ChangeLog index 7e3d83cec..eba252f5a 100644 --- a/sci-chemistry/GromacsWrapper/ChangeLog +++ b/sci-chemistry/GromacsWrapper/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/GromacsWrapper -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/GromacsWrapper: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> GromacsWrapper-9999.ebuild: Switch from git-2 to git-r3 diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml index 13ef0bf5a..43390c986 100644 --- a/sci-chemistry/GromacsWrapper/metadata.xml +++ b/sci-chemistry/GromacsWrapper/metadata.xml @@ -6,4 +6,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">orbeckst/GromacsWrapper</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/avogadro2/ChangeLog b/sci-chemistry/avogadro2/ChangeLog index e2e10ecd5..13b6e53f0 100644 --- a/sci-chemistry/avogadro2/ChangeLog +++ b/sci-chemistry/avogadro2/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/avogadro2 -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/avogadro2: Updating remote-id in metadata.xml + 16 Jan 2014; Justin Lecher <jlec@gentoo.org> avogadro2-0.7.2.ebuild: fix USE deps; don't install license file @@ -10,4 +13,3 @@ 16 Jan 2014; Justin Lecher <jlec@gentoo.org> +avogadro2-0.7.2.ebuild, +metadata.xml: New package, written by me - diff --git a/sci-chemistry/avogadro2/metadata.xml b/sci-chemistry/avogadro2/metadata.xml index 807ce86d3..9a5ff7dd0 100644 --- a/sci-chemistry/avogadro2/metadata.xml +++ b/sci-chemistry/avogadro2/metadata.xml @@ -8,4 +8,7 @@ <use> <flag name="rpc">Enable RPC server</flag> </use> + <upstream> + <remote-id type="sourceforge">avogadro</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/burrow-owl/ChangeLog b/sci-chemistry/burrow-owl/ChangeLog index c6289f3f0..6e36684f8 100644 --- a/sci-chemistry/burrow-owl/ChangeLog +++ b/sci-chemistry/burrow-owl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/burrow-owl -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/burrow-owl: Updating remote-id in metadata.xml + 28 Dec 2013; Justin Lecher <jlec@gentoo.org> burrow-owl-9999.ebuild, metadata.xml: Bump to git-r3.eclass and virtualx.eclass @@ -66,4 +69,3 @@ +metadata.xml: moved from dberkholz overlay to sci. fix for glibc-2.10.1 and gcc-4.4 - diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml index 51fdedab1..9849d77b1 100644 --- a/sci-chemistry/burrow-owl/metadata.xml +++ b/sci-chemistry/burrow-owl/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">burrow-owl</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/cnsface/ChangeLog b/sci-chemistry/cnsface/ChangeLog index 91fb75e01..5026f9466 100644 --- a/sci-chemistry/cnsface/ChangeLog +++ b/sci-chemistry/cnsface/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/cnsface -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/cnsface: Updating remote-id in metadata.xml + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> cnsface-0.0.12.ebuild, metadata.xml: Bump to EAPI5 and distutils-r1.eclass @@ -11,4 +14,3 @@ 01 Dec 2010; Justin Lecher <jlec@gentoo.org> +files/0.0.12-binary.patch, +cnsface-0.0.12.ebuild, +metadata.xml: New addition - diff --git a/sci-chemistry/cnsface/metadata.xml b/sci-chemistry/cnsface/metadata.xml index 9ac9ffdb3..07ea2e9d8 100644 --- a/sci-chemistry/cnsface/metadata.xml +++ b/sci-chemistry/cnsface/metadata.xml @@ -1,5 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-chemistry</herd> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">cnsface</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 1e2a646c0..c7bcab9a5 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2015; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild: + Drop unneeded hack + 08 Mar 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild, metadata.xml: removed openmm build diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index b50184a7c..9b8bf869a 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -247,13 +247,6 @@ src_install() { rm -f "${ED}"usr/bin/gmx-completion* rm -f "${ED}"usr/bin/g_options* rm -f "${ED}"usr/bin/GMXRC* - rm -f "${ED}"usr/lib*/libtng*.a - - #workaround for libtng - if [[ $(get_libdir) != lib ]]; then - mv "${ED}"usr/lib/libtng* "${ED}usr/$(get_libdir)" || die - rmdir "${ED}"usr/lib || die - fi readme.gentoo_create_doc } diff --git a/sci-chemistry/mage/Manifest b/sci-chemistry/mage/Manifest index 5bcae5fc9..588fdd9d3 100644 --- a/sci-chemistry/mage/Manifest +++ b/sci-chemistry/mage/Manifest @@ -1 +1 @@ -DIST mage.6.44.060606.src.tgz 726357 SHA256 c812202138cfee6b6434c51206286d460e83a12828e694013ecb16f2d5e839b3 +DIST mage.6.44.060606.src.tgz 726357 SHA256 c812202138cfee6b6434c51206286d460e83a12828e694013ecb16f2d5e839b3 SHA512 dceb63cc9806690539d0838079c2b57d6e62164049ca178d158e9c7eae759988c28d7e911942fd50f1ea880e61b2e9d7a38cc64bc5c229a4e5d442357c1f9227 WHIRLPOOL 30954a3a314c91acfce89eeffd37ae4600db76b602216c98a0d4f808a8e39b702a6076bcbb7d6c93a3fccfa58135942392cd6dd78e5b1dc5dd88bcb95415e452 diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog index d90a33d0d..a3307e9d0 100644 --- a/sci-chemistry/mdsctk/ChangeLog +++ b/sci-chemistry/mdsctk/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/mdsctk: Add github to remote-id in metadata.xml + 08 Mar 2015; Justin Lecher <jlec@gentoo.org> mdsctk-1.2.0.ebuild, metadata.xml: fix SLOT operator; drop KEYWORDS as deps are missing diff --git a/sci-chemistry/mdsctk/metadata.xml b/sci-chemistry/mdsctk/metadata.xml index a60809e1c..d9fa95a3a 100644 --- a/sci-chemistry/mdsctk/metadata.xml +++ b/sci-chemistry/mdsctk/metadata.xml @@ -9,4 +9,7 @@ <use> <flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag> </use> + <upstream> + <remote-id type="github">douradopalmares/mdsctk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-psico/ChangeLog b/sci-chemistry/pymol-plugins-psico/ChangeLog index 00cfae7b4..dd34ca921 100644 --- a/sci-chemistry/pymol-plugins-psico/ChangeLog +++ b/sci-chemistry/pymol-plugins-psico/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/pymol-plugins-psico -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/pymol-plugins-psico: Add github to remote-id in metadata.xml + 14 Nov 2013; Justin Lecher <jlec@gentoo.org> pymol-plugins-psico-9999.ebuild: bump to git-r3 eclass @@ -17,4 +20,3 @@ 21 Mar 2012; Justin Lecher <jlec@gentoo.org> +pymol-plugins-psico-9999.ebuild, +metadata.xml: New addition, written by me, #408995 - diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml index ae9ec7c5f..3eff7c70c 100644 --- a/sci-chemistry/pymol-plugins-psico/metadata.xml +++ b/sci-chemistry/pymol-plugins-psico/metadata.xml @@ -5,4 +5,7 @@ <maintainer> <email>jlec@gentoo.org</email> </maintainer> + <upstream> + <remote-id type="github">speleo3/pymol-psico</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/pyquante/ChangeLog b/sci-chemistry/pyquante/ChangeLog index f854df533..a44c5e8fa 100644 --- a/sci-chemistry/pyquante/ChangeLog +++ b/sci-chemistry/pyquante/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/pyquante -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/pyquante: Updating remote-id in metadata.xml + *pyquante-1.6.4 (07 Dec 2013) 07 Dec 2013; Nicolas Bock <nicolasbock@gmail.com> +pyquante-1.6.4.ebuild: diff --git a/sci-chemistry/pyquante/metadata.xml b/sci-chemistry/pyquante/metadata.xml index 51fdedab1..12ca64b3a 100644 --- a/sci-chemistry/pyquante/metadata.xml +++ b/sci-chemistry/pyquante/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">pyquante</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-electronics/player/ChangeLog b/sci-electronics/player/ChangeLog index f6e4fa099..95f7f30b5 100644 --- a/sci-electronics/player/ChangeLog +++ b/sci-electronics/player/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-electronics/player -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-electronics/player: Updating remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> player-2.0.4.ebuild: Fix deps diff --git a/sci-electronics/player/metadata.xml b/sci-electronics/player/metadata.xml index 50de93857..822054cc9 100644 --- a/sci-electronics/player/metadata.xml +++ b/sci-electronics/player/metadata.xml @@ -8,4 +8,7 @@ <flag name="openssl">Automatically generated description for openssl</flag> <flag name="festival">Automatically generated description for festival</flag> </use> + <upstream> + <remote-id type="sourceforge">playerstage</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-electronics/stage/ChangeLog b/sci-electronics/stage/ChangeLog index d99de0a8c..64514c649 100644 --- a/sci-electronics/stage/ChangeLog +++ b/sci-electronics/stage/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-electronics/stage: Updating remote-id in metadata.xml + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> stage-2.0.3.ebuild: Bump to EAPI=5 diff --git a/sci-electronics/stage/metadata.xml b/sci-electronics/stage/metadata.xml index 53ae7d77c..6c801c492 100644 --- a/sci-electronics/stage/metadata.xml +++ b/sci-electronics/stage/metadata.xml @@ -1,5 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-electronics</herd> + <herd>sci-electronics</herd> + <upstream> + <remote-id type="sourceforge">playerstage</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-electronics/tnt/ChangeLog b/sci-electronics/tnt/ChangeLog index 24b19c3df..d70be2df2 100644 --- a/sci-electronics/tnt/ChangeLog +++ b/sci-electronics/tnt/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-electronics/tnt -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-electronics/tnt: Updating remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> tnt-1.2.2.ebuild, +files/tnt-1.2.2-autotools.patch, metadata.xml: Punt base.eclass diff --git a/sci-electronics/tnt/metadata.xml b/sci-electronics/tnt/metadata.xml index ce0e016bb..87d1cd2b1 100644 --- a/sci-electronics/tnt/metadata.xml +++ b/sci-electronics/tnt/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-electronics</herd> + <upstream> + <remote-id type="sourceforge">mmtl</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap/metadata.xml b/sci-geosciences/pydap/metadata.xml index c1ce68b21..e86bec391 100644 --- a/sci-geosciences/pydap/metadata.xml +++ b/sci-geosciences/pydap/metadata.xml @@ -9,4 +9,7 @@ <longdescription lang="en"> Pydap is a pure Python library implementing the Data Access Protocol. </longdescription> + <upstream> + <remote-id type="pypi">Pydap</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_cdms/metadata.xml b/sci-geosciences/pydap_handlers_cdms/metadata.xml index 329458eb3..8bf200966 100644 --- a/sci-geosciences/pydap_handlers_cdms/metadata.xml +++ b/sci-geosciences/pydap_handlers_cdms/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_cdms allows Pydap server to serve GRADS formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.cdms</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_csv/metadata.xml b/sci-geosciences/pydap_handlers_csv/metadata.xml index 41d8db5a9..16bc3644d 100644 --- a/sci-geosciences/pydap_handlers_csv/metadata.xml +++ b/sci-geosciences/pydap_handlers_csv/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_csv allows Pydap server to serve CSV formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.csv</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_hdf5/metadata.xml b/sci-geosciences/pydap_handlers_hdf5/metadata.xml index 439a3377c..d4e710a9a 100644 --- a/sci-geosciences/pydap_handlers_hdf5/metadata.xml +++ b/sci-geosciences/pydap_handlers_hdf5/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_hdf5 allows Pydap server to serve hdf5 formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.hdf5</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_nca/metadata.xml b/sci-geosciences/pydap_handlers_nca/metadata.xml index 71fadebd8..2ed0280b3 100644 --- a/sci-geosciences/pydap_handlers_nca/metadata.xml +++ b/sci-geosciences/pydap_handlers_nca/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_nca allows Pydap server to serve aggregated NetCDF formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.nca</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_netcdf/metadata.xml b/sci-geosciences/pydap_handlers_netcdf/metadata.xml index a77356106..4e08c2427 100644 --- a/sci-geosciences/pydap_handlers_netcdf/metadata.xml +++ b/sci-geosciences/pydap_handlers_netcdf/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_netcdf allows Pydap server to serve NetCDF formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.netcdf</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_proxy/metadata.xml b/sci-geosciences/pydap_handlers_proxy/metadata.xml index 48f54b60b..52831c518 100644 --- a/sci-geosciences/pydap_handlers_proxy/metadata.xml +++ b/sci-geosciences/pydap_handlers_proxy/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_proxy allows Pydap server to serve data from other web sites. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.proxy</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_sql/metadata.xml b/sci-geosciences/pydap_handlers_sql/metadata.xml index 0a32c7494..a91b2e0e2 100644 --- a/sci-geosciences/pydap_handlers_sql/metadata.xml +++ b/sci-geosciences/pydap_handlers_sql/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_sql allows Pydap server to serve data from SQL databases. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.sql</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_sqlite/metadata.xml b/sci-geosciences/pydap_handlers_sqlite/metadata.xml index 2709f644d..9c67dc99b 100644 --- a/sci-geosciences/pydap_handlers_sqlite/metadata.xml +++ b/sci-geosciences/pydap_handlers_sqlite/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_sqlite allows Pydap server to serve data from SQLite files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.sqlite</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_kml/metadata.xml b/sci-geosciences/pydap_responses_kml/metadata.xml index a558e81e7..e329976f7 100644 --- a/sci-geosciences/pydap_responses_kml/metadata.xml +++ b/sci-geosciences/pydap_responses_kml/metadata.xml @@ -11,4 +11,7 @@ pydap_responses_kml allows Pydap server to use Google Earth to visualize data. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.kml</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_matlab/metadata.xml b/sci-geosciences/pydap_responses_matlab/metadata.xml index 42f4380fb..b08b16747 100644 --- a/sci-geosciences/pydap_responses_matlab/metadata.xml +++ b/sci-geosciences/pydap_responses_matlab/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_responses_matlab allows Pydap server to deliver data to Matlab. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.matlab</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_netcdf/metadata.xml b/sci-geosciences/pydap_responses_netcdf/metadata.xml index 974f6cb20..491527de1 100644 --- a/sci-geosciences/pydap_responses_netcdf/metadata.xml +++ b/sci-geosciences/pydap_responses_netcdf/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_responses_netcdf allows Pydap server to serve NetCDF formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.netcdf</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_wms/metadata.xml b/sci-geosciences/pydap_responses_wms/metadata.xml index d7bbe41b5..da0b5304a 100644 --- a/sci-geosciences/pydap_responses_wms/metadata.xml +++ b/sci-geosciences/pydap_responses_wms/metadata.xml @@ -11,4 +11,7 @@ pydap_responses_wms allows Pydap server to deliver maps via Web Mapping Service protocol. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.wms</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_xls/metadata.xml b/sci-geosciences/pydap_responses_xls/metadata.xml index 523b428a6..097b4dafd 100644 --- a/sci-geosciences/pydap_responses_xls/metadata.xml +++ b/sci-geosciences/pydap_responses_xls/metadata.xml @@ -11,4 +11,7 @@ pydap_responses_xls allows Pydap server to deliver an Excel file of the data. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.xls</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/armadillo/ChangeLog b/sci-libs/armadillo/ChangeLog index a6559b6d3..908a93a3b 100644 --- a/sci-libs/armadillo/ChangeLog +++ b/sci-libs/armadillo/ChangeLog @@ -2,6 +2,19 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/armadillo: Updating remote-id in metadata.xml + + 26 May 2015; Marius Brehler <marbre@linux.sungazer.de> + -armadillo-5.000.1.ebuild, -armadillo-5.100.1.ebuild: + Drop old + +*armadillo-5.200.1 (26 May 2015) + + 26 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +armadillo-5.200.1.ebuild: + Version bump + *armadillo-5.100.2 (12 May 2015) 12 May 2015; Marius Brehler <marbre@linux.sungazer.de> diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest index 10f7eeaef..e8c1fa6b7 100644 --- a/sci-libs/armadillo/Manifest +++ b/sci-libs/armadillo/Manifest @@ -1,4 +1,3 @@ DIST armadillo-4.650.4.tar.gz 5408567 SHA256 ccc56580ec932ec9beade5679b07ecbed889e9b602866f673d1a05a7692b4bf8 SHA512 a548150ba5484fce35b0bc6023982939946f2f00b733dff2cd5b46101b1c344342061389cb4363cdaa04c5e3cca3278a40febe2ed705316552dd71f841c46037 WHIRLPOOL 331493d8b9c92b9e1908880c6f6510edb12e93193a9ceb77d0b8ce9d0bfb493dc48e590ea949d39c3c19f6fc3b05446b7e00525512e3055be0f907427c28f7d4 -DIST armadillo-5.000.1.tar.gz 5425382 SHA256 8ca55fbfce220517374a879ddc0c79e1afd3993f89cc58621aa502e9533f3cdb SHA512 a1c109313734c1d1c8a5caf7c12f088c5acaaafd0738812b0692ee8353653d25d798dce2b8ec8706fa5cd546f3247155b94b416ad780b5d847d8a5d6ad4399ff WHIRLPOOL 6eeabb373d5fae740ba3debc0cbf63aa7e8fc6cb77e94ce77e0a05741ebe6da3192b18c43d93a19ad46ffa5e2cbc07922f1a8a4ca5eb2cac8cf9159fbf952da7 -DIST armadillo-5.100.1.tar.gz 5428805 SHA256 cf4c3c700e163689b187dd987756d963e24ca5f0834b6dad59832300d55860c7 SHA512 16fffab262d89d9f625e4405dadc20f3117e1682d5bf67810eccab2c08ff0690bdf89e11b87948dafc25547078eeab1745e73e33c4f50223fb632643f692a9b6 WHIRLPOOL 371168e591bb1fa6bd4a506d3f0aaa3c0ff01d6d92815c2210e6e3cb8f73a351e5e5e5ad9128e0ea96f9cc02d04b30a0a03e2c156210a6c19d2093ed565156ba DIST armadillo-5.100.2.tar.gz 5429961 SHA256 63150f12bf7c7c598ea55b7271d99fce349ff386a3dc2cae3904b244f6e35320 SHA512 2777b525bc62daddfb16eae7b74c29b6b695a7985c56d9dca727ae1e13aa4ea20ee85ea82233a5310b37c738838af07bb0fa7eea782e68e72cbe1cf46a0cc896 WHIRLPOOL df85a508875587651b187520b78900634402f2ca0fc2e64f43bd4a793e382e8cc6abd5b988267645bb02b3133d9aa99ab6d6ff5e200d1277093d4f7ce6e9d240 +DIST armadillo-5.200.1.tar.gz 5430678 SHA256 3673fc7cbeefca826108efe7c36e21322f259809f874c161ca284a114fb7f693 SHA512 750e18a7c464bfe17ed113014312cce54793780d2c5d1f6510faaedac44bc6c055955b0ffba6884ab1111be5c22740a0b3ddcd9533caf51afe1bda33074177f4 WHIRLPOOL ec7bffdb57943350fe31fce8926657c98de5e0a847d3ba04872c3644e8feed1cdcf467dc8359f302241f8b520f46465e5cd7843b55641bceb1d039e314f32474 diff --git a/sci-libs/armadillo/armadillo-5.100.1.ebuild b/sci-libs/armadillo/armadillo-5.100.1.ebuild deleted file mode 100644 index 8d63e069b..000000000 --- a/sci-libs/armadillo/armadillo-5.100.1.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/armadillo/armadillo-4.650.4.ebuild,v 1.1 2015/04/03 12:32:07 jlec Exp $ - -EAPI=5 - -CMAKE_IN_SOURCE_BUILD=1 - -inherit cmake-utils toolchain-funcs multilib eutils - -DESCRIPTION="Streamlined C++ linear algebra library" -HOMEPAGE="http://arma.sourceforge.net/" -SRC_URI="mirror://sourceforge/arma/${P}.tar.gz" - -LICENSE="MPL-2.0" -SLOT="0/4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="arpack atlas blas debug doc examples hdf5 lapack mkl tbb test" -REQUIRED_USE="test? ( lapack )" - -RDEPEND=" - dev-libs/boost - arpack? ( sci-libs/arpack ) - atlas? ( sci-libs/atlas[lapack] ) - blas? ( virtual/blas ) - lapack? ( virtual/lapack )" -DEPEND="${RDEPEND} - arpack? ( virtual/pkgconfig ) - atlas? ( virtual/pkgconfig ) - blas? ( virtual/pkgconfig ) - hdf5? ( sci-libs/hdf5 ) - lapack? ( virtual/pkgconfig ) - mkl? ( sci-libs/mkl ) - tbb? ( dev-cpp/tbb )" -PDEPEND="${RDEPEND} - hdf5? ( sci-libs/hdf5 ) - mkl? ( sci-libs/mkl ) - tbb? ( dev-cpp/tbb )" - -src_prepare() { - # avoid the automagic cmake macros - sed -i -e '/ARMA_Find/d' CMakeLists.txt || die - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)" - $(cmake-utils_use debug ARMA_EXTRA_DEBUG) - $(cmake-utils_use mkl ARMA_USE_MKL_ALLOC) - $(cmake-utils_use tbb ARMA_USE_TBB_ALLOC) - ) - if use arpack; then - mycmakeargs+=( - -DARPACK_FOUND=ON - -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)" - ) - fi - if use atlas; then - local c=atlas-cblas l=atlas-clapack - $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads - $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads - mycmakeargs+=( - -DCBLAS_FOUND=ON - -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')" - -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})" - -DCLAPACK_FOUND=ON - -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')" - -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})" - ) - fi - if use blas; then - mycmakeargs+=( - -DBLAS_FOUND=ON - -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" - ) - fi - if use hdf5; then - mycmakeargs+=( - -DHDF5_FOUND=ON - -DHDF5_LIBRARIES="-lhdf5" - ) - fi - if use lapack; then - mycmakeargs+=( - -DLAPACK_FOUND=ON - -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" - ) - fi - cmake-utils_src_configure -} - -src_test() { - pushd examples > /dev/null - emake \ - CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \ - EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)" - LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die - LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die - emake clean - popd > /dev/null -} - -src_install() { - cmake-utils_src_install - dodoc README.txt - use doc && dodoc *pdf && dohtml *html - if use examples; then - insinto /usr/share/examples/${PF} - doins -r examples/* - fi -} diff --git a/sci-libs/armadillo/armadillo-5.000.1.ebuild b/sci-libs/armadillo/armadillo-5.200.1.ebuild index 8d63e069b..8d63e069b 100644 --- a/sci-libs/armadillo/armadillo-5.000.1.ebuild +++ b/sci-libs/armadillo/armadillo-5.200.1.ebuild diff --git a/sci-libs/armadillo/metadata.xml b/sci-libs/armadillo/metadata.xml index 385357d8a..dfc8f3007 100644 --- a/sci-libs/armadillo/metadata.xml +++ b/sci-libs/armadillo/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> Armadillo is a C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a @@ -14,20 +14,23 @@ need for temporaries. This is accomplished through recursive templates and template meta-programming. </longdescription> -<use> - <flag name="atlas"> + <use> + <flag name="atlas"> Link with <pkg>sci-libs/atlas</pkg> libraries for cblas and clapack </flag> - <flag name="arpack"> + <flag name="arpack"> Link with <pkg>sci-libs/arpack</pkg> libraries for eigen decomposition </flag> - <flag name='mkl'> + <flag name="mkl"> Use matrix allocation from the Intel MKL <pkg>sci-libs/mkl</pkg> - </flag> - <flag name='tbb'> + </flag> + <flag name="tbb"> Use matrix allocation from the Threads Building Blocks <pkg>dev-cpp/tbb</pkg> - </flag> -</use> + </flag> + </use> + <upstream> + <remote-id type="sourceforge">arma</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/atlas/ChangeLog b/sci-libs/atlas/ChangeLog index d0a2ccaf8..cf7b7732c 100644 --- a/sci-libs/atlas/ChangeLog +++ b/sci-libs/atlas/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/atlas -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/atlas: Updating remote-id in metadata.xml + 02 Feb 2014; Reinis Danne <rei4dan@gmail.com> atlas-3.10.1-r1.ebuild, atlas-3.10.1-r2.ebuild: Fix cpu governor check. diff --git a/sci-libs/atlas/metadata.xml b/sci-libs/atlas/metadata.xml index fde6aff3c..31d8b7462 100644 --- a/sci-libs/atlas/metadata.xml +++ b/sci-libs/atlas/metadata.xml @@ -13,4 +13,7 @@ <use> <flag name="generic">Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)</flag> </use> + <upstream> + <remote-id type="sourceforge">math-atlas</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/cgnstools/ChangeLog b/sci-libs/cgnstools/ChangeLog index 5c8516431..504626e52 100644 --- a/sci-libs/cgnstools/ChangeLog +++ b/sci-libs/cgnstools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/cgnstools: Updating remote-id in metadata.xml + 07 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> cgnstools-2.5.4-r1.ebuild: Move to EAPI=5 @@ -29,4 +32,3 @@ 26 Aug 2008; Oliver Borm (boroli) <oli.borm@web.de> +cgnstools-2.5.2.ebuild, +metadata.xml: Ebuild for cgnstools from bug 176455 - diff --git a/sci-libs/cgnstools/metadata.xml b/sci-libs/cgnstools/metadata.xml index b229aec85..f9c8ebc15 100644 --- a/sci-libs/cgnstools/metadata.xml +++ b/sci-libs/cgnstools/metadata.xml @@ -1,5 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> + <herd>sci</herd> + <upstream> + <remote-id type="sourceforge">cgns</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/clblas/ChangeLog b/sci-libs/clblas/ChangeLog index 19053c28b..e6656f8f5 100644 --- a/sci-libs/clblas/ChangeLog +++ b/sci-libs/clblas/ChangeLog @@ -2,6 +2,29 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*clblas-2.4-r1 (06 Jun 2015) + + 06 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> +clblas-2.4-r1.ebuild, + +files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch, + -clblas-2.4.ebuild, clblas-9999.ebuild: + sci-libs/clblas: Fix installation of cmake configuration + + 06 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> -clblas-2.2.ebuild, + -files/clblas-2.2-client_CMakeLists.patch, + -files/clblas-2.2-library_tools_tune_CMakeLists.patch: + sci-libs/clblas: Drop old + + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> clblas-2.2.ebuild, + clblas-2.4.ebuild, clblas-9999.ebuild: + sci-libs/clblas: Cleanup ebuilds + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> clblas-2.2.ebuild, + clblas-9999.ebuild: + sci-libs/clblas: Move to python-single-r1.eclass + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/clblas: Add github to remote-id in metadata.xml + *clblas-2.4 (09 May 2015) 09 May 2015; Marius Brehler <marbre@linux.sungazer.de> +clblas-2.4.ebuild: diff --git a/sci-libs/clblas/Manifest b/sci-libs/clblas/Manifest index b54efe1eb..47dd24365 100644 --- a/sci-libs/clblas/Manifest +++ b/sci-libs/clblas/Manifest @@ -1,2 +1 @@ -DIST clblas-2.2.tar.gz 794888 SHA256 0563e028485d240f8b6e6efcae61677049627b19e924dcb1ef8014065b6416df SHA512 9f094845d854130d3901d639606069050da10a33b05985757d72188b2d8ef6e7836edc105f5ad8bf2d0922eb19e9a178388260b2a9da34e2fe27dc731233ec85 WHIRLPOOL 2f81de82d584ec4f2158c1165d02221cacf3775cdb9c96617ca2e3ea1fbb7844c833e50cbd8c7b2601585771ddb81a48795dd1534200806b560954a069cf4ec1 DIST clblas-2.4.tar.gz 800848 SHA256 3e9b8e138c465df1daff0235d9c93b0005986a7257a3739aea2d4c8b60b7ed37 SHA512 ae8c1fc1bef7573b12279977fc32f9e97c9b81b9167994ca6f352587a670dcee0f486ab2b7d5191092324f5e8fc00f9a2ea29303a026a0c1201be31d384cafe7 WHIRLPOOL a97537d7390055ad608eeac66679362956db7acfa96cf1165581ff8f9adfe309b8ff8231225bd8ca6247c8f588bff24d6f648e131cec52f8e3093168a3f26f82 diff --git a/sci-libs/clblas/clblas-2.2.ebuild b/sci-libs/clblas/clblas-2.4-r1.ebuild index 84342eb5b..00133c2e3 100644 --- a/sci-libs/clblas/clblas-2.2.ebuild +++ b/sci-libs/clblas/clblas-2.4-r1.ebuild @@ -4,22 +4,17 @@ EAPI=5 -inherit cmake-utils +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils python-single-r1 MY_PN="clBLAS" DESCRIPTION="A software library containing BLAS routines for OpenCL" HOMEPAGE="https://github.com/clMathLibraries/clBLAS" - -if [ ${PV} == "9999" ] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" - S="${WORKDIR}/${P}/src" -else - SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" - S="${WORKDIR}/${MY_PN}-${PV}/src" -fi +SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64" +S="${WORKDIR}/${MY_PN}-${PV}/src" LICENSE="Apache-2.0" SLOT="0" @@ -30,7 +25,7 @@ RDEPEND=" virtual/opencl || ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk ) dev-libs/boost - performance? ( dev-lang/python ) + performance? ( ${PYTHON_DEPS} ) " DEPEND="${RDEPEND}" # test? ( @@ -43,10 +38,9 @@ DEPEND="${RDEPEND}" RESTRICT="test" PATCHES=( - "${FILESDIR}/${P}"-client_CMakeLists.patch - "${FILESDIR}/${P}"-library_tools_tune_CMakeLists.patch "${FILESDIR}"/clblas-samples_CMakeLists.patch "${FILESDIR}"/clblas-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch ) pkg_pretend() { diff --git a/sci-libs/clblas/clblas-2.4.ebuild b/sci-libs/clblas/clblas-2.4.ebuild deleted file mode 120000 index 9729dfdc2..000000000 --- a/sci-libs/clblas/clblas-2.4.ebuild +++ /dev/null @@ -1 +0,0 @@ -clblas-9999.ebuild
\ No newline at end of file diff --git a/sci-libs/clblas/clblas-9999.ebuild b/sci-libs/clblas/clblas-9999.ebuild index 34e3840d6..bb47c0d37 100644 --- a/sci-libs/clblas/clblas-9999.ebuild +++ b/sci-libs/clblas/clblas-9999.ebuild @@ -4,22 +4,16 @@ EAPI=5 -inherit cmake-utils +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils git-r3 python-single-r1 MY_PN="clBLAS" DESCRIPTION="A software library containing BLAS routines for OpenCL" HOMEPAGE="https://github.com/clMathLibraries/clBLAS" - -if [ ${PV} == "9999" ] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" - S="${WORKDIR}/${P}/src" -else - SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" - S="${WORKDIR}/${MY_PN}-${PV}/src" -fi +EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" +S="${WORKDIR}/${P}/src" LICENSE="Apache-2.0" SLOT="0" @@ -30,7 +24,7 @@ RDEPEND=" virtual/opencl || ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk ) dev-libs/boost - performance? ( dev-lang/python ) + performance? ( ${PYTHON_DEPS} ) " DEPEND="${RDEPEND}" # test? ( @@ -45,6 +39,7 @@ RESTRICT="test" PATCHES=( "${FILESDIR}"/clblas-samples_CMakeLists.patch "${FILESDIR}"/clblas-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch ) pkg_pretend() { diff --git a/sci-libs/clblas/files/clblas-2.2-client_CMakeLists.patch b/sci-libs/clblas/files/clblas-2.2-client_CMakeLists.patch deleted file mode 100644 index 552e230e3..000000000 --- a/sci-libs/clblas/files/clblas-2.2-client_CMakeLists.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- client/CMakeLists.txt 2014-06-19 22:53:25.000000000 +0200 -+++ client/CMakeLists.txt.new 2015-03-23 16:30:39.164046584 +0100 -@@ -52,7 +52,7 @@ include_directories( - - add_executable(client ${CLIENT_SRC} ${CLIENT_HEADER}) - target_link_libraries(client ${Boost_LIBRARIES} ${OPENCL_LIBRARIES} clBLAS) --set_target_properties( client PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" ) -+set_target_properties( client PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" OUTPUT_NAME clBLAS-client ) - - add_executable(testPerfWrapper ${WRAPPER_SRC}) - target_link_libraries(testPerfWrapper ${Boost_LIBRARIES}) diff --git a/sci-libs/clblas/files/clblas-2.2-library_tools_tune_CMakeLists.patch b/sci-libs/clblas/files/clblas-2.2-library_tools_tune_CMakeLists.patch deleted file mode 100644 index 5f1f763fe..000000000 --- a/sci-libs/clblas/files/clblas-2.2-library_tools_tune_CMakeLists.patch +++ /dev/null @@ -1,14 +0,0 @@ -Install tune as clBLAS-tune. - -Patch by Marius Brehler. ---- library/tools/tune/CMakeLists.txt -+++ library/tools/tune/CMakeLists.txt -@@ -138,7 +138,7 @@ endif() - add_executable(tune ${TOOLS_SRC} ${TOOLS_EXTERNAL_SRC}) - add_dependencies(tune GENERATE_CLT) - target_link_libraries(tune ${OPENCL_LIBRARIES} ${TIME_LIBRARY} ${MATH_LIBRARY}) --set_target_properties( tune PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" ) -+set_target_properties( tune PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" OUTPUT_NAME clBLAS-tune ) - - # CPack configuration; include the executable into the package - install( TARGETS tune diff --git a/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch b/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch new file mode 100644 index 000000000..32cb7b553 --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch @@ -0,0 +1,25 @@ +From b83750ab917b12500f9755dc4c81f99eb55bb67e Mon Sep 17 00:00:00 2001 +From: Marius Brehler <marius.brehler@tu-dortmund.de> +Date: Sat, 6 Jun 2015 10:35:32 +0200 +Subject: [PATCH] Install cmake configuration to lib/cmake/clBLAS + +--- + src/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index a23cd37..5c378dc 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -300,7 +300,7 @@ endif( ) + if(WIN32) + set(destdir CMake) + else() +- set(destdir share/clBLAS) ++ set(destdir lib${SUFFIX_LIB}/cmake/clBLAS) + endif() + string(REGEX REPLACE "[^/]+" ".." reldir "${destdir}") + configure_file( +-- +2.3.6 + diff --git a/sci-libs/clblas/metadata.xml b/sci-libs/clblas/metadata.xml index fe45c3c20..1541b5a57 100644 --- a/sci-libs/clblas/metadata.xml +++ b/sci-libs/clblas/metadata.xml @@ -20,4 +20,7 @@ Copy performance scripts that can measure and graph performance. </flag> </use> + <upstream> + <remote-id type="github">clMathLibraries/clBLAS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/clfft/ChangeLog b/sci-libs/clfft/ChangeLog index 92fa54017..eb0991326 100644 --- a/sci-libs/clfft/ChangeLog +++ b/sci-libs/clfft/ChangeLog @@ -2,6 +2,21 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*clfft-2.4-r1 (05 Jun 2015) + + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> +clfft-2.4-r1.ebuild, + +files/clfft-2.4-fix-cmake-config-install.patch, + +files/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch, + -clfft-2.2.ebuild, -clfft-2.4.ebuild, clfft-0.9999.ebuild, clfft-9999.ebuild: + sci-libs/clfft: Drop old; Install cmake configuration + + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> clfft-0.9999.ebuild, + clfft-2.4.ebuild, clfft-9999.ebuild: + sci-libs/clfft: Cleanup ebuilds + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/clfft: Add github to remote-id in metadata.xml + *clfft-0.9999 (11 May 2015) 11 May 2015; Marius Brehler <marbre@linux.sungazer.de> +clfft-0.9999.ebuild, diff --git a/sci-libs/clfft/Manifest b/sci-libs/clfft/Manifest index 6d6894071..65c5acaf2 100644 --- a/sci-libs/clfft/Manifest +++ b/sci-libs/clfft/Manifest @@ -1,2 +1 @@ -DIST clfft-2.2.tar.gz 678144 SHA256 eed3cc196c1b18785291261294655daa4c7d4d9e8b4a3aad26004db55f544e0d SHA512 b7a2e7e3c0c1f7126c37e4a39f09c72c2ac0d3a29e12a3f86deaae7090114dae8e925a03fcc8d39f8530c200de7ec6e3cfc4c8ad76ed5a39f555e76082c86850 WHIRLPOOL 8f7a1919aff1e5cd1044ba4c17cd2b98b652e65b74b7dc8400020071d9a949f0981ed1c578d0916397ca5c171bd8a378788f3cedaf70a9d255de96de67ce4718 DIST clfft-2.4.tar.gz 678262 SHA256 d77506af774bbe8ccf4226a58e623c8a29587edcf02984e72851099be0efe04b SHA512 3450f3ee962e1722c765e962178c57df0bf298508603ac5b4ec12bd6396dc10279136d5b91383b9da56d95cebd0e552bf78e2c01ccaeb8cd43ed947b7d536209 WHIRLPOOL 6ec21e182deac2a8c0a102a96c974289e56cf3f9908fbf067d7105f50646270bee2e17cf98fdf6cecf8ce28c8714c710ce46f514f7cfc1de205d5ef48bb5a0ed diff --git a/sci-libs/clfft/clfft-0.9999.ebuild b/sci-libs/clfft/clfft-0.9999.ebuild index b6c165da9..0aebebb39 120000..100644 --- a/sci-libs/clfft/clfft-0.9999.ebuild +++ b/sci-libs/clfft/clfft-0.9999.ebuild @@ -1 +1,53 @@ -clfft-9999.ebuild
\ No newline at end of file +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils git-r3 + +MY_PN="clFFT" + +DESCRIPTION="A software library containing FFT functions written in OpenCL" +HOMEPAGE="https://github.com/clMathLibraries/clFFT" +EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" +S="${WORKDIR}/${P}/src" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="test" + +RDEPEND=" + >=sys-devel/gcc-4.6:* + virtual/opencl + dev-libs/boost" +DEPEND="${RDEPEND}" +# test? ( +# dev-cpp/gtest +# sci-libs/fftw:3.0 +# )" + +# The tests only get compiled to an executable named Test, which is not recogniozed by cmake. +# Therefore src_test() won't execute any test. +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/clfft-client_CMakeLists.patch + "${FILESDIR}"/clfft-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clfft-2.4-fix-cmake-config-install.patch +) + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then + die "Compilation with gcc older than 4.6 is not supported." + fi + fi +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/clfft/clfft-2.2.ebuild b/sci-libs/clfft/clfft-2.2.ebuild deleted file mode 120000 index b6c165da9..000000000 --- a/sci-libs/clfft/clfft-2.2.ebuild +++ /dev/null @@ -1 +0,0 @@ -clfft-9999.ebuild
\ No newline at end of file diff --git a/sci-libs/clfft/clfft-2.4-r1.ebuild b/sci-libs/clfft/clfft-2.4-r1.ebuild new file mode 100644 index 000000000..6b9893890 --- /dev/null +++ b/sci-libs/clfft/clfft-2.4-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils + +MY_PN="clFFT" + +DESCRIPTION="A software library containing FFT functions written in OpenCL" +HOMEPAGE="https://github.com/clMathLibraries/clFFT" +SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64" +S="${WORKDIR}/${MY_PN}-${PV}/src" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="test" + +RDEPEND=" + >=sys-devel/gcc-4.6:* + virtual/opencl + dev-libs/boost" +DEPEND="${RDEPEND}" +# test? ( +# dev-cpp/gtest +# sci-libs/fftw:3.0 +# )" + +# The tests only get compiled to an executable named Test, which is not recogniozed by cmake. +# Therefore src_test() won't execute any test. +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/clfft-client_CMakeLists.patch + "${FILESDIR}"/clfft-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clfft-2.4-fix-cmake-config-install.patch +) + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then + die "Compilation with gcc older than 4.6 is not supported." + fi + fi +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/clfft/clfft-2.4.ebuild b/sci-libs/clfft/clfft-2.4.ebuild deleted file mode 120000 index b6c165da9..000000000 --- a/sci-libs/clfft/clfft-2.4.ebuild +++ /dev/null @@ -1 +0,0 @@ -clfft-9999.ebuild
\ No newline at end of file diff --git a/sci-libs/clfft/clfft-9999.ebuild b/sci-libs/clfft/clfft-9999.ebuild index 994dad99c..96b7dcdf3 100644 --- a/sci-libs/clfft/clfft-9999.ebuild +++ b/sci-libs/clfft/clfft-9999.ebuild @@ -4,25 +4,15 @@ EAPI=5 -inherit cmake-utils +inherit cmake-utils git-r3 MY_PN="clFFT" DESCRIPTION="A software library containing FFT functions written in OpenCL" HOMEPAGE="https://github.com/clMathLibraries/clFFT" - -if [ ${PV} == "9999" ] || [ ${PV} == "0.9999" ]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" - S="${WORKDIR}/${P}/src" - if [ ${PV} == "9999" ]; then - EGIT_BRANCH="develop" - fi -else - SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" - S="${WORKDIR}/${MY_PN}-${PV}/src" -fi +EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" +EGIT_BRANCH="develop" +S="${WORKDIR}/${P}/src" LICENSE="Apache-2.0" SLOT="0" @@ -42,13 +32,9 @@ DEPEND="${RDEPEND}" # Therefore src_test() won't execute any test. RESTRICT="test" -# Patches are only needed for the recent master and releases <= 2.4 -if [ ${PV} != "9999" ]; then - PATCHES=( - "${FILESDIR}"/clfft-client_CMakeLists.patch - "${FILESDIR}"/clfft-scripts_perf_CMakeLists.patch - ) -fi +PATCHES=( + "${FILESDIR}"/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch +) pkg_pretend() { if [[ ${MERGE_TYPE} != binary ]]; then diff --git a/sci-libs/clfft/files/clfft-2.4-fix-cmake-config-install.patch b/sci-libs/clfft/files/clfft-2.4-fix-cmake-config-install.patch new file mode 100644 index 000000000..6dd1e15db --- /dev/null +++ b/sci-libs/clfft/files/clfft-2.4-fix-cmake-config-install.patch @@ -0,0 +1,128 @@ +Upstream patch, with modified destdir +https://github.com/clMathLibraries/clFFT/pull/88 + + +Description: install missing cmake config module +Author: <kent.knox@amd> +Origin: upstream +Forwarded: not-needed +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -283,6 +283,29 @@ else( ) + message( "GoogleTest unit tests will NOT be built" ) + endif( ) + ++if( BUILD_EXAMPLES ) ++ add_subdirectory( examples ) ++endif() ++ ++if(WIN32) ++ set(destdir CMake) ++else() ++ set(destdir lib${SUFFIX_LIB}/cmake/clFFT) ++endif() ++string(REGEX REPLACE "[^/]+" ".." reldir "${destdir}") ++configure_file( ++ ${CMAKE_CURRENT_SOURCE_DIR}/clFFTConfigVersion.cmake.in ++ ${CMAKE_CURRENT_BINARY_DIR}/clFFTConfigVersion.cmake ++ @ONLY) ++configure_file( ++ ${CMAKE_CURRENT_SOURCE_DIR}/clFFTConfig.cmake.in ++ ${CMAKE_CURRENT_BINARY_DIR}/clFFTConfig.cmake ++ @ONLY) ++install(EXPORT Library DESTINATION ${destdir} FILE clFFTTargets.cmake) ++install(FILES ${CMAKE_CURRENT_BINARY_DIR}/clFFTConfigVersion.cmake ++ ${CMAKE_CURRENT_BINARY_DIR}/clFFTConfig.cmake ++ DESTINATION ${destdir}) ++ + # The following code is setting variables to control the behavior of CPack to generate our + if( WIN32 ) + set( CPACK_SOURCE_GENERATOR "ZIP" ) +diff --git a/src/clFFTConfig.cmake.in b/src/clFFTConfig.cmake.in +new file mode 100644 +index 0000000..5b58c35 +--- /dev/null ++++ b/src/clFFTConfig.cmake.in +@@ -0,0 +1,3 @@ ++include(${CMAKE_CURRENT_LIST_DIR}/clFFTTargets.cmake) ++get_filename_component(CLFFT_INCLUDE_DIRS ${CMAKE_CURRENT_LIST_DIR}/@reldir@/include ABSOLUTE) ++set(CLFFT_LIBRARIES clFFT) +diff --git a/src/clFFTConfigVersion.cmake.in b/src/clFFTConfigVersion.cmake.in +new file mode 100644 +index 0000000..e358473 +--- /dev/null ++++ b/src/clFFTConfigVersion.cmake.in +@@ -0,0 +1,46 @@ ++# This is a basic version file for the Config-mode of find_package(). ++# It is used by write_basic_package_version_file() as input file for configure_file() ++# to create a version-file which can be installed along a config.cmake file. ++# ++# The created file sets PACKAGE_VERSION_EXACT if the current version string and ++# the requested version string are exactly the same and it sets ++# PACKAGE_VERSION_COMPATIBLE if the current version is >= requested version, ++# but only if the requested major version is the same as the current one. ++# The variable CLFFT_VERSION must be set before calling configure_file(). ++ ++ ++set(PACKAGE_VERSION "@CLFFT_VERSION@") ++ ++if("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}" ) ++ set(PACKAGE_VERSION_COMPATIBLE FALSE) ++else() ++ ++ if("@CLFFT_VERSION@" MATCHES "^([0-9]+)\\.") ++ set(CLFFT_VERSION_MAJOR "${CMAKE_MATCH_1}") ++ else() ++ set(CLFFT_VERSION_MAJOR "@CLFFT_VERSION@") ++ endif() ++ ++ if("${PACKAGE_FIND_VERSION_MAJOR}" STREQUAL "${CLFFT_VERSION_MAJOR}") ++ set(PACKAGE_VERSION_COMPATIBLE TRUE) ++ else() ++ set(PACKAGE_VERSION_COMPATIBLE FALSE) ++ endif() ++ ++ if( "${PACKAGE_FIND_VERSION}" STREQUAL "${PACKAGE_VERSION}") ++ set(PACKAGE_VERSION_EXACT TRUE) ++ endif() ++endif() ++ ++ ++# if the installed or the using project don't have CMAKE_SIZEOF_VOID_P set, ignore it: ++if("${CMAKE_SIZEOF_VOID_P}" STREQUAL "" OR "@CMAKE_SIZEOF_VOID_P@" STREQUAL "") ++ return() ++endif() ++ ++# check that the installed version has the same 32/64bit-ness as the one which is currently searching: ++if(NOT "${CMAKE_SIZEOF_VOID_P}" STREQUAL "@CMAKE_SIZEOF_VOID_P@") ++ math(EXPR installedBits "@CMAKE_SIZEOF_VOID_P@ * 8") ++ set(PACKAGE_VERSION "${PACKAGE_VERSION} (${installedBits}bit)") ++ set(PACKAGE_VERSION_UNSUITABLE TRUE) ++endif() +diff --git a/src/library/CMakeLists.txt b/src/library/CMakeLists.txt +index 63ac0f9..0d400d8 100644 +--- a/src/library/CMakeLists.txt ++++ b/src/library/CMakeLists.txt +@@ -95,6 +95,7 @@ endif( ) + + # CPack configuration; include the executable into the package + install( TARGETS clFFT ++ EXPORT Library + RUNTIME DESTINATION bin${SUFFIX_BIN} + LIBRARY DESTINATION lib${SUFFIX_LIB} + ARCHIVE DESTINATION lib${SUFFIX_LIB}/import +diff --git a/src/statTimer/CMakeLists.txt b/src/statTimer/CMakeLists.txt +index a635bf1..3dc026f 100644 +--- a/src/statTimer/CMakeLists.txt ++++ b/src/statTimer/CMakeLists.txt +@@ -80,6 +80,7 @@ endif( ) + + # CPack configuration; include the executable into the package + install( TARGETS StatTimer ++ EXPORT Library + RUNTIME DESTINATION bin${SUFFIX_BIN} + LIBRARY DESTINATION lib${SUFFIX_LIB} + ARCHIVE DESTINATION lib${SUFFIX_LIB}/import +-- +2.1.4 + diff --git a/sci-libs/clfft/files/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch b/sci-libs/clfft/files/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch new file mode 100644 index 000000000..dc317d40d --- /dev/null +++ b/sci-libs/clfft/files/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch @@ -0,0 +1,25 @@ +From 6a3ba77529987d5906ba6f734bc2fa66a9155a1c Mon Sep 17 00:00:00 2001 +From: Marius Brehler <marbre@linux.sungazer.de> +Date: Fri, 5 Jun 2015 14:59:29 +0200 +Subject: [PATCH] Install cmake configuration to lib/cmake/clFFT + +--- + src/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index ad15e4a..73200fa 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -290,7 +290,7 @@ endif() + if(WIN32) + set(destdir CMake) + else() +- set(destdir share/clFFT) ++ set(destdir lib${SUFFIX_LIB}/cmake/clFFT) + endif() + string(REGEX REPLACE "[^/]+" ".." reldir "${destdir}") + configure_file( +-- +2.0.5 + diff --git a/sci-libs/clfft/metadata.xml b/sci-libs/clfft/metadata.xml index 14184f9aa..910e9921c 100644 --- a/sci-libs/clfft/metadata.xml +++ b/sci-libs/clfft/metadata.xml @@ -14,4 +14,7 @@ clFFT is part of the clMath sofware library, which is the successor of APPML. </longdescription> + <upstream> + <remote-id type="github">clMathLibraries/clFFT</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/clrng/ChangeLog b/sci-libs/clrng/ChangeLog index eb82a27f0..1e0a15e1f 100644 --- a/sci-libs/clrng/ChangeLog +++ b/sci-libs/clrng/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/clrng: Add github to remote-id in metadata.xml + *clrng-9999 (11 May 2015) 11 May 2015; Marius Brehler <marbre@linux.sungazer.de> +clrng-9999.ebuild, diff --git a/sci-libs/clrng/metadata.xml b/sci-libs/clrng/metadata.xml index 09f500831..25fe2a5cf 100644 --- a/sci-libs/clrng/metadata.xml +++ b/sci-libs/clrng/metadata.xml @@ -7,4 +7,7 @@ Build a command line clRNG client program. </flag> </use> + <upstream> + <remote-id type="github">clMathLibraries/clRNG</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/dealii/ChangeLog b/sci-libs/dealii/ChangeLog index b3491fe13..c900cbe52 100644 --- a/sci-libs/dealii/ChangeLog +++ b/sci-libs/dealii/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> dealii-8.1.0-r2.ebuild, + dealii-8.2.1-r1.ebuild, dealii-9999.ebuild: + sci-libs/dealii: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/dealii: Add github to remote-id in metadata.xml + *dealii-8.2.1-r1 (28 Mar 2015) 28 Mar 2015; Matthias Maier <tamiko@gentoo.org> +dealii-8.2.1-r1.ebuild, diff --git a/sci-libs/dealii/dealii-8.1.0-r2.ebuild b/sci-libs/dealii/dealii-8.1.0-r2.ebuild index e1bce5e4a..0703aa8af 100644 --- a/sci-libs/dealii/dealii-8.1.0-r2.ebuild +++ b/sci-libs/dealii/dealii-8.1.0-r2.ebuild @@ -46,7 +46,7 @@ RDEPEND="dev-libs/boost mumps? ( sci-libs/mumps[mpi] ) netcdf? ( sci-libs/netcdf-cxx:0 ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) diff --git a/sci-libs/dealii/dealii-8.2.1-r1.ebuild b/sci-libs/dealii/dealii-8.2.1-r1.ebuild index 145cb29e6..331dd0dce 100644 --- a/sci-libs/dealii/dealii-8.2.1-r1.ebuild +++ b/sci-libs/dealii/dealii-8.2.1-r1.ebuild @@ -53,9 +53,9 @@ RDEPEND="dev-libs/boost mumps? ( sci-libs/mumps[mpi] ) muparser? ( dev-cpp/muParser ) netcdf? ( sci-libs/netcdf-cxx:0 ) - opencascade? ( sci-libs/opencascade ) + opencascade? ( sci-libs/opencascade:* ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild index dc836023b..c00c3835f 100644 --- a/sci-libs/dealii/dealii-9999.ebuild +++ b/sci-libs/dealii/dealii-9999.ebuild @@ -51,9 +51,9 @@ RDEPEND="dev-libs/boost mpi? ( virtual/mpi ) muparser? ( dev-cpp/muParser ) netcdf? ( sci-libs/netcdf-cxx:0 ) - opencascade? ( sci-libs/opencascade ) + opencascade? ( sci-libs/opencascade:* ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) diff --git a/sci-libs/dealii/metadata.xml b/sci-libs/dealii/metadata.xml index e838dc172..bce7b01bc 100644 --- a/sci-libs/dealii/metadata.xml +++ b/sci-libs/dealii/metadata.xml @@ -31,4 +31,7 @@ and extra output. If you want to get meaningful backtraces see <flag name="tbb">Add threading support with the help of the tbb library (<pkg>dev-cpp/tbb</pkg>)</flag> <flag name="trilinos">Add support for trilinos (<pkg>sci-libs/trilinos</pkg>)</flag> </use> + <upstream> + <remote-id type="github">dealii/dealii</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/elmer-eio/Manifest b/sci-libs/elmer-eio/Manifest index 4b4383312..2fe59554f 100644 --- a/sci-libs/elmer-eio/Manifest +++ b/sci-libs/elmer-eio/Manifest @@ -1 +1 @@ -DIST elmer-eio-6.0_p4651.tar.gz 147064 SHA256 98979ce8f3d3ee9f0f06a1c07a9021d5ffdc7e16a739ba90724257cc21fc0c88 SHA512 744615444f131fe4a1dd789ff4197cc86d24991a21a9c04b1ea3815ca7c6346b7d211ae47bc77bf49ca2e763a5daf6b0fef3b2b1d71697ed93fbc557ca5825a7 WHIRLPOOL 207abde5b60b5527cb5ea538746a4cf7d30f76a1979f84ddad697b741dd9abb391e1ef5ceee0f461c207aec709743723fcd8846b6b76f1c09ae22ecf07eada4b +DIST elmer-eio-6.0_p4651.tar.gz 147064 SHA256 80748e1386f03ef4b3a4c68271b1c724563a8960ffffcc36ba23e70e8519426e SHA512 52ce490810787e5100524858d41f3ad3d17ebfe5b747ea042acd8b8106028bb3aa7dd87ef80d3ce4ae2ffbf9439ad86c5f1a5f2e2c3cfb1cca5800c0fa166924 WHIRLPOOL 28837ee89756d81db5be96909f9682b1c627f31955179b668097c4d9c3efd55936a8e4c7334eda76051664dbb7043b246ad5d77a6b8950bb20f11a88ae53aa89 diff --git a/sci-libs/framewave/ChangeLog b/sci-libs/framewave/ChangeLog index 86d49d70e..9cb20eeb1 100644 --- a/sci-libs/framewave/ChangeLog +++ b/sci-libs/framewave/ChangeLog @@ -2,5 +2,8 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/framewave: Updating remote-id in metadata.xml + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> framewave-1.3.1.ebuild: Bump to EAPI=5; Cleanup diff --git a/sci-libs/framewave/metadata.xml b/sci-libs/framewave/metadata.xml index 14ebbb547..cef6a6f41 100644 --- a/sci-libs/framewave/metadata.xml +++ b/sci-libs/framewave/metadata.xml @@ -7,4 +7,7 @@ routines designed to accelerate application development, debugging, multi-threading and optimization on x86-class processor platforms. </longdescription> + <upstream> + <remote-id type="sourceforge">framewave</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/geom/ChangeLog b/sci-libs/geom/ChangeLog index d488d7f8e..8e017978d 100644 --- a/sci-libs/geom/ChangeLog +++ b/sci-libs/geom/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/geom: Updating remote-id in metadata.xml + 23 May 2015; Marius Brehler <marbre@linux.sungazer.de> geom-5.1.2.7.ebuild: Bump to EAPI=5 diff --git a/sci-libs/geom/metadata.xml b/sci-libs/geom/metadata.xml index 2974a0288..f97ec5f49 100644 --- a/sci-libs/geom/metadata.xml +++ b/sci-libs/geom/metadata.xml @@ -1,7 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> + <herd>sci</herd> <use> </use> + <upstream> + <remote-id type="sourceforge">salomegeometry</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/gotoblas2/ChangeLog b/sci-libs/gotoblas2/ChangeLog index 77c5817c8..77caeaac5 100644 --- a/sci-libs/gotoblas2/ChangeLog +++ b/sci-libs/gotoblas2/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-libs/gotoblas2 -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Jun 2015; Justin Lecher <jlec@gentoo.org> gotoblas2-1.13.ebuild, + metadata.xml: + sci-libs/gotoblas2: Bump EAPI + 15 Mar 2012; François Bissey <francois.bissey@canterbury.ac.nz> gotoblas2-1.13.ebuild, files/gotoblas2-1.13-sharedlibs.patch: More OS X fixes @@ -40,4 +44,3 @@ +gotoblas2-1.13.ebuild, +files/gotoblas2-1.13-dynamic.patch, +files/gotoblas2-1.13-sharedlibs.patch, +metadata.xml: Initial import - diff --git a/sci-libs/gotoblas2/gotoblas2-1.13.ebuild b/sci-libs/gotoblas2/gotoblas2-1.13.ebuild index 49022f82f..b96298bd7 100644 --- a/sci-libs/gotoblas2/gotoblas2-1.13.ebuild +++ b/sci-libs/gotoblas2/gotoblas2-1.13.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit eutils toolchain-funcs alternatives-2 multilib diff --git a/sci-libs/gotoblas2/metadata.xml b/sci-libs/gotoblas2/metadata.xml index 7ec44c058..300266bab 100644 --- a/sci-libs/gotoblas2/metadata.xml +++ b/sci-libs/gotoblas2/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> The GotoBLAS codes are one of the fastest implementations of the Basic Linear Algebra Subroutines(BLAS). To achieve performance it starts by observing that for current @@ -11,9 +11,9 @@ is also taken into consideration, it is the minimization of such TLB misses that drives the approach. </longdescription> -<use> - <flag name='int64'>Build the 64 bits integer library</flag> - <flag name='incblas'>Build the CBLAS interface</flag> - <flag name='dynamic'>Build dynamic architecture detection at run time (for multi targets)</flag> -</use> + <use> + <flag name="int64">Build the 64 bits integer library</flag> + <flag name="incblas">Build the CBLAS interface</flag> + <flag name="dynamic">Build dynamic architecture detection at run time (for multi targets)</flag> + </use> </pkgmetadata> diff --git a/sci-libs/gsl/ChangeLog b/sci-libs/gsl/ChangeLog index 0ffe3bda8..936c4dff6 100644 --- a/sci-libs/gsl/ChangeLog +++ b/sci-libs/gsl/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-libs/gsl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-libs/gsl/ChangeLog,v 1.77 2010/08/09 09:32:55 xarthisius Exp $ + 16 Jun 2015; Justin Lecher <jlec@gentoo.org> -gsl-1.16-r1.ebuild, + gsl-1.16-r2.ebuild, metadata.xml: + sci-libs/gsl: Fix problems during installation with multilib and alternatives, + https://github.com/gentoo-science/sci/issues/438 + *gsl-1.16-r2 (10 Nov 2014) 10 Nov 2014; Christoph Junghans <ottxor@gentoo.org> +gsl-1.16-r2.ebuild: diff --git a/sci-libs/gsl/gsl-1.16-r1.ebuild b/sci-libs/gsl/gsl-1.16-r1.ebuild deleted file mode 100644 index f19bba153..000000000 --- a/sci-libs/gsl/gsl-1.16-r1.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -AUTOTOOLS_AUTORECONF=1 - -inherit alternatives-2 autotools-utils eutils toolchain-funcs - -DESCRIPTION="GNU Scientific Library" -HOMEPAGE="http://www.gnu.org/software/gsl/" -SRC_URI="mirror://gnu/${PN}/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~x86-interix ~amd64-linux ~x86-linux ~x86-macos ~x64-macos ~sparc-solaris ~x86-solaris" -IUSE="cblas-external static-libs" - -RDEPEND="cblas-external? ( virtual/cblas )" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}"/${P}-cblas-external.patch ) - -src_configure() { - if use cblas-external; then - export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)" - export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)" - fi - local myeconfargs=( - $(use_with cblas-external) - ) - autotools-utils_src_configure -} - -src_install() { - autotools-utils_src_install - local libname=gslcblas - - cat <<-EOF > ${libname}.pc - prefix=${EPREFIX}/usr - libdir=\${prefix}/$(get_libdir) - includedir=\${prefix}/include - Name: ${libname} - Description: ${DESCRIPTION} CBLAS implementation - Version: ${PV} - URL: ${HOMEPAGE} - Libs: -L\${libdir} -l${libname} - Libs.private: -lm - Cflags: -I\${includedir} - EOF - insinto /usr/$(get_libdir)/pkgconfig - doins ${libname}.pc - - # Don't add gsl as a cblas alternative if using cblas-external - use cblas-external || alternatives_for cblas gsl 0 \ - /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc \ - /usr/include/cblas.h gsl/gsl_cblas.h -} diff --git a/sci-libs/gsl/gsl-1.16-r2.ebuild b/sci-libs/gsl/gsl-1.16-r2.ebuild index 7cf440230..fada1472a 100644 --- a/sci-libs/gsl/gsl-1.16-r2.ebuild +++ b/sci-libs/gsl/gsl-1.16-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -53,8 +53,12 @@ multilib_src_install() { insinto /usr/$(get_libdir)/pkgconfig doins ${libname}.pc + GSL_ALTERNATIVES+=( /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc ) +} + +multilib_src_install_all() { # Don't add gsl as a cblas alternative if using cblas-external use cblas-external || alternatives_for cblas gsl 0 \ - /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc \ + ${GSL_ALTERNATIVES[@]} \ /usr/include/cblas.h gsl/gsl_cblas.h } diff --git a/sci-libs/gsl/metadata.xml b/sci-libs/gsl/metadata.xml index 9be87cabc..2d7f4e76e 100644 --- a/sci-libs/gsl/metadata.xml +++ b/sci-libs/gsl/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing @@ -15,8 +15,8 @@ differential equations, quadrature, Monte Carlo integration, special functions, physical constants, and much more. </longdescription> -<use> - <flag name="cblas-external">Link gsl with external cblas provided by + <use> + <flag name="cblas-external">Link gsl with external cblas provided by (<pkg>virtual/cblas</pkg>) instead of shipped internal version</flag> -</use> + </use> </pkgmetadata> diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog index f623cac73..e20aac9e9 100644 --- a/sci-libs/itk/ChangeLog +++ b/sci-libs/itk/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/itk: Updating remote-id in metadata.xml + 01 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> itk-4.4.2.ebuild, itk-4.4.2-r1.ebuild, itk-4.5.1.ebuild: Convert sse2 to cpu_flags_x86_sse2 diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml index 7789e7619..ca42e5f1f 100644 --- a/sci-libs/itk/metadata.xml +++ b/sci-libs/itk/metadata.xml @@ -15,4 +15,7 @@ <flag name="review">Enable compilation of methods under review</flag> <flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag> </use> + <upstream> + <remote-id type="sourceforge">itk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/jhdf5/ChangeLog b/sci-libs/jhdf5/ChangeLog new file mode 100644 index 000000000..48f71af49 --- /dev/null +++ b/sci-libs/jhdf5/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-libs/jhdf5 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*jhdf5-14.12.1 (10 Jun 2015) + + 10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +jhdf5-14.12.1.ebuild, +metadata.xml: + a skeleton for a java package diff --git a/sci-libs/jhdf5/Manifest b/sci-libs/jhdf5/Manifest new file mode 100644 index 000000000..f3fa49b3f --- /dev/null +++ b/sci-libs/jhdf5/Manifest @@ -0,0 +1 @@ +DIST sis-jhdf5-14.12.1-r33502.zip 30916751 SHA256 6ec8979ca84f13201b0fad8fe5b678827e7c79511f4eb08a06d9ac447a656bb9 SHA512 bc6104a829f50639cf913b3497c6ca815aff70782de0c509d9091087d7bcbd01649d5955e2df91d23ed4e058cdf90f7acfa40f1170059ca4039ba376ca11f800 WHIRLPOOL 83cb95d95f33fb73617bdc7cc604f6ab55bef51e2103f414e4a8b8cabb02b6c6628cf6dd84f73742203007e948a050fc59934cbcb88df433bb204e9cf203c2c8 diff --git a/sci-libs/jhdf5/jhdf5-14.12.1.ebuild b/sci-libs/jhdf5/jhdf5-14.12.1.ebuild new file mode 100644 index 000000000..da6b58456 --- /dev/null +++ b/sci-libs/jhdf5/jhdf5-14.12.1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java binding for HDF5 compatible with HDF5 1.6/1.8" +HOMEPAGE="https://wiki-bsse.ethz.ch/display/JHDF5 + https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113" +SRC_URI="https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip" +# first SIS release: https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.0-r33145.zip +# last CISD release: https://wiki-bsse.ethz.ch/download/attachments/26609237/cisd-jhdf5-13.06.2-r29633.zip + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="" +IUSE="" + +# versions <=12.02 required >=java-1.5 +DEPEND=">=virtual/jdk-1.6:*" +RDEPEND="${DEPEND} + >=virtual/jre-1.6:*" + +S="${WORKDIR}"/sis-jhdf5 diff --git a/sci-libs/jhdf5/metadata.xml b/sci-libs/jhdf5/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-libs/jhdf5/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/lapackpp/ChangeLog b/sci-libs/lapackpp/ChangeLog index 53d273f9c..f467421ce 100644 --- a/sci-libs/lapackpp/ChangeLog +++ b/sci-libs/lapackpp/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/lapackpp -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/lapackpp: Updating remote-id in metadata.xml + 12 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> lapackpp-2.5.4.ebuild: sci-libs/lapackpp: Use latest pkg-config diff --git a/sci-libs/lapackpp/metadata.xml b/sci-libs/lapackpp/metadata.xml index 717c30874..5789093f2 100644 --- a/sci-libs/lapackpp/metadata.xml +++ b/sci-libs/lapackpp/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> LAPACK++ (Linear Algebra PACKage in C++) is a software library for numerical linear algebra that solves systems of linear equations and eigenvalue problems on high performance computer architectures. @@ -14,4 +14,7 @@ matrices, symmetric positive definite systems, and solving linear least-square systems. </longdescription> + <upstream> + <remote-id type="sourceforge">lapackpp</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/libmaus/ChangeLog b/sci-libs/libmaus/ChangeLog new file mode 100644 index 000000000..57677bce1 --- /dev/null +++ b/sci-libs/libmaus/ChangeLog @@ -0,0 +1,6 @@ +# ChangeLog for sci-libs/libmaus +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/libmaus: Add github to remote-id in metadata.xml diff --git a/sci-libs/libmaus/metadata.xml b/sci-libs/libmaus/metadata.xml index 72461eb47..c0feca39e 100644 --- a/sci-libs/libmaus/metadata.xml +++ b/sci-libs/libmaus/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-biology</herd> -<longdescription lang="en"> + <herd>sci-biology</herd> + <longdescription lang="en"> libmaus is a collection of data structures and algorithms. It contains I/O classes (single byte and UTF-8) @@ -11,4 +11,7 @@ I/O classes (single byte and UTF-8) BAM sequence alignment files input/output (simple and collating) and many lower level support classes. </longdescription> + <upstream> + <remote-id type="github">gt1/libmaus</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/libsc/ChangeLog b/sci-libs/libsc/ChangeLog index db89785ac..6925e4156 100644 --- a/sci-libs/libsc/ChangeLog +++ b/sci-libs/libsc/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/libsc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> libsc-1.0.ebuild: + sci-libs/libsc: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/libsc: Add github to remote-id in metadata.xml + *libsc-1.1 (13 Oct 2014) 13 Oct 2014; Matthias Maier <tamiko@gentoo.org> +libsc-1.1.ebuild, diff --git a/sci-libs/libsc/libsc-1.0.ebuild b/sci-libs/libsc/libsc-1.0.ebuild index c0cb21288..64b597f49 100644 --- a/sci-libs/libsc/libsc-1.0.ebuild +++ b/sci-libs/libsc/libsc-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,19 +8,19 @@ WANT_AUTOMAKE=1.11 inherit autotools-utils toolchain-funcs eutils multilib -DESCRIPTION="The SC Library provides support for parallel scientific applications." +DESCRIPTION="Support for parallel scientific applications" HOMEPAGE="http://www.p4est.org/" SRC_URI="https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz -> ${P}.tar.gz" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" LICENSE="LGPL-2.1+" SLOT="0" - +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="debug examples mpi romio static-libs" + REQUIRED_USE="romio? ( mpi )" RDEPEND=" - dev-lang/lua + dev-lang/lua:* sys-apps/util-linux virtual/blas virtual/lapack @@ -55,8 +55,7 @@ src_configure() { src_install() { autotools-utils_src_install - if use examples - then + if use examples; then docinto examples dodoc -r example/* docompress -x /usr/share/doc/${PF}/examples diff --git a/sci-libs/libsc/metadata.xml b/sci-libs/libsc/metadata.xml index 6d4eba7c1..b145b03cb 100644 --- a/sci-libs/libsc/metadata.xml +++ b/sci-libs/libsc/metadata.xml @@ -13,4 +13,7 @@ This support library is primarily used by the p4est library. <use> <flag name="romio">Build with support for the ROMIO MPI-IO component</flag> </use> + <upstream> + <remote-id type="github">cburstedde/libsc</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/libsufr/ChangeLog b/sci-libs/libsufr/ChangeLog index 5e752b2ca..d45f80c94 100644 --- a/sci-libs/libsufr/ChangeLog +++ b/sci-libs/libsufr/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/libsufr: Updating remote-id in metadata.xml + *libsufr-0.6.4 (09 May 2015) 09 May 2015; AstroFloyd <AstroFloyd@gmail.com> -libsufr-0.6.2.ebuild, @@ -53,4 +56,3 @@ +files/libsufr-0.3.0-multilib.patch, +metadata.xml: Initial import, ebuild written by AstroFloyd <AstroFloyd@gmail.com>, edited by me - diff --git a/sci-libs/libsufr/metadata.xml b/sci-libs/libsufr/metadata.xml index ec7105731..009574ec1 100644 --- a/sci-libs/libsufr/metadata.xml +++ b/sci-libs/libsufr/metadata.xml @@ -1,13 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>AstroFloyd@gmail.com</email> - <name>AstroFloyd</name> - </maintainer> - <maintainer> - <email>xarthisius@gentoo.org</email> - <name>Kacper Kowalik</name> - </maintainer> + <herd>sci</herd> + <maintainer> + <email>AstroFloyd@gmail.com</email> + <name>AstroFloyd</name> + </maintainer> + <maintainer> + <email>xarthisius@gentoo.org</email> + <name>Kacper Kowalik</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">libsufr</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/lwpr/ChangeLog b/sci-libs/lwpr/ChangeLog index bc8987cf1..48ee04760 100644 --- a/sci-libs/lwpr/ChangeLog +++ b/sci-libs/lwpr/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/lwpr -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/lwpr: Updating remote-id in metadata.xml + *lwpr-1.2.5 (25 Jun 2013) 25 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +lwpr-1.2.5.ebuild, diff --git a/sci-libs/lwpr/metadata.xml b/sci-libs/lwpr/metadata.xml index b9d1fd6a7..a8ec3ab22 100644 --- a/sci-libs/lwpr/metadata.xml +++ b/sci-libs/lwpr/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> -<longdescription> + <herd>sci-mathematics</herd> + <longdescription> Locally Weighted Projection Regression (LWPR) is a recent algorithm that achieves nonlinear function approximation in high dimensional spaces with redundant and irrelevant input dimensions. At its core, it uses @@ -11,7 +11,10 @@ weighted variant of Partial Least Squares (PLS) is employed for doing the dimensionality reduction. </longdescription> -<use> - <flag name='octave'>Add <pkg>sci-mathematics/octave</pkg> support</flag> -</use> + <use> + <flag name="octave">Add <pkg>sci-mathematics/octave</pkg> support</flag> + </use> + <upstream> + <remote-id type="sourceforge">lwpr</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/matc/ChangeLog b/sci-libs/matc/ChangeLog index 37a972540..ea7705062 100644 --- a/sci-libs/matc/ChangeLog +++ b/sci-libs/matc/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-libs/matc -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*matc-8.0 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> +matc-8.0.ebuild: + Version bump + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> matc-9999.ebuild: + Source moved from sf.net to github; Fix LICENSE + 03 Dec 2013; Justin Lecher <jlec@gentoo.org> -matc-5.4.1.ebuild, +matc-6.0_p4651.ebuild, matc-9999.ebuild, -files/matc-5.4.1-shared.patch, +files/matc-6.0_p4651-shared.patch: @@ -14,4 +22,3 @@ +metadata.xml: Bump EAPI; fix license; fix DESCRIPTION; drop keywords from live ebuild; use correct phase functions; simplify configure; build shared libraries - diff --git a/sci-libs/matc/Manifest b/sci-libs/matc/Manifest index f4abaedf9..90b95448c 100644 --- a/sci-libs/matc/Manifest +++ b/sci-libs/matc/Manifest @@ -1,2 +1,3 @@ -DIST MATCManual.pdf 82222 SHA256 a32d6201021d988242e7ab193c865c1aef3e51b7c7a509978edd9360dcef7c52 SHA512 7703f05a9d23b683e9a7030fbbad0b5438de5dbfb22479a2c070e02830ef233697ea2d1f67efbdd958ada537388f1b3449dd2e73a2bd86c66338636cef0c4ea1 WHIRLPOOL 72aca6508a12cc4370e996caf60b61740ecd4aa7eab460d601cfcf5d6a0ee11a3556ef7637c85a6a747cc3d6529c5ac514f95510813720dd093054af48346893 -DIST matc-6.0_p4651.tar.gz 203543 SHA256 e49d5599231ee68f4b0e46a75d4cb2c476eab5608b881b7741aed9b125f92f8d SHA512 1675c880929031caaceb67091903ae306db30810847886fb1f56cb4c0f5e05ee4a9a11eaed8f29d3fbca4bf222268fe62ffddabc62a3b08322c362dd9ce566e0 WHIRLPOOL 73de50b2ee9cd9183b503eedc51a3cfa06eeb9e99fa3929ee610a5fc0be9a3ebb9c963553986f00e9ef9ce1f4d3ce5a17c6be9205d0eff080c4ab7240cfc0816 +DIST MATCManual.pdf 103341 SHA256 a49945c6965cdb28dfaa98f36d46813a56c7f792c4b5634d02e6afc0ae361e9c SHA512 0f9efea84ed2f6848c431b0a9647c8d300b3bcf06a83c4f6bc7cd3640ec5fc003516b442f90b022a246b3cac54f2cdac1118283e929d2c9547f5469f2b9912cb WHIRLPOOL 27eedcf4b62cedacaaa8821d87e2d2ee8a0623cf7e48f99c3310e292d0ee5a3f412546e8cbfcce34a274cf318be2b86c96af6053ff2add24c7c8569a75f670fd +DIST matc-6.0_p4651.tar.gz 203543 SHA256 b174036ebafa2d0bff51db283831e4f9a165e6fa9798224dc3658dc2dc5e99b1 SHA512 ada3e4a1d02a0125ee5ccb7a791975d3f728d89ff21fac6461060e4458b086edb34adef058f3aa84f924f28b7d652a539d63f61d9bfce208d0b8540b812ef7be WHIRLPOOL b47b025bff1fbb88ccbabb0c42a8656c905f09ce4345c12cd83e8effb6b9c12f5cfece69741c2655fc3c60dd4e652a9867c14989d9043ae23b338815f800927a +DIST matc-8.0.tar.gz 45051199 SHA256 ac7cb29e1dba205113ed9705a5852ee11117252495fa2b125adecd2b057c8a8f SHA512 bc34c6dbbdb2c24f2110d377e02c4515cb4886de36b30bc3caf79c9b954e5b7ba81cabedaa35fad1802287c396ab88ef074505efc904411061f7c98c9bea3497 WHIRLPOOL 99004464347f58fd388e52eb7457f2739efc3ba19fd69c328c49c2998a6131c46682417c176a39239fdb92574a4df5244b8d657e584d644fdb7c550279b8e631 diff --git a/sci-libs/matc/matc-8.0.ebuild b/sci-libs/matc/matc-8.0.ebuild new file mode 100644 index 000000000..565962490 --- /dev/null +++ b/sci-libs/matc/matc-8.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Finite element programs, libraries, and visualization tools - math C library" +HOMEPAGE="http://www.csc.fi/english/pages/elmer" +SRC_URI=" + https://github.com/ElmerCSC/elmerfem/archive/release-${PV}.tar.gz -> ${P}.tar.gz + doc? ( http://www.nic.funet.fi/pub/sci/physics/elmer/doc/MATCManual.pdf )" + +LICENSE="GPL-2 LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc debug static-libs" + +RDEPEND=" + sys-libs/ncurses + sys-libs/readline:0" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/elmerfem-release-${PV}/${PN}" + +#PATCHES=( "${FILESDIR}"/${P}-shared.patch ) + +src_configure() { + local myeconfargs=( + --enable-shared + $(use_with debug) + ) + autotools-utils_src_configure +} + +src_install() { + use doc && DOCS=( "${DISTDIR}"/MATCManual.pdf ) + autotools-utils_src_install +} diff --git a/sci-libs/matc/matc-9999.ebuild b/sci-libs/matc/matc-9999.ebuild index b787716a9..2b8aa00c6 100644 --- a/sci-libs/matc/matc-9999.ebuild +++ b/sci-libs/matc/matc-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,7 +6,7 @@ EAPI=5 AUTOTOOLS_AUTORECONF=true -inherit autotools-utils subversion +inherit autotools-utils git-r3 ELMER_ROOT="elmerfem" MY_PN=${PN/elmer-/} @@ -14,27 +14,21 @@ MY_PN=${PN/elmer-/} DESCRIPTION="Finite element programs, libraries, and visualization tools - math C library" HOMEPAGE="http://www.csc.fi/english/pages/elmer" SRC_URI="doc? ( http://www.nic.funet.fi/pub/sci/physics/elmer/doc/MATCManual.pdf )" -ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}" -ESVN_PROJECT="${MY_PN}" +EGIT_REPO_URI="https://github.com/ElmerCSC/elmerfem.git git://github.com/ElmerCSC/elmerfem.git" -LICENSE="GPL-2" +LICENSE="GPL-2 LGPL-2.1" SLOT="0" KEYWORDS="" IUSE="doc debug static-libs" RDEPEND=" sys-libs/ncurses - sys-libs/readline" + sys-libs/readline:0" DEPEND="${RDEPEND}" -S="${WORKDIR}"/${PN} +S="${WORKDIR}/${P}/${PN}" -PATCHES=( "${FILESDIR}"/${PN}-6.0_p4651-shared.patch ) - -src_prepare() { - subversion_src_prepare - autotools-utils_src_prepare -} +#PATCHES=( "${FILESDIR}"/${PN}-6.0_p4651-shared.patch ) src_configure() { local myeconfargs=( diff --git a/sci-libs/nibabel/ChangeLog b/sci-libs/nibabel/ChangeLog index c31cec79e..237f97ecf 100644 --- a/sci-libs/nibabel/ChangeLog +++ b/sci-libs/nibabel/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for sci-libs/nibabel -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 11 Jun 2015; Chymera <chymera@gentoo.org> nibabel-1.3.0.ebuild: + now downloading as tarball + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> nibabel-1.3.0.ebuild, nibabel-9999.ebuild, metadata.xml: Switch from git-2 to git-r3 - diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest index e3f8516ac..0c4e51b19 100644 --- a/sci-libs/nibabel/Manifest +++ b/sci-libs/nibabel/Manifest @@ -1 +1 @@ -DIST 1.3.0.zip 2266889 SHA256 70f7bb33f7c49c94cd264001a89c2df8c455f21d8530e5fb0780e432259edc40 SHA512 31c524385ef68cd6a4693d739d8bcda6c73e48a66417d59fe3825bfacf512117346f610d3aeef1adc62bb95564f52e6a29a64f72de57c86e8e6205fff2c24522 WHIRLPOOL 65ec60d7726eb323522d2efbad4b12747a084fb6b8dd720338a42bc47c7a814217b9ed6fd0c09dfb5fb02188bf2827cd9287f4dea24db920c53c42173513127f +DIST nibabel-1.3.0.tar.gz 2184060 SHA256 21488202a655eae76bb0c1170271c894bbf08bfae8246e79c71706233d4964b1 SHA512 6970a1345ce9c4ead484a15696bdcd918a292c354d0d5799359f1260a26e0b49a32507511ad5a9446a50c1d374113863e4d717c9b7bd16feecbe49d4f3da6119 WHIRLPOOL d117160713d9e2557cc957ffecc29a339f6ef14c0e60d962768cd4c8b2bbd4ef6a498b3f96f084256a4638a8264b6c8cd0189979329168d2d47c1ea119581541 diff --git a/sci-libs/nibabel/nibabel-1.3.0.ebuild b/sci-libs/nibabel/nibabel-1.3.0.ebuild index c3d5d279e..886434fba 100644 --- a/sci-libs/nibabel/nibabel-1.3.0.ebuild +++ b/sci-libs/nibabel/nibabel-1.3.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -10,7 +10,7 @@ inherit distutils-r1 DESCRIPTION="Access a cacophony of neuro-imaging file formats" HOMEPAGE="http://nipy.org/nibabel/" -SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.zip" +SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" KEYWORDS="~amd64 ~x86" diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml index 05f4d5beb..2468f9eb6 100644 --- a/sci-libs/nipy/metadata.xml +++ b/sci-libs/nipy/metadata.xml @@ -9,4 +9,7 @@ <longdescription lang="en"> NIPY is a python project for analysis of structural and functional neuroimaging data. </longdescription> + <upstream> + <remote-id type="pypi">nipy</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/nipype/ChangeLog b/sci-libs/nipype/ChangeLog index e4f160f49..09e140793 100644 --- a/sci-libs/nipype/ChangeLog +++ b/sci-libs/nipype/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for sci-libs/nipype -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Horea Christian <h.chr@mail.ru> nipype-9999.ebuild: + no longer depending on outdated version + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> nipype-9999.ebuild, metadata.xml: Switch from git-2 to git-r3 - diff --git a/sci-libs/nipype/nipype-9999.ebuild b/sci-libs/nipype/nipype-9999.ebuild index 0b833f8f2..018340f60 100644 --- a/sci-libs/nipype/nipype-9999.ebuild +++ b/sci-libs/nipype/nipype-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -23,7 +23,7 @@ IUSE="" DEPEND=" dev-python/setuptools[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] - >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]" + sci-libs/nibabel[${PYTHON_USEDEP}]" RDEPEND=" sci-libs/scipy[${PYTHON_USEDEP}] dev-python/traits[${PYTHON_USEDEP}] diff --git a/sci-libs/o2scl/ChangeLog b/sci-libs/o2scl/ChangeLog index 37af49301..e0817cd7a 100644 --- a/sci-libs/o2scl/ChangeLog +++ b/sci-libs/o2scl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/o2scl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/o2scl: Updating remote-id in metadata.xml + *o2scl-0.915 (02 Jun 2014) 02 Jun 2014; Sébastien Fabbro <bicatali@gentoo.org> +o2scl-0.915.ebuild, diff --git a/sci-libs/o2scl/metadata.xml b/sci-libs/o2scl/metadata.xml index 6f32b1540..dd14258df 100644 --- a/sci-libs/o2scl/metadata.xml +++ b/sci-libs/o2scl/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> O2scl is a C++ class library for object-oriented numerical programming. It includes classes based on numerical routines from GSL and CERNLIB and two sub-libraries: thermodynamics of ideal and nearly-ideal particles with quantum statistics and e quations of state for finite density relevant for neutron stars. </longdescription> + <upstream> + <remote-id type="sourceforge">o2scl</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/openblas/ChangeLog b/sci-libs/openblas/ChangeLog index 0912ff190..e783b9d38 100644 --- a/sci-libs/openblas/ChangeLog +++ b/sci-libs/openblas/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> openblas-0.2.11.ebuild, + openblas-0.2.8.ebuild, openblas-9999.ebuild: + sci-libs/openblas: Add missing eclass + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/openblas: Add github to remote-id in metadata.xml + 02 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> openblas-9999.ebuild: Fix Bug 528974 diff --git a/sci-libs/openblas/metadata.xml b/sci-libs/openblas/metadata.xml index 32441d18a..6ef9b5417 100644 --- a/sci-libs/openblas/metadata.xml +++ b/sci-libs/openblas/metadata.xml @@ -10,4 +10,7 @@ <flag name="int64">Build the 64 bits integer library</flag> <flag name="dynamic">Build dynamic architecture detection at run time (for multi targets)</flag> </use> + <upstream> + <remote-id type="github">xianyi/OpenBLAS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/openblas/openblas-0.2.11.ebuild b/sci-libs/openblas/openblas-0.2.11.ebuild index 2b5f76db2..c69932e42 100644 --- a/sci-libs/openblas/openblas-0.2.11.ebuild +++ b/sci-libs/openblas/openblas-0.2.11.ebuild @@ -5,7 +5,7 @@ EAPI=5 EBASE_PROFNAME="openblas" -inherit alternatives-2 eutils fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 +inherit alternatives-2 eutils multilib fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 SRC_URI+="http://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch" if [[ ${PV} == "9999" ]] ; then diff --git a/sci-libs/openblas/openblas-0.2.8.ebuild b/sci-libs/openblas/openblas-0.2.8.ebuild index 96ca05b80..565215bb9 100644 --- a/sci-libs/openblas/openblas-0.2.8.ebuild +++ b/sci-libs/openblas/openblas-0.2.8.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -inherit eutils toolchain-funcs alternatives-2 multilib fortran-2 +inherit eutils multilib toolchain-funcs alternatives-2 multilib fortran-2 DESCRIPTION="Optimized BLAS library based on GotoBLAS2" HOMEPAGE="http://xianyi.github.com/OpenBLAS/" diff --git a/sci-libs/openblas/openblas-9999.ebuild b/sci-libs/openblas/openblas-9999.ebuild index db150b020..c5166a35f 100644 --- a/sci-libs/openblas/openblas-9999.ebuild +++ b/sci-libs/openblas/openblas-9999.ebuild @@ -5,7 +5,7 @@ EAPI=5 EBASE_PROFNAME="openblas" -inherit alternatives-2 eutils fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 +inherit alternatives-2 eutils multilib fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 SRC_URI+="http://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch" if [[ ${PV} == "9999" ]] ; then diff --git a/sci-libs/p4est/ChangeLog b/sci-libs/p4est/ChangeLog index 61500661e..42e91d06a 100644 --- a/sci-libs/p4est/ChangeLog +++ b/sci-libs/p4est/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/p4est -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> p4est-1.0.ebuild: + sci-libs/p4est: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/p4est: Add github to remote-id in metadata.xml + 13 Oct 2014; Matthias Maier <tamiko@gentoo.org> p4est-1.0.ebuild: sci-libs/p4est: Fix build dependencies diff --git a/sci-libs/p4est/metadata.xml b/sci-libs/p4est/metadata.xml index c8a9acb72..85fc0a1a7 100644 --- a/sci-libs/p4est/metadata.xml +++ b/sci-libs/p4est/metadata.xml @@ -16,4 +16,7 @@ processor cores. <flag name="vtk-binary">Enable binary vtk output. If disabled vtk files will be written in ASCII text format.</flag> <flag name="romio">Build with support for the ROMIO MPI-IO component</flag> </use> + <upstream> + <remote-id type="github">cburstedde/libsc</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/p4est/p4est-1.0.ebuild b/sci-libs/p4est/p4est-1.0.ebuild index 4c6946d94..e753ed7e1 100644 --- a/sci-libs/p4est/p4est-1.0.ebuild +++ b/sci-libs/p4est/p4est-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -24,7 +24,7 @@ REQUIRED_USE="romio? ( mpi )" RDEPEND=" >=sci-libs/libsc-1.0[mpi,romio] - dev-lang/lua + dev-lang/lua:* sys-apps/util-linux virtual/blas virtual/lapack diff --git a/sci-libs/pg2plplot/ChangeLog b/sci-libs/pg2plplot/ChangeLog index 45e2bb9f5..64756b86b 100644 --- a/sci-libs/pg2plplot/ChangeLog +++ b/sci-libs/pg2plplot/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/pg2plplot -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/pg2plplot: Updating remote-id in metadata.xml + *pg2plplot-0.3.1 (28 Apr 2014) 28 Apr 2014; Sébastien Fabbro <bicatali@gentoo.org> +pg2plplot-0.3.1.ebuild, diff --git a/sci-libs/pg2plplot/metadata.xml b/sci-libs/pg2plplot/metadata.xml index d843d11b1..e39c33fca 100644 --- a/sci-libs/pg2plplot/metadata.xml +++ b/sci-libs/pg2plplot/metadata.xml @@ -1,13 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>AstroFloyd@gmail.com</email> - <name>AstroFloyd</name> -</maintainer> -<longdescription> + <herd>sci</herd> + <maintainer> + <email>AstroFloyd@gmail.com</email> + <name>AstroFloyd</name> + </maintainer> + <longdescription> PG2PLplot is code intended to help the transition from Fortran code linked against PGPlot to linking it against PLplot. </longdescription> + <upstream> + <remote-id type="sourceforge">pg2plplot</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/pydicom/ChangeLog b/sci-libs/pydicom/ChangeLog index dd3589ee2..9f5b12ac9 100644 --- a/sci-libs/pydicom/ChangeLog +++ b/sci-libs/pydicom/ChangeLog @@ -1,8 +1,34 @@ # ChangeLog for sci-libs/pydicom -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 May 2015; Horea Christian <h.chr@mail.ru> pydicom-0.9.8.ebuild, + pydicom-9999.ebuild: + updated homepage + + 06 Apr 2015; Horea Christian <h.chr@mail.ru> pydicom-9999.ebuild: + no keywords in live ebuilds + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> pydicom-0.9.8.ebuild, + pydicom-9999.ebuild: + gentoo does not support python 2.6 and 3.2 + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> pydicom-9999.ebuild: + new live ebuild supporting various python versions + +*pydicom-9999 (31 Mar 2015) + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> +pydicom-9999.ebuild: + new live ebuild + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> pydicom-0.9.8.ebuild: + removed python 3 support (only inofficial: + https://dcmstack.readthedocs.org/en/latest/Introduction.html#dependencies ) + added python 2.6 support + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> pydicom-0.9.8.ebuild: + added python 3.3 compatibility + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> pydicom-0.9.8.ebuild, +metadata.xml: Add missing metadata.xml - diff --git a/sci-libs/pydicom/pydicom-0.9.8.ebuild b/sci-libs/pydicom/pydicom-0.9.8.ebuild index 923ef5a19..ad575a675 100644 --- a/sci-libs/pydicom/pydicom-0.9.8.ebuild +++ b/sci-libs/pydicom/pydicom-0.9.8.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 DESCRIPTION="A pure python package for parsing DICOM files" -HOMEPAGE="https://code.google.com/p/pydicom/" +HOMEPAGE="http://www.pydicom.org/" SRC_URI="https://pydicom.googlecode.com/files/${P}.zip" LICENSE="MIT" diff --git a/sci-libs/pydicom/pydicom-9999.ebuild b/sci-libs/pydicom/pydicom-9999.ebuild new file mode 100644 index 000000000..bc09e8ca9 --- /dev/null +++ b/sci-libs/pydicom/pydicom-9999.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_3 python3_4 ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="A pure python package for parsing DICOM files" +HOMEPAGE="http://www.pydicom.org/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/darcymason/pydicom" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="" + +S="${S}/source" diff --git a/sci-libs/xraylib/ChangeLog b/sci-libs/xraylib/ChangeLog index d29b543b2..38be18a88 100644 --- a/sci-libs/xraylib/ChangeLog +++ b/sci-libs/xraylib/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> xraylib-2.16.0.ebuild, + xraylib-3.1.0.ebuild: + sci-libs/xraylib: Add slot operators + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/xraylib: Add github to remote-id in metadata.xml + *xraylib-3.1.0 (03 Apr 2015) 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> +xraylib-3.1.0.ebuild: diff --git a/sci-libs/xraylib/metadata.xml b/sci-libs/xraylib/metadata.xml index a592314d3..16a3a5861 100644 --- a/sci-libs/xraylib/metadata.xml +++ b/sci-libs/xraylib/metadata.xml @@ -35,4 +35,7 @@ </longdescription> <use> </use> + <upstream> + <remote-id type="github">tschoonj/xraylib</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/xraylib/xraylib-2.16.0.ebuild b/sci-libs/xraylib/xraylib-2.16.0.ebuild index 6917f657c..5d9e764cf 100644 --- a/sci-libs/xraylib/xraylib-2.16.0.ebuild +++ b/sci-libs/xraylib/xraylib-2.16.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -23,13 +23,13 @@ IUSE="examples fortran java lua perl python" REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" RDEPEND=" - java? ( >=virtual/jre-1.4 ) - lua? ( dev-lang/lua ) + java? ( >=virtual/jre-1.4:* ) + lua? ( dev-lang/lua:0 ) perl? ( dev-lang/perl ) python? ( ${PYTHON_DEPS} )" DEPEND="${RDEPEND} - java? ( >=virtual/jdk-1.4 )" + java? ( >=virtual/jdk-1.4:* )" S="${WORKDIR}/${PN}-${P}" diff --git a/sci-libs/xraylib/xraylib-3.1.0.ebuild b/sci-libs/xraylib/xraylib-3.1.0.ebuild index 3f9991e32..5d9e764cf 100644 --- a/sci-libs/xraylib/xraylib-3.1.0.ebuild +++ b/sci-libs/xraylib/xraylib-3.1.0.ebuild @@ -23,13 +23,13 @@ IUSE="examples fortran java lua perl python" REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" RDEPEND=" - java? ( >=virtual/jre-1.4 ) - lua? ( dev-lang/lua ) + java? ( >=virtual/jre-1.4:* ) + lua? ( dev-lang/lua:0 ) perl? ( dev-lang/perl ) python? ( ${PYTHON_DEPS} )" DEPEND="${RDEPEND} - java? ( >=virtual/jdk-1.4 )" + java? ( >=virtual/jdk-1.4:* )" S="${WORKDIR}/${PN}-${P}" diff --git a/sci-libs/zarja/ChangeLog b/sci-libs/zarja/ChangeLog index 173c5ec59..8028e709c 100644 --- a/sci-libs/zarja/ChangeLog +++ b/sci-libs/zarja/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/zarja -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/zarja: Updating remote-id in metadata.xml + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> zarja-1.1.1.ebuild, metadata.xml: Move to EAPI=5; fix slot for fftw dep; move to virtual/pkgconfig; clean @@ -12,4 +15,3 @@ 16 Apr 2009; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml, +zarja-1.1.1.ebuild: Initial import to science overlay - bug #254832 - Thanks Hynek Lavička - diff --git a/sci-libs/zarja/metadata.xml b/sci-libs/zarja/metadata.xml index 65dfd5ca8..a5548374a 100644 --- a/sci-libs/zarja/metadata.xml +++ b/sci-libs/zarja/metadata.xml @@ -7,4 +7,7 @@ simulations on graphs. Its functionality was proved in Classical or Quantum mechanical models. </longdescription> + <upstream> + <remote-id type="sourceforge">zarja</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/acl2/ChangeLog b/sci-mathematics/acl2/ChangeLog index baff65ab7..108ca3f59 100644 --- a/sci-mathematics/acl2/ChangeLog +++ b/sci-mathematics/acl2/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*acl2-7.1 (16 Jun 2015) + + 16 Jun 2015; zcj <ustcscgy@163.com> +acl2-7.1.ebuild, -acl2-7.0.ebuild, + metadata.xml: + sci-mathematics/acl2: sci-mathematics/acl2: Version bump; Upstream url + changes. + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/acl2: Add github to remote-id in metadata.xml + *acl2-7.0 (25 Mar 2015) 25 Mar 2015; zcj <ustcscgy@163.com> +acl2-7.0.ebuild, -acl2-6.3.ebuild, diff --git a/sci-mathematics/acl2/Manifest b/sci-mathematics/acl2/Manifest index abf3d42ae..1444f00a9 100644 --- a/sci-mathematics/acl2/Manifest +++ b/sci-mathematics/acl2/Manifest @@ -1 +1 @@ -DIST acl2-7.0.tar.gz 58301172 SHA256 dbbe63ddbe342072fa0504e05f9e02fb01bb654b6befcc1e34ba7ceab2b1e0eb SHA512 25746df91de3b418d0be8f5b6aa906b5456eb95e46745362f4c8697cd5dc57ad44fa25151ebffa6ad3efc28efd9ecdb830dedc136c79082d3fbc71e9393fa2cc WHIRLPOOL 1b7232d0c7c9c68bd3ee8bfc9d2a6547e533dfac5681313e513f7f72bc4aff6a727f36b1704020c21f2d44a8bf36baac91ac411633ff67cf7a3f46071e671fa8 +DIST acl2-7.1.tar.gz 63345284 SHA256 1a8503095a4e1deb6a6b0f3bc51823ba65cad38466def8d6845f193d73338f9d SHA512 5875b88615930fc841cd1d7ed30ada7c04b241a391eeee22184b4e3630e57cc6304a51e445e33ca1284576c2b4110c269f9eb59c47bd2eb47659134450151e27 WHIRLPOOL 632012e3d8998c67f70cd19b8fa7c7ff8000dbdba2d87dfdd56d5b4b39ebb390503d243e051c308c8a5aea0097bb48fa4e5c510b24478886a4a8bfca2c8d0645 diff --git a/sci-mathematics/acl2/acl2-7.0.ebuild b/sci-mathematics/acl2/acl2-7.1.ebuild index c1bfb9036..8378eafb5 100644 --- a/sci-mathematics/acl2/acl2-7.0.ebuild +++ b/sci-mathematics/acl2/acl2-7.1.ebuild @@ -8,7 +8,8 @@ inherit eutils DESCRIPTION="Industrial strength theorem prover" HOMEPAGE="http://www.cs.utexas.edu/users/moore/acl2/" -SRC_URI="https://github.com/acl2/acl2/archive/${PV}.tar.gz -> ${P}.tar.gz" +MY_PN=${PN}-devel +SRC_URI="https://github.com/${MY_PN}/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" SLOT="0" LICENSE="BSD" @@ -19,6 +20,7 @@ DEPEND=" dev-lisp/sbcl:= books? ( dev-lang/perl )" RDEPEND="${DEPEND}" +S="${WORKDIR}/${MY_PN}-${PV}" src_compile() { emake LISP="sbcl --noinform --noprint \ @@ -28,19 +30,18 @@ src_compile() { echo einfo "Building certificates ..." einfo "(this may take hours to finish)" - emake regression + emake certify-books fi } src_install() { - SAVED_NAME=saved_acl2h + SAVED_NAME=saved_acl2 sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die if use books; then sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \ -i ${SAVED_NAME} || die fi dobin ${SAVED_NAME} - dosym ${SAVED_NAME} /usr/bin/saved_acl2 insinto /usr/share/acl2 doins TAGS ${SAVED_NAME}.core diff --git a/sci-mathematics/acl2/metadata.xml b/sci-mathematics/acl2/metadata.xml index 47ab9cabf..0782df404 100644 --- a/sci-mathematics/acl2/metadata.xml +++ b/sci-mathematics/acl2/metadata.xml @@ -1,21 +1,24 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-mathematics</herd> - <maintainer> - <email>dongxuli2011@gmail.com</email> - <name>Dongxu Li</name> - <description>Industrial strength theorem prover</description> - </maintainer> - <longdescription> + <herd>sci-mathematics</herd> + <maintainer> + <email>dongxuli2011@gmail.com</email> + <name>Dongxu Li</name> + <description>Industrial strength theorem prover</description> + </maintainer> + <longdescription> ACL2 is both a programming language in which you can model computer systems and a tool to help you prove properties of those models. ACL2 is part of the Boyer-Moore family of provers, for which its authors have received the 2005 ACM Software System Award. </longdescription> - <use> - <flag name="books"> + <use> + <flag name="books"> build community books, the canonical collection of open-source libraries </flag> - </use> + </use> + <upstream> + <remote-id type="github">acl2-devel/acl2-devel</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/burrtools/ChangeLog b/sci-mathematics/burrtools/ChangeLog index bec5130ec..25b103241 100644 --- a/sci-mathematics/burrtools/ChangeLog +++ b/sci-mathematics/burrtools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/burrtools -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/burrtools: Updating remote-id in metadata.xml + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> burrtools-0.5.2-r1.ebuild: Corrected Slot of fltk to 1 @@ -16,4 +19,3 @@ 13 Jan 2010; Sébastien Fabbro <bicatali@gentoo.org> +burrtools-0.5.2.ebuild, +metadata.xml: Initial import. Ebuild initially submitted by Andreas Röver, bug #171816 - diff --git a/sci-mathematics/burrtools/metadata.xml b/sci-mathematics/burrtools/metadata.xml index cd544f35c..aff4a5140 100644 --- a/sci-mathematics/burrtools/metadata.xml +++ b/sci-mathematics/burrtools/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> -<longdescription lang='en'> + <herd>sci-mathematics</herd> + <longdescription lang="en"> This (set of) program(s) will help you solve a certain kind of puzzle. Namely puzzles that are made out of square or dice shaped units, spheres or prisms with an equilateral triangle as base and where the pieces are also aligned along those grids in the solutions. </longdescription> + <upstream> + <remote-id type="sourceforge">burrtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/cipi/ChangeLog b/sci-mathematics/cipi/ChangeLog index 523a1f16f..5e2475db6 100644 --- a/sci-mathematics/cipi/ChangeLog +++ b/sci-mathematics/cipi/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/cipi -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/cipi: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> cipi-1.0.ebuild, metadata.xml: Use tarball instead of git pull @@ -15,4 +18,3 @@ 20 Jul 2010; Thomas Kahle <tom111@gmx.de> +cipi-1.0.ebuild, +metadata.xml: initial upload for bug 329169 - diff --git a/sci-mathematics/cipi/metadata.xml b/sci-mathematics/cipi/metadata.xml index ff77aadc4..bc37ee723 100644 --- a/sci-mathematics/cipi/metadata.xml +++ b/sci-mathematics/cipi/metadata.xml @@ -10,4 +10,7 @@ cipi is a threaded implementation of iterative proportional fitting. It is used to compute information projections iteratively. </longdescription> + <upstream> + <remote-id type="github">tom111/cipi</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/dolfin/ChangeLog b/sci-mathematics/dolfin/ChangeLog index 980a24abe..f5a0b74b1 100644 --- a/sci-mathematics/dolfin/ChangeLog +++ b/sci-mathematics/dolfin/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/dolfin -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/dolfin: Updating remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> dolfin-0.9.9.ebuild, metadata.xml: Bump EAPI to 5; Bump to python-single-r1 eclass @@ -19,4 +22,3 @@ +dolfin-0.9.9.ebuild, +files/dolfin-0.9.9-find-armadillo.patch, +metadata.xml: Initial import. - diff --git a/sci-mathematics/dolfin/metadata.xml b/sci-mathematics/dolfin/metadata.xml index 9c1b5e566..c3247869e 100644 --- a/sci-mathematics/dolfin/metadata.xml +++ b/sci-mathematics/dolfin/metadata.xml @@ -12,4 +12,7 @@ DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Proble <flag name="scotch">Adds support for graph partitioning with <pkg>sci-libs/scotch</pkg></flag> <flag name="umfpack">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag> </use> + <upstream> + <remote-id type="launchpad">dolfin</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/gambit/ChangeLog b/sci-mathematics/gambit/ChangeLog index 3d3d1a6d3..6643075ff 100644 --- a/sci-mathematics/gambit/ChangeLog +++ b/sci-mathematics/gambit/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/gambit -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/gambit: Updating remote-id in metadata.xml + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> gambit-0.2010.09.01.ebuild, metadata.xml: Fix header and move to EAPI=5 @@ -15,4 +18,3 @@ 15 Apr 2011; Dongxu Li <dongxuli2011@gmail.com> +gambit-0.2010.09.01.ebuild +Manifest +metadata.html +ChangeLog: Initial port. #47670 - diff --git a/sci-mathematics/gambit/metadata.xml b/sci-mathematics/gambit/metadata.xml index 917e7fd9e..63f1ab756 100644 --- a/sci-mathematics/gambit/metadata.xml +++ b/sci-mathematics/gambit/metadata.xml @@ -11,4 +11,7 @@ Enable gui support using wxWidgets. </flag> </use> + <upstream> + <remote-id type="sourceforge">gambit</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/kayali/ChangeLog b/sci-mathematics/kayali/ChangeLog index 293899f57..ae495b18d 100644 --- a/sci-mathematics/kayali/ChangeLog +++ b/sci-mathematics/kayali/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/kayali -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/kayali: Updating remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> kayali-0.3.2.ebuild, metadata.xml: Bump EAPI to 5; Bump to python-single-r1 eclass diff --git a/sci-mathematics/kayali/metadata.xml b/sci-mathematics/kayali/metadata.xml index 82fef4f2e..4be31a565 100644 --- a/sci-mathematics/kayali/metadata.xml +++ b/sci-mathematics/kayali/metadata.xml @@ -8,4 +8,7 @@ used as an advanced replacement for KDE KCalc. It is essentially a front end GUI forMaxima (and is easily extended to other CAS back-ends) and Gnuplot. </longdescription> + <upstream> + <remote-id type="sourceforge">kayali</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/netgen/ChangeLog b/sci-mathematics/netgen/ChangeLog index 665d587c2..4484817eb 100644 --- a/sci-mathematics/netgen/ChangeLog +++ b/sci-mathematics/netgen/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/netgen: Updating remote-id in metadata.xml + 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> netgen-5.0.0.ebuild: Bump to EAPI=5; Update Manifest (Bug #407) diff --git a/sci-mathematics/netgen/metadata.xml b/sci-mathematics/netgen/metadata.xml index 450140bdd..a4ba975d8 100644 --- a/sci-mathematics/netgen/metadata.xml +++ b/sci-mathematics/netgen/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> - <use> - <flag name="opencascade"> Enable OpenCASCADE support</flag> - </use> + <herd>sci-mathematics</herd> + <use> + <flag name="opencascade"> Enable OpenCASCADE support</flag> + </use> + <upstream> + <remote-id type="sourceforge">netgen-mesher</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/open-axiom/ChangeLog b/sci-mathematics/open-axiom/ChangeLog index ad2fb6847..71aa09fd0 100644 --- a/sci-mathematics/open-axiom/ChangeLog +++ b/sci-mathematics/open-axiom/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/open-axiom -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/open-axiom: Updating remote-id in metadata.xml + 29 Dec 2013; Justin Lecher <jlec@gentoo.org> open-axiom-1.4.2.ebuild, metadata.xml: Drop src_install in favour of default and use DOCS @@ -11,4 +14,3 @@ 22 Jan 2010; Sébastien Fabbro <bicatali@gentoo.org> +open-axiom-1.3.0.ebuild, +metadata.xml: Initial experimental ebuild of open-axiom - diff --git a/sci-mathematics/open-axiom/metadata.xml b/sci-mathematics/open-axiom/metadata.xml index 7485722c6..123d02826 100644 --- a/sci-mathematics/open-axiom/metadata.xml +++ b/sci-mathematics/open-axiom/metadata.xml @@ -8,4 +8,7 @@ programming language, a compiler, a large set of mathematical libraries of interest to researchers and practitioners of computational sciences. </longdescription> + <upstream> + <remote-id type="sourceforge">open-axiom</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/pulp/metadata.xml b/sci-mathematics/pulp/metadata.xml index 897aa2e6b..fda7a636f 100644 --- a/sci-mathematics/pulp/metadata.xml +++ b/sci-mathematics/pulp/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="pypi">PuLP</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/ufc/ChangeLog b/sci-mathematics/ufc/ChangeLog index 3e9549b60..fefc01844 100644 --- a/sci-mathematics/ufc/ChangeLog +++ b/sci-mathematics/ufc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/ufc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/ufc: Add bitbucket to remote-id in metadata.xml + 16 Jul 2014; Andrew Reisner <andrew@reisner.co> ufc-2.3.0.ebuild: added keyword diff --git a/sci-mathematics/ufc/metadata.xml b/sci-mathematics/ufc/metadata.xml index 132ec13b6..497df0887 100644 --- a/sci-mathematics/ufc/metadata.xml +++ b/sci-mathematics/ufc/metadata.xml @@ -1,9 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> -<longdescription lang="en"> + <herd>sci-mathematics</herd> + <longdescription lang="en"> UFC (Unified Form-assembly Code) is a unified framework for finite element assembly. More precisely, it defines a fixed interface for communicating low level routines (functions) for evaluating and assembling finite element variational forms. The UFC interface consists of a single header file ufc.h that specifies a C++ interface that must be implemented by code that complies with the UFC specification. </longdescription> + <upstream> + <remote-id type="bitbucket">fenics-project/ufc-deprecated</remote-id> + </upstream> </pkgmetadata> - diff --git a/sci-mathematics/yorick/ChangeLog b/sci-mathematics/yorick/ChangeLog index cadcebccc..2d5679755 100644 --- a/sci-mathematics/yorick/ChangeLog +++ b/sci-mathematics/yorick/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/yorick -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/yorick: Updating remote-id in metadata.xml + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> yorick-2.1.06.ebuild, metadata.xml: Move to EAPI=5; add missing multilib.eclass diff --git a/sci-mathematics/yorick/metadata.xml b/sci-mathematics/yorick/metadata.xml index 754d00e96..5770e5a45 100644 --- a/sci-mathematics/yorick/metadata.xml +++ b/sci-mathematics/yorick/metadata.xml @@ -11,4 +11,7 @@ Yorick is a language for scientific computing and rapid prototyping, similar to matlab. It can easily call C functions and libraries, has multidimensional arrays and built-in plot functions. </longdescription> + <upstream> + <remote-id type="sourceforge">yorick</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/hfst/ChangeLog b/sci-misc/hfst/ChangeLog index 550fcb04d..7ef0a3c11 100644 --- a/sci-misc/hfst/ChangeLog +++ b/sci-misc/hfst/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/hfst -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/hfst: Updating remote-id in metadata.xml + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> hfst-3.0.2.ebuild, hfst-3.3.12.ebuild, metadata.xml: Add ~amd64 or ~x86 keywords for revdeps @@ -28,4 +31,3 @@ 17 Nov 2009; <flammie@gentoo.org> +hfst-2.2.ebuild, +metadata.xml: Initial ebuild for HFST - diff --git a/sci-misc/hfst/metadata.xml b/sci-misc/hfst/metadata.xml index 1e603324b..4be3eac8d 100644 --- a/sci-misc/hfst/metadata.xml +++ b/sci-misc/hfst/metadata.xml @@ -1,28 +1,31 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <longdescription lang="en"> + <longdescription lang="en"> Open Source API for FSTs, a set of command line tools, and clones of traditional FST-based linguistic morphology tools. </longdescription> - <use> - <flag name="openfst"> + <use> + <flag name="openfst"> Add optional support for openfst backend library (<pkg>sci-misc/openfst</pkg>) </flag> - <flag name="foma"> + <flag name="foma"> Add optional support for foma backend library (<pkg>sci-misc/foma</pkg>)</flag> - <flag name="sfst"> + <flag name="sfst"> Add optional support for sfst backend library (<pkg>sci-misc/sfst</pkg>) </flag> - <flag name="glib"> + <flag name="glib"> Parse UTF-8 and collate unicode using glib instead of homebrewn methods </flag> - <flag name="xml"> + <flag name="xml"> Include parsers for grammars and formats that require XML support </flag> - </use> + </use> + <upstream> + <remote-id type="sourceforge">hfst</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/irstlm/ChangeLog b/sci-misc/irstlm/ChangeLog index cb6f0303c..36a33d004 100644 --- a/sci-misc/irstlm/ChangeLog +++ b/sci-misc/irstlm/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/irstlm: Updating remote-id in metadata.xml + *irstlm-5.80.08 (28 Feb 2015) 28 Feb 2015; Pavel Denisov <pavel.a.denisov@gmail.com> diff --git a/sci-misc/irstlm/metadata.xml b/sci-misc/irstlm/metadata.xml index 5d16554ed..e74038ce8 100644 --- a/sci-misc/irstlm/metadata.xml +++ b/sci-misc/irstlm/metadata.xml @@ -1,14 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>pavel.a.denisov@gmail.com</email> - </maintainer> - <longdescription lang="en"> + <maintainer> + <email>pavel.a.denisov@gmail.com</email> + </maintainer> + <longdescription lang="en"> The IRST Language Modeling Toolkit features algorithms and data structures suitable to estimate, store, and access very large LMs. The software has been integrated into a popular open source Statistical Machine Translation decoder called Moses, and is compatible with language models created with other tools, such as the SRILM Tooolkit. </longdescription> + <upstream> + <remote-id type="sourceforge">irstlm</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/jwnl/ChangeLog b/sci-misc/jwnl/ChangeLog index 9a050012b..4e38184d2 100644 --- a/sci-misc/jwnl/ChangeLog +++ b/sci-misc/jwnl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/jwnl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/jwnl: Updating remote-id in metadata.xml + 12 Nov 2014; Justin Lecher <jlec@gentoo.org> jwnl-1.3_rc3.ebuild, metadata.xml: Bump to EAPI=5 diff --git a/sci-misc/jwnl/metadata.xml b/sci-misc/jwnl/metadata.xml index faf15b461..dc7c73e44 100644 --- a/sci-misc/jwnl/metadata.xml +++ b/sci-misc/jwnl/metadata.xml @@ -8,4 +8,7 @@ Java based programming interface for accessing wordnet style dictionary data. </longdescription> + <upstream> + <remote-id type="sourceforge">jwordnet</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/nltk/ChangeLog b/sci-misc/nltk/ChangeLog index 613b269e1..d91ac2a39 100644 --- a/sci-misc/nltk/ChangeLog +++ b/sci-misc/nltk/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/nltk -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/nltk: Add github to remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> -nltk-2.0.1_rc1.ebuild, +nltk-2.0.4.ebuild, metadata.xml: Version Bump; Bump to distutils-r1 eclass diff --git a/sci-misc/nltk/metadata.xml b/sci-misc/nltk/metadata.xml index eefdbc160..8cf6c1d55 100644 --- a/sci-misc/nltk/metadata.xml +++ b/sci-misc/nltk/metadata.xml @@ -8,4 +8,7 @@ NLTK is collection of natural language tools written in python language. It also contains huge corpora. </longdescription> + <upstream> + <remote-id type="github">nltk/nltk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/opennlp-maxent/ChangeLog b/sci-misc/opennlp-maxent/ChangeLog index 388545bd0..f38888dba 100644 --- a/sci-misc/opennlp-maxent/ChangeLog +++ b/sci-misc/opennlp-maxent/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/opennlp-maxent -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/opennlp-maxent: Updating remote-id in metadata.xml + 12 Nov 2014; Justin Lecher <jlec@gentoo.org> opennlp-maxent-2.4.0.ebuild, metadata.xml: Bump to EAPI=5 diff --git a/sci-misc/opennlp-maxent/metadata.xml b/sci-misc/opennlp-maxent/metadata.xml index a9988e63d..74e102484 100644 --- a/sci-misc/opennlp-maxent/metadata.xml +++ b/sci-misc/opennlp-maxent/metadata.xml @@ -8,4 +8,7 @@ Implementation of statistical classification using maximum entropy models in opennlp framework. </longdescription> + <upstream> + <remote-id type="sourceforge">maxent</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/opennlp-tools/ChangeLog b/sci-misc/opennlp-tools/ChangeLog index 717e1908c..ea33a006b 100644 --- a/sci-misc/opennlp-tools/ChangeLog +++ b/sci-misc/opennlp-tools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/opennlp-tools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/opennlp-tools: Updating remote-id in metadata.xml + 12 Nov 2014; Justin Lecher <jlec@gentoo.org> opennlp-tools-1.3.0.ebuild, metadata.xml: Bump to EAPI=5 diff --git a/sci-misc/opennlp-tools/metadata.xml b/sci-misc/opennlp-tools/metadata.xml index 3d05bed34..8a0ae8ca7 100644 --- a/sci-misc/opennlp-tools/metadata.xml +++ b/sci-misc/opennlp-tools/metadata.xml @@ -11,4 +11,7 @@ <use> <flag name="models">Automatically generated description for models</flag> </use> + <upstream> + <remote-id type="sourceforge">opennlp</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/pywordnet/ChangeLog b/sci-misc/pywordnet/ChangeLog index e1b6547ae..9a7ca7d64 100644 --- a/sci-misc/pywordnet/ChangeLog +++ b/sci-misc/pywordnet/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/pywordnet -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/pywordnet: Updating remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> pywordnet-2.0.1.ebuild, metadata.xml: Bump to distutils-r1 eclass diff --git a/sci-misc/pywordnet/metadata.xml b/sci-misc/pywordnet/metadata.xml index 822a0ca76..41b4345f3 100644 --- a/sci-misc/pywordnet/metadata.xml +++ b/sci-misc/pywordnet/metadata.xml @@ -7,4 +7,7 @@ <longdescription> Pywordnet contains python bindings to handle wordnet databases. </longdescription> + <upstream> + <remote-id type="sourceforge">pywordnet</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/simx/ChangeLog b/sci-misc/simx/ChangeLog index 1907c83c6..2ac2ee578 100644 --- a/sci-misc/simx/ChangeLog +++ b/sci-misc/simx/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/simx -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/simx: Add github to remote-id in metadata.xml + *simx-0.2 (07 Feb 2014) 07 Feb 2014; Christoph Junghans <ottxor@gentoo.org> +simx-0.2.ebuild, diff --git a/sci-misc/simx/metadata.xml b/sci-misc/simx/metadata.xml index 897aa2e6b..6e9c32417 100644 --- a/sci-misc/simx/metadata.xml +++ b/sci-misc/simx/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="github">sim-x</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/bigdft/ChangeLog b/sci-physics/bigdft/ChangeLog index 4d205e731..700368c77 100644 --- a/sci-physics/bigdft/ChangeLog +++ b/sci-physics/bigdft/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/bigdft: Updating remote-id in metadata.xml + *bigdft-1.7.6 (22 Apr 2015) *bigdft-1.7.1 (22 Apr 2015) diff --git a/sci-physics/bigdft/metadata.xml b/sci-physics/bigdft/metadata.xml index 855d625ca..88bc4b9af 100644 --- a/sci-physics/bigdft/metadata.xml +++ b/sci-physics/bigdft/metadata.xml @@ -27,4 +27,7 @@ BigDFT is a DFT massively parallel electronic structure code (GPL license) using Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing </flag> </use> + <upstream> + <remote-id type="launchpad">bigdft</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/clip/ChangeLog b/sci-physics/clip/ChangeLog new file mode 100644 index 000000000..0876cda74 --- /dev/null +++ b/sci-physics/clip/ChangeLog @@ -0,0 +1,6 @@ +# ChangeLog for sci-physics/clip +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/clip: Updating remote-id in metadata.xml diff --git a/sci-physics/clip/metadata.xml b/sci-physics/clip/metadata.xml index 8a9f75597..fab4f8637 100644 --- a/sci-physics/clip/metadata.xml +++ b/sci-physics/clip/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <longdescription> @@ -6,4 +6,7 @@ Clip can simulate Laue patterns for arbitrary settings of crystal and detection plane. Moreover it allows to determine the crystal orientation from spots and zones marked on a Laue photograph. </longdescription> + <upstream> + <remote-id type="sourceforge">clip4</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/elk/ChangeLog b/sci-physics/elk/ChangeLog index 9f01d7650..a1e52cc3a 100644 --- a/sci-physics/elk/ChangeLog +++ b/sci-physics/elk/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-physics/elk -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/elk: Updating remote-id in metadata.xml + *elk-2.1.25 (23 Jul 2013) 23 Jul 2013; Honza Macháček <Hloupy.Honza@centrum.cz> +elk-2.1.25.ebuild, @@ -43,4 +46,3 @@ failed tests miserably, even with a lot of segfaults. Using its internal lapack with USE=-lapack, it looks well. Tested OK with USE="-lapack libxc mpi openmp". - diff --git a/sci-physics/elk/metadata.xml b/sci-physics/elk/metadata.xml index a7ed67ff3..ecc6af8e1 100644 --- a/sci-physics/elk/metadata.xml +++ b/sci-physics/elk/metadata.xml @@ -20,4 +20,7 @@ Elk is an all-electron full-potential linearised augmented-plane wave (FP-LAPW) Install python scripts. </flag> </use> + <upstream> + <remote-id type="sourceforge">elk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/espresso++/ChangeLog b/sci-physics/espresso++/ChangeLog index ca71bfef9..7a589edd3 100644 --- a/sci-physics/espresso++/ChangeLog +++ b/sci-physics/espresso++/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/espresso++: Add github to remote-id in metadata.xml + 20 Mar 2015; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild: added test feature diff --git a/sci-physics/espresso++/metadata.xml b/sci-physics/espresso++/metadata.xml index a556ddb82..25acc4649 100644 --- a/sci-physics/espresso++/metadata.xml +++ b/sci-physics/espresso++/metadata.xml @@ -6,4 +6,7 @@ <email>ottxor@gentoo.org</email> <name>Christoph Junghans</name> </maintainer> + <upstream> + <remote-id type="github">espressopp/espressopp</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/looptools/ChangeLog b/sci-physics/looptools/ChangeLog index 6e5903308..407587aa5 100644 --- a/sci-physics/looptools/ChangeLog +++ b/sci-physics/looptools/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-physics/looptools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*looptools-2.12 (07 Jun 2015) + + 07 Jun 2015; Jauhien Piatlicki <jauhien@gentoo.org> +looptools-2.12.ebuild: + version bump + *looptools-2.11 (31 Aug 2014) *looptools-2.10 (31 Aug 2014) *looptools-2.9 (31 Aug 2014) diff --git a/sci-physics/looptools/Manifest b/sci-physics/looptools/Manifest index 3c4607565..f4810e3a2 100644 --- a/sci-physics/looptools/Manifest +++ b/sci-physics/looptools/Manifest @@ -1,4 +1,5 @@ DIST LoopTools-2.10.tar.gz 550654 SHA256 141ab2153006ca3f1cc01e66e1552c02bf8164b9216304ff1829370b7b5c77bb SHA512 1fc9ef5a9ced8ea08ddc5f494338fb27b55bacdd23a968ca4379e5ca63f8d74ea947fb0bb98a80dfd6dddc0db1e80d2d454433abdcfeac323b51c27432046954 WHIRLPOOL b118d3f5f13b6e23920f7680b4b1a0b1d2c4079ac78c0763e73d30e9750d14ae57cd00f889e5b7392bc2ef53f88122be4d7f52de96f999676aa4e1e603353eae DIST LoopTools-2.11.tar.gz 546351 SHA256 efe14e774fcd66bdd46bbeb8065138793e3c1f5c73594c84c116edbab74c842d SHA512 fbe6c43b857561d0e7f35acdea32c34f2430c2faf23172790ad4426c469e39cd0df413d2c3cdc080ce9c4dcfb95773b7dc70b13738341c9d0438f4445cdbf6ab WHIRLPOOL 74b30ebe59998f2217b7e5cfb6e90671193159e5e3adfb2c26fee9c6f7b4021932ea8158e191f2e538e2e6d037fc86382659a697f638dc22ea3d068dfb92340c +DIST LoopTools-2.12.tar.gz 545153 SHA256 df04d944de15ec73665edaf76f655d1db797cbc02b54baa7664ac761ecfa2f70 SHA512 70726493bd138fb80b85a46955fbe28b7f1432d9b67a100fe3ff74c2fa22232a07e461a6742745b0ead81793bb64b81cc4265d09b91fa048e7bdd32cf6956b27 WHIRLPOOL af3abaf31a4a868e0f65bdb0b21405c413c470063e4c8130e31b2a9e05a4f0e65e9999323e3cdf0b4277e48e84d767288852e984d486468abab3aaa664f66879 DIST LoopTools-2.8.tar.gz 546810 SHA256 2395518d0eac9b0883a2c249b9a5ba80df443929c520c45e60f5a4284166eb42 SHA512 32211669fd092d2d5bb38e26a6471a95df0647d9e7ea0cc4e99ff4fd7c3e3fee107f6432ed9075e3102224f0041fac6f7075b1f0a91f7744ec3890b4b36d276e WHIRLPOOL c8dff8030d7ea1bfc6b65bef3370c5acfec69fa73f223a63b7424163b81a3bdf788eb3ffecd07e9bf61a31a63138b1fd126b6442a298c8fad1f4b04b69663a47 DIST LoopTools-2.9.tar.gz 548404 SHA256 e3cdc10fdbc9fe68e56402d34c6d3abd1ec6d727db8914b0cec0119273f7aa4d SHA512 3a46c94a5ff72079c930d7ec2076b0f5278e897130383fdd656173218840f04e03ebb9fdef362af36a207a71a87c038fec6e008a231ef259120073760aa05534 WHIRLPOOL 50591b6aa4e7e624282ad2102c78060cd421c6f5b7abd293bb18b2ca6844857bdcdbafab8e33c86ff4bd464f1245ba0cd13978800ac4786411a658ffd947cc38 diff --git a/sci-physics/looptools/looptools-2.12.ebuild b/sci-physics/looptools/looptools-2.12.ebuild new file mode 100644 index 000000000..66a959c4a --- /dev/null +++ b/sci-physics/looptools/looptools-2.12.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils fortran-2 multilib + +MYP=LoopTools-${PV} + +DESCRIPTION="Tools for evaluation of scalar and tensor one-loop integrals" +HOMEPAGE="http://www.feynarts.de/looptools" +SRC_URI="http://www.feynarts.de/looptools/${MYP}.tar.gz" + +LICENSE="LGPL-3" + +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +DEPEND="virtual/fortran" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MYP}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.10-makefile.patch + export VER="${PV}" + # necessary fix for prefix + sed -i "s/lib\$(LIBDIRSUFFIX)/$(get_libdir)/" makefile.in || die +} + +src_install() { + default + # another one of these package building archive with pic + # no: ooptools is not a typo + use static-libs || rm "${ED}"/usr/$(get_libdir)/libooptools.a + use doc && dodoc manual/*.pdf +} diff --git a/sci-visualization/gnuplot/ChangeLog b/sci-visualization/gnuplot/ChangeLog index 224469137..70dc9bcbd 100644 --- a/sci-visualization/gnuplot/ChangeLog +++ b/sci-visualization/gnuplot/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-visualization/gnuplot -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 May 2015; Christoph Junghans <ottxor@gentoo.org> -gnuplot-4.6.9999.ebuild, + metadata.xml: + remove old + + 25 May 2015; Christoph Junghans <ottxor@gentoo.org> gnuplot-5.0.9999.ebuild, + gnuplot-5.1.9999.ebuild, metadata.xml: + added compat use flag (bug #550370) + *gnuplot-5.1.9999 (08 Nov 2014) 08 Nov 2014; Christoph Junghans <ottxor@gentoo.org> +gnuplot-5.1.9999.ebuild, diff --git a/sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild b/sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild deleted file mode 100644 index 9330bbacd..000000000 --- a/sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild +++ /dev/null @@ -1,194 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils flag-o-matic multilib readme.gentoo toolchain-funcs wxwidgets - -DESCRIPTION="Command-line driven interactive plotting program" -HOMEPAGE="http://www.gnuplot.info/" - -if [[ -z ${PV%%*9999} ]]; then - inherit autotools cvs - ECVS_SERVER="gnuplot.cvs.sourceforge.net:/cvsroot/gnuplot" - ECVS_MODULE="gnuplot" - ECVS_BRANCH="branch-4-6-stable" - ECVS_USER="anonymous" - ECVS_CVS_OPTIONS="-dP" - MY_P="${PN}" - SRC_URI="" -else - MY_P="${P/_/.}" - SRC_URI="mirror://sourceforge/gnuplot/${MY_P}.tar.gz - mirror://gentoo/${PN}.info-4.6.2.tar.xz" -fi - -LICENSE="gnuplot bitmap? ( free-noncomm )" -SLOT="0" -KEYWORDS="" -IUSE="aqua bitmap cairo doc examples +gd ggi latex lua plotutils qt4 readline svga thin-splines wxwidgets X" - -RDEPEND=" - cairo? ( - x11-libs/cairo - x11-libs/pango ) - gd? ( >=media-libs/gd-2.0.35-r3[png] ) - ggi? ( media-libs/libggi ) - latex? ( - virtual/latex-base - lua? ( - dev-tex/pgf - >=dev-texlive/texlive-latexrecommended-2008-r2 ) ) - lua? ( dev-lang/lua ) - plotutils? ( media-libs/plotutils ) - qt4? ( >=dev-qt/qtcore-4.5:4 - >=dev-qt/qtgui-4.5:4 - >=dev-qt/qtsvg-4.5:4 ) - readline? ( sys-libs/readline ) - svga? ( media-libs/svgalib ) - wxwidgets? ( - x11-libs/wxGTK:2.8[X] - x11-libs/cairo - x11-libs/pango - x11-libs/gtk+:2 ) - X? ( x11-libs/libXaw )" -DEPEND="${RDEPEND} - virtual/pkgconfig - doc? ( - virtual/latex-base - dev-texlive/texlive-latexextra - app-text/ghostscript-gpl )" - -S="${WORKDIR}/${MY_P}" - -GP_VERSION="${PV%.*}" -E_SITEFILE="lisp/50${PN}-gentoo.el" -TEXMF="${EPREFIX}/usr/share/texmf-site" - -src_prepare() { - if [[ -n ${PV%%*9999} ]]; then - epatch "${FILESDIR}/${PN}-4.6.1-eldoc.patch" - epatch "${FILESDIR}/${PN}-4.6.2-gdversion.patch" #462996 - else - local dir - for dir in config demo m4 term tutorial; do - emake -C "$dir" -f Makefile.am.in Makefile.am - done - eautoreconf - fi - - # Add special version identification as required by provision 2 - # of the gnuplot license - sed -i -e "1s/.*/& (Gentoo revision ${PR})/" PATCHLEVEL || die - - # hacky workaround - # Please hack the buildsystem if you like - if use prefix && use qt4; then - append-ldflags -Wl,-rpath,"${EPREFIX}"/usr/$(get_libdir)/qt4 - fi - - DOC_CONTENTS='Gnuplot no longer links against pdflib, see the ChangeLog - for details. You can use the "pdfcairo" terminal for PDF output.' - use cairo || DOC_CONTENTS+=' It is available with USE="cairo".' - use svga && DOC_CONTENTS+='\n\nIn order to enable ordinary users to use - SVGA console graphics, gnuplot needs to be set up as setuid root. - Please note that this is usually considered to be a security hazard. - As root, manually "chmod u+s /usr/bin/gnuplot".' - use gd && DOC_CONTENTS+='\n\nFor font support in png/jpeg/gif output, - you may have to set the GDFONTPATH and GNUPLOT_DEFAULT_GDFONT - environment variables. See the FAQ file in /usr/share/doc/${PF}/ - for more information.' -} - -src_configure() { - if ! use latex; then - sed -i -e '/SUBDIRS/s/LaTeX//' share/Makefile.in || die - fi - - if use wxwidgets; then - WX_GTK_VER="2.8" - need-wxwidgets unicode - fi - - tc-export CC CXX #453174 - - econf \ - --without-pdf \ - --with-texdir="${TEXMF}/tex/latex/${PN}" \ - --with-readline=$(usex readline gnu builtin) \ - --without-lisp-files \ - $(use_with bitmap bitmap-terminals) \ - $(use_with cairo) \ - $(use_with doc tutorial) \ - $(use_with gd) \ - "$(use_with ggi ggi "${EPREFIX}/usr/$(get_libdir)")" \ - "$(use_with ggi xmi "${EPREFIX}/usr/$(get_libdir)")" \ - $(use_with lua) \ - "$(use_with plotutils plot "${EPREFIX}/usr/$(get_libdir)")" \ - $(use_with svga linux-vga) \ - $(use_with X x) \ - --enable-stats \ - $(use_enable qt4 qt) \ - $(use_enable thin-splines) \ - $(use_enable wxwidgets) \ - DIST_CONTACT="http://bugs.gentoo.org/" \ - EMACS=no -} - -src_compile() { - # Prevent access violations, see bug 201871 - VARTEXFONTS="${T}/fonts" - - # We believe that the following line is no longer needed. - # In case of problems file a bug report at bugs.gentoo.org. - #addwrite /dev/svga:/dev/mouse:/dev/tts/0 - - emake all - - if use doc; then - # Avoid sandbox violation in epstopdf/ghostscript - addpredict /var/cache/fontconfig - emake -C docs pdf - emake -C tutorial pdf - fi -} - -src_install () { - emake DESTDIR="${D}" install - - dodoc BUGS ChangeLog NEWS PGPKEYS PORTING README* - newdoc term/PostScript/README README-ps - newdoc term/js/README README-js - use lua && newdoc term/lua/README README-lua - readme.gentoo_create_doc - - if use examples; then - # Demo files - insinto /usr/share/${PN}/${GP_VERSION} - doins -r demo - rm -f "${ED}"/usr/share/${PN}/${GP_VERSION}/demo/Makefile* - rm -f "${ED}"/usr/share/${PN}/${GP_VERSION}/demo/binary* - fi - - if use doc; then - # Manual, tutorial, FAQ - dodoc docs/gnuplot.pdf tutorial/{tutorial.dvi,tutorial.pdf} FAQ.pdf - # Documentation for making PostScript files - docinto psdoc - dodoc docs/psdoc/{*.doc,*.tex,*.ps,*.gpi,README} - fi -} - -src_test() { - GNUTERM="unknown" default_src_test -} - -pkg_postinst() { - use latex && texmf-update - readme.gentoo_print_elog -} - -pkg_postrm() { - use latex && texmf-update -} diff --git a/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild b/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild index ba3a990ef..fbc18cfe7 100644 --- a/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild +++ b/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -22,13 +22,13 @@ if [[ -z ${PV%%*9999} ]]; then else MY_P="${P/_/.}" SRC_URI="mirror://sourceforge/gnuplot/${MY_P}.tar.gz" - KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~s390 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~s390 ~sparc ~x86 ~ppc-aix ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris" inherit autotools fi LICENSE="gnuplot bitmap? ( free-noncomm )" SLOT="0" -IUSE="aqua bitmap cairo doc examples +gd ggi latex libcaca libcerf lua qt4 readline svga wxwidgets X" +IUSE="aqua bitmap cairo compat doc examples +gd ggi latex libcaca libcerf lua qt4 readline svga wxwidgets X" RDEPEND=" cairo? ( @@ -42,11 +42,11 @@ RDEPEND=" dev-tex/pgf >=dev-texlive/texlive-latexrecommended-2008-r2 ) ) libcaca? ( media-libs/libcaca ) - lua? ( dev-lang/lua ) + lua? ( dev-lang/lua:0 ) qt4? ( >=dev-qt/qtcore-4.5:4 >=dev-qt/qtgui-4.5:4 >=dev-qt/qtsvg-4.5:4 ) - readline? ( sys-libs/readline ) + readline? ( sys-libs/readline:0 ) libcerf? ( sci-libs/libcerf ) svga? ( media-libs/svgalib ) wxwidgets? ( @@ -75,9 +75,6 @@ src_prepare() { emake -C "$dir" -f Makefile.am.in Makefile.am done eautoreconf - else - epatch "${FILESDIR}/${PN}-5.0_rc1-libcerf.patch" - eautoreconf fi # Add special version identification as required by provision 2 @@ -121,6 +118,7 @@ src_configure() { --with-readline=$(usex readline gnu builtin) \ $(use_with bitmap bitmap-terminals) \ $(use_with cairo) \ + $(use_enable compat backwards-compatibility) \ $(use_with doc tutorial) \ $(use_with gd) \ "$(use_with ggi ggi "${EPREFIX}/usr/$(get_libdir)")" \ diff --git a/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild b/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild index 05eabe319..f8f88c274 100644 --- a/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild +++ b/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -28,7 +28,7 @@ fi LICENSE="gnuplot bitmap? ( free-noncomm )" SLOT="0" -IUSE="aqua bitmap cairo doc examples +gd ggi latex libcaca libcerf lua qt4 readline svga wxwidgets X" +IUSE="aqua bitmap cairo compat doc examples +gd ggi latex libcaca libcerf lua qt4 readline svga wxwidgets X" RDEPEND=" cairo? ( @@ -42,11 +42,11 @@ RDEPEND=" dev-tex/pgf >=dev-texlive/texlive-latexrecommended-2008-r2 ) ) libcaca? ( media-libs/libcaca ) - lua? ( dev-lang/lua ) + lua? ( dev-lang/lua:0 ) qt4? ( >=dev-qt/qtcore-4.5:4 >=dev-qt/qtgui-4.5:4 >=dev-qt/qtsvg-4.5:4 ) - readline? ( sys-libs/readline ) + readline? ( sys-libs/readline:0 ) libcerf? ( sci-libs/libcerf ) svga? ( media-libs/svgalib ) wxwidgets? ( @@ -121,6 +121,7 @@ src_configure() { --with-readline=$(usex readline gnu builtin) \ $(use_with bitmap bitmap-terminals) \ $(use_with cairo) \ + $(use_enable compat backwards-compatibility) \ $(use_with doc tutorial) \ $(use_with gd) \ "$(use_with ggi ggi "${EPREFIX}/usr/$(get_libdir)")" \ diff --git a/sci-visualization/gnuplot/metadata.xml b/sci-visualization/gnuplot/metadata.xml index 1a66c9402..cccec8e78 100644 --- a/sci-visualization/gnuplot/metadata.xml +++ b/sci-visualization/gnuplot/metadata.xml @@ -16,11 +16,11 @@ three-dimensional plots in many different formats. It is designed primarily for the visual display of scientific data. </longdescription> - <use> +<use> + <flag name="compat">Enable backwards compatibility with version 4 syntax</flag> <flag name="gd">Add support for <pkg>media-libs/gd</pkg>. Needed for GIF, JPEG, and PNG image output.</flag> <flag name="libcerf">Enable special functions from <pkg>sci-libs/libcerf</pkg></flag> - <flag name="thin-splines">Enable thin plate splines</flag> <flag name="bitmap">Enable dot-matrix printers and pbm terminal</flag> </use> <upstream> diff --git a/sci-visualization/mantid/ChangeLog b/sci-visualization/mantid/ChangeLog index 642a8f282..dc58dbba4 100644 --- a/sci-visualization/mantid/ChangeLog +++ b/sci-visualization/mantid/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-visualization/mantid: Updating remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> mantid-3.3.0.ebuild, metadata.xml: sci-visualization/mantid: fix SLOT operators; fix whitespaces diff --git a/sci-visualization/mantid/metadata.xml b/sci-visualization/mantid/metadata.xml index 52e887f3c..6a018c74f 100644 --- a/sci-visualization/mantid/metadata.xml +++ b/sci-visualization/mantid/metadata.xml @@ -20,4 +20,7 @@ <flag name="paraview">Enable the Visualisation and Analysis Toolkit ExtensionS (VATES)</flag> <flag name="tcmalloc">Use thread-caching malloc</flag> </use> + <upstream> + <remote-id type="sourceforge">mantid</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-visualization/mayavi/ChangeLog b/sci-visualization/mayavi/ChangeLog index f0c228bda..588ac41ad 100644 --- a/sci-visualization/mayavi/ChangeLog +++ b/sci-visualization/mayavi/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: Exp $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-visualization/mayavi: Add github to remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> mayavi-4.4.0.ebuild, metadata.xml: sci-visualization/mayavi: fix SLOT operators diff --git a/sci-visualization/mayavi/metadata.xml b/sci-visualization/mayavi/metadata.xml index a76fa19f9..023851c52 100644 --- a/sci-visualization/mayavi/metadata.xml +++ b/sci-visualization/mayavi/metadata.xml @@ -21,4 +21,7 @@ used as an Envisage plug-in which allows it to be embedded in other Envisage based applications natively. </longdescription> + <upstream> + <remote-id type="github">enthought/mayavi</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-visualization/yt/metadata.xml b/sci-visualization/yt/metadata.xml index fc0769f7f..ebd98f7b5 100644 --- a/sci-visualization/yt/metadata.xml +++ b/sci-visualization/yt/metadata.xml @@ -1,15 +1,18 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>xarthisius@gentoo.org</email> - <name>Kacper Kowalik</name> - </maintainer> - <longdescription>yt is an analysis and visualization system written in Python, + <herd>sci</herd> + <maintainer> + <email>xarthisius@gentoo.org</email> + <name>Kacper Kowalik</name> + </maintainer> + <longdescription>yt is an analysis and visualization system written in Python, designed for use with Astrophysical Simulation codes. yt can process data in a myriad of ways and make a variety of visualizations. It is designed to be portable across simulation codes, and it is developed by developers from a variety of institutions and backgrounds. </longdescription> + <upstream> + <remote-id type="pypi">yt</remote-id> + </upstream> </pkgmetadata> diff --git a/sys-cluster/htcondor/ChangeLog b/sys-cluster/htcondor/ChangeLog index 7215000f4..959952f85 100644 --- a/sys-cluster/htcondor/ChangeLog +++ b/sys-cluster/htcondor/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sys-cluster/htcondor: Add github to remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> htcondor-8.0.0.ebuild, htcondor-8.3.2.ebuild: sys-cluster/htcondor: fix SLOT operators diff --git a/sys-cluster/htcondor/metadata.xml b/sys-cluster/htcondor/metadata.xml index 6485807ae..7767e2fac 100644 --- a/sys-cluster/htcondor/metadata.xml +++ b/sys-cluster/htcondor/metadata.xml @@ -26,4 +26,7 @@ <flag name="minimal">Don't support standard universe jobs</flag> <flag name="X">Enable the HTCondor Keyboard Daemon to monitor logged in X users for activity</flag> </use> + <upstream> + <remote-id type="github">htcondor/htcondor</remote-id> + </upstream> </pkgmetadata> diff --git a/sys-cluster/pyslice/metadata.xml b/sys-cluster/pyslice/metadata.xml index 65f154a4c..d2d79a4da 100644 --- a/sys-cluster/pyslice/metadata.xml +++ b/sys-cluster/pyslice/metadata.xml @@ -5,4 +5,7 @@ <longdescription> Templating system for parametric modeling. </longdescription> + <upstream> + <remote-id type="pypi">pyslice</remote-id> + </upstream> </pkgmetadata> diff --git a/x11-misc/envytools/ChangeLog b/x11-misc/envytools/ChangeLog index 87328eb68..b9a57bd18 100644 --- a/x11-misc/envytools/ChangeLog +++ b/x11-misc/envytools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for x11-misc/envytools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + x11-misc/envytools: Add github to remote-id in metadata.xml + 16 Apr 2014; Wilhelm Erasmus <webmaster@wilhelm.co.za> envytools-9999.ebuild: x11-misc/envytools: Updated github url, Resolves gentoo-science/sci#103 diff --git a/x11-misc/envytools/metadata.xml b/x11-misc/envytools/metadata.xml index 098ac091a..cff6c9ef4 100644 --- a/x11-misc/envytools/metadata.xml +++ b/x11-misc/envytools/metadata.xml @@ -6,4 +6,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">pathscale/envytools</remote-id> + </upstream> </pkgmetadata> |