sci-chemistry/ccpn: Version Bump

Package-Manager: portage-2.2.0_alpha99/cvs/Linux x86_64

4 files changed, 233 insertions, 6 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index fc0fe42ef64c..15d7869a79fe 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.80 2012/03/04 09:18:53 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.81 2012/04/03 14:45:33 jlec Exp $
+
+*ccpn-2.2.2 (03 Apr 2012)
+
+  03 Apr 2012; Justin Lecher <jlec@gentoo.org> +files/2.2.2-parallel.patch,
+  +ccpn-2.2.2.ebuild:
+  Version Bump
 
 *ccpn-2.2.1_p120304 (04 Mar 2012)
 *ccpn-2.1.5_p120304 (04 Mar 2012)
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index e45f8e1ee318..74b188f8fcca 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -6,6 +6,7 @@ AUX 2.1.3_1-impl-dec.patch 2818 RMD160 182cb26478750711916c73b7f9ba5e0caeb30bde
 AUX 2.1.3_1-parallel.patch 577 RMD160 8bafa14bec766aaca0e55f33f9b51f10f5f29c43 SHA1 e95891313f669e0908374aa98a725596140150cf SHA256 7e650ef2fa1ff0626349affdf1bc9578fe1da3b8cee7dd9125d33a2164978b69
 AUX 2.1.5-parallel.patch 850 RMD160 8120e0ff579b6ec575cb96b51b8babec63116e0c SHA1 1389f1703ecf86d5ce98a3854314bd85d5c350e1 SHA256 5d9a1a4f1392057167312a844972608fa25afb821453b2057ac1acd03b8711d5
 AUX 2.2.1-parallel.patch 850 RMD160 c2d0c523637325de3109894e564cfdea77e9c11e SHA1 beca108b9d2d17ea550bb26b95fa83160d38eb3a SHA256 318bbf3ae5b04e8cbe0e8e93a7e81a7e793fffa9a0d754464367092d6b79f04d
+AUX 2.2.2-parallel.patch 850 RMD160 c2d0c523637325de3109894e564cfdea77e9c11e SHA1 beca108b9d2d17ea550bb26b95fa83160d38eb3a SHA256 318bbf3ae5b04e8cbe0e8e93a7e81a7e793fffa9a0d754464367092d6b79f04d
 AUX analysis 319 RMD160 90f2fadd0c95c6d7d5f38c9a59bb6f72ea610c6a SHA1 7433d87b0eea322a67a3d3dfe71ff3075ebcc864 SHA256 0731b9a1624259b373c7163c6ad095c82f77965f0b61880e84bc8e3c30b83d6e
 AUX dangle 315 RMD160 5e0e4a03ecf427687157677e2fd64316312fefc7 SHA1 570799f08e63e32bf3767b755de82ce691a5bafb SHA256 03101ba39fc9fef1380315c2c64f9d027fb95b79d82c35b9971445613ad5774d
 AUX dataShifter 318 RMD160 c9054be6091ace5e80aef1fb2a226c5658d16ee3 SHA1 8144ab11963c25bb6f57e8a91efa31a35e0c85f8 SHA256 891f87e2eaae88253ffddd4e71b060f8b8e7711d54a02492117500186f04f45d
@@ -18,6 +19,7 @@ AUX xeasy2azara 324 RMD160 88b4967ef4822ff04264f2b632a1dbfca3fe23f0 SHA1 1c877d6
 DIST analysis2.1.3_1.tar.gz 18932918 RMD160 5f19ea6fe47c2910d16fcba8d1a78f0e1dead731 SHA1 683bdfb17d14979eb6477aaa99e4c4af5003beb2 SHA256 bbc1ba5434f896d38b6745c1dc9adc470a78d3be7b879160edcd635a19228b74
 DIST analysis2.1.5.tar.gz 20338459 RMD160 b0706c859c1ee4da2ab80ee41534197268f73d44 SHA1 70dc5e6b2752d6b7d5c8673fc992ebd0a88e6ad0 SHA256 9f91f1bd56fb73fd24e71d396c96c0f0d31b92287664b6a2e756f6efc630b31b
 DIST analysis2.2.1.tar.gz 20974926 RMD160 5905f43fc1399a656f018808c4a2f8dd3d247ca9 SHA1 eed30da55a719ef6c29431e3b3c5a76f521010dc SHA256 d1252811b3db3a30d96a73368bae8abcb05de02fcd2f1f9c502d71dff5e00d13
+DIST analysis2.2.2.tar.gz 21044504 RMD160 cbf3c0d320747b0057afeac0e3ca9a2d889136ba SHA1 825ad7487ef6191baac0e5aa3d0ec6a6ed94a04f SHA256 8e46d12b8fb7763d282933e14ddfa9ce197954ed9fbfa2333e22602ac841b6e5
 DIST ccpn-update-100806.patch.bz2 187965 RMD160 3297162fe3314aa405ee58737ce45cda084834e5 SHA1 338423d9f36da3fb10dc9d9a3b8aeb932ae3bfd0 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4
 DIST ccpn-update-2.1.5-111213.patch.xz 104892 RMD160 d2a83a0b809a91f8f8422a24c11ce20a8e2cde8d SHA1 ae819afdf4cb6aa39c9059cd1bb96d3d188a86fb SHA256 72bbe7f2a68ee20eca029685b8b3daaf15f71d164767b3aa5d222c3a5de779b1
 DIST ccpn-update-2.1.5-111220.patch.xz 105472 RMD160 f8c358e7bc7757a4f645a2f26fa38e0159e5bc2f SHA1 21721845d3f0df77c548a3e5774ed5a82f3d12df SHA256 a4d8d4982c8bf63031cd11cbe67121a598b97f1c490862c363555bf9c2f11140
@@ -40,12 +42,13 @@ EBUILD ccpn-2.2.1_p111220.ebuild 5788 RMD160 abb85d91207669ef94be18d38b4e9efc5dc
 EBUILD ccpn-2.2.1_p111221.ebuild 5788 RMD160 e722eaef088dbe8f273190fed6331157ab57c553 SHA1 97328118dcde05d92d7d5410f61a8c2b9b5badc5 SHA256 72216a2ec437f6cafa02eb435fffcf97bc274c5d6009f303a3eb214bd08badf5
 EBUILD ccpn-2.2.1_p120109.ebuild 5784 RMD160 c6279bd8aab43037353347299c139da99c4d4bda SHA1 7cd2a6425cc8fd62396891874f16e1bfa7f33010 SHA256 b4b08ff9094119e5bd50066f72d41927bd3bbe840c0985f49c585501925ba593
 EBUILD ccpn-2.2.1_p120304.ebuild 5784 RMD160 e4278559ae4129bf56c73b7df807d73898910322 SHA1 c3e8b18e7a42c7e4d9e786e580ed40ae73b96710 SHA256 387882b2a69b312bfe9d7edaaf8a2dc399e1d3d16f62e3b250d91207e64c3f72
-MISC ChangeLog 16455 RMD160 8f55d4c31ab61d3171977692951efa465644b32a SHA1 ce11f27aef0cd91c2d5ba997eac00ecf9c73d396 SHA256 8b34994ce18407c55221ef78bc279eb4d94765b7086690150bb06ad11b4dfa19
+EBUILD ccpn-2.2.2.ebuild 4792 RMD160 66866605d58520d45257e277f9b8a483ccae9fbc SHA1 977794e3110f24e8b63bca12e9f9ca96a632b9fb SHA256 268766d35ac9f38942d7bb5143daeb2e02cde8d72716aaa0c6cf4924642e6145
+MISC ChangeLog 16596 RMD160 3bc0fc4100f9c313b85045cbae54926f2d944706 SHA1 b3e74b9df51f819f9c9acb230e42748da0012c13 SHA256 56019706822ddbbab114f3e9c1844c009d2445662fd6702417d6c56edeaa2725
 MISC metadata.xml 322 RMD160 9fd5fba7405b689fc39a089d81ffdaa9f961b514 SHA1 0c31132b25fca04cff97ef11fdc11940f90c77d0 SHA256 7468ba4c27b879e7ed5f82274f5837e51f1f389673a33b9e26e1756a6b0783df
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+Version: GnuPG v2.0.19 (GNU/Linux)
 
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diff --git a/sci-chemistry/ccpn/ccpn-2.2.2.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2.ebuild
new file mode 100644
index 000000000000..b358c83ac114
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.2.ebuild
@@ -0,0 +1,180 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.2.ebuild,v 1.1 2012/04/03 14:45:33 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="2:2.5"
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python toolchain-funcs versionator
+
+#PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+MY_MAJOR="$(get_version_component_range 1-3)"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="extendnmr +opengl"
+
+RDEPEND="
+	dev-lang/tk[threads]
+	dev-python/numpy
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet )"
+# We need to fix this
+#		sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+PDEPEND="
+	extendnmr? (
+		>=sci-chemistry/aria-2.3.2-r1
+		sci-chemistry/prodecomp )"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+	sed \
+		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+		-e "s:weights_s:weights:g" \
+		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_TRUE"
+		GL_DIR="${EPREFIX}/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
+
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+	fi
+
+	GLUT_NOT_IN_GL=""
+	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+	rm -rf data model doc license || die
+
+	sed \
+		-e "s|/usr|${EPREFIX}/usr|g" \
+		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
+		-e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
+		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
+		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
+		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
+		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
+		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
+		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
+		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
+		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
+		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
+		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
+		c/environment_default.txt > c/environment.txt || die
+
+	sed \
+		-e 's:ln -s:cp -f:g' \
+		-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C c all
+	emake -C c links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type f -delete
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
+	use extendnmr && _wrapper="${_wrapper} extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+			-e "s|gentoopython|$(PYTHON -a)|g" \
+			-e "s|gentoousr|${EPREFIX}/usr|g" \
+			-e "s|//|/|g" \
+			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper}
+	done
+
+	local in_path=$(python_get_sitedir)/${PN}
+	local files
+	local pydocs
+
+	pydocs="$(find python -name doc -type d)"
+	rm -rf ${pydocs} || die
+
+	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+	sed \
+		-e 's|#from __future__|from __future__|g' \
+		-i ${i} || die
+	done
+
+	insinto ${in_path}
+
+	dodir ${in_path}/c
+
+	ebegin "Installing main files"
+		doins -r python
+	eend
+
+	ebegin "Adjusting permissions"
+
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/ccpn/files/2.2.2-parallel.patch b/sci-chemistry/ccpn/files/2.2.2-parallel.patch
new file mode 100644
index 000000000000..9223ea8828c2
--- /dev/null
+++ b/sci-chemistry/ccpn/files/2.2.2-parallel.patch
@@ -0,0 +1,38 @@
+diff --git a/ccpnmr2.2/c/Makefile b/ccpnmr2.2/c/Makefile
+index 01fb25a..8e8e1fe 100644
+--- a/ccpnmr2.2/c/Makefile
++++ b/ccpnmr2.2/c/Makefile
+@@ -5,22 +5,22 @@ all: compile
+ compile: global structure analysis clouds dynamics bayes
+ 
+ global:
+-	cd memops/global && $(MAKE)
++	$(MAKE) -C memops/global
+ 
+-structure:
+-	cd ccp/structure && $(MAKE)
++structure: global
++	$(MAKE) -C ccp/structure
+ 
+-analysis:
+-	cd ccpnmr/analysis && $(MAKE)
++analysis: global
++	$(MAKE) -C ccpnmr/analysis
+ 
+-clouds:
+-	cd ccpnmr/clouds && $(MAKE)
++clouds: global
++	$(MAKE) -C ccpnmr/clouds
+ 
+-dynamics:
+-	cd ccpnmr/dynamics && $(MAKE)
++dynamics: global
++	$(MAKE) -C ccpnmr/dynamics
+ 
+-bayes:
+-	cd other/cambridge/bayes && $(MAKE)
++bayes: global
++	$(MAKE) -C other/cambridge/bayes
+ 
+ clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean
+