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2022-05-03gnu: sundials: Add 5.8.0.Paul A. Patience
* gnu/packages/maths.scm (sundials-5, sundials-openmpi-5): New variables. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-03gnu: sundials: Update to 6.2.0.Paul A. Patience
* gnu/packages/maths.scm (sundials): Update to 6.2.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-03gnu: sundials-openmpi: Add HYPRE dependency.Paul A. Patience
* gnu/packages/maths.scm (sundials-openmpi)[propagated-inputs]: Add hypre-openmpi. [arguments]<#:configure-flags>: Add -DENABLE_HYPRE, -DHYPRE_INCLUDE_DIR and -DHYPRE_LIBRARY_DIR. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-03gnu: sundials: Fix various issues.Paul A. Patience
This commit fixes various issues. First, some of SUNDIALS's CMake variables were renamed at some point between 5.2.0 and 5.7.0, in particular KLU_ENABLE, which was changed to ENABLE_KLU. Since sundials-julia is essentially SUNDIALS 5.2.0, its configure flags need to be different from those of the sundials package. Second, commit 61bcd648ca215e3d8e75b3a3f49bfb94d66f7c79, which updated SUNDIALS to 6.1.1, accidentally completely disabled PETSc support for sundials-openmpi (PETSc is supported only with MPI) by removing the relevant configure flags. Third, SUNDIALS's default index size is 64 bits, but PETSc's is 32 bits, and they need to be the same; this issue is discussed in the next three paragraphs. The default index size in SUNDIALS 3.1.1 (which was the sundials package's version previous to the aforementioned commit) was also 64 bits (though it was configured through the SUNDIALS_INDEX_TYPE CMake variable, which could take the values INT64_T or INT32_T), but SUNDIALS's configure script didn't warn of any incompatibility with PETSc's 32-bit indices. I don't know if this was an accidental omission from the configure script or if SUNDIALS's index size didn't have to correspond to PETSc's at the time. Keeping 64-bit indices in SUNDIALS would require adding a package for PETSc with 64-bit indices (using the --with-64-bit-indices configure flag), possibly named petsc64-openmpi (to follow the style of the SCOTCH packages, i.e., scotch, scotch32, etc., though there the unadorned package name represents the 64-bit version, unlike the unadorned petsc), which would in turn require a package for METIS with 64-bit indices (using IDXTYPEWIDTH=64). However, SUNDIALS is an optional dependency of deal.II, both of which have PETSc as an optional dependency, and deal.II's index size (which defaults to 32 bits) must match PETSc's. In other words, the current deal.II package can build with SUNDIALS only if SUNDIALS has 32-bit indices. Furthermore, users needing 64-bit indices in SUNDIALS probably also need them in PETSc and other libraries. If and when 64-bit indices are deemed necessary, we can add all the package variations at once (for SUNDIALS, PETSc, METIS, deal.II and any others). * gnu/packages/maths.scm (sundials)[source]: Reuse version in URL. [native-inputs]: Capitalize and punctuate comment. [inputs]: Remove petsc, now unnecessary gfortran, and obsolete comment. Move TODO item to sundials-openmpi. [arguments]<#:configure-flags>: Add -DSUNDIALS_INDEX_SIZE=32 to match PETSc's 32-bit indices. Remove obsolete -DEXAMPLES_ENABLE_F77, -DEXAMPLES_ENABLE_F90 and -DFCMIX_ENABLE. Mention new but currently unusable -DBUILD_FORTRAN_MODULE_INTERFACE and -DEXAMPLES_ENABLE_F2003. Rename KLU_ENABLE to ENABLE_KLU. (sundials-openmpi): Use package/inherit. [inputs]: Move openmpi and petsc-openmpi from here... [propagated-inputs]: ...to here. Clarify comment. [arguments]<#:configure-flags>: Add -DENABLE_PETSC and -DPETSC_DIR, the equivalents of which were accidentally removed in commit 61bcd648ca215e3d8e75b3a3f49bfb94d66f7c79. <#:phases>: Replace a tab with spaces. [synopsis]: Replace OpenMPI with MPI to conform to other package synopses. (sundials-julia)[inputs]: Add gfortran. [arguments]<#:configure-flags>: Set only, and manually, -DCMAKE_C_FLAGS, -DSUNDIALS_INDEX_SIZE, -DKLU_ENABLE, -DKLU_INCLUDE_DIR, -DKLU_LIBRARY_DIR and -DLAPACK_ENABLE instead of inheriting from the sundials package, because some of SUNDIALS's CMake variables have changed name. [synopsis]: Capitalize “LAPACK”. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-03gnu: petsc-openmpi: Fix header inclusions.Paul A. Patience
* gnu/packages/maths.scm (petsc-openmpi)[arguments]: Add 'patch-header-inclusions' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-04-26gnu: nomad-optimizer: Disable failing test.Paul A. Patience
* gnu/packages/maths.scm (nomad-optimizer)[arguments]: Disable the examples/advanced/library/PSDMads test. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-04-19gnu: lrslib: Update to 7.2.Andreas Enge
* gnu/packages/maths.scm (lrslib): Update to 7.2.
2022-04-19gnu: nomad-optimizer: Fix some tests.Paul A. Patience
* gnu/packages/maths.scm (nomad-optimizer)[arguments]<#:phases> [fix-sources-for-tests]: Enable the pipefail option in the (generated) script that runs tests. Enable the basic batch example3 test. Fix the advanced library FixedVariable test (and seemingly the neighbor PSDMads test). Expand some comments. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-04-19gnu: nomad-optimizer: Update to 4.2.0.Paul A. Patience
* gnu/packages/maths.scm (nomad-optimizer): Update to 4.2.0. [arguments]: Accommodate updated build process. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-04-19gnu: nomad-optimizer: Remove trailing booleans.Paul A. Patience
* gnu/packages/maths.scm (nomad-optimizer)[arguments]: Remove trailing booleans. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-04-19gnu: nomad-optimizer: Remove input labels.Paul A. Patience
* gnu/packages/maths.scm (nomad-optimizer)[native-inputs]: Remove labels. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-04-19gnu: gmsh: Update to 4.9.5.Paul A. Patience
* gnu/packages/maths.scm (gmsh): Update to 4.9.5. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-04-19gnu: gnuplot: Update to 5.4.3.Paul A. Patience
* gnu/packages/maths.scm (gnuplot): Update to 5.4.3. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-04-14gnu: sundials: Remove input labels.Ludovic Courtès
* gnu/packages/maths.scm (sundials)[native-inputs, inputs]: Remove labels. (sundials-openmpi)[inputs]: Remove labels.
2022-04-14gnu: sundials: Update to 6.1.1.Ludovic Courtès
* gnu/packages/maths.scm (sundials): Update to 6.1.1. [inputs]: Add PETSC. (sundials-openmpi)[inputs]: Remove PETSC. [arguments]: Remove now unnecessary flags. Change "MPI_ENABLE" to "ENABLE_MPI".
2022-03-31gnu: gsl: Force bootstrap when cross-compiling to riscv64-linux.Arun Isaac
* gnu/packages/maths.scm (gsl)[arguments]: Force an autotools bootstrap when cross-compiling to riscv64-linux. [native-inputs]: Add autoconf, automake and libtool when cross-compiling to riscv64-linux. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-18gnu: petsc-openmpi: Remove input labels.Ludovic Courtès
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Use 'modify-inputs'. [arguments]: Adjust label name for hdf5.
2022-03-18gnu: petsc-openmpi: Fix compilation with Scotch 7.0.Ludovic Courtès
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add SCOTCH:METIS. [arguments]: Add 'adjust-pt-scotch-library-names' phase.
2022-03-07gnu: scotch: Explicitly pass "-DINTSIZE" to CMake.Ludovic Courtès
Previously, the 'scotch' and 'pt-scotch' packages would use the default int size, which turned out to be 32 on x86_64-linux instead of 64 as it used to be in Scotch 6.x. * gnu/packages/maths.scm (scotch)[arguments]: Add "-DINTSIZE" to #:configure-flags. (scotch32)[arguments]: Likewise. (pt-scotch)[arguments]: Likewise. (pt-scotch32)[arguments]: Likewise.
2022-03-02gnu: hypre: Remove input labels.Ludovic Courtès
* gnu/packages/maths.scm (hypre)[native-inputs, inputs]: Remove labels. (hypre-openmpi)[inputs]: Use 'modify-inputs'.
2022-03-02gnu: texlive-latex-wrapfig: Rename to "texlive-wrapfig".Ludovic Courtès
* gnu/packages/tex.scm (texlive-latex-wrapfig): Rename to... (texlive-wrapfig): ... this. (texlive-latex-wrapfig): Define as deprecated. * gnu/packages/maths.scm (hypre)[native-inputs]: Use new name. * gnu/packages/python-xyz.scm (python-ipython-documentation) (python-numpy-documentation): Likewise.
2022-03-02gnu: why3: Update to 1.4.1.Julien Lepiller
* gnu/packages/maths.scm (why3): Update to 1.4.1.
2022-02-15gnu: Remove unneeded uses of 'libiconv'.Marius Bakke
iconv is part of glibc, there is no need to add it as input. * gnu/packages/accessibility.scm (brltty)[inputs]: Remove LIBICONV. * gnu/packages/compression.scm (innoextract)[inputs]: Likewise. * gnu/packages/haskell-apps.scm (darcs)[inputs]: Likewise. * gnu/packages/kde-multimedia.scm (k3b)[inputs]: Likewise. * gnu/packages/linphone.scm (liblinphone)[inputs]: Likewise. * gnu/packages/mail.scm (mailutils)[inputs]: Likewise. * gnu/packages/maths.scm (libqalculate)[inputs]: Likewise. * gnu/packages/pep.scm (pep-engine)[inputs]: Likewise. * gnu/packages/vim.scm (neovim)[inputs]: Likewise. * gnu/packages/wget.scm (wget2)[inputs]: Likewise. * gnu/packages/telegram.scm (telegram-desktop)[inputs]: Likewise. * gnu/packages/video.scm (transcode)[native-inputs]: Likewise.
2022-02-15gnu: mumps: Remove input labels.Ludovic Courtès
* gnu/packages/maths.scm (mumps)[inputs]: Remove labels. [arguments]: Adjust 'configure' phase to not rely on the "mpi" and "blas" labels. (mumps-metis, mumps-openmpi, mumps-metis-openmpi): Use 'modify-inputs'.
2022-02-15gnu: scotch: Update to 7.0.1.Ludovic Courtès
* gnu/packages/maths.scm (scotch): Update to 7.0.1. [source]: Switch to 'git-fetch'. [build-system]: Switch to CMAKE-BUILD-SYSTEM. [arguments]: Add #:configure-flags. Remove #:make-flags. Remove 'chdir-to-src', 'configure', and 'build-esmumps' phases. [properties]: Update 'release-monitoring-url' property. (scotch32, pt-scotch, pt-scotch32): Update accordingly, replacing now useless build phases with #:configure-flags. (scotch-shared, pt-scotch-shared): Mark as deprecated. (mumps)[arguments]: In 'configure' phase, use '-lesmumps' unconditionally, since that's now how pt-scotch calls it.
2022-02-11gnu: opencascade-occt: Update to 7.6.0.Petr Hodina
* gnu/packages/maths.scm (opencascade-occt): Update to 7.6.0. [native-inputs]: Add fontconfig. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-02-05gnu: superlu: Update to 5.3.0.Eric Bavier
* gnu/packages/maths.scm (superlu): Update to 5.3.0. [source]: Adjust to new url.
2022-02-01gnu: openblas: Fix building on riscv64-linux.Efraim Flashner
* gnu/packages/maths.scm (openblas)[arguments]: Adjust make-flags on riscv64-linux to target the correct architecture when building for riscv64-linux.
2022-01-28gnu: Properly deprecate texlive-generic-ulem.Nicolas Goaziou
* gnu/packages/python-xyz.scm (python-nbconvert): * gnu/packages/maths.scm (hypre): Apply deprecation. * gnu/packages/tex.scm (texlive-generic-ulem): Fix typo in deprecation command.
2022-01-28gnu: Remove occurrences of deprecated texlive-latex-capt-of.Nicolas Goaziou
* gnu/packages/maths.scm (hypre): * gnu/packages/python-xyz.scm (python-numpy-documentation): (python-ipython-documentation): Use texlive-capt-of instead of texlive-latex-capt-of.
2022-01-22gnu: jacal: Update to 1c7.Morgan Smith
* gnu/packages/patches/jacal-fix-texinfo.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Delete this. * gnu/packages/maths.scm (jacal)[source]: Delete this patch. [version]: Update to 1c7. Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
2022-01-20gnu: dune-pdelab: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-pdelab): Update to 2.7.1. [version]: Use `git-version` to compute the version string. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-functions: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-functions): Update to 2.7.1. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-typetree: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-typetree): Update to 2.7.1. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-subgrid: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-subgrid): Update to 2.7.1. [version]: Use `git-version` to compute the version string. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-alugrid: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-alugrid): Update to 2.7.1. [version]: Use `git-version` to compute the version string. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-localfunctions: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-localfunctions): Update to 2.7.1. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-istl: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-istl): Update to 2.7.1. [arguments]: Parallelize build-tests phase. [source](patches) Remove patch that is no longer needed. * gnu/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove above patch. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-grid: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-grid): Update to 2.7.1. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-uggrid: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-uggrid): Update to 2.7.1. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-geometry: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-geometry): Update to 2.7.1. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: dune-common: Update to 2.7.1.Felix Gruber
* gnu/packages/maths.scm (dune-common): Update to 2.7.1. [arguments]: Parallelize build-tests phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-20gnu: Modernize add-openmpi-to-dune-packageFelix Gruber
* gnu/packages/maths.scm (add-openmpi-to-dune-package): Use modify-inputs. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-12gnu: Remove python2-cvxopt.Felix Gruber
* gnu/packages/maths.scm (python2-cvxopt): Remove variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2022-01-12gnu: python-cvxopt: Update to 1.2.7.Felix Gruber
* gnu/packages/maths.scm (python-cvxopt): Update to 1.2.7. Signed-off-by: Leo Famulari <leo@famulari.name>
2022-01-11gnu: ceres: Update to 2.0.0.Felix Gruber
* gnu/packages/maths.scm (ceres): Update to 2.0.0. [inputs]: Use simplified format. (ceres-solver-benchmarks)[phases]: Add schur_eliminator_benchmark. Replace autodiff_cost_function_benchmark with new autodiff_benchmarks. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-01-11gnu: dealii: Update to 9.3.2.Felix Gruber
* gnu/packages/maths.scm (dealii): Update to 9.3.2. [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and dealii-fix-sundials.patch. [inputs]: Use simplified format. [native-inputs]: Use simplified format. * gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch: New file. * gnu/packages/patches/dealii-fix-sundials.patch: New file. * gnu/local.mk: Add new patch files. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2022-01-01gnu: gsl: Add 'tunable?' property.Ludovic Courtès
* gnu/packages/maths.scm (gsl)[properties]: New field.
2022-01-01gnu: Add ceres-solver-benchmarks.Ludovic Courtès
* gnu/packages/maths.scm (ceres-solver-benchmarks): New variable.
2022-01-01gnu: ceres-solver: Mark as tunable.Ludovic Courtès
* gnu/packages/maths.scm (ceres)[properties]: New field.
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