sci-chemistry/ccpn: Todays python patches

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 189 insertions, 16 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 6ae320aa86fd..b364dab79261 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.155 2015/01/05 13:51:04 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.156 2015/01/08 07:58:02 jlec Exp $
+
+*ccpn-2.4.1_p150108 (08 Jan 2015)
+
+  08 Jan 2015; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.1_p150108.ebuild:
+  Todays python patches
 
 *ccpn-2.4.1_p150105 (05 Jan 2015)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index d5247f3c553c..46cd82f17d35 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -31,6 +31,7 @@ DIST ccpn-update-2.4.1-141022.patch.xz 2552 SHA256 6ec6ab3246b42ebe385056b8d2555
 DIST ccpn-update-2.4.1-141117.patch.xz 5120 SHA256 ce02985d32f1764ee7e05b8aa0628ac263fbe56da10411217cadeabccf0de17f SHA512 7762c479e23f9f54760d003099bfa3449b3f32a2c0ac464ec3d26bff54a1cc86f0b0b34d909b48726e849f45b4bcc54ad897380d1d9f895ff05f4c1eba75f579 WHIRLPOOL 7acb7233abcf48ce6eed6985ebad1f5ebeab255f45100803f2ea89c05d53e6c97dd62f56747d96aadf450509f97eac9e060e4b66a329ae8f5cb2eb833a7b20bb
 DIST ccpn-update-2.4.1-141204.patch.xz 6460 SHA256 502cba7654e415d8d1e08ca48ca966b2b5a25eb4238c03c0457a9633044d5aa0 SHA512 a5af54cc8b9056546c65463e335f28f9d0fe63db2edbab95b9b0a673f602970be635b8f571bd0522ddbe1fac24cdbc1553a596a49a17b0b3c2b569d06802c29c WHIRLPOOL 0e85f6f80b304ef578e319b0e6d08901860671ca707fa4149c3f05aab91c4d941aa2c8cb736a4b5d902f604eb8fad22476fbb0e0bdab6d19cbb7d27d06090477
 DIST ccpn-update-2.4.1-150105.patch.xz 7072 SHA256 f9f448ffa4baddabc8e7870dfcd5ad82a67254147088dd87e35fb34fa129ce3b SHA512 1a57a54ca3b810d2fcff665b339c8b909375dd97a7d9daf00894bf49b6c54dfdf89a07f8ea2d112cebd1d46d5ed502f8cab571a4ec871f9b89e5d05c0a60dd7e WHIRLPOOL 7197c77b3615edc8736c6a5e29014e5c463d0eafdefb6e9862f8f2ba0277ac3db7488e151da8f5e1f84f9bee90054488ca14b336e4b658945ed1a6665af346fb
+DIST ccpn-update-2.4.1-150108.patch.xz 8364 SHA256 a2223d89dc279573871263093fedd9cca1a4ee3f29036d329c50448d6132c8f2 SHA512 32dcc3ff75db61cedeb2ef317b8a9bba1edeefedaeb8a0bd29735842c0b6f596aebe9a511f1ea447323786d092fc9930b3029d1c1a236c4c365a616841d79608 WHIRLPOOL 97ade62a3a8e735bc867e897478466524288929c8f20a19ac6a9bf6e8f524dc1010a8941e90ce51af3722e7775bebf78b5ed80b7a3b80318e83cd623bb8a6f9b
 EBUILD ccpn-2.3.1_p140425.ebuild 4703 SHA256 8bdc74da4c23ab1c25147abd87ef87a8567bdf21a15a511d1ee966f09ef2c6c3 SHA512 a22af894d808cb5ca19190fb9dfdfe21e47b3626e2b18eebc1946fca28bbd463fb1bd4fca0a2b2ff57558ec2f004798c58253ccc7740f18174df258d07499ef8 WHIRLPOOL abc9ac85b431e2acc5ec8bf760ff52ae77c60df8e72dab823cb83c0040f895b6234b28b7e63ca854422bd311cf17079cacf03e702d3cc6e5907bcd13080b2208
 EBUILD ccpn-2.4.0_p140915.ebuild 4692 SHA256 32847b9452cab2d8579eb372548812497425f25715f4597a9c967abdf8ccf687 SHA512 67b2c0c969cf83194435667dfb92719d8b75be049cafa708c124e91a60519ae8b43843278004ecac92dc1035cd8391cd8531f58b82cf1fffe5151d0a4595b340 WHIRLPOOL e5de10a8838cfee05a23e81f1f3f032e23263633b67504afe71ae5a7d06a4097eba4ec32714907380ce17d82619fb8db9e0217b16952e19f0babe19dd3e30c79
 EBUILD ccpn-2.4.0_p140917.ebuild 4692 SHA256 9f4acfd7e56f6f0ccd12037b91bbd7e739e932e4543b8f34214273c0d2954012 SHA512 a7abfe87f100596d9f1c1bb22c43f35833a7f256c153fe2e52d2be4570eecb82b641081b35fd62478800a579ce4a5eb84f917095cd6172665b1d3e6c6db117ec WHIRLPOOL f0bc39c7ffd2b4b74919eec8d4b5bb619c3b45d1fc19f6cc5de6ca762b13189e5067e0e397f0ffe2e13e46ddfa6d18df78e8ef2def28426bdeab479bd9aee075
@@ -42,24 +43,25 @@ EBUILD ccpn-2.4.1_p141022.ebuild 4692 SHA256 bc559064a91bf4d92d17714c6d67f1dd7b4
 EBUILD ccpn-2.4.1_p141117.ebuild 4692 SHA256 9ddc2b8b9fef6302f5adaea918a05b6c5307663f4c41e099a68c1a113f4cd440 SHA512 cfb181c616ff4d80a6a22b0f5d0e2321ff4fd61e50bd1cfce3502db45056f55c50d57c57079a51d559d0660bd93496e308f66eefcf22220d9a0376f9aa3e57ae WHIRLPOOL 42b842692007dfe752b37301acba95455febf8da2ddac27ed163c099a9b9be8db1cd0cfee196ab668df25830a4826362c4328c5e624c40f2a1325ef38d597e85
 EBUILD ccpn-2.4.1_p141204.ebuild 4692 SHA256 dce86e7384ab436c6da05d38d2668eb71607d58ad0edb89e5970f0399cc17012 SHA512 0f4052811f3aa6c033984263b81e37e962539f68403ffe7e98ca79cea9fd309044d0d0ffbd8005092a70a9cefdd8debfe260da78a0db2a85b4632c17dac3c25e WHIRLPOOL 6f1f347073a25b622ed7d966a9e7b252cb6d674d8e8c11ff4ce5675c3ebc1b6476ddbabcb3067de257260109a29ee59fccc9cff9ae354fb40b27b8f046df72c7
 EBUILD ccpn-2.4.1_p150105.ebuild 4692 SHA256 3eae14889135e60f8c67b5c92e92621bf6a759bc25ca14ad59f076f145558df6 SHA512 2edf083f46dffbcc0366bd3156c19822bff7762d1b736406daacf3af6af41683f0c1506fcdae59e3db3e91c0fe1096d5b30a7c4a92c508ee71fad200e2bae5d6 WHIRLPOOL 94cf022891b2ed7e189abeec8bc05f8df4e4187ec21a981dfedc400d1a2cf5eb513baccdc3f871a245e002bbb072c055c90808b816b1207b7f8776f7066ef25e
-MISC ChangeLog 29153 SHA256 3d5a9ba38152b8d0ff52697125ae122ea7788f385003b000f64a42ef9cf3392a SHA512 e45dff5c43cec80f424886a858a1cf73769470d554ae3ff03877af44c38a8dbd71c56b972f8ca3b4111e39843999f0335ea8d6629726c528216d76b2996a088d WHIRLPOOL e5211cb1b1f7e5f7728996274db0071819024bb404a560741266e3fa99ec62963a3611cf6c0666211ae82f0256255599e7bdeec74b7d78867c204fa5153003dd
+EBUILD ccpn-2.4.1_p150108.ebuild 4692 SHA256 cd8f2a9327714d07a88b714353299e078b6177444d746510e55dc7cb4c4b6e91 SHA512 94b835c77fec900191f3819934951938e864fa061e25c8a6e885af527947fd60510ec4dd8a65661996233d3de97fa0143803c7ba59508c79900676341e628721 WHIRLPOOL 638ec09624e702b0fc585a8eb63bf4070cd598e3b49032cfd4bd5f82219a77a16c832caec032f59b30e6ee1d4fbb41cbe7611a4d3b4e8c14f1f61a5942f79109
+MISC ChangeLog 29288 SHA256 faabcdc89c4f3ee2b8ee5490e1251320385cdf040dc5d219ea9d52b828f17a73 SHA512 0ee551413c94bca07b7b2595b32bda7f859be7aafc7beabbb9473d8a72cbec37d3fdad5c7d58cc54ad86c34d6cd2469950ce8fdd023d0a8823c16116422bd1f5 WHIRLPOOL c76935a486fadcd91dc23f7d2966b9582365e740cf67c17971edeede0ffa713d554c668f81bfd843a71c31df76bf542ba515ce79a9c18406d124f761c9a19bc5
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150108.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150108.ebuild
new file mode 100644
index 000000000000..0ba4565df18b
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.1_p150108.ebuild
@@ -0,0 +1,166 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.1_p150108.ebuild,v 1.1 2015/01/08 07:58:02 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_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}.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 "${FILESDIR}"/2.3.1-parallel.patch
+
+	append-lfs-flags
+
+	sed \
+		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+		-e "s:weights_s:weights:g" \
+		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(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
+}