From 17ed872c6334185fdebf3d60b2aa219fc1fe7516 Mon Sep 17 00:00:00 2001 From: Aaron Bauman Date: Fri, 3 Jul 2020 22:22:37 -0400 Subject: */*: drop last-rited py2 packages Signed-off-by: Aaron Bauman --- sci-chemistry/hollow/Manifest | 1 - sci-chemistry/hollow/hollow-1.2-r1.ebuild | 38 ------ sci-chemistry/hollow/metadata.xml | 11 -- sci-chemistry/modeller/Manifest | 2 - sci-chemistry/modeller/metadata.xml | 8 -- sci-chemistry/modeller/modeller-9.20.ebuild | 145 --------------------- sci-chemistry/modeller/modeller-9.22.ebuild | 145 --------------------- sci-chemistry/pymol-plugins-msms/Manifest | 1 - .../pymol-plugins-msms/files/100415-msms.patch | 33 ----- sci-chemistry/pymol-plugins-msms/metadata.xml | 17 --- .../pymol-plugins-msms-100415-r1.ebuild | 43 ------ 11 files changed, 444 deletions(-) delete mode 100644 sci-chemistry/hollow/Manifest delete mode 100644 sci-chemistry/hollow/hollow-1.2-r1.ebuild delete mode 100644 sci-chemistry/hollow/metadata.xml delete mode 100644 sci-chemistry/modeller/Manifest delete mode 100644 sci-chemistry/modeller/metadata.xml delete mode 100644 sci-chemistry/modeller/modeller-9.20.ebuild delete mode 100644 sci-chemistry/modeller/modeller-9.22.ebuild delete mode 100644 sci-chemistry/pymol-plugins-msms/Manifest delete mode 100644 sci-chemistry/pymol-plugins-msms/files/100415-msms.patch delete mode 100644 sci-chemistry/pymol-plugins-msms/metadata.xml delete mode 100644 sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/hollow/Manifest b/sci-chemistry/hollow/Manifest deleted file mode 100644 index 9c9dec2ce5a3..000000000000 --- a/sci-chemistry/hollow/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST hollow-1.2.zip 62554 BLAKE2B 825ebbd5b9085d47be3487331ecabf80a6af73eda4525e1d073eea05b5fb0c1892b115f669c8ce3227bfb573f266d1a0225c7aaeee844338496bceb55d88edd6 SHA512 e253680cc0fae286ec697b2dac822b9e165d509cc7eefb27bbcafae6ab2617c3edc8cd9c8beefcc9ef2eb920c9d839fd0bc25f79d22160d857b1705cefbc05ca diff --git a/sci-chemistry/hollow/hollow-1.2-r1.ebuild b/sci-chemistry/hollow/hollow-1.2-r1.ebuild deleted file mode 100644 index d1db2c19db3f..000000000000 --- a/sci-chemistry/hollow/hollow-1.2-r1.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit python-r1 vcs-clean - -DESCRIPTION="Production of surface images of proteins" -HOMEPAGE="http://hollow.sourceforge.net/" -#SRC_URI="mirror://sourceforge/${P}.zip" -SRC_URI="http://hollow.sourceforge.net/${P}.zip" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="GPL-3" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - sci-chemistry/pymol[${PYTHON_USEDEP}]" -DEPEND="${PYTHON_DEPS} - app-arch/unzip" - -src_install() { - python_setup - esvn_clean - python_foreach_impl python_domodule pdbstruct - python_moduleinto ${PN} - python_foreach_impl python_domodule *.py hollow.txt - - python_foreach_impl python_newscript ${PN}.py ${PN} - - dodoc README - python_optimize -} diff --git a/sci-chemistry/hollow/metadata.xml b/sci-chemistry/hollow/metadata.xml deleted file mode 100644 index 266ef9d56913..000000000000 --- a/sci-chemistry/hollow/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - - hollow - - diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest deleted file mode 100644 index 69e1780c97f5..000000000000 --- a/sci-chemistry/modeller/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST modeller-9.20.tar.gz 34909796 BLAKE2B d89c81823c4d7784a7b3d64fdb01158a973edc7d8b316c773e038ba8645797c543d5bc58c1bff5462ae5975a6c2796f4b2d500641d226c3b2281cf794cfeba8d SHA512 667edeeda0a9038258f6932b3cef22a1e9d0fe47f47bd2ac612e7bac7f23a863f5a65cfd93abfa405310e7fb7b305d53e71d6c6e930613b0dbd43b24dcd5919a -DIST modeller-9.22.tar.gz 34953371 BLAKE2B 3bf8828b38f22955dea973cfe54cbd2f77bf021900bd5aa3c75f083b12e2a7199c3173de526acfeab005c0606816bac347b9bdfb6b62d5e3db9c9e18fed99ac4 SHA512 0056f09a07d6e2b565c8f4accca48ad176c9d32634b75bc4db60a187d56f22ef1710296dfd31bf27f496c5ed100146420be7cfdb135ca8b2b0fac7d7f5fa877f diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml deleted file mode 100644 index da36ecbfcd6a..000000000000 --- a/sci-chemistry/modeller/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - diff --git a/sci-chemistry/modeller/modeller-9.20.ebuild b/sci-chemistry/modeller/modeller-9.20.ebuild deleted file mode 100644 index 641395067b0d..000000000000 --- a/sci-chemistry/modeller/modeller-9.20.ebuild +++ /dev/null @@ -1,145 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 eutils multilib versionator - -DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" -HOMEPAGE="https://salilab.org/modeller/" -SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz" - -LICENSE="modeller" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc examples" -SLOT="0" - -RESTRICT="mirror" - -DEPEND=">=dev-lang/swig-1.3" -RDEPEND="" - -INPATH="${EPREFIX}"/opt/modeller${ver} - -QA_PREBUILT="/opt/*" - -pkg_setup() { - case ${ARCH} in - x86) - EXECTYPE="i386-intel8";; - amd64) - EXECTYPE="x86_64-intel8";; - *) - die "Your arch "${ARCH}" does not appear supported at this time.";; - esac -} - -python_prepare_all() { - sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die - distutils-r1_python_prepare_all -} - -python_compile() { - cd src/swig || die - swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die - distutils-r1_python_compile -} - -python_install() { - cd src/swig || die - distutils-r1_python_install -} - -python_install_all() { - cd "${S}" || die - sed \ - -e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \ - -e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \ - -i bin/modscript || die - - sed -e "s;@TOPDIR\@;\"${INPATH}\";" \ - -e "s;@EXETYPE\@;${EXECTYPE};" \ - bin/modpy.sh.in > "${T}/modpy.sh" - - insinto ${INPATH} - doins -r modlib - python_foreach_impl python_domodule modlib/modeller - - insinto ${INPATH}/bin - doins -r bin/{lib,*top} - - exeinto ${INPATH}/bin - doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh - - python_foreach_impl python_doscript bin/modslave.py - dosym ${INPATH}/bin/modscript /opt/bin/mod${PV} - dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh - - exeinto ${INPATH}/lib/${EXECTYPE}/ - doexe lib/${EXECTYPE}/lib* - dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so - dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8 - - use doc && HTML_DOCS=( doc/. ) - distutils-r1_python_install_all - - if use examples; then - insinto /usr/share/${PN}/ - doins -r examples - fi - - insinto /etc/revdep-rebuild - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/" - EOF - doins "${T}"/40-${PN} -} - -pkg_postinst() { - if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then - echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py - fi - - if grep -q license ${INPATH}/modlib/modeller/config.py; then - einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py" - else - ewarn "Obtain a license Key from" - ewarn "http://salilab.org/modeller/registration.html" - ewarn "And run this before using modeller:" - ewarn "emerge --config =${CATEGORY}/${PF}" - ewarn "That way you can [re]enter your license key." - fi -} - -pkg_postrm() { - ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py" - ewarn "that you need to remove to completely get rid of modeller." -} - -pkg_config() { - ewarn "Your license key is NOT checked for validity here." - ewarn " Make sure you type it in correctly." - eerror "If you CTRL+C out of this, modeller will not run!" - while true - do - einfo "Please enter your license key:" - read license_key1 - einfo "Please re-enter your license key:" - read license_key2 - if [[ "$license_key1" == "" ]] - then - echo "You entered a blank license key. Try again." - else - if [[ "$license_key1" == "$license_key2" ]] - then - echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py" - einfo "Thank you!" - break - else - eerror "Your license key entries do not match. Try again." - fi - fi - done -} diff --git a/sci-chemistry/modeller/modeller-9.22.ebuild b/sci-chemistry/modeller/modeller-9.22.ebuild deleted file mode 100644 index 2bc08bd43d4e..000000000000 --- a/sci-chemistry/modeller/modeller-9.22.ebuild +++ /dev/null @@ -1,145 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 eutils multilib - -DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" -HOMEPAGE="https://salilab.org/modeller/" -SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz" - -LICENSE="modeller" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc examples" -SLOT="0" - -RESTRICT="mirror" - -DEPEND=">=dev-lang/swig-1.3" -RDEPEND="" - -INPATH="${EPREFIX}"/opt/modeller${ver} - -QA_PREBUILT="/opt/*" - -pkg_setup() { - case ${ARCH} in - x86) - EXECTYPE="i386-intel8";; - amd64) - EXECTYPE="x86_64-intel8";; - *) - die "Your arch "${ARCH}" does not appear supported at this time.";; - esac -} - -python_prepare_all() { - sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die - distutils-r1_python_prepare_all -} - -python_compile() { - cd src/swig || die - swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die - distutils-r1_python_compile -} - -python_install() { - cd src/swig || die - distutils-r1_python_install -} - -python_install_all() { - cd "${S}" || die - sed \ - -e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \ - -e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \ - -i bin/modscript || die - - sed -e "s;@TOPDIR\@;\"${INPATH}\";" \ - -e "s;@EXETYPE\@;${EXECTYPE};" \ - bin/modpy.sh.in > "${T}/modpy.sh" - - insinto ${INPATH} - doins -r modlib - python_foreach_impl python_domodule modlib/modeller - - insinto ${INPATH}/bin - doins -r bin/{lib,*top} - - exeinto ${INPATH}/bin - doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh - - python_foreach_impl python_doscript bin/modslave.py - dosym ${INPATH}/bin/modscript /opt/bin/mod${PV} - dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh - - exeinto ${INPATH}/lib/${EXECTYPE}/ - doexe lib/${EXECTYPE}/lib* - dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so - dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8 - - use doc && HTML_DOCS=( doc/. ) - distutils-r1_python_install_all - - if use examples; then - insinto /usr/share/${PN}/ - doins -r examples - fi - - insinto /etc/revdep-rebuild - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/" - EOF - doins "${T}"/40-${PN} -} - -pkg_postinst() { - if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then - echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py - fi - - if grep -q license ${INPATH}/modlib/modeller/config.py; then - einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py" - else - ewarn "Obtain a license Key from" - ewarn "http://salilab.org/modeller/registration.html" - ewarn "And run this before using modeller:" - ewarn "emerge --config =${CATEGORY}/${PF}" - ewarn "That way you can [re]enter your license key." - fi -} - -pkg_postrm() { - ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py" - ewarn "that you need to remove to completely get rid of modeller." -} - -pkg_config() { - ewarn "Your license key is NOT checked for validity here." - ewarn " Make sure you type it in correctly." - eerror "If you CTRL+C out of this, modeller will not run!" - while true - do - einfo "Please enter your license key:" - read license_key1 - einfo "Please re-enter your license key:" - read license_key2 - if [[ "$license_key1" == "" ]] - then - echo "You entered a blank license key. Try again." - else - if [[ "$license_key1" == "$license_key2" ]] - then - echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py" - einfo "Thank you!" - break - else - eerror "Your license key entries do not match. Try again." - fi - fi - done -} diff --git a/sci-chemistry/pymol-plugins-msms/Manifest b/sci-chemistry/pymol-plugins-msms/Manifest deleted file mode 100644 index 3e5c1d3ef747..000000000000 --- a/sci-chemistry/pymol-plugins-msms/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pymol-plugins-msms-100415.py 62320 BLAKE2B 2778221bd0138764b9f0b75202de8bc46d71005b26d0e23faba582d5f49fc0c3edca04d0ffcddf8f3be541a2142b739afe8a2904912a29d2443d9e6974f453a5 SHA512 924d89836f92d0be52d7534cbe6dc9338dac1c2263a51900ab62dbe96e4f54f565dbaa6bdf51236d8ea8e9042aa09283a117f5285561b252177a5a32f3876489 diff --git a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch deleted file mode 100644 index 0d26fb31c5f1..000000000000 --- a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch +++ /dev/null @@ -1,33 +0,0 @@ - pymol-plugins-msms-100415.py | 18 ++++++++++-------- - 1 files changed, 10 insertions(+), 8 deletions(-) - -diff --git a/pymol-plugins-msms-100415.py b/pymol-plugins-msms-100415.py -index 725934d..7ea00bf 100644 ---- a/pymol-plugins-msms-100415.py -+++ b/pymol-plugins-msms-100415.py -@@ -99,15 +99,17 @@ class MSMSPlugin: - self.cleanup_saved_pymol_sel.set(True) # by default, clean up - - self.pdb_fn.set('') -- if 'MSMS_BIN' in os.environ: -- if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN'] -- self.msms_bin.set(os.environ['MSMS_BIN']) -- else: -- if VERBOSE: print 'MSMS_BIN not found in environmental variables.' -- self.msms_bin.set('') -+ self.msms_bin.set('GENTOOMSMS') -+## if 'MSMS_BIN' in os.environ: -+## if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN'] -+## self.msms_bin.set(os.environ['MSMS_BIN']) -+## else: -+## if VERBOSE: print 'MSMS_BIN not found in environmental variables.' -+## self.msms_bin.set('') - ## self.pdb2xyzr_bin.set('') -- if 'PDB2XYZRN' in os.environ: self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN']) -- else: self.pdb2xyzrn_bin.set('') -+ self.pdb2xyzrn_bin.set('GENTOOXYZRN') -+## if 'PDB2XYZRN' in os.environ: self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN']) -+## else: self.pdb2xyzrn_bin.set('') - self.tmp_dir.set('/tmp') - self.cleanup_msms_output = Tkinter.BooleanVar() - self.cleanup_msms_output.set(True) # by default, clean up msms output diff --git a/sci-chemistry/pymol-plugins-msms/metadata.xml b/sci-chemistry/pymol-plugins-msms/metadata.xml deleted file mode 100644 index 214696c4a1f7..000000000000 --- a/sci-chemistry/pymol-plugins-msms/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - -MSMS is an excellent tool for computing protein solvent excluded surface (SES). -MSMS Plugin for PyMOL provides a graphical user interface for running MSMS and -displaying its results in PyMOL. - -1. Citation for this plugin: - Hongbo Zhu. MSMS plugin for PyMOL, 2010, Biotechnology Center (BIOTEC), TU Dresden. -2. Citation for PyMOL can be found at: http://pymol.sourceforge.net/faq.html#CITE - - diff --git a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild deleted file mode 100644 index 33c7dbf9be7d..000000000000 --- a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils python-r1 - -DESCRIPTION="GUI for MSMS and displaying its results in PyMOL" -HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html" -SRC_URI="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/pymol_script/msms_pymol.py -> ${P}.py" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="BSD pymol" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - sci-chemistry/msms-bin - sci-chemistry/pymol[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" - -src_unpack() { - mkdir "${S}" || die - cp "${DISTDIR}"/${A} "${S}/" || die -} - -src_prepare() { - epatch "${FILESDIR}"/${PV}-msms.patch - sed \ - -e "s:GENTOOMSMS:${EPREFIX}/opt/bin/msms:g" \ - -e "s:GENTOOXYZRN:${EPREFIX}/usr/bin/pdb_to_xyzrn:g" \ - -i ${A} || die -} - -src_install() { - python_moduleinto pmg_tk/startup - python_foreach_impl python_domodule ${P}.py - python_foreach_impl python_optimize -} -- cgit v1.2.3-65-gdbad