Todays python patches

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 200 insertions, 24 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index b34e5b283c9e..fb4371cb2ac2 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.164 2015/03/11 15:23:47 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.165 2015/03/25 12:17:39 jlec Exp $
+
+*ccpn-2.4.2_p150325 (25 Mar 2015)
+
+  25 Mar 2015; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.2_p150325.ebuild,
+  ccpn-2.4.1_p150226.ebuild, ccpn-2.4.2.ebuild:
+  Todays python patches
 
 *ccpn-2.4.2 (11 Mar 2015)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index f12c4d71570b..e4791f800844 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -15,26 +15,28 @@ AUX xeasy2azara 288 SHA256 e116e19f3cb7bb10a75b75608ae6efb93dfb710e86fece357f300
 DIST analysis2.4.1.tar.gz 36088236 SHA256 1cb089dcc739e8536d938a68536f556094f5d728907b251fe337758ba5bef106 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1 WHIRLPOOL b53fc0438a878a8f8ce0244f5c1ce9edb616665149a699364e3bcd38c5db548c22b80ef67b4183ad5321b71b69a3b85aecc7d912893bba947700003a411651ac
 DIST analysis2.4.2.tar.gz 36390919 SHA256 14941131033cbd4b0b13d6d4fe3f9253360a7c2ace8ece9194be00c1fe4b2903 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b WHIRLPOOL 4499dcb074d445bfc972f9dea43e6f3e3c28722d513dce0fec4e1b2b5dab8be098f53f82565d86a4e7935f0595ef303465668230aa61021cf88e13cce8606214
 DIST ccpn-update-2.4.1-150226.patch.xz 10732 SHA256 74e8723d310d336cd4215ed4e9a1a1c0b2c0efdb4c03aaacba7ecd0575b38287 SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb WHIRLPOOL 3a2357d4fcb086206d45edd5b9cc807313b5f62be2f2a70e8f011f5521cf8729371b8c7149837c4ea1f6f059e26a49c1d20492f338a844e15f38ccf543faf6e1
-EBUILD ccpn-2.4.1_p150226.ebuild 4663 SHA256 6c1dabe2bc98de950634a6d70539ed1fb459e6197e1745f93254ad5cf0652d12 SHA512 43d771890afced54c29c2a30118a622125f9c47e137e1662b9f3ce048498a137dd495d61844ea1514868b94767538c0f368c2f00da6e72709429943267ee03d1 WHIRLPOOL 7f81b441dae290999ee4e50f0f9e95dc20835f35b658ebd76b316441d250dbcb8ab209b1b85ff2f310205c1425bd25c7ad4496b9e19efbdc70b622f407b05be4
-EBUILD ccpn-2.4.2.ebuild 4656 SHA256 08661857f887ef9da418d500dafbba34c7a80910d19a17f287f7f9607ec0a860 SHA512 bd862d9e20b320aca7c28261cd16071c300fa94f36bec2f6640e39b5a985f642257cb3513c198fc9ebf1c994f14c57ba3b93f385364698e5f1f26db3b90e8c59 WHIRLPOOL 3b87bc53a3fb2bf88d602dc5684f3de7cf3616896d814cb793132aefd4d78bf2830c057dea0b4644edc5488dcb3781d9223fb0e2603d5c03ba3c8b264d01cf52
-MISC ChangeLog 31102 SHA256 1425aadbe7b89d0548accb5fe662d87d8a23e3bdb44b41de89f045dcd24bd035 SHA512 93e0859fc144af9fb90744f131a4d87f7c06a3ad1dc4eab3454c66a8d7b2975fcc396ed1ffe1c21c4be823b73da1551d43d826cff54e2e9062c1f8329dbabe96 WHIRLPOOL 8ee3bc52c06b8457fb72b1f3c2e1d481df55cb4bec430144d1633b985d8bf0e4a5c1ed1a11d26c3c3cbb203b89c8d7434f2a5159409dbecc191918aad43a301f
+DIST ccpn-update-2.4.2-150325.patch.xz 2096 SHA256 d33676fd93aaa5814aa43179f221df69f4bae9b8ec98ce5b6cc57ce6aacab732 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873 WHIRLPOOL f2e9780eb3216185cc6b89ca490e14c2de1130393eda4308fc71e6a2eb0460fc97f83ab3c92fb6a488a1926ba2f3099c7ae5f0a4bd216f8ffa24bfd87e360838
+EBUILD ccpn-2.4.1_p150226.ebuild 4668 SHA256 5b0cda2b0270173831f07760c9c3d39f46e8e84a5ef3a4ada3ff5b3435375147 SHA512 59e43c3c2f9c6dce01633f4c3a6bbd51e14ec98b962777e027e634f70405013737cd2741b7e0cc78d407ab954fa9869a45a0daa2583d3306b030433896132dba WHIRLPOOL 64febf20e9b842370f16d848ce7087d3e663f87e2836e2eea4d10940919bd34638497b731cbd8c121237781e90ddc272b45cd39ea999f94b18420bba4713cce9
+EBUILD ccpn-2.4.2.ebuild 4661 SHA256 2d389f8474981d4f9b5888a2c1a54ef7615d7ef98db4ab919bafe5c694d925d2 SHA512 baecfdc6617a5c3e353fe9b459ed3fdec5bfc84ebc62418dbcc2ffb6e245e1c2c229721e305a54de9a02b1610d7e7dcd69aef953f4f5840ce58eb8d58bd60a2a WHIRLPOOL 334210c94184145054f84a2b0863d4a4cafbddce30ee862c257fc2eec50794eef2e297d7f6250d7fb54a01d75704b00fa1cc4ccf7248376cdb683672af7ac436
+EBUILD ccpn-2.4.2_p150325.ebuild 4668 SHA256 e5db889d53056bb80310bdbeacfa0dd942785eff48fbb5057aa5afd8b74c0316 SHA512 d297d0508eb624102f74a062cac56cac2193b2102ed1036669f9d0cabfa74717f0de312455f8bd7ed8392313c7afac2d4d670b5696f38555f18c075724737ce7 WHIRLPOOL 0da3cabff804429a020401b88d12240b8ad7eb973005a92bc3b2a51b71ce8f4889bced5f81962c11391a180e7d051ae8b428756cb060ed9387d5c3583c8d5af6
+MISC ChangeLog 31285 SHA256 6fd1b85c258fd4878a4ceab1b4ca0b73986a4d22591de81d212a7a546f7f8e96 SHA512 7d02a27e461fa6ce51282557a40f2562e261c46fbd2c8e6b2145f6972d7f36b457a2e6327feb3df0bfa32aa8c10a8931b2e1a0e72690f76eb21fc7adb5337ee3 WHIRLPOOL 874858792c1789be11bbc66932d31424c300820e69b83da62377c81190b5799c34fd752757b77a0dec57ce49043bb5cabe745eff47df36bf5044e3778dd2a665
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild
index 1333b404c9e1..48334c029ff4 100644
--- a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild
@@ -1,6 +1,6 @@
 # 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_p150226.ebuild,v 1.2 2015/03/11 15:23:47 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild,v 1.3 2015/03/25 12:17:39 jlec Exp $
 
 EAPI=5
 
@@ -29,7 +29,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
 	${PYTHON_DEPS}
-	dev-lang/tk[threads]
+	dev-lang/tk:0=[threads]
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-tcltk/tix
 	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
@@ -38,7 +38,8 @@ RDEPEND="
 	x11-libs/libX11
 	opengl? (
 		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}] )"
+		dev-python/pyglet[${PYTHON_USEDEP}]
+		)"
 DEPEND="${RDEPEND}"
 
 RESTRICT="mirror"
diff --git a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild
index c7092b446957..c676c4f3a3c5 100644
--- a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild
@@ -1,6 +1,6 @@
 # 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-2.4.2.ebuild,v 1.1 2015/03/11 15:23:47 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.2.ebuild,v 1.2 2015/03/25 12:17:39 jlec Exp $
 
 EAPI=5
 
@@ -29,7 +29,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
 	${PYTHON_DEPS}
-	dev-lang/tk[threads]
+	dev-lang/tk:0=[threads]
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-tcltk/tix
 	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
@@ -38,7 +38,8 @@ RDEPEND="
 	x11-libs/libX11
 	opengl? (
 		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}] )"
+		dev-python/pyglet[${PYTHON_USEDEP}]
+		)"
 DEPEND="${RDEPEND}"
 
 RESTRICT="mirror"
diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild
new file mode 100644
index 000000000000..f253352532b0
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.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-2.4.2_p150325.ebuild,v 1.1 2015/03/25 12:17:39 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="
+	${PYTHON_DEPS}
+	dev-lang/tk:0=[threads]
+	dev-python/numpy[${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="${EPREFIX}/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS=""
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+	fi
+
+	GLUT_NOT_IN_GL=""
+	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+	rm -rf data model doc license || die
+
+	sed \
+		-e "s|/usr|${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
+}