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path: root/sci-chemistry/pymol
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* sci-chemistry/pymol: Multiple bugfixesPacho Ramos2024-09-287-0/+485
| | | | | | | | | | | | | | | | | 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>
* sci-chemistry/pymol: mark as LTO-unsafeEli Schwartz2024-09-051-0/+5
| | | | | Closes: https://bugs.gentoo.org/933235 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-chemistry/pymol: drop a bunch of dependencies to runtime-onlyEli Schwartz2024-09-051-6/+7
| | | | | | | | | | | | 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>
* sci-chemistry/pymol: Update to 3.0.0 and drop oldAlexey Shvetsov2024-05-173-105/+6
| | | | | | | 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>
* sci-chemistry/pymol: OFL license has been renamed to OFL-1.0Ulrich Müller2024-05-132-4/+4
| | | | | Bug: https://bugs.gentoo.org/931823 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-chemistry/pymol: Fix install on prefixPacho Ramos2023-07-201-1/+1
| | | | | | Thanks-to: hsk17 Bug: https://bugs.gentoo.org/910021 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Use PEP517 buildPacho Ramos2023-07-202-0/+123
| | | | | Closes: https://bugs.gentoo.org/910021 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: drop 2.5.0-r2Pacho Ramos2023-07-191-98/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Fix distutils-r1 usagePacho Ramos2023-07-191-7/+9
| | | | | | Thanks-to: Sam James Closes: https://bugs.gentoo.org/851588 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Drop dev-libs/msgpack[cxx(-)] to workaround portage bugPacho Ramos2023-06-241-0/+98
| | | | | Bug: https://bugs.gentoo.org/872227 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: enable py3.11Pacho Ramos2023-05-021-1/+1
| | | | | Closes: https://bugs.gentoo.org/897202 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: support msgpack-5Marek Szuba2023-02-072-100/+1
| | | | | | | 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>
* sci-chemistry/pymol: account for dev-libs/msgpack without IUSE=cxxMarek Szuba2023-02-052-2/+2
| | | | | | | | 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>
* */*: remove py3.8 from PYTHON_COMPATDavid Seifert2023-01-142-4/+4
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/pymol: add github upstream metadataSam James2022-07-311-10/+11
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/pymol: Fix desktop file, LICENSE and restrict valuesPacho Ramos2022-05-221-0/+98
| | | | | | | | Also port to eapi8 Thanks-to: Ulrich Müller Closes: https://bugs.gentoo.org/844991 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: enable py3.10Alexey Shvetsov2022-04-081-17/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: drop 2.4.0-r1David Seifert2021-10-243-151/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* **/metadata.xml: Replace http by https in DOCTYPE elementUlrich Müller2021-09-111-1/+1
| | | | | Bug: https://bugs.gentoo.org/552720 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-chemistry/pymol: apbs_tools.py is not createdPacho Ramos2021-05-201-10/+12
| | | | | | | | 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>
* sci-chemistry/pymol: Version bumpAlexey Shvetsov2021-05-162-0/+112
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: Re-host distfilesPacho Ramos2021-05-021-1/+1
| | | | | Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* */*: Remove obsolete values from PYTHON_COMPATMichał Górny2021-01-311-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/pymol: Remove oldJakov Smolic2021-01-181-115/+0
| | | | | Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr> Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/pymol: Ensure proper prepare phase is runPacho Ramos2021-01-151-2/+1
| | | | | | | | | 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>
* sci-chemistry/pymol: Fix netcdf handlingPacho Ramos2021-01-132-0/+151
| | | | | | | | | | 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>
* sci-chemistry/pymol: drop x86-macosFabian Groffen2021-01-061-2/+2
| | | | | Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Fabian Groffen <grobian@gentoo.org>
* sci-chemistry/pymol: Fix distutils warningAlexey Shvetsov2020-11-281-0/+1
| | | | | Package-Manager: Portage-3.0.10, Repoman-3.0.2 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: Version bumpAlexey Shvetsov2020-11-272-1/+1
| | | | | | Closes: https://bugs.gentoo.org/701868 Package-Manager: Portage-3.0.10, Repoman-3.0.2 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: add pmw as depAlexey Shvetsov2020-11-271-0/+1
| | | | | | Closes: https://bugs.gentoo.org/725480 Package-Manager: Portage-3.0.10, Repoman-3.0.2 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: Added py39Alexey Shvetsov2020-10-141-1/+1
| | | | | Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: Inherit optfeature.eclassDavid Seifert2020-09-071-2/+2
| | | | | Package-Manager: Portage-3.0.5, Repoman-3.0.1 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/pymol: Drop 2.3.0-r2Andreas Sturmlechner2020-08-021-118/+0
| | | | | Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-chemistry/pymol: Works with py38Alexey Shvetsov2020-06-041-1/+1
| | | | | Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: pymol works with py3Alexey Shvetsov2020-03-042-1/+113
| | | | | Package-Manager: Portage-2.3.88, Repoman-2.3.20 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: chemical-mime-data needed for .desktop Mime defsPacho Ramos2020-02-071-1/+3
| | | | | | Closes: https://bugs.gentoo.org/703000 Package-Manager: Portage-2.3.87, Repoman-2.3.20 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: Remove old (drop to ~arch)Michał Górny2020-01-282-112/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/pymol: Revbump post dep changeMichał Górny2020-01-222-0/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/pymol: Use HTTPSMichał Górny2020-01-162-4/+4
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/pymol: Permit numpy-python2Michał Górny2020-01-162-2/+8
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/pymol: Dep on dev-python/pmw directlyMichał Górny2019-09-272-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/pymol: Change depsAlexey Shvetsov2019-06-013-119/+3
| | | | | | | 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>
* sci-chemistry/pymol: Version bumpAlexey Shvetsov2019-02-262-0/+116
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: Fix missing depAlexey Shvetsov2018-11-131-0/+1
| | | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11
* sci-chemistry/pymol: Version bumpAlexey Shvetsov2018-11-083-116/+6
| | | | | Package-Manager: Portage-2.3.51, Repoman-2.3.12 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/pymol: Version bumpAlexey Shvetsov2018-03-292-0/+114
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-chemistry/*: Update Manifest hashesMichał Górny2017-12-101-3/+3
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* sci-chemistry/pymol: dropped ppc keywordsMatt Turner2017-09-121-1/+1
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* sci-chemistry/pymol: Version bumpAlexey Shvetsov2017-03-272-0/+110
| | | | | | Warning: Pymol now depends on dev-libs/msgpack Package-Manager: Portage-2.3.3, Repoman-2.3.1
* Drop $Id$ per council decision in bug #611234.Robin H. Johnson2017-02-281-1/+0
| | | | Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>