sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.0/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 189 insertions, 15 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 796172391561..20342a9777c5 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 1.115 2013/08/14 07:46:36 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.116 2013/08/19 14:47:41 jlec Exp $
+
+*ccpn-2.3.1_p130819 (19 Aug 2013)
+
+  19 Aug 2013; Justin Lecher <jlec@gentoo.org> +ccpn-2.3.1_p130819.ebuild:
+  Todays python patches
 
 *ccpn-2.3.1_p130814 (14 Aug 2013)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index b28a34c3255a..771834b8d468 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -19,6 +19,7 @@ AUX xeasy2azara 324 SHA256 89945dae1c7bd78aefdd19c81c79571a13aaa149d6c50e12cc0ec
 DIST analysis2.1.3_1.tar.gz 18932918 SHA256 bbc1ba5434f896d38b6745c1dc9adc470a78d3be7b879160edcd635a19228b74 SHA512 ee95119a972ada7949d646e0fd634d1828bba7562d7ea3a3be1c2b17d22f194dbd1267716f21ce86fffb3eadec136b0b613705f862747ab7933cb2ad57e063b8 WHIRLPOOL 1fb19a4bc676955eca4168595fad0661054061e18fa6e25e7f4ed5026cf31faba75b7644a8e2e18ece10e9641efc81feaccf580d3c766bda1d5232a346d99133
 DIST analysis2.2.2.tar.gz 21044504 SHA256 8e46d12b8fb7763d282933e14ddfa9ce197954ed9fbfa2333e22602ac841b6e5 SHA512 efe8a82381521dbfb95b12dd553f401f200aee3763f9e739c37a9141a14bf038865b2a860b0353adc532582697b58079034386be42161aecbe231952b8abaac7 WHIRLPOOL c9d7fc936dc25b952e711e8fa439ada5a67e68497b6d4ad034586e604bcbd9d1ff7dd48d1a3baace347fc9bab5c17d2f7852906f921708a16ce8c8eb4a8659b9
 DIST analysis2.3.1.tar.gz 21702376 SHA256 892df0e2d999a9cac75438c5357d8766c9aa5f7d0d575e798d92638df26165e6 SHA512 34a86020e764bed9e85870a55896f9aaafdab4b50be6fca17d35830d013a314fbdc3d1609024b1d5ce8bfa306a3e5a39af9c70a751823adc12d38a26a424ff3e WHIRLPOOL aa7b4a3fd9350c9b98fa9226547635692eaff4a311951b2e89b493b258c1dc8353b9945fde46fc0fee4990cb4caa5615326e81532c579db34807221bdcb72e20
+DIST analysis2.3.1r2.tar.gz 21683215 SHA256 a9e47a24d84f7b8261c6c23a8607af5a6ba2f2db9e161a7f873794c1ba8663ef SHA512 96bf75d1e958340d83836348f5a3045e5b2632913c66d9d74272140085800ea096f1ae53eadfb5bc0eba76804f1864553e82a517d637bdc3bace71b0c1c785ee WHIRLPOOL 2d1e55a4d8e62decc649a885d767dc5a2bdec701447a97ef8bc5e15ddde8c6add5fb0606c0cdd5871bbb9af74c163a13a28207b3e254fb41ba56293c88d6bc85
 DIST ccpn-update-100806.patch.bz2 187965 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4 SHA512 ab145f14137955bcb4dcc4d242eb718a806152bf3376e4cc9ff5e8186ed54812051ad07de1c9d2316ce3379c8c74db4af36f714aa3291ea7a1d11d4f432df06f WHIRLPOOL 2a0cbf62aca74e22fc0e00a0a91c3c185c10fb07277ba30791511565a2fa645b123a8c5164389eb9fb5a2d1f591e26c6416c46038acceefa2f1ecf347b631a66
 DIST ccpn-update-2.2.2-121125.patch.xz 223556 SHA256 996f453d7d6a143715a94b1201bd7b8b9c037f6d0baa342f5c0645d500aa5c79 SHA512 d213e072a63110ec478c3ee64792b01c818d3c9052ae6d7dac903508536f78c432c72d5a4756665045579d72f4f54ef5ac9db1fb02eb5ea3111eaa47e72866b0 WHIRLPOOL c268761e4d9cf4c845964c7c865e20439a9cacd00bc56d89d8558e0f601fc9840d4288307c4a4f47ba6d478eb9da9dacd1e149c657d2e6506ef5e32d6b0b75d1
 DIST ccpn-update-2.2.2-130110.patch.xz 226800 SHA256 6c0f4d71322e45ef24a15f1e26eb5d4104499fc2391660e575158dc08ae0380a SHA512 2fa7e782ca30402c91793032dc0d4555d9e866ba11b03f8f4b06891c8c80d256f5598bccfc99e9a97ae9b3618b1c24307814de4656087e2c0b40d378df743e47 WHIRLPOOL 5a49c0480328e7b03691a1e63fea339e2a9a29afd845babcce70e57b6e8d6ce21a5cb612d856c22bd3a9033a9ab565b0149e61435bc31ffdf02e247051e29d6d
@@ -30,6 +31,7 @@ DIST ccpn-update-2.2.2-130618.patch.xz 242764 SHA256 c605c92a547e50e64f5c97ae5ee
 DIST ccpn-update-2.2.2-130705.patch.xz 248520 SHA256 12951d154579b23e110f4f326fe880c998ca0027aaddfb602a4eceb9b493ee77 SHA512 6fa4f6e83ac5d02b74d36ba9eea311c4c5764b5898280310ab9e0ba8f580ae53bbce17da49990aaf82e67b389019e0836534463777f8c6c0245cf51901a562f7 WHIRLPOOL 8fff3c93e8f985b36bacc00142b8289e9ef0a3726f5b9bc8d6be70c5ee1b3cffe3c504ce935ae219d98fb9500c56cd4e3b86a7397f70fc30378cae455315d5e9
 DIST ccpn-update-2.3.1-130813.patch.xz 1108 SHA256 5f6b5c5e1d5bb221585f23e7e60484ec35a07d418a2b0ff0cd2d26a3974c2e54 SHA512 b4afc4d8a2ee8ea1c1883055960ac9d14ec2496b26c2966f1a972ee7d46c1d484a11badd639426d9c2afa09b259ff125c34346355ea79ab5393936df22aa60c7 WHIRLPOOL 12bbc548b7d871bf0c6a836067209e13671aeefc66f3d8a326256bf5bfa4c15858acac0c5d7bcd8a69bf6218a010058b7497d7b6a5385868df92236200aec50a
 DIST ccpn-update-2.3.1-130814.patch.xz 1308 SHA256 67e29aa7e4c43b2249d230937e8b8ba25991de9dadc57ac9f8e30f0712591546 SHA512 2ec9f81ce5a6607f227119fcce31477d9017406a14fdced6832b7464f0b684e340c21b9402653641aaf3112c7956366106d86c881ff25ebc0b4af1fb7161759a WHIRLPOOL 96d43d3b53a35088d8c162573ddc1db6368371fbe932b43954604e8b1343d13f5a3ca61ca75ab9be44af814e68fcb0eb921dfee34e4f11fb3f947675c5177739
+DIST ccpn-update-2.3.1-130819.patch.xz 648 SHA256 6b5702663cff8a85c42158ff777f5fb5c8d5af25329a26b3bec43b0d3c079c8c SHA512 945f5a66b6f68e0b217f05bed45e791b568b39c32deeeaa22ec16d887167b6bc701caf6f4545ec4a49b3a9156dd80437575bca0202fad18d21ddcba6c1c7a8b9 WHIRLPOOL 78f839f4c89dea5aa86c265301cee73236482ea4c4dd3fa7e514bcbec52701723e2bb3a8cf71dc3c55e614a0a2e85e50537b2ef3600f391f6dc4505c47914f1e
 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
@@ -43,22 +45,23 @@ EBUILD ccpn-2.2.2_p130705.ebuild 4649 SHA256 1b3a3af9673c488457fc4b62074178c04c6
 EBUILD ccpn-2.3.1.ebuild 4709 SHA256 ee3050fc0fd62efdbb32fc84e89cd11bed3570f3021909490d1080f76fc260fe SHA512 a03d3c1a8f517b9be2e093872288e0a8a14a93b5131b3b1de7a2d20f3e9569c5d0887e268b8b6a182195b7f595e2ab05e4f77716351e4ef8d8375af325e71bd3 WHIRLPOOL 4f810a4c972bc77a08b18d816606844f5f58556dfda2045907b549165a0638f99b55281677d958e19c8e84d87a75f46e7df55998427e706d1fba9f71a6b95f94
 EBUILD ccpn-2.3.1_p130813.ebuild 4716 SHA256 ff440c877003610b978bdecedd9a32a57eb2e5e54ed67a5868c3d0295978755b SHA512 a3661b1a67af7a912ed42482f3e5b6917eba5280f35fad5941e75882bec8c8b80c7d13ab243f2e46005f8683250ce66a31aaf9076e9bb653acf26883438e8aae WHIRLPOOL 84d89a81a13a373d566d078a12b68609117ceed2f89fd4a6ecf0c97c3d368e0a038971fe2675e1de05c6eace3490701e1160536de806bc6a0b590cf7022b86fe
 EBUILD ccpn-2.3.1_p130814.ebuild 4716 SHA256 31d9cdcfdf1c00a5c7dea719ec8de5585cf9d5899fd09debfb2bbaa310ca56d8 SHA512 dd6f4e26e049938f9ffb393e33ceea23f30c4d371f1bf71aec05b05faf387631c7dd7a8efe8aa4f64321a8c30cefd30cce3bc3408d6f19a56515537b640a44b2 WHIRLPOOL 1566c78e6d4171ecb7fc6935531aed1bda6b2a7d576cc140cab0b6053cb914b5ff8544b8bd2d18a3f37e2ec1f7f83fc4997fbda228e3af6aadeffe7941d52c1d
-MISC ChangeLog 22317 SHA256 5f03e6604b5ec0552e9e2d55604f726eeeac519d255c859dc0a9a4bdffdfff7e SHA512 328db46d6a1b3fc54d0a94dfd614d9252ecc84af73dbbde0cc6454a20360bede8012b6fbcee58e589647876c094f9d924d2a446899f96df89b8070c29049028f WHIRLPOOL 75f3d9fbe3271b39e2cc16c59b9539ee2cad14885605fa02bf49ff7edd550cbe9e316d385139de5fc295585aff884880fe3f6054fd31f65ac231e943ead0b820
+EBUILD ccpn-2.3.1_p130819.ebuild 4689 SHA256 fa517d0862b59f448f7bb0f55509f587c311a7b5d6885e00ce667812552e772e SHA512 a51c5a691e8112278810cba5c3f2008c4511b280612e697219e22eafedf5e62aa30030d2f20398b3babb8a8ee9b07c525bf194e15a53bb630a1576e59c0ea693 WHIRLPOOL a7b935333604262590dda581723853b57c2737cd501801d511228ddead6f502e9a0d2caa442c62378e2b86fa84a7ee3276644c46568be0b587bdaaccb4cdd205
+MISC ChangeLog 22452 SHA256 81624a6f0d7af2c44f8ed36511558d3b5c5ec68cbc57efb2f379f4ef3a75668a SHA512 2f4fc6dba16031bca626e42ae5ee553eac36c50f2ff71ffb622e4109db905bfc59cea0aba63ef7db5cbe621f2c5044840d504d0b1b63d1fafc6a11df46e34c75 WHIRLPOOL 3e756487acab451ddc94b3df0e7c4c5d03e2782d9e02780a1027f7046ed7eb9d58496c56f36d99298b64ffd3e764645786e5eb8477978ba4403907e061017046
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.3.1_p130819.ebuild b/sci-chemistry/ccpn/ccpn-2.3.1_p130819.ebuild
new file mode 100644
index 000000000000..fc9a777bd56d
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.3.1_p130819.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_p130819.ebuild,v 1.1 2013/08/19 14:47:41 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_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
+}