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 6a679992f8a0..535332a0eefe 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 1.123 2013/10/10 10:22:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.124 2013/10/15 10:35:48 jlec Exp $
+
+*ccpn-2.3.1_p131015 (15 Oct 2013)
+
+  15 Oct 2013; Justin Lecher <jlec@gentoo.org> +ccpn-2.3.1_p131015.ebuild:
+  Todays python patches
 
 *ccpn-2.3.1_p131010 (10 Oct 2013)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 84eaff616bb9..8a8a5148d980 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -36,6 +36,7 @@ DIST ccpn-update-2.3.1-130918.patch.xz 1408 SHA256 331a3019492da127bb8a2de225277
 DIST ccpn-update-2.3.1-130930.patch.xz 3540 SHA256 311cbf0e3bbb77b68ae77fe2f7092c6e1ec98dd4d45d36daac584e90a1af28e5 SHA512 0bc23e01824040e32149f30af729b1baee8a0d53092c0610227df17c08fcbb9ab9df4d9c17d75f710c7a79ab5c5738c91cd4e1cf523dd9dbcc498755cb7537c7 WHIRLPOOL cfaaeb8834a2b1fe02fb9e0c63c07482ad5fd32cadb9898c00a43e235eead1633ee3a2b488385cbf96f73a161d06bd7fb1d8d76dce79f177abdd75ce7e3fbc13
 DIST ccpn-update-2.3.1-131008.patch.xz 4980 SHA256 f52ee972d459f6f3169b24b2858b1e912c950ebcd57905bbb1633e54dbf00a4e SHA512 12db64c4f03e5f14f1998fd713459f1d7ffc7355c2ac2cdcc8d5b48a46b59956f6ec6bc0b9f37c785c70630b3736886c9b8818612563d73840699e976a65cd9a WHIRLPOOL be9bde47b0373cf463d94720d9f8b342f12cf6afe57c07f1d6a541beb3decb604eddbaac886d23b9eb4806d8bf049e6d1fde4ba2caff19fdc27b1dcb347818f2
 DIST ccpn-update-2.3.1-131010.patch.xz 7352 SHA256 f447df5334aac40847c9796421b5af8c4d290355b8f4a7de67ea6735683efca4 SHA512 865f3c39398f0c55a1f219d816c5a0395e9c7fa71b6f145c05959c39a4971c451f7162e9d23e5e0b000e0a2f7754bac6d458875b897bf3c3d4ed9a72f80a5561 WHIRLPOOL 60616ccaf6bdd2cabf6bf23813a761e00d8dca31ecb0e8d34c8a7ddc2983c8643a12392ccd7e1b5c356cc40456df9140801b842bc7170fa311c273cc5ed762db
+DIST ccpn-update-2.3.1-131015.patch.xz 7676 SHA256 df46e2f39ff6a9feda6bd9d4480d94af0f0282e318f6e3e27fc3d5b6ee1888db SHA512 c1ba9a0b9766a5317564978159a7e7c3176d382ff0e5d4547a372666309c614079254e772921761010e23ce61a81b1cdf4f99b3b58880ab9901ab372adea1055 WHIRLPOOL 4d008ac4c4861083091c557485afe0efd9dcfd982f1c241987743cb494f36ab084b27449cf2e528c2b95e2048dc67e90e58a4e0e3de283b81e17478b6900cff9
 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
@@ -54,22 +55,23 @@ EBUILD ccpn-2.3.1_p130918.ebuild 4685 SHA256 4a784b756590ee61b193d44e1addb0680cd
 EBUILD ccpn-2.3.1_p130930.ebuild 4685 SHA256 e1a004b4a163e0268943618080b315b39be7296585dee708b64948c93f77b514 SHA512 5a7a7496ecd4cf6d36b6f7215b17ac6565fb39e2f7f77bec5de225e012b732394df9bd82a7a7ecf948ff97ff5b8c476d72254d0edb0f57103bb7c11b02dd051d WHIRLPOOL f31e77528477a92e2c6acd13e6c9837effa830a00097ac075e8c7bed86eebc6f4e6f760e47793708f1eefcc45c638432d10f83b23802ed11816e6354fb52e4b5
 EBUILD ccpn-2.3.1_p131008.ebuild 4685 SHA256 ae08a4a528ecc7828b6e176fed7ebe967352c3fbe6306e12348e3504b0e37f4c SHA512 a14bcb3596fdd130b5f8986d50983381f61289aab7c81f9a3619359836b7fb27008957dcfc1bb6d0f0322b3858291e5d107c5974e09031a022e124a4db990b0c WHIRLPOOL 6ec92ea8ef6ebf990880f800ce9e633fa44d9339c88d746db2665555117497377ab4c0b717732f26237c04905856ea47fbac37fb75f90fe9ede41b2fc7be268b
 EBUILD ccpn-2.3.1_p131010.ebuild 4685 SHA256 8d98fd88b576a617f7b55d9b0de3ee5441828545e54baebaca1dc2914e188199 SHA512 400ca5f0efa2e5865544f0ca7a810fa3d1825b693b194cd5b58c84dff028c1aa8678c06c6f17a0f1cbfad4eb852c4d102429fba04803fae825e10522849866c4 WHIRLPOOL 5b9da2f81b0909037385988096f37937243a4110b752850c8f6505f06b372a4ce55534ae1a896f86040a17601a293c6caad765924efcd5f6d34236a3b0a851f4
-MISC ChangeLog 23575 SHA256 1c6933ecac5243af9946093e200346445a4fca3b09a117d7cd6d3398950b23c6 SHA512 dc7ae89a440ba31c44569d5debcd296342ac25776ec1c5d3a2c93c572f681d3623326a48d6d04ae9af74b38494f62870befa453f90f13afa6cadb75fe39d48f3 WHIRLPOOL 3d0839050d4be806106fe879465bb519c1991780e2e5f40f2491ab36d3f5b47a834207b346395e8f0bd99122493a5ce4d7f579e5758db6c55bd09a3c0c9c3cce
+EBUILD ccpn-2.3.1_p131015.ebuild 4685 SHA256 0215b6ff8c9ee7247a3b4fbb48a9c37f9e7c95623d08afb7a50590134fca5e7e SHA512 fea0e8f85e82d0b4af0551465546cd78226126d7dbb2315949309a09854245db798f9054140f2355b687937c308c5365c672ccb3315cad8bd5e09f99b8a89bdf WHIRLPOOL 68ce200e5efbba9fbee4e0fa95f4a479868881655b51f76a2989a8079d2b30ad05a305270cbc862b9b39f259b9854bb8b6e4b66d7c446526e35ceef71b787984
+MISC ChangeLog 23710 SHA256 945062300cf72e901d8b135af2f35ff121b9aa9102b7d7f1a6c7ab7b7b6880cd SHA512 2d0fbb143cf7173c54d0428d54b59958c00afee2762769e0ad6a71dc4ab34b7d98e2e987a2a57ab216169bdf0d3d58753a2fda6ccb158a30023e00f50ac8ac81 WHIRLPOOL 0ec1e02364f8fdbadf7e729155549c7081bc12f65ac399fc8d46ecc70386bbb9f45fd5b5c810882ca7d8f06535a6c1d2c3b441334238ff34c8996cb0f728f258
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.3.1_p131015.ebuild b/sci-chemistry/ccpn/ccpn-2.3.1_p131015.ebuild
new file mode 100644
index 000000000000..9a5eee87b0c5
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.3.1_p131015.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_p131015.ebuild,v 1.1 2013/10/15 10:35:48 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
+}