+++ /dev/null
-DIST PyClimate-1.2.2.tar.gz 1417758 BLAKE2B 96e9768f3487c97edd4ff4a6017ccf36a76611b5642545be62839910c0418e68f5937e1a763237f9d924dc50e1cd60634a1af1fca86d081dafced9fad70555ac SHA512 b217991873e99ad147e0f4e05bfa900a60486852a803ed6c224321f6fc1f1b6700ad2ad1d6c7c7f8ed8ec94340220c5277456c98ccb408f0bef6888c0adf018f
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <maintainer type="project">
- <email>python@gentoo.org</email>
- <name>Python</name>
- </maintainer>
- <longdescription>
- A package designed to accomplish some usual tasks during the analysis of
- climate variability using Python. It provides functions to perform some
- simple IO operations, operations with COARDS-compliant netCDF files, EOF
- analysis, SVD and CCA analysis of coupled data sets, some linear digital
- filters, kernel based probability density function estimation and access
- to DCDFLIB.C library.
- </longdescription>
- <longdescription lang="ja">
- このパッケージはPython言語を使った気候の変化を分析する必要なタスクを終えるために
- デザインされました。幾つかの単純なI/O操作、COARDS-compliant netCDFファイルの操作
- 、EOF解析、カップル・データのSVDとCCA解析、幾つかのリニア・デジタル・フィルター、カーネル・ベースのプロバビリティ・デンシティ・ファンクション・エスティメーショ
- ンとDCDFLIB.Cライブラリへのアクセス等の機能を提供します。
- </longdescription>
-</pkgmetadata>
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-DISTUTILS_SINGLE_IMPL=1
-
-inherit distutils-r1
-
-MY_P="${P/pyclimate/PyClimate}"
-
-DESCRIPTION="Climate Data Analysis Module for Python"
-HOMEPAGE="http://www.pyclimate.org/"
-SRC_URI="http://fisica.ehu.es/jsaenz/pyclimate_files/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="examples"
-
-DEPEND=""
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- >=dev-python/scientificpython-2.8[${PYTHON_USEDEP}]
- >=sci-libs/netcdf-3.0"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
- python-single-r1_pkg_setup
-}
-
-python_install_all() {
- use examples && local EXAMPLES=( examples/. )
- distutils-r1_python_install_all
- dodoc doc/manual.ps doc/dcdflib_doc/dcdflib*
-}
+++ /dev/null
-DIST ScientificPython-2.9.4.tar.gz 688704 BLAKE2B 8f125f11aa466ca2dd3afe5642385ac06350ea299e377aa4c368b3090ad0606e9d20e86a0b0f0a8b80408d11f558eb08abc630b185973318fa9df7f02b9b959f SHA512 8bd3ce3ead090832582711c25f7d4c7a5a55642ef9a1e845fb68b4b3dba833ba86baf9c444fd9948ce761a5357dbf388a2c1a860a66ee13fdf1f26d1010cc8c8
+++ /dev/null
---- Src/MPI/compile.py
-+++ Src/MPI/compile.py
-@@ -4,7 +4,7 @@
- # Normally nothing needs to be changed below
- import distutils
- import distutils.sysconfig
--import os, sys
-+import os, subprocess, sys
- from Scientific import N
-
- cfgDict = distutils.sysconfig.get_config_vars()
-@@ -32,16 +32,16 @@
- items[i] = os.path.join(frameworkdir[0], items[i])
- linkforshared = ' '.join(items)
-
--cmd = '%s %s -o mpipython -I%s %s %s -L%s -lpython%s %s %s' % \
-- (mpicompiler,
-- linkforshared,
-- cfgDict['INCLUDEPY'],
-- extra_compile_args,
-- sources,
-- cfgDict['LIBPL'],
-- cfgDict['VERSION'],
-- cfgDict['LIBS'],
-- cfgDict['LIBM'])
-+cmd = [mpicompiler]
-+cmd.extend(linkforshared.split())
-+cmd.extend(os.environ.get("CFLAGS", "").split())
-+cmd.extend(os.environ.get("LDFLAGS", "").split())
-+cmd.extend(["-o", "mpipython"])
-+cmd.extend(["-I" + x for x in cfgDict['INCLUDEPY'].split()])
-+cmd.extend(["-I../../Include"])
-+cmd.extend(extra_compile_args.split())
-+cmd.extend(sources.split())
-+cmd.extend(["-lpython%s" % cfgDict['VERSION']])
-
--print 'cmd = ', cmd
--os.system(cmd)
-+print 'cmd =', " ".join(cmd)
-+sys.exit(subprocess.call(cmd))
+++ /dev/null
-From 71a5e881290c1cec2506a346e2740a1b821c36aa Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org>
-Date: Thu, 13 Mar 2014 15:29:33 +0100
-Subject: [PATCH] Include MPI cflags/ldflags for netcdf.
-
----
- setup.py | 7 +++++--
- 1 file changed, 5 insertions(+), 2 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 7f01656..71ac92a 100644
---- a/setup.py
-+++ b/setup.py
-@@ -2,7 +2,7 @@
-
- from distutils.core import setup, Extension
- from distutils.command.install_headers import install_headers
--import os, sys, platform
-+import os, sys, platform, subprocess
- from glob import glob
-
- class Dummy:
-@@ -92,13 +92,16 @@ else:
- netcdf_include = os.path.join(netcdf_prefix, 'include')
- netcdf_h_file = os.path.join(netcdf_prefix, 'include', 'netcdf.h')
- netcdf_lib = os.path.join(netcdf_prefix, 'lib')
-+ mpi_cflags = subprocess.Popen(["mpicc", "-showme:compile"], stdout=subprocess.PIPE).communicate()[0].rstrip().split()
-+ mpi_ldflags = subprocess.Popen(["mpicc", "-showme:link"], stdout=subprocess.PIPE).communicate()[0].rstrip().split()
- ext_modules = [Extension('Scientific._netcdf',
- ['Scientific/_netcdf.c'],
- include_dirs=['Include', netcdf_include]
- + numpy_include,
- library_dirs=[netcdf_lib],
- libraries = ['netcdf'],
-- extra_compile_args=extra_compile_args)]
-+ extra_compile_args=extra_compile_args + mpi_cflags,
-+ extra_link_args=mpi_ldflags)]
-
- try:
- # Add code for including documentation in Mac packages
---
-1.9.0
-
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <maintainer type="project">
- <email>python@gentoo.org</email>
- <name>Python</name>
- </maintainer>
- <longdescription lang="en">
- ScientificPython is a collection of Python modules that are useful for
- scientific computing. In this collection you will find modules that
- cover basic geometry (vectors, tensors, transformations, vector and
- tensor fields), quaternions, automatic derivatives, linear
- interpolation, polynomials, elementary statistics, nonlinear
- least-squares fits, unit calculations, Fortran-compatible text
- formatting, 3D visualization via VRML, and two Tk widgets for simple
- line plots and 3D wireframe models.
-</longdescription>
-</pkgmetadata>
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-MY_PN="ScientificPython"
-MY_P="${MY_PN}-${PV}"
-DOWNLOAD_NUMBER=4570
-
-DESCRIPTION="Scientific Module for Python"
-SRC_URI="http://sourcesup.cru.fr/frs/download.php/${DOWNLOAD_NUMBER}/${MY_P}.tar.gz"
-HOMEPAGE="http://sourcesup.cru.fr/projects/scientific-py/"
-
-LICENSE="CeCILL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc mpi test"
-
-RDEPEND="
- <dev-python/numpy-1.9[${PYTHON_USEDEP}]
- dev-python/pyro:3[${PYTHON_USEDEP}]
- sci-libs/netcdf
- mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}
- test? ( dev-python/nose[${PYTHON_USEDEP}] )"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.9-mpi.patch )
-DOCS=( README README.MPI Doc/CHANGELOG Examples/demomodule.c Examples/netcdf_demo.py )
-
-python_prepare_all() {
- use mpi && PATCHES+=( "${FILESDIR}"/${PN}-2.9.3-mpi-netcdf.patch )
- distutils-r1_python_prepare_all
-}
-
-python_compile() {
- distutils-r1_python_compile
-
- if use mpi; then
- cd Src/MPI || die
- ${PYTHON} compile.py || die
- mv -f mpipython mpipython-${EPYTHON} || die
- fi
-}
-
-python_test() {
- cd "${S}"/Tests || die
- nosetests -v -v || die
-}
-
-python_install() {
- distutils-r1_python_install
-
- if use mpi; then
- cd Src/MPI || die
- python_newexe mpipython-${EPYTHON} mpipython
- fi
-}
-
-python_install_all() {
- use doc && HTML_DOCS=( Doc/Reference/. )
- use mpi && EXAMPLES=( Examples/mpi.py )
- distutils-r1_python_install_all
-}
# EAPI=4. Removal in 30 days
app-admin/durep
-# Michał Górny <mgorny@gentoo.org> (2019-11-08)
-# Ancient vulnerable version of NumPy, plus all its revdeps.
-# Removal in 30 days. Bug #627962.
-<dev-python/numpy-1.14.5
-dev-python/pyclimate
-dev-python/scientificpython
-sci-chemistry/parassign
-sci-chemistry/pymol-plugins-psico
-sci-libs/mmtk
-
# Michał Górny <mgorny@gentoo.org> (2019-11-08)
# Obsolete binary version. Please use www-apps/trickster instead.
# Removal in 30 days. Bug #694884.
+++ /dev/null
-DIST PARAssign_Linux_x64_86.tgz 76693208 BLAKE2B 9141b7f3e6b50efd84cfc2af13c170946220b3f02f90422c4759a6aab8073a0d28cf44e045f305f392055816e50052826dd403f1d71ff7edb04950bf5dfc5f2b SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
- <longdescription>
-The use of paramagnetic NMR data for the refinement of structures of proteins
-and protein complexes is widespread. However, the power of paramagnetism for
-protein assignment has not yet been fully exploited. PARAssign is software that
-uses pseudocontact shift data derived from several paramagnetic centers attached
-to the protein to obtain amide and methyl assignments. The ability of PARAssign
-to perform assignment when the positions of the paramagnetic centers are known
-and unknown is demonstrated. PARAssign has been tested using synthetic data for
-methyl assignment of a 47 kDa protein, and using both synthetic and experimental
-data for amide assignment of a 14 kDa protein. The complex fitting space
-involved in such an assignment procedure necessitates that good starting
-conditions are found, both regarding placement and strength of paramagnetic
-centers. These starting conditions are obtained through automated tensor
-placement and user-defined tensor parameters. The results presented herein
-demonstrate that PARAssign is able to successfully perform resonance assignment
-in large systems with a high degree of reliability. This software provides a
-method for obtaining the assignments of large systems, which may previously have
-been unassignable, by using 2D NMR spectral data and a known protein structure.
-</longdescription>
-</pkgmetadata>
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 python-r1
-
-DESCRIPTION="Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)"
-HOMEPAGE="http://protchem.lic.leidenuniv.nl/software/parassign/registration"
-SRC_URI="PARAssign_Linux_x64_86.tgz"
-RESTRICT="fetch"
-
-SLOT="0"
-LICENSE="Apache-2.0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scientificpython[${PYTHON_USEDEP}]
- sci-biology/biopython[${PYTHON_USEDEP}]
- sci-libs/scipy[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}"/PARAssign_Linux_x64_86/
-
-src_prepare() {
- sed \
- -e '1i#!/usr/bin/python2' \
- -i code/*py || die
-
- if use x86; then
- sed \
- -e "s:munkres64:munkres:g" \
- -i modules/setup.py || die
- elif use amd64; then
- sed \
- -e "s:munkres:munkres64:g" \
- -i code/*py || die
- fi
- cd modules || die
- rm *o *c || die
- distutils-r1_src_prepare
-}
-
-src_compile() {
- cd modules || die
- distutils-r1_src_compile
-}
-
-src_install() {
- python_foreach_impl python_doscript code/* || die
-
- dodoc PARAssign_Tutorial.pdf README
-
- cd modules || die
- distutils-r1_src_install
-}
+++ /dev/null
-DIST pymol-plugins-psico-3.1.tar.gz 76136 BLAKE2B d1218b0d9da9326a47fb5e0d6268c43ee2d6266066260b83686aa664c500609fb87d61886a83d46a59a2270c3671cfdb7e2f3f761f7898b52932d5f92b2b4b31 SHA512 b0f57049ea6fc290a5abd48e0c98d4fda3c3f947898597b80e11cb3ab9ac14038aade0a016b21a525bf0ab4cf68e3be35c64b8ec34422268058414c20a755b0e
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">speleo3/pymol-psico</remote-id>
- </upstream>
-</pkgmetadata>
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 vcs-snapshot
-
-DESCRIPTION="Pymol ScrIpt COllection"
-HOMEPAGE="https://github.com/speleo3/pymol-psico/"
-SRC_URI="https://github.com/speleo3/pymol-psico/tarball/${PV} -> ${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="BSD-2"
-IUSE="minimal"
-
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- sci-biology/biopython[${PYTHON_USEDEP}]
- sci-libs/mmtk[${PYTHON_USEDEP}]
- sci-chemistry/pymol[${PYTHON_USEDEP}]
- !minimal? (
- media-libs/qhull
- media-video/mplayer
- sci-biology/stride
- sci-chemistry/dssp
- sci-chemistry/mm-align
- sci-chemistry/pdbmat
- sci-chemistry/theseus
- sci-chemistry/tm-align
- sci-mathematics/diagrtb
- )"
-
-pkg_postinst() {
- if ! use minimal; then
- elog "For full functionality you need to get DynDom from"
- elog "http://fizz.cmp.uea.ac.uk/dyndom/dyndomMain.do"
- fi
-}
+++ /dev/null
-DIST MMTK-2.7.9.tar.gz 1213599 BLAKE2B 66fb7bcb93a100661bc9aaa2b45162b4946fb0aae36f88d328e04e577eb01752e18ade7c2fb6d50db2141279b57069b0e62738d951ba9f363611841c4515fd18 SHA512 66819048aec4d8bdd370bb063f702c828145ecc9b7cb3247fcdd067486c78e00110a4e316f5c76df0b57a7885e05c347fa1616944daabfaa6d8b35933a79a7d8
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
+++ /dev/null
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-# This number identifies each release on the CRU website.
-# Can't figure out how to avoid hardcoding it.
-NUMBER="4324"
-
-MY_PN=${PN/mmtk/MMTK}
-MY_P=${MY_PN}-${PV}
-
-DESCRIPTION="Molecular Modeling ToolKit for Python"
-HOMEPAGE="http://dirac.cnrs-orleans.fr/MMTK/"
-SRC_URI="http://sourcesup.cru.fr/frs/download.php/${NUMBER}/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="CeCILL-2"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-RDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- <dev-python/numpy-1.9[${PYTHON_USEDEP}]
- dev-python/scientificpython[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-python_prepare_all() {
- export MMTK_USE_CYTHON="1"
- sed \
- -e "/ext_package/d" \
- -e "/^if sphinx/s|:| == 3:|g" \
- -e "s:import sphinx:sphinx = None:g" \
- -i "${S}"/setup.py || die
- distutils-r1_python_prepare_all
-}
-
-python_install_all() {
- DOCS=( README* Doc/CHANGELOG )
- HTML_DOCS=( Doc/HTML/. )
-
- distutils-r1_python_install_all
-
- if use examples; then
- insinto /usr/share/${P}
- doins -r Examples
- fi
-}
projects / gentoo.git / commitdiff