sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.7/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 188 insertions, 15 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 36fae526b327..0c7eca7cd02c 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.120 2013/09/18 12:58:56 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.121 2013/09/30 10:38:24 jlec Exp $
+
+*ccpn-2.3.1_p130930 (30 Sep 2013)
+
+  30 Sep 2013; Justin Lecher <jlec@gentoo.org> +ccpn-2.3.1_p130930.ebuild:
+  Todays python patches
 
 *ccpn-2.3.1_p130918 (18 Sep 2013)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 5670973e405d..a61fe41aaad9 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -33,6 +33,7 @@ DIST ccpn-update-2.3.1-130813.patch.xz 1108 SHA256 5f6b5c5e1d5bb221585f23e7e6048
 DIST ccpn-update-2.3.1-130814.patch.xz 1308 SHA256 67e29aa7e4c43b2249d230937e8b8ba25991de9dadc57ac9f8e30f0712591546 SHA512 2ec9f81ce5a6607f227119fcce31477d9017406a14fdced6832b7464f0b684e340c21b9402653641aaf3112c7956366106d86c881ff25ebc0b4af1fb7161759a WHIRLPOOL 96d43d3b53a35088d8c162573ddc1db6368371fbe932b43954604e8b1343d13f5a3ca61ca75ab9be44af814e68fcb0eb921dfee34e4f11fb3f947675c5177739
 DIST ccpn-update-2.3.1-130822.patch.xz 648 SHA256 5d240fc2a0c79c72c4d2aeffd08a5c7505a26ecaf6372e03a965c3b580e33edb SHA512 0e4987e583489d17f20c08679c6fa8a1521a83569804256e542dcaa97c16e8770765a53fece0091c6f2de1faf1d94c8c000e69677aabd7ce7629693838f02be3 WHIRLPOOL 0c594b19e86181e5326543a6a91f758fcb14800eb0e210d7d1c4e1ebc75579ca3ca8c3a01b269e86c5efa76ddaa3e975d88865dc1f5e9d0bb1bac4cbd1c1f3bd
 DIST ccpn-update-2.3.1-130918.patch.xz 1408 SHA256 331a3019492da127bb8a2de2252776d20b5bc1ec586f5a3176fc8eb2cfdb8fc8 SHA512 b63e6467dd8344b208cf6f2ce66c7aeca464b5921fe49ad1043be841a95bb07c749f359449e0f6c5a0fa55053805013420390f9db6b44762720b8f49eabe59dd WHIRLPOOL 4de6669ee58bf8ad296f2c69b5ebe5d177fdee604f8a483f116a0aad7aa8c137a1e260849cae6f5df5361d4852b79a2ac727099c88ed211a60fe3025352b5cd8
+DIST ccpn-update-2.3.1-130930.patch.xz 3540 SHA256 311cbf0e3bbb77b68ae77fe2f7092c6e1ec98dd4d45d36daac584e90a1af28e5 SHA512 0bc23e01824040e32149f30af729b1baee8a0d53092c0610227df17c08fcbb9ab9df4d9c17d75f710c7a79ab5c5738c91cd4e1cf523dd9dbcc498755cb7537c7 WHIRLPOOL cfaaeb8834a2b1fe02fb9e0c63c07482ad5fd32cadb9898c00a43e235eead1633ee3a2b488385cbf96f73a161d06bd7fb1d8d76dce79f177abdd75ce7e3fbc13
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5181 SHA256 c3ba268461da63ea23ee7f621a8e4837a368eb3e4c85bcc5245250fb6b377b58 SHA512 701ea90a13dc44e5bf1ea17c0f69adea56b1c14788ab79c67fa4b9726cae532998717515568045aec9bb4e1dd4c352227130115d90c50bf07e7fd132cdee385d WHIRLPOOL 898a618f95b254785739e6fab20af333cb3a44bff12cd6840d1b111f1588a60e48055e8af7ca88457173452f6acba86ebd3bada96390211bc4cd063fe4160fd5
 EBUILD ccpn-2.2.2_p121125.ebuild 4612 SHA256 08a4b0682c049a6301138ea6f24d665edb0a8d8d709ed2c2f2529aa0a5e648a1 SHA512 f8c45f0b19a721775dab3147cced933e8db969e8443c15cd2bd2a31ffc3fcd0eda95acc75a93df5d0dd51dabd80fde8311a7b02bf3f6a051bc0855cb156755a5 WHIRLPOOL 427cacc0c080197cc79a867f1cf1d5bed45cbfbb0f8c5dc6456548218895ff25023ea30090e751af78b77fffd47f87f7aac3869a8ed13aa3727f2f12bac743b1
 EBUILD ccpn-2.2.2_p130110.ebuild 4649 SHA256 53125900943ea89ba3d3483de29a240a0e7282098af869a04bc926c34f3bf51f SHA512 8406a93562897aadfefd03e098b393af5fb29f9bfde8e5727b73ceb6cbe004b73cfd97b61e942189d9fba717761b20cc4914e5c9d858f36bbdbdeea1369490e7 WHIRLPOOL 112e9cab77898ef9246b127d5ef8529948cfaf91157a25bbe39899560af8340f8e5cbd1e2a3935dae083a9291f0d569d3cc5b7588dc2029f3342ecbe5590cb0f
@@ -48,22 +49,23 @@ EBUILD ccpn-2.3.1_p130813.ebuild 4714 SHA256 69a4206eb202fc4e7262ba9a2900094ee10
 EBUILD ccpn-2.3.1_p130814.ebuild 4714 SHA256 c50e78f7506b1b9f6bced8c745f514a5148518a14ce4f7b58b55c8a31ba2bce7 SHA512 72aa9b929d0f7e43fd2d4a537d84d5184e052d6d3e7ca6167e69026e5a6879699cda1f46ae480b847fbe900677e0cf7a10db4b018d8ed8b58daa7ca96f81e9ad WHIRLPOOL 9bdb917f84ca139e6a9aad4c7f159ce11589e9084459f092a2e0f4e712dffef6777a7c1bb86ecb40214fae23cc5d005799d9abfbf02025a1682a887c9dd267de
 EBUILD ccpn-2.3.1_p130822.ebuild 4687 SHA256 63a8d24b2cef235985bc0c7d3f34f22dac2b214155c67dccb12c75471f61b759 SHA512 f709dc1be89b66cffa9818e139fb012f3cf45552b0699a62dc0e3e7b47e251abd554fb03b9e810fc82bf2e0ba13bddffffea005d3716dce90a7035fcfea01649 WHIRLPOOL e7edb15638c826355e87881c21894569a5460b65c607ec8ffadb7f74ad337dc4ba225eaacc776b28e2115fbcb6cbce73eaa3d0dcff1a468ca4cca5d9d2df9e00
 EBUILD ccpn-2.3.1_p130918.ebuild 4685 SHA256 4a784b756590ee61b193d44e1addb0680cdae07675c1ffdd4478c44858651680 SHA512 e283a670a0d31ab9bb5a2286615c605e4c05dc9b5c96ba6d56fbbb9f75768d52c290257340a1bae3db9883d9b5a04e89dfd831b891b2d265ceb0884fd2aaee2e WHIRLPOOL 2923f87daeb23fa3eca9a7bbccaf931d3503df32400884e58193d9c2b6fccd662a9d27911aa6b9d3de10b2f81d71ce45ebf01d80184257636b6374d2cdbfee71
-MISC ChangeLog 23166 SHA256 b9d461733920afa863a0a9f9e5e2fa3adc9f66360f0aee08e386ebe6131ad382 SHA512 f5e203ee96c82390d51a2d690b2648a1faf69d701d5e0434997c1ae09b4316419ef1d267a55660bbe761b2409ed22b89fd378c839b3d890c0c1dfc89338b5257 WHIRLPOOL 86a2ec8fe4039954811d5e87c24ec05ac91262c26738b5c9bd8f7032e2907edbb26e65c477397822146f5efd59c3c1e679427710fec0713955adc91845a046ea
+EBUILD ccpn-2.3.1_p130930.ebuild 4685 SHA256 e1a004b4a163e0268943618080b315b39be7296585dee708b64948c93f77b514 SHA512 5a7a7496ecd4cf6d36b6f7215b17ac6565fb39e2f7f77bec5de225e012b732394df9bd82a7a7ecf948ff97ff5b8c476d72254d0edb0f57103bb7c11b02dd051d WHIRLPOOL f31e77528477a92e2c6acd13e6c9837effa830a00097ac075e8c7bed86eebc6f4e6f760e47793708f1eefcc45c638432d10f83b23802ed11816e6354fb52e4b5
+MISC ChangeLog 23301 SHA256 42575e8c7f66e8c98e3c383005d1ca31f98a7d6654b223b5ca7db0f37726bf67 SHA512 ce0655e6637542d9dc9785ebc7ee9f60dd93531a2e7c86618f5d95b3877842e8429f8ea2da30a0c821624e9bbab5cd68baf186c6e01c1414725ece1742c9c39b WHIRLPOOL 75c7088f4edbfb63ae38ff00912c3e6d75b97d9b359bd6bdd5e3231c3310ef1d7f86c755723b12a648414e048cc0f1e02d6fdb10d84f015811db2df3b0927ea9
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.3.1_p130930.ebuild b/sci-chemistry/ccpn/ccpn-2.3.1_p130930.ebuild
new file mode 100644
index 000000000000..efda014d1fa4
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.3.1_p130930.ebuild
@@ -0,0 +1,166 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.3.1_p130930.ebuild,v 1.1 2013/09/30 10:38:24 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+PYTHON_REQ_USE="ssl,tk"
+
+inherit eutils flag-o-matic multilib portability python-single-r1 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"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}r2.tar.gz"
+[[ -n ${PATCHSET} ]] \
+	&& SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-lang/tk[threads]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+	append-lfs-flags
+
+	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 ${CPPFLAGS} ${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|^\(TK_LIB =\).*|\1 -ltk|g" \
+		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
+		c/environment_default.txt > c/environment.txt || die
+
+	sed \
+		-e 's:ln -s:cp -f:g' \
+		-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C c all
+	emake -C c links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type f -delete || die
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|$(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|${EPYTHON}|g" \
+			-e "s|gentoousr|${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
+
+	dodir ${in_path#${EPREFIX}}/c
+
+	ebegin "Installing main files"
+		python_moduleinto ${PN}
+		python_domodule python
+	eend
+
+	ebegin "Adjusting permissions"
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+	python_optimize
+}