3 files changed, 190 insertions, 17 deletions
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 38c9de4d2379..fa3eebdff53f 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 1.167 2015/04/13 08:01:37 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.168 2015/04/21 13:00:03 jlec Exp $
+
+*ccpn-2.4.2_p150421 (21 Apr 2015)
+
+  21 Apr 2015; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.2_p150421.ebuild:
+  Today's python patches
 
 *ccpn-2.4.2_p150413 (13 Apr 2015)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 12478e132d2b..78d5b842a45a 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -17,28 +17,30 @@ DIST analysis2.4.2.tar.gz 36390919 SHA256 14941131033cbd4b0b13d6d4fe3f9253360a7c
 DIST ccpn-update-2.4.1-150226.patch.xz 10732 SHA256 74e8723d310d336cd4215ed4e9a1a1c0b2c0efdb4c03aaacba7ecd0575b38287 SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb WHIRLPOOL 3a2357d4fcb086206d45edd5b9cc807313b5f62be2f2a70e8f011f5521cf8729371b8c7149837c4ea1f6f059e26a49c1d20492f338a844e15f38ccf543faf6e1
 DIST ccpn-update-2.4.2-150325.patch.xz 2096 SHA256 d33676fd93aaa5814aa43179f221df69f4bae9b8ec98ce5b6cc57ce6aacab732 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873 WHIRLPOOL f2e9780eb3216185cc6b89ca490e14c2de1130393eda4308fc71e6a2eb0460fc97f83ab3c92fb6a488a1926ba2f3099c7ae5f0a4bd216f8ffa24bfd87e360838
 DIST ccpn-update-2.4.2-150413.patch.xz 3132 SHA256 c0796e1f739f799003304c8b8d23ea0ee42b2e0a6dd59b292cb2a1167b5725f5 SHA512 99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d WHIRLPOOL 48a355ef4824d41517d618178be4cd4efc42a6f5e190bac88348041504da0807aa1b34bafbc3937d7f6fc3b5b52fe469431fb6ce9df40bb1c56d7faad88cfe51
+DIST ccpn-update-2.4.2-150421.patch.xz 3788 SHA256 df8f7dd81281f3f7ddd266b8bd90a089f61a9e8f0cda3bcba8b495a6f4be6238 SHA512 0e8a10b6d9721b52574cd2fe0413dca0fac32a948eb31d3db6e2c4d4f7d85c341e8d53d70954341792ea598a37ec87e4392a615e1c2f6f8bbfc0e42a750be648 WHIRLPOOL 2673ac33b2eca1a3fb873567784f1d77937e7ec6aec3ab7eef6065f9322513326993786bd3865a50c50c58e05bf874ba25df02d15083f50aef9acb404ca4e1ef
 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
 EBUILD ccpn-2.4.2_p150413.ebuild 4668 SHA256 378d49c75aa0b89d9c615125c36c479f3584b70913d50ecb3ddfcfa8b59a3df6 SHA512 f9ee3e61a27bf424e64dfd36e70834ec8e82aa99cbf160a8c49e0de37372ad7bed5d9a837b1892e1925fa9a68c937fc101078afd3931853955c68bf1c01474bc WHIRLPOOL 73c94ed2eeb89ce2f8a96e6a440dfcb19793402ff772c3a757dff0aa9236fe5743029c9a64092fe5e68788911657514e4f70aebfd89b088d90054fadffbb3641
-MISC ChangeLog 31421 SHA256 770b12176f120a35eba8cc5ee481407b7c1679422d8369a49ce7469cae205dcf SHA512 5966f3136c575a5a0d057518c8ee09cc4d520216ff8453672cb8a7b41fd508fd649a39131b053197ea785b59f1726e2c3c5b1130b017be486b500a8ae09baa49 WHIRLPOOL f65579fb6c34b2a1f028eab3a006d4a7e3d586d0f29294f0a275751b1137ebe07997ed2ebc2c9d32bf5a875517934884713e5791824732964593e3f39d27af18
+EBUILD ccpn-2.4.2_p150421.ebuild 4668 SHA256 ec197dfe02a735e41b954bfbe23bee94929736e325a5f2c83003d9b99aa659dd SHA512 2c3e5ea5dad421fcbe4d50cd3cb74d26bd8d2076b28dc5c2e071dfa8d6c69c8245079702141b8cdba5d1e7e20aeedb2556176ea83701929d6b02ae54e99cc94a WHIRLPOOL a549a7dd60d6c3281dd295301d1cd02f2a6097c2978e302898d94ec9883899f22aa19f92f2b2f50e4074bf0aa3f59588c1b898828bdeed5860267500ae40942b
+MISC ChangeLog 31557 SHA256 042c0bc173a82407f009a4fca2a0104631a6b468bad8c7cccdcebc13d2af3d7d SHA512 7ed05524d32beab53d2f5436af7f7f737b10f482ca2d04b94bd0f9e8d6554a579ce59404e8c366b42e3f7debb35981242a6579ebebe9a135ecb5efe6c91c299e WHIRLPOOL e486e6dce0ce4080dd7f3084b3c5743cb03f3f871b1b638d7b5ae4c6eeac986e1b0aafb2d49015d02990816e4968b8098b9b1bf2e9a47ce9a8abdd0be1d78d29
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild
new file mode 100644
index 000000000000..f39e4711579f
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.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_p150421.ebuild,v 1.1 2015/04/21 13:00:03 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
+}