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

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* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2015-08-27 15:01 Justin Lecher
  0 siblings, 0 replies; 55+ messages in thread
From: Justin Lecher @ 2015-08-27 15:01 UTC (permalink / raw
  To: gentoo-commits

commit:     c5965f615e9e9688b5fa7bc50e67ecded48f3b07
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 27 15:01:11 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Aug 27 15:01:16 2015 +0000
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


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2015-09-24 10:57 Agostino Sarubbo
  0 siblings, 0 replies; 55+ messages in thread
From: Agostino Sarubbo @ 2015-09-24 10:57 UTC (permalink / raw
  To: gentoo-commits

commit:     78f9911612d1a9931f742d6eb18085973d4487c2
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 24 10:57:25 2015 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Thu Sep 24 10:57:25 2015 +0000
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="


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2015-11-11 10:39 Agostino Sarubbo
  0 siblings, 0 replies; 55+ messages in thread
From: Agostino Sarubbo @ 2015-11-11 10:39 UTC (permalink / raw
  To: gentoo-commits

commit:     9075bb32c413e50a4995f15dfdce92fd4a4338f0
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 11 10:38:39 2015 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Wed Nov 11 10:38:39 2015 +0000
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="


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2015-11-11 11:35 Justin Lecher
  0 siblings, 0 replies; 55+ messages in thread
From: Justin Lecher @ 2015-11-11 11:35 UTC (permalink / raw
  To: gentoo-commits

commit:     bab728c8989c1ad152efa0fad4bb25c2ff11d733
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 11 11:22:39 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Nov 11 11:35:20 2015 +0000
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 <jlec <AT> 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 1467a9746abe60e371162e6065253fbb23453f80a4757a18936f5b6509f63657b7073ee5e118c7e4faf333371cd38c78917e1f4b0a3a684b4807972546180d69
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d 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 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
   <herd>sci-chemistry</herd>

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..0000000
--- 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="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.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() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2015-11-11 11:35 Justin Lecher
  0 siblings, 0 replies; 55+ messages in thread
From: Justin Lecher @ 2015-11-11 11:35 UTC (permalink / raw
  To: gentoo-commits

commit:     49442c76f58b64b302c908ec67b7a4b47ccb9323
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 11 11:34:16 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Nov 11 11:35:20 2015 +0000
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 <jlec <AT> 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 1467a9746abe60e371162e6065253fbb23453f80a4757a18936f5b6509f63657b7073ee5e118c7e4faf333371cd38c78917e1f4b0a3a684b4807972546180d69
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d 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 0000000..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 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}-1.7.0.0.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() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2015-11-11 15:00 Agostino Sarubbo
  0 siblings, 0 replies; 55+ messages in thread
From: Agostino Sarubbo @ 2015-11-11 15:00 UTC (permalink / raw
  To: gentoo-commits

commit:     58f810bf66c0e4c89faa0335c012f7a5cdb695ee
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 11 15:00:09 2015 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Wed Nov 11 15:00:09 2015 +0000
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="


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2015-11-11 15:01 Agostino Sarubbo
  0 siblings, 0 replies; 55+ messages in thread
From: Agostino Sarubbo @ 2015-11-11 15:01 UTC (permalink / raw
  To: gentoo-commits

commit:     50f0bc9e1c73375f64124100989390ba9ff37bc2
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 11 15:01:02 2015 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Wed Nov 11 15:01:02 2015 +0000
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="


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2015-11-12 16:20 Justin Lecher
  0 siblings, 0 replies; 55+ messages in thread
From: Justin Lecher @ 2015-11-12 16:20 UTC (permalink / raw
  To: gentoo-commits

commit:     01222e4f46e52148f0c9e200129a6420d6b3f8fb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 12 16:20:32 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov 12 16:20:32 2015 +0000
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 <jlec <AT> 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 1467a9746abe60e371162e6065253fbb23453f80a4757a18936f5b6509f63657b7073ee5e118c7e4faf333371cd38c78917e1f4b0a3a684b4807972546180d69
 DIST pymol-1.7.6.0.tar.xz 6510380 SHA256 31d4924378b38b65fae5b294e0755ee15916f9e845ef2efe5e2421f463bf3b91 SHA512 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d 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 @@
     <email>jlec@gentoo.org</email>
   </maintainer>
   <use>
-    <flag name="apbs">Install the apbs plugin</flag>
     <flag name="web">Install Pymodule needed for web app support</flag>
   </use>
   <upstream>

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..0000000
--- 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' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	python_export python2_7 EPYTHON
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="$(python_get_sitedir)/${PN}"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${PN}-1.7.0.0.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() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}

diff --git a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
index c163b24..4033493 100644
--- a/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.6.0.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 PYTHON_COMPAT=( python2_7 )
 PYTHON_REQ_USE="tk"
 
-inherit distutils-r1 fdo-mime flag-o-matic versionator
+inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://www.pymol.org/"
@@ -21,7 +21,7 @@ SRC_URI="
 LICENSE="PSF-2.2"
 SLOT="0"
 KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
+IUSE="web"
 
 DEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
@@ -33,11 +33,7 @@ DEPEND="
 	media-video/mpeg-tools
 	sys-libs/zlib
 	virtual/python-pmw[${PYTHON_USEDEP}]
-	apbs? (
-		sci-chemistry/apbs[${PYTHON_USEDEP}]
-		sci-chemistry/pdb2pqr[${PYTHON_USEDEP}]
-		!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
+	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
 	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
 RDEPEND="${DEPEND}"
 
@@ -105,6 +101,7 @@ python_install_all() {
 pkg_postinst() {
 	fdo-mime_desktop_database_update
 	fdo-mime_mime_database_update
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
 }
 
 pkg_postrm() {

diff --git a/sci-chemistry/pymol/pymol-1.7.7.2.ebuild b/sci-chemistry/pymol/pymol-1.7.7.2.ebuild
index a16c696..7d6aab4 100644
--- a/sci-chemistry/pymol/pymol-1.7.7.2.ebuild
+++ b/sci-chemistry/pymol/pymol-1.7.7.2.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 PYTHON_COMPAT=( python2_7 )
 PYTHON_REQ_USE="tk"
 
-inherit distutils-r1 fdo-mime flag-o-matic versionator
+inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://www.pymol.org/"
@@ -21,7 +21,7 @@ SRC_URI="
 LICENSE="PSF-2.2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="apbs web"
+IUSE="web"
 
 DEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
@@ -33,11 +33,7 @@ DEPEND="
 	media-video/mpeg-tools
 	sys-libs/zlib
 	virtual/python-pmw[${PYTHON_USEDEP}]
-	apbs? (
-		sci-chemistry/apbs[${PYTHON_USEDEP}]
-		sci-chemistry/pdb2pqr[${PYTHON_USEDEP}]
-		!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	)
+	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
 	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
 RDEPEND="${DEPEND}"
 
@@ -105,6 +101,7 @@ python_install_all() {
 pkg_postinst() {
 	fdo-mime_desktop_database_update
 	fdo-mime_mime_database_update
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
 }
 
 pkg_postrm() {


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2016-09-24 15:56 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2016-09-24 15:56 UTC (permalink / raw
  To: gentoo-commits

commit:     bbd5edbc744481ae2f9827b4a424aabcf5957309
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 24 15:55:43 2016 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sat Sep 24 15:56:22 2016 +0000
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 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d 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 00000000..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 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}-1.7.0.0.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() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2016-10-23 20:25 Justin Lecher
  0 siblings, 0 replies; 55+ messages in thread
From: Justin Lecher @ 2016-10-23 20:25 UTC (permalink / raw
  To: gentoo-commits

commit:     e55d1db83008e1d11d18727843a4c8f0d14b36f5
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 23 08:09:44 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Oct 23 20:25:08 2016 +0000
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 <jlec <AT> 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 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d 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 00000000..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
+
+	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}-1.7.0.0.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() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2017-02-12 19:51 Justin Lecher
  0 siblings, 0 replies; 55+ messages in thread
From: Justin Lecher @ 2017-02-12 19:51 UTC (permalink / raw
  To: gentoo-commits

commit:     4252a802ac78527b992745cd631c082d7599158f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 12 19:35:12 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 12 19:51:49 2017 +0000
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 <jlec <AT> 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 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d 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;"


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2017-02-13 11:13 Agostino Sarubbo
  0 siblings, 0 replies; 55+ messages in thread
From: Agostino Sarubbo @ 2017-02-13 11:13 UTC (permalink / raw
  To: gentoo-commits

commit:     a1320339bc92cd57fef4a64bf24fe33dc005aba5
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 13 11:11:56 2017 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Mon Feb 13 11:11:56 2017 +0000
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 <ago <AT> 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="


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2017-02-14 15:39 Agostino Sarubbo
  0 siblings, 0 replies; 55+ messages in thread
From: Agostino Sarubbo @ 2017-02-14 15:39 UTC (permalink / raw
  To: gentoo-commits

commit:     1719d0a9f6852ff037f0cd1f5bf8a123fd5ed9bb
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 14 15:38:09 2017 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Tue Feb 14 15:38:09 2017 +0000
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 <ago <AT> 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="


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2017-02-25 20:56 Justin Lecher
  0 siblings, 0 replies; 55+ messages in thread
From: Justin Lecher @ 2017-02-25 20:56 UTC (permalink / raw
  To: gentoo-commits

commit:     e4d2f4aa20dd3df7e3fa7b34da4f5c597b506830
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 20:56:17 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 20:56:27 2017 +0000
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 <jlec <AT> 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 ff8c37de07e0ed8dc1176224eea439109f2bd5e42b5c08316f5737a2fdcf5a1f267b625c166fa740296c20ef089873ae1ad6cb89b11111e9d3aeda0b6035d55d 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..0000000000
--- 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 "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}"/${PN}-1.7.0.0.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() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}

diff --git a/sci-chemistry/pymol/pymol-1.7.7.2.ebuild b/sci-chemistry/pymol/pymol-1.7.7.2.ebuild
deleted file mode 100644
index 7d6aab4313..0000000000
--- a/sci-chemistry/pymol/pymol-1.7.7.2.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 "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}"/${PN}-1.7.0.0.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() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}

diff --git a/sci-chemistry/pymol/pymol-1.8.2.1.ebuild b/sci-chemistry/pymol/pymol-1.8.2.1.ebuild
deleted file mode 100644
index e86a042c8d..0000000000
--- a/sci-chemistry/pymol/pymol-1.8.2.1.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# 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 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}-1.7.0.0.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() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2017-03-27 14:09 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2017-03-27 14:09 UTC (permalink / raw
  To: gentoo-commits

commit:     f7f304a16a0f4530e49dc100bc4a542b457a5e28
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 27 14:08:53 2017 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Mar 27 14:09:21 2017 +0000
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 00000000000..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="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${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() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	fdo-mime_mime_database_update
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2017-09-12 22:58 Matt Turner
  0 siblings, 0 replies; 55+ messages in thread
From: Matt Turner @ 2017-09-12 22:58 UTC (permalink / raw
  To: gentoo-commits

commit:     50b3a1044867e51acc08e53433633e2964643436
Author:     Matt Turner <mattst88 <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 12 22:56:19 2017 +0000
Commit:     Matt Turner <mattst88 <AT> gentoo <DOT> org>
CommitDate: Tue Sep 12 22:58:17 2017 +0000
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="


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2018-03-29 11:43 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2018-03-29 11:43 UTC (permalink / raw
  To: gentoo-commits

commit:     326f87e6afac2433c7e131c6a5126e03c845b811
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 29 11:42:27 2018 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Mar 29 11:42:27 2018 +0000
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 00000000000..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 >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH="${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
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2018-11-08 10:05 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2018-11-08 10:05 UTC (permalink / raw
  To: gentoo-commits

commit:     d6a556d0bb073db14a6091c0d705ea08f76ee5bb
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Nov  8 10:02:20 2018 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Nov  8 10:05:29 2018 +0000
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 <alexxy <AT> 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..00000000000
--- 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' \
-		"${D}/$(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() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}

diff --git a/sci-chemistry/pymol/pymol-2.1.0.ebuild b/sci-chemistry/pymol/pymol-2.2.0.ebuild
similarity index 92%
rename from sci-chemistry/pymol/pymol-2.1.0.ebuild
rename to sci-chemistry/pymol/pymol-2.2.0.ebuild
index f29f29694f2..5c2dc1f498f 100644
--- a/sci-chemistry/pymol/pymol-2.1.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.2.0.ebuild
@@ -1,18 +1,18 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 PYTHON_REQ_USE="tk"
 
-inherit distutils-r1 eutils xdg-utils flag-o-matic versionator
+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/${PN}-1.8.4.0.png.xz
-	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1)/${PN}-v${PV}.tar.bz2
+	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
 	"
 # git archive -v --prefix=${P}/ master -o ${P}.tar.xz
 RESTRICT="mirror"
@@ -36,7 +36,7 @@ DEPEND="
 	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
 RDEPEND="${DEPEND}"
 
-S="${WORKDIR}"/${PN}
+S="${WORKDIR}"/${PN}-open-source-${PV}
 
 python_prepare_all() {
 	sed \


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2018-11-13 10:13 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2018-11-13 10:13 UTC (permalink / raw
  To: gentoo-commits

commit:     922495f0a1938669ae1c819cca68276adb76a98d
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 13 10:13:34 2018 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Nov 13 10:13:34 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=922495f0

sci-chemistry/pymol: Fix missing dep

Signed-off-by: Alexey Shvetsov <alexxy <AT> 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


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2019-02-26 14:15 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2019-02-26 14:15 UTC (permalink / raw
  To: gentoo-commits

commit:     6608559d020df9dc6c0e7364bc7c058a1c2ab1fd
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 26 14:15:06 2019 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Feb 26 14:15:06 2019 +0000
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 <alexxy <AT> 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 00000000000..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 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
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2019-06-01  8:40 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2019-06-01  8:40 UTC (permalink / raw
  To: gentoo-commits

commit:     dd358f4227f9021e21150582702536055324017b
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  1 08:37:56 2019 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sat Jun  1 08:37:56 2019 +0000
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 <alexxy <AT> 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..00000000000
--- 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 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
-}

diff --git a/sci-chemistry/pymol/pymol-2.3.0.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
similarity index 95%
rename from sci-chemistry/pymol/pymol-2.3.0.ebuild
rename to sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
index 0f197578023..89aef82c8e9 100644
--- a/sci-chemistry/pymol/pymol-2.3.0.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild
@@ -4,9 +4,8 @@
 EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
 
-inherit distutils-r1 eutils xdg-utils flag-o-matic
+inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
 
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://www.pymol.org/"
@@ -14,7 +13,6 @@ 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 ${P}.tar.xz
 RESTRICT="mirror"
 LICENSE="PSF-2.2"
 SLOT="0"
@@ -26,7 +24,8 @@ DEPEND="
 	dev-libs/mmtf-cpp
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freeglut
+	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
 	media-libs/freetype:2
 	media-libs/glew:0=
 	media-libs/glm


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2019-09-27 17:33 Michał Górny
  0 siblings, 0 replies; 55+ messages in thread
From: Michał Górny @ 2019-09-27 17:33 UTC (permalink / raw
  To: gentoo-commits

commit:     e879367f72e6f019c005cb19ea0d337841834654
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 27 17:30:47 2019 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Fri Sep 27 17:33:43 2019 +0000
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 <mgorny <AT> 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}"


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-01-16  6:39 Michał Górny
  0 siblings, 0 replies; 55+ messages in thread
From: Michał Górny @ 2020-01-16  6:39 UTC (permalink / raw
  To: gentoo-commits

commit:     d1a502c6076dba392a82e7a3a476f65f4ac8cf55
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 06:27:31 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 06:38:04 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d1a502c6

sci-chemistry/pymol: Permit numpy-python2

Signed-off-by: Michał Górny <mgorny <AT> 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}]


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-01-16  6:39 Michał Górny
  0 siblings, 0 replies; 55+ messages in thread
From: Michał Górny @ 2020-01-16  6:39 UTC (permalink / raw
  To: gentoo-commits

commit:     903ca8dc261b929d0b6d57f62e2ec18129cb14ec
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 06:36:25 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 06:38:24 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=903ca8dc

sci-chemistry/pymol: Use HTTPS

Signed-off-by: Michał Górny <mgorny <AT> 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


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-01-22 21:50 Michał Górny
  0 siblings, 0 replies; 55+ messages in thread
From: Michał Górny @ 2020-01-22 21:50 UTC (permalink / raw
  To: gentoo-commits

commit:     6db822a4c7759eacbe5c96503d3c629f1256b187
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 22 21:44:04 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed Jan 22 21:49:53 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6db822a4

sci-chemistry/pymol: Revbump post dep change

Signed-off-by: Michał Górny <mgorny <AT> 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


^ permalink raw reply	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-01-28 18:24 Michał Górny
  0 siblings, 0 replies; 55+ messages in thread
From: Michał Górny @ 2020-01-28 18:24 UTC (permalink / raw
  To: gentoo-commits

commit:     fffd22f3ab77845f870f93d08b75722ce474ef32
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 28 16:48:52 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Tue Jan 28 18:24:07 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fffd22f3

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

Signed-off-by: Michał Górny <mgorny <AT> 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..00000000000
--- 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 ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-pkg_postinst() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-02-07 18:41 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2020-02-07 18:41 UTC (permalink / raw
  To: gentoo-commits

commit:     68bc99ce88a667735c8b723fdb48d9e9c399a25c
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Fri Feb  7 18:40:38 2020 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Fri Feb  7 18:41:08 2020 +0000
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 <pacho <AT> 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}
 


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-03-04 18:02 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2020-03-04 18:02 UTC (permalink / raw
  To: gentoo-commits

commit:     de879cad418f2e55fb037c9a063dde7c3ae3dec3
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Mar  4 18:01:25 2020 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Mar  4 18:01:50 2020 +0000
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 <alexxy <AT> 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
 "


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-06-03 21:22 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2020-06-03 21:22 UTC (permalink / raw
  To: gentoo-commits

commit:     d8f901f6451dcefa90b1e467d2819a85717bae56
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Jun  3 21:20:53 2020 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Jun  3 21:20:53 2020 +0000
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 <alexxy <AT> 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
 


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-08-01 23:20 Andreas Sturmlechner
  0 siblings, 0 replies; 55+ messages in thread
From: Andreas Sturmlechner @ 2020-08-01 23:20 UTC (permalink / raw
  To: gentoo-commits

commit:     e6cc55210919cbdee58bcaa282cf6ef2064aa7c2
Author:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 29 18:47:25 2020 +0000
Commit:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sat Aug  1 23:19:34 2020 +0000
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 <asturm <AT> 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..00000000000
--- 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
-}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-09-07  8:55 David Seifert
  0 siblings, 0 replies; 55+ messages in thread
From: David Seifert @ 2020-09-07  8:55 UTC (permalink / raw
  To: gentoo-commits

commit:     45a1aa11ca88530be7230c350a47c17604ab5018
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Sep  7 08:53:51 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Sep  7 08:53:51 2020 +0000
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 <soap <AT> 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"


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-10-14 10:43 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2020-10-14 10:43 UTC (permalink / raw
  To: gentoo-commits

commit:     10a72e4fd89f88032a5f6af84975b99777b02a13
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 14 10:31:34 2020 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Oct 14 10:31:34 2020 +0000
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 <alexxy <AT> 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
 


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-11-27 13:31 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2020-11-27 13:31 UTC (permalink / raw
  To: gentoo-commits

commit:     e9c0ee13ce43b45b33796326e41049f3d020310d
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 27 13:31:48 2020 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Nov 27 13:31:48 2020 +0000
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 <alexxy <AT> 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


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-11-27 13:39 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2020-11-27 13:39 UTC (permalink / raw
  To: gentoo-commits

commit:     fb417c1f224725f3f0b986113865d3de8bb38741
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 27 13:39:23 2020 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Nov 27 13:39:23 2020 +0000
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 <alexxy <AT> 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


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2020-11-28 19:36 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2020-11-28 19:36 UTC (permalink / raw
  To: gentoo-commits

commit:     5517c82efb9b793cd9b0533d5371080199789543
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 28 19:36:37 2020 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sat Nov 28 19:36:37 2020 +0000
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 <alexxy <AT> 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
 


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2021-01-06 15:10 Fabian Groffen
  0 siblings, 0 replies; 55+ messages in thread
From: Fabian Groffen @ 2021-01-06 15:10 UTC (permalink / raw
  To: gentoo-commits

commit:     a748077bb6ede1a43ca3d798a14ef278a9dfdd26
Author:     Fabian Groffen <grobian <AT> gentoo <DOT> org>
AuthorDate: Wed Jan  6 15:09:56 2021 +0000
Commit:     Fabian Groffen <grobian <AT> gentoo <DOT> org>
CommitDate: Wed Jan  6 15:09:56 2021 +0000
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 <grobian <AT> 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="


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2021-01-14 23:11 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2021-01-14 23:11 UTC (permalink / raw
  To: gentoo-commits

commit:     d707db016087c78a6a39b8f6607f9304e90361ed
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 14 23:11:09 2021 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu Jan 14 23:11:09 2021 +0000
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 <pacho <AT> 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 \


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2021-01-18 10:14 David Seifert
  0 siblings, 0 replies; 55+ messages in thread
From: David Seifert @ 2021-01-18 10:14 UTC (permalink / raw
  To: gentoo-commits

commit:     ed702145ff6aa7244042d67bf68f6e17b621cd94
Author:     Jakov Smolic <jakov.smolic <AT> sartura <DOT> hr>
AuthorDate: Mon Jan 18 10:14:15 2021 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Jan 18 10:14:15 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ed702145

sci-chemistry/pymol: Remove old

Signed-off-by: Jakov Smolic <jakov.smolic <AT> sartura.hr>
Signed-off-by: David Seifert <soap <AT> 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..00000000000
--- 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
-}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2021-05-02 19:22 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2021-05-02 19:22 UTC (permalink / raw
  To: gentoo-commits

commit:     c4ec1ee42400be04414a8ab1b728ec21add16fff
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun May  2 19:20:06 2021 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun May  2 19:22:22 2021 +0000
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 <pacho <AT> 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"


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2021-05-16 20:41 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2021-05-16 20:41 UTC (permalink / raw
  To: gentoo-commits

commit:     428de16e86460563d0e465331e301cc0dedf91ac
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Sun May 16 20:41:00 2021 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sun May 16 20:41:15 2021 +0000
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 <alexxy <AT> 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 00000000000..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 "${T}"/20pymol
+
+	newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png
+	make_desktop_entry ${PN} PyMol ${PN} \
+		"Graphics;Education;Science;Chemistry;" \
+		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
+
+	if ! use web; then
+		rm -rf "${D}/$(python_get_sitedir)/web" || die
+	fi
+
+	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
+}
+
+pkg_postinst() {
+	xdg_pkg_postinst
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2021-05-20 15:07 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2021-05-20 15:07 UTC (permalink / raw
  To: gentoo-commits

commit:     319a93dd7c1b57253d978f4491df7dfb6e9d3108
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu May 20 15:07:07 2021 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu May 20 15:07:21 2021 +0000
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 <pacho <AT> 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
+#}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2022-04-08  9:54 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2022-04-08  9:54 UTC (permalink / raw
  To: gentoo-commits

commit:     7ed232b26caa687abd38b7079d9f4e19a86a3bc3
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Apr  8 09:52:06 2022 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Apr  8 09:52:06 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7ed232b2

sci-chemistry/pymol: enable py3.10

Signed-off-by: Alexey Shvetsov <alexxy <AT> 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
-#}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2022-05-22 11:18 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2022-05-22 11:18 UTC (permalink / raw
  To: gentoo-commits

commit:     b1b098bea1c8a0d165b298ee37805f0b334c0363
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun May 22 11:17:48 2022 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun May 22 11:17:54 2022 +0000
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 <pacho <AT> 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 000000000000..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
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2022-07-31  8:27 Sam James
  0 siblings, 0 replies; 55+ messages in thread
From: Sam James @ 2022-07-31  8:27 UTC (permalink / raw
  To: gentoo-commits

commit:     5fdce3209a4873ddc9ded828ac8fd2ff5339ec13
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sun Jul 31 07:39:24 2022 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sun Jul 31 08:25:22 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5fdce320

sci-chemistry/pymol: add github upstream metadata

Signed-off-by: Sam James <sam <AT> 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 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <use>
-    <flag name="web">Install Pymodule needed for web app support</flag>
-  </use>
-  <upstream>
-    <remote-id type="sourceforge">pymol</remote-id>
-  </upstream>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+	<use>
+		<flag name="web">Install Pymodule needed for web app support</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">schrodinger/pymol-open-source</remote-id>
+		<remote-id type="sourceforge">pymol</remote-id>
+	</upstream>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2023-02-05 21:01 Marek Szuba
  0 siblings, 0 replies; 55+ messages in thread
From: Marek Szuba @ 2023-02-05 21:01 UTC (permalink / raw
  To: gentoo-commits

commit:     3a660afed239c168c7f62df1517dddaab03738d6
Author:     Marek Szuba <marecki <AT> gentoo <DOT> org>
AuthorDate: Sun Feb  5 20:56:02 2023 +0000
Commit:     Marek Szuba <marecki <AT> gentoo <DOT> org>
CommitDate: Sun Feb  5 21:01:41 2023 +0000
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 <marecki <AT> 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}]


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2023-02-07  9:42 Marek Szuba
  0 siblings, 0 replies; 55+ messages in thread
From: Marek Szuba @ 2023-02-07  9:42 UTC (permalink / raw
  To: gentoo-commits

commit:     c0dd21f4fceff481c9a02396ea9db26b9e4ff20a
Author:     Marek Szuba <marecki <AT> gentoo <DOT> org>
AuthorDate: Tue Feb  7 09:35:49 2023 +0000
Commit:     Marek Szuba <marecki <AT> gentoo <DOT> org>
CommitDate: Tue Feb  7 09:36:41 2023 +0000
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 <marecki <AT> 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..000000000000
--- 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
-}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2023-05-02 18:42 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2023-05-02 18:42 UTC (permalink / raw
  To: gentoo-commits

commit:     27714ff93e785287397f31049027fea2357828f7
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 18:32:28 2023 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Tue May  2 18:42:45 2023 +0000
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 <pacho <AT> 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


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2023-06-24 17:44 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2023-06-24 17:44 UTC (permalink / raw
  To: gentoo-commits

commit:     b79fe624316f1410e0ac77c10ded47222fcd9d57
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 24 17:17:02 2023 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sat Jun 24 17:17:02 2023 +0000
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 <pacho <AT> 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 000000000000..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
+}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2023-07-19  8:28 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2023-07-19  8:28 UTC (permalink / raw
  To: gentoo-commits

commit:     5e4cabe39a1ad71a44b89b696142bab6226291a4
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 19 08:26:10 2023 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Wed Jul 19 08:28:05 2023 +0000
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 <pacho <AT> 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.


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2023-07-19  8:28 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2023-07-19  8:28 UTC (permalink / raw
  To: gentoo-commits

commit:     61839b4959858697d83224ddca44839af364100d
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 19 08:27:44 2023 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Wed Jul 19 08:28:06 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61839b49

sci-chemistry/pymol: drop 2.5.0-r2

Signed-off-by: Pacho Ramos <pacho <AT> 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..000000000000
--- 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
-}


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2023-07-20 11:31 Pacho Ramos
  0 siblings, 0 replies; 55+ messages in thread
From: Pacho Ramos @ 2023-07-20 11:31 UTC (permalink / raw
  To: gentoo-commits

commit:     7c1155b0a87a8388154a392f173e0399394cd681
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 20 11:30:51 2023 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu Jul 20 11:31:44 2023 +0000
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 <pacho <AT> 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.


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2024-05-13 16:11 Ulrich Müller
  0 siblings, 0 replies; 55+ messages in thread
From: Ulrich Müller @ 2024-05-13 16:11 UTC (permalink / raw
  To: gentoo-commits

commit:     3408011f5a9237398ad50fc9441f958008c8488e
Author:     Ulrich Müller <ulm <AT> gentoo <DOT> org>
AuthorDate: Sun May 12 14:50:39 2024 +0000
Commit:     Ulrich Müller <ulm <AT> gentoo <DOT> org>
CommitDate: Mon May 13 16:05:30 2024 +0000
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 <ulm <AT> 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"


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2024-05-17 19:21 Alexey Shvetsov
  0 siblings, 0 replies; 55+ messages in thread
From: Alexey Shvetsov @ 2024-05-17 19:21 UTC (permalink / raw
  To: gentoo-commits

commit:     dfe0f62750dadf6273bd4146db194c7165181781
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri May 17 19:20:35 2024 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri May 17 19:20:35 2024 +0000
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 <alexxy <AT> 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..000000000000
--- 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 ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}

diff --git a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild
similarity index 97%
rename from sci-chemistry/pymol/pymol-2.5.0-r5.ebuild
rename to sci-chemistry/pymol/pymol-3.0.0.ebuild
index 3e0e1d344ac6..150f7732d930 100644
--- a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild
+++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{9..12} )
 DISTUTILS_USE_PEP517="setuptools"
 DISTUTILS_EXT=1
 
@@ -15,6 +15,9 @@ 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 -> ${P}.tar.gz
 	"
+
+S="${WORKDIR}"/${PN}-open-source-${PV}
+
 LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
@@ -39,8 +42,6 @@ RDEPEND="${DEPEND}
 	sci-chemistry/chemical-mime-data
 "
 
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
 PATCHES=(
 	"${FILESDIR}/${PN}-2.5.0-format-security.patch"
 )
@@ -59,7 +60,7 @@ python_prepare_all() {
 		-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
 		-i setup.py || die
 
-	append-cxxflags -std=c++0x
+	append-cxxflags -std=c++17
 
 	distutils-r1_python_prepare_all
 }


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2024-09-05  4:08 Eli Schwartz
  0 siblings, 0 replies; 55+ messages in thread
From: Eli Schwartz @ 2024-09-05  4:08 UTC (permalink / raw
  To: gentoo-commits

commit:     045fb68f62b66b2d85d685eeaa49d2903621817a
Author:     Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  4 21:20:25 2024 +0000
Commit:     Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Thu Sep  5 04:07:44 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=045fb68f

sci-chemistry/pymol: drop a bunch of dependencies to runtime-only

They aren't needed to run setup.py (whether via gpep517 or otherwise).
They are only used by the runtime code. The distinction between
dependency types is sometimes seen as a bit academic, but it matters for
--buildpkgonly. This is especially useful as one of the runtime-only
dependencies will, in turn, depend on python[tk], and moving it out of
DEPEND means the package can be test-compiled with --buildpkgonly,
without rebuilding and reinstalling python.

Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>

 sci-chemistry/pymol/pymol-3.0.0.ebuild | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/sci-chemistry/pymol/pymol-3.0.0.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild
index 150f7732d930..f589a6cd9584 100644
--- a/sci-chemistry/pymol/pymol-3.0.0.ebuild
+++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild
@@ -26,19 +26,20 @@ 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}]
+	sys-libs/zlib
 	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}
+RDEPEND="
+	${DEPEND}
+	media-video/mpeg-tools
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+	dev-python/pmw[${PYTHON_USEDEP}]
 	sci-chemistry/chemical-mime-data
 "
 


^ permalink raw reply related	[flat|nested] 55+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/
@ 2024-09-05  4:08 Eli Schwartz
  0 siblings, 0 replies; 55+ messages in thread
From: Eli Schwartz @ 2024-09-05  4:08 UTC (permalink / raw
  To: gentoo-commits

commit:     05e449791a34defa3ab40141bf4b122e00f2f174
Author:     Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  4 21:42:58 2024 +0000
Commit:     Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Thu Sep  5 04:07:45 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=05e44979

sci-chemistry/pymol: mark as LTO-unsafe

Closes: https://bugs.gentoo.org/933235
Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>

 sci-chemistry/pymol/pymol-3.0.0.ebuild | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/sci-chemistry/pymol/pymol-3.0.0.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild
index f589a6cd9584..b6ec9fbef1e3 100644
--- a/sci-chemistry/pymol/pymol-3.0.0.ebuild
+++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild
@@ -67,6 +67,11 @@ python_prepare_all() {
 }
 
 python_configure_all() {
+	# -Werror=odr
+	# https://bugs.gentoo.org/933235
+	# https://github.com/schrodinger/pymol-open-source/issues/395
+	filter-lto
+
 	use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins )
 }
 


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2015-11-11 11:35 [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/pymol/ Justin Lecher
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2024-09-05  4:08 Eli Schwartz
2024-09-05  4:08 Eli Schwartz
2024-05-17 19:21 Alexey Shvetsov
2024-05-13 16:11 Ulrich Müller
2023-07-20 11:31 Pacho Ramos
2023-07-19  8:28 Pacho Ramos
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2023-06-24 17:44 Pacho Ramos
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2023-02-07  9:42 Marek Szuba
2023-02-05 21:01 Marek Szuba
2022-07-31  8:27 Sam James
2022-05-22 11:18 Pacho Ramos
2022-04-08  9:54 Alexey Shvetsov
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2021-05-16 20:41 Alexey Shvetsov
2021-05-02 19:22 Pacho Ramos
2021-01-18 10:14 David Seifert
2021-01-14 23:11 Pacho Ramos
2021-01-06 15:10 Fabian Groffen
2020-11-28 19:36 Alexey Shvetsov
2020-11-27 13:39 Alexey Shvetsov
2020-11-27 13:31 Alexey Shvetsov
2020-10-14 10:43 Alexey Shvetsov
2020-09-07  8:55 David Seifert
2020-08-01 23:20 Andreas Sturmlechner
2020-06-03 21:22 Alexey Shvetsov
2020-03-04 18:02 Alexey Shvetsov
2020-02-07 18:41 Pacho Ramos
2020-01-28 18:24 Michał Górny
2020-01-22 21:50 Michał Górny
2020-01-16  6:39 Michał Górny
2020-01-16  6:39 Michał Górny
2019-09-27 17:33 Michał Górny
2019-06-01  8:40 Alexey Shvetsov
2019-02-26 14:15 Alexey Shvetsov
2018-11-13 10:13 Alexey Shvetsov
2018-11-08 10:05 Alexey Shvetsov
2018-03-29 11:43 Alexey Shvetsov
2017-09-12 22:58 Matt Turner
2017-03-27 14:09 Alexey Shvetsov
2017-02-25 20:56 Justin Lecher
2017-02-14 15:39 Agostino Sarubbo
2017-02-13 11:13 Agostino Sarubbo
2017-02-12 19:51 Justin Lecher
2016-10-23 20:25 Justin Lecher
2016-09-24 15:56 Alexey Shvetsov
2015-11-12 16:20 Justin Lecher
2015-11-11 15:01 Agostino Sarubbo
2015-11-11 15:00 Agostino Sarubbo
2015-11-11 11:35 Justin Lecher
2015-11-11 10:39 Agostino Sarubbo
2015-09-24 10:57 Agostino Sarubbo
2015-08-27 15:01 Justin Lecher

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