Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci

11 files changed, 65 insertions, 66 deletions

diff --git a/dev-python/RecSQL/ChangeLog b/dev-python/RecSQL/ChangeLog
index 554723499..16c58e071 100644
--- a/dev-python/RecSQL/ChangeLog
+++ b/dev-python/RecSQL/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Mar 2013; Justin Lecher <jlec@gentoo.org> RecSQL-9999.ebuild,
+  metadata.xml:
+  Enhance python r1 eclass usage
+
   25 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> -Manifest,
   -RecSQL-0.7.8.ebuild, RecSQL-9999.ebuild:
   Update deps
diff --git a/dev-python/RecSQL/RecSQL-9999.ebuild b/dev-python/RecSQL/RecSQL-9999.ebuild
index 1c7d4db23..f823e082a 100644
--- a/dev-python/RecSQL/RecSQL-9999.ebuild
+++ b/dev-python/RecSQL/RecSQL-9999.ebuild
@@ -5,6 +5,7 @@
 EAPI=5
 
 PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+PYTHON_REQ_USE="sqlite"
 
 if [[ $PV = *9999* ]]; then
 	scm_eclass=git-2
@@ -21,13 +22,12 @@ fi
 
 inherit eutils distutils-r1 ${scm_eclass}
 
-DESCRIPTION="RecSQL - simple SQL analysis of python records"
+DESCRIPTION="Simple SQL analysis of python records"
 HOMEPAGE="http://orbeckst.github.com/RecSQL/"
+
 LICENSE="GPL-3"
 SLOT="0"
 IUSE=""
 
-DEPEND="
-	dev-lang/python[sqlite]
-	dev-python/numpy"
+DEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
 RDEPEND="${DEPEND}"
diff --git a/dev-python/RecSQL/metadata.xml b/dev-python/RecSQL/metadata.xml
index fe317282e..098ac091a 100644
--- a/dev-python/RecSQL/metadata.xml
+++ b/dev-python/RecSQL/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci</herd>
-	<maintainer>
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
+  <herd>sci</herd>
+  <maintainer>
+    <email>alexxy@gentoo.org</email>
+    <name>Alexey Shvetsov</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/GromacsWrapper/ChangeLog b/sci-chemistry/GromacsWrapper/ChangeLog
index 48c310a17..f8c6e3290 100644
--- a/sci-chemistry/GromacsWrapper/ChangeLog
+++ b/sci-chemistry/GromacsWrapper/ChangeLog
@@ -2,6 +2,16 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Mar 2013; Justin Lecher <jlec@gentoo.org> GromacsWrapper-9999.ebuild:
+  Drop py 2.5 support
+
+  26 Mar 2013; Justin Lecher <jlec@gentoo.org> GromacsWrapper-9999.ebuild:
+  Enhance python r1 eclass usage
+
+  26 Mar 2013; Justin Lecher <jlec@gentoo.org> -GromacsWrapper-0.3.1.ebuild,
+  metadata.xml:
+  Drop in tree version
+
   23 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org>
   +files/0001-Drop-chmod-hack.patch, GromacsWrapper-0.3.1.ebuild,
   GromacsWrapper-9999.ebuild:
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild
deleted file mode 100644
index dd94e8c72..000000000
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_5,2_6,2_7} )
-
-if [[ $PV = *9999* ]]; then
-	scm_eclass=git-2
-	EGIT_REPO_URI="
-		git://github.com/orbeckst/${PN}.git
-		https://github.com/orbeckst/${PN}.git"
-	EGIT_BRANCH="develop"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	scm_eclass=vcs-snapshot
-	SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-inherit eutils distutils-r1 ${scm_eclass}
-
-DESCRIPTION="GromacsWrapper - a python framework for Gromacs"
-HOMEPAGE="http://orbeckst.github.com/GromacsWrapper/"
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND="
-		>=dev-python/matplotlib-0.91.3
-		>=dev-python/RecSQL-0.3
-		>=sci-libs/scipy-0.9
-		"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}/0001-Drop-chmod-hack.patch"
-)
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild
index dd94e8c72..4d8864dca 100644
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild
+++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+PYTHON_COMPAT=( python{2_6,2_7} )
 
 if [[ $PV = *9999* ]]; then
 	scm_eclass=git-2
@@ -22,16 +22,17 @@ fi
 
 inherit eutils distutils-r1 ${scm_eclass}
 
-DESCRIPTION="GromacsWrapper - a python framework for Gromacs"
+DESCRIPTION="Python framework for Gromacs"
 HOMEPAGE="http://orbeckst.github.com/GromacsWrapper/"
+
 LICENSE="GPL-3 LGPL-3"
 SLOT="0"
 IUSE=""
 
 DEPEND="
-		>=dev-python/matplotlib-0.91.3
-		>=dev-python/RecSQL-0.3
-		>=sci-libs/scipy-0.9
+		>=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}]
+		>=dev-python/RecSQL-0.3[${PYTHON_USEDEP}]
+		>=sci-libs/scipy-0.9[${PYTHON_USEDEP}]
 		"
 RDEPEND="${DEPEND}"
 
diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest
deleted file mode 100644
index 22a8baa34..000000000
--- a/sci-chemistry/GromacsWrapper/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST GromacsWrapper-0.3.1.tar.gz 1575486 SHA256 ddd2668060668528878370961a9a33257cf3643fd0d9e9191b1d26d4f78e803b SHA512 655dae431bf575963af58a5f75abe6703fe1ecdddba5839b671d9237ddee0e33ab19b528e89bcba4db9063fe30622d44e8f47c7b6452b4d1eed8c7400873a012 WHIRLPOOL 3b848aff931190eabd49426d61186a3c1eef9779a9fabf95b4d21d47793e5543adbcba5ac2b39c8a9af7c2479930a8ea65bb336e2155dfca98378df56ba4cb3e
diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml
index fe317282e..098ac091a 100644
--- a/sci-chemistry/GromacsWrapper/metadata.xml
+++ b/sci-chemistry/GromacsWrapper/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci</herd>
-	<maintainer>
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
+  <herd>sci</herd>
+  <maintainer>
+    <email>alexxy@gentoo.org</email>
+    <name>Alexey Shvetsov</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index dad76a97c..f5e0f9b41 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Mar 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild, metadata.xml:
+  Sync with tree
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Fix missing DOCTYPE
 
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 0ced419a9..bca2106bc 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -7,5 +7,6 @@
   </maintainer>
   <use>
     <flag name="apbs">Pymol supprt for sci-chemistry/apbs</flag>
+    <flag name="web">Install Pymodule needed for web app support</flag>
   </use>
 </pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 6f6c5f732..564732c2f 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 PYTHON_COMPAT=( python2_7 )
 PYTHON_REQ_USE="tk"
 
-inherit distutils-r1 fdo-mime prefix subversion versionator
+inherit distutils-r1 fdo-mime subversion versionator
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://pymol.sourceforge.net/"
@@ -17,10 +17,10 @@ ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
 LICENSE="PSF-2.2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs"
+IUSE="apbs web"
 
 DEPEND="
-	dev-python/numpy
+	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/pmw[${PYTHON_USEDEP}]
 	media-libs/freetype:2
 	media-libs/glew
@@ -34,7 +34,7 @@ DEPEND="
 		sci-chemistry/pdb2pqr
 		sci-chemistry/pymol-apbs-plugin
 	)
-	!dev-python/webpy"
+	web? ( !dev-python/webpy )"
 RDEPEND="${DEPEND}"
 
 src_unpack() {
@@ -50,9 +50,12 @@ python_prepare_all() {
 
 	rm ./modules/pmg_tk/startup/apbs_tools.py || die
 
-	distutils-r1_python_prepare_all
+	sed \
+		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e '/ext_comp_args/s:\[.*\]:[]:g' \
+		-i setup.py || die
 
-	eprefixify setup.py
+	distutils-r1_python_prepare_all
 }
 
 src_prepare() {
@@ -67,8 +70,26 @@ python_install() {
 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
+
 	doicon "${WORKDIR}"/${PN}.{xpm,png}
 	make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;"
+
+	if ! use web; then
+		rm -rvf "${D}/$(python_get_sitedir)/web" || die
+	fi
+
+	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
 }
 
 pkg_postinst() {