sci-chemistry/pymol: Version Bump

Package-Manager: portage-2.2.14_rc1/cvs/Linux x86_64
RepoMan-Options: --force
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 142 insertions, 16 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index ca274c591808..eadece7d5c3c 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.118 2014/09/15 08:20:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.119 2014/10/17 06:54:03 jlec Exp $
+
+*pymol-1.7.3.1 (17 Oct 2014)
+
+  17 Oct 2014; Justin Lecher <jlec@gentoo.org> +pymol-1.7.3.1.ebuild,
+  +files/pymol-1.7.3.1-maeffplugin.cpp.patch:
+  Version Bump
 
 *pymol-1.7.3.0 (15 Sep 2014)
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 22a6eb742dd6..e37ad10a45d2 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -13,6 +13,7 @@ AUX pymol-1.6.0.0-bg_rgb.patch 9264 SHA256 12fa3a5a83f77ecbff3f5958e40b7c8f0b5f9
 AUX pymol-1.6.0.0-labels.patch 17150 SHA256 b1385696a5f781e51adcd61774362f76c4f8443e168e5232b1b577f06a6821b0 SHA512 190353d690656685da0e7912cb74426c161659a177d3cc8b1e9bdeb02513756b9d36b32c0ee351905b5dd31e7a7ea6dfe7ca685533b0ef7651bd51190e2060bc WHIRLPOOL e79fd2debc7b3bb80f0d83fe49c9b90de24d5e3f0e373e2b91452965059874c2d007b3e2731028a2ab4005ddef3c75404ee7f4b6bde6216e930eb5ff2fd1fbf3
 AUX pymol-1.6.0.0-stereo.patch 1839 SHA256 accbb7e142d2f4709605d156c169146836d78d29514af5eeffc5c6121d5e056c SHA512 bd32c26dce36b2a44613470f20ef8916111acc20f6525185b9c4b33c25b03efea4ee00f35ab391f8c12874d3bc9e1be665b5706864e660c85b2432b97a9c80b8 WHIRLPOOL 16a30e3830c17420bc53dc86191dbf6b366be94ef5484798e945600b3fc97f83df742d7cdbcbcfa574cb4a4e7c9ff5501f7301d1f33c3a11682f99aadd52dd82
 AUX pymol-1.7.0.4-fix-broken-label-scaling-on-Linux.patch 3073 SHA256 a5bbfc21e3d47e70e597d0b6509251b0720480beb118dff1f85113fc7e59c643 SHA512 96ade2f3d47966fb2322c32d5ab055cc927a065b5ac84bc1de20d798ea6b358a153b6b8c8f85e66f3e3ac04790df416294eb4bbde1b8aad7737c83ecf82158fe WHIRLPOOL bae9e9f38ff0e5bb3fb94d9e4c1d1082d80b40a0ab14e6098733c8a18c5c5289a9dc63725d06299eac917b3f2c6b6b4df68e36ef6fb959f30aa2f2cb283fa79d
+AUX pymol-1.7.3.1-maeffplugin.cpp.patch 407 SHA256 852a4e0c104caf4ea2c297dcc25a522831504b9a185a10c9de03c9a0c727986a SHA512 7c9557f3a1ef69469c2fa2569959130a9a73ad0bbeea4a48ed996dc09de65ae09748b6834b7d3b528aaf393bae6f3706f744ac3feacf67f5cb5f58397c47ed03 WHIRLPOOL 7a24cbc80e3565dd3fa305443940c9ced9a82ea5182152824d4a32b51d3503f5b03ef635ddf8601c0dfb3e551d8b2e6295ad2c7cdd3594553f3da028700c1f5a
 DIST pymol-1.5.0.3.tar.xz 7412080 SHA256 b304c2839bc944bd2619403474d36cb846b372ba281c8f05931d3f155a0aec7a SHA512 a3f1dd3089fa4158840f2cb8c3848ef70284d1f859429cfab6ac9b00f649d7274a3ac7697a7fb4996d7643068a916f9ad7b1952c5ff27003cedcc7c89e795485 WHIRLPOOL 82788bf6fce52d76ff00d1d7243e8f3962027b4512addaf0fc2f881aaf5f0da6582cb3b3b56a178ed36572947273a999be3d67ba49845eb887da6cf242c5b5f3
 DIST pymol-1.6.0_rc1.tar.xz 6592108 SHA256 7353c9bdfa272b516bd43efaea7df16a6e1632b013ac6091eb5ec34b1f8676bc SHA512 971f03b41db1ed6b1095e91cea49ca5ffb819bf9b97e34dab215112462da02d7bb1b608c462d07556998dfd49631663f3d2cbf27368980f3d69bf134002224a8 WHIRLPOOL 2368fb3a20cbb2d490b1f4b370f770aa7b89921c5827414715ec7616ad66e991bb7f378ed7c379db78b9391dea0bcae9d56362bd705978d667858af8ef46ebb4
 DIST pymol-1.7.0.0.png.xz 5392 SHA256 4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105 WHIRLPOOL 395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b
@@ -23,6 +24,7 @@ DIST pymol-1.7.1.3.tar.xz 6566460 SHA256 837b5df679887a2b7bd749972da2200f61508da
 DIST pymol-1.7.2.0.tar.xz 6571040 SHA256 3a4ac5b5e865bc539f122636317b69c3ae4b321b8dcf658bfc24b95f74c3c772 SHA512 a140dfdb8d84d4e4a02be2b173e70447d11e2855caa4bcecf156f069973a9fc4e589e37b39470267191ef1e772bb63f0ae2c74632e3a3742d5ca744e86dc8dc5 WHIRLPOOL 204e3dc9d8e0e2f9c0c932276e9f2dbe00750eac4af6d6e09d94f2ad1dceb31fd702582af259f86f1134e734c69fd268b08cbba12ec87e016266f1f295f31552
 DIST pymol-1.7.2.1.tar.xz 6570132 SHA256 b8538b3c4de20a630c6282a3b0a0204bf259dbbf952a3246366ffee8cee57b8c SHA512 db176351a624fb270e5aa8b5fc2d96ec93098ce0fa5c424df7eb24b58320766dc3c4563e4848adc0d723350a881689b19a92f5f8f471d763dc339eadfc22ee32 WHIRLPOOL c98a4414579e54358687134e1284b12c42b405b68366d8406d329788bbeed936bd906091f47c4fb234905cdf1b6a0deeac577dd7639a4e982217e0ca90c19e8e
 DIST pymol-1.7.3.0.tar.xz 6505060 SHA256 0a4f89a5cfd19859804794842bc0eb51554d86fb75ee650007e87f0af8b45464 SHA512 03f53c77321fe2837b43f9cb2e5962f04f5cb430c63f49a2a84e6fe010371ffae1c3542d3546b9f2eff07f9aa7b4fdee6c70124096f4071017a77cf48bf60e5c WHIRLPOOL 7a39d9cb89197c141ab8d4808e9d7c3f43a3de5147a75b3a15cb1a4d3cfa2027e59571108b79563150df81c75608cbd92d82d319c455f203c4af76413477a524
+DIST pymol-1.7.3.1.tar.xz 6516580 SHA256 688a4fc07bb88e80bd757ef9c6f9fadd3b2e09ef76cf4032e1119acb06d14d7e SHA512 2cc710ab772189e6eba38a3e44552f43fc53c3014379536139702bd24923ae85630ad2658ac4e4690820145f4cef4146d28025701d98e4c1540cc523c2553fd1 WHIRLPOOL f2d38ec9497d5a10982c00f07176acbeca0513057ff592dcd68ea27663d4dab386f423fad9686a624b420e11e7861f1d5db3a8ab8b5f978e6044d616c2d81392
 DIST pymol-icons.tar.xz 38100 SHA256 03500f28256f67abfbb7d08b798b11aaa208f0ae1473ef2a7205b3c012ddb06a SHA512 5af51014d4fcbc85ef1fecd7667224709c9305b9b72bfdfd89ece2b4420fa8a81bf8c85fcc5903e2a670f44403f12764808f6a16ef42f111bbd0e7ed8e412d54 WHIRLPOOL 6104d378928c56b39f8cbe29184629b73f87da09e81e41ddc08b9b291876f1a30ccaf9ec257f47798c6d03253816f80c14567073c419fa48dd1520fa3fa58ecd
 DIST pymol-v1.6.0.0.tar.bz2 8695114 SHA256 a37eb1a1bd882da14ac9c03617f62f6a49eea5a6dacd0d7202fb3b7cba84e62b SHA512 afe4a9e9c9501b3e636ca97eac3e4204da2cbafd7dc85ad6fd43227c68b448de435f190eea9c75b3403f11786bc512b6366bdf092c591432440032ddc018b0b2 WHIRLPOOL 30302badde84ad63e4a402a54046da63812051879bdb707782589b4bfaa09a8f590e58b5bdd89d0deefd9d2127f17406dd862f36f6a0e33e3e410f8a9d47a937
 DIST pymol-v1.7.0.0.tar.bz2 8775358 SHA256 f4c1b6f0dfc9b1b8419d92e39d436d4ea3462bdfcd17df1025877379bf647a4d SHA512 f5a1dc255aefe14f1cbb716687af959a53757bb77d9858650ea8b021f34bf9f2a48ac04fbfe40f67fe0219def5cfea1e30d78f50fd68930c5bbd4983ea58d8ac WHIRLPOOL c0a4b7f93a4140af44d5b3aa0824426482e65f5dc7c6a598435388ac3dc912ad220dc38a619165b921cedb131069d02a41bbcda8ce218dc3f8c052a3dc7a022f
@@ -41,24 +43,25 @@ EBUILD pymol-1.7.1.3.ebuild 2536 SHA256 f7f3f87e6b313bdfb17ccbcd129fcb860c642789
 EBUILD pymol-1.7.2.0.ebuild 2590 SHA256 e2f0fda771211143ea680aaeb70c30b61ef1af4b61d794847b96cb12fab06209 SHA512 d0582936d481aebd8892778e3419fc32c9546f4b26012ab05d54b635911f3059cf65200c34870171dcc02105054b808513f395ecab3dd74664f01d59665e5d37 WHIRLPOOL 3000d82af7189be8ec5ad3e95a5912e8d9df2dda45d1ba07eadf09ea0c7b6c4b127a6e83df5f350692beb50eb647bd11a2d70301314efa76daafbbd19ef641d0
 EBUILD pymol-1.7.2.1.ebuild 2590 SHA256 24ced99d2801103f09868ef9df1c65b7e28a840ea01f00fe353ad99f28123f80 SHA512 0950f1386f87e95d485f804fdeba72b6d34c62f922501ee3252610d227aad873d6b8abd0d0cab5cb7464c70bcd326dff1d3a37285142541cfcaf07c4126abe97 WHIRLPOOL 159092231777d7c17dc64c050e8ffa85be704d56f44a7322d86733499488ae62afd839cc06e914fc95b3d15ba8683af0d2632051b9fb621c486ab5da3186f47f
 EBUILD pymol-1.7.3.0.ebuild 2590 SHA256 41a7158fd607a267f3f670e96482a5428b8da4160b3e45fe30e21d75ad2583e5 SHA512 568e0f1384e6d6406f1e5ca7bf3b4eaac8e61d03151fcd055a2b56201b4e6601ee59df4f640858379b26362e1ec2dea9bdbcdddea8af288898d7b9c26d0028d7 WHIRLPOOL bc14a06ee2280f5189366ff7988133f41b0336b835fc281e294de4cbe16f07a4e9beb161fdc8def2f125f5a3e20a669ddd9768d5a85b97db41942ad1689d9377
-MISC ChangeLog 7101 SHA256 1d85b4db0a20ab22ed5d65788b5d60d7212ae65b66c185ed0790ce5ca32c0377 SHA512 9586e3e6fbffc44ab4ab0829f2e59a4a400d4adedcd070cb5bb12a245d5105ecebb9d7c9233de602ad28a632a3a7c113ea8f52636265bb1e827a6785488a275b WHIRLPOOL 7c00dbbc449db42b96d10fe3ca04886ef00a43a6ecfdb2f6203a6f26bbfb86c1d2cc90603baf72ed7b8a69a5ca871a38f0a27bfc23b7c042e6be25ea6e7db8f8
+EBUILD pymol-1.7.3.1.ebuild 2773 SHA256 d53a6204866d76c3a6eed1cf17243463fe77c31bf910d252faf58d0d2c104b90 SHA512 ec233aea7f21645ce08be3ee85eaa3bd9e0da03c5c83bdfc45df7192eb855225f599aa874436d737f354dfade4fcc6feabf52281f7d16a7321c4950b27c2bc25 WHIRLPOOL f4b5aab663650f6a009dad439972f83320e80c1f9199c4a5c094bcddbce6a9ba408808479a0f02d700b46e294a2c52768cf561a30e34c7616b54a6b477dd14c6
+MISC ChangeLog 7263 SHA256 a50ae8886bcf40ca9d6088b7015fd4a299c2e38909ef6e5eb3e5286ea3bc0cf1 SHA512 e82a15d332119c0e199571dcb4368bc7a1a185f6d3cf8623429136dd50037a0cbb0a913b28dd81359c7494773b624ee0fa05dc98bb7c4e4d8ebda300745bff2e WHIRLPOOL 17ead09b3450269919f1da805a6147f0b0c895406d15340d4cb0c327c975ad78b98ec73f7cbed6a1c17e7a6458c56ae0d913b7d3db5bc6c7dc56e1bd80277c63
 MISC metadata.xml 491 SHA256 7370aee92bf4088e8dc054dc8812cc30e98be7995570afae89dfacc49eec711b SHA512 319f8924b56ecb64e35892fa10ab94adbca68dc3d9dffc760d54e44fe19feb0e3bf87110aa7e94f25a353792e84610353f2f8684b6032426cd4eaa70fa5a9fdc WHIRLPOOL 93baebbb622f81fd48b7396bb3f98c8ce0d97db41c6a09e28da0cd923261961100cd715ada8f4ff70f79638cca88b0f1ab0b0ff78f9656323efcb871ea0958cf
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diff --git a/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch b/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch
new file mode 100644
index 000000000000..cd4650bbf4e0
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch
@@ -0,0 +1,11 @@
+--- contrib/uiuc/plugins/molfile_plugin/src/maeffplugin_orig.cpp	2014-02-07 19:50:50.132261610 -0800
++++ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp	2014-02-07 19:52:12.527797099 -0800
+@@ -1983,7 +1983,7 @@
+       }
+     }
+     catch (std::exception &e) {
+-      fprintf(stderr, e.what());
++      fprintf(stderr, "%s", e.what());
+       return MOLFILE_ERROR;
+     }
+     return MOLFILE_SUCCESS;
diff --git a/sci-chemistry/pymol/pymol-1.7.3.1.ebuild b/sci-chemistry/pymol/pymol-1.7.3.1.ebuild
new file mode 100644
index 000000000000..37b77d5f35be
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.7.3.1.ebuild
@@ -0,0 +1,106 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.7.3.1.ebuild,v 1.1 2014/10/17 06:54:03 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 fdo-mime versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/"
+SRC_URI="
+	http://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
+	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
+"
+#	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="apbs web"
+
+DEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pmw[${PYTHON_USEDEP}]
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	media-libs/freetype:2
+	media-libs/glew
+	media-libs/libpng
+	media-video/mpeg-tools
+	sys-libs/zlib
+	media-libs/freeglut
+	apbs? (
+		sci-chemistry/apbs
+		sci-chemistry/pdb2pqr
+		sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+	)
+	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${P}/${PN}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-maeffplugin.cpp.patch
+	)
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
+		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+		-e "/import/s:argparse:argparseX:g" \
+		-i setup.py || die
+
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
+	sed \
+		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e '/ext_comp_args/s:\[.*\]:[]:g' \
+		-i setup.py || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_install() {
+	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+
+	python_export python2_7 EPYTHON
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH="$(python_get_sitedir)/${PN}"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol
+
+	newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
+	make_desktop_entry ${PN} PyMol ${PN} \
+		"Graphics;Education;Science;Chemistry;" \
+		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
+
+	if ! use web; then
+		rm -rf "${D}/$(python_get_sitedir)/web" || die
+	fi
+
+	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}