commit: 730740b74ec2c133b225870c4f6ee620b3f3dab5
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 2 20:21:16 2020 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Jan 2 20:21:16 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=730740b7
sci-chemistry/gromacs: Version bump
Package-Manager: Portage-2.3.83, Repoman-2.3.20
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/gromacs/Manifest | 4 +-
...cs-2020_rc1.ebuild => gromacs-2020.9999.ebuild} | 2 +-
...gromacs-2020_rc1.ebuild => gromacs-2020.ebuild} | 2 +-
sci-chemistry/gromacs/gromacs-9999.ebuild | 75 ++++++++++++++++++----
4 files changed, 67 insertions(+), 16 deletions(-)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 867bba59978..68cba940949 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,8 +1,8 @@
DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B
8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015
SHA512
6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B
bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09
SHA512
da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183
DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B
1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb
SHA512
fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6
-DIST gromacs-2020-rc1.tar.gz 29077110 BLAKE2B
5d5e6e63bd6b4dd03b688913b2da923547daddb270bca1a7d6ab8e625c26fb1031eea65330bd2e772f958e72e5a096c662633fbc71e7ee32ad83d99dcfb09170
SHA512
9dac945c5de9be2dc79bdde4d5f4afa3f2818334437ef8b4d1c57e46bdb80a0623ed7b16e1a8100395820b7eec367ea14195d420d3564f0f4eef0c88c52e78f9
+DIST gromacs-2020.tar.gz 28928068 BLAKE2B
72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c
SHA512
15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B
34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275
SHA512
3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B
4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45
SHA512
c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff
DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B
c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d
SHA512
7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce
-DIST regressiontests-2020-rc1.tar.gz 48537816 BLAKE2B
f9f4cde7a29691459d36e5f3fac91e75f4ebc6d95302c760722f4731a63a5e0695c8bc5106d38bb7b7266f6bac19bcb988496b572dca3f500f6c323c72615c60
SHA512
fb082479a3f3e03aaac4653682680ba8409f42a47f6e64e2a67e497467fce28e013b4fed8f9d3a1ce2db52237eb0e92e6e5c8de9be33beb7324d855de20b6ec7
+DIST regressiontests-2020.tar.gz 48536146 BLAKE2B
9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10
SHA512
5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821
diff --git a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild
b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
similarity index 99%
copy from sci-chemistry/gromacs/gromacs-2020_rc1.ebuild
copy to sci-chemistry/gromacs/gromacs-2020.9999.ebuild
index 162d64c983f..859628fa107 100644
--- a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
diff --git a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild
b/sci-chemistry/gromacs/gromacs-2020.ebuild
similarity index 99%
rename from sci-chemistry/gromacs/gromacs-2020_rc1.ebuild
rename to sci-chemistry/gromacs/gromacs-2020.ebuild
index 162d64c983f..859628fa107 100644
--- a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild
b/sci-chemistry/gromacs/gromacs-9999.ebuild
index f9d980d7c0f..859628fa107 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,11 +1,15 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1
toolchain-funcs xdg-utils
+PYTHON_COMPAT=( python3_{5,6,7} )
+
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib
readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -30,7 +34,7 @@ HOMEPAGE="http://www.gromacs.org/";
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib,
memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? (
BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit
mkl mpi +offensive opencl openmp +single-precision test +threads +tng
${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc
lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test
+threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
@@ -47,13 +51,16 @@ CDEPEND="
lmfit? ( sci-libs/lmfit )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
+ ${PYTHON_DEPS}
+ !sci-chemistry/gmxapi
"
-DEPEND="${CDEPEND}
+BDEPEND="${CDEPEND}
virtual/pkgconfig
doc? (
app-doc/doxygen
- dev-python/sphinx
+ dev-python/sphinx[${PYTHON_USEDEP}]
media-gfx/mscgen
+ media-gfx/graphviz
dev-texlive/texlive-latex
dev-texlive/texlive-latexextra
media-gfx/imagemagick
@@ -64,7 +71,8 @@ REQUIRED_USE="
|| ( single-precision double-precision )
cuda? ( single-precision )
cuda? ( !opencl )
- mkl? ( !blas !fftw !lapack )"
+ mkl? ( !blas !fftw !lapack )
+ ${PYTHON_REQUIRED_USE}"
DOCS=( AUTHORS README )
@@ -74,12 +82,18 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
+PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by
gromacs"
use openmp && ! tc-has-openmp && \
die "Please switch to an openmp compatible compiler"
}
+pkg_setup() {
+ python-single-r1_pkg_setup
+}
+
src_unpack() {
if [[ ${PV} != *9999 ]]; then
default
@@ -116,6 +130,28 @@ src_prepare() {
fi
DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file
formats"
+
+ # try to create policy for imagemagik
+ mkdir -p ${HOME}/.config/ImageMagick
+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
+ name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights
NMTOKEN #IMPLIED
+ stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
}
src_configure() {
@@ -172,6 +208,7 @@ src_configure() {
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-DBUILD_TESTING=$(usex test)
-DGMX_BUILD_UNITTESTS=$(usex test)
+ -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
${extra}
)
@@ -193,11 +230,13 @@ src_configure() {
-DGMX_MPI=OFF
-DGMX_THREAD_MPI=$(usex threads)
-DGMXAPI=$(usex gmxapi)
+ -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
"${opencl[@]}"
"${cuda[@]}"
"$(use test && echo
-DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-DGMX_BINARY_SUFFIX="${suffix}"
-DGMX_LIBS_SUFFIX="${suffix}"
+ -DGMX_PYTHON_PACKAGE=$(usex python)
)
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
[[ ${CHOST} != *-darwin* ]] || \
@@ -207,9 +246,11 @@ src_configure() {
mycmakeargs=(
${mycmakeargs_pre[@]} ${p}
-DGMX_THREAD_MPI=OFF
- -DGMX_MPI=ON ${cuda}
+ -DGMX_MPI=ON
-DGMX_OPENMM=OFF
-DGMXAPI=OFF
+ "${opencl[@]}"
+ "${cuda[@]}"
-DGMX_BUILD_MDRUN_ONLY=ON
-DBUILD_SHARED_LIBS=OFF
-DGMX_BUILD_MANUAL=OFF
@@ -227,6 +268,12 @@ src_compile() {
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_compile
+ if use python; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_compile python_packaging/all
+ BUILD_DIR="${WORKDIR}/${P}" \
+ distutils-r1_src_compile
+ fi
# not 100% necessary for rel ebuilds as available from website
if use doc; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
@@ -250,6 +297,10 @@ src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake-utils_src_install
+ if use python; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake-utils_src_install python_packaging/install
+ fi
if use doc; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf
"${PN}-manual-${PV}.pdf"
fi
@@ -263,14 +314,14 @@ src_install() {
doins src/external/tng_io/include/tng/*h
fi
# drop unneeded stuff
- rm "${ED}"usr/bin/GMXRC* || die
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+ rm "${ED}"/usr/bin/GMXRC* || die
+ for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
local n=${x##*/gmx-completion-}
n="${n%.bash}"
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+ cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" ||
die
newbashcomp "${T}"/"${n}" "${n}"
done
- rm "${ED}"usr/bin/gmx-completion*.bash || die
+ rm "${ED}"/usr/bin/gmx-completion*.bash || die
readme.gentoo_create_doc
}
