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author | Donnie Berkholz <dberkholz@gentoo.org> | 2009-07-11 17:51:53 -0700 |
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committer | Donnie Berkholz <dberkholz@gentoo.org> | 2009-07-11 17:51:53 -0700 |
commit | 30f280ac7197f046d652fec61f36fcc032d92ae9 (patch) | |
tree | 40b9409b758568fca63eb0b2157bb419e4b8a823 /sci-chemistry | |
parent | biskit: a few fixups (diff) | |
download | dberkholz-30f280ac7197f046d652fec61f36fcc032d92ae9.tar.gz dberkholz-30f280ac7197f046d652fec61f36fcc032d92ae9.tar.bz2 dberkholz-30f280ac7197f046d652fec61f36fcc032d92ae9.zip |
pymol: live version is in the science overlay now
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/pymol/Manifest | 7 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/apbs-070604.patch.bz2 | bin | 20034 -> 0 bytes | |||
-rw-r--r-- | sci-chemistry/pymol/files/nosplash-gentoo.patch | 9 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch | 51 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/pymol-1.1-r1-shaders.patch | 11 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/pymol-9999-data-path.patch | 30 | ||||
-rw-r--r-- | sci-chemistry/pymol/files/pymol-9999-shaders.patch | 11 | ||||
-rw-r--r-- | sci-chemistry/pymol/pymol-9999.ebuild | 116 |
8 files changed, 0 insertions, 235 deletions
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest deleted file mode 100644 index 9d6b93e..0000000 --- a/sci-chemistry/pymol/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX apbs-070604.patch.bz2 20034 RMD160 0244e60a99143fbfd43e849910da798d14259cf5 SHA1 0b4c86a7cd34282efa580866c3f80809a27e3348 SHA256 8d694a2fe726fc1176228beec42bbde9df1bced0148cbef2b2b853995cf0376f -AUX nosplash-gentoo.patch 467 RMD160 a6be474aab95e8c8ffd37f509fe3d40cf4db23f7 SHA1 14862bab327fea0cdc8198070f01827d6f832899 SHA256 c4b5384485242165aa517fe2caf83241201c2354d5c964554f6d82c51ba7fba3 -AUX pymol-1.1-r1-data-path.patch 2584 RMD160 c5fdd7884241a493578be5a2b658ac0cd0bff000 SHA1 1e4cd368ad08b87627ef465fad4ca96dcfbef00b SHA256 39e06459105969e0156bfe71f61bdccd3da4c8d7f2ba6e783aa34e63dc62b0a7 -AUX pymol-1.1-r1-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0 -AUX pymol-9999-data-path.patch 1585 RMD160 e8d505a25869f0abd7b1ef77e1176c5fe7b2a312 SHA1 89464b3780fc48bd239c0e0662dbd1d61665984f SHA256 c89862e631b7bb0e05426ad0550be51501380d4522820a7600708d5290e5dfa8 -AUX pymol-9999-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0 -EBUILD pymol-9999.ebuild 3080 RMD160 d3f1e4b79da10cc654ded67145bbde5b485f5b26 SHA1 94135388aadc09523435bc104dca0c16544425e7 SHA256 8c8b5b36a184624e148008ba7e931202e133194b08e6e22cc3b7e8e6aebc6763 diff --git a/sci-chemistry/pymol/files/apbs-070604.patch.bz2 b/sci-chemistry/pymol/files/apbs-070604.patch.bz2 Binary files differdeleted file mode 100644 index b5095ec..0000000 --- a/sci-chemistry/pymol/files/apbs-070604.patch.bz2 +++ /dev/null diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch deleted file mode 100644 index 0ef65b1..0000000 --- a/sci-chemistry/pymol/files/nosplash-gentoo.patch +++ /dev/null @@ -1,9 +0,0 @@ ---- 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-1.1-r1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch deleted file mode 100644 index 329b682..0000000 --- a/sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch +++ /dev/null @@ -1,51 +0,0 @@ -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-1.1-r1-shaders.patch b/sci-chemistry/pymol/files/pymol-1.1-r1-shaders.patch deleted file mode 100644 index 7f4a24f..0000000 --- a/sci-chemistry/pymol/files/pymol-1.1-r1-shaders.patch +++ /dev/null @@ -1,11 +0,0 @@ -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/files/pymol-9999-data-path.patch b/sci-chemistry/pymol/files/pymol-9999-data-path.patch deleted file mode 100644 index 86c3fe1..0000000 --- a/sci-chemistry/pymol/files/pymol-9999-data-path.patch +++ /dev/null @@ -1,30 +0,0 @@ -diff -arNu -uarN pymol/modules/pymol/commanding.py pymol.new/modules/pymol/commanding.py ---- pymol/modules/pymol/commanding.py 2009-03-31 12:43:14.585834066 +0200 -+++ pymol.new/modules/pymol/commanding.py 2009-03-31 12:44:26.436354330 +0200 -@@ -219,11 +219,11 @@ - _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 -arNu -uarN pymol/modules/pymol/importing.py pymol.new/modules/pymol/importing.py ---- pymol/modules/pymol/importing.py 2009-03-31 12:43:14.546250540 +0200 -+++ pymol.new/modules/pymol/importing.py 2009-03-31 12:44:48.876657949 +0200 -@@ -191,7 +191,7 @@ - ''' - 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-9999-shaders.patch b/sci-chemistry/pymol/files/pymol-9999-shaders.patch deleted file mode 100644 index 7f4a24f..0000000 --- a/sci-chemistry/pymol/files/pymol-9999-shaders.patch +++ /dev/null @@ -1,11 +0,0 @@ -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/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild deleted file mode 100644 index fcefe73..0000000 --- a/sci-chemistry/pymol/pymol-9999.ebuild +++ /dev/null @@ -1,116 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -NEED_PYTHON=2.4 -PYTHON_MODNAME="chempy pmg_tk pymol" - -inherit distutils eutils multilib subversion - -ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol" - -DESCRIPTION="A Python-extensible molecular graphics system." -HOMEPAGE="http://pymol.sourceforge.net/" - -LICENSE="PSF-2.2" -IUSE="apbs shaders" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-python/pmw - dev-python/numeric - dev-lang/tk - media-libs/libpng - sys-libs/zlib - virtual/glut - apbs? ( dev-libs/maloc - sci-chemistry/apbs - sci-chemistry/pdb2pqr - )" -DEPEND="${RDEPEND}" - -pkg_setup() { - if ! built_with_use dev-lang/python tk; then - eerror "Please reemerge dev-lang/python with 'tk' support or pymol will" - eerror "not work. In order to fix this, execute the following:" - eerror "echo \"dev-lang/python tk\" >> /etc/portage/package.use" - eerror "and reemerge dev-lang/python before emerging pymol." - die "requires dev-lang/python with use-flag 'tk'!!" - fi -} - -src_unpack() { - subversion_src_unpack - - python_version - - epatch "${FILESDIR}"/${PF}-data-path.patch - - # Turn off splash screen. Please do make a project contribution - # if you are able though. - [[ -z "$WANT_SPLASH" ]] && epatch "${FILESDIR}"/nosplash-gentoo.patch - - # Respect CFLAGS - sed -i \ - -e "s:\(ext_comp_args=\).*:\1[]:g" \ - "${S}"/setup.py - - if use shaders; then - epatch "${FILESDIR}"/${PF}-shaders.patch - fi - - if use apbs; then -# epatch "${FILESDIR}"/apbs-070604.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}/usr/$(get_libdir)/python${PYVER}/site-packages" ${python} setup2.py - - # These environment variables should not go in the wrapper script, or else - # it will be impossible to use the PyMOL libraries from Python. - cat >> "${T}"/20pymol <<- EOF - PYMOL_PATH=/usr/$(get_libdir)/python${PYVER}/site-packages/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}"/usr/$(get_libdir)/python${PYVER}/site-packages/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 - - if use apbs; then - [[ -e /usr/share/apbs-0.5* ]] && \ - ewarn "You need to reemerge sci-chemistry/apbs!" - fi -} |