sci-chemistry/relax: Version BUmp

Package-Manager: portage-2.2.7/cvs/Linux x86_64
RepoMan-Options: --force
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 118 insertions, 15 deletions

diff --git a/sci-chemistry/relax/ChangeLog b/sci-chemistry/relax/ChangeLog
index b20fb1f59e4f..2fd134f6d94d 100644
--- a/sci-chemistry/relax/ChangeLog
+++ b/sci-chemistry/relax/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/relax
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/relax/ChangeLog,v 1.10 2013/11/27 11:27:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/relax/ChangeLog,v 1.11 2013/11/29 08:38:42 jlec Exp $
+
+*relax-3.1.0 (29 Nov 2013)
+
+  29 Nov 2013; Justin Lecher <jlec@gentoo.org> +relax-3.1.0.ebuild,
+  +files/relax-3.1.0-sample-script.patch:
+  Version BUmp
 
 *relax-3.0.2-r2 (27 Nov 2013)
 
diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest
index afcdeed29da3..cb66120618c3 100644
--- a/sci-chemistry/relax/Manifest
+++ b/sci-chemistry/relax/Manifest
@@ -6,32 +6,35 @@ AUX relax-2.2.1-gentoo.patch 1676 SHA256 8c31035e6d9abbca876a5d29ce25abe2a6daf6e
 AUX relax-3.0.1-gentoo.patch 1645 SHA256 266faa00ccfae77171785800825ec16ad518e0e22ac2ade74154ab01d547fa17 SHA512 6869b5dca42d7428ab177ee3134feded9788d61cf0fe870dd1198039b9f520b4e7e745feae0ba01189f832fd21a6141ca53f8929694d25207f08667b2744606c WHIRLPOOL c74adb00570006e0c515d4b88234044d76ac7ca15e0c1224ed626d05efd71b114abdc8d14196921cf022db55f67fc250bf95a86d339c2052f99672724c1f1366
 AUX relax-3.0.2-wxpython-2.patch 2258 SHA256 281440662cd3aacbf0c77269c3216be5df34aedd7bfa24bdde2ad22d4cbfec1c SHA512 f0d49f3870c28c776a300264a4656711db4e01f5ac065a3d079887ad299c50ab66bb899403ef13a13ad1dde80cde7f5cf44f8a6f25a8ec80b62e068cf55717b4 WHIRLPOOL 02601f57d0573bd0da665fd15da0e3196cd550c2403b700088e224e83925c03c5a1e54838bf52485f3625b067f2e5ff9775fce5964e0c571a3cfbdcc616de820
 AUX relax-3.0.2-wxpython.patch 26526 SHA256 e027848934357fabe880bf99792cfebbbe9285c5a62bf806e1b547158b3f7f7f SHA512 1c98220c4eda426fac0c8b463e9360bff74ab9b5923c3c068c90b02971860a267ded2b39e7f41ddc71fd15bd92fab911ab5b879b66715bc0953b3a4184901b22 WHIRLPOOL 5db39eaf6219faa48efe4609c45f0cf22f333a499032e2ec03a33c4afe64c9153629b25379a72853e83ee4a0457e172a963a358a4e2497a9d020992aa2d2ec93
+AUX relax-3.1.0-sample-script.patch 1809 SHA256 7201cd4d6b9379e3fc2d6115847f1134ac80505922d91ba56ab96507facfcfd7 SHA512 aaca5fe9294f4c013cda8d3f10e24badcd0b6e4a5cdc757bd023a3d55dd8f2d8a671b5c52d3fa064811dcf0bf0d40b8a8004d5447dfebfafb9908e7fcac5fe6a WHIRLPOOL a9e9980f45353eee1ac5e5a537706ca4bff82663ffc0518b2f66a59bf7071ba8ab807ab60afc1f68f062aba9e6d07e9db1f133f24061028ca0dac864de73c7f1
 DIST relax-2.1.0.src.tar.bz2 22054720 SHA256 e7908dbf774e1eb866f45fc222d14935624ce9fe4453da979d1b6cb7e1204dd4 SHA512 e42fb050097de6c79751477e1b9e8ff76f8d495fae446380785d8bf8a0e384df4837b283d95c6988e9e5a2aec9af54369a53cc5584d233c58448882f07235dd0 WHIRLPOOL 51b62e2515780248345c14e1fd11511e8dba1832c69178dca1afb0784b2d411ddb21d3f305e04216ef8e041ea1ce560a40135617f91a5bb5e94d19c76ec0cab6
 DIST relax-2.2.1.src.tar.bz2 58950056 SHA256 532fabd9f8e3c7503ee9b75f690869898f639526e0b36c858f66faddba6d3831 SHA512 d6bc574d9ff0baed5f08599df585354b2e0aec263adb33773aeec5392bb26efe43d8626cea13e789b2d1346bfe763511882dfe2c3ee8935ae4c9c0955f76ba79 WHIRLPOOL a561c0c25e0642aa9190233e4ed7fb045f7f891c690d662a559cc3e6f1f7da27977fc8e27c0cc27ab3c0b9624ac9bd606ffa6f7cb77e77bef8dae7b88430116d
 DIST relax-2.2.5.src.tar.bz2 59081139 SHA256 1f62d5e3294accab2baee912216d1651d9ec43b8b33d7f8d434c125c200991fe SHA512 bffdde3fd4644e730d41b1a67e1f43f07f6a9426bd9f714aea59a92c2868e5467adc5bc57326e1c8904708b13b13482867e040fc28373d1b5029b577b400895f WHIRLPOOL d3e5817e7de0d9bae830cb195be1d90a83020c544bdb06b31958f07e7b0309189ae48a3f21a12955f457fa86a21c8764b619a62a6d8a966be46bcdd4b5c52a90
 DIST relax-3.0.1.src.tar.bz2 60536002 SHA256 472b0446c3611a06c4f5bbc338e7986e31993f31a4289a2c211fa0510a0566b1 SHA512 0e1cf46324a52363c4ceb18c2817e0d57cf38ea781a213822156601c05aecd56af0fdb39a1e7ff996dd6c20b5d8c8cc6aa27fcbd6082f51d712d5fc843e3fdc6 WHIRLPOOL d9445e76fc70fb57384ea7aa86a672575ca702dd098fe3b37fd494744d75187a62827a72c3ad5253069be4d6e00ea47443e6a13123a911d599bb0ae57713e175
 DIST relax-3.0.2.src.tar.bz2 60546216 SHA256 647fa4b05ae4e7f5072ee1c3c88af5b6eaf7a81a32d1b9a506d69ae8e37c865b SHA512 e90f97ee62ae56b899e0d70a2272c9411a56e71a0f14032985870a781a2fac530bdbff1669b46faae599a047141904a6718d351513b1f2d1afed8b92709d9501 WHIRLPOOL ec93521174c34357a06e82ee1ac5fdf3af5b341e951f5c263451a2bc90e9067f99e689455a4b3c966cb128661cb69bfd7aa355d7ca3fad7686139d8c1deea835
+DIST relax-3.1.0.src.tar.bz2 66036287 SHA256 900454b3b84749c35c824065bd61425e8cf53a4b2cb2d3cfa82fd54e3ffc091a SHA512 95536807247f0bc7721c5af40275445e20cf554bf8318b7e6f4bda6d0e15d96681e68b03d14f63438203814eba31d8b4a927e098194ca2572364a84cd6249a75 WHIRLPOOL 1bb244eedf76743e7914c1620fa056dadb983da93c3118427447cef9f251405bc5b791e5b293f59921f1b8e6adcd1001a6a4bee7ddc61c8c0e844430d6a76dca
 EBUILD relax-2.1.0.ebuild 1128 SHA256 2d49d317cc424da9f9f2bf86ec802dae614952d506e385a60fa95e262b0c0da3 SHA512 fa76e538545bb5a2d520d3b063ba255f2d4c0279332631f061444a697528f78c6709f3d91a946289bf80828059ff7423b0d3d5374117bf89625f360212540614 WHIRLPOOL 4e0686ab5f70ddd7243c53437978b617ee2a9be55da1eb78022863babeafffae80536048471526e6076553761ea968129e7100c960d6fc7f970b281911d4ba09
 EBUILD relax-2.2.1.ebuild 1337 SHA256 4c65b74e17d1928bfc0f42230e1ccbc6abd5963901a751a7782f3c19bf25008c SHA512 70c78139ba9a9a08404673fc970082f9e3c868b2651b80d9f7cac4c5680bec846c69d3c65e68240139dfe37957607845b0ac66f595151ee7051b745d500d095e WHIRLPOOL 219ca572d15297a779da98b2a9f7a12edd80bec89710be07d0d2b02716534c831893a0bc14a0a9f177e6cebc0283c4d25872c4265a7f6f20610c0b17feafd236
 EBUILD relax-2.2.5.ebuild 1521 SHA256 f9192d970b2e70dcebdfc6ebd4658459cf5ac88a1b74886cf456108633ccf2c3 SHA512 7a4f13a4be29ef48082e82e6ec7bc6f6b3e1da72ed32e914b9f202c83f61868d850f3c4f2410407ad4c1be5ce5939fb16330d403bcdbdea12fc69e0070a15007 WHIRLPOOL ba6768c596b799456d18f85450520b7de81b5688df9ec3762023b54bf82f3398ed9eea862d242a064ffd3f71f8f73315b15d8734ace7a0196e4fc0b82be8ad99
 EBUILD relax-3.0.1.ebuild 1510 SHA256 640d9964245a7c7b42db8e31f59cbb33c6c136481f9cedc46ad80e425e05d1df SHA512 773004e05d60024ba2b793cbe1cc0b95e9f2b788d5cd2a667e4d182598662181e82b03ca084f7690a6755b8bb6926a81b19190b8343f6e2b70ab7e781dd5b683 WHIRLPOOL d2eac52a53b0f7f6389b128ab4433aead2394e64ff1a10006b73a6633a407030918030e859d64657bd139d326cd38faba05f86094f7a684660dc08f48a761cb9
 EBUILD relax-3.0.2-r2.ebuild 1681 SHA256 15d6aa55fc61b7541b5855c96be559b381b3263b8193fbc2fa04a007bf50b39b SHA512 b80c1a5857df64e1e4c9015a4d65396ef186ac66713720ebead7cd72b6045524fba2103da6f5f4018c7c04453a9b89bf4018e237cda64834e003319ef2bfbb61 WHIRLPOOL 59f856b9b638384c3015a705ffcc391d209dc207fae07e9cb27e68bfa51668ad5c4ef8cc037a8ed04f6cae16c4732e69b465344b2eaaeeaf101170d6db77e030
-MISC ChangeLog 1786 SHA256 40e536aa5bf7f15441d85cae8e27f0fe20ad4905d3b6dfa8fa2e53080c3ff28c SHA512 8552325fc3f3caf8c98a8d33f4e61b7095b7adbc69a744d716be4165dfcd33ff6e925be8fac5462ca4f1eba4c3e6f84160cf2faa72f05158fae370ab9c345e09 WHIRLPOOL 3c9f0f435a1a250619e08b013d8c3e748b7644c510211f7b15e64d8182e14cbd509cad052eea22fbd79cf7f21e428eaede4da0378b42c0cebc827c25a40151de
+EBUILD relax-3.1.0.ebuild 1609 SHA256 19b52e4b492705815850c2073403214d3774cdc0ab4755ff3840cc8f567aec38 SHA512 72415c6207f79182cc5990e92c84b1edecce14aca5495660161d34abf09f63e5ead19fc79888959c2eb3d8155bd4d97c84a074d65556c21382654fae6e4ed11c WHIRLPOOL a031272eb826e199774b1921d8ef126a1316da431d1e8ba9c06e8e758669fc64fcdf84a1160f284ed7114c69df4deb631e40d41d5a6c6b68b5b4c655f3aadc55
+MISC ChangeLog 1940 SHA256 bf3f9de5b7af33f5fce38fdfb589638a60153b20304c84ced77d8bcf216e4665 SHA512 548074aca569cff90bd03f5933d86d65619f2615d397788842ed9c3b9c47d583cf34e07d89a662033829b6be66fa44f0cf0f77a143d86213c4b0cd21e75a0672 WHIRLPOOL 1c17884299dfedd44abbf611a96ba328f0e4675a45e95f397998f42af43f82f03408457d7c73a26d140ec60edc0e8422f1ae26dddf4e65bd32ebbccb70765f77
 MISC metadata.xml 1315 SHA256 58aef1b2b940b7211a85032dfc7212025aca6a3cd313b1a6e203854bbd3dd03e SHA512 dcb1d935782546693b79aa74dc37d55701ff4cb1756860a7f0d9919534ad2ae6f1dcad20cace867b10297c577cb6444dd5e212b13f57c3d81b30b382d8458c04 WHIRLPOOL e2de7c85fb3494a98c2ee1b08dd06d28676f43f64367ad29a8723f712e12e9052daa82794bb6626506de568701b1ea09efe059a8d3a13f6aee5fd607a913e441
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diff --git a/sci-chemistry/relax/files/relax-3.1.0-sample-script.patch b/sci-chemistry/relax/files/relax-3.1.0-sample-script.patch
new file mode 100644
index 000000000000..c1eefd2cb736
--- /dev/null
+++ b/sci-chemistry/relax/files/relax-3.1.0-sample-script.patch
@@ -0,0 +1,25 @@
+ sample_scripts/relax_disp/R1rho_analysis.py | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/sample_scripts/relax_disp/R1rho_analysis.py b/sample_scripts/relax_disp/R1rho_analysis.py
+index 1dcbf68..11d6f97 100644
+--- a/sample_scripts/relax_disp/R1rho_analysis.py
++++ b/sample_scripts/relax_disp/R1rho_analysis.py
+@@ -77,7 +77,7 @@ spin.isotope(isotope='15N')
+ 
+ # The spectral data - spectrum ID, peak list file name, spin-lock field strength (Hz), the spin-lock offset (ppm), the relaxation time (s), spectrometer frequency (Hz), and experimental error (RMSD of the base plane noise for each spectrum).
+ data = [
+-    ['ref_500MHz',       'ref_500MHz.list',     ,   None, 110.0, 0.1, 500e6, 200000.0]
++    ['ref_500MHz',       'ref_500MHz.list',         None, 110.0, 0.1, 500e6, 200000.0]
+     ['nu_1000.0_500MHz', 'nu_1000.0_500MHz.list', 1000.0, 110.0, 0.1, 500e6, 200000.0]
+     ['nu_1500.0_500MHz', 'nu_1500.0_500MHz.list', 1500.0, 110.0, 0.1, 500e6, 200000.0]
+     ['nu_2000.0_500MHz', 'nu_2000.0_500MHz.list', 2000.0, 110.0, 0.1, 500e6, 200000.0]
+@@ -89,7 +89,7 @@ data = [
+     ['nu_5000.0_500MHz', 'nu_5000.0_500MHz.list', 5000.0, 110.0, 0.1, 500e6, 200000.0]
+     ['nu_5500.0_500MHz', 'nu_5500.0_500MHz.list', 5500.0, 110.0, 0.1, 500e6, 200000.0]
+     ['nu_6000.0_500MHz', 'nu_6000.0_500MHz.list', 6000.0, 110.0, 0.1, 500e6, 200000.0]
+-    ['ref_800MHz',       'ref_800MHz.list',     ,   None, 110.0, 0.1, 800e6, 200000.0]
++    ['ref_800MHz',       'ref_800MHz.list',         None, 110.0, 0.1, 800e6, 200000.0]
+     ['nu_1000.0_800MHz', 'nu_1000.0_800MHz.list', 1000.0, 110.0, 0.1, 800e6, 200000.0]
+     ['nu_1500.0_800MHz', 'nu_1500.0_800MHz.list', 1500.0, 110.0, 0.1, 800e6, 200000.0]
+     ['nu_2000.0_800MHz', 'nu_2000.0_800MHz.list', 2000.0, 110.0, 0.1, 800e6, 200000.0]
diff --git a/sci-chemistry/relax/relax-3.1.0.ebuild b/sci-chemistry/relax/relax-3.1.0.ebuild
new file mode 100644
index 000000000000..f8dde3d0958c
--- /dev/null
+++ b/sci-chemistry/relax/relax-3.1.0.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/relax/relax-3.1.0.ebuild,v 1.1 2013/11/29 08:38:42 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+WX_GTK_VER="2.9"
+
+inherit eutils python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx
+
+DESCRIPTION="Molecular dynamics by NMR data analysis"
+HOMEPAGE="http://www.nmr-relax.com/"
+SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}]
+	sci-chemistry/molmol
+	sci-chemistry/pymol[${PYTHON_USEDEP}]
+	sci-chemistry/vmd
+	>=sci-libs/bmrblib-1.0.1_pre198[${PYTHON_USEDEP}]
+	>=sci-libs/minfx-1.0.4_pre98[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	sci-visualization/grace
+	sci-visualization/opendx
+	x11-libs/wxGTK:${WX_GTK_VER}[X]"
+DEPEND="${RDEPEND}"
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	rm -rf minfx bmrblib || die
+	epatch \
+		"${FILESDIR}"/${PN}-3.0.1-gentoo.patch \
+		"${FILESDIR}"/${P}-sample-script.patch
+	tc-export CC
+}
+
+src_compile() {
+	escons
+}
+
+src_test() {
+	VIRTUALX_COMMAND="${EPYTHON}"
+	virtualmake ./${PN}.py -x || die
+}
+
+src_install() {
+	dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf,prompt_screenshot.txt}
+
+	python_moduleinto ${PN}
+	python_domodule *
+
+	rm ${PN} README || die
+
+	make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@"
+}