[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: dfe0f62750dadf6273bd4146db194c7165181781
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Fri May 17 19:20:35 2024 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Fri May 17 19:20:35 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dfe0f627

sci-chemistry/pymol: Update to 3.0.0 and drop old

Closes: https://bugs.gentoo.org/862441
Closes: https://bugs.gentoo.org/910511
Closes: https://bugs.gentoo.org/929762
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/Manifest   |   2 +-
 sci-chemistry/pymol/pymol-2.5.0-r3.ebuild  | 100 -
 .../{pymol-2.5.0-r5.ebuild => pymol-3.0.0.ebuild}  |   9 +-
 3 files changed, 6 insertions(+), 105 deletions(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 2c6723b71c25..2ef25b2b27fa 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,2 +1,2 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B 
f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b
 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
-DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B 
ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9
 SHA512 
19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91
+DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B 
b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1
 SHA512 
eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
deleted file mode 100644
index 317350640580..
--- a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-DISTUTILS_USE_SETUPTOOLS=no
-DISTUTILS_EXT=1
-
-inherit desktop 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 
-> ${P}.tar.gz
-   "
-LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" 
#844991
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="+netcdf web"
-
-DEPEND="
-   dev-cpp/msgpack-cxx
-   dev-libs/mmtf-cpp
-   dev-python/pyopengl[${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-${PV}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${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
-
-   distutils-r1_python_prepare_all
-}
-
-python_configure_all() {
-   use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins )
-}
-
-python_install() {
-   distutils-r1_python_install \
-   --pymol-path="${EPREFIX}/usr/share/pymol"
-
-   sed \
-   -e '1i#!/usr/bin/env python' \
-   "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} 
|| die
-   python_doscript "${T}"/${PN}
-}
-
-python_install_all() {
-   distutils-r1_python_install_all
-
-   # These environment variables should not go in the wrapper script, or 
else
-   # it will be impossible to use the PyMOL libraries from Python.
-   cat >> "${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} %u"  PyMol ${PN} \
-   "Graphics;Education;Science;Chemistry;" \
-   

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Ulrich Müller]

commit: 3408011f5a9237398ad50fc9441f958008c8488e
Author: Ulrich Müller  gentoo  org>
AuthorDate: Sun May 12 14:50:39 2024 +
Commit: Ulrich Müller  gentoo  org>
CommitDate: Mon May 13 16:05:30 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3408011f

sci-chemistry/pymol: OFL license has been renamed to OFL-1.0

Bug: https://bugs.gentoo.org/931823
Signed-off-by: Ulrich Müller  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0-r3.ebuild| 4 ++--
 sci-chemistry/pymol/{pymol-2.5.0-r4.ebuild => pymol-2.5.0-r5.ebuild} | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
index ae7eda57d7a6..317350640580 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -15,7 +15,7 @@ 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
"
-LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991
+LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" 
#844991
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="+netcdf web"

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild
similarity index 95%
rename from sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
rename to sci-chemistry/pymol/pymol-2.5.0-r5.ebuild
index e4b4d3e2eadb..3e0e1d344ac6 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -15,7 +15,7 @@ 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
"
-LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991
+LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" 
#844991
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="+netcdf web"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: 7c1155b0a87a8388154a392f173e0399394cd681
Author: Pacho Ramos  gentoo  org>
AuthorDate: Thu Jul 20 11:30:51 2023 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Thu Jul 20 11:31:44 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7c1155b0

sci-chemistry/pymol: Fix install on prefix

Thanks-to: hsk17
Bug: https://bugs.gentoo.org/910021
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0-r4.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
index 0bc61b40744a..e4b4d3e2eadb 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
@@ -83,7 +83,7 @@ python_install_all() {
 
# Move data to correct location
dodir /usr/share/pymol
-   mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* 
"${D}/usr/share/pymol" || die
+   mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* 
"${ED}/usr/share/pymol" || die
 
# These environment variables should not go in the wrapper script, or 
else
# it will be impossible to use the PyMOL libraries from Python.

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/files/, sci-chemistry/pymol/

[Pacho Ramos]

commit: e7319a218c29e15bae4b0dd617db10d286adfef6
Author: Pacho Ramos  gentoo  org>
AuthorDate: Thu Jul 20 08:01:11 2023 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Thu Jul 20 08:01:11 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e7319a21

sci-chemistry/pymol: Use PEP517 build

Closes: https://bugs.gentoo.org/910021
Signed-off-by: Pacho Ramos  gentoo.org>

 .../pymol/files/pymol-2.5.0-format-security.patch  |  15 +++
 sci-chemistry/pymol/pymol-2.5.0-r4.ebuild  | 108 +
 2 files changed, 123 insertions(+)

diff --git a/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch 
b/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch
new file mode 100644
index ..080e5e8960e4
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch
@@ -0,0 +1,15 @@
+Author: Michael Banck 
+Description: Fix "error: format not a string literal and no format arguments 
[-Werror=format-security]" (#759860)
+Forwarded: yes
+
+--- a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
 b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
+@@ -2004,7 +2004,7 @@ namespace {
+   }
+ }
+ catch (std::exception ) {
+-  fprintf(stderr, "%s", e.what());
++  fprintf(stderr, "Cannot write timestamp to mae file: %s\n", e.what());
+   return MOLFILE_ERROR;
+ }
+ return MOLFILE_SUCCESS;

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
new file mode 100644
index ..0bc61b40744a
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.5.0-r4.ebuild
@@ -0,0 +1,108 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_PEP517="setuptools"
+DISTUTILS_EXT=1
+
+inherit desktop 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 
-> ${P}.tar.gz
+   "
+LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="+netcdf web"
+
+DEPEND="
+   dev-cpp/msgpack-cxx
+   dev-libs/mmtf-cpp
+   dev-python/pyopengl[${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-${PV}
+
+PATCHES=(
+   "${FILESDIR}/${PN}-2.5.0-format-security.patch"
+)
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${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
+
+   distutils-r1_python_prepare_all
+}
+
+python_configure_all() {
+   use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins )
+}
+
+python_install() {
+   distutils-r1_python_install \
+   --pymol-path="${EPREFIX}/usr/share/pymol"
+
+   sed \
+   -e '1i#!/usr/bin/env python' \
+   "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} 
|| die
+   python_doscript "${T}"/${PN}
+}
+
+python_install_all() {
+   distutils-r1_python_install_all
+
+   # Move data to correct location
+   dodir /usr/share/pymol
+   mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* 
"${D}/usr/share/pymol" || die
+
+   # 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} %u"  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" || 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: 61839b4959858697d83224ddca44839af364100d
Author: Pacho Ramos  gentoo  org>
AuthorDate: Wed Jul 19 08:27:44 2023 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Wed Jul 19 08:28:06 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61839b49

sci-chemistry/pymol: drop 2.5.0-r2

Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0-r2.ebuild | 98 ---
 1 file changed, 98 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
deleted file mode 100644
index 8a5317d06c11..
--- a/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-DISTUTILS_USE_SETUPTOOLS=no
-
-inherit desktop 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 
-> ${P}.tar.gz
-   "
-LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="+netcdf web"
-
-DEPEND="
-   || ( dev-cpp/msgpack-cxx dev-libs/msgpack[cxx(-)] )
-   dev-libs/mmtf-cpp
-   dev-python/pyopengl[${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-${PV}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${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="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-   distutils-r1_python_install_all
-
-   sed \
-   -e '1i#!/usr/bin/env python' \
-   "${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} %u"  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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: 5e4cabe39a1ad71a44b89b696142bab6226291a4
Author: Pacho Ramos  gentoo  org>
AuthorDate: Wed Jul 19 08:26:10 2023 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Wed Jul 19 08:28:05 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5e4cabe3

sci-chemistry/pymol: Fix distutils-r1 usage

Thanks-to: Sam James
Closes: https://bugs.gentoo.org/851588
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0-r3.ebuild | 16 +---
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
index 92415ecd58a6..ae7eda57d7a6 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
@@ -5,6 +5,7 @@ EAPI=8
 
 PYTHON_COMPAT=( python3_{9..11} )
 DISTUTILS_USE_SETUPTOOLS=no
+DISTUTILS_EXT=1
 
 inherit desktop flag-o-matic xdg distutils-r1
 
@@ -56,24 +57,25 @@ python_prepare_all() {
 
append-cxxflags -std=c++0x
 
-   use !netcdf && mydistutilsargs=( --no-vmd-plugins )
-
distutils-r1_python_prepare_all
 }
 
+python_configure_all() {
+   use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins )
+}
+
 python_install() {
distutils-r1_python_install \
--pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-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_doscript "${T}"/${PN}
+}
 
-   python_foreach_impl python_doscript "${T}"/${PN}
+python_install_all() {
+   distutils-r1_python_install_all
 
# These environment variables should not go in the wrapper script, or 
else
# it will be impossible to use the PyMOL libraries from Python.

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: b79fe624316f1410e0ac77c10ded47222fcd9d57
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sat Jun 24 17:17:02 2023 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sat Jun 24 17:17:02 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b79fe624

sci-chemistry/pymol: Drop dev-libs/msgpack[cxx(-)] to workaround portage bug

Bug: https://bugs.gentoo.org/872227
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0-r3.ebuild | 98 +++
 1 file changed, 98 insertions(+)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
new file mode 100644
index ..92415ecd58a6
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild
@@ -0,0 +1,98 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_SETUPTOOLS=no
+
+inherit desktop 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 
-> ${P}.tar.gz
+   "
+LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="+netcdf web"
+
+DEPEND="
+   dev-cpp/msgpack-cxx
+   dev-libs/mmtf-cpp
+   dev-python/pyopengl[${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-${PV}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${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="${EPREFIX}/usr/share/pymol"
+}
+
+python_install_all() {
+   distutils-r1_python_install_all
+
+   sed \
+   -e '1i#!/usr/bin/env python' \
+   "${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} %u"  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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: 27714ff93e785287397f31049027fea2357828f7
Author: Pacho Ramos  gentoo  org>
AuthorDate: Tue May  2 18:32:28 2023 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Tue May  2 18:42:45 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=27714ff9

sci-chemistry/pymol: enable py3.11

Closes: https://bugs.gentoo.org/897202
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0-r2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
index a4653ad70c83..8a5317d06c11 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..10} )
+PYTHON_COMPAT=( python3_{9..11} )
 DISTUTILS_USE_SETUPTOOLS=no
 
 inherit desktop flag-o-matic xdg distutils-r1

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Marek Szuba]

commit: c0dd21f4fceff481c9a02396ea9db26b9e4ff20a
Author: Marek Szuba  gentoo  org>
AuthorDate: Tue Feb  7 09:35:49 2023 +
Commit: Marek Szuba  gentoo  org>
CommitDate: Tue Feb  7 09:36:41 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c0dd21f4

sci-chemistry/pymol: support msgpack-5

Tested, builds fine against =dev-cpp/msgpack-cxx-5.0.0.

Closes: https://bugs.gentoo.org/893314
Signed-off-by: Marek Szuba  gentoo.org>

 ...pymol-2.5.0-r1.ebuild => pymol-2.5.0-r2.ebuild} |  2 +-
 sci-chemistry/pymol/pymol-2.5.0.ebuild | 99 --
 2 files changed, 1 insertion(+), 100 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
similarity index 97%
rename from sci-chemistry/pymol/pymol-2.5.0-r1.ebuild
rename to sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
index 287c6e3776bc..a4653ad70c83 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0-r2.ebuild
@@ -20,7 +20,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="+netcdf web"
 
 DEPEND="
-   dev-libs/msgpack[cxx(-)]
+   || ( dev-cpp/msgpack-cxx dev-libs/msgpack[cxx(-)] )
dev-libs/mmtf-cpp
dev-python/pyopengl[${PYTHON_USEDEP}]
dev-python/PyQt5[opengl,${PYTHON_USEDEP}]

diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0.ebuild
deleted file mode 100644
index febb99f21a88..
--- a/sci-chemistry/pymol/pymol-2.5.0.ebuild
+++ /dev/null
@@ -1,99 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{9..10} )
-DISTUTILS_USE_SETUPTOOLS=no
-
-inherit desktop 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-${PV}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${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="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-   distutils-r1_python_install_all
-
-   sed \
-   -e '1i#!/usr/bin/env python' \
-   "${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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Marek Szuba]

commit: 3a660afed239c168c7f62df1517dddaab03738d6
Author: Marek Szuba  gentoo  org>
AuthorDate: Sun Feb  5 20:56:02 2023 +
Commit: Marek Szuba  gentoo  org>
CommitDate: Sun Feb  5 21:01:41 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3a660afe

sci-chemistry/pymol: account for dev-libs/msgpack without IUSE=cxx

No revbump because this isn't finished yet - for newer versions of
msgpack PyMol should depend on dev-cpp/msgpack-cxx, however
compatibility with that package has not been tested yet.

Signed-off-by: Marek Szuba  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0-r1.ebuild | 2 +-
 sci-chemistry/pymol/pymol-2.5.0.ebuild| 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild
index d237e0916f57..287c6e3776bc 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild
@@ -20,7 +20,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="+netcdf web"
 
 DEPEND="
-   dev-libs/msgpack[cxx]
+   dev-libs/msgpack[cxx(-)]
dev-libs/mmtf-cpp
dev-python/pyopengl[${PYTHON_USEDEP}]
dev-python/PyQt5[opengl,${PYTHON_USEDEP}]

diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0.ebuild
index 80803df67e5d..febb99f21a88 100644
--- a/sci-chemistry/pymol/pymol-2.5.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0.ebuild
@@ -21,7 +21,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="+netcdf web"
 
 DEPEND="
-   dev-libs/msgpack[cxx]
+   dev-libs/msgpack[cxx(-)]
dev-libs/mmtf-cpp
dev-python/pyopengl[${PYTHON_USEDEP}]
dev-python/PyQt5[opengl,${PYTHON_USEDEP}]

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Sam James]

commit: 5fdce3209a4873ddc9ded828ac8fd2ff5339ec13
Author: Sam James  gentoo  org>
AuthorDate: Sun Jul 31 07:39:24 2022 +
Commit: Sam James  gentoo  org>
CommitDate: Sun Jul 31 08:25:22 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5fdce320

sci-chemistry/pymol: add github upstream metadata

Signed-off-by: Sam James  gentoo.org>

 sci-chemistry/pymol/metadata.xml | 21 +++--
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index d28a87c8e563..8a087408c332 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -1,14 +1,15 @@
 
 https://www.gentoo.org/dtd/metadata.dtd;>
 
-  
-sci-chemis...@gentoo.org
-Gentoo Chemistry Project
-  
-  
-Install Pymodule needed for web app support
-  
-  
-pymol
-  
+   
+   sci-chemis...@gentoo.org
+   Gentoo Chemistry Project
+   
+   
+   Install Pymodule needed for web app 
support
+   
+   
+   schrodinger/pymol-open-source
+   pymol
+   
 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: b1b098bea1c8a0d165b298ee37805f0b334c0363
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sun May 22 11:17:48 2022 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sun May 22 11:17:54 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b1b098be

sci-chemistry/pymol: Fix desktop file, LICENSE and restrict values

Also port to eapi8

Thanks-to: Ulrich Müller
Closes: https://bugs.gentoo.org/844991
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0-r1.ebuild | 98 +++
 1 file changed, 98 insertions(+)

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild
new file mode 100644
index ..cf2591c61323
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.5.0-r1.ebuild
@@ -0,0 +1,98 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=no
+
+inherit desktop 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 
-> ${P}.tar.gz
+   "
+LICENSE="BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA" #844991
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="+netcdf web"
+
+DEPEND="
+   dev-libs/msgpack[cxx]
+   dev-libs/mmtf-cpp
+   dev-python/pyopengl[${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-${PV}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${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="${EPREFIX}/usr/share/pymol"
+}
+
+python_install_all() {
+   distutils-r1_python_install_all
+
+   sed \
+   -e '1i#!/usr/bin/env python' \
+   "${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} %u"  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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: 7ed232b26caa687abd38b7079d9f4e19a86a3bc3
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Fri Apr  8 09:52:06 2022 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Fri Apr  8 09:52:06 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7ed232b2

sci-chemistry/pymol: enable py3.10

Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0.ebuild | 20 +++-
 1 file changed, 3 insertions(+), 17 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0.ebuild
index a7fc5fdc127c..93464f4a28be 100644
--- a/sci-chemistry/pymol/pymol-2.5.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{7..10} )
 DISTUTILS_USE_SETUPTOOLS=no
 
-inherit desktop optfeature flag-o-matic xdg distutils-r1
+inherit desktop flag-o-matic xdg distutils-r1
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="https://www.pymol.org/;
@@ -65,15 +65,6 @@ python_prepare_all() {
 python_install() {
distutils-r1_python_install \
--pymol-path="${EPREFIX}/usr/share/pymol"
-
-# File is not created as apbs was dropped from the tree
-# https://bugs.gentoo.org/790629
-#  sed \
-#  -e '1d' \
-#  -e "/APBS_BINARY_LOCATION/s:None:\"${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() {
@@ -106,8 +97,3 @@ python_install_all() {
 
rm -f "${ED}"/usr/share/${PN}/LICENSE || die
 }
-
-#pkg_postinst() {
-#  xdg_pkg_postinst
-#  optfeature "Electrostatic calculations" sci-chemistry/apbs 
sci-chemistry/pdb2pqr
-#}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

[David Seifert]

commit: 95a31681e14af07ba21add4cdb655fe3211eedeb
Author: David Seifert  gentoo  org>
AuthorDate: Sun Oct 24 11:20:28 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Oct 24 11:20:28 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=95a31681

sci-chemistry/pymol: drop 2.4.0-r1

Signed-off-by: David Seifert  gentoo.org>

 sci-chemistry/pymol/Manifest   |   1 -
 .../pymol/files/pymol-2.4.0-fix_bug119.patch   |  34 --
 sci-chemistry/pymol/pymol-2.4.0-r1.ebuild  | 116 -
 3 files changed, 151 deletions(-)

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..000
--- 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 
-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/pymol-2.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
deleted file mode 100644
index c710896747d..000
--- 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' \
-   

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: 319a93dd7c1b57253d978f4491df7dfb6e9d3108
Author: Pacho Ramos  gentoo  org>
AuthorDate: Thu May 20 15:07:07 2021 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Thu May 20 15:07:21 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=319a93dd

sci-chemistry/pymol: apbs_tools.py is not created

as apbs package was dropped from the tree

Closes: https://bugs.gentoo.org/790629
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.5.0.ebuild | 22 --
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0.ebuild
index 6d7ecd4e09c..a7fc5fdc127 100644
--- a/sci-chemistry/pymol/pymol-2.5.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.5.0.ebuild
@@ -66,12 +66,14 @@ 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}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || 
die
+# File is not created as apbs was dropped from the tree
+# https://bugs.gentoo.org/790629
+#  sed \
+#  -e '1d' \
+#  -e "/APBS_BINARY_LOCATION/s:None:\"${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() {
@@ -105,7 +107,7 @@ python_install_all() {
rm -f "${ED}"/usr/share/${PN}/LICENSE || die
 }
 
-pkg_postinst() {
-   xdg_pkg_postinst
-   optfeature "Electrostatic calculations" sci-chemistry/apbs 
sci-chemistry/pdb2pqr
-}
+#pkg_postinst() {
+#  xdg_pkg_postinst
+#  optfeature "Electrostatic calculations" sci-chemistry/apbs 
sci-chemistry/pdb2pqr
+#}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: 428de16e86460563d0e465331e301cc0dedf91ac
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Sun May 16 20:41:00 2021 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Sun May 16 20:41:15 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=428de16e

sci-chemistry/pymol: Version bump

Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/Manifest   |   1 +
 sci-chemistry/pymol/pymol-2.5.0.ebuild | 111 +
 2 files changed, 112 insertions(+)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index cfd2bae6b9a..dec8f0b1525 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,2 +1,3 @@
 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/pymol-2.5.0.ebuild 
b/sci-chemistry/pymol/pymol-2.5.0.ebuild
new file mode 100644
index 000..6d7ecd4e09c
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.5.0.ebuild
@@ -0,0 +1,111 @@
+# 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-${PV}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${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 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: c4ec1ee42400be04414a8ab1b728ec21add16fff
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sun May  2 19:20:06 2021 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sun May  2 19:22:22 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c4ec1ee4

sci-chemistry/pymol: Re-host distfiles

Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.4.0-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
index 7fb154b6850..c710896747d 100644
--- a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
@@ -11,7 +11,7 @@ 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/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+   https://dev.gentoo.org/~pacho/${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"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[David Seifert]

commit: ed702145ff6aa7244042d67bf68f6e17b621cd94
Author: Jakov Smolic  sartura  hr>
AuthorDate: Mon Jan 18 10:14:15 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Jan 18 10:14:15 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ed702145

sci-chemistry/pymol: Remove old

Signed-off-by: Jakov Smolic  sartura.hr>
Signed-off-by: David Seifert  gentoo.org>

 sci-chemistry/pymol/pymol-2.4.0.ebuild | 115 -
 1 file changed, 115 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.4.0.ebuild 
b/sci-chemistry/pymol/pymol-2.4.0.ebuild
deleted file mode 100644
index 5dd5d436776..000
--- a/sci-chemistry/pymol/pymol-2.4.0.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6,7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=no
-
-inherit distutils-r1 desktop optfeature flag-o-matic xdg-utils
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="https://www.pymol.org/;
-SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
-   https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz 
-> ${P}.tar.gz
-   "
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="web"
-
-DEPEND="
-   dev-libs/msgpack[cxx]
-   dev-libs/mmtf-cpp
-   dev-python/pyopengl[${PYTHON_USEDEP}]
-   dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
-   dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/pmw[${PYTHON_USEDEP}]
-   media-libs/freetype:2
-   media-libs/glew:0=
-   media-libs/glm
-   media-libs/libpng:0=
-   media-video/mpeg-tools
-   sys-libs/zlib
-"
-RDEPEND="${DEPEND}
-   sci-chemistry/chemical-mime-data
-"
-
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
-   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-   -e "/import/s:argparse:argparseX: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
-
-   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_desktop_database_update
-   xdg_mimeinfo_database_update
-   optfeature "Electrostatic calculations" sci-chemistry/apbs 
sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-   xdg_desktop_database_update
-   xdg_mimeinfo_database_update
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: d707db016087c78a6a39b8f6607f9304e90361ed
Author: Pacho Ramos  gentoo  org>
AuthorDate: Thu Jan 14 23:11:09 2021 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Thu Jan 14 23:11:09 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d707db01

sci-chemistry/pymol: Ensure proper prepare phase is run

and don't drop argparse

Thanks-to: Soren Harward
Closes: https://bugs.gentoo.org/757798
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.4.0-r1.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
index 540097824ec..a21a210f478 100644
--- a/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=7
 PYTHON_COMPAT=( python3_{6..9} )
 DISTUTILS_USE_SETUPTOOLS=no
 
-inherit distutils-r1 desktop optfeature flag-o-matic xdg
+inherit desktop optfeature flag-o-matic xdg distutils-r1
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="https://www.pymol.org/;
@@ -50,7 +50,6 @@ python_prepare_all() {
sed \
-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-   -e "/import/s:argparse:argparseX:g" \
-i setup.py || die
 
sed \

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

[Pacho Ramos]

commit: 85e6d34ad04bc76ea9a8f9fa04eb46af9ebf433d
Author: Pacho Ramos  gentoo  org>
AuthorDate: Wed Jan 13 19:05:06 2021 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Wed Jan 13 19:11:11 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=85e6d34a

sci-chemistry/pymol: Fix netcdf handling

Also fix upstream bug and use xdg.eclass to not need to redefine every pkg_
phase

Closes: https://bugs.gentoo.org/757798
Thanks-to: Soren Harward
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Pacho Ramos  gentoo.org>

 .../pymol/files/pymol-2.4.0-fix_bug119.patch   |  34 ++
 sci-chemistry/pymol/pymol-2.4.0-r1.ebuild  | 117 +
 2 files changed, 151 insertions(+)

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
new file mode 100644
index 000..62512053fd7
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-2.4.0-fix_bug119.patch
@@ -0,0 +1,34 @@
+From 885891cf60371674406cdff16b395e25cc13d8ae Mon Sep 17 00:00:00 2001
+From: Sebastian Keller 
+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/pymol-2.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
new file mode 100644
index 000..540097824ec
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.4.0-r1.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+DISTUTILS_USE_SETUPTOOLS=no
+
+inherit distutils-r1 desktop optfeature flag-o-matic xdg
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="https://www.pymol.org/;
+SRC_URI="
+   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+   https://github.com/schrodinger/pymol-open-source/archive/v${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" \
+   -e "/import/s:argparse:argparseX: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' \
+   

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Fabian Groffen]

commit: a748077bb6ede1a43ca3d798a14ef278a9dfdd26
Author: Fabian Groffen  gentoo  org>
AuthorDate: Wed Jan  6 15:09:56 2021 +
Commit: Fabian Groffen  gentoo  org>
CommitDate: Wed Jan  6 15:09:56 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a748077b

sci-chemistry/pymol: drop x86-macos

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Fabian Groffen  gentoo.org>

 sci-chemistry/pymol/pymol-2.4.0.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.4.0.ebuild 
b/sci-chemistry/pymol/pymol-2.4.0.ebuild
index 6ff6e2326d9..5dd5d436776 100644
--- a/sci-chemistry/pymol/pymol-2.4.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.4.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -17,7 +17,7 @@ SRC_URI="
 RESTRICT="mirror"
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="web"
 
 DEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: 5517c82efb9b793cd9b0533d5371080199789543
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Sat Nov 28 19:36:37 2020 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Sat Nov 28 19:36:37 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5517c82e

sci-chemistry/pymol: Fix distutils warning

Package-Manager: Portage-3.0.10, Repoman-3.0.2
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/pymol-2.4.0.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-chemistry/pymol/pymol-2.4.0.ebuild 
b/sci-chemistry/pymol/pymol-2.4.0.ebuild
index 04ac2f9895a..6ff6e2326d9 100644
--- a/sci-chemistry/pymol/pymol-2.4.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.4.0.ebuild
@@ -4,6 +4,7 @@
 EAPI=7
 
 PYTHON_COMPAT=( python3_{6,7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=no
 
 inherit distutils-r1 desktop optfeature flag-o-matic xdg-utils
 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: fb417c1f224725f3f0b986113865d3de8bb38741
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Fri Nov 27 13:39:23 2020 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Fri Nov 27 13:39:23 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fb417c1f

sci-chemistry/pymol: Version bump

Closes: https://bugs.gentoo.org/701868
Package-Manager: Portage-3.0.10, Repoman-3.0.2
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/Manifest  | 2 +-
 sci-chemistry/pymol/{pymol-2.3.0-r3.ebuild => pymol-2.4.0.ebuild} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 5204b446eb8..cfd2bae6b9a 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,2 +1,2 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B 
f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b
 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
-DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 
0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05
 SHA512 
e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
+DIST pymol-2.4.0.tar.gz 10552539 BLAKE2B 
34e31dce99c1e838b00389c3d7c29657534dd037349769bd6c8cb17028cfaaa856d5729760d3768fd43f61086cac30749a864fb4156c14eda07f9027430f0523
 SHA512 
2b19294197d58a808bf7bb7fa9f829c2ec582ba47a4380783a2b1eedda2ce4118cd398e01885db8c449e7fd5e4c08a1c40508e679ef42d8e183a6a52b031c02a

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.4.0.ebuild
similarity index 100%
rename from sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
rename to sci-chemistry/pymol/pymol-2.4.0.ebuild

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: e9c0ee13ce43b45b33796326e41049f3d020310d
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Fri Nov 27 13:31:48 2020 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Fri Nov 27 13:31:48 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e9c0ee13

sci-chemistry/pymol: add pmw as dep

Closes: https://bugs.gentoo.org/725480
Package-Manager: Portage-3.0.10, Repoman-3.0.2
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/pymol-2.3.0-r3.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
index 0a2e041f0da..04ac2f9895a 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -25,6 +25,7 @@ DEPEND="
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

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: 10a72e4fd89f88032a5f6af84975b99777b02a13
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Wed Oct 14 10:31:34 2020 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Wed Oct 14 10:31:34 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=10a72e4f

sci-chemistry/pymol: Added py39

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/pymol-2.3.0-r3.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
index e469b6431e8..0a2e041f0da 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6,7,8} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 
 inherit distutils-r1 desktop optfeature flag-o-matic xdg-utils
 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[David Seifert]

commit: 45a1aa11ca88530be7230c350a47c17604ab5018
Author: David Seifert  gentoo  org>
AuthorDate: Mon Sep  7 08:53:51 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Sep  7 08:53:51 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=45a1aa11

sci-chemistry/pymol: Inherit optfeature.eclass

Package-Manager: Portage-3.0.5, Repoman-3.0.1
Signed-off-by: David Seifert  gentoo.org>

 sci-chemistry/pymol/pymol-2.3.0-r3.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
index 58c0d6707c4..e469b6431e8 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 PYTHON_COMPAT=( python3_{6,7,8} )
 
-inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
+inherit distutils-r1 desktop optfeature flag-o-matic xdg-utils
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="https://www.pymol.org/;
@@ -81,7 +81,7 @@ python_install_all() {
 
# These environment variables should not go in the wrapper script, or 
else
# it will be impossible to use the PyMOL libraries from Python.
-   cat >> "${T}"/20pymol <<- EOF
+   cat >> "${T}"/20pymol <<- EOF || die
PYMOL_PATH="${EPREFIX}/usr/share/pymol"
PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Andreas Sturmlechner]

commit: e6cc55210919cbdee58bcaa282cf6ef2064aa7c2
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Wed Jul 29 18:47:25 2020 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sat Aug  1 23:19:34 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e6cc5521

sci-chemistry/pymol: Drop 2.3.0-r2

Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: Andreas Sturmlechner  gentoo.org>

 sci-chemistry/pymol/pymol-2.3.0-r2.ebuild | 118 --
 1 file changed, 118 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
deleted file mode 100644
index 5eadc9a8512..000
--- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="https://www.pymol.org/;
-SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
-   https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz 
-> ${P}.tar.gz
-   "
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="web"
-
-DEPEND="
-   dev-libs/msgpack[cxx]
-   dev-libs/mmtf-cpp
-   || (
-   dev-python/numpy-python2[${PYTHON_USEDEP}]
-   dev-python/numpy[${PYTHON_USEDEP}]
-   )
-   dev-python/pmw:py2[${PYTHON_USEDEP}]
-   dev-python/pyopengl[${PYTHON_USEDEP}]
-   dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
-   media-libs/freetype:2
-   media-libs/glew:0=
-   media-libs/glm
-   media-libs/libpng:0=
-   media-video/mpeg-tools
-   sys-libs/zlib
-   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}
-   sci-chemistry/chemical-mime-data
-"
-
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
-   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-   -e "/import/s:argparse:argparseX: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
-
-   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 >> "${T}"/20pymol <<- EOF
-   PYMOL_PATH="${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_desktop_database_update
-   xdg_mimeinfo_database_update
-   optfeature "Electrostatic calculations" sci-chemistry/apbs 
sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-   xdg_desktop_database_update
-   xdg_mimeinfo_database_update
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-promol/

[Andreas K. Hüttel]

commit: 5326d0eddaaa497b7fad715cd8c1b7766e20138f
Author: Alexey Sokolov  google  com>
AuthorDate: Sat Jun 20 16:17:52 2020 +
Commit: Andreas K. Hüttel  gentoo  org>
CommitDate: Sat Jun 27 20:45:04 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5326d0ed

sci-chemistry/pymol-plugins-promol: update homepage

Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Alexey Sokolov  asokolov.org>
Signed-off-by: Andreas K. Hüttel  gentoo.org>

 .../pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git 
a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild 
b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
index d1c826850f6..6cd842f3703 100644
--- a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
+++ b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
@@ -8,8 +8,8 @@ PYTHON_COMPAT=( python2_7 )
 inherit python-r1
 
 DESCRIPTION="Fast and accurate regognition of active sites"
-HOMEPAGE="http://www.rit.edu/cos/ezviz/ProMOL_dl.html;
-SRC_URI="http://www.rit.edu/cos/ezviz/ProMOL.zip -> ${P}.zip"
+HOMEPAGE="https://www.rit.edu/cos/ezviz/ProMOL_dl.html;
+SRC_URI="https://www.rit.edu/cos/ezviz/ProMOL.zip -> ${P}.zip"
 
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: d8f901f6451dcefa90b1e467d2819a85717bae56
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Wed Jun  3 21:20:53 2020 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Wed Jun  3 21:20:53 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d8f901f6

sci-chemistry/pymol: Works with py38

Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/pymol-2.3.0-r3.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
index 675c8b36880..58c0d6707c4 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: de879cad418f2e55fb037c9a063dde7c3ae3dec3
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Wed Mar  4 18:01:25 2020 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Wed Mar  4 18:01:50 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=de879cad

sci-chemistry/pymol: pymol works with py3

Package-Manager: Portage-2.3.88, Repoman-2.3.20
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/pymol-2.3.0-r2.ebuild  |  1 -
 .../pymol/{pymol-2.3.0-r2.ebuild => pymol-2.3.0-r3.ebuild} | 10 ++
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
index 36cc913f7b0..5eadc9a8512 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
@@ -29,7 +29,6 @@ DEPEND="
dev-python/pmw:py2[${PYTHON_USEDEP}]
dev-python/pyopengl[${PYTHON_USEDEP}]
dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
-   dev-python/numpy[${PYTHON_USEDEP}]
media-libs/freetype:2
media-libs/glew:0=
media-libs/glm

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
similarity index 92%
copy from sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
copy to sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
index 36cc913f7b0..675c8b36880 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7} )
 
 inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
 
@@ -22,11 +22,6 @@ IUSE="web"
 DEPEND="
dev-libs/msgpack[cxx]
dev-libs/mmtf-cpp
-   || (
-   dev-python/numpy-python2[${PYTHON_USEDEP}]
-   dev-python/numpy[${PYTHON_USEDEP}]
-   )
-   dev-python/pmw:py2[${PYTHON_USEDEP}]
dev-python/pyopengl[${PYTHON_USEDEP}]
dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
@@ -36,8 +31,7 @@ DEPEND="
media-libs/libpng:0=
media-video/mpeg-tools
sys-libs/zlib
-   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+"
 RDEPEND="${DEPEND}
sci-chemistry/chemical-mime-data
 "

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Pacho Ramos]

commit: 68bc99ce88a667735c8b723fdb48d9e9c399a25c
Author: Pacho Ramos  gentoo  org>
AuthorDate: Fri Feb  7 18:40:38 2020 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Fri Feb  7 18:41:08 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=68bc99ce

sci-chemistry/pymol: chemical-mime-data needed for .desktop Mime defs

Closes: https://bugs.gentoo.org/703000
Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/pymol/pymol-2.3.0-r2.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
index 6e8433b403e..36cc913f7b0 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
@@ -38,7 +38,9 @@ DEPEND="
sys-libs/zlib
!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+   sci-chemistry/chemical-mime-data
+"
 
 S="${WORKDIR}"/${PN}-open-source-${PV}
 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Michał Górny]

commit: fffd22f3ab77845f870f93d08b75722ce474ef32
Author: Michał Górny  gentoo  org>
AuthorDate: Tue Jan 28 16:48:52 2020 +
Commit: Michał Górny  gentoo  org>
CommitDate: Tue Jan 28 18:24:07 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fffd22f3

sci-chemistry/pymol: Remove old (drop to ~arch)

Signed-off-by: Michał Górny  gentoo.org>

 sci-chemistry/pymol/Manifest|   1 -
 sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild | 111 
 2 files changed, 112 deletions(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index ab400768a37..5204b446eb8 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-2.3.0.tar.gz 10448674 BLAKE2B 
0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05
 SHA512 
e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
-DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B 
a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3
 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild
deleted file mode 100644
index f60de8dcb18..000
--- a/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="https://www.pymol.org/;
-SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${P}.png.xz
-   mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
-   "
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="web"
-
-DEPEND="
-   || (
-   dev-python/numpy-python2[${PYTHON_USEDEP}]
-   dev-python/numpy[${PYTHON_USEDEP}]
-   )
-   dev-python/pmw:py2[${PYTHON_USEDEP}]
-   dev-python/pyopengl[${PYTHON_USEDEP}]
-   media-libs/freeglut
-   media-libs/freetype:2
-   media-libs/glew:0=
-   media-libs/libpng:0=
-   media-video/mpeg-tools
-   sys-libs/zlib
-   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
-   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-   -e "/import/s:argparse:argparseX:g" \
-   -i setup.py || die
-
-   sed \
-   -e "s:/opt/local:${EPREFIX}/usr:g" \
-   -e '/ext_comp_args/s:\[.*\]:[]:g' \
-   -i setup.py || die
-
-   append-cxxflags -std=c++0x
-
-   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 >> "${T}"/20pymol <<- EOF
-   PYMOL_PATH="${EPREFIX}/usr/share/pymol"
-   PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-   PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-   EOF
-
-   doenvd "${T}"/20pymol
-
-   newicon "${WORKDIR}"/${P}.png ${PN}.png
-   make_desktop_entry ${PN} PyMol ${PN} \
-   

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Michał Górny]

commit: 6db822a4c7759eacbe5c96503d3c629f1256b187
Author: Michał Górny  gentoo  org>
AuthorDate: Wed Jan 22 21:44:04 2020 +
Commit: Michał Górny  gentoo  org>
CommitDate: Wed Jan 22 21:49:53 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6db822a4

sci-chemistry/pymol: Revbump post dep change

Signed-off-by: Michał Górny  gentoo.org>

 sci-chemistry/pymol/{pymol-1.8.4.0-r1.ebuild => pymol-1.8.4.0-r2.ebuild} | 0
 sci-chemistry/pymol/{pymol-2.3.0-r1.ebuild => pymol-2.3.0-r2.ebuild} | 0
 2 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild
similarity index 100%
rename from sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
rename to sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
similarity index 100%
rename from sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
rename to sci-chemistry/pymol/pymol-2.3.0-r2.ebuild

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Michał Górny]

commit: d1a502c6076dba392a82e7a3a476f65f4ac8cf55
Author: Michał Górny  gentoo  org>
AuthorDate: Thu Jan 16 06:27:31 2020 +
Commit: Michał Górny  gentoo  org>
CommitDate: Thu Jan 16 06:38:04 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d1a502c6

sci-chemistry/pymol: Permit numpy-python2

Signed-off-by: Michał Górny  gentoo.org>

 sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild | 5 -
 sci-chemistry/pymol/pymol-2.3.0-r1.ebuild   | 5 -
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
index 0bcafb2e322..d6864f00a97 100644
--- a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
@@ -22,7 +22,10 @@ KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos 
~x86-macos"
 IUSE="web"
 
 DEPEND="
-   dev-python/numpy[${PYTHON_USEDEP}]
+   || (
+   dev-python/numpy-python2[${PYTHON_USEDEP}]
+   dev-python/numpy[${PYTHON_USEDEP}]
+   )
dev-python/pmw:py2[${PYTHON_USEDEP}]
dev-python/pyopengl[${PYTHON_USEDEP}]
media-libs/freeglut

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
index b84c2769806..7591fe38393 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
@@ -22,7 +22,10 @@ IUSE="web"
 DEPEND="
dev-libs/msgpack[cxx]
dev-libs/mmtf-cpp
-   dev-python/numpy[${PYTHON_USEDEP}]
+   || (
+   dev-python/numpy-python2[${PYTHON_USEDEP}]
+   dev-python/numpy[${PYTHON_USEDEP}]
+   )
dev-python/pmw:py2[${PYTHON_USEDEP}]
dev-python/pyopengl[${PYTHON_USEDEP}]
dev-python/PyQt5[opengl,${PYTHON_USEDEP}]

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Michał Górny]

commit: 903ca8dc261b929d0b6d57f62e2ec18129cb14ec
Author: Michał Górny  gentoo  org>
AuthorDate: Thu Jan 16 06:36:25 2020 +
Commit: Michał Górny  gentoo  org>
CommitDate: Thu Jan 16 06:38:24 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=903ca8dc

sci-chemistry/pymol: Use HTTPS

Signed-off-by: Michał Górny  gentoo.org>

 sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild | 4 ++--
 sci-chemistry/pymol/pymol-2.3.0-r1.ebuild   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
index d6864f00a97..f60de8dcb18 100644
--- a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -9,7 +9,7 @@ PYTHON_REQ_USE="tk"
 inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
 
 DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/;
+HOMEPAGE="https://www.pymol.org/;
 SRC_URI="
https://dev.gentoo.org/~jlec/distfiles/${P}.png.xz
mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
index 7591fe38393..6e8433b403e 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
 
 DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/;
+HOMEPAGE="https://www.pymol.org/;
 SRC_URI="
https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz 
-> ${P}.tar.gz

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Michał Górny]

commit: e879367f72e6f019c005cb19ea0d337841834654
Author: Michał Górny  gentoo  org>
AuthorDate: Fri Sep 27 17:30:47 2019 +
Commit: Michał Górny  gentoo  org>
CommitDate: Fri Sep 27 17:33:43 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e879367f

sci-chemistry/pymol: Dep on dev-python/pmw directly

Signed-off-by: Michał Górny  gentoo.org>

 sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild | 2 +-
 sci-chemistry/pymol/pymol-2.3.0-r1.ebuild   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
index c2bedf7ca9d..0bcafb2e322 100644
--- a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
@@ -23,6 +23,7 @@ IUSE="web"
 
 DEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pmw:py2[${PYTHON_USEDEP}]
dev-python/pyopengl[${PYTHON_USEDEP}]
media-libs/freeglut
media-libs/freetype:2
@@ -30,7 +31,6 @@ DEPEND="
media-libs/libpng:0=
media-video/mpeg-tools
sys-libs/zlib
-   virtual/python-pmw[${PYTHON_USEDEP}]
!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
 RDEPEND="${DEPEND}"

diff --git a/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
index 89aef82c8e9..b84c2769806 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
@@ -23,6 +23,7 @@ DEPEND="
dev-libs/msgpack[cxx]
dev-libs/mmtf-cpp
dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pmw:py2[${PYTHON_USEDEP}]
dev-python/pyopengl[${PYTHON_USEDEP}]
dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
@@ -32,7 +33,6 @@ DEPEND="
media-libs/libpng:0=
media-video/mpeg-tools
sys-libs/zlib
-   virtual/python-pmw[${PYTHON_USEDEP}]
!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
 RDEPEND="${DEPEND}"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-promol/

[Michał Górny]

commit: e92ae77f7325ea8db5144c1fe34228fe3cad2b5a
Author: Michał Górny  gentoo  org>
AuthorDate: Fri Sep 27 17:31:03 2019 +
Commit: Michał Górny  gentoo  org>
CommitDate: Fri Sep 27 17:33:44 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e92ae77f

sci-chemistry/pymol-plugins-promol: Dep on dev-python/pmw directly

Signed-off-by: Michał Górny  gentoo.org>

 sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git 
a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild 
b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
index 1c0b12a6a76..030ecde978e 100644
--- a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
+++ b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
@@ -22,7 +22,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
${PYTHON_DEPS}
-   virtual/python-pmw[${PYTHON_USEDEP}]
+   dev-python/pmw:py2[${PYTHON_USEDEP}]
sci-chemistry/pymol[${PYTHON_USEDEP}]"
 DEPEND=""
 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-caver/

[Michał Górny]

commit: f70cad2cf2b9ef4d61a866c986e5a15aa7805aac
Author: Michał Górny  gentoo  org>
AuthorDate: Fri Sep 20 21:49:22 2019 +
Commit: Michał Górny  gentoo  org>
CommitDate: Fri Sep 20 21:59:21 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f70cad2c

sci-chemistry/pymol-plugins-caver: Add missing RESTRICT=bindist

Signed-off-by: Michał Górny  gentoo.org>

 sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild 
b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild
index 7da3317b59b..e189f885dcc 100644
--- a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild
+++ b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild
@@ -27,7 +27,7 @@ RDEPEND="
 DEPEND="app-arch/unzip
${PYTHON_DEPS}"
 
-RESTRICT="fetch"
+RESTRICT="bindist fetch"
 
 S="${WORKDIR}/${MY_P}"/linux_mac
 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-promol/

[David Seifert]

commit: 23932c30cbd5647cbc698b37c51ba0baaeeaa6b3
Author: David Seifert  gentoo  org>
AuthorDate: Sun Aug 11 11:50:11 2019 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Aug 11 11:50:11 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=23932c30

sci-chemistry/pymol-plugins-promol: [QA] Fix double-prefix

Package-Manager: Portage-2.3.71, Repoman-2.3.17
Signed-off-by: David Seifert  gentoo.org>

 .../pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git 
a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild 
b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
index bda6bd69481..1c0b12a6a76 100644
--- a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
+++ b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -33,7 +33,7 @@ src_prepare() {
preparation() {
cd "${BUILD_DIR}" || die
sed \
-   -e 
"s:./modules/pmg_tk/startup:${EPREFIX}/$(python_get_sitedir)/pmg_tk/startup/ProMol:g"
 \
+   -e 
"s:./modules/pmg_tk/startup:$(python_get_sitedir)/pmg_tk/startup/ProMol:g" \
-i ProMOL_302.py || die
}
python_foreach_impl preparation

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: dd358f4227f9021e21150582702536055324017b
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Sat Jun  1 08:37:56 2019 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Sat Jun  1 08:37:56 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dd358f42

sci-chemistry/pymol: Change deps

Now pymol depends on PyQt5, since freeglut interface is deprecated

Package-Manager: Portage-2.3.67, Repoman-2.3.13
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/Manifest   |   1 -
 sci-chemistry/pymol/pymol-2.2.0.ebuild | 114 -
 .../{pymol-2.3.0.ebuild => pymol-2.3.0-r1.ebuild}  |   7 +-
 3 files changed, 3 insertions(+), 119 deletions(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 4e293b43050..ab400768a37 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,3 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B 
f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b
 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
-DIST pymol-2.2.0.tar.gz 10514753 BLAKE2B 
54bf7c639ec1af0c318438f6dcbe5878aded5cc360dee3a5f1dee4b6eea588f4242865ae8adf1e044628ad5f71aa8f6d58d0cc71baf7c1f20eed3045ed3a1cb1
 SHA512 
56776586276208d42cc4bd4c3cb7d6b9a08e7239186b8f398c75cb57f85e05ebf51aaa8cdec5672e56beeda26f1cd9d14c6de7fba1a741f9c8ec22c1292b9c63
 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 
0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05
 SHA512 
e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
 DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B 
a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3
 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe

diff --git a/sci-chemistry/pymol/pymol-2.2.0.ebuild 
b/sci-chemistry/pymol/pymol-2.2.0.ebuild
deleted file mode 100644
index 1e53d9ab339..000
--- a/sci-chemistry/pymol/pymol-2.2.0.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils xdg-utils flag-o-matic
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/;
-SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
-   https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz 
-> ${P}.tar.gz
-   "
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="web"
-
-DEPEND="
-   dev-libs/msgpack[cxx]
-   dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/pyopengl[${PYTHON_USEDEP}]
-   media-libs/freeglut
-   media-libs/freetype:2
-   media-libs/glew:0=
-   media-libs/glm
-   media-libs/libpng:0=
-   media-video/mpeg-tools
-   sys-libs/zlib
-   virtual/python-pmw[${PYTHON_USEDEP}]
-   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
-   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-   -e "/import/s:argparse:argparseX: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
-
-   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 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-dynamics/

[Mikle Kolyada]

commit: 75c9c71805f8564d1aecc61bdbef54ace5261038
Author: Mikle Kolyada  gentoo  org>
AuthorDate: Mon Apr 15 07:31:19 2019 +
Commit: Mikle Kolyada  gentoo  org>
CommitDate: Mon Apr 15 07:31:19 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=75c9c718

sci-chemistry/pymol-plugins-dynamics: remove last rited package

Signed-off-by: Mikle Kolyada  gentoo.org>

 sci-chemistry/pymol-plugins-dynamics/Manifest  |  2 --
 sci-chemistry/pymol-plugins-dynamics/metadata.xml  | 11 ---
 .../pymol-plugins-dynamics-2.0.7.ebuild| 37 --
 .../pymol-plugins-dynamics-2.1.1.ebuild| 37 --
 4 files changed, 87 deletions(-)

diff --git a/sci-chemistry/pymol-plugins-dynamics/Manifest 
b/sci-chemistry/pymol-plugins-dynamics/Manifest
deleted file mode 100644
index ea60811a63b..000
--- a/sci-chemistry/pymol-plugins-dynamics/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST pymol-plugins-dynamics-2.0.7.tar.gz 822680 BLAKE2B 
3c8b3418dff65d9cad4f632b5062f13626bdf267190a9b11a96d63fec345532eed4d54014f5caf2c62a7d6e86705fb667f42bba378aa8ba0dab19c6bcd212984
 SHA512 
0d57e3e90a86a59cb96b11371ff1227b2b3e8f5b82cce713f4a855d6e7f5a10524508d4cb4dad7d9f77562fc1753b1af3c9240d4333e0189dabeef07c40d78a1
-DIST pymol-plugins-dynamics-2.1.1.tar.gz 816623 BLAKE2B 
bd065b176f3f779962c4f48e715a74afefbac2ee6dd31bb9f52208fae171f16847ff70692a7df3739dbaa23be215f73e4fe265328b05c4fb3dd598def48c9ff1
 SHA512 
e872c131e7d4ae37bd0e33e56d5d51e83ad732a125a46802ad9fa08648906d49de166bf75fbeca1431726aa9df781671c29578a799f580a94dc1fd89fb398b3c

diff --git a/sci-chemistry/pymol-plugins-dynamics/metadata.xml 
b/sci-chemistry/pymol-plugins-dynamics/metadata.xml
deleted file mode 100644
index d0be20ea989..000
--- a/sci-chemistry/pymol-plugins-dynamics/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-  
-sci-chemis...@gentoo.org
-Gentoo Chemistry Project
-  
-  
-tomaszmakarewicz/Dynamics
-  
-

diff --git 
a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild 
b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild
deleted file mode 100644
index a860012cf6f..000
--- a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-MY_PN="Dynamics"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Molecular dynamics in Pymol"
-HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics;
-SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="
-   ${PYTHON_DEPS}
-   sci-chemistry/prody[${PYTHON_USEDEP}]
-   "
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( manual.odt )
-
-src_install() {
-   python_moduleinto pmg_tk/startup
-   python_foreach_impl python_domodule pymol_plugin_dynamics.py
-}

diff --git 
a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild 
b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild
deleted file mode 100644
index a860012cf6f..000
--- a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-MY_PN="Dynamics"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Molecular dynamics in Pymol"
-HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics;
-SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="
-   ${PYTHON_DEPS}
-   sci-chemistry/prody[${PYTHON_USEDEP}]
-   "
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( manual.odt )
-
-src_install() {
-   python_moduleinto pmg_tk/startup
-   python_foreach_impl python_domodule pymol_plugin_dynamics.py
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: 6608559d020df9dc6c0e7364bc7c058a1c2ab1fd
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Tue Feb 26 14:15:06 2019 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Tue Feb 26 14:15:06 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6608559d

sci-chemistry/pymol: Version bump

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/Manifest   |   1 +
 sci-chemistry/pymol/pymol-2.3.0.ebuild | 115 +
 2 files changed, 116 insertions(+)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index d308fc6a065..4e293b43050 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,3 +1,4 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B 
f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b
 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-2.2.0.tar.gz 10514753 BLAKE2B 
54bf7c639ec1af0c318438f6dcbe5878aded5cc360dee3a5f1dee4b6eea588f4242865ae8adf1e044628ad5f71aa8f6d58d0cc71baf7c1f20eed3045ed3a1cb1
 SHA512 
56776586276208d42cc4bd4c3cb7d6b9a08e7239186b8f398c75cb57f85e05ebf51aaa8cdec5672e56beeda26f1cd9d14c6de7fba1a741f9c8ec22c1292b9c63
+DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 
0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05
 SHA512 
e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
 DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B 
a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3
 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe

diff --git a/sci-chemistry/pymol/pymol-2.3.0.ebuild 
b/sci-chemistry/pymol/pymol-2.3.0.ebuild
new file mode 100644
index 000..0f197578023
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.3.0.ebuild
@@ -0,0 +1,115 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 eutils xdg-utils flag-o-matic
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/;
+SRC_URI="
+   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+   https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz 
-> ${P}.tar.gz
+   "
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+   dev-libs/msgpack[cxx]
+   dev-libs/mmtf-cpp
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pyopengl[${PYTHON_USEDEP}]
+   media-libs/freeglut
+   media-libs/freetype:2
+   media-libs/glew:0=
+   media-libs/glm
+   media-libs/libpng:0=
+   media-video/mpeg-tools
+   sys-libs/zlib
+   virtual/python-pmw[${PYTHON_USEDEP}]
+   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}-open-source-${PV}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
+   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+   -e "/import/s:argparse:argparseX: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
+
+   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 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-caver/

[Ben Kohler]

commit: 1dcfc41b64e612b5e5ac77a19ae9bf983c6f5f95
Author: Ben Kohler  gentoo  org>
AuthorDate: Tue Feb  5 18:35:29 2019 +
Commit: Ben Kohler  gentoo  org>
CommitDate: Tue Feb  5 18:45:10 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1dcfc41b

sci-chemistry/pymol-plugins-caver: don't reference ${DISTDIR}

Package-Manager: Portage-2.3.59, Repoman-2.3.12
Signed-off-by: Ben Kohler  gentoo.org>

 sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild 
b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild
index ffc1c59074a..7da3317b59b 100644
--- a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild
+++ b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -34,7 +34,7 @@ S="${WORKDIR}/${MY_P}"/linux_mac
 pkg_nofetch() {
elog "Download ${A}"
elog "from ${HOMEPAGE}. This requires registration."
-   elog "Place tarballs in ${DISTDIR}."
+   elog "Place tarballs into your DISTDIR directory."
 }
 
 src_install() {

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: 922495f0a1938669ae1c819cca68276adb76a98d
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Tue Nov 13 10:13:34 2018 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Tue Nov 13 10:13:34 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=922495f0

sci-chemistry/pymol: Fix missing dep

Signed-off-by: Alexey Shvetsov  gentoo.org>
Package-Manager: Portage-2.3.51, Repoman-2.3.11

 sci-chemistry/pymol/pymol-2.2.0.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-chemistry/pymol/pymol-2.2.0.ebuild 
b/sci-chemistry/pymol/pymol-2.2.0.ebuild
index 5c2dc1f498f..1e53d9ab339 100644
--- a/sci-chemistry/pymol/pymol-2.2.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.2.0.ebuild
@@ -28,6 +28,7 @@ DEPEND="
media-libs/freeglut
media-libs/freetype:2
media-libs/glew:0=
+   media-libs/glm
media-libs/libpng:0=
media-video/mpeg-tools
sys-libs/zlib

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: d6a556d0bb073db14a6091c0d705ea08f76ee5bb
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Thu Nov  8 10:02:20 2018 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Thu Nov  8 10:05:29 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d6a556d0

sci-chemistry/pymol: Version bump

Package-Manager: Portage-2.3.51, Repoman-2.3.12
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/pymol/Manifest   |   3 +-
 sci-chemistry/pymol/pymol-1.8.6.0.ebuild   | 109 -
 .../{pymol-2.1.0.ebuild => pymol-2.2.0.ebuild} |  10 +-
 3 files changed, 6 insertions(+), 116 deletions(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 64fe4abc321..d308fc6a065 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,3 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B 
f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b
 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
+DIST pymol-2.2.0.tar.gz 10514753 BLAKE2B 
54bf7c639ec1af0c318438f6dcbe5878aded5cc360dee3a5f1dee4b6eea588f4242865ae8adf1e044628ad5f71aa8f6d58d0cc71baf7c1f20eed3045ed3a1cb1
 SHA512 
56776586276208d42cc4bd4c3cb7d6b9a08e7239186b8f398c75cb57f85e05ebf51aaa8cdec5672e56beeda26f1cd9d14c6de7fba1a741f9c8ec22c1292b9c63
 DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B 
a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3
 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
-DIST pymol-v1.8.6.0.tar.bz2 8717164 BLAKE2B 
ddcabb81e15b2409ee551900ed09daaf681c7ef0e196eecea36773c131586f6379cd41c50bfa9df8f396ddb1a5da761e8b3409e9656a8f6ac7a87818f4375895
 SHA512 
bd08e6890382af1503d6af16b27b43af09b372a1229cc9d8e2de311873918b5e7b06e8a2365ce73a5f52cb31ac795f5d91b2ae6ef62890d9c2bf0ea25f856658
-DIST pymol-v2.1.0.tar.bz2 8779083 BLAKE2B 
819846a9963ddf3953f53e29a8396ed104dbdafc55fe39ad91363366c7647af3ad833704aff3d4c11f39829545500e00bb18916b6963de4b986423adf700845c
 SHA512 
67175c0668a13826febcb73f7c62a43cfa03a7f86bb80113d52fb337e7d29008684c03163fc06338c4d68edd9246ffcf63aec1ee3110ae91c8a71ef24ab7b605

diff --git a/sci-chemistry/pymol/pymol-1.8.6.0.ebuild 
b/sci-chemistry/pymol/pymol-1.8.6.0.ebuild
deleted file mode 100644
index 8fd0a78a12a..000
--- a/sci-chemistry/pymol/pymol-1.8.6.0.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/;
-SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
-   mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
-   "
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="web"
-
-DEPEND="
-   dev-libs/msgpack[cxx]
-   dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/pyopengl[${PYTHON_USEDEP}]
-   media-libs/freeglut
-   media-libs/freetype:2
-   media-libs/glew:0=
-   media-libs/libpng:0=
-   media-video/mpeg-tools
-   sys-libs/zlib
-   virtual/python-pmw[${PYTHON_USEDEP}]
-   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
-   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-   -e "/import/s:argparse:argparseX:g" \
-   -i setup.py || die
-
-   sed \
-   -e "s:/opt/local:${EPREFIX}/usr:g" \
-   -e '/ext_comp_args/s:\[.*\]:[]:g' \
-   -i setup.py || die
-
-   append-cxxflags -std=c++0x
-
-   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' \
- 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: 326f87e6afac2433c7e131c6a5126e03c845b811
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Thu Mar 29 11:42:27 2018 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Thu Mar 29 11:42:27 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=326f87e6

sci-chemistry/pymol: Version bump

Package-Manager: Portage-2.3.24, Repoman-2.3.6

 sci-chemistry/pymol/Manifest   |   1 +
 sci-chemistry/pymol/pymol-2.1.0.ebuild | 113 +
 2 files changed, 114 insertions(+)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index efd53bc3a1a..64fe4abc321 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,3 +1,4 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B 
f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b
 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B 
a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3
 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
 DIST pymol-v1.8.6.0.tar.bz2 8717164 BLAKE2B 
ddcabb81e15b2409ee551900ed09daaf681c7ef0e196eecea36773c131586f6379cd41c50bfa9df8f396ddb1a5da761e8b3409e9656a8f6ac7a87818f4375895
 SHA512 
bd08e6890382af1503d6af16b27b43af09b372a1229cc9d8e2de311873918b5e7b06e8a2365ce73a5f52cb31ac795f5d91b2ae6ef62890d9c2bf0ea25f856658
+DIST pymol-v2.1.0.tar.bz2 8779083 BLAKE2B 
819846a9963ddf3953f53e29a8396ed104dbdafc55fe39ad91363366c7647af3ad833704aff3d4c11f39829545500e00bb18916b6963de4b986423adf700845c
 SHA512 
67175c0668a13826febcb73f7c62a43cfa03a7f86bb80113d52fb337e7d29008684c03163fc06338c4d68edd9246ffcf63aec1ee3110ae91c8a71ef24ab7b605

diff --git a/sci-chemistry/pymol/pymol-2.1.0.ebuild 
b/sci-chemistry/pymol/pymol-2.1.0.ebuild
new file mode 100644
index 000..f29f29694f2
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.1.0.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 eutils xdg-utils flag-o-matic versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/;
+SRC_URI="
+   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+   mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1)/${PN}-v${PV}.tar.bz2
+   "
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+   dev-libs/msgpack[cxx]
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pyopengl[${PYTHON_USEDEP}]
+   media-libs/freeglut
+   media-libs/freetype:2
+   media-libs/glew:0=
+   media-libs/libpng:0=
+   media-video/mpeg-tools
+   sys-libs/zlib
+   virtual/python-pmw[${PYTHON_USEDEP}]
+   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
+   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+   -e "/import/s:argparse:argparseX: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
+
+   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
+ 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-caver/

[Justin Lecher]

commit: 756e4e06cd7ffd5b0b780820c58f8ab4dfc0ad63
Author: Justin Lecher  gentoo  org>
AuthorDate: Sun Dec 17 19:46:09 2017 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Dec 18 14:03:47 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=756e4e06

sci-chemistry/pymol-plugins-caver: Update to latest hashing algos

Signed-off-by: Justin Lecher  gentoo.org>
Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-chemistry/pymol-plugins-caver/Manifest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol-plugins-caver/Manifest 
b/sci-chemistry/pymol-plugins-caver/Manifest
index ecfe07a54c4..4d7abe5d823 100644
--- a/sci-chemistry/pymol-plugins-caver/Manifest
+++ b/sci-chemistry/pymol-plugins-caver/Manifest
@@ -1 +1 @@
-DIST Caver2_1_2_pymol_plugin.zip 5698331 SHA256 
1dcc61ba13247c05710c4cd68491d0c867ce1d0c11c824be85a516250b2874e3 SHA512 
9d28e059bb20f30cf6a0d25ed2eb080dcf9dbb753e9d4578d95e293b31c5cf5fe23d5177dccdb79c192ab3e65bb484b6eb22b26c267637b125404f871e01a52c
 WHIRLPOOL 
33e6893d2114b5ce197fc098d09dfc67ce88f38741e30f1fa574873836c636b5e0c180301849fd98f1f93de5ce51554d2245d0bd615b938d39a802e91e68ebb9
+DIST Caver2_1_2_pymol_plugin.zip 5698331 BLAKE2B 
e1accfaea6faf1e8c545b88c965228ccb62710d4015ff681506971feba6bd18a4a8b0b6e6caf621c99830ba529a6ec17873cdd3d5e52ad6dc6f67d9457e4eb87
 SHA512 
9d28e059bb20f30cf6a0d25ed2eb080dcf9dbb753e9d4578d95e293b31c5cf5fe23d5177dccdb79c192ab3e65bb484b6eb22b26c267637b125404f871e01a52c

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-dynamics/

[Justin Lecher]

commit: 94f68b4448debca63c4a7d98a95aabc16f5a116d
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct  2 19:31:26 2017 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct  2 19:31:52 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=94f68b44

sci-chemistry/pymol-plugins-dynamics: Version Bump

Package-Manager: Portage-2.3.10, Repoman-2.3.3
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol-plugins-dynamics/Manifest  |  1 +
 .../pymol-plugins-dynamics-2.1.1.ebuild| 37 ++
 2 files changed, 38 insertions(+)

diff --git a/sci-chemistry/pymol-plugins-dynamics/Manifest 
b/sci-chemistry/pymol-plugins-dynamics/Manifest
index 90b61c6d2ce..9e488a83d19 100644
--- a/sci-chemistry/pymol-plugins-dynamics/Manifest
+++ b/sci-chemistry/pymol-plugins-dynamics/Manifest
@@ -1 +1,2 @@
 DIST pymol-plugins-dynamics-2.0.7.tar.gz 822680 SHA256 
282e806b088a8d059ff5c722bb1e4789591cc263e9911d9129d3c3863ed4a5e0 SHA512 
0d57e3e90a86a59cb96b11371ff1227b2b3e8f5b82cce713f4a855d6e7f5a10524508d4cb4dad7d9f77562fc1753b1af3c9240d4333e0189dabeef07c40d78a1
 WHIRLPOOL 
51d866d45e172751151f4fd0bfb4d6cb102b0279e0c4a3aff68242a23fbaaaf9dfa347842192c1cef0d182708d6f17c383fc87707e543d9ccec6bc2d8aaa7d9d
+DIST pymol-plugins-dynamics-2.1.1.tar.gz 816623 SHA256 
31b7ebca39e4922af9a5d05d7e1e81688ba096e6ed4355291362a7bf94d6f5e9 SHA512 
e872c131e7d4ae37bd0e33e56d5d51e83ad732a125a46802ad9fa08648906d49de166bf75fbeca1431726aa9df781671c29578a799f580a94dc1fd89fb398b3c
 WHIRLPOOL 
a8396f962bfd0571d09696aa2f1ee73e0da120db70beac6f871fcf971854320b3b07e03e926c192fc137765d0249197fc5ab432e845adbaac8f817245736e866

diff --git 
a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild 
b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild
new file mode 100644
index 000..a860012cf6f
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-r1
+
+MY_PN="Dynamics"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Molecular dynamics in Pymol"
+HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics;
+SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+   ${PYTHON_DEPS}
+   sci-chemistry/prody[${PYTHON_USEDEP}]
+   "
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${MY_P}
+
+DOCS=( manual.odt )
+
+src_install() {
+   python_moduleinto pmg_tk/startup
+   python_foreach_impl python_domodule pymol_plugin_dynamics.py
+}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Matt Turner]

commit: 50b3a1044867e51acc08e53433633e2964643436
Author: Matt Turner  gentoo  org>
AuthorDate: Tue Sep 12 22:56:19 2017 +
Commit: Matt Turner  gentoo  org>
CommitDate: Tue Sep 12 22:58:17 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=50b3a104

sci-chemistry/pymol: dropped ppc keywords

 sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
index ad66fbb6ceb..c2bedf7ca9d 100644
--- a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
@@ -18,7 +18,7 @@ SRC_URI="
 RESTRICT="mirror"
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="web"
 
 DEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-dynamics/

[Justin Lecher]

commit: 98de0462e35852cfb2cad1ee7ac06d682fd5cb0c
Author: Justin Lecher  gentoo  org>
AuthorDate: Sat Jun  3 19:07:42 2017 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Sat Jun  3 19:36:43 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=98de0462

sci-chemistry/pymol-plugins-dynamics: Version Bump

Drop old

Package-Manager: Portage-2.3.6, Repoman-2.3.2
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol-plugins-dynamics/Manifest  |  3 +-
 .../pymol-plugins-dynamics-1.2.0.ebuild| 42 --
 ebuild => pymol-plugins-dynamics-2.0.7.ebuild} |  4 +--
 3 files changed, 3 insertions(+), 46 deletions(-)

diff --git a/sci-chemistry/pymol-plugins-dynamics/Manifest 
b/sci-chemistry/pymol-plugins-dynamics/Manifest
index 258493d5b26..90b61c6d2ce 100644
--- a/sci-chemistry/pymol-plugins-dynamics/Manifest
+++ b/sci-chemistry/pymol-plugins-dynamics/Manifest
@@ -1,2 +1 @@
-DIST pymol-plugins-dynamics-1.2.0.tar.gz 725163 SHA256 
edf9bddbbce41ee5319bfd0b28d6e0b0eba56e8b2d8a300d510be8ff5894704f SHA512 
7e8d62ea58cb88348136fccd132d9a1faaa3474c0a0f821e729ced777620e2083b1b0606d79fc75802755c96c5eb0b90e08b00e5c865ecbaaee2b837f56987de
 WHIRLPOOL 
07061d3b0840fef0025be55b90fca013afc1ea58308d6ee11a8b74321de4f1c24760b1cf141b0a86678c5cf652c8890cdf2c4e0da60403c8454e04b003e20aaa
-DIST pymol-plugins-dynamics-2.0.4.tar.gz 821563 SHA256 
358452e0d8589ffae28fe486eeca0be353f17f1fdde9f05f548025b241afabe5 SHA512 
befad8b5c09ddba89b9e00bd712a2af7202e312b2ebee7722cbeec5698125dd7614463465d79c17c805714ba23ca1188c64610789e90c93bb0ad7572841ebf25
 WHIRLPOOL 
039e40c7c57a242476e72a351ecc099201021f479762c2eb29bdad25b72c11c33295e8f9707ece486235efb1b205524e479cd4ae57639d1410515a75d2221989
+DIST pymol-plugins-dynamics-2.0.7.tar.gz 822680 SHA256 
282e806b088a8d059ff5c722bb1e4789591cc263e9911d9129d3c3863ed4a5e0 SHA512 
0d57e3e90a86a59cb96b11371ff1227b2b3e8f5b82cce713f4a855d6e7f5a10524508d4cb4dad7d9f77562fc1753b1af3c9240d4333e0189dabeef07c40d78a1
 WHIRLPOOL 
51d866d45e172751151f4fd0bfb4d6cb102b0279e0c4a3aff68242a23fbaaaf9dfa347842192c1cef0d182708d6f17c383fc87707e543d9ccec6bc2d8aaa7d9d

diff --git 
a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-1.2.0.ebuild 
b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-1.2.0.ebuild
deleted file mode 100644
index 99dc00e3668..000
--- a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-1.2.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-MY_PN="Dynamics"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Molecular dynamics in Pymol"
-HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics;
-SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v1.2.0.tar.gz -> 
${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${MY_P}
-
-DOCS=( manual.odt )
-
-src_prepare() {
-   sed \
-   -e "/sys.path.insert/d" \
-   -e "s:import dynamics_pymol_plugin:from pmg_tk.startup import 
dynamics_pymol_plugin:g" \
-   -i pydynamics* || die
-}
-
-src_install() {
-   python_moduleinto pmg_tk/startup
-   python_foreach_impl python_domodule dynamics_pymol_plugin.py
-   python_foreach_impl python_doscript pydynamics*
-}

diff --git 
a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.4.ebuild 
b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild
similarity index 93%
rename from 
sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.4.ebuild
rename to 
sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild
index 53644f17020..a860012cf6f 100644
--- a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.4.ebuild
+++ b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: f7f304a16a0f4530e49dc100bc4a542b457a5e28
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Mon Mar 27 14:08:53 2017 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Mon Mar 27 14:09:21 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f7f304a1

sci-chemistry/pymol: Version bump

Warning: Pymol now depends on dev-libs/msgpack

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-chemistry/pymol/Manifest |   1 +
 sci-chemistry/pymol/pymol-1.8.6.0.ebuild | 109 +++
 2 files changed, 110 insertions(+)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 1f72685ea0c..b4695e66d6d 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,2 +1,3 @@
 DIST pymol-1.8.4.0.png.xz 19528 SHA256 
e2c956b39965130a3dc51c2c1b1090bee6bf591885069b2ddb77c0991e9e4928 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 WHIRLPOOL 
1336c20e068b71cdf35118c84b5df8485c86bc51eed7f542a483fb78ce374ca76e4aed3518aced0a6f8ea49e0b180004e567cc059ac52a27a3d616adb282cea2
 DIST pymol-v1.8.4.0.tar.bz2 8717344 SHA256 
b6147befe74844dd23550461b831b2fa6d170d4456f0059cf93fb1e8cb43d279 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
 WHIRLPOOL 
3943a619ca00cc2bfb51ff4dffa0166856b4425c7518d91b1ff2a048caa53dcb7411c64b246014b860b7f036de582e9efdc09783b3918283f0a96ee5130c7287
+DIST pymol-v1.8.6.0.tar.bz2 8717164 SHA256 
7eaaf90ac1e1be0969291cdb1154b3631b5b6403cce1d697133d90cd37a3c565 SHA512 
bd08e6890382af1503d6af16b27b43af09b372a1229cc9d8e2de311873918b5e7b06e8a2365ce73a5f52cb31ac795f5d91b2ae6ef62890d9c2bf0ea25f856658
 WHIRLPOOL 
950d655a48b3801de2657b6d8935404ca0069525719b9c88a117ad819c37366a55e42dbe51a253b960b79413e5df9d781b9ada8839ca06e1e01dde965044efe4

diff --git a/sci-chemistry/pymol/pymol-1.8.6.0.ebuild 
b/sci-chemistry/pymol/pymol-1.8.6.0.ebuild
new file mode 100644
index 000..8fd0a78a12a
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.8.6.0.ebuild
@@ -0,0 +1,109 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/;
+SRC_URI="
+   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+   mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
+   "
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+   dev-libs/msgpack[cxx]
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pyopengl[${PYTHON_USEDEP}]
+   media-libs/freeglut
+   media-libs/freetype:2
+   media-libs/glew:0=
+   media-libs/libpng:0=
+   media-video/mpeg-tools
+   sys-libs/zlib
+   virtual/python-pmw[${PYTHON_USEDEP}]
+   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
+   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+   -e "/import/s:argparse:argparseX:g" \
+   -i setup.py || die
+
+   sed \
+   -e "s:/opt/local:${EPREFIX}/usr:g" \
+   -e '/ext_comp_args/s:\[.*\]:[]:g' \
+   -i setup.py || die
+
+   append-cxxflags -std=c++0x
+
+   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 >> "${T}"/20pymol <<- EOF
+   PYMOL_PATH="${EPREFIX}/usr/share/pymol"
+   PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+   

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Justin Lecher]

commit: e4d2f4aa20dd3df7e3fa7b34da4f5c597b506830
Author: Justin Lecher  gentoo  org>
AuthorDate: Sat Feb 25 20:56:17 2017 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Sat Feb 25 20:56:27 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4d2f4aa

sci-chemistry/pymol: Drop old

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol/Manifest |   4 --
 sci-chemistry/pymol/pymol-1.7.6.0.ebuild | 110 ---
 sci-chemistry/pymol/pymol-1.7.7.2.ebuild | 110 ---
 sci-chemistry/pymol/pymol-1.8.2.1.ebuild | 109 --
 4 files changed, 333 deletions(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index d7e893dc07..1f72685ea0 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,6 +1,2 @@
-DIST pymol-1.7.0.0.png.xz 5392 SHA256 
4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 
24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105
 WHIRLPOOL 
395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b
-DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 
31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 
ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b1e9d3aeda0b6035d55d
 WHIRLPOOL 
3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2
-DIST pymol-1.7.7.2.tar.xz 6527780 SHA256 
fc15fc8fbf23b422c5d19babd20e19b7d7ab8ee9532012c7b3a27b87af44fdae SHA512 
faf3715cd6b9e7115f6501fc4480a6f71fe53d3b02b2eeefdd07a57d7c15b3621c05fd3894bb92ac4042edaa224d99c2be7488a762254d069c581974a0146179
 WHIRLPOOL 
b52683ce1dc265fe302c974ccc1bfa9e55365e8502f944cf6527c0071f207fcb54e8b3ad38fd684b66c66f85fa6a03f2f1178b90fd406b9f7561d956c704fb9a
 DIST pymol-1.8.4.0.png.xz 19528 SHA256 
e2c956b39965130a3dc51c2c1b1090bee6bf591885069b2ddb77c0991e9e4928 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 WHIRLPOOL 
1336c20e068b71cdf35118c84b5df8485c86bc51eed7f542a483fb78ce374ca76e4aed3518aced0a6f8ea49e0b180004e567cc059ac52a27a3d616adb282cea2
-DIST pymol-v1.8.2.1.tar.bz2 8694029 SHA256 
fc5d33d7e36364567462cee19b9b132530a83cbab3fafcf373f2a17f127b3f4e SHA512 
c6768ab75f715e48fbaa3d0c0664f717b05212c6d004cacea0e9a79ead98375ae7773b4a5c4c476a3b3731be910e3df585b2980fd97fd3fb2afb5ec91304adce
 WHIRLPOOL 
4ad164a3629e15df12ce75a769e34b1af2f87f68f88988919c0d0e8d80fe4062283102003d222040b9a8f0bd91e756eac494e67477242b48cd04947d34cb7c48
 DIST pymol-v1.8.4.0.tar.bz2 8717344 SHA256 
b6147befe74844dd23550461b831b2fa6d170d4456f0059cf93fb1e8cb43d279 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
 WHIRLPOOL 
3943a619ca00cc2bfb51ff4dffa0166856b4425c7518d91b1ff2a048caa53dcb7411c64b246014b860b7f036de582e9efdc09783b3918283f0a96ee5130c7287

diff --git a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild 
b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
deleted file mode 100644
index 4033493c22..00
--- a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/;
-SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-   https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#  mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="web"
-
-DEPEND="
-   dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/pyopengl[${PYTHON_USEDEP}]
-   media-libs/freeglut
-   media-libs/freetype:2
-   media-libs/glew:0=
-   media-libs/libpng:0=
-   media-video/mpeg-tools
-   sys-libs/zlib
-   virtual/python-pmw[${PYTHON_USEDEP}]
-   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
-   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-   -e "/import/s:argparse:argparseX:g" \
-   -i setup.py || die
-
-   sed \
-   -e 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Agostino Sarubbo]

commit: 1719d0a9f6852ff037f0cd1f5bf8a123fd5ed9bb
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Tue Feb 14 15:38:09 2017 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Tue Feb 14 15:38:09 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1719d0a9

sci-chemistry/pymol: x86 stable wrt bug #609166

Package-Manager: portage-2.3.3
RepoMan-Options: --include-arches="x86"
Signed-off-by: Agostino Sarubbo  gentoo.org>

 sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
index aeb672e9e5..155e5d4565 100644
--- a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
@@ -19,7 +19,7 @@ SRC_URI="
 RESTRICT="mirror"
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="web"
 
 DEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Agostino Sarubbo]

commit: a1320339bc92cd57fef4a64bf24fe33dc005aba5
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Mon Feb 13 11:11:56 2017 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Mon Feb 13 11:11:56 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a1320339

sci-chemistry/pymol: amd64 stable wrt bug #609166

Package-Manager: portage-2.3.3
RepoMan-Options: --include-arches="amd64"
Signed-off-by: Agostino Sarubbo  gentoo.org>

 sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
index 165c113fc1..aeb672e9e5 100644
--- a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
@@ -19,7 +19,7 @@ SRC_URI="
 RESTRICT="mirror"
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="web"
 
 DEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Justin Lecher]

commit: 4252a802ac78527b992745cd631c082d7599158f
Author: Justin Lecher  gentoo  org>
AuthorDate: Sun Feb 12 19:35:12 2017 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Sun Feb 12 19:51:49 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4252a802

sci-chemistry/pymol: Update icon

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=608744

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol/Manifest| 1 +
 .../pymol/{pymol-1.8.4.0.ebuild => pymol-1.8.4.0-r1.ebuild} | 6 +++---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 104bc1a850..d7e893dc07 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,5 +1,6 @@
 DIST pymol-1.7.0.0.png.xz 5392 SHA256 
4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 
24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105
 WHIRLPOOL 
395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 
31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 
ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b1e9d3aeda0b6035d55d
 WHIRLPOOL 
3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2
 DIST pymol-1.7.7.2.tar.xz 6527780 SHA256 
fc15fc8fbf23b422c5d19babd20e19b7d7ab8ee9532012c7b3a27b87af44fdae SHA512 
faf3715cd6b9e7115f6501fc4480a6f71fe53d3b02b2eeefdd07a57d7c15b3621c05fd3894bb92ac4042edaa224d99c2be7488a762254d069c581974a0146179
 WHIRLPOOL 
b52683ce1dc265fe302c974ccc1bfa9e55365e8502f944cf6527c0071f207fcb54e8b3ad38fd684b66c66f85fa6a03f2f1178b90fd406b9f7561d956c704fb9a
+DIST pymol-1.8.4.0.png.xz 19528 SHA256 
e2c956b39965130a3dc51c2c1b1090bee6bf591885069b2ddb77c0991e9e4928 SHA512 
40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 WHIRLPOOL 
1336c20e068b71cdf35118c84b5df8485c86bc51eed7f542a483fb78ce374ca76e4aed3518aced0a6f8ea49e0b180004e567cc059ac52a27a3d616adb282cea2
 DIST pymol-v1.8.2.1.tar.bz2 8694029 SHA256 
fc5d33d7e36364567462cee19b9b132530a83cbab3fafcf373f2a17f127b3f4e SHA512 
c6768ab75f715e48fbaa3d0c0664f717b05212c6d004cacea0e9a79ead98375ae7773b4a5c4c476a3b3731be910e3df585b2980fd97fd3fb2afb5ec91304adce
 WHIRLPOOL 
4ad164a3629e15df12ce75a769e34b1af2f87f68f88988919c0d0e8d80fe4062283102003d222040b9a8f0bd91e756eac494e67477242b48cd04947d34cb7c48
 DIST pymol-v1.8.4.0.tar.bz2 8717344 SHA256 
b6147befe74844dd23550461b831b2fa6d170d4456f0059cf93fb1e8cb43d279 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
 WHIRLPOOL 
3943a619ca00cc2bfb51ff4dffa0166856b4425c7518d91b1ff2a048caa53dcb7411c64b246014b860b7f036de582e9efdc09783b3918283f0a96ee5130c7287

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
similarity index 95%
rename from sci-chemistry/pymol/pymol-1.8.4.0.ebuild
rename to sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
index 44305d6d1d..165c113fc1 100644
--- a/sci-chemistry/pymol/pymol-1.8.4.0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -12,7 +12,7 @@ inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://www.pymol.org/;
 SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
+   https://dev.gentoo.org/~jlec/distfiles/${P}.png.xz
mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
"
 # git archive -v --prefix=${P}/ master -o ${P}.tar.xz
@@ -85,7 +85,7 @@ python_install_all() {
 
doenvd "${T}"/20pymol
 
-   newicon "${WORKDIR}"/${PN}-1.7.0.0.png ${PN}.png
+   newicon "${WORKDIR}"/${P}.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;"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/files/

[David Seifert]

commit: bc146ad2a6e93d07096060ed14fa26b84450944e
Author: Michael Mair-Keimberger (asterix)  gmail 
 com>
AuthorDate: Mon Jan 30 17:53:55 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Jan 31 08:41:33 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bc146ad2

sci-chemistry/pymol: remove unused patch

Closes: https://github.com/gentoo/gentoo/pull/3730

 sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch | 11 ---
 1 file changed, 11 deletions(-)

diff --git a/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch 
b/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch
deleted file mode 100644
index cd4650b..
--- a/sci-chemistry/pymol/files/pymol-1.7.3.1-maeffplugin.cpp.patch
+++ /dev/null
@@ -1,11 +0,0 @@
 contrib/uiuc/plugins/molfile_plugin/src/maeffplugin_orig.cpp   
2014-02-07 19:50:50.132261610 -0800
-+++ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp2014-02-07 
19:52:12.527797099 -0800
-@@ -1983,7 +1983,7 @@
-   }
- }
- catch (std::exception ) {
--  fprintf(stderr, e.what());
-+  fprintf(stderr, "%s", e.what());
-   return MOLFILE_ERROR;
- }
- return MOLFILE_SUCCESS;

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-dssp/

[Pacho Ramos]

commit: 41a097077d1c14e6bd9037f285fa619883bcc09c
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sun Jan 15 11:01:27 2017 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sun Jan 15 11:19:54 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=41a09707

sci-chemistry/pymol-plugins-dssp: Drop old

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 .../pymol-plugins-dssp-110430.ebuild   | 49 --
 1 file changed, 49 deletions(-)

diff --git a/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430.ebuild 
b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430.ebuild
deleted file mode 100644
index 9a85ed0..
--- a/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.* *-jython"
-
-inherit python
-
-DESCRIPTION="DSSP Plugin for PyMOL"
-HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/dssp_pymol/dssp_pymol.html;
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.py.xz;
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="BSD pymol"
-IUSE=""
-
-RDEPEND="
-   sci-chemistry/dssp
-   sci-biology/stride
-   sci-chemistry/pymol"
-DEPEND=""
-
-src_prepare() {
-   sed \
-   -e "s:GENTOO_DSSP:${EPREFIX}/usr/bin/dssp:g" \
-   -e "s:GENTOO_STRIDE:${EPREFIX}/usr/bin/stride:g" \
-   -i ${P}.py || die
-}
-
-src_install() {
-   installation() {
-   insinto $(python_get_sitedir)/pmg_tk/startup
-   doins ${P}.py
-   }
-   python_execute_function installation
-}
-
-pkg_postinst() {
-   python_mod_optimize pmg_tk/startup/${P}.py
-}
-
-pkg_postrm() {
-   python_mod_cleanup pmg_tk/startup/${P}.py
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-msms/

[Pacho Ramos]

commit: ab797c2d2a3444ec63a8d23dea23057bd35d5300
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sun Jan 15 11:01:49 2017 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sun Jan 15 11:19:56 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ab797c2d

sci-chemistry/pymol-plugins-msms: Drop old

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 .../pymol-plugins-msms-100415.ebuild   | 54 --
 1 file changed, 54 deletions(-)

diff --git a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild 
b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild
deleted file mode 100644
index e226003..
--- a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.* *-jython"
-
-inherit eutils python
-
-DESCRIPTION="GUI for MSMS and displaying its results in PyMOL"
-HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html;
-SRC_URI="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/pymol_script/msms_pymol.py
 -> ${P}.py"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="BSD pymol"
-IUSE=""
-
-RDEPEND="
-   sci-chemistry/msms-bin
-   sci-chemistry/pymol"
-DEPEND="${RDEPEND}"
-
-src_unpack() {
-   mkdir "${S}"
-   cp "${DISTDIR}"/${A} "${S}/"
-}
-
-src_prepare() {
-   epatch "${FILESDIR}"/${PV}-msms.patch
-   sed \
-   -e "s:GENTOOMSMS:${EPREFIX}/opt/bin/msms:g" \
-   -e "s:GENTOOXYZRN:${EPREFIX}/usr/bin/pdb_to_xyzrn:g" \
-   -i ${A} || die
-}
-
-src_install() {
-   installation() {
-   insinto $(python_get_sitedir)/pmg_tk/startup
-   doins ${P}.py
-   }
-   python_execute_function installation
-}
-
-pkg_postinst() {
-   python_mod_optimize pmg_tk/startup/${P}.py
-}
-
-pkg_postrm() {
-   python_mod_cleanup pmg_tk/startup/${P}.py
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-bni-tools/

[Pacho Ramos]

commit: 61d3e010f8eec9695af79b8c8a6eb6e0be4b1736
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sun Jan 15 11:01:11 2017 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sun Jan 15 11:19:52 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61d3e010

sci-chemistry/pymol-plugins-bni-tools: Drop old

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-chemistry/pymol-plugins-bni-tools/Manifest |  1 -
 .../pymol-plugins-bni-tools-0.25.1.ebuild  | 41 --
 2 files changed, 42 deletions(-)

diff --git a/sci-chemistry/pymol-plugins-bni-tools/Manifest 
b/sci-chemistry/pymol-plugins-bni-tools/Manifest
index 532cf76..04874b3 100644
--- a/sci-chemistry/pymol-plugins-bni-tools/Manifest
+++ b/sci-chemistry/pymol-plugins-bni-tools/Manifest
@@ -1,2 +1 @@
-DIST bni-tools-0.251.zip 32596 SHA256 
79f77ecb5797de49249c571eda958a97647f34f456bcda952e4b63ffd0c412d2 SHA512 
0d28433679fff1d4473469078ef3b9091f4ed13ccf414d4c54afadcde2f120768f26c0aaee378f04fd9cc71159f21ad7f9281a163a365106dadc3f641b743b76
 WHIRLPOOL 
4f869b2a357b6c1be6077f478b7356e4bba14ae7a4ef7c17357f6729888439d4c3b09cb27271585258024f39f2fe2437016dd7bec3301e849de453add25330d9
 DIST bni-tools-027.zip 33753 SHA256 
9ddb9785146b12c5c2ff03d34262fec8ff04bfaa9c56ec4665bac5e33879cd7c SHA512 
9c0ef1ca5bbb3040192ab2668f354f947e93d42c91a0cfdde5d05be273e6ba9f29ec3c6ee86367f18d87316282b4e0141183b8d6259bd36d44010b7bbb7666e5
 WHIRLPOOL 
7e14a2ef86009237f53e28f6ac95b56687dd7275e8bd8a856c4d408a6c57cffb7131cb9a505d01da7b2f58bf20bae9b400e478d994bb04f9e799ecf09a60edd3

diff --git 
a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.25.1.ebuild 
b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.25.1.ebuild
deleted file mode 100644
index 640cf96..
--- 
a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.25.1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-SUPPORT_PYTHON_ABIS="1"
-
-inherit python versionator
-
-MY_PN="${PN#pymol-plugins-}"
-MY_P="${MY_PN}-$(delete_version_separator 2)"
-
-DESCRIPTION="Gives Pymol additional functionalities and presets to the PyMOL 
GUI"
-HOMEPAGE="http://bni-tools.sourceforge.net/;
-SRC_URI="mirror://sourceforge/${MY_PN}/${MY_P}.zip"
-
-LICENSE="CNRI"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="sci-chemistry/pymol"
-DEPEND="app-arch/unzip"
-RESTRICT_PYTHON_ABIS="2.4 3.*"
-
-src_install(){
-   installation() {
-   insinto $(python_get_sitedir)/pmg_tk/startup/
-   doins bni-tools.py || die "Failed to install ${P}"
-   }
-   python_execute_function installation
-   dodoc readme.txt || die "No dodoc"
-}
-
-pkg_postinst(){
-   python_mod_optimize pmg_tk/startup
-}
-
-pkg_postrm() {
-   python_mod_cleanup pmg_tk/startup
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Justin Lecher]

commit: e55d1db83008e1d11d18727843a4c8f0d14b36f5
Author: Justin Lecher  gentoo  org>
AuthorDate: Sun Oct 23 08:09:44 2016 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Sun Oct 23 20:25:08 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e55d1db8

sci-chemistry/pymol: Version Bump

Package-Manager: portage-2.3.2
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol/Manifest |   1 +
 sci-chemistry/pymol/pymol-1.8.4.0.ebuild | 109 +++
 2 files changed, 110 insertions(+)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 31c3176..104bc1a 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -2,3 +2,4 @@ DIST pymol-1.7.0.0.png.xz 5392 SHA256 
4c554a5c4f47946b6f7bae00209d51163051625342
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 
31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 
ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b1e9d3aeda0b6035d55d
 WHIRLPOOL 
3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2
 DIST pymol-1.7.7.2.tar.xz 6527780 SHA256 
fc15fc8fbf23b422c5d19babd20e19b7d7ab8ee9532012c7b3a27b87af44fdae SHA512 
faf3715cd6b9e7115f6501fc4480a6f71fe53d3b02b2eeefdd07a57d7c15b3621c05fd3894bb92ac4042edaa224d99c2be7488a762254d069c581974a0146179
 WHIRLPOOL 
b52683ce1dc265fe302c974ccc1bfa9e55365e8502f944cf6527c0071f207fcb54e8b3ad38fd684b66c66f85fa6a03f2f1178b90fd406b9f7561d956c704fb9a
 DIST pymol-v1.8.2.1.tar.bz2 8694029 SHA256 
fc5d33d7e36364567462cee19b9b132530a83cbab3fafcf373f2a17f127b3f4e SHA512 
c6768ab75f715e48fbaa3d0c0664f717b05212c6d004cacea0e9a79ead98375ae7773b4a5c4c476a3b3731be910e3df585b2980fd97fd3fb2afb5ec91304adce
 WHIRLPOOL 
4ad164a3629e15df12ce75a769e34b1af2f87f68f88988919c0d0e8d80fe4062283102003d222040b9a8f0bd91e756eac494e67477242b48cd04947d34cb7c48
+DIST pymol-v1.8.4.0.tar.bz2 8717344 SHA256 
b6147befe74844dd23550461b831b2fa6d170d4456f0059cf93fb1e8cb43d279 SHA512 
73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
 WHIRLPOOL 
3943a619ca00cc2bfb51ff4dffa0166856b4425c7518d91b1ff2a048caa53dcb7411c64b246014b860b7f036de582e9efdc09783b3918283f0a96ee5130c7287

diff --git a/sci-chemistry/pymol/pymol-1.8.4.0.ebuild 
b/sci-chemistry/pymol/pymol-1.8.4.0.ebuild
new file mode 100644
index ..44305d6
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.8.4.0.ebuild
@@ -0,0 +1,109 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/;
+SRC_URI="
+   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
+   mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
+   "
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pyopengl[${PYTHON_USEDEP}]
+   media-libs/freeglut
+   media-libs/freetype:2
+   media-libs/glew:0=
+   media-libs/libpng:0=
+   media-video/mpeg-tools
+   sys-libs/zlib
+   virtual/python-pmw[${PYTHON_USEDEP}]
+   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
+   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+   -e "/import/s:argparse:argparseX:g" \
+   -i setup.py || die
+
+   sed \
+   -e "s:/opt/local:${EPREFIX}/usr:g" \
+   -e '/ext_comp_args/s:\[.*\]:[]:g' \
+   -i setup.py || die
+
+   append-cxxflags -std=c++0x
+
+   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

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Alexey Shvetsov]

commit: bbd5edbc744481ae2f9827b4a424aabcf5957309
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Sat Sep 24 15:55:43 2016 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Sat Sep 24 15:56:22 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bbd5edbc

sci-chemistry/pymol: Version bump

Package-Manager: portage-2.3.0

 sci-chemistry/pymol/Manifest |   1 +
 sci-chemistry/pymol/pymol-1.8.2.1.ebuild | 109 +++
 2 files changed, 110 insertions(+)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 1d654d7..31c3176 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,3 +1,4 @@
 DIST pymol-1.7.0.0.png.xz 5392 SHA256 
4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 
24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105
 WHIRLPOOL 
395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 
31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 
ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b1e9d3aeda0b6035d55d
 WHIRLPOOL 
3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2
 DIST pymol-1.7.7.2.tar.xz 6527780 SHA256 
fc15fc8fbf23b422c5d19babd20e19b7d7ab8ee9532012c7b3a27b87af44fdae SHA512 
faf3715cd6b9e7115f6501fc4480a6f71fe53d3b02b2eeefdd07a57d7c15b3621c05fd3894bb92ac4042edaa224d99c2be7488a762254d069c581974a0146179
 WHIRLPOOL 
b52683ce1dc265fe302c974ccc1bfa9e55365e8502f944cf6527c0071f207fcb54e8b3ad38fd684b66c66f85fa6a03f2f1178b90fd406b9f7561d956c704fb9a
+DIST pymol-v1.8.2.1.tar.bz2 8694029 SHA256 
fc5d33d7e36364567462cee19b9b132530a83cbab3fafcf373f2a17f127b3f4e SHA512 
c6768ab75f715e48fbaa3d0c0664f717b05212c6d004cacea0e9a79ead98375ae7773b4a5c4c476a3b3731be910e3df585b2980fd97fd3fb2afb5ec91304adce
 WHIRLPOOL 
4ad164a3629e15df12ce75a769e34b1af2f87f68f88988919c0d0e8d80fe4062283102003d222040b9a8f0bd91e756eac494e67477242b48cd04947d34cb7c48

diff --git a/sci-chemistry/pymol/pymol-1.8.2.1.ebuild 
b/sci-chemistry/pymol/pymol-1.8.2.1.ebuild
new file mode 100644
index ..e86a042
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.8.2.1.ebuild
@@ -0,0 +1,109 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/;
+SRC_URI="
+   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
+   mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
+   "
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pyopengl[${PYTHON_USEDEP}]
+   media-libs/freeglut
+   media-libs/freetype:2
+   media-libs/glew:0=
+   media-libs/libpng:0=
+   media-video/mpeg-tools
+   sys-libs/zlib
+   virtual/python-pmw[${PYTHON_USEDEP}]
+   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
+   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+   -e "/import/s:argparse:argparseX:g" \
+   -i setup.py || die
+
+   sed \
+   -e "s:/opt/local:${EPREFIX}/usr:g" \
+   -e '/ext_comp_args/s:\[.*\]:[]:g' \
+   -i setup.py || die
+
+   append-cxxflags -std=c++0x
+
+   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 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-apbs-plugin/files/, sci-chemistry/pymol-apbs-plugin/, ...

[Justin Lecher]

commit: 3b2fcdb2a906620608ddcb217ca3c0727575841e
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Feb 22 15:19:40 2016 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Feb 22 15:19:40 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b2fcdb2

Drop sci-chemistry/pymol-apbs-plugin

Signed-off-by: Justin Lecher  gentoo.org>

 profiles/package.mask  |   5 -
 sci-chemistry/pymol-apbs-plugin/Manifest   |   4 -
 .../files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch | 176 -
 sci-chemistry/pymol-apbs-plugin/metadata.xml   |  11 --
 .../pymol-apbs-plugin-0_p15.ebuild |  57 ---
 .../pymol-apbs-plugin-0_p18.ebuild |  57 ---
 .../pymol-apbs-plugin-2.1_p24.ebuild   |  57 ---
 .../pymol-apbs-plugin-2.1_p26-r1.ebuild|  56 ---
 .../pymol-apbs-plugin-2.1_p26.ebuild   |  56 ---
 9 files changed, 479 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 1f63929..2e82221 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -303,11 +303,6 @@ www-apps/389-dsgw
 dev-lang/php:5.4
 ~virtual/httpd-php-5.4
 
-# Justin Lecher  (12 Nov 2015)
-# deprecated version of the plugin. 
-# sci-chemistry/pymol includes the newer version
-sci-chemistry/pymol-apbs-plugin
-
 # Brian Evans  (11 Nov 2015)
 # Mask latest xdebug{,-client} beta versions
 # Upstream keeps changing the tarballs causing Manifest errors.

diff --git a/sci-chemistry/pymol-apbs-plugin/Manifest 
b/sci-chemistry/pymol-apbs-plugin/Manifest
deleted file mode 100644
index 8d2bd38..000
--- a/sci-chemistry/pymol-apbs-plugin/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST pymol-apbs-plugin-0_p15.py 104351 SHA256 
c5a259ddc1931f1ec4efe0ffc3ae9e9ac4a84a28c83a4f93a06ebb7c1bef0c1d SHA512 
1bfba44aed8ca03300430e00b6b2a3297bda5820b06a7a8914e5396c6720005ea5acaebc07bdf5d27d82f563afb8210e59af145422c7cacab92160f6f22874e1
 WHIRLPOOL 
a0737250151503b431aa302c3ca175088b068a5aaf7e55c6673a9dd077d28ff7f58f40d2080426484a704ecc4e43f2845ae0d9ef6b5fc3ad850fff5bdffe36c0
-DIST pymol-apbs-plugin-0_p18.py 108766 SHA256 
ec09c5a0903ac965cc29fcf0a3c1999bd939f9791d037915596092698855d12c SHA512 
e736c2852851014eb412dcb573ee177f57dd9dd163673d5c7df1240f0f9c21fdc4277c647ba2a9e510d1cf8e53fabc6671da5a5b90b989cbcfc0835552c4ffdb
 WHIRLPOOL 
3b418afc7198752e7d3578574238756c9a992b6c7c3a16d474a7d5363533d91cedc8300033f6005efae478a2606b9b5e1a6e6b74aed8a0ec46842b8b02ac
-DIST pymol-apbs-plugin-2.1_p24.py 113049 SHA256 
d51bb1bbbf641777ee36713c0c47696d7906179e42cac8cdd0e8e156ef081c9f SHA512 
49141ea7e4a3a3430d342fb4fbb497d522ce6485c6d9e3527414519574eab7b8218fe240f26920013676528c40059a46341d58153bfe9d05bf747ead926b2cfd
 WHIRLPOOL 
17a4f9ed9670b9a7f82395a9cf1ad465635f840b7389c10ad8c8eae3262c3696383bbacadf5aee9fed817eff7370008cc85a1666896fed56dffb0163e4c3d7e1
-DIST pymol-apbs-plugin-2.1_p26.py 113086 SHA256 
552242b4f5b47f298eeb0616e0d51924b4a7649dc8a16e4809e923dbcb97738d SHA512 
3561d077875a1880d6badccf835db3d17e0c45416accd6127cbef7c550711908b47ccb392563e3d29ecb7d6527c098584eeabb6490d1033720ed7efe751d0fb0
 WHIRLPOOL 
dccd32b0193e74e505d69922b441323fb24b0ba30aa85f4d69b94663ab406a57b772985ca2c56146e2c4b929f73b321095c3ae2caf95f297f14d8b31671f475e

diff --git 
a/sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch
 
b/sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch
deleted file mode 100644
index c3675cf..000
--- 
a/sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch
+++ /dev/null
@@ -1,176 +0,0 @@
 pymol-apbs-plugin-2.1_p26.py.orig2013-08-16 20:29:27.0 
-0400
-+++ pymol-apbs-plugin-2.1_p26.py2013-08-16 20:31:35.0 -0400
-@@ -560,7 +560,8 @@
- # Set up the Main page
- page = self.notebook.add('Main')
- group = Pmw.Group(page,tag_text='Main options')
--group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+#group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.selection = Pmw.EntryField(group.interior(),
- labelpos='w',
- label_text='Selection to use: ',
-@@ -606,7 +607,8 @@
- page = self.notebook.add('Configuration')
- 
- group = Pmw.Group(page,tag_text='Dielectric Constants')
--group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+#group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
- group.grid(column=0, row=0)
- self.interior_dielectric = 
Pmw.EntryField(group.interior(),labelpos='w',
-label_text = 'Protein Dielectric:',
-@@ -625,7 +627,8 @@
- 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-emovie/

[Justin Lecher]

commit: ca4803f9e53d7108d632e78f91265e72ade4c9be
Author: Justin Lecher  gentoo  org>
AuthorDate: Thu Dec 10 15:00:43 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Dec 10 15:00:55 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ca4803f9

sci-chemistry/pymol-plugins-emovie: Bump to EAPI=5 and python-r1.eclass

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=567928

Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol-plugins-emovie/metadata.xml|  6 +--
 .../pymol-plugins-emovie-1.0.4.ebuild  | 46 +++---
 2 files changed, 17 insertions(+), 35 deletions(-)

diff --git a/sci-chemistry/pymol-plugins-emovie/metadata.xml 
b/sci-chemistry/pymol-plugins-emovie/metadata.xml
index 18330bb..1837bbc 100644
--- a/sci-chemistry/pymol-plugins-emovie/metadata.xml
+++ b/sci-chemistry/pymol-plugins-emovie/metadata.xml
@@ -2,7 +2,7 @@
 http://www.gentoo.org/dtd/metadata.dtd;>
 
sci-chemistry
-
-   j...@gentoo.org
-
+   
+   j...@gentoo.org
+   
 

diff --git 
a/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild 
b/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild
index 38a48fd..667dcf3 100644
--- a/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild
+++ b/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI="3"
+EAPI=5
 
-SUPPORT_PYTHON_ABIS="1"
+PYTHON_COMPAT=( python2_7 )
 
-inherit eutils python
+inherit eutils python-r1
 
-DESCRIPTION="eMovie is a plug-in tool for the molecular visualization program 
PyMOL"
+DESCRIPTION="PyMOL plugin for convinient movie creation"
 SRC_URI="http://www.weizmann.ac.il/ISPC/eMovie_package.zip;
 HOMEPAGE="http://www.weizmann.ac.il/ISPC/eMovie.html;
 
@@ -17,38 +17,20 @@ LICENSE="GPL-2"
 KEYWORDS="~x86 ~amd64 ~x86-linux ~amd64-linux"
 IUSE=""
 
-RDEPEND=">sci-chemistry/pymol-0.99"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+   >sci-chemistry/pymol-0.99[${PYTHON_USEDEP}]"
 DEPEND="app-arch/unzip"
-#RESTRICT_PYTHON_ABIS="3.*"
+
+S="${WORKDIR}"
 
 src_prepare() {
epatch "${FILESDIR}"/${PV}-indent.patch
-
-   mkdir ${P}
-   mv e* ${P}/
-
-   python_copy_sources
-
-   conversion() {
-   [[ "${PYTHON_ABI}" == 2.* ]] && return
-
-   2to3-${PYTHON_ABI} -w eMovie.py > /dev/null
-   }
-   python_execute_function --action-message 'Applying patches for Python 
${PYTHON_ABI}' --failure-message 'Applying patches for Python ${PYTHON_ABI} 
failed' -s conversion
 }
 
 src_install(){
-   installation() {
-   insinto $(python_get_sitedir)/pmg_tk/startup/
-   doins eMovie.py || die
-   }
-   python_execute_function -s installation
-}
-
-pkg_postinst(){
-   python_mod_optimize pmg_tk/startup
-}
-
-pkg_postrm() {
-   python_mod_cleanup pmg_tk/startup
+   python_moduleinto pmg_tk/startup
+   python_foreach_impl python_domodule eMovie.py
+   python_foreach_impl python_optimize
 }

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Justin Lecher]

commit: 01222e4f46e52148f0c9e200129a6420d6b3f8fb
Author: Justin Lecher  gentoo  org>
AuthorDate: Thu Nov 12 16:20:32 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Nov 12 16:20:32 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=01222e4f

sci-chemistry/pymol: Always use included apbs plugin

Correctly block files collisions

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=565600

Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol/Manifest |   1 -
 sci-chemistry/pymol/metadata.xml |   1 -
 sci-chemistry/pymol/pymol-1.7.4.0.ebuild | 106 ---
 sci-chemistry/pymol/pymol-1.7.6.0.ebuild |  11 ++--
 sci-chemistry/pymol/pymol-1.7.7.2.ebuild |  11 ++--
 5 files changed, 8 insertions(+), 122 deletions(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index b660c66..1d654d7 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,3 @@
 DIST pymol-1.7.0.0.png.xz 5392 SHA256 
4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 
24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105
 WHIRLPOOL 
395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b
-DIST pymol-1.7.4.0.tar.xz 6528964 SHA256 
5a732aeb8a02797a185f54c3bd8bb477a1a11976eb9f982f6cf79ce887ce3a4a SHA512 
fa53e90413cb1e02797a30b21b4254901504edc029104567fd2d4c5ef630eb8c2eb9f5065b2b9e65f657aaa30ca8ac85c3314c6c7fbb89148d89a9a0964de3cf
 WHIRLPOOL 
1467a9746abe60e371162e6065253fbb23453f80a4757a18936f5b6509f63657b7073ee5e118c7e4faf71cd38c78917e1f4b0a3a684b4807972546180d69
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 
31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 
ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b1e9d3aeda0b6035d55d
 WHIRLPOOL 
3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2
 DIST pymol-1.7.7.2.tar.xz 6527780 SHA256 
fc15fc8fbf23b422c5d19babd20e19b7d7ab8ee9532012c7b3a27b87af44fdae SHA512 
faf3715cd6b9e7115f6501fc4480a6f71fe53d3b02b2eeefdd07a57d7c15b3621c05fd3894bb92ac4042edaa224d99c2be7488a762254d069c581974a0146179
 WHIRLPOOL 
b52683ce1dc265fe302c974ccc1bfa9e55365e8502f944cf6527c0071f207fcb54e8b3ad38fd684b66c66f85fa6a03f2f1178b90fd406b9f7561d956c704fb9a

diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index 9af014e..6a64062 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -6,7 +6,6 @@
 j...@gentoo.org
   
   
-Install the apbs plugin
 Install Pymodule needed for web app support
   
   

diff --git a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild 
b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
deleted file mode 100644
index 2e0475c..000
--- a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/;
-SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-   https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#  mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-   dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/pyopengl[${PYTHON_USEDEP}]
-   media-libs/freeglut
-   media-libs/freetype:2
-   media-libs/glew:0=
-   media-libs/libpng:0=
-   media-video/mpeg-tools
-   sys-libs/zlib
-   virtual/python-pmw[${PYTHON_USEDEP}]
-   apbs? (
-   sci-chemistry/apbs[${PYTHON_USEDEP}]
-   sci-chemistry/pdb2pqr[${PYTHON_USEDEP}]
-   sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-   )
-   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-PATCHES=(
-   "${FILESDIR}"/${PN}-1.7.3.1-maeffplugin.cpp.patch
-   )
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
-   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-   -e "/import/s:argparse:argparseX:g" \
-   -i setup.py || die
-
-   rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-   sed \
-   -e "s:/opt/local:${EPREFIX}/usr:g" \
-   -e '/ext_comp_args/s:\[.*\]:[]:g' \
-   

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Justin Lecher]

commit: bab728c8989c1ad152efa0fad4bb25c2ff11d733
Author: Justin Lecher  gentoo  org>
AuthorDate: Wed Nov 11 11:22:39 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Wed Nov 11 11:35:20 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bab728c8

sci-chemistry/pymol: Drop old

obsoletes

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=543018

Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol/Manifest |   1 -
 sci-chemistry/pymol/metadata.xml |   2 +-
 sci-chemistry/pymol/pymol-1.7.0.1.ebuild | 101 ---
 3 files changed, 1 insertion(+), 103 deletions(-)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 3e0a1ca..6779a07 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,3 @@
 DIST pymol-1.7.0.0.png.xz 5392 SHA256 
4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 
24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105
 WHIRLPOOL 
395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b
-DIST pymol-1.7.0.1.tar.xz 6550492 SHA256 
e8c6f6a465aec78171daf5cd981ebd1614dfa5e014e13c85a044cfbb591841c8 SHA512 
a09277cd827f832c4f4e307f6117613d2ee8250643d129a5c34a30ceab2bfe8cea195c71a138fff09b6c69e9427153b917d7d3a7262d154ada5f323ec9635087
 WHIRLPOOL 
1803b55ade1b04de5963fd4a3bbe1354cda8759e15254c644952e25d7dcc904bc7b9fd91da75fdb8c6a96fd118a5a21bec9c8bba368744b44436747faca5cd9c
 DIST pymol-1.7.4.0.tar.xz 6528964 SHA256 
5a732aeb8a02797a185f54c3bd8bb477a1a11976eb9f982f6cf79ce887ce3a4a SHA512 
fa53e90413cb1e02797a30b21b4254901504edc029104567fd2d4c5ef630eb8c2eb9f5065b2b9e65f657aaa30ca8ac85c3314c6c7fbb89148d89a9a0964de3cf
 WHIRLPOOL 
1467a9746abe60e371162e6065253fbb23453f80a4757a18936f5b6509f63657b7073ee5e118c7e4faf71cd38c78917e1f4b0a3a684b4807972546180d69
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 
31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 
ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b1e9d3aeda0b6035d55d
 WHIRLPOOL 
3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2

diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
index f92fc92..9af014e 100644
--- a/sci-chemistry/pymol/metadata.xml
+++ b/sci-chemistry/pymol/metadata.xml
@@ -1,4 +1,4 @@
-
+
 http://www.gentoo.org/dtd/metadata.dtd;>
 
   sci-chemistry

diff --git a/sci-chemistry/pymol/pymol-1.7.0.1.ebuild 
b/sci-chemistry/pymol/pymol-1.7.0.1.ebuild
deleted file mode 100644
index af90249..000
--- a/sci-chemistry/pymol/pymol-1.7.0.1.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 fdo-mime versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="http://www.pymol.org/;
-SRC_URI="
-   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
-   https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
-"
-#  mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
-
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
-
-DEPEND="
-   dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/pyopengl[${PYTHON_USEDEP}]
-   media-libs/freeglut
-   media-libs/freetype:2
-   media-libs/glew:0=
-   media-libs/libpng:0=
-   media-video/mpeg-tools
-   sys-libs/zlib
-   virtual/python-pmw[${PYTHON_USEDEP}]
-   apbs? (
-   sci-chemistry/apbs
-   sci-chemistry/pdb2pqr
-   sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-   )
-   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${P}/${PN}
-
-python_prepare_all() {
-   sed \
-   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
-   -e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
-   -e "/import/s:argparse:argparseX:g" \
-   -i setup.py || die
-
-   rm ./modules/pmg_tk/startup/apbs_tools.py || die
-
-   sed \
-   -e "s:/opt/local:${EPREFIX}/usr:g" \
-   -e '/ext_comp_args/s:\[.*\]:[]:g' \
-   -i setup.py || die
-
-   distutils-r1_python_prepare_all
-}
-
-python_install() {
-   distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-   distutils-r1_python_install_all
-
-   python_export python2_7 EPYTHON
-
-   # These environment variables should not go in the wrapper script, or 
else
- 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Justin Lecher]

commit: 49442c76f58b64b302c908ec67b7a4b47ccb9323
Author: Justin Lecher  gentoo  org>
AuthorDate: Wed Nov 11 11:34:16 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Wed Nov 11 11:35:20 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=49442c76

sci-chemistry/pymol: Version Bump

Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol/Manifest |   1 +
 sci-chemistry/pymol/pymol-1.7.7.2.ebuild | 113 +++
 2 files changed, 114 insertions(+)

diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 6779a07..b660c66 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,3 +1,4 @@
 DIST pymol-1.7.0.0.png.xz 5392 SHA256 
4c554a5c4f47946b6f7bae00209d5116305162534292735d30ae0794c56a8a0b SHA512 
24bb1584b28688f5d5824e938f8500ca9887838adf490b4284c52f8c0da4c5ec4a56051ee80f48e4f34541ab53f9a4e00c849c382f1fd37c232fbea12d700105
 WHIRLPOOL 
395f978eb9ea3a8f8f39bf0694f71986ac9f8ebb307b90283c53fed85c4412d84e54af472f8646fcbd99c650039cb395a8f02b281168802c73ddb9bad175512b
 DIST pymol-1.7.4.0.tar.xz 6528964 SHA256 
5a732aeb8a02797a185f54c3bd8bb477a1a11976eb9f982f6cf79ce887ce3a4a SHA512 
fa53e90413cb1e02797a30b21b4254901504edc029104567fd2d4c5ef630eb8c2eb9f5065b2b9e65f657aaa30ca8ac85c3314c6c7fbb89148d89a9a0964de3cf
 WHIRLPOOL 
1467a9746abe60e371162e6065253fbb23453f80a4757a18936f5b6509f63657b7073ee5e118c7e4faf71cd38c78917e1f4b0a3a684b4807972546180d69
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 
31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 
ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b1e9d3aeda0b6035d55d
 WHIRLPOOL 
3582cc846695ca580a4bcd31db8079f32d3cb0d84b8fa1afeb0b210d7004642bf58eab42cafd552f360a5e20b546e554cf5420b7dd2e8cefa5b956a9453215e2
+DIST pymol-1.7.7.2.tar.xz 6527780 SHA256 
fc15fc8fbf23b422c5d19babd20e19b7d7ab8ee9532012c7b3a27b87af44fdae SHA512 
faf3715cd6b9e7115f6501fc4480a6f71fe53d3b02b2eeefdd07a57d7c15b3621c05fd3894bb92ac4042edaa224d99c2be7488a762254d069c581974a0146179
 WHIRLPOOL 
b52683ce1dc265fe302c974ccc1bfa9e55365e8502f944cf6527c0071f207fcb54e8b3ad38fd684b66c66f85fa6a03f2f1178b90fd406b9f7561d956c704fb9a

diff --git a/sci-chemistry/pymol/pymol-1.7.7.2.ebuild 
b/sci-chemistry/pymol/pymol-1.7.7.2.ebuild
new file mode 100644
index 000..a16c696
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.7.7.2.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit distutils-r1 fdo-mime flag-o-matic versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="http://www.pymol.org/;
+SRC_URI="
+   https://dev.gentoo.org/~jlec/distfiles/${PN}-1.7.0.0.png.xz
+   https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
+"
+#  mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 
1-2)/${PN}-v${PV}.tar.bz2
+# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="apbs web"
+
+DEPEND="
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pyopengl[${PYTHON_USEDEP}]
+   media-libs/freeglut
+   media-libs/freetype:2
+   media-libs/glew:0=
+   media-libs/libpng:0=
+   media-video/mpeg-tools
+   sys-libs/zlib
+   virtual/python-pmw[${PYTHON_USEDEP}]
+   apbs? (
+   sci-chemistry/apbs[${PYTHON_USEDEP}]
+   sci-chemistry/pdb2pqr[${PYTHON_USEDEP}]
+   !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
+   )
+   web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${P}/${PN}
+
+python_prepare_all() {
+   sed \
+   -e "s:\"/usr:\"${EPREFIX}/usr:g" \
+   -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+   -e "/import/s:argparse:argparseX:g" \
+   -i setup.py || die
+
+   sed \
+   -e "s:/opt/local:${EPREFIX}/usr:g" \
+   -e '/ext_comp_args/s:\[.*\]:[]:g' \
+   -i setup.py || die
+
+   append-cxxflags -std=c++0x
+
+   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 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Agostino Sarubbo]

commit: 58f810bf66c0e4c89faa0335c012f7a5cdb695ee
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Wed Nov 11 15:00:09 2015 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Wed Nov 11 15:00:09 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=58f810bf

sci-chemistry/pymol: amd64 stable wrt bug #565494

Package-Manager: portage-2.2.20.1
RepoMan-Options: --include-arches="amd64"

 sci-chemistry/pymol/pymol-1.7.6.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild 
b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
index a16c696..8924903 100644
--- a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
@@ -20,7 +20,7 @@ SRC_URI="
 
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="apbs web"
 
 DEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Agostino Sarubbo]

commit: 50f0bc9e1c73375f64124100989390ba9ff37bc2
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Wed Nov 11 15:01:02 2015 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Wed Nov 11 15:01:02 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=50f0bc9e

sci-chemistry/pymol: x86 stable wrt bug #565494

Package-Manager: portage-2.2.20.1
RepoMan-Options: --include-arches="x86"

 sci-chemistry/pymol/pymol-1.7.6.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild 
b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
index 8924903..c163b24 100644
--- a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
@@ -20,7 +20,7 @@ SRC_URI="
 
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="apbs web"
 
 DEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Agostino Sarubbo]

commit: 9075bb32c413e50a4995f15dfdce92fd4a4338f0
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Wed Nov 11 10:38:39 2015 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Wed Nov 11 10:38:39 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9075bb32

sci-chemistry/pymol: x86 stable wrt bug #543020

Package-Manager: portage-2.2.20.1
RepoMan-Options: --include-arches="x86"

 sci-chemistry/pymol/pymol-1.7.4.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild 
b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
index 54729a0..2e0475c 100644
--- a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
@@ -20,7 +20,7 @@ SRC_URI="
 
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="apbs web"
 
 DEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-dynamics/

[Justin Lecher]

commit: 95f69d625aa06e2e47289e0044eca43b6c85a3c9
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct 12 08:05:00 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct 12 08:06:33 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=95f69d62

sci-chemistry/pymol-plugins-dynamics: Version Bump

Package-Manager: portage-2.2.22
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol-plugins-dynamics/Manifest  |  1 +
 .../pymol-plugins-dynamics-2.0.4.ebuild| 38 ++
 2 files changed, 39 insertions(+)

diff --git a/sci-chemistry/pymol-plugins-dynamics/Manifest 
b/sci-chemistry/pymol-plugins-dynamics/Manifest
index a607e37..258493d 100644
--- a/sci-chemistry/pymol-plugins-dynamics/Manifest
+++ b/sci-chemistry/pymol-plugins-dynamics/Manifest
@@ -1 +1,2 @@
 DIST pymol-plugins-dynamics-1.2.0.tar.gz 725163 SHA256 
edf9bddbbce41ee5319bfd0b28d6e0b0eba56e8b2d8a300d510be8ff5894704f SHA512 
7e8d62ea58cb88348136fccd132d9a1faaa3474c0a0f821e729ced777620e2083b1b0606d79fc75802755c96c5eb0b90e08b00e5c865ecbaaee2b837f56987de
 WHIRLPOOL 
07061d3b0840fef0025be55b90fca013afc1ea58308d6ee11a8b74321de4f1c24760b1cf141b0a86678c5cf652c8890cdf2c4e0da60403c8454e04b003e20aaa
+DIST pymol-plugins-dynamics-2.0.4.tar.gz 821563 SHA256 
358452e0d8589ffae28fe486eeca0be353f17f1fdde9f05f548025b241afabe5 SHA512 
befad8b5c09ddba89b9e00bd712a2af7202e312b2ebee7722cbeec5698125dd7614463465d79c17c805714ba23ca1188c64610789e90c93bb0ad7572841ebf25
 WHIRLPOOL 
039e40c7c57a242476e72a351ecc099201021f479762c2eb29bdad25b72c11c33295e8f9707ece486235efb1b205524e479cd4ae57639d1410515a75d2221989

diff --git 
a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.4.ebuild 
b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.4.ebuild
new file mode 100644
index 000..c61
--- /dev/null
+++ b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.4.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-r1
+
+MY_PN="Dynamics"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Molecular dynamics in Pymol"
+HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics;
+SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+   ${PYTHON_DEPS}
+   sci-chemistry/prody[${PYTHON_USEDEP}]
+   "
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${MY_P}
+
+DOCS=( manual.odt )
+
+src_install() {
+   python_moduleinto pmg_tk/startup
+   python_parallel_foreach_impl python_domodule pymol_plugin_dynamics.py
+}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Agostino Sarubbo]

commit: 78f9911612d1a9931f742d6eb18085973d4487c2
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Thu Sep 24 10:57:25 2015 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Thu Sep 24 10:57:25 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=78f99116

sci-chemistry/pymol: amd64 stable wrt bug #543020

Package-Manager: portage-2.2.20.1
RepoMan-Options: --include-arches="amd64"

 sci-chemistry/pymol/pymol-1.7.4.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild 
b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
index eb857b6..6e3f8c8 100644
--- a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
@@ -20,7 +20,7 @@ SRC_URI="
 
 LICENSE="PSF-2.2"
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="apbs web"
 
 DEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-psico/

[Justin Lecher]

commit: 2cfb1698008322be44bf72f8090c3e8d866fa196
Author: Justin Lecher  gentoo  org>
AuthorDate: Tue Sep 15 13:53:39 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Tue Sep 15 14:03:53 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2cfb1698

sci-chemistry/pymol-plugins-psico: Drop optional dep

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild | 1 -
 1 file changed, 1 deletion(-)

diff --git 
a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild 
b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild
index 2b4d116..1d9d37f 100644
--- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild
+++ b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild
@@ -26,7 +26,6 @@ RDEPEND="
media-libs/qhull
media-video/mplayer
sci-biology/stride
-   sci-chemistry/ccp4-apps[${PYTHON_USEDEP}]
sci-chemistry/dssp
sci-chemistry/mm-align
sci-chemistry/pdbmat

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol-plugins-emovie/, sci-chemistry/aqua/, sci-chemistry/surf/, ...

[Justin Lecher]

commit: 9a0f124e713e3ee2a76dbe92fb9956911859be88
Author: Justin Lecher  gentoo  org>
AuthorDate: Tue Sep 15 14:02:51 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Tue Sep 15 14:03:54 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9a0f124e

sci-chemistry: Update Checksums

Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/aqua/Manifest | 2 +-
 sci-chemistry/balbes/Manifest   | 2 +-
 sci-chemistry/mead/Manifest | 2 +-
 sci-chemistry/mm-align/Manifest | 2 +-
 sci-chemistry/moldy/Manifest| 2 +-
 sci-chemistry/mrbump/Manifest   | 2 +-
 sci-chemistry/msms-bin/Manifest | 4 ++--
 sci-chemistry/mustang/Manifest  | 2 +-
 sci-chemistry/p3d/Manifest  | 2 +-
 sci-chemistry/pdb-extract/Manifest  | 4 ++--
 sci-chemistry/pdbcns/Manifest   | 2 +-
 sci-chemistry/prekin/Manifest   | 2 +-
 sci-chemistry/pymol-plugins-emovie/Manifest | 2 +-
 sci-chemistry/surf/Manifest | 2 +-
 sci-chemistry/threeV/Manifest   | 2 +-
 15 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest
index 7f6594d..187beb2 100644
--- a/sci-chemistry/aqua/Manifest
+++ b/sci-chemistry/aqua/Manifest
@@ -1,2 +1,2 @@
 DIST aqua-3.2-nmr_manual.tar.gz 632031 SHA256 
89bbc2501831e547fec2fe755bbc0081f672e5e2c7adb83618699e6825f73996
-DIST aqua3.2.tar.gz 688408 SHA256 
895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f
+DIST aqua3.2.tar.gz 688408 SHA256 
895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f SHA512 
1939f662a68122da613368aa106d7a31525903014420035eba9d10c3bd99b04d654d156328d308673003854233a02c1da48c036f3187fa1f0f303cc5928edd6a
 WHIRLPOOL 
458fc0e574273fd9d2647ef8b2788c98669c9f96133f7132eddc9cbfb981e42894f5e4fd0e8d67f52ddb4c6424399b21973d4d87a175b440d81b7b955fe3fe41

diff --git a/sci-chemistry/balbes/Manifest b/sci-chemistry/balbes/Manifest
index ac3f2cd..1358fcf 100644
--- a/sci-chemistry/balbes/Manifest
+++ b/sci-chemistry/balbes/Manifest
@@ -1,2 +1,2 @@
 DIST balbes-1.0.0_p100317.tar.gz 506464 SHA256 
c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 
1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
+DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 
1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 
413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20
 WHIRLPOOL 
faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c

diff --git a/sci-chemistry/mead/Manifest b/sci-chemistry/mead/Manifest
index b86a2a2..c2c39f4 100644
--- a/sci-chemistry/mead/Manifest
+++ b/sci-chemistry/mead/Manifest
@@ -1 +1 @@
-DIST mead-2.2.7.tar.gz 806319 RMD160 9adf9743e44061779f9ac3b9064abb9164ad3e58 
SHA1 6d3bbda29a5f8fdf26600e036ca8debacc37b90e SHA256 
fd2a4b357bbd847ac9b255563034d7e71bf16cf59efa371d966b6fbbe9b4cd7c
+DIST mead-2.2.7.tar.gz 806319 SHA256 
fd2a4b357bbd847ac9b255563034d7e71bf16cf59efa371d966b6fbbe9b4cd7c

diff --git a/sci-chemistry/mm-align/Manifest b/sci-chemistry/mm-align/Manifest
index a1e08c4..ccce82f 100644
--- a/sci-chemistry/mm-align/Manifest
+++ b/sci-chemistry/mm-align/Manifest
@@ -1 +1 @@
-DIST MM-align-20120321.tar.xz 20072 SHA256 
0158a93a06257b885630ab7bed3b7bf8dca2ee12217c84d019829a1e34f3eeb3
+DIST MM-align-20120321.tar.xz 20072 SHA256 
0158a93a06257b885630ab7bed3b7bf8dca2ee12217c84d019829a1e34f3eeb3 SHA512 
193c3b16b2d9fb0aaacf18b203fcf0240de7b11b4c0ce99fc571c277aa6e624b7b8b4df625e34433a5dec4349bb5bf6ae0368609c1738337923cf3b4d06428bc
 WHIRLPOOL 
42ccb05d05d668f7a99c6d1f60ca55663e68568fb7b4277ac9db3c05c8739969c1a1c63dfd8edca7cd1fa0e064bc9a12721759a0418c6d3f7656cd775b89db87

diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest
index 9e0e388..836dc88 100644
--- a/sci-chemistry/moldy/Manifest
+++ b/sci-chemistry/moldy/Manifest
@@ -1 +1 @@
-DIST moldy-2.16e.tar.gz 488410 RMD160 ef9c1c6cf1afa6e28e78a51a6a771d127aac2c83 
SHA1 e7984f59170a11b5dab0beae89c5f4cf4da20ad1 SHA256 
51abefc5e7de355022f48084382c30e72738cc1f21cd3d67fde7f047f1822ea8
+DIST moldy-2.16e.tar.gz 488410 SHA256 
51abefc5e7de355022f48084382c30e72738cc1f21cd3d67fde7f047f1822ea8

diff --git a/sci-chemistry/mrbump/Manifest b/sci-chemistry/mrbump/Manifest
index db81a16..206c2c7 100644
--- a/sci-chemistry/mrbump/Manifest
+++ b/sci-chemistry/mrbump/Manifest
@@ -1 +1 @@
-DIST mrbump-0.4.4.tar.gz 9220116 RMD160 
2b81e1aee9d2cf697c14712a7a7afe3f06c67a68 SHA1 
eb474602bbfc3ec8e3d1282b2c6b3000c7194558 SHA256 
499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a
+DIST mrbump-0.4.4.tar.gz 9220116 SHA256 
499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a

diff --git 

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/

[Justin Lecher]

commit: c5965f615e9e9688b5fa7bc50e67ecded48f3b07
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Thu Aug 27 15:01:11 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Thu Aug 27 15:01:16 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c5965f61

sci-chemistry/pymol: React on subslot changes

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher jlec AT gentoo.org

 sci-chemistry/pymol/pymol-1.7.0.1.ebuild | 2 +-
 sci-chemistry/pymol/pymol-1.7.4.0.ebuild | 2 +-
 sci-chemistry/pymol/pymol-1.7.6.0.ebuild | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-1.7.0.1.ebuild 
b/sci-chemistry/pymol/pymol-1.7.0.1.ebuild
index d71b5ab..f43ba4f 100644
--- a/sci-chemistry/pymol/pymol-1.7.0.1.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.0.1.ebuild
@@ -27,7 +27,7 @@ DEPEND=
dev-python/pyopengl[${PYTHON_USEDEP}]
media-libs/freeglut
media-libs/freetype:2
-   media-libs/glew
+   media-libs/glew:0=
media-libs/libpng:0=
media-video/mpeg-tools
sys-libs/zlib

diff --git a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild 
b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
index 4836600..eb857b6 100644
--- a/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.4.0.ebuild
@@ -28,7 +28,7 @@ DEPEND=
dev-python/pyopengl[${PYTHON_USEDEP}]
media-libs/freeglut
media-libs/freetype:2
-   media-libs/glew
+   media-libs/glew:0=
media-libs/libpng:0=
media-video/mpeg-tools
sys-libs/zlib

diff --git a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild 
b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
index 4c0590e..c119920 100644
--- a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
@@ -28,7 +28,7 @@ DEPEND=
dev-python/pyopengl[${PYTHON_USEDEP}]
media-libs/freeglut
media-libs/freetype:2
-   media-libs/glew
+   media-libs/glew:0=
media-libs/libpng:0=
media-video/mpeg-tools
sys-libs/zlib