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author | Justin Lecher (jlec) <jlec@j-schmitz.net> | 2009-02-06 09:43:10 +0100 |
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committer | Justin Lecher (jlec) <jlec@j-schmitz.net> | 2009-02-06 09:43:10 +0100 |
commit | 8a40732473de580f15fdc11f5c13f42cd640a618 (patch) | |
tree | e6d6bf915b75e46a6144ee28c68613e62ebe56be | |
parent | [QA]: Add missing diags USE flag to IUSE (diff) | |
download | sci-8a40732473de580f15fdc11f5c13f42cd640a618.tar.gz sci-8a40732473de580f15fdc11f5c13f42cd640a618.tar.bz2 sci-8a40732473de580f15fdc11f5c13f42cd640a618.zip |
sci-chemistry/pymol-1.2_beta added. I will maintain all beta versions in sci overlay.
-rw-r--r-- | sci-chemistry/pymol/ChangeLog | 12 | ||||
-rw-r--r-- | sci-chemistry/pymol/Manifest | 7 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2 | bin | 0 -> 20283 bytes | |||
-rw-r--r-- | sci-chemistry/pymol/files/nosplash-gentoo.patch | 9 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/pymol-1.2_beta2-data-path.patch | 51 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch | 11 | ||||
-rw-r--r-- | sci-chemistry/pymol/metadata.xml | 11 | ||||
-rw-r--r-- | sci-chemistry/pymol/pymol-1.2_beta2.ebuild | 112 |
8 files changed, 213 insertions, 0 deletions
diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog new file mode 100644 index 000000000..d612299b4 --- /dev/null +++ b/sci-chemistry/pymol/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-chemistry/pymol +# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 06 Feb 2009; justin Lecher (jlec) <jlec@j-schmitz.net> + +sci-chemistry/pymol/files/pymol-1.2_beta2-data-path.patch, + +sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch, + +sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2, + +sci-chemistry/pymol/files/nosplash-gentoo.patch, + +sci-chemistry/pymol/metadata.xml: + Initial checkin of pymol to sci-overlay + diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest new file mode 100644 index 000000000..45a40a721 --- /dev/null +++ b/sci-chemistry/pymol/Manifest @@ -0,0 +1,7 @@ +AUX apbs-070604-r3550.patch.bz2 20283 RMD160 e7fc42934dea043000ba81e4f27b99b6062e4b12 SHA1 1708de792a53ac4819dfe4ec11cc9ee54b3d5fb9 SHA256 ad8ce064ee2ce3310f862b60b8f762ef713f9952fef0ebd329204a2d25b42db5 +AUX nosplash-gentoo.patch 467 RMD160 a6be474aab95e8c8ffd37f509fe3d40cf4db23f7 SHA1 14862bab327fea0cdc8198070f01827d6f832899 SHA256 c4b5384485242165aa517fe2caf83241201c2354d5c964554f6d82c51ba7fba3 +AUX pymol-1.2_beta2-data-path.patch 2584 RMD160 c5fdd7884241a493578be5a2b658ac0cd0bff000 SHA1 1e4cd368ad08b87627ef465fad4ca96dcfbef00b SHA256 39e06459105969e0156bfe71f61bdccd3da4c8d7f2ba6e783aa34e63dc62b0a7 +AUX pymol-1.2_beta2-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0 +EBUILD pymol-1.2_beta2.ebuild 2758 RMD160 073aed8dcc3012a1b921ed53f1dd83bfa39f391a SHA1 e206d6f2b7b39b559868c62022914cf5dbcea420 SHA256 276b9ea9c4c4ce9c07f931b46005dddafff6df871e76f761ba411e4cd24f7e44 +MISC ChangeLog 489 RMD160 9a85d57d2087e8ac772d3df0f311487ee1d62f88 SHA1 759c8b8d1bd512fe2a92d4a13896dc3a885498c4 SHA256 c75c41133c6e44ce26865740908f001097e411e38fb57c4cfb16624dde32098f +MISC metadata.xml 297 RMD160 431061f6875f90a251ae90c5fc5be499da78c9d8 SHA1 b01c71fad62ac24b76a45536f6ddeae3904558dd SHA256 fbe32692a4ff6e595966ca094d9d12912952aaeb639d248fdbd0ed2a9a088d75 diff --git a/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2 b/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2 Binary files differnew file mode 100644 index 000000000..396a4d26d --- /dev/null +++ b/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2 diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch new file mode 100644 index 000000000..0ef65b1d8 --- /dev/null +++ b/sci-chemistry/pymol/files/nosplash-gentoo.patch @@ -0,0 +1,9 @@ +--- modules/pymol/invocation.py.orig 2008-06-26 20:55:25.000000000 +0200 ++++ modules/pymol/invocation.py 2008-06-26 20:56:06.000000000 +0200 +@@ -373,6 +373,4 @@ + if loaded_something and (options.after_load_script!=""): + options.deferred.append(options.after_load_script) + options.deferred.extend(final_actions) +- if options.show_splash and not options.no_gui: +- options.deferred.insert(0,"_do__ cmd.splash(1)") + diff --git a/sci-chemistry/pymol/files/pymol-1.2_beta2-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2_beta2-data-path.patch new file mode 100644 index 000000000..329b68292 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-1.2_beta2-data-path.patch @@ -0,0 +1,51 @@ +diff -urN pymol-9999.orig/modules/pymol/commanding.py pymol-9999/modules/pymol/commanding.py +--- pymol-9999.orig/modules/pymol/commanding.py 2008-01-11 13:23:32.000000000 +0100 ++++ pymol-9999/modules/pymol/commanding.py 2008-01-11 13:22:57.000000000 +0100 +@@ -198,11 +198,11 @@ + _self.unlock(0,_self) + r = DEFAULT_SUCCESS + if show_splash==1: # generic / open-source +- png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png") ++ png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png") + elif show_splash==2: # evaluation builds +- png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png") ++ png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png") + else: # incentive builds +- png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png") ++ png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png") + if os.path.exists(png_path): + _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path) + else: +#diff -urN pymol-9999.orig/modules/pymol/fitting.py pymol-9999/modules/pymol/fitting.py +#--- pymol-9999.orig/modules/pymol/fitting.py 2008-01-11 13:23:32.000000000 +0100 +#+++ pymol-9999/modules/pymol/fitting.py 2008-01-11 13:23:00.000000000 +0100 +#@@ -68,7 +68,7 @@ +# if string.lower(matrix)=='none': +# matrix='' +# if len(matrix): +#- mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix) +#+ mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix) +# else: +# mfile = '' +# # delete existing alignment object (if asked to reset it) +#@@ -135,7 +135,7 @@ +# if string.lower(matrix)=='none': +# matrix='' +# if len(matrix): +#- mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix) +#+ mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix) +# else: +# mfile = '' +# if object==None: object='' +diff -urN pymol-9999.orig/modules/pymol/importing.py pymol-9999/modules/pymol/importing.py +--- pymol-9999.orig/modules/pymol/importing.py 2008-01-11 13:23:32.000000000 +0100 ++++ pymol-9999/modules/pymol/importing.py 2008-01-11 13:23:02.000000000 +0100 +@@ -171,7 +171,7 @@ + r = DEFAULT_ERROR + + +- tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png", ++ tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png", + 'pymol' : 'pymol', + 'rgb' : 'rgb' } + diff --git a/sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch new file mode 100644 index 000000000..7f4a24f48 --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch @@ -0,0 +1,11 @@ +diff -uarN pymol-9999.orig/setup.py pymol-9999/setup.py +--- pymol-9999.orig/setup.py 2008-06-18 11:47:58.000000000 +0200 ++++ pymol-9999/setup.py 2008-06-18 11:48:52.000000000 +0200 +@@ -143,6 +143,7 @@ + def_macros=[("_PYMOL_MODULE",None), + ("_PYMOL_INLINE",None), + ("_PYMOL_FREETYPE",None), ++ ("_PYMOL_OPENGL_SHADERS",None), + # Numeric Python support + # ("_PYMOL_NUMPY",None), + # VMD plugin support diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml new file mode 100644 index 000000000..1b9609b2a --- /dev/null +++ b/sci-chemistry/pymol/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<pkgmetadata> +<herd>sci-chemistry</herd> +<maintainer> + <email>jlec@j-schmitz.net</email> +</maintainer> +<use> + <flag name='apbs'>Pymol supprt for sci-chemistry/apbs</flag> + <flag name='shaders'>Enable shaders support for Pymol</flag> +</use> +</pkgmetadata> diff --git a/sci-chemistry/pymol/pymol-1.2_beta2.ebuild b/sci-chemistry/pymol/pymol-1.2_beta2.ebuild new file mode 100644 index 000000000..18ca53e26 --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.2_beta2.ebuild @@ -0,0 +1,112 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +NEED_PYTHON=2.4 +PYTHON_MODNAME="chempy pmg_tk pymol" +APBS_PATCH="070604-r3550" + +inherit distutils subversion + +ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol@3580" + +DESCRIPTION="A Python-extensible molecular graphics system." +HOMEPAGE="http://pymol.sourceforge.net/" + +LICENSE="PSF-2.2" +IUSE="apbs shaders" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND="dev-python/pmw + dev-python/numpy + dev-lang/tk + media-libs/libpng + sys-libs/zlib + virtual/glut + apbs? ( dev-libs/maloc + sci-chemistry/apbs + sci-chemistry/pdb2pqr + )" + +RDEPEND="${DEPEND}" + +pkg_setup(){ + python_tkinter_exists + python_version +} + +src_unpack() { + subversion_src_unpack + + epatch "${FILESDIR}"/${PF}-data-path.patch || die + + # Turn off splash screen. Please do make a project contribution + # if you are able though. + [[ -z "$WANT_NOSPLASH" ]] && epatch "${FILESDIR}"/nosplash-gentoo.patch ||die + + # Respect CFLAGS + sed -i \ + -e "s:\(ext_comp_args=\).*:\1[]:g" \ + "${S}"/setup.py + + if use shaders; then + epatch "${FILESDIR}"/${PF}-shaders.patch || die + fi + + if use apbs; then + epatch "${FILESDIR}"/apbs-${APBS_PATCH}.patch.bz2 + sed "s:LIBANDPYTHON:$(get_libdir)/python${PYVER}:g" \ + -i modules/pmg_tk/startup/apbs_tools.py || die + fi +} + +src_install() { + distutils_src_install + cd "${S}" + + #The following three lines probably do not do their jobs and should be + #changed + PYTHONPATH="${D}$(python_get_sitedir)" ${python} setup2.py + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF + PYMOL_PATH=$(python_get_sitedir)/pymol + PYMOL_DATA="/usr/share/pymol/data" + PYMOL_SCRIPTS="/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol || die "Failed to install env.d file." + + # Make our own wrapper + cat >> "${T}"/pymol <<- EOF + #!/bin/sh + ${python} -O \${PYMOL_PATH}/__init__.py \$* + EOF + + if ! use apbs; then + rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py + fi + + exeinto /usr/bin + doexe "${T}"/pymol || die "Failed to install wrapper." + dodoc DEVELOPERS || die "Failed to install docs." + + mv examples "${D}"/usr/share/doc/${PF}/ || die "Failed moving docs." + + dodir /usr/share/pymol + mv test "${D}"/usr/share/pymol/ || die "Failed moving test files." + mv data "${D}"/usr/share/pymol/ || die "Failed moving data files." + mv scripts "${D}"/usr/share/pymol/ || die "Failed moving scripts." +} + +pkg_postinst(){ + distutils_pkg_postinst + + # The apbs ebuild was just corrected and not bumped #213616 + if use apbs; then + [ -e /usr/share/apbs-0.5* ] && \ + ewarn "You need to reemerge sci-chemistry/apbs!" + fi +} |