Latest Python patches

Package-Manager: portage-2.2.8-r1/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 5ae77d92098f..dfeab9944d85 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.132 2014/01/31 10:02:12 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.133 2014/02/05 15:32:06 jlec Exp $
+
+*ccpn-2.3.1_p140205 (05 Feb 2014)
+
+  05 Feb 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.3.1_p140205.ebuild:
+  Latest Python patches
 
 *ccpn-2.3.1_p140131-r1 (31 Jan 2014)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index af387c9e92e9..e0726c6a0e14 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -26,6 +26,7 @@ DIST ccpn-update-2.3.1-131125.patch.xz 10160 SHA256 a386e70114b61de2957eccbfdd39
 DIST ccpn-update-2.3.1-131127.patch.xz 10488 SHA256 513252fc6376d89e6bbbb1da1206cf0044513c896c8ea01af8262fcfcdb5a4df SHA512 ac4115d48cc0c8d707978216732fe1f29a0b4e8b9900f029707f483a16fb1b5f1e7055bf33d828455babe52afff13485d32de4729bebc567ffa2d19575ecad80 WHIRLPOOL f05d2149f16c6decc93d30ad55a2f1232e913cefc2fa6f1d6bde42534f0695fe68f3a245164b4408f063a1297df5e01add60e01cd9a77528a5833da7c0d78c91
 DIST ccpn-update-2.3.1-140120.patch.xz 11404 SHA256 b01310884ccf27450d767b63e2f49516f6005259bbf859747b26b95371038f62 SHA512 51c23407c7e5018434f84ade50681156f2d59e6b9e83195967959ccf83bef25406ab0438b3f241de0a00ee923c24e93616c3893e78f4dde82c80e43475de18c5 WHIRLPOOL 8063fb5c78e1e6527f37f82d297414d74edeef78daeff19676648b192a6b30684df5e8afd81d1f1fec2268b4fbbeeae5cb54c27f7ad4f100aee450a218822267
 DIST ccpn-update-2.3.1-140131.patch.xz 12620 SHA256 58906f4c2ee0845743d4b90e01bc95cd5051f05274dcc811040769e3b412345d SHA512 2e34f76ab396ebd925054f62d83a6dfca23ccffe6410f14149a39cf570700919e312f02b9e30db0d74a505cba4602e6b8d089d08035a52f22f4a59d2f77fadeb WHIRLPOOL 431f4fc1eb36b33fa306d75232e31ded222da20d345cad1d9715a255352ef0462720a8df6e7412927cf05ddce40b33805dd18edc2943906769634115d39829a0
+DIST ccpn-update-2.3.1-140205.patch.xz 14572 SHA256 b21b45375f52a968acbfd4c3371ba1b0417a0399ca7362214818467b1e4552d2 SHA512 8b9d5d35b0555341b5219a511fcf54a3f00249234a594f66c84c4e62f99bde7ff21937662fdd0c1c561bf3fd4d83830088b772e2bb474a071a1a7fe5ba970913 WHIRLPOOL 2f031e7540efa0c88db7e2b9c122210f9fd1a09c6c1d0eccaecbdebee116f8c1ac6baa65bc62b95e68296aa76072f090e4db9c2066631a787d4d3897bed66900
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5181 SHA256 c3ba268461da63ea23ee7f621a8e4837a368eb3e4c85bcc5245250fb6b377b58 SHA512 701ea90a13dc44e5bf1ea17c0f69adea56b1c14788ab79c67fa4b9726cae532998717515568045aec9bb4e1dd4c352227130115d90c50bf07e7fd132cdee385d WHIRLPOOL 898a618f95b254785739e6fab20af333cb3a44bff12cd6840d1b111f1588a60e48055e8af7ca88457173452f6acba86ebd3bada96390211bc4cd063fe4160fd5
 EBUILD ccpn-2.3.1.ebuild 4707 SHA256 b97f41d2321679a416127920c8457e2e019dd98ad79a3e563677c7f2d0f66735 SHA512 54a181c71e47659bc448845c2043f04358dec626162a8c72f392ba91833cb8cbabfc524da5239060531c5d4ca0b3f8d1c81a9a102e14d5014bf57e27e50aede7 WHIRLPOOL 1fe18f4b7349e96ed46648a29aa774fc8ccb6be3880b0f5558914d908bd080462152f3f6d461e961ccbace7d4f4ba6deb36770fa7304d796e6f359c202f5856f
 EBUILD ccpn-2.3.1_p131119.ebuild 4712 SHA256 304c3c6a3748eaa478d98b3af95668cef50262c5f6c7a872dbace8c828bca594 SHA512 678ea73d436550565828f682cf90382ed7f3fd166f9daea8643998781099a561899e7b6db5a53b691950f0c67440caabf3b087608db9532c17db2ac02e277c0c WHIRLPOOL 5f19462b456bae09a6983351c894735dd5c58f244154c8b30a54bda1d564d9728cb13fe779d47b46d2bbedb4a27fd7d575f73613fdcb10484b694ba6117e3d60
@@ -33,22 +34,23 @@ EBUILD ccpn-2.3.1_p131125.ebuild 4712 SHA256 4b138cb7a05107ae9feeb6a2827fba1f385
 EBUILD ccpn-2.3.1_p131127.ebuild 4712 SHA256 341087325444fd25568d06905b467f33748d66b3e9f31943251cf40bfa657122 SHA512 3b3dfe6ecc4a117b64e4168ae6131186e6a205b5f1ff29561db0fb0bea9cd775259b86e93df59fdd715ab92b7acd03b98441f2a9ae8ce0a029fb09dc92f0d993 WHIRLPOOL 04e36b31ca326a0f1e6983e0714c560a9d60fd0470341742da51aaa4e131e2f7b6726d8f8ceb89ad8ba43d464376a9684609b85df588481eef474f7b8fdfe957
 EBUILD ccpn-2.3.1_p140120.ebuild 4712 SHA256 1bb42d83a252cdd6b9ad8289f8e22467cab4382984a807fc7b12ba1532a2f6a9 SHA512 999a0daf88c62d4118b0c71ebb020f462a018878c3e1981bb4df3275e352b5f8c3e294f02644d8035c4943fe63ba0150af1542d6df16656bc1aaee59add48a9e WHIRLPOOL 8b49fa1654d8d3ede51ed83ce7b21069da41a6094e803d2cda9a0cd37d3acbb8331777031a9dbdfebf9dc57fcc130267c89890dc6beff2156f82abde0b37b8f5
 EBUILD ccpn-2.3.1_p140131-r1.ebuild 4715 SHA256 f8382a429ff50a9813587a6d989d568787db1eb16bc8b03b551063abbbad2559 SHA512 8df236d946e046ec8a0c0fe54d5b5904a551bdb6a29da02283cf8b88ff4fc25661c65bb7b3a6fcb1a362078449277a97c9e71fec60dadec867d6953cf11ea8a5 WHIRLPOOL 2c341e959059c9391e203718461a9ddecd6913c5c02cd68e6cc43c34a6e3a3a7a828fa60f5b8074ac6c459ab2e1875f9ec5c69b86e236de2d5d31795b2f01c39
-MISC ChangeLog 25411 SHA256 6029e832081489e6e248a2c701e53eac099bf7c840acfd7b1ffef157f69d6f63 SHA512 2c644534e32c9a7abc29271b61901d321333f6109e079de69b926fe5f97281690b6e777a20a2bff74a99ac286c3ee970af484770cd449714575c03299b23ee3a WHIRLPOOL 6af9346b4e3e2af33e3c90104ab24c4035ea2b177f4721fe361201c62421f80d1c714385e8e41f8073544c260178c04ddae4327ecfc7f2f29359e714336338be
+EBUILD ccpn-2.3.1_p140205.ebuild 4703 SHA256 be8bfc524ba2650dc2d86f86a2a73bfbd585073ed62feee666e23de40618daf5 SHA512 d399edc3044efb66024f0cad3a8623813708490408d4bfdbd0875ae10dd8c8987f83ea46d0ca90e1cd8fc232aa96cd138c3a705316605a4b9264c9d0668717b9 WHIRLPOOL c113c5afd5dddf34bca47128fdac3894c0716e4817d8d1c858aab31fe3a6830b6d5ac60a998070fb1392e468af6b7bd89eb45a3eca854a16e70dc8c78942e97b
+MISC ChangeLog 25546 SHA256 3344b69f2bc8825d362310bef6c04599a7294fd63b409054510db5dee35f614c SHA512 68c81416365b553616a01c184a0de793494e4f15d6a8854e6066183d45d15e319c3d1373e25a76b944c0f65b5f44f312cb0b86e06d21ebf4d32e45251a3c2f75 WHIRLPOOL b980c0ee13d3f3211e0a4ac24724fc137f9e1d0cafc193e65c4ada6f28ae2e4d1787f01a0b4ffd0d9200813f19aadda8fd59f5de3480cad2c05930b45846a5ec
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.22 (GNU/Linux)
 
-iQIcBAEBCgAGBQJS63SlAAoJELnU8jG9FVirZW8QAJMFLEe7nimZ8FMF8tlomSSd
-tzPBrvMqlaIxkkj+H70uLNznbFMxcXDk9vg/wdqnNN9qeOo6z9SDqq1miHSwPVjJ
-xmAuiIdz1+Ft8uMXYxBkG31tSpQhZgVFwuIRukouAI2YUKwlt1u3Rp4pbNc8mvZg
-dfOfx0KszAmyuDkETeD2tEC9wIv7bnBl3Ws1OLC1PBDraIkrx2r+pZo8i5qzIzU+
-7UpXuION7GDxJ+IqHP5z56my6qukm+EZDBbP6o/xiIxmty7D+7Xx0+nD0I6NT1GW
-MVz/NrjqK78LEvB6VXu6OmClvE3P+hN6eO/dW0HoSbj6AnSMVWxtzINPZCZLjcaf
-08BVjiu36wPjRoswQ2Rmq8SnBWDd6Gl6o9gPFkDDyo78irXQbvqrstpm17m79jb/
-yFu0UqEELf9kA1hBIqGeNoKzdQFeoJpFq5pRn4d8Ctb1Kfi3HipEcci+YtUOvd4O
-/HYyLc/CvR3uwN6xS43xl676TtXIH8WiC0x44fxYP1t+ym7cxzerkiPyxO5KOwtr
-hNopMf7sZNEwnmN/StGf2qAvNiAoZG6IvvHrIVZSPhn5vzqaD0/pFckUqvWZSjVE
-HJ5KU+yRqIOsSB2o1/rsS2CS2JwUVs65ZP9zB8WHTR4SA0tSMGbQqKyg/yw3YFkY
-OQnh7vkXPKY98221SSm3
-=MR5L
+iQIcBAEBCgAGBQJS8ll3AAoJELnU8jG9FVirATIQAIt9JWiUZVXUsSCpo06pHrh3
+b+dZ1xyCdkvyyW7AagJb/1+u31SldtzXGCt9MGUz9C+RaWmV1jbyVWl/0ZBJffpt
+a4I6hycpGQlUhzFdz6rtM4oMASrbLyY9oJzHDqjmvCJHtw+iK0WVJ0jmzJSgNnbI
+SKVu3vy8ah2ltFml6xUql8VE8Yx44uQU507wO0Dv0QUNxMApo/BJCejz+7hLy0U1
+MFnmYGxLI3vu/+jMd4UsfQ4v87bPx1W8OVMyK7aKRl3ksTZLFovTLky7zI9wo1xJ
+Yh3qfPVomCCz57i8676t1yTRNgTv1zsXR91gBdGsfVBKY4zcIRV8f+PAYd+KqU5w
+K3ovMk9ftoyOQxDb3X7S1+1YEzaw+BX1BiSyBQJ7njEKPeusa+rXU1sHI0Gn+e8D
+soM+d99eAJUV26TyIof980Aq2993ZuT2AmTTYcaWN75hEYRpKW1EO/ZYyLbeSDhj
+ntRTaqvxEdVoxuW5Lx49tOJA79+hS+jiU/FzXC6rW13AIUYQxpyprgcKXGwlN3y3
+fONwymMyNGNXSNhhIPV3rCtwZKeSvOnN4t7zPeHAFrAxiUV/8xBoFGatrC+LjoCf
+3TyXimb6llA3n/GB59qJfsfUDbwceuR0jK9ogHKBkF6TQ6//p5a8L+5QTAZ/B2td
+zGv03e9Hv7Q2QcQECPrZ
+=jQq5
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ccpn/ccpn-2.3.1_p140205.ebuild b/sci-chemistry/ccpn/ccpn-2.3.1_p140205.ebuild
new file mode 100644
index 000000000000..898bb3a7d806
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.3.1_p140205.ebuild
@@ -0,0 +1,166 @@
+# Copyright 1999-2014 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_p140205.ebuild,v 1.1 2014/02/05 15:32:06 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 ${PATCHSET} ]] && \
+		EPATCH_OPTS="-p2" epatch "${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
+}