Add missing wrong usage of PYMOL_PATH, #409971

Package-Manager: portage-2.2.0_alpha96/cvs/Linux x86_64

4 files changed, 145 insertions, 14 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 3aa6322d350e..b32f325782c0 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pymol
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.86 2012/03/10 09:31:31 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.87 2012/03/28 12:34:56 jlec Exp $
+
+*pymol-1.5.0.3-r1 (28 Mar 2012)
+
+  28 Mar 2012; Justin Lecher <jlec@gentoo.org>
+  files/pymol-1.5.0.1-data-path.patch, +pymol-1.5.0.3-r1.ebuild:
+  Add missing wrong usage of PYMOL_PATH, #409971
 
 *pymol-1.5.0.3 (10 Mar 2012)
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index b55c37e028e8..e943bdb14e82 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -13,7 +13,7 @@ AUX pymol-1.4-vmd.patch 1414 RMD160 c7de92c73a0f91e6f95a7208b912cb6105f6d972 SHA
 AUX pymol-1.4.1-data-path.patch 3898 RMD160 842548be0710bb4f80791fdb98654b36cb777e84 SHA1 f3dedae4a97ee4916ca7ce4733506d6b8221e79f SHA256 911f69cb428f91a284102580b73f771648f6a1a059a53c1bcc31c51ab492b010
 AUX pymol-1.4.1-shaders.patch 2507 RMD160 2dea0805fcc8a993d7f5fa8668257be860c7d5e8 SHA1 4548f93fbe92a511dc0d2425c86402a776567cb4 SHA256 b0cbb5bc81bb8f85bef8cbb6cd76f91b02b076ef5798075e152626becf3b5ae5
 AUX pymol-1.4.1-web.patch 550 RMD160 fc15b0e428b9376a9d7f2e87d06035555ceab2fe SHA1 06db70ef92ce981715cde9ac1578291b653341d9 SHA256 2545245c4c18c96faf76e0ba4a754402cb2081e56f945da1732b63fddda4fb2b
-AUX pymol-1.5.0.1-data-path.patch 6577 RMD160 42fa714d39bd36398505db2430e29330a72c2454 SHA1 a126b73c983ffa1ac16fba0a9146f6349fef9e53 SHA256 5a0f5f4fb0308b750cfbca5007683363102a6675be9ae93466dcb53177375c61
+AUX pymol-1.5.0.1-data-path.patch 6765 RMD160 a548821472f105424422c97047413877b89e0fa2 SHA1 466c1723444af5e93765d0b6caab520e54f35c15 SHA256 ad3ba9a519cc2a97c37868ce4d27a9868710be0dd32687327abd920c57db8661
 AUX pymol-1.5.0.1-flags.patch 521 RMD160 0a8788c55de42a24f97c96594f7065fcd26e1469 SHA1 9405af5a709bc626524bb5730f6c08e2f5c4aa1b SHA256 7a92d5ea975dcef50ea9614b87c56d7b4f1b976210608800413a80de98c69a3f
 AUX pymol-1.5.0.1-prefix.patch 1746 RMD160 2bab80e0881a7180887a0259121c46fd09b73b67 SHA1 ae54823d5eb48e3dcfc57d5635b25df9728703ef SHA256 95ccc4b626ff1a6bd21da6825e647740bcda8c003ca4cf10a1bcd3940b562247
 AUX pymol-1.5.0.1-setup.py.patch 893 RMD160 3060484fe43632743eec4503d8b73cff28d9b3a4 SHA1 01353b2578867a413b31a6b063f5ca561a218ddb SHA256 3a03cb19878a772caff5c6931ff7bb1fdcd022147ec0e8a23593d4ae61cf1593
@@ -31,13 +31,14 @@ EBUILD pymol-1.3.1_pre3925-r1.ebuild 2703 RMD160 73f891e9c3d8f56b154c38c8b18261d
 EBUILD pymol-1.4.1.ebuild 2807 RMD160 f3d2f58327812613dc80aeb1b1287cc637fc6aa3 SHA1 9b0ca9e0abbcb6b7459ae28ea22b10a943a10528 SHA256 c4713c5d289c6a00093a2c89afb918c5411de8dee91082fe22fc708b38463067
 EBUILD pymol-1.5.0.1.ebuild 2800 RMD160 253f9636af0a4611c36ea5bc0871d914af6f270a SHA1 f915cd2add9592fd2a597b0fb552f5b70f596ba6 SHA256 df5d9ba7bf2c044ae4fff1d50948f1be519b96feee97b2f6b4416fc4a54a55f3
 EBUILD pymol-1.5.0.2.ebuild 2814 RMD160 7d177d6ece8a5ffb095e03ba0c4b5e4136abf6a0 SHA1 793b74bb2d08b242b785b1047321e7eb6c44432c SHA256 e30f4c555c3e4278d97b4e7638ffb7dbfecb9f16e939e7168023e82fd7921b77
+EBUILD pymol-1.5.0.3-r1.ebuild 2799 RMD160 a756d9347d67a386d2babb4847a74876ce19ca95 SHA1 4856a57c77a5da1bcb1315a0d72566957bf7abbf SHA256 872920f8fb563b20d0af8782f3303421f697bd4bc6fc779633ee70d3e761713b
 EBUILD pymol-1.5.0.3.ebuild 2796 RMD160 b6dfb9807830d8e9c0030e7bb350802e54a808b4 SHA1 19992731ba6d8c52fb3bf77c1b3ff13e717c22b6 SHA256 41d6dd2821a207bd7a3bd4f79b5c70489690dff01b07db810437969d23a0598f
-MISC ChangeLog 2081 RMD160 d70a82eebeb784bf5017c38de1845183d8adab3d SHA1 18a518d469d553310486efde2ec7ac73ec58fee9 SHA256 53a48b1d113cff204c52892eb871c1e1cfa9c7b773ba7b3f13f34b10b0b6a0a5
+MISC ChangeLog 2276 RMD160 c179ea40f1e91cc6dd009a977ae740f67c17144c SHA1 5bce3cca406b4598ac843a3633ea18f3b2ce1c90 SHA256 02715ba4345ec3cb1a621ca2805263ac873c62b3f97614f2557d8575281e35da
 MISC metadata.xml 569 RMD160 edfb6f78a19d49eb7f18fb0d8336a0c5f97c3f34 SHA1 c75951bdda3dcb4564d23b873e30773bc9ed7fc7 SHA256 6f2b2746c7b2182262554076f11159b11d671695c40509bf7014c7546d719ff2
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0.19 (GNU/Linux)
 
-iEYEAREKAAYFAk9bH3gACgkQgAnW8HDreRbvqQCgiZoYP7X/7tUxF/HgxQ86RqpK
-8XAAn1dGCPlqxORs8/pArURKAdF3s5+8
-=soL5
+iEYEAREKAAYFAk9zBXUACgkQgAnW8HDreRaI2gCgmlzfVdTxdrTgYVcXJ/IOfB4f
+YQQAoJZjdgTBLlqb5zv0gH2b5HiMH45r
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diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch
index e865bfd04174..a2b09bb9eee3 100644
--- a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch
+++ b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch
@@ -4,8 +4,8 @@
  modules/chempy/tinker/__init__.py   |    2 +-
  modules/pymol/commanding.py         |    6 +++---
  modules/pymol/importing.py          |    2 +-
- modules/pymol/wizard/mutagenesis.py |    4 ++--
- 7 files changed, 17 insertions(+), 17 deletions(-)
+ modules/pymol/wizard/mutagenesis.py |    8 ++++----
+ 7 files changed, 19 insertions(+), 19 deletions(-)
 
 diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
 index cc760ae..364277f 100644
@@ -74,7 +74,7 @@ index 23dbe45..795a223 100644
      path = os.environ['PYMOL_DATA'] + '/chempy/'
  elif os.environ.has_key('PYMOL_PATH'):
 -    path = os.environ['PYMOL_PATH'] + '/data/chempy/'   
-+    path = os.environ['PYMOL_PATH'] + '/chempy/'   
++    path = os.environ['PYMOL_PATH'] + '/chempy/'
  elif os.environ.has_key('FREEMOL_MODULES'):
      path = os.environ['FREEMOL_MODULES'] + '/chempy/'
  else:
@@ -127,20 +127,24 @@ diff --git a/modules/pymol/wizard/mutagenesis.py b/modules/pymol/wizard/mutagene
 index 8a5250d..6c1b26c 100644
 --- a/modules/pymol/wizard/mutagenesis.py
 +++ b/modules/pymol/wizard/mutagenesis.py
-@@ -53,7 +53,7 @@ class Mutagenesis(Wizard):
+@@ -52,8 +52,8 @@ class Mutagenesis(Wizard):
+         
          self.dep = default_dep
  
-         self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
+-        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
 -                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
++        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
 +                                           "/chempy/sidechains/sc_bb_ind.pkl")
          self.load_library()
          self.status = 0 # 0 no selection, 1 mutagenizing
          self.bump_check = 1
-@@ -218,7 +218,7 @@ class Mutagenesis(Wizard):
+@@ -217,8 +217,8 @@ class Mutagenesis(Wizard):
+     def load_library(self):
          if self.dep == 'dep':
              if not hasattr(self,'dep_library'):
-                 self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
+-                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
 -                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
++                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
 +                                           "/chempy/sidechains/sc_bb_dep.pkl")
              
      def set_mode(self,mode):
diff --git a/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild
new file mode 100644
index 000000000000..c3a348f84c11
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild
@@ -0,0 +1,120 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild,v 1.1 2012/03/28 12:34:56 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="2:2.7"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.* *-jython 2.7-pypy-*"
+PYTHON_USE_WITH="tk"
+PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
+
+inherit distutils eutils fdo-mime prefix versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="
+	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
+	http://dev.gentoo.org/~jlec/distfiles/${PN}.xpm.tar"
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="apbs numpy vmd web"
+
+DEPEND="
+	dev-python/numpy
+	dev-python/pmw
+	media-libs/freetype:2
+	media-libs/glew
+	media-libs/libpng
+	media-video/mpeg-tools
+	sys-libs/zlib
+	media-libs/freeglut
+	apbs? (
+		dev-libs/maloc
+		sci-chemistry/apbs
+		sci-chemistry/pdb2pqr
+		sci-chemistry/pymol-apbs-plugin
+	)
+	web? ( !dev-python/webpy )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-1.5.0.1-setup.py.patch \
+		"${FILESDIR}"/${PN}-1.5.0.1-data-path.patch \
+		"${FILESDIR}"/${PN}-1.5.0.1-flags.patch
+
+	use web || epatch "${FILESDIR}"/${P}-web.patch
+
+	epatch "${FILESDIR}"/${P}-prefix.patch && \
+		eprefixify setup.py
+
+	use vmd && epatch "${FILESDIR}"/${PN}-1.5.0.1-vmd.patch
+
+	if use numpy; then
+		sed \
+			-e '/PYMOL_NUMPY/s:^#::g' \
+			-i setup.py || die
+	fi
+
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
+	echo "site_packages = \'$(python_get_sitedir -f)\'" > setup3.py || die
+
+	# python 3.* fix
+	# sed '452,465d' -i setup.py
+	distutils_src_prepare
+}
+
+src_configure() {
+	:
+}
+
+src_install() {
+	distutils_src_install
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol
+
+	cat >> "${T}"/pymol <<- EOF
+	#!/bin/sh
+	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$*
+	EOF
+
+	dobin "${T}"/pymol
+
+	insinto /usr/share/pymol
+	doins -r test data scripts
+
+	insinto /usr/share/pymol/examples
+	doins -r examples
+
+	dodoc DEVELOPERS README
+
+	doicon "${WORKDIR}"/${PN}.xpm
+	make_desktop_entry pymol PyMol ${PN} "Graphics;Science;Chemistry"
+}
+
+pkg_postinst() {
+	elog "\t USE=shaders was removed,"
+	elog "please use pymol config settings"
+	elog "\t set use_shaders, 1"
+	distutils_pkg_postinst
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}