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* sci-chemistry/votca: initial importChristoph Junghans2021-12-164-0/+159
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Christoph Junghans <junghans@gentoo.org>
* sci-chemistry/gnome-chemistry-utils: Drop oldPacho Ramos2021-12-161-74/+0
| | | | | Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gnome-chemistry-utils: Fix compat with openbabelPacho Ramos2021-12-161-0/+76
| | | | | | | Bump eapi too Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/openbabel: bump EAPI=8, add python310Andrew Ammerlaan2021-12-152-4/+4
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/openbabel: Bump openbabel-3.1.1_p20210225Peter Levine2021-12-152-0/+273
| | | | | | | | | | | | | | Closes: https://bugs.gentoo.org/664124 Closes: https://bugs.gentoo.org/716208 Closes: https://bugs.gentoo.org/722860 Closes: https://bugs.gentoo.org/723434 Closes: https://bugs.gentoo.org/766003 Closes: https://bugs.gentoo.org/770493 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Peter Levine <plevine457@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/16182 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/openbabel: Add openbabel-9999Peter Levine2021-12-154-0/+381
| | | | | | | | | Add an up-to-date live ebuild with a templated versioning scheme, and match the bindings to USE flags. Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Peter Levine <plevine457@gmail.com> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-chemistry/probe: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-1/+1
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-chemistry/mopac7: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-1/+1
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-chemistry/molscript: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-1/+1
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-chemistry/molmol: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-2/+2
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-chemistry/moldy: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-2/+2
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-chemistry/tm-align: de-stabilize for ~ppc, bug #823768Georgy Yakovlev2021-11-181-2/+2
| | | | | Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org>
* sci-chemistry/dssp: Stabilize 3.0.11 amd64, #823826Jakov Smolić2021-11-161-1/+1
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/dssp: x86 stable wrt bug #823826Agostino Sarubbo2021-11-161-1/+1
| | | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-chemistry/dssp: don't run useless (for downstream) cppcheck testSam James2021-11-161-1/+2
| | | | | | | | It's not useful for us to determine if the package is working correctly so skip it. Closes: https://bugs.gentoo.org/823894 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/chemex: Update tests handlingPacho Ramos2021-11-121-1/+1
| | | | | | | Closes: https://bugs.gentoo.org/815079 Thanks-to: Agostino Sarubbo Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: Drop oldPacho Ramos2021-11-113-91/+0
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: Version bumpPacho Ramos2021-11-112-0/+47
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/vmd: Bump to alpha55Pacho Ramos2021-11-112-0/+270
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: version bump to 2021.4Alexey Shvetsov2021-11-092-0/+359
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: fix v2019 build on newer glibcChristoph Junghans2021-11-072-0/+293
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Christoph Junghans <junghans@gentoo.org>
* sci-chemistry/openbabel: Drop 2.4.1-r1Andreas Sturmlechner2021-11-073-130/+0
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-chemistry/dssp: Drop oldPacho Ramos2021-11-063-79/+0
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/dssp: gromacs-2022 will support dssp-4Pacho Ramos2021-11-061-1/+1
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: needs mpi[cxx]Sam James2021-11-043-3/+3
| | | | | Closes: https://bugs.gentoo.org/821712 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: Fix depsAlexey Shvetsov2021-11-043-3/+3
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Unbundle muParserAlexey Shvetsov2021-11-043-30/+27
| | | | | | Closes: https://bugs.gentoo.org/820620 Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: Add 2022_beta1Alexey Shvetsov2021-10-284-11/+708
| | | | | Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: revbump for subslot operator changesSam James2021-10-268-12/+12
| | | | | | | | | | Needed to have the changes apply. Also propagate the changes to the other ebuilds for consistency. Added to FFTW as well while at it. See: 7ad99109ba539795b0ca4ee887734b4930937679 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: Needs to be rebuilt with lmfit soname changesPacho Ramos2021-10-265-7/+7
| | | | | | | Also fix hwloc dep for old gromacs Package-Manager: Portage-3.0.28, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/pymol: drop 2.4.0-r1David Seifert2021-10-243-151/+0
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-chemistry/cluster: Port to EAPI 8Jakov Smolić2021-10-211-9/+10
| | | | Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* sci-chemistry/chemex: Drop oldPacho Ramos2021-10-192-41/+0
| | | | | Package-Manager: Portage-3.0.24, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: Version bumpPacho Ramos2021-10-192-0/+47
| | | | | Package-Manager: Portage-3.0.24, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/gromacs: fix confusing indentationSam James2021-10-143-18/+18
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: fix configure with -custom-cflagsSam James2021-10-143-3/+6
| | | | | | | | Need to default to AUTO and let it be overridden as appropriate later. Bug: https://bugs.gentoo.org/818055 Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/dssp: Keyword 4.0.1_p20210831 x86, #811417Sam James2021-10-101-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: Stabilize 2021.3 arm, #814101Sam James2021-10-071-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/gromacs: Stabilize 2021.3 amd64, #814101Sam James2021-10-071-1/+1
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-chemistry/dssp: x86 stable wrt bug #816123Agostino Sarubbo2021-10-051-1/+1
| | | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-chemistry/dssp: amd64 stable wrt bug #816123Agostino Sarubbo2021-10-041-1/+1
| | | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-chemistry/dssp: Bump to 4.0.3Pacho Ramos2021-10-032-0/+32
| | | | | Package-Manager: Portage-3.0.24, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/chemex: Version bumpPacho Ramos2021-09-262-0/+44
| | | | | | | Closes: https://bugs.gentoo.org/809764 Closes: https://bugs.gentoo.org/809761 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
* sci-chemistry/votca-xtp: version bumpChristoph Junghans2021-09-192-0/+52
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Christoph Junghans <junghans@gentoo.org>
* sci-chemistry/votca-csg: version bumpChristoph Junghans2021-09-192-0/+89
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Christoph Junghans <junghans@gentoo.org>
* sci-chemistry/gromacs: Check patchesAlexey Shvetsov2021-09-151-6/+1
| | | | | Package-Manager: Portage-3.0.23, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/gromacs: version bumpAlexey Shvetsov2021-09-152-0/+363
| | | | | Package-Manager: Portage-3.0.23, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
* sci-chemistry/mdtraj: Fix DISTUTILS_USE_SETUPTOOLSJakov Smolić2021-09-131-2/+1
| | | | | Closes: https://bugs.gentoo.org/809767 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
* **/metadata.xml: Replace http by https in DOCTYPE elementUlrich Müller2021-09-1165-65/+65
| | | | | Bug: https://bugs.gentoo.org/552720 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-chemistry/dssp: Bump to 3.0.11Pacho Ramos2021-09-022-0/+43
| | | | | | | | | | It is the latest version that seems to work with gmx do_dssp from my tests, also the one packaged in Fedora currently Closes: https://bugs.gentoo.org/802417 Closes: https://bugs.gentoo.org/808669 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org>