From: Aaron Bauman Date: Sun, 8 Dec 2019 19:01:43 +0000 (-0500) Subject: profiles/package.mask: drop last-rited pkgs X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=c83b48420b7ee012f156338a86b6f976519019c9;p=gentoo.git profiles/package.mask: drop last-rited pkgs Signed-off-by: Aaron Bauman --- diff --git a/dev-python/pyclimate/Manifest b/dev-python/pyclimate/Manifest deleted file mode 100644 index 8446f30d24b1..000000000000 --- a/dev-python/pyclimate/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST PyClimate-1.2.2.tar.gz 1417758 BLAKE2B 96e9768f3487c97edd4ff4a6017ccf36a76611b5642545be62839910c0418e68f5937e1a763237f9d924dc50e1cd60634a1af1fca86d081dafced9fad70555ac SHA512 b217991873e99ad147e0f4e05bfa900a60486852a803ed6c224321f6fc1f1b6700ad2ad1d6c7c7f8ed8ec94340220c5277456c98ccb408f0bef6888c0adf018f diff --git a/dev-python/pyclimate/metadata.xml b/dev-python/pyclimate/metadata.xml deleted file mode 100644 index aa2237b317d7..000000000000 --- a/dev-python/pyclimate/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ - - - - - sci@gentoo.org - Gentoo Science Project - - - python@gentoo.org - Python - - - 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. - - - 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。 - - diff --git a/dev-python/pyclimate/pyclimate-1.2.2-r2.ebuild b/dev-python/pyclimate/pyclimate-1.2.2-r2.ebuild deleted file mode 100644 index 009559ff3ff8..000000000000 --- a/dev-python/pyclimate/pyclimate-1.2.2-r2.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# 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* -} diff --git a/dev-python/scientificpython/Manifest b/dev-python/scientificpython/Manifest deleted file mode 100644 index 8ed2616faa61..000000000000 --- a/dev-python/scientificpython/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ScientificPython-2.9.4.tar.gz 688704 BLAKE2B 8f125f11aa466ca2dd3afe5642385ac06350ea299e377aa4c368b3090ad0606e9d20e86a0b0f0a8b80408d11f558eb08abc630b185973318fa9df7f02b9b959f SHA512 8bd3ce3ead090832582711c25f7d4c7a5a55642ef9a1e845fb68b4b3dba833ba86baf9c444fd9948ce761a5357dbf388a2c1a860a66ee13fdf1f26d1010cc8c8 diff --git a/dev-python/scientificpython/files/scientificpython-2.9-mpi.patch b/dev-python/scientificpython/files/scientificpython-2.9-mpi.patch deleted file mode 100644 index 3140779c74a9..000000000000 --- a/dev-python/scientificpython/files/scientificpython-2.9-mpi.patch +++ /dev/null @@ -1,40 +0,0 @@ ---- 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)) diff --git a/dev-python/scientificpython/files/scientificpython-2.9.3-mpi-netcdf.patch b/dev-python/scientificpython/files/scientificpython-2.9.3-mpi-netcdf.patch deleted file mode 100644 index c9672948f2f8..000000000000 --- a/dev-python/scientificpython/files/scientificpython-2.9.3-mpi-netcdf.patch +++ /dev/null @@ -1,43 +0,0 @@ -From 71a5e881290c1cec2506a346e2740a1b821c36aa Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= -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 - diff --git a/dev-python/scientificpython/metadata.xml b/dev-python/scientificpython/metadata.xml deleted file mode 100644 index ead81e593755..000000000000 --- a/dev-python/scientificpython/metadata.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - - - sci@gentoo.org - Gentoo Science Project - - - python@gentoo.org - Python - - - 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. - - diff --git a/dev-python/scientificpython/scientificpython-2.9.4.ebuild b/dev-python/scientificpython/scientificpython-2.9.4.ebuild deleted file mode 100644 index a760b97ee758..000000000000 --- a/dev-python/scientificpython/scientificpython-2.9.4.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# 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=" - (2019-11-08) -# Ancient vulnerable version of NumPy, plus all its revdeps. -# Removal in 30 days. Bug #627962. - (2019-11-08) # Obsolete binary version. Please use www-apps/trickster instead. # Removal in 30 days. Bug #694884. diff --git a/sci-chemistry/parassign/Manifest b/sci-chemistry/parassign/Manifest deleted file mode 100644 index 2407156632e3..000000000000 --- a/sci-chemistry/parassign/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST PARAssign_Linux_x64_86.tgz 76693208 BLAKE2B 9141b7f3e6b50efd84cfc2af13c170946220b3f02f90422c4759a6aab8073a0d28cf44e045f305f392055816e50052826dd403f1d71ff7edb04950bf5dfc5f2b SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79 diff --git a/sci-chemistry/parassign/metadata.xml b/sci-chemistry/parassign/metadata.xml deleted file mode 100644 index f230593f73e9..000000000000 --- a/sci-chemistry/parassign/metadata.xml +++ /dev/null @@ -1,27 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - -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. - - diff --git a/sci-chemistry/parassign/parassign-20130522.ebuild b/sci-chemistry/parassign/parassign-20130522.ebuild deleted file mode 100644 index c49d09b2ab0a..000000000000 --- a/sci-chemistry/parassign/parassign-20130522.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# 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 -} diff --git a/sci-chemistry/pymol-plugins-psico/Manifest b/sci-chemistry/pymol-plugins-psico/Manifest deleted file mode 100644 index 3efb39319f8c..000000000000 --- a/sci-chemistry/pymol-plugins-psico/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pymol-plugins-psico-3.1.tar.gz 76136 BLAKE2B d1218b0d9da9326a47fb5e0d6268c43ee2d6266066260b83686aa664c500609fb87d61886a83d46a59a2270c3671cfdb7e2f3f761f7898b52932d5f92b2b4b31 SHA512 b0f57049ea6fc290a5abd48e0c98d4fda3c3f947898597b80e11cb3ab9ac14038aade0a016b21a525bf0ab4cf68e3be35c64b8ec34422268058414c20a755b0e diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml deleted file mode 100644 index 29f0c024a2f1..000000000000 --- a/sci-chemistry/pymol-plugins-psico/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - - speleo3/pymol-psico - - diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild deleted file mode 100644 index 0fca945ebee8..000000000000 --- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# 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[${PYTHON_USEDEP}] - !minimal? ( - media-libs/qhull - media-video/mplayer - sci-biology/stride - sci-chemistry/dssp - sci-chemistry/mm-align - sci-chemistry/pdbmat - sci-chemistry/theseus - sci-chemistry/tm-align - sci-mathematics/diagrtb - )" - -pkg_postinst() { - if ! use minimal; then - elog "For full functionality you need to get DynDom from" - elog "http://fizz.cmp.uea.ac.uk/dyndom/dyndomMain.do" - fi -} diff --git a/sci-libs/mmtk/Manifest b/sci-libs/mmtk/Manifest deleted file mode 100644 index 413128ed78ea..000000000000 --- a/sci-libs/mmtk/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST MMTK-2.7.9.tar.gz 1213599 BLAKE2B 66fb7bcb93a100661bc9aaa2b45162b4946fb0aae36f88d328e04e577eb01752e18ade7c2fb6d50db2141279b57069b0e62738d951ba9f363611841c4515fd18 SHA512 66819048aec4d8bdd370bb063f702c828145ecc9b7cb3247fcdd067486c78e00110a4e316f5c76df0b57a7885e05c347fa1616944daabfaa6d8b35933a79a7d8 diff --git a/sci-libs/mmtk/metadata.xml b/sci-libs/mmtk/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-libs/mmtk/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - diff --git a/sci-libs/mmtk/mmtk-2.7.9.ebuild b/sci-libs/mmtk/mmtk-2.7.9.ebuild deleted file mode 100644 index 6b4bc3559c26..000000000000 --- a/sci-libs/mmtk/mmtk-2.7.9.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 - -# This number identifies each release on the CRU website. -# Can't figure out how to avoid hardcoding it. -NUMBER="4324" - -MY_PN=${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}] -