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* sci-libs/geos: Drop no-op USE=pythonAndreas Sturmlechner2020-01-301-2/+2
| | | | | | | Reported-by: Jouni Kosonen <jouni.kosonen@tukesoft.com> Bug: https://bugs.gentoo.org/707516 Package-Manager: Portage-2.3.86, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/proj: Drop 6.0.0 and 6.2.0Andreas Sturmlechner2020-01-303-95/+0
| | | | | Package-Manager: Portage-2.3.86, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/proj: bump to 6.3.0Andrey Grozin2020-01-302-0/+49
| | | | | | Closes: https://bugs.gentoo.org/show_bug.cgi?id=706306 Package-Manager: Portage-2.3.85, Repoman-2.3.20 Signed-off-by: Andrey Grozin <grozin@gentoo.org>
* sci-libs/Shapely: x86 stable wrt bug #704214Agostino Sarubbo2020-01-301-1/+1
| | | | | | Package-Manager: Portage-2.3.84, Repoman-2.3.20 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-libs/gdal: ppc stable wrt bug #707320Agostino Sarubbo2020-01-301-2/+2
| | | | | | Package-Manager: Portage-2.3.84, Repoman-2.3.20 RepoMan-Options: --include-arches="ppc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-libs/gdal: Drop 2.4.1-r2Andreas Sturmlechner2020-01-291-322/+0
| | | | | Package-Manager: Portage-2.3.86, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/gdal: local HTML_DOCS, some slot opsAndreas Sturmlechner2020-01-291-5/+5
| | | | | Package-Manager: Portage-2.3.86, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/gdal: version bump 3.0.2Chris Mayo2020-01-294-0/+459
| | | | | | | | Bug: https://bugs.gentoo.org/686732 Package-Manager: Portage-2.3.79, Repoman-2.3.16 Signed-off-by: Chris Mayo <aklhfex@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/14061 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/Rtree: Remove py2Michał Górny2020-01-281-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/Rtree: Remove old (py2)Michał Górny2020-01-282-21/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scipy-python2: Split from scipyMichał Górny2020-01-283-0/+152
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scikits_learn: fix MissingTestRestrict CI issueJoonas Niilola2020-01-282-0/+4
| | | | Signed-off-by: Joonas Niilola <juippis@gentoo.org>
* sci-libs/scipy: Revert "fixing numpy deps"Michał Górny2020-01-271-2/+1
| | | | | | Change done in explicit violation of maintainer's request. Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scipy: fixing numpy depsRick Farina2020-01-271-1/+2
| | | | | Package-Manager: Portage-2.3.85, Repoman-2.3.20 Signed-off-by: Rick Farina <zerochaos@gentoo.org>
* sci-libs/proj: stable 6.2.1 for ppc64, bug #706442Sergei Trofimovich2020-01-271-2/+2
| | | | | | Package-Manager: Portage-2.3.85, Repoman-2.3.20 RepoMan-Options: --include-arches="ppc64" Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-libs/scipy: disable parallel build completely.Benda Xu2020-01-271-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | After 4 years discussion and debugging, we conclude that Python 3 is deeply broken in parallel builds for anything involving compiling of C/C++/fortran code. The problem is universal, regardless how dev-python/numpy is built. Numpy and scipy upstream cannot do anything about this. We bite the bullet and disable parallel build of scipy completely. Thanks to all who have contributed to this heroic marathon debugging. We regret that only a workaround can be provided at this moment. Credit: Andrés Becerra Sandoval, Hendrik v. Raven, younky.yang@yahoo.com Credit: matoro, Denis Descheneaux, Mathy Vanvoorden, email200202@yahoo.com Credit: jon R-B, Anton Kochkov, Jonas Stein, edes, David Duchesne Credit: thulle, Mathy Vanvoorden, Sasha Medvedev, rtgiskard@gmail.com Credit: Lukasz Ligowski, Zentoo, Jouni Kosonen, Neil, Harris Landgarten Credit: Markus Oehme, Andreas Proteus Suggested-By: François Bissey, Arfrever Frehtes Taifersar Arahesis Reference: https://github.com/numpy/numpy/issues/13080 Reference: https://github.com/scipy/scipy/issues/7112 Closes: https://bugs.gentoo.org/614464 Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* sci-libs/mpfi: Remove old 1.5.1David Seifert2020-01-262-22/+0
| | | | | Package-Manager: Portage-2.3.85, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-libs/libgeodecomp: Fix VisIt removalKurt Kanzenbach2020-01-262-4/+1
| | | | | | | | | | | Commit 06a2e799559c ("sci-libs/libgeodecomp: Fix file collision with libflatarray") started the removal of the VisIt use flag. However, it's not complete. Remove the last references to it. Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Kurt Kanzenbach <kurt@kmk-computers.de> Closes: https://github.com/gentoo/gentoo/pull/14455 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/tensorflow: bump 2.1.0Jason Zaman2020-01-264-47/+7
| | | | | | | | Closes: https://bugs.gentoo.org/701334 Closes: https://bugs.gentoo.org/704490 Closes: https://bugs.gentoo.org/701342 Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Jason Zaman <perfinion@gentoo.org>
* */*: Drop stable alpha keywordsMatt Turner2020-01-2524-24/+24
| | | | Signed-off-by: Matt Turner <mattst88@gentoo.org>
* sci-libs/getdata: Revbump post dep changeMichał Górny2020-01-221-0/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/mathgl: Revbump post dep changeMichał Górny2020-01-221-0/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/nlopt: Revbump post dep changeMichał Górny2020-01-221-0/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/pymmlib: Revbump post dep changeMichał Górny2020-01-221-0/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/libgeodecomp: Fix file collision with libflatarrayKurt Kanzenbach2020-01-212-16/+58
| | | | | | | | | | | | | | | | | | | As of commit 948ee21633c0 ("sci-libs/libgeodecomp: added dependency to libflatarray") libgeodecomp depends on libflatarray which is correct. Therefore, libgeodecomp uses the system installed libflatarray. However, it also bundles its own version libflatarray and installs that one unconditionally which results in the file collision. Thus, simply don't install the libflatarray files whenever the system one is used. That resolves the issue. While here, bump EAPI to 7 and remove visit use flag. VisIt has been removed. Bug: https://bugs.gentoo.org/688932 Package-Manager: Portage-2.3.79, Repoman-2.3.16 Signed-off-by: Kurt Kanzenbach <kurt@kmk-computers.de> Closes: https://github.com/gentoo/gentoo/pull/14368 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/m4ri: various upstreamed patchesFrançois Bissey2020-01-203-1/+175
| | | | | | Package-Manager: Portage-2.3.79, Repoman-2.3.16 Signed-off-by: François René Pierre Bissey <frp.bissey@gmail.com> Signed-off-by: Michael Orlitzky <mjo@gentoo.org>
* sci-libs/m4ri: New upstream release.François Bissey2020-01-202-0/+47
| | | | | | Package-Manager: Portage-2.3.79, Repoman-2.3.16 Signed-off-by: François René Pierre Bissey <frp.bissey@gmail.com> Signed-off-by: Michael Orlitzky <mjo@gentoo.org>
* sci-libs/symmetrica: new C library for representation theory and more.Michael Orlitzky2020-01-203-0/+49
| | | | | | | | | | | | | | | | This package has been forked under the SageMath umbrella, and the build system has been overhauled to the point that maintaining it will not be a punishment. The new v3.0.1 is the first release of the fork if you pretend that v3.0.0 never happened (I forgot to include the documentation in the release tarball). The upstream SageMath project can detect and use the system copy of symmetrica now, so this will allow Gentoo users of SageMath to avoid pointless rebuilds of symmetrica. Closes: https://bugs.gentoo.org/232014 Package-Manager: Portage-2.3.79, Repoman-2.3.16 Signed-off-by: Michael Orlitzky <mjo@gentoo.org>
* sci-libs/shogun: Use HTTPSMichał Górny2020-01-161-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scikits_learn: Use HTTPSMichał Górny2020-01-162-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/shogun: Remove Python 2Michał Górny2020-01-161-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/Shapely: Remove Python 2Michał Górny2020-01-161-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scikits_timeseries: Remove Python 2Michał Górny2020-01-161-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scikits_timeseries: Remove oldMichał Górny2020-01-161-47/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scikits_optimization: Remove Python 2Michał Górny2020-01-161-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scikits_optimization: Remove oldMichał Górny2020-01-161-31/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/scikits_learn: Remove Python 2Michał Górny2020-01-163-3/+3
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/pymmlib: Permit numpy-python2Michał Górny2020-01-161-2/+5
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/plplot: Remove oldMichał Górny2020-01-168-830/+0
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/numkit: Remove Python 2Michał Górny2020-01-161-1/+1
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/nlopt: Permit numpy-python2Michał Górny2020-01-161-2/+5
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/mathgl: Permit numpy-python2Michał Górny2020-01-161-2/+8
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/libsigrok: Remove Python 2Michał Górny2020-01-164-4/+4
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/keras-preprocessing: Remove Python 2Michał Górny2020-01-162-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/keras-applications: Remove Python 2Michał Górny2020-01-162-2/+2
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/getdata: Permit numpy-python2Michał Górny2020-01-161-2/+8
| | | | Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-libs/libbraiding: new library for braid group computation.Michael Orlitzky2020-01-153-0/+60
| | | | | | | | | | François Bissey had an ebuild for the latest version of this package in the sage-on-gentoo overlay, so I've imported that after adding a few comments and an EAPI=7 bump. Closes: https://bugs.gentoo.org/705432 Package-Manager: Portage-2.3.79, Repoman-2.3.16 Signed-off-by: Michael Orlitzky <mjo@gentoo.org>
* sci-libs/cddlib: new version 094j.Michael Orlitzky2020-01-153-8/+81
| | | | | | | | | | | | | | | | | | | | | | | | | François Bissey had an ebuild for the latest version of this package in the sage-on-gentoo overlay, so I've imported it with minor changes: * Updated to EAPI=7 (no related changes). * Dropped the unused autotools.eclass inherit. * Changed GPL-2 to GPL-2+, since the files that do have copyright headers have the "or any later version" bit. * Dropped the DOCS declaration; they're all covered by einstalldocs. * Added IUSE=examples. * Reworked the documentation/example installation logic. The new autotools build system installs everything by default, so if the user doesn't want something, we have to kill it from $ED. I've also added the upstream remote to metadata.xml, and added myself and François as maintainers in the future. SageMath uses two cddlib executables only present as of this version, so it's a prerequisite for moving more of SageMath into the tree. Closes: https://bugs.gentoo.org/705218 Package-Manager: Portage-2.3.79, Repoman-2.3.16 Signed-off-by: Michael Orlitzky <mjo@gentoo.org>
* sci-libs/superlu_mt: amd64 stable wrt bug #705134Agostino Sarubbo2020-01-141-2/+2
| | | | | | Package-Manager: Portage-2.3.79, Repoman-2.3.16 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-libs/sundials: amd64 stable wrt bug #705134Agostino Sarubbo2020-01-141-2/+2
| | | | | | Package-Manager: Portage-2.3.79, Repoman-2.3.16 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>