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2022-08-02gnu: gnuplot: Update to 5.4.4.Paul A. Patience
* gnu/packages/maths.scm (gnuplot): Update to 5.4.4. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-08-02gnu: gnuplot: Use G-expressions.Paul A. Patience
* gnu/packages/maths.scm (gnuplot)[arguments]: Use G-expressions. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-08-02gnu: gnuplot: Remove input labels.Paul A. Patience
* gnu/packages/maths.scm (gnuplot)[inputs]: Move below native-inputs and sort. [native-inputs]: Remove labels. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-08-02gnu: wcalc: Remove pre-generated files.Efraim Flashner
* gnu/packages/maths.scm (wcalc)[source]: Add snippet to remove files generated by bison and flex. [native-inputs]: Add bison, flex.
2022-08-01gnu: trilinos-for-dealii-openmpi: Use G-expressions.Paul A. Patience
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[arguments]: Use G-expressions. <#:phases>: Remove trailing boolean. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: trilinos-for-dealii-openmpi: Remove input labels.Paul A. Patience
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs, inputs, propagated-inputs]: Remove labels. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: dealii: Update to 9.4.0.Paul A. Patience
* gnu/packages/maths.scm (dealii): Update to 9.4.0. [propagated-inputs]: Replace sundials-5 with sundials. (dealii-openmpi)[propagated-inputs]: Replace sundials-openmpi-5 with sundials-openmpi. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: dealii: Use G-expressions.Paul A. Patience
* gnu/packages/maths.scm (dealii)[snippet, arguments]: Use G-expressions. (dealii-openmpi)[arguments]: Same. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: trilinos-for-dealii-openmpi: Fix build.Paul A. Patience
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs]: Add gcc-7 to fix the failing build with newer versions of gcc. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: hdf5-1.8: Add missing comma to linker flag.Paul A. Patience
* gnu/packages/maths.scm (hdf5-1.8)[arguments]<#:phases>: Add missing comma to linker flag. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-07-31gnu: qttools: Rename to qttools-5.Maxim Cournoyer
Automated with: git grep -l qttools | xargs sed 's/\bqttools\b/\0-5/g' -i git checkout NEWS
2022-07-31gnu: qtsvg: Rename variable to qtsvg-5.Maxim Cournoyer
This is in preparation of the qtsvg update to version 6. This change was automated via the following command: git grep -l '\bqtsvg\b' | xargs sed 's/qtsvg/qtsvg-5/g' -i
2022-07-15gnu: gmsh: Update to 4.10.5.Paul A. Patience
* gnu/packages/maths.scm (gmsh): Update to 4.10.5. [source]: Reindent. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-07-15gnu: gmsh: Remove trailing booleans.Paul A. Patience
* gnu/packages/maths.scm (gmsh)[snippet, arguments]: Remove trailing booleans. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-07-15gnu: gmsh: Remove input labels.Paul A. Patience
* gnu/packages/maths.scm (gmsh)[inputs]: Remove labels. Signed-off-by: Christopher Baines <mail@cbaines.net>
2022-07-13gnu: elpa: Update source URL.Maxim Cournoyer
Fixes <https://issues.guix.gnu.org/46460>. * gnu/packages/maths.scm (elpa): Update source URL. Reported-by: Danny Milosavljevic <dannym@scratchpost.org>
2022-07-04gnu: nauty: Update package style.Nicolas Goaziou
* gnu/packages/maths.scm (nauty)[arguments]: Use G-expressions. Remove trailing #T.
2022-07-04gnu: nauty: Update to 2.7r4.Nicolas Goaziou
* gnu/packages/maths.scm (nauty): Update to 2.7r4.
2022-07-04gnu: Add gizaSharlatan Hellseher
* gnu/packages/maths.scm (giza): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-07-04gnu: z3: Prefer CMake to build the package.Zhu Zihao
Z3 developer recommends to use CMake to build Z3 except the OCaml bindings. Use CMake also enable us to cross compile z3. * gnu/packages/maths.scm (z3)[build-system]: Use cmake-build-system. [arguments]<#:configure-flags>: Add flags for CMake. <#:phases>: Remove stale phase 'fix-compatability'. In phase 'check', build the z3 test binary and don't test when cross compiling. Add phase 'compile-python-modules' phase to generate python bytecode cache for z3 python binding. Add phase 'fix-z3-library-path' to help z3 pythong binding to find the z3 shared library. (ocaml-z3)[build-system]: Override the inherited value with 'gnu-build-system'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-07-04gnu: z3: Update to 4.8.17.Zhu Zihao
* gnu/packages/maths.scm (z3): Update to 4.8.17. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-07-04gnu: z3: Use G-expressions.Zhu Zihao
* gnu/packages/maths.scm (z3)[arguments]: Use G-expressions. [native-inputs]: Use label-less style. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-07-01gnu: mcrl2: Update to 202206.0.Jan (janneke) Nieuwenhuizen
* gnu/packages/patches/mcrl2-fix-1687.patch, gnu/packages/patches/mcrl2-fix-counterexample.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/maths.scm (mcrl2): Update to 202206.0 and use them.
2022-06-30gnu: octave: Update to 7.1.0.Greg Hogan
* gnu/packages/maths.scm (octave): Update to 7.1.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-06-23gnu: hypre: Add missing dependencies on latex fonts.Ontje Lünsdorf
* gnu/packages/maths.scm (hypre)[native-inputs]: Add TEXLIVE-COURIER and TEXLIVE-HELVETIC. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-06-08Merge branch 'master' into stagingLudovic Courtès
2022-06-06gnu: itpp: Avoid embedding build dates.Vagrant Cascadian
* gnu/packages/maths.scm (itpp): Add 'set-man-page-date and 'set-force-source-date phases.
2022-06-01Merge remote-tracking branch 'origin/master' into stagingEfraim Flashner
2022-05-31gnu: Remove python2-kiwisolver.Maxim Cournoyer
* gnu/packages/maths.scm (python2-kiwisolver): Delete variable.
2022-05-31gnu: Remove python2-numpy.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python2-numpy): Delete variable. (python2-numpy-1.8): Likewise. (python-numpy)[properties]: Delete field. * gnu/packages/maths.scm (flann): Delete comment. * gnu/packages/chemistry.scm (with-numpy-1.8): Delete procedure.
2022-06-04gnu: ruby-asciimath: Update to 2.0.4.SeerLite
gnu/packages/math.scm (ruby-asciimath): Update to 2.0.4. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-28gnu: nlopt: Update to 2.7.1.Ricardo Wurmus
* gnu/packages/maths.scm (nlopt): Update to 2.7.1. [source]: Fetch from git. [build-system]: Use cmake-build-system. [arguments]: Adjuts 'set-libnlopt-file-name phase. [inputs]: Replace guile-2.0 with guile-3.0; add octave and python. [native-inputs]: Add swig.
2022-05-15gnu: openblas: Remove input labels.Ludovic Courtès
* gnu/packages/maths.scm (openblas)[inputs, native-inputs]: Remove labels. [arguments]: In 'set-extralib' phase, use 'search-input-file'.
2022-05-15gnu: openblas: Update to 0.3.20Aurora
* gnu/packages/maths.scm (openblas): Update to 0.3.20. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-05gnu: Add n2p2.Pierre-Antoine Bouttier
* gnu/packages/maths.scm (n2p2): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2022-05-03gnu: dealii: Update to 9.3.3.Paul A. Patience
* gnu/packages/maths.scm (dealii): Update to 9.3.3. * gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch: Delete file. * gnu/packages/patches/dealii-fix-sundials.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-03gnu: dealii: Add SUNDIALS dependency.Paul A. Patience
* gnu/packages/maths.scm (dealii)[propagated-inputs]: Add sundials-5. Reformat list to clarify comment. (dealii-openmpi)[propagated-inputs]: Add sundials-openmpi-5. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-03gnu: dealii-openmpi: Remove input labels.Paul A. Patience
* gnu/packages/maths.scm (dealii-openmpi)[inputs]: Remove labels. [propagated-inputs]: Same. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-03gnu: dealii: Remove trailing booleans.Paul A. Patience
* gnu/packages/maths.scm (dealii)[snippet]: Remove trailing boolean (and therefore the 'begin'). [native-inputs, inputs]: Reindent. [arguments]<#:phases>: Remove trailing boolean. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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>
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