sci-chemistry/ccpn: Todays python patches; fix for generic tcl/tk; drop unused local use description

Package-Manager: portage-2.2.0_alpha153/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

5 files changed, 193 insertions, 13 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index c0dc7ce3b597..def0157fb74a 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.100 2013/01/10 17:41:33 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.101 2013/01/16 11:43:05 jlec Exp $
+
+*ccpn-2.2.2_p130116 (16 Jan 2013)
+
+  16 Jan 2013; Justin Lecher <jlec@gentoo.org> ccpn-2.2.2_p130110.ebuild,
+  +ccpn-2.2.2_p130116.ebuild, metadata.xml:
+  Todays python patches; fix for generic tcl/tk; drop unused local use
+  description
 
 *ccpn-2.2.2_p130110 (10 Jan 2013)
 
@@ -8,7 +15,7 @@
   -ccpn-2.2.2_p120912.ebuild, -ccpn-2.2.2_p121012.ebuild,
   -ccpn-2.2.2_p121112.ebuild, -ccpn-2.2.2_p121119.ebuild,
   +ccpn-2.2.2_p130110.ebuild, metadata.xml:
-  Todays python patches
+  Todays python patches, Drop old
 
 *ccpn-2.2.2_p121125 (25 Nov 2012)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 4a1fcacf8953..39437e80fa9e 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -20,15 +20,17 @@ DIST analysis2.2.2.tar.gz 21044504 SHA256 8e46d12b8fb7763d282933e14ddfa9ce197954
 DIST ccpn-update-100806.patch.bz2 187965 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4 SHA512 ab145f14137955bcb4dcc4d242eb718a806152bf3376e4cc9ff5e8186ed54812051ad07de1c9d2316ce3379c8c74db4af36f714aa3291ea7a1d11d4f432df06f WHIRLPOOL 2a0cbf62aca74e22fc0e00a0a91c3c185c10fb07277ba30791511565a2fa645b123a8c5164389eb9fb5a2d1f591e26c6416c46038acceefa2f1ecf347b631a66
 DIST ccpn-update-2.2.2-121125.patch.xz 223556 SHA256 996f453d7d6a143715a94b1201bd7b8b9c037f6d0baa342f5c0645d500aa5c79 SHA512 d213e072a63110ec478c3ee64792b01c818d3c9052ae6d7dac903508536f78c432c72d5a4756665045579d72f4f54ef5ac9db1fb02eb5ea3111eaa47e72866b0 WHIRLPOOL c268761e4d9cf4c845964c7c865e20439a9cacd00bc56d89d8558e0f601fc9840d4288307c4a4f47ba6d478eb9da9dacd1e149c657d2e6506ef5e32d6b0b75d1
 DIST ccpn-update-2.2.2-130110.patch.xz 226800 SHA256 6c0f4d71322e45ef24a15f1e26eb5d4104499fc2391660e575158dc08ae0380a SHA512 2fa7e782ca30402c91793032dc0d4555d9e866ba11b03f8f4b06891c8c80d256f5598bccfc99e9a97ae9b3618b1c24307814de4656087e2c0b40d378df743e47 WHIRLPOOL 5a49c0480328e7b03691a1e63fea339e2a9a29afd845babcce70e57b6e8d6ce21a5cb612d856c22bd3a9033a9ab565b0149e61435bc31ffdf02e247051e29d6d
+DIST ccpn-update-2.2.2-130116.patch.xz 227144 SHA256 df7ea8439f58a32d3e9c9fe9dc187bb7fa6d51cbfdcaa0fa3dfec8e055cb2538 SHA512 34396fcc1688b2f1c6de62d6c89cbc6cbce606fc4191dd1c6f04bc5fb372f88dc9e54b94d4d42ecf1f49c5db1300a983e8fc8020c07911fc0656d48888f7a84a WHIRLPOOL 956ca65b9e42d2c2cd4f917284772ff94911da8aba138e7dfb955eb865dc02481f44305702d7f8343ceb45ae2fe840cd301446caa2f58234ecae2af4755b722a
 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 4658 SHA256 395ccae5b36353eea07585cff86ced8d52a44705694459e8ceac33d986f9fa9e SHA512 7729cf7d61a9b725775ec34ec3186f4bf9297ee10d3b76d889a9014d0b64b8c7b6dad434d09a20b554c7c336f54732ce83b50a38feb443816a805fd2e56df2a7 WHIRLPOOL 536b13159432085336e2079cadc4a382272e2963856972c4b2759580871026b8ba601de177c645bf21cfe0de540965ee7aad0b9bcd6bdaf4c81c3871d8b49ada
-MISC ChangeLog 19815 SHA256 91a36a46f04a07ee6a72a3b48fd95fa168a1d57dd508e7403e7ec53f04b11389 SHA512 8a7d6535eade4d5f7fd3c3c90022500c5aae825cc56582d8965b657897c59e288dd66cd4f15b64457a23d0e8c4edcea3f44139bbdb01c11a115f5599419704a6 WHIRLPOOL cbee84a842eabe82e1255dec25e4bc380aacac10426da72ad587225c769df254d627fd4a7a9eb85dfbb6ab8a41a784462c616ab1b570696a9472f04901674354
-MISC metadata.xml 331 SHA256 94d753ba1d3240defd1d9b5f6a60545874c498f65fc33a0bf8dbbb5690cd5f96 SHA512 353f8d2445a091abf398a4c6087d76d709880cc4f6f1b535bf2c59c433669a4f6c43283ec55e6ed137e7019559db1cd82a95e4451c0016c384356c128d5b8d59 WHIRLPOOL adf01cbf6b28a72f29abb737edfde82f90365ddb97a04cdb977e401bfde172c5f800d8cae3199c114bc3063bb47798dc6a2c356915277452b0d8d22d6803f1c2
+EBUILD ccpn-2.2.2_p130110.ebuild 4649 SHA256 53125900943ea89ba3d3483de29a240a0e7282098af869a04bc926c34f3bf51f SHA512 8406a93562897aadfefd03e098b393af5fb29f9bfde8e5727b73ceb6cbe004b73cfd97b61e942189d9fba717761b20cc4914e5c9d858f36bbdbdeea1369490e7 WHIRLPOOL 112e9cab77898ef9246b127d5ef8529948cfaf91157a25bbe39899560af8340f8e5cbd1e2a3935dae083a9291f0d569d3cc5b7588dc2029f3342ecbe5590cb0f
+EBUILD ccpn-2.2.2_p130116.ebuild 4649 SHA256 b1832e30ba4cf40a79a8781f0e84c49f35245ea36a42e7ca5adf2019bcacfdca SHA512 52fe7e59bb3a801ac30f0fb1d503622a0d6e18357fec14a73c9b83d05fdbac33d594e636ab5e72df6eea15dc796ab90c113d0715f1dc06d3ecebfcfcf9fc186e WHIRLPOOL 617306f09808d9bdad288990ffc3da5cacfcae8bfa8c07dbde20c879d9e5308a4d7d9d64afb217be0ef46801d22230a2b8a6152b461332b94448a01f813e4ffd
+MISC ChangeLog 20064 SHA256 097eda07f9ccd3723001d60016ddfc5ca57fec3d54dafedc4e3e16f6bb962a48 SHA512 f72b72f595897f10e799817e48ba9ec06eb18168453a586f7e3c52fef4a838e3785aafedcecafddf7f0f3dd581b0a9da0a4ee0c57abeff94bddb9da95892b59a WHIRLPOOL 190064103b521cc1c5fb004b9b32ad3d986b94b099148491f961b0a397d38450ef11290e2a8c423ee2056b3f0bfd8b5389e7fc9b1507f17038517eb94824a70b
+MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild
index 71c969df6198..5db6c4bb9349 100644
--- a/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild
@@ -1,6 +1,6 @@
 # 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-2.2.2_p130110.ebuild,v 1.1 2013/01/10 17:41:33 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.2_p130110.ebuild,v 1.2 2013/01/16 11:43:05 jlec Exp $
 
 EAPI=4
 
@@ -97,7 +97,7 @@ src_prepare() {
 		-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${tk_ver}|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${EPREFIX}/$(python_get_includedir)|g" \
 		-e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p130116.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p130116.ebuild
new file mode 100644
index 000000000000..9e83f3d33e37
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p130116.ebuild
@@ -0,0 +1,174 @@
+# 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-2.2.2_p130116.ebuild,v 1.1 2013/01/16 11:43:05 jlec Exp $
+
+EAPI=5
+
+PYTHON_DEPEND="2:2.5"
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python 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}-${PATCHSET}.patch.xz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+RDEPEND="
+	dev-lang/tk[threads]
+	dev-python/numpy
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+	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 ${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${EPREFIX}/$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
+		c/environment_default.txt > c/environment.txt || die
+
+	sed \
+		-e 's:ln -s:cp -f:g' \
+		-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C c all
+	emake -C c links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type f -delete
+
+	libdir=$(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 ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
+		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+			-e "s|gentoopython|$(PYTHON -a)|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
+
+	insinto ${in_path}
+
+	dodir ${in_path}/c
+
+	ebegin "Installing main files"
+		doins -r python
+	eend
+
+	ebegin "Adjusting permissions"
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/ccpn/metadata.xml b/sci-chemistry/ccpn/metadata.xml
index 8a82c7657734..ae9ec7c5f6a4 100644
--- a/sci-chemistry/ccpn/metadata.xml
+++ b/sci-chemistry/ccpn/metadata.xml
@@ -5,7 +5,4 @@
   <maintainer>
     <email>jlec@gentoo.org</email>
   </maintainer>
-  <use>
-    <flag name="extendnmr">Install needed packages for extendNMR support</flag>
-  </use>
 </pkgmetadata>