sci-chemistry / pymol

A Python-extensible molecular graphics system

Official package sites : https://www.pymol.org/ ·

v2.5.0-r4 :: 0 :: gentoo

Modified
License
BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA
Keywords
~amd64 ~amd64-linux ~x64-macos ~x86 ~x86-linux
USE flags
debug netcdf web

v2.5.0-r3 :: 0 :: gentoo

Modified
License
BitstreamVera BSD freedist HPND OFL public-domain UoI-NCSA
Keywords
~amd64 ~amd64-linux ~x64-macos ~x86 ~x86-linux
USE flags
debug netcdf web

General

debug
Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces
netcdf
Enable NetCDF data format support
web
Install Pymodule needed for web app support

python_targets

python3_10
Build with Python 3.10
python3_11
Build with Python 3.11

dev-cpp / msgpack-cxx : MessagePack for C++

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-libs / mmtf-cpp : The pure C++ implementation of the MMTF API, decoder and encoder

dev-python / PyQt5 : Python bindings for the Qt framework

dev-python / numpy : Fast array and numerical python library

dev-python / pmw : Toolkit for building high-level compound Python widgets using the Tkinter module

dev-python / pyopengl : Python OpenGL bindings

media-libs / freetype : High-quality and portable font engine

media-libs / glew : The OpenGL Extension Wrangler Library

media-libs / glm : OpenGL Mathematics

media-libs / libpng : Portable Network Graphics library

media-video / mpeg-tools : Tools for MPEG video

sci-libs / netcdf : Scientific library and interface for array oriented data access

sys-libs / zlib : Standard (de)compression library

dev-cpp / msgpack-cxx : MessagePack for C++

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-libs / mmtf-cpp : The pure C++ implementation of the MMTF API, decoder and encoder

dev-python / PyQt5 : Python bindings for the Qt framework

dev-python / numpy : Fast array and numerical python library

dev-python / pmw : Toolkit for building high-level compound Python widgets using the Tkinter module

dev-python / pyopengl : Python OpenGL bindings

media-libs / freetype : High-quality and portable font engine

media-libs / glew : The OpenGL Extension Wrangler Library

media-libs / glm : OpenGL Mathematics

media-libs / libpng : Portable Network Graphics library

media-video / mpeg-tools : Tools for MPEG video

sci-chemistry / chemical-mime-data : A collection of data files to add support for chemical MIME types

sci-libs / netcdf : Scientific library and interface for array oriented data access

sys-libs / zlib : Standard (de)compression library

862441
sci-chemistry/pymol-2.5.0-r1 fails to compile (lto): ReadPARM7.h:62:16: error: type struct parm violates the C++ One Definition Rule [-Werror=odr]
910511
sci-chemistry/pymol-2.5.0-r3 segfaults when loading a PDB
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Pacho Ramos · gentoo
sci-chemistry/pymol: Fix install on prefix
Thanks-to: hsk17 Bug: https://bugs.gentoo.org/910021 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Pacho Ramos · gentoo
sci-chemistry/pymol: Use PEP517 build
Closes: https://bugs.gentoo.org/910021 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Pacho Ramos · gentoo
sci-chemistry/pymol: drop 2.5.0-r2
Signed-off-by: Pacho Ramos <pacho@gentoo.org>
Pacho Ramos · gentoo
sci-chemistry/pymol: Fix distutils-r1 usage
Thanks-to: Sam James Closes: https://bugs.gentoo.org/851588 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Pacho Ramos · gentoo
sci-chemistry/pymol: Drop dev-libs/msgpack[cxx(-)] to workaround portage bug
Bug: https://bugs.gentoo.org/872227 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Pacho Ramos · gentoo
sci-chemistry/pymol: enable py3.11
Closes: https://bugs.gentoo.org/897202 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Marek Szuba · gentoo
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@gentoo.org>
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Marek Szuba · gentoo
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@gentoo.org>
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David Seifert · gentoo
*/*: remove py3.8 from PYTHON_COMPAT
Signed-off-by: David Seifert <soap@gentoo.org>
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Pacho Ramos · gentoo
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@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: enable py3.10
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
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David Seifert · gentoo
sci-chemistry/pymol: drop 2.4.0-r1
Signed-off-by: David Seifert <soap@gentoo.org>
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Pacho Ramos · gentoo
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@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: Version bump
Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
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Pacho Ramos · gentoo
sci-chemistry/pymol: Re-host distfiles
Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Michał Górny · gentoo
*/*: Remove obsolete values from PYTHON_COMPAT
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Jakov Smolic · gentoo
sci-chemistry/pymol: Remove old
Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
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Pacho Ramos · gentoo
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@gentoo.org>
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Pacho Ramos · gentoo
sci-chemistry/pymol: Fix netcdf handling
Also fix upstream bug and use xdg.eclass to not need to redefine every pkg_ phase Closes: https://bugs.gentoo.org/757798 Thanks-to: Soren Harward Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Fabian Groffen · gentoo
sci-chemistry/pymol: drop x86-macos
Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Fabian Groffen <grobian@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: Fix distutils warning
Package-Manager: Portage-3.0.10, Repoman-3.0.2 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
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Alexey Shvetsov · gentoo
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@gentoo.org>
Alexey Shvetsov · gentoo
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@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: Added py39
Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
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David Seifert · gentoo
sci-chemistry/pymol: Inherit optfeature.eclass
Package-Manager: Portage-3.0.5, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
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Andreas Sturmlechner · gentoo
sci-chemistry/pymol: Drop 2.3.0-r2
Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: Works with py38
Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: pymol works with py3
Package-Manager: Portage-2.3.88, Repoman-2.3.20 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
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Pacho Ramos · gentoo
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@gentoo.org>
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Michał Górny · gentoo
sci-chemistry/pymol: Remove old (drop to ~arch)
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Michał Górny · gentoo
sci-chemistry/pymol: Revbump post dep change
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Michał Górny · gentoo
sci-chemistry/pymol: Use HTTPS
Signed-off-by: Michał Górny <mgorny@gentoo.org>
Michał Górny · gentoo
sci-chemistry/pymol: Permit numpy-python2
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Michał Górny · gentoo
sci-chemistry/pymol: Dep on dev-python/pmw directly
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Alexey Shvetsov · gentoo
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@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: Version bump
Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: Fix missing dep
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11
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Alexey Shvetsov · gentoo
sci-chemistry/pymol: Version bump
Package-Manager: Portage-2.3.51, Repoman-2.3.12 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
Alexey Shvetsov · gentoo
sci-chemistry/pymol: Version bump
Package-Manager: Portage-2.3.24, Repoman-2.3.6
Matt Turner · gentoo
sci-chemistry/pymol: dropped ppc keywords
Alexey Shvetsov · gentoo
sci-chemistry/pymol: Version bump
Warning: Pymol now depends on dev-libs/msgpack Package-Manager: Portage-2.3.3, Repoman-2.3.1
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Justin Lecher · gentoo
sci-chemistry/pymol: Drop old
Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Agostino Sarubbo · gentoo
sci-chemistry/pymol: ppc stable wrt bug #609166
Package-Manager: portage-2.3.3 RepoMan-Options: --include-arches="ppc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
Agostino Sarubbo · gentoo
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@gentoo.org>
Agostino Sarubbo · gentoo
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@gentoo.org>
Justin Lecher · gentoo
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@gentoo.org>
T. Malfatti · gentoo
media-libs/portaudio: Version bump
Justin Lecher · gentoo
sci-chemistry/pymol: Version Bump
Package-Manager: portage-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Alexey Shvetsov · gentoo
sci-chemistry/pymol: Version bump
Package-Manager: portage-2.3.0
Justin Lecher · gentoo
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@gentoo.org>
Agostino Sarubbo · gentoo
sci-chemistry/pymol: x86 stable wrt bug #565494
Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="x86"
Agostino Sarubbo · gentoo
sci-chemistry/pymol: amd64 stable wrt bug #565494
Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="amd64"
Justin Lecher · gentoo
sci-chemistry/pymol: Version Bump
Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Justin Lecher · gentoo
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@gentoo.org>
Agostino Sarubbo · gentoo
sci-chemistry/pymol: x86 stable wrt bug #543020
Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="x86"
Justin Lecher · gentoo
Sanitize virtual namespace of python packages
Rename virtual/MODULE to virtual/python-MODULE Signed-off-by: Justin Lecher <jlec@gentoo.org>
Agostino Sarubbo · gentoo
sci-chemistry/pymol: amd64 stable wrt bug #543020
Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="amd64"
Justin Lecher · gentoo
sci-chemistry/pymol: React on subslot changes
Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Justin Lecher · gentoo
Use https by default
Convert all URLs for sites supporting encrypted connections from http to https Signed-off-by: Justin Lecher <jlec@gentoo.org>
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed