Versions
v3.0.0-r1 :: 0 :: gentoo
- Modified
- License
- BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA
- Keywords
- ~amd64 ~amd64-linux ~x64-macos ~x86 ~x86-linux
- USE flags
- debug netcdf test web
USE flags
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
- test
- Enable dependencies and/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)
- web
- Install Pymodule needed for web app support
python_targets
- python3_11
- Build with Python 3.11
- python3_12
- Build with Python 3.12
- python3_13
- Build with Python 3.13
Dependencies
dev-cpp / msgpack-cxx : MessagePack for C++
dev-lang / python : Freethreading (no-GIL) version of Python programming language
dev-libs / mmtf-cpp : The pure C++ implementation of the MMTF API, decoder and encoder
dev-python / numpy : Fast array and numerical python library
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
sci-libs / netcdf : Scientific library and interface for array oriented data access
Runtime Dependencies
dev-cpp / msgpack-cxx : MessagePack for C++
dev-lang / python : Freethreading (no-GIL) version of Python programming language
dev-libs / mmtf-cpp : The pure C++ implementation of the MMTF API, decoder and encoder
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
dev-python / pyqt5 : Python bindings for the Qt framework
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
Bugs
Change logs
- Repository mirror & CI · gentoo
Merge updates from master - Alexey Shvetsov · gentoo
sci-chemistry/pymol: enable py3.13 and disable py3.10
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/pymol: drop 3.0.0
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
Rename dev-python/{PyQt5 → pyqt5}
Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Pacho Ramos · gentoo
sci-chemistry/pymol: Multiple bugfixes
Upstream fixes for multiple bugs, also fixing python 3.12 and numpy2 compat, and fixing LTO building. Format-security patch looks to not be needed anymore (at least I couldn't reproduce the problem). If the problem reappears, please report the bug to upstream to follow its progress properly. Use icon from the pymol tarball and update desktop file. Update ebuild to try to run the tests, but keep them restricted for now as they keep failing. Bug: https://bugs.gentoo.org/932127 Signed-off-by: Pacho Ramos <pacho@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Eli Schwartz · gentoo
sci-chemistry/pymol: mark as LTO-unsafe
Closes: https://bugs.gentoo.org/933235 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org> - Eli Schwartz · gentoo
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@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Alexey Shvetsov · gentoo
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@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Ulrich Müller · gentoo
sci-chemistry/pymol: OFL license has been renamed to OFL-1.0
Bug: https://bugs.gentoo.org/931823 Signed-off-by: Ulrich Müller <ulm@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - Pacho Ramos · gentoo
sci-chemistry/pymol: Use PEP517 build
Closes: https://bugs.gentoo.org/910021 Signed-off-by: Pacho Ramos <pacho@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - Pacho Ramos · gentoo
sci-chemistry/pymol: enable py3.11
Closes: https://bugs.gentoo.org/897202 Signed-off-by: Pacho Ramos <pacho@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
*/*: remove py3.8 from PYTHON_COMPAT
Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - Alexey Shvetsov · gentoo
sci-chemistry/pymol: enable py3.10
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
sci-chemistry/pymol: drop 2.4.0-r1
Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
*/*: Remove obsolete values from PYTHON_COMPAT
Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
sci-chemistry/pymol: Remove old (drop to ~arch)
Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
sci-chemistry/pymol: Revbump post dep change
Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
sci-chemistry/pymol: Dep on dev-python/pmw directly
Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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> - Repository mirror & CI · gentoo
Merge updates from master - 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 - Repository mirror & CI · gentoo
Merge updates from master - 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