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* sci-chemistry/mopac7: mark as LTO-unsafeEli Schwartz2024-09-091-1/+7
| | | | | | | Unmaintained, treecleaning candidate. Still, it is unsafe so say so. Closes: https://bugs.gentoo.org/927389 Signed-off-by: Eli Schwartz <eschwartz@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/tinker: mark as LTO-unsafeEli Schwartz2024-08-051-1/+6
| | | | | | | | At least, the tests fail if you use LTO. So it is apparently unsafe, though unsafe here means the results you get are wrong! Closes: https://bugs.gentoo.org/878059 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
* sci-chemistry/votca: sync live ebuildPacho Ramos2024-07-311-3/+3
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/votca: support py3.12Pacho Ramos2024-07-311-2/+2
| | | | | Closes: https://bugs.gentoo.org/929764 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/openbabel: sync live ebuildPacho Ramos2024-07-301-4/+8
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/openbabel: enable py3.12Pacho Ramos2024-07-301-1/+1
| | | | | Closes: https://bugs.gentoo.org/929759 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/propka: add 3.5.1Pacho Ramos2024-07-302-0/+29
| | | | | Closes: https://bugs.gentoo.org/929761 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/procheck: treecleanArthur Zamarin2024-07-195-182/+0
| | | | | Bug: https://bugs.gentoo.org/928067 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/aqua: treecleanArthur Zamarin2024-07-194-191/+0
| | | | | Bug: https://bugs.gentoo.org/928068 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/xyza2pipe: treecleanArthur Zamarin2024-07-194-211/+0
| | | | | Bug: https://bugs.gentoo.org/934232 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/namd: treecleanArthur Zamarin2024-07-195-271/+0
| | | | | | | | Bug: https://bugs.gentoo.org/686856 Bug: https://bugs.gentoo.org/686858 Bug: https://bugs.gentoo.org/686860 Bug: https://bugs.gentoo.org/934228 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/autodock_vina: Stabilize 1.2.5 amd64, #935909Arthur Zamarin2024-07-131-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/autodock_vina: fix build w/ boost-1.85Sam James2024-07-122-0/+22
| | | | | Closes: https://bugs.gentoo.org/932237 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/vmd: Fix compat with numpy-2 and don't mess with linkingPacho Ramos2024-07-111-0/+263
| | | | | | | | | | | Ebuild forcing linking flags break some utils, point to new location for numpy2 include files Closes: https://bugs.gentoo.org/929763 Thanks-to: he.ousia Closes: https://bugs.gentoo.org/835604 Thanks-to: Hypoon Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/molmol: Stabilize 2k_p2-r9 amd64, #935856Jakov Smolić2024-07-111-1/+1
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/wxmacmolplt: drop 7.5-r1Pacho Ramos2024-07-053-60/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/xds-bin: drop 20170930Arthur Zamarin2024-07-052-49/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/xds-bin: add 20240831Markus Meier2024-07-052-1/+59
| | | | | | Bug: https://bugs.gentoo.org/934365 Authored-by: Markus Meier <markus.meier74@gmail.com> Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/openbabel: drop 3.1.1_p20210225Andreas Sturmlechner2024-06-291-280/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* */*: delete some utterly bogus remote-idsEli Schwartz2024-06-281-3/+0
| | | | | | | | | | | | Added in a global rewrite that was apparently not tested as well as it ideally could have been, since it added some pretty wild changes. Non-exhaustive -- I caught these in passing and haven't really vetted the tree. Fixes: 67064ef687e8b3a61f5a4698ae1b029e2e70822c Fixes: 92715265f5e37292e57673f39c5372a268778c44 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/chemex: fix mysterious overdependency on tomliEli Schwartz2024-06-272-2/+0
| | | | | | | | | | | | | | | | | In upstream version 2024.02.09 some "refactoring" was done: https://github.com/gbouvignies/ChemEx/commit/97d6896836e4d5c23e0eff7b1dc1646e3f69ac9e It dropped support for python 3.10 and required the stdlib tomllib rather than trying tomli. And sure enough, when 2024.02.16 was added to ::gentoo, it excluded 3.10 support for this exact reason. But it didn't state why, and it didn't remove the out of date tomli dependency. Remove it now. Bug: https://bugs.gentoo.org/929756 Fixes: c5f2c621136bfc67183c410a60713763fd0f7bdf Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: Add ~riscv keywordAlexey Shvetsov2024-06-234-4/+4
| | | | | | Tested on visionfive2 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/threeV: EAPI 6 -> 8Arthur Zamarin2024-06-211-12/+5
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/chemex: drop 2022.3.6, 2024.02.16Pacho Ramos2024-06-163-90/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: add 2024.05.3Pacho Ramos2024-06-162-0/+46
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/elem: unkeyword 1.0.3-r3 for sparcArthur Zamarin2024-06-131-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/elem: EAPI 6 -> 8Arthur Zamarin2024-06-131-2/+2
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
* sci-chemistry/vmd: enable py3.12Alexey Shvetsov2024-06-051-6/+4
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/MDAnalysis: enable py3.12Alexey Shvetsov2024-06-051-3/+3
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/molequeue: enable py3.12Andreas K. Hüttel2024-06-041-1/+1
| | | | Signed-off-by: Andreas K. Hüttel <dilfridge@gentoo.org>
* sci-chemistry/dssp: Add missing dependencyPacho Ramos2024-06-011-1/+3
| | | | | Closes: https://bugs.gentoo.org/932159 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: add 2024.05.2Pacho Ramos2024-06-012-0/+46
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/molmol: Fix pkgcheck warningsPacho Ramos2024-05-181-4/+1
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/molmol: Fix passing incompatible pointer typeBrahmajit Das2024-05-182-0/+118
| | | | | | | Closes: https://bugs.gentoo.org/923325 Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/36093 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: Fix EmptyGlobalAssignment warningPacho Ramos2024-05-181-1/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: drop 4.3.1, 4.4.1Pacho Ramos2024-05-183-95/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: add 4.4.7Pacho Ramos2024-05-182-0/+55
| | | | | Closes: https://bugs.gentoo.org/924695 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: Fix VariableOrderWrong warningPacho Ramos2024-05-181-1/+1
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: drop 2022.3.5Pacho Ramos2024-05-182-43/+0
| | | | Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: add 2024.02.16Pacho Ramos2024-05-182-0/+46
| | | | | Closes: https://bugs.gentoo.org/929756 Signed-off-by: Pacho Ramos <pacho@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/gromacs: add 2024.2Alexey Shvetsov2024-05-172-0/+338
| | | | Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/modeller: add 10.5, drop 9.25Alexey Shvetsov2024-05-173-9/+37
| | | | 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>
* */*: inline mirror://sourceforgeLucio Sauer2024-04-307-13/+13
| | | | | | | bump copyright of touched ebuilds to 2024 Signed-off-by: Lucio Sauer <watermanpaint@posteo.net> Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/votca: add subslot dep on sci-libs/hdf5Sam James2024-04-232-4/+4
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/mdtraj: Remove last-rited pkgMichał Górny2024-04-134-78/+0
| | | | | Bug: https://bugs.gentoo.org/911646 Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-chemistry/openbabel: Stabilize 3.1.1_p20210225-r1 amd64, #929186Arthur Zamarin2024-04-111-1/+1
| | | | Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>