sci-chemistry/relax: Add another backport for sample scripts; add live ebuild

(Portage version: 2.2.7/cvs/Linux x86_64, RepoMan options: --force, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 194 insertions, 3 deletions

diff --git a/sci-chemistry/relax/ChangeLog b/sci-chemistry/relax/ChangeLog
index b8edf91fe9b6..61f92e695fbd 100644
--- a/sci-chemistry/relax/ChangeLog
+++ b/sci-chemistry/relax/ChangeLog
@@ -1,6 +1,14 @@
 # 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 1.12 2013/11/29 09:14:58 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/relax/ChangeLog,v 1.13 2013/11/29 10:58:24 jlec Exp $
+
+*relax-9999 (29 Nov 2013)
+*relax-3.1.0-r2 (29 Nov 2013)
+
+  29 Nov 2013; Justin Lecher <jlec@gentoo.org> -relax-3.1.0-r1.ebuild,
+  +relax-3.1.0-r2.ebuild, +relax-9999.ebuild,
+  +files/relax-3.1.0-sample-script-backport.patch:
+  Add another backport for sample scripts; add live ebuild
 
 *relax-3.1.0-r1 (29 Nov 2013)
 
diff --git a/sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch b/sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch
new file mode 100644
index 000000000000..7c82da50aaa0
--- /dev/null
+++ b/sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch
@@ -0,0 +1,111 @@
+--- trunk/sample_scripts/relax_disp/R1rho_analysis.py	2013/11/29 09:40:25	21705
++++ trunk/sample_scripts/relax_disp/R1rho_analysis.py	2013/11/29 09:42:22	21706
+@@ -58,16 +58,16 @@
+ # Set up the data pipe.
+ #######################
+ 
++# The path to the data files.
++DATA_PATH = '../../test_suite/shared_data/dispersion/r1rho_off_res_tp02'
++
+ # Create the data pipe.
+ pipe_name = 'base pipe'
+ pipe_bundle = 'relax_disp'
+ pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
+ 
+-# The path to the data files.
+-data_path = 'r1rho_off_res_tp02'
+-
+ # Load the sequence.
+-sequence.read('fake_sequence.in', res_num_col=1, res_name_col=2)
++sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1, res_name_col=2)
+ 
+ # Name the spins so they can be matched to the assignments.
+ spin.name(name='N')
+@@ -77,37 +77,37 @@
+ 
+ # 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]
+-    ['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]
+-    ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, 500e6, 200000.0]
+-    ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, 500e6, 200000.0]
+-    ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, 500e6, 200000.0]
+-    ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, 500e6, 200000.0]
+-    ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, 500e6, 200000.0]
+-    ['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]
+-    ['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]
+-    ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, 800e6, 200000.0]
+-    ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, 800e6, 200000.0]
+-    ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, 800e6, 200000.0]
+-    ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, 800e6, 200000.0]
+-    ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, 800e6, 200000.0]
+-    ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, 800e6, 200000.0]
+-    ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, 800e6, 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],
++    ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, 500e6, 200000.0],
++    ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, 500e6, 200000.0],
++    ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, 500e6, 200000.0],
++    ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, 500e6, 200000.0],
++    ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, 500e6, 200000.0],
++    ['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],
++    ['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],
++    ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, 800e6, 200000.0],
++    ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, 800e6, 200000.0],
++    ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, 800e6, 200000.0],
++    ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, 800e6, 200000.0],
++    ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, 800e6, 200000.0],
++    ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, 800e6, 200000.0],
++    ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, 800e6, 200000.0],
+     ['nu_6000.0_800MHz', 'nu_6000.0_800MHz.list', 6000.0, 110.0, 0.1, 800e6, 200000.0]
+ ]
+ 
+ # Loop over the spectra.
+ for id, file, field, offset, relax_time, H_frq, rmsd in data:
+     # Load the peak intensities and set the errors.
+-    spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id, int_method='height')
+-    spectrum.baseplane_rmsd(spectrum_id=id, error=error)
++    spectrum.read_intensities(file=file, dir=DATA_PATH, spectrum_id=id, int_method='height')
++    spectrum.baseplane_rmsd(spectrum_id=id, error=rmsd)
+ 
+     # Set the relaxation dispersion experiment type.
+     relax_disp.exp_type(spectrum_id=id, exp_type='R1rho')
+@@ -125,18 +125,17 @@
+     spectrometer.frequency(id=id, frq=H_frq)
+ 
+ # Load the R1 data.
+-relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6, file='R1_500MHz.out', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+-relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
++relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6, file='R1_500MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
++relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+ 
+-# Clustering.
+-relax_disp.cluster(cluster_id='cluster', spin_id=':1-50')
++# Clustering (only to be activated after an initial analysis without clustering).
++#relax_disp.cluster(cluster_id='cluster', spin_id=':1-50')
+ 
+ # Read the chemical shift data.
+-chemical_shift.read(file='ref_500MHz.list', dir=data_path)
++chemical_shift.read(file='ref_500MHz.list', dir=DATA_PATH)
+ 
+ # Deselect unresolved spins.
+-deselect.read(file='unresolved', dir='500_MHz', res_num_col=1)
+-deselect.read(file='unresolved', dir='800_MHz', res_num_col=1)
++deselect.read(file='unresolved', dir=DATA_PATH, res_num_col=1)
+ 
+ 
+ 
diff --git a/sci-chemistry/relax/relax-3.1.0-r1.ebuild b/sci-chemistry/relax/relax-3.1.0-r2.ebuild
index 355ce100f4b9..e138260b198d 100644
--- a/sci-chemistry/relax/relax-3.1.0-r1.ebuild
+++ b/sci-chemistry/relax/relax-3.1.0-r2.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/relax/relax-3.1.0-r1.ebuild,v 1.1 2013/11/29 09:14:58 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/relax/relax-3.1.0-r2.ebuild,v 1.1 2013/11/29 10:58:24 jlec Exp $
 
 EAPI=5
 
@@ -51,7 +51,7 @@ src_prepare() {
 	rm -rf minfx bmrblib || die
 	epatch \
 		"${FILESDIR}"/${PN}-3.0.1-gentoo.patch \
-		"${FILESDIR}"/${P}-sample-script.patch
+		"${FILESDIR}"/${P}-sample-script{,-backport}.patch
 	tc-export CC
 
 	ebegin "Fixing png files"
diff --git a/sci-chemistry/relax/relax-9999.ebuild b/sci-chemistry/relax/relax-9999.ebuild
new file mode 100644
index 000000000000..c8e8914035eb
--- /dev/null
+++ b/sci-chemistry/relax/relax-9999.ebuild
@@ -0,0 +1,72 @@
+# 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-9999.ebuild,v 1.1 2013/11/29 10:58:24 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+WX_GTK_VER="2.9"
+
+inherit eutils python-single-r1 scons-utils subversion toolchain-funcs wxwidgets virtualx
+
+DESCRIPTION="Molecular dynamics by NMR data analysis"
+HOMEPAGE="http://www.nmr-relax.com/"
+SRC_URI=""
+ESVN_REPO_URI="svn://svn.gna.org/svn/relax/trunk"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS=""
+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() {
+	local png
+	rm -rf minfx bmrblib || die
+	epatch \
+		"${FILESDIR}"/${PN}-3.0.1-gentoo.patch
+	tc-export CC
+}
+
+src_compile() {
+	escons
+	escons user_manual_pdf_nofetch
+	escons user_manual_html_nofetch
+}
+
+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 $@"
+}