sci-chemistry/ccpn: Move to new python eclasses; add latest python patches

Package-Manager: portage-2.2.0_alpha166/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

3 files changed, 175 insertions, 6 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 558861470b75..7a386d44b019 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 1.102 2013/02/13 11:56:42 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.103 2013/03/18 12:36:30 jlec Exp $
+
+*ccpn-2.2.2_p130318 (18 Mar 2013)
+
+  18 Mar 2013; Justin Lecher <jlec@gentoo.org> +ccpn-2.2.2_p130318.ebuild:
+  Move to new python eclasses; add latest python patches
 
 *ccpn-2.2.2_p130213 (13 Feb 2013)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index ae0567051cef..0fb11304d99f 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX 2.1.3_1-dynamics.patch 825 SHA256 53577b6f9621a707b1b5d676d57ed16f3963f3172598d944b823133908226edb SHA512 56d89056a2916cf7c5a90084b151a46a39a456ad84c1d9d4042bfa1bd236b576e3f3232a2e34c0adbeff77a4f954d73b1565e0df701a29a0eca1e0a654728e74 WHIRLPOOL 084bdee6ca240491db0a718e23529887c3b4341217a036be4f87e3172cdb01db364ff4adc6a63d66aa146c605e05891d2d1c879cf0576084c5662e016314b74e
 AUX 2.1.3_1-impl-dec.patch 2818 SHA256 f175a1b4a9cc4f1636bf36928883d37a266af830234aa3d7676f4fe4f7f1ddd8 SHA512 11d54abe5578424c601f97e28f7af613284b789ad977c6b1f4e737116828ad0eee3183f65ba20e609065d602028a3cc59ebd6fe232d0c06133b0dcaea5f3dbea WHIRLPOOL 597d03fab86dcd61991a256a06644df0edb3edbbcbc6b916b8b3dd6808f5809a473383facabd46bf1ac343a9d75f9c49cac36c1a1a8cc60974f66b43237634fe
@@ -22,17 +22,19 @@ DIST ccpn-update-2.2.2-121125.patch.xz 223556 SHA256 996f453d7d6a143715a94b1201b
 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
 DIST ccpn-update-2.2.2-130213.patch.xz 228908 SHA256 45d6fde3aff5f1d4c6f324501867a4177c0500b8e427541e31c74d9fd65a220b SHA512 2ade631eb7123eb67573294debcf5ac25c47f9b68e88942e7d2680e1bd813dedbf1a9b36cba86b8bbb48378310fed6a4211eb0af7177a739b634415b80c0081a WHIRLPOOL 5ca9808940a87652ce01cf54163bad035edfa204f8dfedee7868ae7438daeebca8217cf7963788e996307164e785b2d3be2869ff509505c6f72f65db9202dab6
+DIST ccpn-update-2.2.2-130318.patch.xz 231912 SHA256 ada36dce0c715ad39ab0446a2f6462a983feb6f3dbaa966222bce42a7e2c0ece SHA512 1fa319007405ca15e97ed68a9c703203c93f0dc5a2e6b06d36b5570ac3787f250f5335eda4cc38768a5b37870aafe6cef47e5a96378747c46858040e8bfc4b61 WHIRLPOOL 0315de7b0e3f4843de56e6c7f7612b99e5feae1887832ebf0fa19dddafb4a82759b3fbcbfd17904cc2cbcc9d0daea6fe93a310732e799bc40c1ae36ec8a5e8ff
 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
 EBUILD ccpn-2.2.2_p130116.ebuild 4649 SHA256 b1832e30ba4cf40a79a8781f0e84c49f35245ea36a42e7ca5adf2019bcacfdca SHA512 52fe7e59bb3a801ac30f0fb1d503622a0d6e18357fec14a73c9b83d05fdbac33d594e636ab5e72df6eea15dc796ab90c113d0715f1dc06d3ecebfcfcf9fc186e WHIRLPOOL 617306f09808d9bdad288990ffc3da5cacfcae8bfa8c07dbde20c879d9e5308a4d7d9d64afb217be0ef46801d22230a2b8a6152b461332b94448a01f813e4ffd
 EBUILD ccpn-2.2.2_p130213.ebuild 4649 SHA256 bf5b16abe8e4a864b6b8629634464cc026aaf80b45361ca85adb774f1f282d2f SHA512 2fbe3dfe634a43bfa543af91cf7778f178ed5725ad034cbf815c202de6a781b0cf2448efe6e99ff721872c168fa1d1efed784112bf3085d7f1174fc3d2e013db WHIRLPOOL 9c83b89f53e34fc65b169c22686f472b6f2adf92feaa965608b7b725fc7d2507866c7fe32f09100a76d58d0c53e47ef61534612c933199017203a72213642a07
-MISC ChangeLog 20199 SHA256 8e29aa24618e90d8a1f0082fc675812183008dafd4cf6ee212ded0ed72da1b7a SHA512 7192aa23e0de59724c8da6844c09316fed215e4da6066cde56fdbc0bf7af2f46a38f8ccd5083600d6caf0c987f085f30e0547c05fa2df0b0d91d9816d8ac6586 WHIRLPOOL f920bed66ebeb1dd9f214d37f14053c8d5394ed8282a7cab218dd459b72a13927bf73f19e43b8296702f2687e57b62b2fd22884b3a88d0f92b51baec64dbf4c1
+EBUILD ccpn-2.2.2_p130318.ebuild 4574 SHA256 cb82394e883319e956dcd49de1c924f3d1c7abac65a155711cf40081087b43f9 SHA512 af77c2e6c0059f9f474fbececa819b13018391a04397adc53ebe07ab77227f0ae4b65054794aecc94a59284d9f7e4c6f5bb9bf89da7e552dab47f0ad41dfbbe5 WHIRLPOOL 08e14c30d250a8229c6ab163479f82836756b28c6d104d6fa9c6ec12a00545a7ac8ba6033087b932f4c8f70489144fe22f2ce8e0fe9620f00d7ce8f9b00684e6
+MISC ChangeLog 20367 SHA256 fdcc47e21d1715d5562f9ac615ec47ba548e595df98aa1215ff1043cc5fd7887 SHA512 d86f775350f6903c42506369e6edc7f2f559f797498287a5450af0704f934e365b12a3107cb5248dc68cbbc2c57ec8d2bef89cbdc8b2b5ededba1401066fbf4d WHIRLPOOL 546ac45b31f3dbad40df69855f26a0c0cef774eee753dce298aa7a8acebb0bb6953f627743f12bb45c3fec9484337ef31bd4b694a8fb29e548cf8b8dc1285d44
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.19 (GNU/Linux)
 
-iEYEAREIAAYFAlEbf4EACgkQgAnW8HDreRZUPwCgqkSo4oOYyX5+WF/mRR5FJO/M
-+hsAn3guSgEluFimnE9o5fRKyWN4sZzs
-=vW/t
+iEYEAREKAAYFAlFHCk8ACgkQgAnW8HDreRaDxgCeKWbuWNgVmIY4S+uu4QUpcK52
+ctoAoMbHOc69N6y7bvToiclxXOnbb4a4
+=XDOj
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ccpn/ccpn-2.2.2_p130318.ebuild b/sci-chemistry/ccpn/ccpn-2.2.2_p130318.ebuild
new file mode 100644
index 000000000000..9d5ba37dfa11
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.2.2_p130318.ebuild
@@ -0,0 +1,162 @@
+# 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_p130318.ebuild,v 1.1 2013/03/18 12:36:30 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+PYTHON_REQ_USE="ssl tk"
+
+inherit eutils 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}-${PATCHSET}.patch.xz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+RDEPEND="
+	dev-lang/tk[threads]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+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 -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 ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|${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${tkver}|g" \
+			-e "s|gentoopython|${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
+
+	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
+	python_optimize
+}