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* sci-libs/gloo: addpredict for cudaAlfredo Tupone2024-04-021-0/+2
| | | | Signed-off-by: Alfredo Tupone <tupone@gentoo.org>
* sci-libs/netcdf: cmake rework, fix bug 886155Paul Zander2024-04-022-1/+105
| | | | | | | | | | | Remove cmake automagic for file filters. Make test run in parallel that failed due to mpi failures. Filter cmake targets file further. Closes: https://bugs.gentoo.org/886155 Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/35786 Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/netcdf-fortran: mark as LTO-unsafeEli Schwartz2024-04-013-3/+18
| | | | | | Closes: https://bugs.gentoo.org/927588 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/lis: add missing dep for switch to zip distfileEli Schwartz2024-04-011-0/+1
| | | | | | | | | Dunno why upstream had to change. :( Also dunno why PMS doesn't use libarchive. :( Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/dcmtk: update LTO comment (fixed upstream in git!)Sam James2024-04-011-2/+1
| | | | | | | Thank you dcmtk maintainers :) Bug: https://bugs.gentoo.org/862699 Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/lis: add 2.1.3Eli Schwartz2024-04-013-0/+493
| | | | | | | | | Current release is from 2016. Try to rebase onto a newer release. Does not fix LTO, unfortunately. Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/lis: update EAPI 6 -> 8Eli Schwartz2024-04-011-1/+1
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/lis: mark as LTO-unsafeEli Schwartz2024-04-011-2/+7
| | | | | | Closes: https://bugs.gentoo.org/927587 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/caffe2: disable py3.9Alfredo Tupone2024-03-301-1/+1
| | | | Signed-off-by: Alfredo Tupone <tupone@gentoo.org>
* sci-libs/caffe2: addpredict /proc/self/taskAlfredo Tupone2024-03-301-0/+1
| | | | | Closes: https://bugs.gentoo.org/926116 Signed-off-by: Alfredo Tupone <tupone@gentoo.org>
* sci-libs/givaro: fix build with gcc-14Michael Orlitzky2024-03-302-0/+32
| | | | | | | There was already an upstream patch for this that I missed. Closes: https://bugs.gentoo.org/928020 Signed-off-by: Michael Orlitzky <mjo@gentoo.org>
* sci-libs/volk: add 3.1.2Rick Farina2024-03-292-0/+59
| | | | Signed-off-by: Rick Farina <zerochaos@gentoo.org>
* sci-libs/libticalcs2: fix erroneous bashism during buildingEli Schwartz2024-03-292-0/+44
| | | | | | | | | | | * QA Notice: Abnormal configure code * * checking for the host compiler... ./configure: 17678: test: xx86_64-pc-linux-gnu: unexpected operator Bug: https://github.com/debrouxl/tilibs/pull/87 Closes: https://bugs.gentoo.org/723452 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/libticalcs2: update EAPI 6 -> 8Eli Schwartz2024-03-291-3/+5
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/libticalcs2: mark as LTO-unsafeEli Schwartz2024-03-291-2/+6
| | | | | | Closes: https://bugs.gentoo.org/927586 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/ignition-fuel-tools: drop 4.4.0Andreas Sturmlechner2024-03-272-45/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/getdata: fix bashisms in configureSam James2024-03-272-0/+67
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/getdata: add libltdl depSam James2024-03-272-1/+3
| | | | | Closes: https://bugs.gentoo.org/923316 Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/getdata: mark as LTO-unsafeEli Schwartz2024-03-271-1/+7
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/getdata: add github upstream metadataEli Schwartz2024-03-271-0/+1
| | | | | | | | | | In theory the sourceforge site claims to be defunct. In practice the github repo is abandoned immediately after switching too... https://sourceforge.net/p/getdata/code/1178/ Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/netcdf-cxx: make sure elibtoolize is appliedEli Schwartz2024-03-273-3/+24
| | | | | | | | | | Since the libtool available for 4.2 is very old, that means running a full eautoreconf. Needed to e.g. pass LTO warning flags through to the linker. Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/matio: make sure elibtoolize is appliedEli Schwartz2024-03-271-0/+7
| | | | | | | Needed to e.g. pass LTO warning flags through to the linker. Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/opencascade: mark as LTO-unsafeEli Schwartz2024-03-265-5/+30
| | | | | | Closes: https://bugs.gentoo.org/862912 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/gmsh: add 4.12.2Eli Schwartz2024-03-262-0/+138
| | | | | | | | Fixes LTO issues. Includes a backported patch. Closes: https://bugs.gentoo.org/862711 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/htslib: add 1.19.1David Seifert2024-03-262-0/+53
| | | | Signed-off-by: David Seifert <soap@gentoo.org>
* sci-libs/opencascade: fix 927629, 927592, 925441Paul Zander2024-03-254-70/+95
| | | | | | | | | Closes: https://bugs.gentoo.org/927629 Closes: https://bugs.gentoo.org/927592 Closes: https://bugs.gentoo.org/925441 Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/35912 Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/gmsh: drop 4.9.5-r3, 4.10.3-r1Andreas Sturmlechner2024-03-243-200/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/plplot: drop 5.15.0-r105Andreas Sturmlechner2024-03-248-627/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/mathgl: drop 2.4.4-r1Andreas Sturmlechner2024-03-242-161/+0
| | | | Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/metis: drop 5.1.0-r5Andreas Sturmlechner2024-03-245-132/+0
| | | | | Closes: https://bugs.gentoo.org/906314 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
* sci-libs/ta-lib: mark as LTO-unsafeEli Schwartz2024-03-241-2/+11
| | | | | | Closes: https://bugs.gentoo.org/862936 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/sundials: mark as LTO-unsafeEli Schwartz2024-03-243-3/+21
| | | | | | | | | | | | It fails with linking errors that are probably fortran related. An upstream ticket exists since 2021 but no sign anything is being done about it. Bug: https://github.com/LLNL/sundials/issues/97 Closes: https://bugs.gentoo.org/862933 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/opencascade: add 7.7.1, 7.7.2, 7.8.0, 9999Paul Zander2024-03-239-21/+1539
| | | | | | | | | Closes: https://bugs.gentoo.org/923350 Closes: https://bugs.gentoo.org/911578 Closes: https://bugs.gentoo.org/908889 Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/35374 Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/opencascade: drop obsolete blockPaul Zander2024-03-232-2/+0
| | | | | Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/caffe2: drop 1.13.1-r6, 2.0.1-r5Alfredo Tupone2024-03-227-920/+0
| | | | Signed-off-by: Alfredo Tupone <tupone@gentoo.org>
* sci-libs/pytorch: drop 1.13.1-r2, 2.0.1-r1Alfredo Tupone2024-03-227-203/+0
| | | | Signed-off-by: Alfredo Tupone <tupone@gentoo.org>
* sci-libs/cgnslib: fix SLOT to correctly describe sonameEli Schwartz2024-03-221-1/+1
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/cdf: backport LTO filter to stableSam James2024-03-221-2/+6
| | | | | | Closes: https://bugs.gentoo.org/927487 Bug: https://bugs.gentoo.org/862675 Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/cdf: add 3.9.0Sam James2024-03-223-0/+242
| | | | | | | | Reported the aliasing issue upstream by email. Closes: https://bugs.gentoo.org/804951 Closes: https://bugs.gentoo.org/862675 Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/cddlib: update EAPI 7 -> 8Eli Schwartz2024-03-221-0/+62
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/cddlib: make sure elibtoolize is appliedEli Schwartz2024-03-221-1/+8
| | | | | | | Needed to e.g. pass LTO warning flags through to the linker. Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/libmuscle: update EAPI 6 -> 8Eli Schwartz2024-03-221-3/+2
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/libmuscle: mark as LTO-unsafe, strict-aliasing unsafeEli Schwartz2024-03-221-1/+9
| | | | | | Closes: https://bugs.gentoo.org/862897 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/oc: update EAPI 7 -> 8Eli Schwartz2024-03-211-1/+1
| | | | | Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/oc: mark as LTO-unsafe, strict-aliasing unsafeEli Schwartz2024-03-211-1/+12
| | | | | | | | | | | | | | Upstream is libdap. They exist. They have lots of maintained software, it is simply that oc isn't one of them as far as I can tell. What happened to it? I don't know. Maybe it's legacy abandoned software. Their distfiles server still has it, but that's it. Possibly we should delete the package instead... Closes: https://bugs.gentoo.org/862906 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/mumps: mark as LTO-unsafe, strict-aliasing unsafeEli Schwartz2024-03-211-0/+10
| | | | | | | | | | | | I would like to report this upstream. However, the only contact method is their mailing list. And their mailing list may or may not work -- I find it hard to tell because I've never seen the interface before, but it is mostly in French and the bit that I recognized doesn't seem to have working links to e.g. the archive. Closes: https://bugs.gentoo.org/862903 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/mumps: update HOMEPAGE, SRC_URIEli Schwartz2024-03-211-3/+3
| | | | | | | | The previous upstream website was dead, but in fact it just has a new domain and the old domain doesn't exist anymore. Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/scotch: remove redundant double sedEli Schwartz2024-03-211-2/+1
| | | | | | | | Introduced in commit 4af10b0593cbc3fa93b62b3755ba2bed748dbf7d as part of other changes. Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-libs/ceres-solver: 2.2.0 fix automagic cuda dependencyPaul Zander2024-03-181-3/+23
| | | | | | Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/35779 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-libs/libint: add 2.9.0Sam James2024-03-172-0/+75
| | | | | | | | Filter LTO given it's a tonne of code generating stuff and it takes hours to build. Filld with reinterpret_cast. Closes: https://bugs.gentoo.org/862894 Signed-off-by: Sam James <sam@gentoo.org>