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-rw-r--r--sci-chemistry/GromacsWrapper/metadata.xml2
-rw-r--r--sci-chemistry/MDAnalysis/metadata.xml2
-rw-r--r--sci-chemistry/aqua/metadata.xml2
-rw-r--r--sci-chemistry/autodock/metadata.xml2
-rw-r--r--sci-chemistry/autodock_vina/metadata.xml2
-rw-r--r--sci-chemistry/avogadro2/metadata.xml2
-rw-r--r--sci-chemistry/bodr/bodr-10.ebuild15
-rw-r--r--sci-chemistry/bodr/metadata.xml2
-rw-r--r--sci-chemistry/cara-bin/metadata.xml2
-rw-r--r--sci-chemistry/chemex/Manifest3
-rw-r--r--sci-chemistry/chemex/chemex-2021.4.0_p2.ebuild (renamed from sci-chemistry/chemex/chemex-2018.10.3.ebuild)21
-rw-r--r--sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild46
-rw-r--r--sci-chemistry/chemex/metadata.xml2
-rw-r--r--sci-chemistry/chemical-mime-data/metadata.xml2
-rw-r--r--sci-chemistry/chemtool/metadata.xml2
-rw-r--r--sci-chemistry/clashlist/metadata.xml2
-rw-r--r--sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild19
-rw-r--r--sci-chemistry/cluster/metadata.xml2
-rw-r--r--sci-chemistry/dssp/Manifest3
-rw-r--r--sci-chemistry/dssp/dssp-2.2.1-r3.ebuild41
-rw-r--r--sci-chemistry/dssp/dssp-3.0.11.ebuild42
-rw-r--r--sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild33
-rw-r--r--sci-chemistry/dssp/dssp-4.0.3.ebuild31
-rw-r--r--sci-chemistry/dssp/files/30-dssp1
-rw-r--r--sci-chemistry/dssp/metadata.xml9
-rw-r--r--sci-chemistry/easychem/easychem-0.6-r1.ebuild20
-rw-r--r--sci-chemistry/easychem/metadata.xml2
-rw-r--r--sci-chemistry/elem/metadata.xml2
-rw-r--r--sci-chemistry/gelemental/metadata.xml2
-rw-r--r--sci-chemistry/gnome-chemistry-utils/metadata.xml2
-rw-r--r--sci-chemistry/gperiodic/metadata.xml2
-rw-r--r--sci-chemistry/gromacs/Manifest3
-rw-r--r--sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild (renamed from sci-chemistry/gromacs/gromacs-2018.8.ebuild)4
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild (renamed from sci-chemistry/gromacs/gromacs-2019.6.ebuild)6
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild (renamed from sci-chemistry/gromacs/gromacs-2020.4.ebuild)6
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.6-r1.ebuild (renamed from sci-chemistry/gromacs/gromacs-2020.6.ebuild)6
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild (renamed from sci-chemistry/gromacs/gromacs-2021.2.ebuild)6
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild356
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.9999.ebuild21
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild21
-rw-r--r--sci-chemistry/gromacs/metadata.xml2
-rw-r--r--sci-chemistry/ksdssp/metadata.xml2
-rw-r--r--sci-chemistry/mars/Manifest1
-rw-r--r--sci-chemistry/mars/mars-1.2.ebuild43
-rw-r--r--sci-chemistry/mars/metadata.xml8
-rw-r--r--sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild3
-rw-r--r--sci-chemistry/mdtraj/metadata.xml2
-rw-r--r--sci-chemistry/metadata.xml2
-rw-r--r--sci-chemistry/mm-align/metadata.xml2
-rw-r--r--sci-chemistry/modeller/metadata.xml2
-rw-r--r--sci-chemistry/molden/metadata.xml2
-rw-r--r--sci-chemistry/moldy/metadata.xml2
-rw-r--r--sci-chemistry/molequeue/metadata.xml2
-rw-r--r--sci-chemistry/molmol/metadata.xml2
-rw-r--r--sci-chemistry/molscript/metadata.xml2
-rw-r--r--sci-chemistry/molsketch/metadata.xml2
-rw-r--r--sci-chemistry/mopac7/metadata.xml2
-rw-r--r--sci-chemistry/mopac7/mopac7-1.15-r1.ebuild17
-rw-r--r--sci-chemistry/mpqc/metadata.xml2
-rw-r--r--sci-chemistry/msms-bin/metadata.xml2
-rw-r--r--sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch5
-rw-r--r--sci-chemistry/mustang/metadata.xml2
-rw-r--r--sci-chemistry/mustang/mustang-3.2.2.ebuild10
-rw-r--r--sci-chemistry/namd/metadata.xml2
-rw-r--r--sci-chemistry/nmrglue/metadata.xml2
-rw-r--r--sci-chemistry/numbat/metadata.xml2
-rw-r--r--sci-chemistry/openbabel-perl/metadata.xml2
-rw-r--r--sci-chemistry/openbabel/metadata.xml2
-rw-r--r--sci-chemistry/pdbcat/metadata.xml2
-rw-r--r--sci-chemistry/pdbcns/metadata.xml2
-rw-r--r--sci-chemistry/pdbmat/metadata.xml2
-rw-r--r--sci-chemistry/povscript+/metadata.xml2
-rw-r--r--sci-chemistry/prekin/metadata.xml2
-rw-r--r--sci-chemistry/probe/metadata.xml2
-rw-r--r--sci-chemistry/procheck/metadata.xml2
-rw-r--r--sci-chemistry/propka/metadata.xml2
-rw-r--r--sci-chemistry/psi/metadata.xml2
-rw-r--r--sci-chemistry/pymol/Manifest1
-rw-r--r--sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch34
-rw-r--r--sci-chemistry/pymol/metadata.xml2
-rw-r--r--sci-chemistry/pymol/pymol-2.4.0-r1.ebuild116
-rw-r--r--sci-chemistry/raster3d/metadata.xml2
-rw-r--r--sci-chemistry/suitename/metadata.xml2
-rw-r--r--sci-chemistry/surf/metadata.xml2
-rw-r--r--sci-chemistry/theseus/metadata.xml2
-rw-r--r--sci-chemistry/theseus/theseus-3.3.0-r1.ebuild28
-rw-r--r--sci-chemistry/threeV/metadata.xml2
-rw-r--r--sci-chemistry/tinker/metadata.xml2
-rw-r--r--sci-chemistry/tm-align/metadata.xml2
-rw-r--r--sci-chemistry/vmd/metadata.xml2
-rw-r--r--sci-chemistry/votca-csg/Manifest2
-rw-r--r--sci-chemistry/votca-csg/metadata.xml2
-rw-r--r--sci-chemistry/votca-csg/votca-csg-2021.2.ebuild87
-rw-r--r--sci-chemistry/votca-csgapps/metadata.xml2
-rw-r--r--sci-chemistry/votca-ctp/metadata.xml2
-rw-r--r--sci-chemistry/votca-xtp/Manifest1
-rw-r--r--sci-chemistry/votca-xtp/metadata.xml2
-rw-r--r--sci-chemistry/votca-xtp/votca-xtp-2021.2.ebuild51
-rw-r--r--sci-chemistry/wxmacmolplt/metadata.xml2
-rw-r--r--sci-chemistry/xds-bin/metadata.xml2
-rw-r--r--sci-chemistry/xyza2pipe/metadata.xml2
101 files changed, 872 insertions, 376 deletions
diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml
index e8b6e94ed2a..0096486f68a 100644
--- a/sci-chemistry/GromacsWrapper/metadata.xml
+++ b/sci-chemistry/GromacsWrapper/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>alexxy@gentoo.org</email>
diff --git a/sci-chemistry/MDAnalysis/metadata.xml b/sci-chemistry/MDAnalysis/metadata.xml
index 6b7aa8ce58a..31c543b5ba1 100644
--- a/sci-chemistry/MDAnalysis/metadata.xml
+++ b/sci-chemistry/MDAnalysis/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci@gentoo.org</email>
diff --git a/sci-chemistry/aqua/metadata.xml b/sci-chemistry/aqua/metadata.xml
index da36ecbfcd6..d4ff1000a77 100644
--- a/sci-chemistry/aqua/metadata.xml
+++ b/sci-chemistry/aqua/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/autodock/metadata.xml b/sci-chemistry/autodock/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/autodock/metadata.xml
+++ b/sci-chemistry/autodock/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml
index f363bab631f..f603fd62c19 100644
--- a/sci-chemistry/autodock_vina/metadata.xml
+++ b/sci-chemistry/autodock_vina/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/avogadro2/metadata.xml b/sci-chemistry/avogadro2/metadata.xml
index 8da47dd4e3c..b669d7480d2 100644
--- a/sci-chemistry/avogadro2/metadata.xml
+++ b/sci-chemistry/avogadro2/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/bodr/bodr-10.ebuild b/sci-chemistry/bodr/bodr-10.ebuild
index 4a8ecabc18c..7a957c05b90 100644
--- a/sci-chemistry/bodr/bodr-10.ebuild
+++ b/sci-chemistry/bodr/bodr-10.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=8
DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties"
HOMEPAGE="https://sourceforge.net/projects/bodr"
@@ -10,17 +10,10 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~ppc-macos"
-IUSE=""
-DEPEND="dev-libs/libxslt"
-RDEPEND=""
-
-DOCS=( "THANKS" "AUTHORS" "README" "ChangeLog" )
+BDEPEND="dev-libs/libxslt"
src_prepare() {
+ default
sed -i -e "s/COPYING//g" Makefile.* || die
}
-
-src_configure() {
- econf --docdir="${EPREFIX}"/usr/share/doc/${PF}
-}
diff --git a/sci-chemistry/bodr/metadata.xml b/sci-chemistry/bodr/metadata.xml
index c4fa86e29eb..05ed327d6fa 100644
--- a/sci-chemistry/bodr/metadata.xml
+++ b/sci-chemistry/bodr/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/cara-bin/metadata.xml b/sci-chemistry/cara-bin/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/cara-bin/metadata.xml
+++ b/sci-chemistry/cara-bin/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest
index 1f128ac7b06..594cc24b868 100644
--- a/sci-chemistry/chemex/Manifest
+++ b/sci-chemistry/chemex/Manifest
@@ -1 +1,2 @@
-DIST chemex-2018.10.3.tar.gz 546696 BLAKE2B d283cfb94118686f1974780249641e0ea6f86cdb854c4a256897e361a300a94506813a5035ee2f300fca13263e8452b77e7a0817436cbd620ba16d801a541af7 SHA512 784bd03b354724d6aa52d663c6f661f865d4ef7ca345573bc8aae9ef63e5dbb3e65abba364de3ff441b78adfa588344c718809c5880b3fc70d8ed24be06a0826
+DIST chemex-2021.4.0_p2.tar.gz 2384471 BLAKE2B 1eb609c4e4ad9ac0f7cac8ab523e72e8ab9c12d40671fd598cd26b8de2a3d6e68dfdcaee9202521fc583068f591377842b3e7b9f0e1f95e6cba8da9b0c6d63a4 SHA512 568072eaf0d1c666de2aedacc50cd98da15631e0ef15ba60414be671ac97a50967e5b4d6d00340b1263f730b3a803ccc8995fbb86cfc47517b9521c9920641c8
+DIST chemex-2021.4.0_p4.tar.gz 2387888 BLAKE2B 26b4467756ba1b31775c554906a2ce09556e1fb99dd2ff294620a12b92246f441a2daa07e6bad7cedf903bd18e6ecc0613b6473f54d27d89ed9117ddc6a27269 SHA512 7d93f213317e4cb5a987c0b3cfcce146fb02a15ac9efbde74f9d3fc56a5e86c89ca6b606f45013bf08ed10f3de17cc72fa010ce0e42c5cb746119ede0ce4d38f
diff --git a/sci-chemistry/chemex/chemex-2018.10.3.ebuild b/sci-chemistry/chemex/chemex-2021.4.0_p2.ebuild
index 19f50cce7be..8b5e04b8b08 100644
--- a/sci-chemistry/chemex/chemex-2018.10.3.ebuild
+++ b/sci-chemistry/chemex/chemex-2021.4.0_p2.ebuild
@@ -1,16 +1,16 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DISTUTILS_SINGLE_IMPL="yes"
-DISTUTILS_USE_SETUPTOOLS=rdepend
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
inherit distutils-r1
DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data"
HOMEPAGE="https://github.com/gbouvignies/chemex"
-SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV/_p/-dev}.tar.gz -> ${P}.tar.gz"
SLOT="0"
LICENSE="BSD"
@@ -21,18 +21,21 @@ RESTRICT="!test? ( test )"
RDEPEND="
$(python_gen_cond_dep '
>=dev-python/asteval-0.9.11[${PYTHON_USEDEP}]
- >=dev-python/lmfit-0.9.11[${PYTHON_USEDEP}]
- >=dev-python/matplotlib-1.1[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/jsonschema-3.2.0[${PYTHON_USEDEP}]
+ >=dev-python/lmfit-1.0.2[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-3.4.2[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.21.0[${PYTHON_USEDEP}]
dev-python/setuptools_scm[${PYTHON_USEDEP}]
- >=dev-python/scipy-0.11[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.7.0[${PYTHON_USEDEP}]
+ >=dev-python/tomlkit-0.7.2[${PYTHON_USEDEP}]
+ >=dev-python/tqdm-4.61.1[${PYTHON_USEDEP}]
')
"
DEPEND="${RDEPEND}"
distutils_enable_tests pytest
-S="${WORKDIR}/ChemEx-${PV}"
+S="${WORKDIR}/ChemEx-${PV/_p/-dev}"
src_prepare() {
export SETUPTOOLS_SCM_PRETEND_VERSION="${PV}"
diff --git a/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild b/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild
new file mode 100644
index 00000000000..3a331d48eba
--- /dev/null
+++ b/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+DISTUTILS_SINGLE_IMPL="yes"
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+
+inherit distutils-r1
+
+DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data"
+HOMEPAGE="https://github.com/gbouvignies/chemex"
+SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV/_p/-dev}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64"
+IUSE="test"
+
+#RESTRICT="!test? ( test )"
+# FIXME: Restrict until we figure out how to run tests properly, bug #815079
+RESTRICT="test"
+
+RDEPEND="
+ $(python_gen_cond_dep '
+ >=dev-python/asteval-0.9.25[${PYTHON_USEDEP}]
+ >=dev-python/jsonschema-4.1.0[${PYTHON_USEDEP}]
+ >=dev-python/lmfit-1.0.3[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-3.4.3[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.21.2[${PYTHON_USEDEP}]
+ dev-python/setuptools_scm[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.7.0[${PYTHON_USEDEP}]
+ >=dev-python/tomlkit-0.7.2[${PYTHON_USEDEP}]
+ >=dev-python/tqdm-4.61.1[${PYTHON_USEDEP}]
+ ')
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+S="${WORKDIR}/ChemEx-${PV/_p/-dev}"
+
+src_prepare() {
+ export SETUPTOOLS_SCM_PRETEND_VERSION="${PV}"
+ distutils-r1_src_prepare
+}
diff --git a/sci-chemistry/chemex/metadata.xml b/sci-chemistry/chemex/metadata.xml
index 020b40648ee..572c7daf2cc 100644
--- a/sci-chemistry/chemex/metadata.xml
+++ b/sci-chemistry/chemex/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>pacho@gentoo.org</email>
diff --git a/sci-chemistry/chemical-mime-data/metadata.xml b/sci-chemistry/chemical-mime-data/metadata.xml
index a11dac39018..702a57465bc 100644
--- a/sci-chemistry/chemical-mime-data/metadata.xml
+++ b/sci-chemistry/chemical-mime-data/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/chemtool/metadata.xml b/sci-chemistry/chemtool/metadata.xml
index 8b1591478bc..8847960e68c 100644
--- a/sci-chemistry/chemtool/metadata.xml
+++ b/sci-chemistry/chemtool/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/clashlist/metadata.xml b/sci-chemistry/clashlist/metadata.xml
index a2df83cc0e8..b9fcbfc541c 100644
--- a/sci-chemistry/clashlist/metadata.xml
+++ b/sci-chemistry/clashlist/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
index d274ed0d378..b5f0395734e 100644
--- a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
+++ b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
@@ -1,26 +1,27 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=8
-inherit epatch toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Build lists of collections of interacting items"
HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz"
+S="${WORKDIR}"/${PN}1.3src
-SLOT="0"
LICENSE="richardson"
+SLOT="0"
KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
-S="${WORKDIR}"/${PN}1.3src
+PATCHES=(
+ "${FILESDIR}"/${PV}-ldflags.patch
+ "${FILESDIR}"/${PV}-includes.patch
+)
-src_prepare() {
- epatch \
- "${FILESDIR}"/${PV}-ldflags.patch \
- "${FILESDIR}"/${PV}-includes.patch
+src_configure() {
tc-export CXX
+ default
}
src_install() {
diff --git a/sci-chemistry/cluster/metadata.xml b/sci-chemistry/cluster/metadata.xml
index 62f5e4eb25a..40e82f448b5 100644
--- a/sci-chemistry/cluster/metadata.xml
+++ b/sci-chemistry/cluster/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
index ada8aac8e5c..9fd132f8a29 100644
--- a/sci-chemistry/dssp/Manifest
+++ b/sci-chemistry/dssp/Manifest
@@ -1 +1,4 @@
DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811
+DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d
+DIST dssp-4.0.1_p20210831.tar.gz 121793 BLAKE2B 1e028b086b418772a93db350f8084d1786996ff6ea935d236b1431d8f4a07c0b33ebf374a4c4d5d4d243952f3f56e29a548ce09763863a1e0c529755fba6c211 SHA512 62f1ac781dd3d6f3436e6c155ae1a470d0baf6a6d9f6d6729034a7a5ef41550f76d0473c688d235279336306c9f3598377c056cddd6d00a89a826fbb04c1bfb3
+DIST dssp-4.0.3.tar.gz 122872 BLAKE2B f88c330370645b4bd4e89656ad676e443a33c38d7882145bc60e329f823eb761777713df6c7ae44550d10bcd22256ac16db358587cadd39efd6268dd869655d4 SHA512 31ca481b097c9c59f407e35eb8175638b5e4102991007090b5b4ea30db0b076f97cff45d0aa9ae01a826f7673258464b572d68714f00e210db26020cea4be094
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
new file mode 100644
index 00000000000..208f006e4f5
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/"
+SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz"
+
+LICENSE="Boost-1.0"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="dev-libs/boost:=[bzip2,zlib,threads(+)]"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.1.0-gentoo.patch
+ "${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch
+)
+
+src_configure() {
+ tc-export CXX
+
+ cat >> make.config <<- EOF || die
+ BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)"
+ BOOST_INC_DIR = "${EPREFIX}/usr/include"
+ EOF
+}
+
+src_install() {
+ dobin mkdssp
+ dosym mkdssp /usr/bin/dssp
+ doman doc/mkdssp.1
+ dodoc README.txt changelog
+
+ doenvd "${FILESDIR}"/30-${PN}
+}
diff --git a/sci-chemistry/dssp/dssp-3.0.11.ebuild b/sci-chemistry/dssp/dssp-3.0.11.ebuild
new file mode 100644
index 00000000000..b0771e31047
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-3.0.11.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit autotools
+
+MY_PN="hssp"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/cmbi/hssp"
+SRC_URI="https://github.com/cmbi/${MY_PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Boost-1.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ dev-lang/perl:=
+ dev-libs/boost:=[bzip2,zlib,threads(+)]
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ default
+
+ # Fix version
+ sed -i -e "s/3.0.10/${PV}/" configure.ac || die
+
+ sed -i -e '/-Werror/d' Makefile.am || die
+
+ eautoreconf
+}
+
+src_install() {
+ default
+ dosym mkdssp /usr/bin/dssp
+ doenvd "${FILESDIR}"/30-${PN}
+}
diff --git a/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild
new file mode 100644
index 00000000000..ca051ca5a0d
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+inherit cmake
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
+
+COMMIT="728cc7c6c8d95460d8db453cf7adb25a89ba15f6"
+SRC_URI="https://github.com/PDB-REDO/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+BDEPEND="
+ >=dev-libs/boost-1.70.0:=[bzip2,zlib,threads(+)]
+ >=sci-libs/libcifpp-1.1.1
+"
+DEPEND=""
+RDEPEND="${BDEPEND}"
+
+pkg_postinst() {
+ if has_version sci-chemistry/gromacs; then
+ ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:"
+ ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129"
+ ewarn
+ ewarn "Feel free to mask newer versions if needed."
+ fi
+}
diff --git a/sci-chemistry/dssp/dssp-4.0.3.ebuild b/sci-chemistry/dssp/dssp-4.0.3.ebuild
new file mode 100644
index 00000000000..d9d8a5740c8
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-4.0.3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+inherit cmake
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
+
+SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+BDEPEND="
+ >=dev-libs/boost-1.70.0:=[zlib,threads(+)]
+ >=sci-libs/libcifpp-2.0.0
+"
+DEPEND=""
+RDEPEND="${BDEPEND}"
+
+pkg_postinst() {
+ if has_version sci-chemistry/gromacs; then
+ ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:"
+ ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129"
+ ewarn
+ ewarn "Feel free to mask newer versions if needed."
+ fi
+}
diff --git a/sci-chemistry/dssp/files/30-dssp b/sci-chemistry/dssp/files/30-dssp
new file mode 100644
index 00000000000..e0a5e0ce562
--- /dev/null
+++ b/sci-chemistry/dssp/files/30-dssp
@@ -0,0 +1 @@
+DSSP=/usr/bin/dssp \ No newline at end of file
diff --git a/sci-chemistry/dssp/metadata.xml b/sci-chemistry/dssp/metadata.xml
index 8937bad0b17..572c7daf2cc 100644
--- a/sci-chemistry/dssp/metadata.xml
+++ b/sci-chemistry/dssp/metadata.xml
@@ -1,8 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
+ <maintainer type="person">
+ <email>pacho@gentoo.org</email>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-chemistry/easychem/easychem-0.6-r1.ebuild b/sci-chemistry/easychem/easychem-0.6-r1.ebuild
index 9fbce181512..4d9d43bcf61 100644
--- a/sci-chemistry/easychem/easychem-0.6-r1.ebuild
+++ b/sci-chemistry/easychem/easychem-0.6-r1.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=8
-inherit epatch toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Chemical structure drawing program - focused on presentation"
HOMEPAGE="http://easychem.sourceforge.net/"
@@ -12,18 +12,22 @@ SRC_URI="mirror://sourceforge/easychem/${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
RDEPEND="
- x11-libs/gtk+:2
app-text/ghostscript-gpl
- media-gfx/pstoedit"
-DEPEND="${RDEPEND}
+ media-gfx/pstoedit
+ x11-libs/gtk+:2
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
dev-lang/perl
- virtual/pkgconfig"
+ virtual/pkgconfig
+"
+
+PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch )
src_prepare() {
- epatch "${FILESDIR}"/${PV}-gentoo.patch
+ default
tc-export CC
}
diff --git a/sci-chemistry/easychem/metadata.xml b/sci-chemistry/easychem/metadata.xml
index 6eea2dfe179..7451327b470 100644
--- a/sci-chemistry/easychem/metadata.xml
+++ b/sci-chemistry/easychem/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/elem/metadata.xml b/sci-chemistry/elem/metadata.xml
index ca4cdc816a9..762d19498c8 100644
--- a/sci-chemistry/elem/metadata.xml
+++ b/sci-chemistry/elem/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/gelemental/metadata.xml b/sci-chemistry/gelemental/metadata.xml
index 091878c90ab..a4a8fa434cf 100644
--- a/sci-chemistry/gelemental/metadata.xml
+++ b/sci-chemistry/gelemental/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>tamiko@gentoo.org</email>
diff --git a/sci-chemistry/gnome-chemistry-utils/metadata.xml b/sci-chemistry/gnome-chemistry-utils/metadata.xml
index 0d27f618fe3..fcf8bc4bad0 100644
--- a/sci-chemistry/gnome-chemistry-utils/metadata.xml
+++ b/sci-chemistry/gnome-chemistry-utils/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>pacho@gentoo.org</email>
diff --git a/sci-chemistry/gperiodic/metadata.xml b/sci-chemistry/gperiodic/metadata.xml
index 9220d57f13e..3050b77faba 100644
--- a/sci-chemistry/gperiodic/metadata.xml
+++ b/sci-chemistry/gperiodic/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index c60eb6f9145..0102ae34ad4 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,13 +3,16 @@ DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645
DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a
DIST gromacs-2020.6.tar.gz 29196621 BLAKE2B b350fc62fd8eeb3f2b042fa74a4ed42e43a7b74efd8fddb60ec086a814048a52b8625da65fa5c4cf2cb1e22f8347562bc84d38bf34441fc5ebc6abaa38b0eea0 SHA512 4ce4d6b9ae33e9cd2a1ad3313e80acf63ded21dac897b01dbf87df2e318181796ef64c8a1d3e0a6058b972d8d88d00f710cd0277db12f38fc2c9b29772c98bea
DIST gromacs-2021.2.tar.gz 37976386 BLAKE2B 8818321bbcbdee25356bbf909d9c667f9d7cf180e696a323a61017683234d1269decc8f8d72b8012a8cc207f69e5cd97e2ab48dbbff06d82bbb407bc0578854b SHA512 51b1728f41932274436ab807d569109e2b0e145abcb5cf9c9b7daf6a7396f2f8716dc28fb93cf178c97a7eaeab2a88878d0bc71dd6c6abe7e829d579e7968615
+DIST gromacs-2021.3.tar.gz 37987972 BLAKE2B d71995c7d5a34978246e33dc637ac3d273e547afcf72d1a107026650f03286ecdf27e4b9a70113b3c3a01af59ad49ac5c813aa6e5d2e8eb29fd05582a7a28d34 SHA512 da420917d06de2e192dfbb4e1b9f46989ed05b5c7e641c657104ed8f2bd8b22509bffd1ecfd7c965c80544eafa6af12d6d0aba7e1e7d9d14a4a88fb3fbf394a5
DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
DIST manual-2020.4.pdf 11851608 BLAKE2B 7b7bdf08e8946fcc448543b08391b94a67fee60a8c810597c1f09f70443f9d7db817c99622dd0c21c6317f5fdcd6c4a88589ecac57055cb0cd8597d6021026e7 SHA512 928555663c77de36393e625c29d388d4e1c8c1298e7a993d871839e0d4d8d18d190221ad8f1d975bd072bdd6a061e9ea5b9295f2ecf45f24b6523ea5ea290fed
DIST manual-2020.6.pdf 11850850 BLAKE2B 155e4eb9c200dcd0a38e3669b26077fcf310d437b82d9a593d333dada3989c2c8a936d62c642e195f98bb474b1673b8142405c467348fc96a74d57fb12106d76 SHA512 be508ebec597b82a2c4056029f8bb731b22cb8902628a45462ed21af54c554d28e07d5381efaaa96565202b7b47d33aea67950206cd9e8936211ae721b21b3e1
DIST manual-2021.2.pdf 12252501 BLAKE2B 0dbf9024e1516076b0eeb46e41523b966d1d81f57504fe0501c7bc8575e74fb19e3452ac584757e425bcccbc737367fe83be87fd21a4287f4675cf87184b960b SHA512 14156d3b1017990e0be3ceb7ec055777a1aec4c347ac2e821a042d51c931f84ebca862f60644a90ed7ba4070cb14ff8babcde3e4351e4dbec84df8563e350984
+DIST manual-2021.3.pdf 12255076 BLAKE2B 6ca516b6832507c9d4100679d1f9bc9e3ab17d226849b050764b0d0626247dc57ce49985f9a7fc0061f3df278923a83faa367ca8ab91c37e5624dc584a51a822 SHA512 5d53798f30ea00fcb4e1b35f7eaa4bebfc05dafa4f2d0c197dcf2b57a624ad3a98b74fd90722e40d0ac13a6fff4ca231f9d6340f52ba94659c827c53c2f1cb16
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978
DIST regressiontests-2020.6.tar.gz 48541232 BLAKE2B dbb405bd9168775984de8c9fb9e3fa2398d2790e2e4de23711c51a01dc3ea570d172a35d4924742ad5eda463eb0a885e6924512801e82b241600ceaefd5db70d SHA512 497a9e7d438b0b7b0734a97cf3683baf480ecc056e96b09f1e143c362ff047a4e51e323216750501c954559579716dc024d3c51319bd2c85fa719466ce4330b2
DIST regressiontests-2021.2.tar.gz 48514312 BLAKE2B 81b007d5e5e1d054349c73dc8bc3589db328752e48a66687c0ad36be87ebe580df9cbd93b193a724669bd5765af06ec306f2e12af00a228af616de03943d6f05 SHA512 b687ddfd3dc6ec1051af2a3253633703ef1c82335d1df23379819ea47e44dfcd417e81e29610cc584d4c5fb1ee1cbc76731a3fd31b529d8cdd0b9c22f432c7ec
+DIST regressiontests-2021.3.tar.gz 48515038 BLAKE2B ee79d8adddc9c68f7d59d9e568b12bf4d1fe0e44c2810fee846ad6f689bbcacf60f5c266433946329e64e3127bc2d37a3f81f69c070c636b411b38067650c2cf SHA512 e14baa22ef2902a23125bbd9143ae7a9a4810498b321794ff1989f8d044d47db5db41d5225798fda08016c05e5f7f315178b5a6e35cdf01e3b6604670a8ce7a2
diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild
index 88cd8246d14..5266a60f632 100644
--- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild
@@ -34,8 +34,8 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( <sys-apps/hwloc-2 )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( <sys-apps/hwloc-2:= )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild
index b93b01a654e..0c9aa1c428a 100644
--- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild
@@ -34,10 +34,10 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( sys-apps/hwloc:= )
lapack? ( virtual/lapack )
- lmfit? ( sci-libs/lmfit )
+ lmfit? ( sci-libs/lmfit:= )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
${PYTHON_DEPS}
diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild
index 4acfbb38511..b12df9964c0 100644
--- a/sci-chemistry/gromacs/gromacs-2020.4.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild
@@ -48,10 +48,10 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( sys-apps/hwloc:= )
lapack? ( virtual/lapack )
- lmfit? ( sci-libs/lmfit )
+ lmfit? ( sci-libs/lmfit:= )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
${PYTHON_DEPS}
diff --git a/sci-chemistry/gromacs/gromacs-2020.6.ebuild b/sci-chemistry/gromacs/gromacs-2020.6-r1.ebuild
index ffd92a1f1d7..125ab033266 100644
--- a/sci-chemistry/gromacs/gromacs-2020.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.6-r1.ebuild
@@ -48,10 +48,10 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( sys-apps/hwloc:= )
lapack? ( virtual/lapack )
- lmfit? ( sci-libs/lmfit )
+ lmfit? ( sci-libs/lmfit:= )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
${PYTHON_DEPS}
diff --git a/sci-chemistry/gromacs/gromacs-2021.2.ebuild b/sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild
index 4a9c41ff8ac..5067010bc65 100644
--- a/sci-chemistry/gromacs/gromacs-2021.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.2-r1.ebuild
@@ -48,10 +48,10 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] )
opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( sys-apps/hwloc:= )
lapack? ( virtual/lapack )
- lmfit? ( sci-libs/lmfit )
+ lmfit? ( sci-libs/lmfit:= )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
${PYTHON_DEPS}
diff --git a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild
new file mode 100644
index 00000000000..ade6f56115a
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild
@@ -0,0 +1,356 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{8,9} )
+
+DISTUTILS_USE_SETUPTOOLS=no
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ ${PV} = *9999* ]]; then
+ EGIT_REPO_URI="
+ https://gitlab.com/gromacs/gromacs.git
+ https://github.com/gromacs/gromacs.git
+ git://git.gromacs.org/gromacs.git"
+ [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+ inherit git-r3
+else
+ SRC_URI="
+ http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
+ test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
+ KEYWORDS="amd64 arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+# 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 +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+ X? (
+ x11-libs/libX11
+ x11-libs/libSM
+ x11-libs/libICE
+ )
+ blas? ( virtual/blas )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] )
+ opencl? ( virtual/opencl )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( sys-apps/hwloc:= )
+ lapack? ( virtual/lapack )
+ lmfit? ( sci-libs/lmfit:= )
+ mkl? ( sci-libs/mkl )
+ mpi? ( virtual/mpi )
+ ${PYTHON_DEPS}
+ !sci-chemistry/gmxapi
+ "
+BDEPEND="${CDEPEND}
+ virtual/pkgconfig
+ build-manual? (
+ app-doc/doxygen
+ $(python_gen_cond_dep '
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ ')
+ media-gfx/mscgen
+ media-gfx/graphviz
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ )"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+ || ( single-precision double-precision )
+ doc? ( !build-manual )
+ cuda? ( single-precision )
+ cuda? ( !opencl )
+ mkl? ( !blas !fftw !lapack )
+ ${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+if [[ ${PV} != *9999 ]]; then
+ S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+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 [[ ${PV} != *9999 ]]; then
+ default
+ else
+ git-r3_src_unpack
+ if use test; then
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+ EGIT_BRANCH="${EGIT_BRANCH}" \
+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+ git-r3_src_unpack
+ fi
+ fi
+}
+
+src_prepare() {
+ #notes/todos
+ # -on apple: there is framework support
+
+ xdg_environment_reset #591952
+
+ cmake_src_prepare
+
+ use cuda && cuda_src_prepare
+
+ GMX_DIRS=""
+ use single-precision && GMX_DIRS+=" float"
+ use double-precision && GMX_DIRS+=" double"
+
+ if use test; then
+ for x in ${GMX_DIRS}; do
+ mkdir -p "${WORKDIR}/${P}_${x}" || die
+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+ done
+ fi
+
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+ if use build-manual; then
+ # 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
+ fi
+}
+
+src_configure() {
+ local mycmakeargs_pre=( ) extra fft_opts=( )
+ local acce="AUTO"
+
+ if use custom-cflags; then
+ #go from slowest to fastest acceleration
+ acce="None"
+ if (use amd64 || use x86); then
+ use cpu_flags_x86_sse2 && acce="SSE2"
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+ use cpu_flags_x86_avx && acce="AVX_256"
+ use cpu_flags_x86_avx2 && acce="AVX2_256"
+ use cpu_flags_x86_avx512f && acce="AVX_512"
+ elif (use arm); then
+ use cpu_flags_arm_neon && acce="ARM_NEON"
+ elif (use arm64); then
+ use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
+ fi
+ else
+ strip-flags
+ fi
+
+ #to create man pages, build tree binaries are executed (bug #398437)
+ [[ ${CHOST} = *-darwin* ]] && \
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+ if use fftw; then
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include"
+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+ )
+ elif use mkl; then
+ local bits=$(get_libdir)
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+ )
+ else
+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+ fi
+
+ if use lmfit; then
+ local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
+ else
+ local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
+ fi
+
+ mycmakeargs_pre+=(
+ "${fft_opts[@]}"
+ "${lmfit_opts[@]}"
+ -DGMX_X11=$(usex X)
+ -DGMX_EXTERNAL_BLAS=$(usex blas)
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack)
+ -DGMX_OPENMP=$(usex openmp)
+ -DGMX_COOL_QUOTES=$(usex offensive)
+ -DGMX_USE_TNG=$(usex tng)
+ -DGMX_BUILD_MANUAL=$(usex build-manual)
+ -DGMX_HWLOC=$(usex hwloc)
+ -DGMX_DEFAULT_SUFFIX=off
+ -DGMX_SIMD="$acce"
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+ -DBUILD_TESTING=$(usex test)
+ -DGMX_BUILD_UNITTESTS=$(usex test)
+ -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
+ ${extra}
+ )
+
+ for x in ${GMX_DIRS}; do
+ einfo "Configuring for ${x} precision"
+ local suffix=""
+ #if we build single and double - double is suffixed
+ use double-precision && use single-precision && \
+ [[ ${x} = "double" ]] && suffix="_d"
+ local p
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+ local gpu=( "-DGMX_GPU=OFF" )
+ [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+ use opencl && gpu=( "-DGMX_GPU=OPENCL" )
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_MPI=OFF
+ -DGMX_THREAD_MPI=$(usex threads)
+ -DGMXAPI=$(usex gmxapi)
+ -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+ "${gpu[@]}"
+ "$(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_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+ use mpi || continue
+ einfo "Configuring for ${x} precision with mpi"
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_THREAD_MPI=OFF
+ -DGMX_MPI=ON
+ -DGMX_OPENMM=OFF
+ -DGMXAPI=OFF
+ "${opencl[@]}"
+ "${cuda[@]}"
+ -DGMX_BUILD_MDRUN_ONLY=ON
+ -DBUILD_SHARED_LIBS=OFF
+ -DGMX_BUILD_MANUAL=OFF
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}"
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+ done
+}
+
+src_compile() {
+ for x in ${GMX_DIRS}; do
+ einfo "Compiling for ${x} precision"
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile
+ if use python; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile python_packaging/all
+ BUILD_DIR="${WORKDIR}/${P}" \
+ distutils-r1_src_compile
+ fi
+ # not 100% necessary for rel ebuilds as available from website
+ if use build-manual; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile manual
+ fi
+ use mpi || continue
+ einfo "Compiling for ${x} precision with mpi"
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+ cmake_src_compile
+ done
+}
+
+src_test() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile check
+ done
+}
+
+src_install() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake_src_install
+ if use python; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake_src_install python_packaging/install
+ fi
+ if use build-manual; then
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+ fi
+
+ if use doc; then
+ if [[ ${PV} != *9999* ]]; then
+ newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
+ fi
+ fi
+
+ use mpi || continue
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+ cmake_src_install
+ done
+
+ if use tng; then
+ insinto /usr/include/tng
+ 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
+ local n=${x##*/gmx-completion-}
+ n="${n%.bash}"
+ cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+ newbashcomp "${T}"/"${n}" "${n}"
+ done
+ rm "${ED}"/usr/bin/gmx-completion*.bash || die
+ readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+ einfo
+ einfo "Please read and cite:"
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+ einfo "https://dx.doi.org/10.1021/ct700301q"
+ einfo
+ readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
index cbac7d70f6b..c135dc43d74 100644
--- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
@@ -48,10 +48,10 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] )
opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( sys-apps/hwloc:= )
lapack? ( virtual/lapack )
- lmfit? ( sci-libs/lmfit )
+ lmfit? ( sci-libs/lmfit:= )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
${PYTHON_DEPS}
@@ -161,17 +161,18 @@ src_prepare() {
src_configure() {
local mycmakeargs_pre=( ) extra fft_opts=( )
+ local acce="AUTO"
if use custom-cflags; then
#go from slowest to fastest acceleration
- local acce="None"
+ acce="None"
if (use amd64 || use x86); then
- use cpu_flags_x86_sse2 && acce="SSE2"
- use cpu_flags_x86_sse4_1 && acce="SSE4.1"
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
- use cpu_flags_x86_avx && acce="AVX_256"
- use cpu_flags_x86_avx2 && acce="AVX2_256"
- use cpu_flags_x86_avx512f && acce="AVX_512"
+ use cpu_flags_x86_sse2 && acce="SSE2"
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+ use cpu_flags_x86_avx && acce="AVX_256"
+ use cpu_flags_x86_avx2 && acce="AVX2_256"
+ use cpu_flags_x86_avx512f && acce="AVX_512"
elif (use arm); then
use cpu_flags_arm_neon && acce="ARM_NEON"
elif (use arm64); then
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index cbac7d70f6b..c135dc43d74 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -48,10 +48,10 @@ CDEPEND="
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] )
opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( sys-apps/hwloc )
+ fftw? ( sci-libs/fftw:3.0= )
+ hwloc? ( sys-apps/hwloc:= )
lapack? ( virtual/lapack )
- lmfit? ( sci-libs/lmfit )
+ lmfit? ( sci-libs/lmfit:= )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
${PYTHON_DEPS}
@@ -161,17 +161,18 @@ src_prepare() {
src_configure() {
local mycmakeargs_pre=( ) extra fft_opts=( )
+ local acce="AUTO"
if use custom-cflags; then
#go from slowest to fastest acceleration
- local acce="None"
+ acce="None"
if (use amd64 || use x86); then
- use cpu_flags_x86_sse2 && acce="SSE2"
- use cpu_flags_x86_sse4_1 && acce="SSE4.1"
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
- use cpu_flags_x86_avx && acce="AVX_256"
- use cpu_flags_x86_avx2 && acce="AVX2_256"
- use cpu_flags_x86_avx512f && acce="AVX_512"
+ use cpu_flags_x86_sse2 && acce="SSE2"
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+ use cpu_flags_x86_avx && acce="AVX_256"
+ use cpu_flags_x86_avx2 && acce="AVX2_256"
+ use cpu_flags_x86_avx512f && acce="AVX_512"
elif (use arm); then
use cpu_flags_arm_neon && acce="ARM_NEON"
elif (use arm64); then
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 44134f44362..0b64bbe8abd 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>alexxy@gentoo.org</email>
diff --git a/sci-chemistry/ksdssp/metadata.xml b/sci-chemistry/ksdssp/metadata.xml
index da36ecbfcd6..d4ff1000a77 100644
--- a/sci-chemistry/ksdssp/metadata.xml
+++ b/sci-chemistry/ksdssp/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/mars/Manifest b/sci-chemistry/mars/Manifest
deleted file mode 100644
index dfe88f47338..00000000000
--- a/sci-chemistry/mars/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mars-1.2_linux.tar.gz 2058733 BLAKE2B 3ca8c636e619313c5462b4deda1f1c34b64574d869bd285c2a07cf7a1e36103a38d2a3401a29ef50f1e97478f1d8a5a3eab01a70aa410fd953a8d6261d14595a SHA512 ba7ec4e94cf5918d22405022c75feabf3e5b345d96075eabf50eb24857101575bb41d15e5686822c2b2f25ba554aa7d7a2b65122dd47304939234a4a884ae4d2
diff --git a/sci-chemistry/mars/mars-1.2.ebuild b/sci-chemistry/mars/mars-1.2.ebuild
deleted file mode 100644
index 58667bc6dd8..00000000000
--- a/sci-chemistry/mars/mars-1.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_P="${P}_linux"
-
-DESCRIPTION="Robust automatic backbone assignment of proteins"
-HOMEPAGE="http://www.mpibpc.mpg.de/groups/zweckstetter/_links/software_mars.htm"
-SRC_URI="http://www.mpibpc.mpg.de/groups/zweckstetter/_software_files/_${PN}/${MY_P}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-RESTRICT=mirror
-
-RDEPEND="sci-biology/psipred"
-
-S="${WORKDIR}/${MY_P}"
-
-QA_PREBUILT="opt/mars/*"
-
-src_install() {
- dobin bin/runmars*
-
- exeinto /opt/${PN}/
- doexe bin/{${PN},calcJC-S2,runmars*,*.awk} *.awk
-
- insinto /opt/${PN}/
- doins bin/*.{tab,txt}
-
- if use examples; then
- insinto /usr/share/${PN}/
- doins -r examples
- fi
-
- cat >> "${T}"/23mars <<- EOF || die
- MARSHOME="${EPREFIX}/opt/${PN}"
- EOF
-
- doenvd "${T}"/23mars
-}
diff --git a/sci-chemistry/mars/metadata.xml b/sci-chemistry/mars/metadata.xml
deleted file mode 100644
index 8937bad0b17..00000000000
--- a/sci-chemistry/mars/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?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>
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
index 229f664042a..f618155f139 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
@@ -1,9 +1,8 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
diff --git a/sci-chemistry/mdtraj/metadata.xml b/sci-chemistry/mdtraj/metadata.xml
index 8425c0d53cb..7d3acaf5d25 100644
--- a/sci-chemistry/mdtraj/metadata.xml
+++ b/sci-chemistry/mdtraj/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci@gentoo.org</email>
diff --git a/sci-chemistry/metadata.xml b/sci-chemistry/metadata.xml
index 7c6e6107936..3f779c2ba92 100644
--- a/sci-chemistry/metadata.xml
+++ b/sci-chemistry/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE catmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<catmetadata>
<longdescription lang="en">
The sci-chemistry category contains software that can be used
diff --git a/sci-chemistry/mm-align/metadata.xml b/sci-chemistry/mm-align/metadata.xml
index 5653687f9cf..03c48e987ff 100644
--- a/sci-chemistry/mm-align/metadata.xml
+++ b/sci-chemistry/mm-align/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml
index 7daa2ce7e5f..22631b58bc2 100644
--- a/sci-chemistry/modeller/metadata.xml
+++ b/sci-chemistry/modeller/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>alexxy@gentoo.org</email>
diff --git a/sci-chemistry/molden/metadata.xml b/sci-chemistry/molden/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/molden/metadata.xml
+++ b/sci-chemistry/molden/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/moldy/metadata.xml b/sci-chemistry/moldy/metadata.xml
index da36ecbfcd6..d4ff1000a77 100644
--- a/sci-chemistry/moldy/metadata.xml
+++ b/sci-chemistry/moldy/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/molequeue/metadata.xml b/sci-chemistry/molequeue/metadata.xml
index 070683db0c1..a1173b82214 100644
--- a/sci-chemistry/molequeue/metadata.xml
+++ b/sci-chemistry/molequeue/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci@gentoo.org</email>
diff --git a/sci-chemistry/molmol/metadata.xml b/sci-chemistry/molmol/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/molmol/metadata.xml
+++ b/sci-chemistry/molmol/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/molscript/metadata.xml b/sci-chemistry/molscript/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/molscript/metadata.xml
+++ b/sci-chemistry/molscript/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/molsketch/metadata.xml b/sci-chemistry/molsketch/metadata.xml
index 4ddbdcb92cc..cc6c6d64715 100644
--- a/sci-chemistry/molsketch/metadata.xml
+++ b/sci-chemistry/molsketch/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/mopac7/metadata.xml b/sci-chemistry/mopac7/metadata.xml
index efd0c0d00e5..cd1cacd0abf 100644
--- a/sci-chemistry/mopac7/metadata.xml
+++ b/sci-chemistry/mopac7/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
index 3cb18cba78f..aaf87bceee5 100644
--- a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
+++ b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=8
inherit autotools fortran-2 flag-o-matic toolchain-funcs
@@ -21,6 +21,8 @@ DEPEND="dev-libs/libf2c"
RDEPEND="${DEPEND}"
src_prepare() {
+ default
+
# Install the executable
sed -i \
-e "s:noinst_PROGRAMS = mopac7:bin_PROGRAMS = mopac7:g" \
@@ -44,11 +46,12 @@ src_compile() {
emake
if use gmxmopac7; then
einfo "Making mopac7 lib for gromacs"
- mkdir "${S}"/fortran/libgmxmopac7 && cd "${S}"/fortran/libgmxmopac7
- cp -f ../SIZES ../*.f "${FILESDIR}"/Makefile . || die
+ mkdir "${S}"/fortran/libgmxmopac7 || die
+ cd "${S}"/fortran/libgmxmopac7 || die
+ cp -n ../SIZES ../*.f "${FILESDIR}"/Makefile . || die
emake clean
- cp -f "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die
- sed "s:GENTOOVERSION:${PV}:g" -i Makefile
+ cp -n "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die
+ sed "s:GENTOOVERSION:${PV}:g" -i Makefile || die
emake FC=$(tc-getFC)
fi
}
@@ -61,7 +64,7 @@ src_install() {
default
if use gmxmopac7; then
- cd "${S}"/fortran/libgmxmopac7
+ cd "${S}"/fortran/libgmxmopac7 || die
dolib.so libgmxmopac7.so*
fi
diff --git a/sci-chemistry/mpqc/metadata.xml b/sci-chemistry/mpqc/metadata.xml
index 2a8e4866597..f010ff6d55a 100644
--- a/sci-chemistry/mpqc/metadata.xml
+++ b/sci-chemistry/mpqc/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/msms-bin/metadata.xml b/sci-chemistry/msms-bin/metadata.xml
index ba21fec241d..9a643a85e7b 100644
--- a/sci-chemistry/msms-bin/metadata.xml
+++ b/sci-chemistry/msms-bin/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>alexxy@gentoo.org</email>
diff --git a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
index 9e5dea85afe..20bd300db89 100644
--- a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
+++ b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
@@ -1,8 +1,3 @@
- src/superpose_on_core_2.cpp | 2 ++
- 1 files changed, 2 insertions(+), 0 deletions(-)
-
-diff --git a/src/superpose_on_core_2.cpp b/src/superpose_on_core_2.cpp
-index ae137de..059dfe3 100644
--- a/src/superpose_on_core_2.cpp
+++ b/src/superpose_on_core_2.cpp
@@ -55,6 +55,8 @@ using std::ofstream ;
diff --git a/sci-chemistry/mustang/metadata.xml b/sci-chemistry/mustang/metadata.xml
index da36ecbfcd6..d4ff1000a77 100644
--- a/sci-chemistry/mustang/metadata.xml
+++ b/sci-chemistry/mustang/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/mustang/mustang-3.2.2.ebuild b/sci-chemistry/mustang/mustang-3.2.2.ebuild
index c82add5410d..d15a60e8394 100644
--- a/sci-chemistry/mustang/mustang-3.2.2.ebuild
+++ b/sci-chemistry/mustang/mustang-3.2.2.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=8
-inherit epatch toolchain-funcs
+inherit toolchain-funcs
MY_PN="MUSTANG"
SRC_P="${PN}_v${PV}"
@@ -12,16 +12,16 @@ MY_P="${MY_PN}_v${PV}"
DESCRIPTION="MUltiple STructural AligNment AlGorithm"
HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html"
SRC_URI="http://www.csse.monash.edu.au/~karun/${PN}/${PN}_v${PV}.tgz"
+S="${WORKDIR}/${MY_P}"
LICENSE="BSD"
SLOT="0"
KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
-S="${WORKDIR}/${MY_P}"
+PATCHES=( "${FILESDIR}"/${PN}-3.2.1-gcc-4.7.patch )
src_prepare() {
- epatch "${FILESDIR}"/${PN}-3.2.1-gcc-4.7.patch
+ default
sed -e 's:3.2.1:3.2.2:g' -i Makefile || die
}
diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
index 2fe5325ae7f..11bbcb9bf2c 100644
--- a/sci-chemistry/namd/metadata.xml
+++ b/sci-chemistry/namd/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>nicolasbock@gentoo.org</email>
diff --git a/sci-chemistry/nmrglue/metadata.xml b/sci-chemistry/nmrglue/metadata.xml
index 55fa34fcbc4..71d8eb79fc1 100644
--- a/sci-chemistry/nmrglue/metadata.xml
+++ b/sci-chemistry/nmrglue/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/numbat/metadata.xml b/sci-chemistry/numbat/metadata.xml
index 0f4399d7df6..273753c203e 100644
--- a/sci-chemistry/numbat/metadata.xml
+++ b/sci-chemistry/numbat/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/openbabel-perl/metadata.xml b/sci-chemistry/openbabel-perl/metadata.xml
index e549fb694ab..74da65eec81 100644
--- a/sci-chemistry/openbabel-perl/metadata.xml
+++ b/sci-chemistry/openbabel-perl/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml
index 245451297cd..88ffa5eb106 100644
--- a/sci-chemistry/openbabel/metadata.xml
+++ b/sci-chemistry/openbabel/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/pdbcat/metadata.xml b/sci-chemistry/pdbcat/metadata.xml
index 29177ef0643..ad3b3d086c2 100644
--- a/sci-chemistry/pdbcat/metadata.xml
+++ b/sci-chemistry/pdbcat/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/pdbcns/metadata.xml b/sci-chemistry/pdbcns/metadata.xml
index da36ecbfcd6..d4ff1000a77 100644
--- a/sci-chemistry/pdbcns/metadata.xml
+++ b/sci-chemistry/pdbcns/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/pdbmat/metadata.xml b/sci-chemistry/pdbmat/metadata.xml
index 5116112c89e..3186389b927 100644
--- a/sci-chemistry/pdbmat/metadata.xml
+++ b/sci-chemistry/pdbmat/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/povscript+/metadata.xml b/sci-chemistry/povscript+/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/povscript+/metadata.xml
+++ b/sci-chemistry/povscript+/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/prekin/metadata.xml b/sci-chemistry/prekin/metadata.xml
index 4ac68c154bb..b71795dbfba 100644
--- a/sci-chemistry/prekin/metadata.xml
+++ b/sci-chemistry/prekin/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/probe/metadata.xml b/sci-chemistry/probe/metadata.xml
index da36ecbfcd6..d4ff1000a77 100644
--- a/sci-chemistry/probe/metadata.xml
+++ b/sci-chemistry/probe/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/procheck/metadata.xml
+++ b/sci-chemistry/procheck/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/propka/metadata.xml b/sci-chemistry/propka/metadata.xml
index 6bfad85b400..03810a21807 100644
--- a/sci-chemistry/propka/metadata.xml
+++ b/sci-chemistry/propka/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/psi/metadata.xml b/sci-chemistry/psi/metadata.xml
index e18109f21fc..34f6bdcc537 100644
--- a/sci-chemistry/psi/metadata.xml
+++ b/sci-chemistry/psi/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index dec8f0b1525..2c6723b71c2 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,3 +1,2 @@
DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
-DIST pymol-2.4.0.tar.gz 10552539 BLAKE2B 34e31dce99c1e838b00389c3d7c29657534dd037349769bd6c8cb17028cfaaa856d5729760d3768fd43f61086cac30749a864fb4156c14eda07f9027430f0523 SHA512 2b19294197d58a808bf7bb7fa9f829c2ec582ba47a4380783a2b1eedda2ce4118cd398e01885db8c449e7fd5e4c08a1c40508e679ef42d8e183a6a52b031c02a
DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9 SHA512 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91
diff --git a/sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch b/sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch
deleted file mode 100644
index 62512053fd7..00000000000
--- a/sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-From 885891cf60371674406cdff16b395e25cc13d8ae Mon Sep 17 00:00:00 2001
-From: Sebastian Keller <sebastian-keller@gmx.de>
-Date: Tue, 28 Jul 2020 22:50:53 +0200
-Subject: [PATCH] Don't drop the last model when updating the selector table
-
-The last assigned model in the Obj vector was at position modelCnt.
-Resizing the vector to modelCnt removes the last model, which later
-results in a crash when trying to access it.
-
-See https://github.com/schrodinger/pymol-open-source/issues/119
----
- layer3/Selector.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/layer3/Selector.cpp b/layer3/Selector.cpp
-index 546725b..637cd60 100644
---- a/layer3/Selector.cpp
-+++ b/layer3/Selector.cpp
-@@ -7284,11 +7284,11 @@ static sele_array_t SelectorUpdateTableSingleObject(PyMOLGlobals * G, ObjectMole
- result[obj->SeleBase + at] = tag;
- }
- }
- }
- }
-- I->Obj.resize(modelCnt);
-+ I->Obj.resize(modelCnt + 1);
- I->Table.resize(c);
-
- PRINTFD(G, FB_Selector)
- "SelectorUpdateTableSingleObject-Debug: leaving...\n" ENDFD;
-
---
-libgit2 1.0.1
-
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 156735fe0d3..d28a87c8e56 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
deleted file mode 100644
index c710896747d..00000000000
--- a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
+++ /dev/null
@@ -1,116 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-DISTUTILS_USE_SETUPTOOLS=no
-
-inherit desktop optfeature flag-o-matic xdg distutils-r1
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="https://www.pymol.org/"
-SRC_URI="
- https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz
- https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
- "
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="+netcdf web"
-
-DEPEND="
- dev-libs/msgpack[cxx]
- dev-libs/mmtf-cpp
- dev-python/pyopengl[${PYTHON_USEDEP}]
- dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pmw[${PYTHON_USEDEP}]
- media-libs/freetype:2
- media-libs/glew:0=
- media-libs/glm
- media-libs/libpng:0=
- media-video/mpeg-tools
- sys-libs/zlib
- netcdf? ( sci-libs/netcdf:0= )
-"
-RDEPEND="${DEPEND}
- sci-chemistry/chemical-mime-data
-"
-
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-PATCHES=(
- # https://github.com/schrodinger/pymol-open-source/issues/119
- "${FILESDIR}/${P}-fix_bug119.patch"
-)
-
-python_prepare_all() {
- sed \
- -e "s:\"/usr:\"${EPREFIX}/usr:g" \
- -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
- -i setup.py || die
-
- sed \
- -e "s:/opt/local:${EPREFIX}/usr:g" \
- -e '/ext_comp_args/s:\[.*\]:[]:g' \
- -i setup.py || die
- sed \
- -e "s:\['msgpackc'\]:\['msgpack'\]:g" \
- -i setup.py || die
-
- append-cxxflags -std=c++0x
-
- use !netcdf && mydistutilsargs=( --no-vmd-plugins )
-
- distutils-r1_python_prepare_all
-}
-
-python_install() {
- distutils-r1_python_install \
- --pymol-path="${EPREFIX}/usr/share/pymol"
-
- sed \
- -e '1d' \
- -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
- -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
- -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
- -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
-}
-
-python_install_all() {
- distutils-r1_python_install_all
-
- sed \
- -e '1i#!/usr/bin/env python' \
- "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
-
- python_foreach_impl python_doscript "${T}"/${PN}
-
- # These environment variables should not go in the wrapper script, or else
- # it will be impossible to use the PyMOL libraries from Python.
- cat >> "${T}"/20pymol <<- EOF || die
- PYMOL_PATH="${EPREFIX}/usr/share/pymol"
- PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
- PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
- EOF
-
- doenvd "${T}"/20pymol
-
- newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png
- make_desktop_entry ${PN} PyMol ${PN} \
- "Graphics;Education;Science;Chemistry;" \
- "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
- if ! use web; then
- rm -rf "${D}/$(python_get_sitedir)/web" || die
- fi
-
- rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-pkg_postinst() {
- xdg_pkg_postinst
- optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
diff --git a/sci-chemistry/raster3d/metadata.xml b/sci-chemistry/raster3d/metadata.xml
index 59d8b8360b0..a1d690946ac 100644
--- a/sci-chemistry/raster3d/metadata.xml
+++ b/sci-chemistry/raster3d/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/suitename/metadata.xml b/sci-chemistry/suitename/metadata.xml
index e816416cfd5..432560e7fd5 100644
--- a/sci-chemistry/suitename/metadata.xml
+++ b/sci-chemistry/suitename/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/surf/metadata.xml b/sci-chemistry/surf/metadata.xml
index 4ac68c154bb..b71795dbfba 100644
--- a/sci-chemistry/surf/metadata.xml
+++ b/sci-chemistry/surf/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/theseus/metadata.xml b/sci-chemistry/theseus/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/theseus/metadata.xml
+++ b/sci-chemistry/theseus/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild b/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild
index f9e62b3916d..fe012719670 100644
--- a/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild
+++ b/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild
@@ -1,40 +1,42 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=8
-inherit multilib toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
HOMEPAGE="http://www.theseus3d.org/"
SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
+S="${WORKDIR}"/${PN}_src
-SLOT="0"
LICENSE="GPL-3"
+SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="examples"
RDEPEND="
sci-libs/gsl:=
|| (
+ sci-biology/clustalw:2
+ sci-biology/kalign
+ sci-biology/mafft
sci-biology/muscle
sci-biology/probcons
- sci-biology/mafft
sci-biology/t-coffee
- sci-biology/kalign
- sci-biology/clustalw:2
- )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}"/${PN}_src/
+ )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
src_prepare() {
- cat >> make.inc <<- EOF
+ default
+
+ cat >> make.inc <<- EOF || die
ARCH = $(tc-getAR)
ARCHFLAGS = -rvs
RANLIB = $(tc-getRANLIB)
- LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
+ LOCALLIBDIR = "${EPREFIX}"/usr/$(get_libdir)
SYSLIBS = $($(tc-getPKG_CONFIG) --libs gsl) -lpthread
LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
LIBDIR = -L./lib
diff --git a/sci-chemistry/threeV/metadata.xml b/sci-chemistry/threeV/metadata.xml
index da36ecbfcd6..d4ff1000a77 100644
--- a/sci-chemistry/threeV/metadata.xml
+++ b/sci-chemistry/threeV/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml
index da36ecbfcd6..d4ff1000a77 100644
--- a/sci-chemistry/tinker/metadata.xml
+++ b/sci-chemistry/tinker/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/tm-align/metadata.xml b/sci-chemistry/tm-align/metadata.xml
index f53ebfe8d76..e29234951cb 100644
--- a/sci-chemistry/tm-align/metadata.xml
+++ b/sci-chemistry/tm-align/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
index 25e17d0a8ff..1073cf919a8 100644
--- a/sci-chemistry/vmd/metadata.xml
+++ b/sci-chemistry/vmd/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>alexxy@gentoo.org</email>
diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest
index 1f9bfdbfa13..ce6c049cb04 100644
--- a/sci-chemistry/votca-csg/Manifest
+++ b/sci-chemistry/votca-csg/Manifest
@@ -1,10 +1,12 @@
DIST votca-csg-1.5.1.tar.gz 708319 BLAKE2B 2ea75cf08dc3005bd08ebe85113d95743fe85bae4b7ac3c2e2d9b64be64a7103ecf30b9edf45cffa86b7588d5c57a0256aef02f4590fa6031cb63881480bd0fd SHA512 3559452182c325d5df72918ec6e12122c8214df9733d779c123ff199597fe47fc493fd75adf1f5dbc6b55016373863378ba3cc69fb6b61bc1531c6e591d8131c
DIST votca-csg-1.6.4.tar.gz 537966 BLAKE2B c9ccc3aa28bdc4a2a2c080104b70602d8cf4be19a71e7d0b4a1c03d11f54b645984103d1662823a9308a4e4c4baedef731de06ff314b168f89e7326c0d3c8ee9 SHA512 4cdbf6c0a593720675f48f574ff9a93d038a48037543c1e09a4559d3eb262a2d8bf83d5f5dab85b4820a541e0c57f7cca78315d5b3382763e8acd8cc0fcb65ac
DIST votca-csg-2021.1.tar.gz 4300862 BLAKE2B 4ef287a8b0e14e97bcbc293bebdc3a0c45a08bd0033044ef8aa1ac18bac04928010ab3f5edfb656f1d062926f4572a1f3b0e55b3b3b635fdc388e5b850ec3bba SHA512 e1abdd34a3d88aea253cc10e7832a18d2cffc44286e4591c5a1239bf34e68d6c40054d3eb907a902e5ab6af5a9dea4ec266ff5ce59073b500413f4e122885e94
+DIST votca-csg-2021.2.tar.gz 4300675 BLAKE2B 8db666e77bc7d6d8da34fed97b0466e5296019aa703f324d46531992c0af544c31b2e3e4595883791cef7acd6d2d52eff8edc7eeedecaae0eb9e0cbf334748ab SHA512 5808edd96199cad6e5fc803a0e489f3d2f376da3d64f565536cc37561a0fcd22960563af7d3f86522bcc7336c8d6f7c7f6501b36feb960aae5168904156bfbf6
DIST votca-csg-2021.tar.gz 4300573 BLAKE2B ba589c97f22888b8a1a12c71314133c08c89e44c201bafa6e5f1d74dfe90c87dd84a5d1c2883b26402858b6aa990d37add57bdfb9db6836a7c287f0685a40a59 SHA512 8eacf4045ddc13d33e853cd35a67d03dfb63da60c3e879ea4f16e63f27a92aa13cbf4e367d9258778c9c09462443e4bb2b937c247c6246377ceeecf56bc6fc12
DIST votca-csg-manual-1.5.1.pdf 1263719 BLAKE2B 29e2ce27215787a1121e45ec1e88ce7c61ba81709a2519aa0959eede505498b9aaf4f38666bb1a4f97837c98b862e7ed02405da07294a7ec76cc80390fe72e0d SHA512 7d9fb4c635383e1b9c9547691f8729e19f273fcafc4dab2a6b438b3ce98ea05bd31887d09bc4edc86ceb0b04d71a4371aed7aadc3ba6864f7be2ef3328ede642
DIST votca-csg-manual-1.6.4.pdf 1242124 BLAKE2B 003a255d2869c8185f9e03038f646a80b682be3daceb18757c791f5d52101379402aee20c5dcb65ef8ce651bd6f6590ad5249e835e53ce92e04eb33214017a9e SHA512 36956acd24a21cb0a1dd26d6640b41b7473132948327c05856191b4f9531b4d1d5f98be68a9d1a847935d47633d483e87c2300634233a6e617a010c1fb563690
DIST votca-csg-tutorials-1.5.1.tar.gz 5949467 BLAKE2B c6de6084fbb1d2c4ac2ce75d01a1153eabc63386063de800ff2dc6b483b0568191e7f06ddcb8be46123224ccfd3a97f5fb4e7cd603c0ee99a8636d7143f6c701 SHA512 f2e709ae31d914fe12a4ce37b5019deb878b15ade14972f2a8204bec8970ba2c8946b71b94a5bfd6f7569e41173bfbc75275ea09cbee4358ad1de0e84751049c
DIST votca-csg-tutorials-1.6.4.tar.gz 5944389 BLAKE2B 66f1d4947bb28ec602250226ad2c08cc02278a90776acbcadca2df3078361435fb2353ee0fa299d0d19697d36682f20aab709d45539d5ac7e7070942601ebc3f SHA512 7e40037f2e70c861fd7f5c63806c17ad56672a340a8795fa745414940c55f593bef32b9f6b9050400131ed9e66aa927149e9d324a1c264364d8504baf1921e28
DIST votca-csg-tutorials-2021.1.tar.gz 5941978 BLAKE2B 5e6c5cfc3860e287d93cf8d59862a75e3afe7ac1610e696427e99302a99c86d12ce12f7a23281f36c8859e48a25be138466b9316f4c0667d5bf784f33c27e6df SHA512 8370ac9e2e859153f9a54b2e02cd18692fd06810dafb50a6bf3d81eca5211847e1b75d9832df80b1436ae0f9dcab455aa0bfb4c8122165c584cabd14203408ba
+DIST votca-csg-tutorials-2021.2.tar.gz 5942042 BLAKE2B a03627406a3b56ebf978dc82629e1f0950bfbb121a0f6c7fd60341986efe4892ba8bf1e6b526e6df2df5fb81351177ad97816568521b9dc6a91e72d6853c1e62 SHA512 3ddeb3e57353e6d4e59163ee1303b39d4e3b623309875f280bf8c02dde76d0615b32a27ea960a301b61b81034a538df87dfe97a53dfdd0c81f52629eadd64f1f
DIST votca-csg-tutorials-2021.tar.gz 5942031 BLAKE2B 60ef492c98bf07b5169c6f1be2298b6dac76003ef9981064463de9fdae649c215d469424e253d06b63637bb3eee9383c587a98322ab987995f8b4861bb0002e1 SHA512 844706407cb91d507c6b0433e23f4b27756dd4c882f6cef79d51f2b2acae6cd0114ccd91d626d090d0f61c58a57cc3c1eda0a0d10d6f4bfa522eda7ee8de21b3
diff --git a/sci-chemistry/votca-csg/metadata.xml b/sci-chemistry/votca-csg/metadata.xml
index 795272141d7..e20cfda723e 100644
--- a/sci-chemistry/votca-csg/metadata.xml
+++ b/sci-chemistry/votca-csg/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>junghans@gentoo.org</email>
diff --git a/sci-chemistry/votca-csg/votca-csg-2021.2.ebuild b/sci-chemistry/votca-csg/votca-csg-2021.2.ebuild
new file mode 100644
index 00000000000..eb83c3f2c7a
--- /dev/null
+++ b/sci-chemistry/votca-csg/votca-csg-2021.2.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit bash-completion-r1 cmake
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/${PN/-//}.git"
+else
+ SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )"
+ KEYWORDS="~amd64 ~x86 ~amd64-linux"
+ S="${WORKDIR}/${P#votca-}"
+fi
+
+DESCRIPTION="Votca coarse-graining engine"
+HOMEPAGE="https://www.votca.org/"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+IUSE="examples extras +gromacs hdf5 test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ app-shells/bash:*
+ >=dev-cpp/eigen-3.3
+ dev-lang/perl
+ ~sci-libs/votca-tools-${PV}
+ gromacs? ( sci-chemistry/gromacs:= )
+ hdf5? ( sci-libs/hdf5 )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ >=app-text/txt2tags-2.5
+ virtual/pkgconfig
+"
+
+DOCS=( README.rst NOTICE.rst CHANGELOG.rst )
+
+src_unpack() {
+ if [[ ${PV} == *9999 ]]; then
+ git-r3_src_unpack
+ if use examples; then
+ EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git"
+ EGIT_BRANCH="master"
+ EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials" \
+ git-r3_src_unpack
+ fi
+ else
+ default
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_DISABLE_FIND_PACKAGE_GROMACS=$(usex !gromacs)
+ -DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex !hdf5)
+ -DBUILD_CSGAPPS=$(usex extras)
+ -DENABLE_TESTING=$(usex test)
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+ newbashcomp "${ED}"/usr/share/votca/rc/csg-completion.bash csg_call
+ for i in "${ED}"/usr/bin/csg_*; do
+ [[ ${i} = *csg_call ]] && continue
+ bashcomp_alias csg_call "${i##*/}"
+ done
+ if use examples; then
+ insinto "/usr/share/doc/${PF}/tutorials"
+ docompress -x "/usr/share/doc/${PF}/tutorials"
+ rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake*
+ doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/*
+ fi
+}
+
+pkg_postinst() {
+ einfo
+ einfo "Please read and cite:"
+ einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). "
+ einfo "https://dx.doi.org/10.1021/ct900369w"
+ einfo
+}
diff --git a/sci-chemistry/votca-csgapps/metadata.xml b/sci-chemistry/votca-csgapps/metadata.xml
index b555f7427af..525a7af3b23 100644
--- a/sci-chemistry/votca-csgapps/metadata.xml
+++ b/sci-chemistry/votca-csgapps/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>junghans@gentoo.org</email>
diff --git a/sci-chemistry/votca-ctp/metadata.xml b/sci-chemistry/votca-ctp/metadata.xml
index 7b7ecf65468..a77179a479f 100644
--- a/sci-chemistry/votca-ctp/metadata.xml
+++ b/sci-chemistry/votca-ctp/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>junghans@gentoo.org</email>
diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest
index 0d13f9eb984..b3ede576936 100644
--- a/sci-chemistry/votca-xtp/Manifest
+++ b/sci-chemistry/votca-xtp/Manifest
@@ -1,3 +1,4 @@
DIST votca-xtp-1.6.4.tar.gz 1405299 BLAKE2B 9d4e9d3f87e0c6be886df77bf52f9d8c0b4010fb1d77621a51b739986f3f5d70c85637c0d7b4d6a8a06d7dfc7e70ff5491bdc833a1b9da6fe1e8a9742a82d220 SHA512 f35e9605f4ac92547c801b254de792b5c3bf40200e8636869467997412357251df08f88ad851bc76cb0ba15428f06f28dbd4f64043a7612273468c8d653e52af
DIST votca-xtp-2021.1.tar.gz 2192322 BLAKE2B 8b15f17e1287249ff383fc2b66b5d37c7f78bac071ea6cc2f902811ab56cded26db764cd204371d5bebca55dfce73d840d680a4c62bc458a6cf55955d783a666 SHA512 ad0190f3e9235aec9c6db4ea16de7cd0daad96ff9836821672b46dcf098ed3bc1cdbb98ccf4b495dab172d1c1a971580eef8dbf341a2067964f684871ca6277f
+DIST votca-xtp-2021.2.tar.gz 2192074 BLAKE2B 75b835501d70d1f90010bffce7cdaf3718629c8ec07d0cc10b11e6422c64f37ae32ba30c5b3006cd04863bba1986de1214fe7dbe7a6a12d76c21b4fe3e3b075b SHA512 d79e2e8973ad35a47ac0b1872cc6906aaec3881f4c8dc5ef4d9001b661212592bc309b1a82982db9c4d2827ba7749cd0bbc3134e29798c0bfaf794dee04a7cb6
DIST votca-xtp-2021.tar.gz 2192166 BLAKE2B bcacdfe92b8c9fbbe2fe949d7096c09928ef7ece3cc4e40adbf58f2894036588762f9905bce1a1595bea99d1dfb8bcd99f395bed2ce7b94eeaf51b1c33719558 SHA512 1444fd0a64a684fd2b1327a9c3af067ea812190fa95cab5f3bfcc7aae932cc7469d07fc219871ca594496fbfe74e277d3b6ccfbd7d5c24c162623515ee2fef0b
diff --git a/sci-chemistry/votca-xtp/metadata.xml b/sci-chemistry/votca-xtp/metadata.xml
index 1b28210e37e..979a4dea2e2 100644
--- a/sci-chemistry/votca-xtp/metadata.xml
+++ b/sci-chemistry/votca-xtp/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>junghans@gentoo.org</email>
diff --git a/sci-chemistry/votca-xtp/votca-xtp-2021.2.ebuild b/sci-chemistry/votca-xtp/votca-xtp-2021.2.ebuild
new file mode 100644
index 00000000000..4d4db8635e4
--- /dev/null
+++ b/sci-chemistry/votca-xtp/votca-xtp-2021.2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit bash-completion-r1 cmake
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/${PN/-//}.git"
+else
+ SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86 ~amd64-linux"
+ S="${WORKDIR}/${P#votca-}"
+fi
+
+DESCRIPTION="Votca excitation and charge properties module"
+HOMEPAGE="https://www.votca.org/"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ >=dev-cpp/eigen-3.3
+ ~sci-chemistry/votca-csg-${PV}
+ sci-libs/hdf5[cxx]
+ sci-libs/libxc
+ sci-libs/libint:2
+ ~sci-libs/votca-tools-${PV}
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+DOCS=( README.rst NOTICE.rst CHANGELOG.rst )
+
+src_configure() {
+ local mycmakeargs=(
+ -DENABLE_TESTING=$(usex test)
+ )
+ cmake_src_configure
+}
+
+pkg_postinst() {
+ einfo
+ einfo "Please read and cite:"
+ einfo "VOTCA-XTP, J. Chem. Theo. Comp. 14, 6353 (2018)"
+ einfo "https://doi.org/10.1021/acs.jctc.8b00617"
+ einfo
+}
diff --git a/sci-chemistry/wxmacmolplt/metadata.xml b/sci-chemistry/wxmacmolplt/metadata.xml
index 9e890dd280b..5fe032a3c45 100644
--- a/sci-chemistry/wxmacmolplt/metadata.xml
+++ b/sci-chemistry/wxmacmolplt/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/xds-bin/metadata.xml b/sci-chemistry/xds-bin/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/xds-bin/metadata.xml
+++ b/sci-chemistry/xds-bin/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
diff --git a/sci-chemistry/xyza2pipe/metadata.xml b/sci-chemistry/xyza2pipe/metadata.xml
index 8937bad0b17..e490bcb8aa8 100644
--- a/sci-chemistry/xyza2pipe/metadata.xml
+++ b/sci-chemistry/xyza2pipe/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>