diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
98 files changed, 1544 insertions, 704 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/bedops/default.nix b/nixpkgs/pkgs/applications/science/biology/bedops/default.nix index 407ed0c01f76..e7379ee382a4 100644 --- a/nixpkgs/pkgs/applications/science/biology/bedops/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bedops/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "bedops"; - version = "2.4.39"; + version = "2.4.40"; src = fetchFromGitHub { owner = "bedops"; repo = "bedops"; rev = "v${version}"; - sha256 = "sha256-vPrut3uhZK1Eg9vPcyxVNWW4zKeypdsb28oM1xbbpJo="; + sha256 = "sha256-rJVl3KbzGblyQZ7FtJXeEv/wjQJmzYGNjzhvkoMoBWY="; }; buildInputs = [ zlib bzip2 jansson ]; diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie/default.nix index 916bba5c0512..0722ffe09fc9 100644 --- a/nixpkgs/pkgs/applications/science/biology/bowtie/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bowtie/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "An ultrafast memory-efficient short read aligner"; license = licenses.artistic2; - homepage = "http://bowtie-bio.sf.net/bowtie"; + homepage = "http://bowtie-bio.sourceforge.net"; maintainers = with maintainers; [ prusnak ]; platforms = platforms.all; }; diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix index 205ff9afdca1..818d0fe14ba2 100644 --- a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, cmake, tbb, zlib }: +{ lib, stdenv, fetchFromGitHub, cmake, tbb, zlib, python3, perl }: stdenv.mkDerivation rec { pname = "bowtie2"; @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; - buildInputs = [ tbb zlib ]; + buildInputs = [ tbb zlib python3 perl ]; meta = with lib; { description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; diff --git a/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix b/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix index ba1d6c27ccb1..474c0f292af4 100644 --- a/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { sha256 = "032nva6iiwmw59gjipm1mv0xlcckhxsf45mc2qbnv19lbis0q22i"; }; - propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.PerlMagick ]; + propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.ImageMagick ]; nativeBuildInputs = [ zlib makeWrapper ]; buildInputs = lib.optional stdenv.cc.isClang openmp; diff --git a/nixpkgs/pkgs/applications/science/biology/fastp/default.nix b/nixpkgs/pkgs/applications/science/biology/fastp/default.nix index e396c8597d24..c4cae59d1c4e 100644 --- a/nixpkgs/pkgs/applications/science/biology/fastp/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/fastp/default.nix @@ -5,13 +5,13 @@ stdenv.mkDerivation rec { pname = "fastp"; - version = "0.20.1"; + version = "0.22.0"; src = fetchFromGitHub { owner = "OpenGene"; repo = "fastp"; rev = "v${version}"; - sha256 = "sha256-pANwppkO9pfV9vctB7HmNCzYRtf+Xt+5HMKzvFuvyFM="; + sha256 = "sha256-XR76hNz7iGXQYSBbBandHZ+oU3wyTf1AKlu9Xeq/GyE="; }; buildInputs = [ zlib ]; diff --git a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix index d21ef8b3d7a9..072826c40615 100644 --- a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "minimap2"; - version = "2.17"; + version = "2.22"; src = fetchFromGitHub { repo = pname; owner = "lh3"; rev = "v${version}"; - sha256 = "0qdwlkib3aa6112372hdgvnvk86hsjjkhjar0p53pq4ajrr2cdlb"; + sha256 = "sha256-jYXJr2T1enZfSABVV5Kmd5OBtWZtQ2D/2eAlW2WHtGU="; }; buildInputs = [ zlib ]; diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix index 4815ddf2f75c..715f2ea313b4 100644 --- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix @@ -17,13 +17,13 @@ let in stdenv.mkDerivation rec { pname = "mosdepth"; - version = "0.3.1"; + version = "0.3.2"; src = fetchFromGitHub { owner = "brentp"; repo = "mosdepth"; rev = "v${version}"; - sha256 = "1kcrvamrafz1m0s7mlbhaay8jyg97l1w37p6syl36r2m1plmwxjd"; + sha256 = "sha256-uui4yC7ok+pvbXVKfBVsAarH40fnH4fnP8P4uzOqztQ="; }; nativeBuildInputs = [ nim ]; diff --git a/nixpkgs/pkgs/applications/science/biology/mrbayes/builder.sh b/nixpkgs/pkgs/applications/science/biology/mrbayes/builder.sh deleted file mode 100644 index 5b3a54946fc9..000000000000 --- a/nixpkgs/pkgs/applications/science/biology/mrbayes/builder.sh +++ /dev/null @@ -1,9 +0,0 @@ -# builder for mrbayes - note: only builds on Unix - -source $stdenv/setup - -tar xvfz $src -cd mrbayes-* -make -mkdir -p $out/bin -cp -v mb $out/bin diff --git a/nixpkgs/pkgs/applications/science/biology/mrbayes/default.nix b/nixpkgs/pkgs/applications/science/biology/mrbayes/default.nix index 9acfea1a1463..e4c2bbe65652 100644 --- a/nixpkgs/pkgs/applications/science/biology/mrbayes/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mrbayes/default.nix @@ -1,18 +1,18 @@ -{lib, stdenv, fetchurl, readline}: +{ lib, stdenv, fetchFromGitHub, readline }: stdenv.mkDerivation rec { - # FIXME: replace Makefile so we can build MPI & MAC support + pname = "mrbayes"; + version = "3.2.7a"; - name = "mrbayes-3.1.2"; - src = fetchurl { - url = "mirror://sourceforge/mrbayes/${name}.tar.gz"; - sha256 = "1x7j8ca5wjrqrxmcpvd375ydm3s2pbkzykv8xfhg1jc037g560n6"; + src = fetchFromGitHub { + owner = "NBISweden"; + repo = "MrBayes"; + rev = "v${version}"; + sha256 = "sha256-pkkxZ6YHRn/I1SJpT9A+EK4S5hWGmFdcDBJS0zh5mLA="; }; - builder = ./builder.sh; - buildInputs = [readline]; meta = with lib; { - description = "Bayesian Inference of Phylogeny"; + description = "Bayesian Inference of Phylogeny"; longDescription = '' Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is @@ -22,8 +22,9 @@ stdenv.mkDerivation rec { MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. ''; - license = licenses.gpl2; - homepage = "http://mrbayes.csit.fsu.edu/"; + maintainers = with maintainers; [ ]; + license = licenses.gpl2Plus; + homepage = "https://nbisweden.github.io/MrBayes/"; platforms = platforms.linux; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix index 7bfef3a82fed..804407968e1c 100644 --- a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix @@ -60,13 +60,13 @@ stdenv.mkDerivation rec { else ["--without-mpi"]); - postInstall = lib.optionals (python != null) [ '' + postInstall = lib.optionalString (python != null) '' ## standardise python neuron install dir if any if [[ -d $out/lib/python ]]; then mkdir -p ''${out}/${python.sitePackages} mv ''${out}/lib/python/* ''${out}/${python.sitePackages}/ fi - '']; + ''; propagatedBuildInputs = [ readline ncurses which libtool ]; diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix index ed0d043cd542..345a38ae24a4 100644 --- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,17 +2,17 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.25.1"; + version = "2.26.0"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "sha256-bW5iLWtGX5/HBMN7y6VbDaxa0U0HCIu9vfreXNAn7hw="; + sha256 = "sha256-sz/7MtcCJlUlrNy16W1YB/zXMhYeLLbQOIOdzNsGW7w="; }; nativeBuildInputs = [ makeWrapper ]; buildInputs = [ jre ]; - phases = [ "installPhase" ]; + dontUnpack = true; installPhase = '' mkdir -p $out/libexec/picard diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix index 16091514f154..89ac4c49629e 100644 --- a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "stacks"; - version = "2.55"; + version = "2.59"; src = fetchurl { url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz"; - sha256 = "sha256-p8L0F3A+GdNsPgTQNn9Em5EjFCc9f7gUvyLIRCTd05c="; + sha256 = "sha256-pVFwb4EPba9wL9kDGN2gi7aeH+sPhDG/XLyHxqG4zd4="; }; buildInputs = [ zlib ]; @@ -14,6 +14,6 @@ stdenv.mkDerivation rec { description = "Software pipeline for building loci from short-read sequences"; homepage = "http://catchenlab.life.illinois.edu/stacks/"; maintainers = [ lib.maintainers.bzizou ]; - license = lib.licenses.gpl3; + license = lib.licenses.gpl3Plus; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/varscan/default.nix b/nixpkgs/pkgs/applications/science/biology/varscan/default.nix index 2a232d64693d..7b09f601ad68 100644 --- a/nixpkgs/pkgs/applications/science/biology/varscan/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/varscan/default.nix @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ makeWrapper ]; buildInputs = [ jre ]; - phases = [ "installPhase" ]; + dontUnpack = true; installPhase = '' mkdir -p $out/libexec/varscan diff --git a/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix b/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix new file mode 100644 index 000000000000..437123faafd8 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix @@ -0,0 +1,37 @@ +{ lib, stdenv, fetchFromGitHub, cmake, eigen, avogadrolibs, molequeue, hdf5 +, openbabel, qttools, wrapQtAppsHook +}: + +stdenv.mkDerivation rec { + pname = "avogadro2"; + version = "1.94.0"; + + src = fetchFromGitHub { + owner = "OpenChemistry"; + repo = "avogadroapp"; + rev = version; + sha256 = "6RaiX23YUMfTYAuSighcLGGlJtqeydNgi3PWGF77Jp8="; + }; + + nativeBuildInputs = [ cmake wrapQtAppsHook ]; + + buildInputs = [ + avogadrolibs + molequeue + eigen + hdf5 + qttools + ]; + + propagatedBuildInputs = [ openbabel ]; + + qtWrapperArgs = [ "--prefix PATH : ${openbabel}/bin" ]; + + meta = with lib; { + description = "Molecule editor and visualizer"; + maintainers = with maintainers; [ sheepforce ]; + homepage = "https://github.com/OpenChemistry/avogadroapp"; + platforms = platforms.mesaPlatforms; + license = licenses.bsd3; + }; +} diff --git a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix new file mode 100644 index 000000000000..6bb99ce556dd --- /dev/null +++ b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix @@ -0,0 +1,117 @@ +{ lib, stdenv, fetchFromGitHub, python3, gfortran, blas, lapack +, fftw, libint, libvori, libxc, mpi, gsl, scalapack, openssh, makeWrapper +, libxsmm, spglib, which +} : + +let + cp2kVersion = "psmp"; + arch = "Linux-x86-64-gfortran"; + +in stdenv.mkDerivation rec { + pname = "cp2k"; + version = "8.2.0"; + + src = fetchFromGitHub { + owner = "cp2k"; + repo = "cp2k"; + rev = "v${version}"; + sha256 = "0kykq5p318hxjzd4gzqjwv9gqshbdvbg0gnjbd9bdfjx1r6jkjn3"; + fetchSubmodules = true; + }; + + nativeBuildInputs = [ python3 which openssh makeWrapper ]; + buildInputs = [ + gfortran + fftw + gsl + libint + libvori + libxc + libxsmm + spglib + scalapack + blas + lapack + ]; + + propagatedBuildInputs = [ mpi ]; + propagatedUserEnvPkgs = [ mpi ]; + + makeFlags = [ + "ARCH=${arch}" + "VERSION=${cp2kVersion}" + ]; + + doCheck = true; + + enableParallelBuilding = true; + + postPatch = '' + patchShebangs tools exts/dbcsr/tools/build_utils exts/dbcsr/.cp2k + substituteInPlace exts/dbcsr/.cp2k/Makefile --replace '/usr/bin/env python3' '${python3}/bin/python' + ''; + + configurePhase = '' + cat > arch/${arch}.${cp2kVersion} << EOF + CC = mpicc + CPP = + FC = mpif90 + LD = mpif90 + AR = ar -r + DFLAGS = -D__FFTW3 -D__LIBXC -D__LIBINT -D__parallel -D__SCALAPACK \ + -D__MPI_VERSION=3 -D__F2008 -D__LIBXSMM -D__SPGLIB \ + -D__MAX_CONTR=4 -D__LIBVORI + CFLAGS = -fopenmp + FCFLAGS = \$(DFLAGS) -O2 -ffree-form -ffree-line-length-none \ + -ftree-vectorize -funroll-loops -msse2 \ + -std=f2008 \ + -fopenmp -ftree-vectorize -funroll-loops \ + -I${libxc}/include -I${libxsmm}/include \ + -I${libint}/include + LIBS = -lfftw3 -lfftw3_threads \ + -lscalapack -lblas -llapack \ + -lxcf03 -lxc -lxsmmf -lxsmm -lsymspg \ + -lint2 -lstdc++ -lvori \ + -lgomp -lpthread -lm \ + -fopenmp + LDFLAGS = \$(FCFLAGS) \$(LIBS) + EOF + ''; + + checkPhase = '' + export OMP_NUM_THREADS=1 + + export HYDRA_IFACE=lo # Fix to make mpich run in a sandbox + export OMPI_MCA_rmaps_base_oversubscribe=1 + export CP2K_DATA_DIR=data + + mpirun -np 2 exe/${arch}/libcp2k_unittest.${cp2kVersion} + ''; + + installPhase = '' + mkdir -p $out/bin $out/share/cp2k + + cp exe/${arch}/* $out/bin + + for i in cp2k cp2k_shell graph; do + wrapProgram $out/bin/$i.${cp2kVersion} \ + --set-default CP2K_DATA_DIR $out/share/cp2k + done + + wrapProgram $out/bin/cp2k.popt \ + --set-default CP2K_DATA_DIR $out/share/cp2k \ + --set OMP_NUM_THREADS 1 + + cp -r data/* $out/share/cp2k + ''; + + passthru = { inherit mpi; }; + + meta = with lib; { + description = "Quantum chemistry and solid state physics program"; + homepage = "https://www.cp2k.org"; + license = licenses.gpl2Plus; + maintainers = [ maintainers.sheepforce ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix new file mode 100644 index 000000000000..b7d61848134e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/default.nix @@ -0,0 +1,40 @@ +{ lib, stdenv, fetchurl, blas, lapack } : + +stdenv.mkDerivation rec { + pname = "ergoscf"; + version = "3.8"; + + src = fetchurl { + url = "http://www.ergoscf.org/source/tarfiles/ergo-${version}.tar.gz"; + sha256 = "1s50k2gfs3y6r5kddifn4p0wmj0yk85wm5vf9v3swm1c0h43riix"; + }; + + buildInputs = [ blas lapack ]; + + patches = [ ./math-constants.patch ]; + + postPatch = '' + patchShebangs ./test + ''; + + configureFlags = [ + "--enable-linalgebra-templates" + "--enable-performance" + ] ++ lib.optional stdenv.isx86_64 "--enable-sse-intrinsics"; + + LDFLAGS = "-lblas -llapack"; + + enableParallelBuilding = true; + + OMP_NUM_THREADS = 2; # required for check phase + + doCheck = true; + + meta = with lib; { + description = "Quantum chemistry program for large-scale self-consistent field calculations"; + homepage = "http://www.ergoscf.org"; + license = licenses.gpl3Plus; + maintainers = [ maintainers.markuskowa ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/chemistry/ergoscf/math-constants.patch b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/math-constants.patch new file mode 100644 index 000000000000..62209f1a3d84 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/chemistry/ergoscf/math-constants.patch @@ -0,0 +1,19 @@ +diff --git a/source/dft/functionals.h b/source/dft/functionals.h +index fde49ba..f7a61fc 100644 +--- a/source/dft/functionals.h ++++ b/source/dft/functionals.h +@@ -59,6 +59,14 @@ + #define EXTERN_C + #endif + ++#ifndef M_PI ++#define M_PI 3.14159265358979323846 ++#endif ++ ++#ifndef M_SQRT2 ++#define M_SQRT2 1.41421356237309504880 ++#endif ++ + typedef ergo_real real; + + #if defined(FUNC_PRECISION) && FUNC_PRECISION == 1 diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index 5d2158843ede..a3add93c8f70 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -17,14 +17,14 @@ let }; in stdenv.mkDerivation rec { - version = "14.31.44"; + version = "14.31.49"; pname = "jmol"; src = let baseVersion = "${lib.versions.major version}.${lib.versions.minor version}"; in fetchurl { url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; - sha256 = "sha256-MHfqoQzUEL7nje7Y/hbaA8iktxfN7464TJXum5B6OCc="; + sha256 = "sha256-P+bzimBVammX5LxE6Yd6CmvmBeG8WdyA1T9bHXd+ifI="; }; patchPhase = '' diff --git a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix index af646b514af9..8efe537dcacd 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -5,9 +5,9 @@ } : let - version = "21.02"; + version = "21.06"; # The tag keeps moving, fix a hash instead - gitLabRev = "41cee871945ac712e86ee971425a49a8fc60a936"; + gitLabRev = "dd982ad4bc94dec8ac1e3e99cb6a7dd249ff71de"; python = python3.withPackages (ps : with ps; [ six pyparsing ]); @@ -19,7 +19,7 @@ in stdenv.mkDerivation { owner = "Molcas"; repo = "OpenMolcas"; rev = gitLabRev; - sha256 = "0cap53gy1wds2qaxbijw09fqhvfxphfkr93nhp9xdq84yxh4wzv6"; + sha256 = "07dm73n0s7ckif561yb3s9yqxsv39a73kb9qwny4yp39wdvv52hz"; }; patches = [ diff --git a/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix index 2df8b0e6d473..39bbae77a66e 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/pymol/default.nix @@ -1,8 +1,18 @@ -{ lib, fetchurl, fetchFromGitHub, makeDesktopItem -, python3, python3Packages -, glew, glm, freeglut, libpng, libxml2, tk, freetype, msgpack }: - - +{ lib +, fetchFromGitHub +, makeDesktopItem +, python3 +, python3Packages +, netcdf +, glew +, glm +, freeglut +, libpng +, libxml2 +, tk +, freetype +, msgpack +}: let pname = "pymol"; description = "A Python-enhanced molecular graphics tool"; @@ -20,15 +30,15 @@ let in python3Packages.buildPythonApplication rec { inherit pname; - version = "2.3.0"; + version = "2.5.0"; src = fetchFromGitHub { owner = "schrodinger"; repo = "pymol-open-source"; rev = "v${version}"; - sha256 = "175cqi6gfmvv49i3ws19254m7ljs53fy6y82fm1ywshq2h2c93jh"; + sha256 = "sha256-JdsgcVF1w1xFPZxVcyS+GcWg4a1Bd4SvxFOuSdlz9SM="; }; - buildInputs = [ python3Packages.numpy glew glm freeglut libpng libxml2 tk freetype msgpack ]; + buildInputs = [ python3Packages.numpy glew glm freeglut libpng libxml2 tk freetype msgpack netcdf ]; NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2"; hardeningDisable = [ "format" ]; @@ -49,7 +59,7 @@ python3Packages.buildPythonApplication rec { ''; meta = with lib; { - description = description; + inherit description; homepage = "https://www.pymol.org/"; license = licenses.mit; maintainers = with maintainers; [ samlich ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix index 0628134d9df2..1a900e10197e 100644 --- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix +++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix @@ -66,8 +66,8 @@ let # Make desktop item mkdir -p "$out"/share/applications cp "$desktopItem"/share/applications/* "$out"/share/applications/ - mkdir -p "$out"/share/icons - ln -s "$out/eagle-${version}/bin/eagle-logo.png" "$out"/share/icons/eagle.png + mkdir -p "$out"/share/pixmaps + ln -s "$out/eagle-${version}/bin/eagle-logo.png" "$out"/share/pixmaps/eagle.png ''; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle7.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle7.nix index 2804fc3c8d7c..8ea75a3ec486 100644 --- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle7.nix +++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle7.nix @@ -45,7 +45,7 @@ stdenv.mkDerivation rec { libX11 libXext libXi ]; - phases = [ "installPhase" ]; + dontUnpack = true; # NOTES: # Eagle for Linux comes as a self-extracting shell script with embedded diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix index 596083c27098..d7398f39ec43 100644 --- a/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix +++ b/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix @@ -64,7 +64,7 @@ assert lib.assertMsg (!(sanitizeAddress && sanitizeThreads)) "'sanitizeAddress' and 'sanitizeThreads' are mutually exclusive, use one."; let - inherit (lib) optional optionals; + inherit (lib) optional optionals optionalString; in stdenv.mkDerivation rec { pname = "kicad-base"; @@ -172,7 +172,7 @@ stdenv.mkDerivation rec { dontStrip = debug; - postInstall = optional (withI18n) '' + postInstall = optionalString (withI18n) '' mkdir -p $out/share lndir ${i18n}/share $out/share ''; diff --git a/nixpkgs/pkgs/applications/science/electronics/lepton-eda/default.nix b/nixpkgs/pkgs/applications/science/electronics/lepton-eda/default.nix new file mode 100644 index 000000000000..3e701dc93c4f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/electronics/lepton-eda/default.nix @@ -0,0 +1,61 @@ +{ stdenv +, lib +, pkg-config +, makeWrapper +, texinfo +, fetchurl +, autoreconfHook +, guile +, flex +, gtk2 +, glib +, gtkextra +, gettext +, gawk +, shared-mime-info +, groff +, libstroke +}: + +stdenv.mkDerivation rec { + pname = "lepton-eda"; + version = "1.9.16-20210731"; + + src = fetchurl { + url = "https://github.com/lepton-eda/lepton-eda/releases/download/${version}/lepton-eda-${builtins.head (lib.splitString "-" version)}.tar.gz"; + sha256 = "sha256-xdJ11M4RXNF6ePZD6Y+/DUdO21AFLbydZcq9nWg0+Yk="; + }; + + nativeBuildInputs = [ pkg-config makeWrapper texinfo autoreconfHook ]; + + propagatedBuildInputs = [ guile flex gtk2 glib gtkextra gettext gawk shared-mime-info groff libstroke ]; + + configureFlags = [ + "--disable-update-xdg-database" + ]; + + CFLAGS = [ + "-DSCM_DEBUG_TYPING_STRICTNESS=2" + ]; + + postInstall = '' + libs="${lib.makeLibraryPath propagatedBuildInputs}" + for program in $out/bin/*; do + wrapProgram "$program" \ + --prefix LD_LIBRARY_PATH : "$libs" \ + --prefix LTDL_LIBRARY_PATH : "$out/lib" + done + ''; + + meta = with lib; { + homepage = "https://github.com/lepton-eda"; + description = "Lepton Electronic Design Automation"; + longDescription = '' + Lepton EDA is a suite of free software tools for designing electronics. + It provides schematic capture, netlisting into over 30 netlist formats, and many other features. + ''; + license = licenses.gpl2Plus; + platforms = platforms.linux; + maintainers = with maintainers; [ tesq0 ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix b/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix index d2cdf20ab87c..1b9d7773669c 100644 --- a/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/openhantek6022/default.nix @@ -2,13 +2,13 @@ mkDerivation rec { pname = "openhantek6022"; - version = "3.2.3"; + version = "3.2.4"; src = fetchFromGitHub { owner = "OpenHantek"; repo = "OpenHantek6022"; rev = version; - sha256 = "0hnd3rdmv76dwwlmkykzwhp5sbxd1fr5ss8zdfdybxw28cxlpq8r"; + sha256 = "sha256-Rb0bd2fnnNWEm1n2EVRB2Leb0Or9vxi5oj+FKNY4GSc="; }; nativeBuildInputs = [ cmake makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/openroad/default.nix b/nixpkgs/pkgs/applications/science/electronics/openroad/default.nix new file mode 100644 index 000000000000..1b1eb39cffa0 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/electronics/openroad/default.nix @@ -0,0 +1,94 @@ +{ lib +, mkDerivation +, fetchFromGitHub +, bison +, cmake +, doxygen +, flex +, git +, python3 +, swig4 +, boost172 +, cimg +, eigen +, lcov +, lemon-graph +, libjpeg +, pcre +, qtbase +, readline +, spdlog +, tcl +, tcllib +, xorg +, yosys +, zlib +}: + +mkDerivation rec { + pname = "openroad"; + version = "2.0"; + + src = fetchFromGitHub { + owner = "The-OpenROAD-Project"; + repo = "OpenROAD"; + rev = "v${version}"; + fetchSubmodules = true; + sha256 = "1p677xh16wskfj06jnplhpc3glibhdaqxmk0j09832chqlryzwyx"; + }; + + nativeBuildInputs = [ + bison + cmake + doxygen + flex + git + swig4 + ]; + + buildInputs = [ + boost172 + cimg + eigen + lcov + lemon-graph + libjpeg + pcre + python3 + qtbase + readline + spdlog + tcl + tcllib + yosys + xorg.libX11 + zlib + ]; + + postPatch = '' + patchShebangs --build etc/find_messages.py + ''; + + # Enable output images from the placer. + cmakeFlags = [ "-DUSE_CIMG_LIB=ON" ]; + + # Resynthesis needs access to the Yosys binaries. + qtWrapperArgs = [ "--prefix PATH : ${lib.makeBinPath [ yosys ]}" ]; + + # Upstream uses vendored package versions for some dependencies, so regression testing is prudent + # to see if there are any breaking changes in unstable that should be vendored as well. + doCheck = false; # Disabled pending upstream release with fix for rcx log file creation. + checkPhase = '' + # Regression tests must be run from the project root not from within the CMake build directory. + cd .. + test/regression + ''; + + meta = with lib; { + description = "OpenROAD's unified application implementing an RTL-to-GDS flow"; + homepage = "https://theopenroadproject.org"; + license = licenses.bsd3; + maintainers = with maintainers; [ trepetti ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix b/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix index 5377a7b3d118..159e15cf247d 100644 --- a/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/verilator/default.nix @@ -4,11 +4,11 @@ stdenv.mkDerivation rec { pname = "verilator"; - version = "4.202"; + version = "4.210"; src = fetchurl { url = "https://www.veripool.org/ftp/${pname}-${version}.tgz"; - sha256 = "0ydn4304pminzq8zc1hsrb2fjrfqnb6akr45ky43jd29c4jgznnq"; + sha256 = "sha256-KoIfJeV2aITnwiB2eQgQo4ZyXfMe6erFiGKXezR+IBg="; }; enableParallelBuilding = true; diff --git a/nixpkgs/pkgs/applications/science/electronics/vhd2vl/default.nix b/nixpkgs/pkgs/applications/science/electronics/vhd2vl/default.nix index adce30551071..f0dd990a35bc 100644 --- a/nixpkgs/pkgs/applications/science/electronics/vhd2vl/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/vhd2vl/default.nix @@ -4,6 +4,7 @@ , bison , flex , verilog +, which }: stdenv.mkDerivation rec { @@ -29,6 +30,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ bison flex + which ]; buildInputs = [ @@ -36,8 +38,9 @@ stdenv.mkDerivation rec { ]; installPhase = '' - mkdir -p $out/bin - cp src/vhd2vl $out/bin/ + runHook preInstall + install -D -m755 src/vhd2vl $out/bin/vdh2vl + runHook postInstall ''; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/geometry/gama/default.nix b/nixpkgs/pkgs/applications/science/geometry/gama/default.nix index c5e95d37b510..899e65a7740a 100644 --- a/nixpkgs/pkgs/applications/science/geometry/gama/default.nix +++ b/nixpkgs/pkgs/applications/science/geometry/gama/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, lib, expat, octave, libxml2, texinfo, zip }: stdenv.mkDerivation rec { pname = "gama"; - version = "2.12"; + version = "2.14"; src = fetchurl { url = "mirror://gnu/${pname}/${pname}-${version}.tar.gz"; - sha256 = "0zfilasalsy29b7viw0iwgnl9bkvp0l87gpxl1hx7379l8agwqyj"; + sha256 = "sha256-ltYoJyo4b4Ys70nbZo5gxkjBw/RiEs5Rrdb6he9bsBI="; }; buildInputs = [ expat ]; diff --git a/nixpkgs/pkgs/applications/science/logic/bitwuzla/default.nix b/nixpkgs/pkgs/applications/science/logic/bitwuzla/default.nix new file mode 100644 index 000000000000..a8820b55b746 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/bitwuzla/default.nix @@ -0,0 +1,67 @@ +{ stdenv +, fetchFromGitHub +, lib +, python3 +, cmake +, lingeling +, btor2tools +, gtest +, gmp +, cadical +, minisat +, picosat +, cryptominisat +, zlib +, pkg-config + # "*** internal error in 'lglib.c': watcher stack overflow" on aarch64-linux +, withLingeling ? !stdenv.hostPlatform.isAarch64 +}: + +stdenv.mkDerivation rec { + pname = "bitwuzla"; + version = "unstable-2021-07-01"; + + src = fetchFromGitHub { + owner = "bitwuzla"; + repo = "bitwuzla"; + rev = "58d720598e359b1fdfec4a469c76f1d1f24db51a"; + sha256 = "06ymqsdppyixb918161rmbgqvbnarj4nm4az88lkn3ri4gyimw04"; + }; + + nativeBuildInputs = [ cmake pkg-config ]; + buildInputs = [ + cadical + cryptominisat + picosat + minisat + btor2tools + gmp + zlib + ] ++ lib.optional withLingeling lingeling; + + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=ON" + "-DPicoSAT_INCLUDE_DIR=${lib.getDev picosat}/include/picosat" + "-DBtor2Tools_INCLUDE_DIR=${lib.getDev btor2tools}/include/btor2parser" + "-DBtor2Tools_LIBRARIES=${lib.getLib btor2tools}/lib/libbtor2parser${stdenv.hostPlatform.extensions.sharedLibrary}" + ] ++ lib.optional doCheck "-DTESTING=YES"; + + checkInputs = [ python3 gtest ]; + # two tests fail on darwin and 3 on aarch64-linux + doCheck = stdenv.hostPlatform.isLinux && (!stdenv.hostPlatform.isAarch64); + preCheck = let + var = if stdenv.isDarwin then "DYLD_LIBRARY_PATH" else "LD_LIBRARY_PATH"; + in + '' + export ${var}=$(readlink -f lib) + patchShebangs .. + ''; + + meta = with lib; { + description = "A SMT solver for fixed-size bit-vectors, floating-point arithmetic, arrays, and uninterpreted functions"; + homepage = "https://bitwuzla.github.io"; + license = licenses.mit; + platforms = platforms.unix; + maintainers = with maintainers; [ symphorien ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix index ca5e6b5c4195..f0cb1efb3050 100644 --- a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix @@ -2,23 +2,39 @@ stdenv.mkDerivation rec { pname = "cadical"; - version = "1.3.0"; + version = "1.4.1"; src = fetchFromGitHub { owner = "arminbiere"; repo = "cadical"; rev = "rel-${version}"; - sha256 = "05lvnvapjawgkky38xknb9lgaliiwan4kggmb9yggl4ifpjrh8qf"; + sha256 = "0y44z3np4gssgdh4aj5qila7pshrbphycdxn2083i8ayyyjbxshp"; }; + outputs = [ "out" "dev" "lib" ]; doCheck = true; - dontAddPrefix = true; + + # the configure script is not generated by autotools and does not accept the + # arguments that the default configurePhase passes like --prefix and --libdir + configurePhase = '' + runHook preConfigure + + ./configure + + runHook postConfigure + ''; installPhase = '' + runHook preInstall + install -Dm0755 build/cadical "$out/bin/cadical" install -Dm0755 build/mobical "$out/bin/mobical" - mkdir -p "$out/share/doc/${pname}-${version}/" - install -Dm0755 {LICEN?E,README*,VERSION} "$out/share/doc/${pname}-${version}/" + install -Dm0644 src/ccadical.h "$dev/include/ccadical.h" + install -Dm0644 build/libcadical.a "$lib/lib/libcadical.a" + mkdir -p "$out/share/doc/${pname}/" + install -Dm0755 {LICEN?E,README*,VERSION} "$out/share/doc/${pname}/" + + runHook postInstall ''; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/logic/elan/default.nix b/nixpkgs/pkgs/applications/science/logic/elan/default.nix index a49262e7cb65..1fb4693d64a2 100644 --- a/nixpkgs/pkgs/applications/science/logic/elan/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/elan/default.nix @@ -7,16 +7,16 @@ in rustPlatform.buildRustPackage rec { pname = "elan"; - version = "1.0.6"; + version = "1.0.7"; src = fetchFromGitHub { owner = "leanprover"; repo = "elan"; rev = "v${version}"; - sha256 = "sha256-Ns8vSS/PDlfopigW4Nz3fdR9PCMG8gDoL36+/s0Qkeo="; + sha256 = "sha256-SFY9RbUHoaOXCaK+uIqhnKbzSkbtWiS6os/JvsggagI="; }; - cargoSha256 = "sha256-NDtldiVo4SyE88f6ntKn1WJDFdvwN5Ps4DxQH15iNZE="; + cargoSha256 = "sha256-6TFionZw76V4htYQrz8eLX7ioW7Fbgd63rtz53s0TLU="; nativeBuildInputs = [ pkg-config makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/logic/lean/default.nix b/nixpkgs/pkgs/applications/science/logic/lean/default.nix index ea2cd356e315..5c6ad241cb76 100644 --- a/nixpkgs/pkgs/applications/science/logic/lean/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/lean/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.31.0"; + version = "3.32.1"; src = fetchFromGitHub { owner = "leanprover-community"; @@ -11,8 +11,8 @@ stdenv.mkDerivation rec { # from. this is then used to check whether an olean file should be # rebuilt. don't use a tag as rev because this will get replaced into # src/githash.h.in in preConfigure. - rev = "333783350cd3fe38f25fed1da7d6a433d8f85b77"; - sha256 = "sha256-N8Ju7pSGssvt84/0e1o6G/p7fWM1c0Mzw+ftL1/++J4="; + rev = "35b3a9c4e2d35cccb5ed220ea2f2909a4ed2ca90"; + sha256 = "0s69smknsvycvydbk2f3vcqj1z3jrbv3k048z2r46391dai5iwhf"; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/logic/logisim-evolution/default.nix b/nixpkgs/pkgs/applications/science/logic/logisim-evolution/default.nix new file mode 100644 index 000000000000..10266abffea1 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/logisim-evolution/default.nix @@ -0,0 +1,46 @@ +{ lib, stdenv, fetchurl, jre, makeWrapper, copyDesktopItems, makeDesktopItem, unzip }: + +stdenv.mkDerivation rec { + pname = "logisim-evolution"; + version = "3.5.0"; + + src = fetchurl { + url = "https://github.com/logisim-evolution/logisim-evolution/releases/download/v${version}/logisim-evolution-${version}-all.jar"; + sha256 = "1r6im4gmjbnckx8jig6bxi5lxv06lwdnpxkyfalsfmw4nybd5arw"; + }; + + dontUnpack = true; + + nativeBuildInputs = [ makeWrapper copyDesktopItems unzip ]; + + desktopItems = [ + (makeDesktopItem { + name = pname; + desktopName = "Logisim-evolution"; + exec = "logisim-evolution"; + icon = "logisim-evolution"; + comment = meta.description; + categories = "Education;"; + }) + ]; + + installPhase = '' + runHook preInstall + + mkdir -p $out/bin + makeWrapper ${jre}/bin/java $out/bin/logisim-evolution --add-flags "-jar $src" + + unzip $src resources/logisim/img/logisim-icon.svg + install -D resources/logisim/img/logisim-icon.svg $out/share/pixmaps/logisim-evolution.svg + + runHook postInstall + ''; + + meta = with lib; { + homepage = "https://github.com/logisim-evolution/logisim-evolution"; + description = "Digital logic designer and simulator"; + maintainers = with maintainers; [ angustrau ]; + license = licenses.gpl2Plus; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/logic/logisim/default.nix b/nixpkgs/pkgs/applications/science/logic/logisim/default.nix index 9b3f42dd4ba8..f94f08e43ab2 100644 --- a/nixpkgs/pkgs/applications/science/logic/logisim/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/logisim/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, jre, makeWrapper }: +{ lib, stdenv, fetchurl, jre, makeWrapper, copyDesktopItems, makeDesktopItem, unzip }: stdenv.mkDerivation rec { pname = "logisim"; @@ -11,17 +11,39 @@ stdenv.mkDerivation rec { dontUnpack = true; - nativeBuildInputs = [ makeWrapper ]; + nativeBuildInputs = [ makeWrapper copyDesktopItems unzip ]; + + desktopItems = [ + (makeDesktopItem { + name = pname; + desktopName = "Logisim"; + exec = "logisim"; + icon = "logisim"; + comment = meta.description; + categories = "Education;"; + }) + ]; installPhase = '' + runHook preInstall + mkdir -p $out/bin makeWrapper ${jre}/bin/java $out/bin/logisim --add-flags "-jar $src" + + # Create icons + unzip $src "resources/logisim/img/*" + for size in 16 20 24 48 64 128 + do + install -D "./resources/logisim/img/logisim-icon-$size.png" "$out/share/icons/hicolor/''${size}x''${size}/apps/logisim.png" + done + + runHook postInstall ''; meta = with lib; { - homepage = "http://ozark.hendrix.edu/~burch/logisim"; + homepage = "http://www.cburch.com/logisim/"; description = "Educational tool for designing and simulating digital logic circuits"; - maintainers = with maintainers; [ ]; + maintainers = with maintainers; [ angustrau ]; license = licenses.gpl2Plus; platforms = platforms.unix; }; diff --git a/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix b/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix index 1681d4545904..fd22b7b1add8 100644 --- a/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix @@ -6,13 +6,13 @@ stdenv.mkDerivation rec { pname = "opensmt"; - version = "2.0.1"; + version = "2.1.0"; src = fetchFromGitHub { owner = "usi-verification-and-security"; repo = "opensmt"; rev = "v${version}"; - sha256 = "uoIcXWsxxRsIuFsou3RcN9e48lc7cWMgRPVJLFVslDE="; + sha256 = "sha256-m8TpMBY1r0h8GJTHM4FLBuZtX+WK/Q7RTXUnNmUWV+o="; }; nativeBuildInputs = [ cmake bison flex ]; diff --git a/nixpkgs/pkgs/applications/science/logic/poly/default.nix b/nixpkgs/pkgs/applications/science/logic/poly/default.nix index 75ad91bc54de..c80b9bf1f0c4 100644 --- a/nixpkgs/pkgs/applications/science/logic/poly/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/poly/default.nix @@ -2,14 +2,14 @@ stdenv.mkDerivation rec { pname = "libpoly"; - version = "0.1.9"; + version = "0.1.10"; src = fetchFromGitHub { owner = "SRI-CSL"; repo = "libpoly"; # they've pushed to the release branch, use explicit tag rev = "refs/tags/v${version}"; - sha256 = "sha256-E2lHo8Bt4ujoGQ623fjkQbqRnDYJYilXdRt4lnF4wJk="; + sha256 = "sha256-22Y4L5NFnCzKwZt0A/ChMuGPU4Dk1Qyke6mdvfN063w="; }; # https://github.com/SRI-CSL/libpoly/pull/52 diff --git a/nixpkgs/pkgs/applications/science/logic/saw-tools/default.nix b/nixpkgs/pkgs/applications/science/logic/saw-tools/default.nix index 3eabc9422e38..df99d067f08c 100644 --- a/nixpkgs/pkgs/applications/science/logic/saw-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/saw-tools/default.nix @@ -48,8 +48,6 @@ stdenv.mkDerivation { done ''; - phases = "unpackPhase installPhase fixupPhase"; - meta = { description = "Tools for software verification and analysis"; homepage = "https://saw.galois.com"; diff --git a/nixpkgs/pkgs/applications/science/logic/tlaplus/tlaps.nix b/nixpkgs/pkgs/applications/science/logic/tlaplus/tlaps.nix index 89bdd979fea0..90a4aeb4f8ab 100644 --- a/nixpkgs/pkgs/applications/science/logic/tlaplus/tlaps.nix +++ b/nixpkgs/pkgs/applications/science/logic/tlaplus/tlaps.nix @@ -1,6 +1,12 @@ { fetchurl -, lib, stdenv -, ocaml, isabelle, cvc3, perl, wget, which +, lib +, stdenv +, ocaml +, isabelle +, cvc3 +, perl +, wget +, which }: stdenv.mkDerivation rec { @@ -13,8 +19,6 @@ stdenv.mkDerivation rec { buildInputs = [ ocaml isabelle cvc3 perl wget which ]; - phases = [ "unpackPhase" "installPhase" ]; - installPhase = '' mkdir -pv "$out" export HOME="$out" @@ -45,9 +49,9 @@ stdenv.mkDerivation rec { and scalable to large system specifications. It provides a consistent abstraction over the various “backend” verifiers. ''; - homepage = "https://tla.msr-inria.inria.fr/tlaps/content/Home.html"; - license = lib.licenses.bsd2; - platforms = lib.platforms.unix; + homepage = "https://tla.msr-inria.inria.fr/tlaps/content/Home.html"; + license = lib.licenses.bsd2; + platforms = lib.platforms.unix; maintainers = [ ]; }; diff --git a/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix b/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix index ef2d97ef6bfc..21c60d03ac1e 100644 --- a/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix +++ b/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix @@ -1,5 +1,13 @@ -{ lib, fetchzip, makeWrapper, makeDesktopItem, stdenv -, gtk3, libXtst, glib, zlib, wrapGAppsHook +{ lib +, fetchzip +, makeWrapper +, makeDesktopItem +, stdenv +, gtk3 +, libXtst +, glib +, zlib +, wrapGAppsHook }: let @@ -17,7 +25,8 @@ let }; -in stdenv.mkDerivation rec { +in +stdenv.mkDerivation rec { pname = "tla-toolbox"; version = "1.7.1"; src = fetchzip { @@ -31,8 +40,6 @@ in stdenv.mkDerivation rec { dontWrapGApps = true; - phases = [ "installPhase" ]; - installPhase = '' runHook preInstall diff --git a/nixpkgs/pkgs/applications/science/logic/verifast/default.nix b/nixpkgs/pkgs/applications/science/logic/verifast/default.nix index e426f7b80989..c610256ccaef 100644 --- a/nixpkgs/pkgs/applications/science/logic/verifast/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/verifast/default.nix @@ -20,11 +20,11 @@ let in stdenv.mkDerivation rec { pname = "verifast"; - version = "19.12"; + version = "21.04"; src = fetchurl { url = "https://github.com/verifast/verifast/releases/download/${version}/${pname}-${version}-linux.tar.gz"; - sha256 = "169kshjq4cf4i9v92azv0xaflrnik5686w7fwcgdhd6qkbzflzl6"; + sha256 = "sha256-PlRsf4wFXoM+E+60SbeKzs/RZK0HNVirX47AnI6NeYM="; }; dontConfigure = true; @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { meta = { description = "Verification for C and Java programs via separation logic"; - homepage = "http://people.cs.kuleuven.be/~bart.jacobs/verifast/"; + homepage = "https://people.cs.kuleuven.be/~bart.jacobs/verifast/"; license = lib.licenses.mit; platforms = [ "x86_64-linux" ]; maintainers = [ lib.maintainers.thoughtpolice ]; diff --git a/nixpkgs/pkgs/applications/science/logic/why3/default.nix b/nixpkgs/pkgs/applications/science/logic/why3/default.nix index 924ff3fd9fd2..b9f14332f9d8 100644 --- a/nixpkgs/pkgs/applications/science/logic/why3/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/why3/default.nix @@ -1,12 +1,12 @@ { callPackage, fetchurl, fetchpatch, lib, stdenv , ocamlPackages, coqPackages, rubber, hevea, emacs }: -stdenv.mkDerivation { +stdenv.mkDerivation rec { pname = "why3"; version = "1.4.0"; src = fetchurl { - url = "https://gforge.inria.fr/frs/download.php/file/38425/why3-1.4.0.tar.gz"; + url = "https://gforge.inria.fr/frs/download.php/file/38425/why3-${version}.tar.gz"; sha256 = "0lw0cpx347zz9vvwqibmbxgs80fsd16scgk3isscvwxnajpc3rv8"; }; diff --git a/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix b/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix index d4fdbfd6937c..fc08f5d7c85e 100644 --- a/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix +++ b/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix @@ -1,31 +1,30 @@ { stdenv, makeWrapper, runCommand, symlinkJoin, why3 }: provers: let configAwkScript = runCommand "why3-conf.awk" { inherit provers; } - '' - for p in $provers; do - for b in $p/bin/*; do - BASENAME=$(basename $b) - echo "/^command =/{ gsub(\"$BASENAME\", \"$b\") }" >> $out - done + '' + for p in $provers; do + for b in $p/bin/*; do + BASENAME=$(basename $b) + echo "/^command =/{ gsub(\"$BASENAME\", \"$b\") }" >> $out done - echo '{ print }' >> $out - ''; -in stdenv.mkDerivation { + done + echo '{ print }' >> $out + ''; +in +stdenv.mkDerivation { name = "${why3.name}-with-provers"; - phases = [ "buildPhase" "installPhase" ]; - nativeBuildInputs = [ makeWrapper ]; buildInputs = [ why3 ] ++ provers; buildPhase = '' - mkdir -p $out/share/why3/ - why3 config --detect-provers -C $out/share/why3/why3.conf - awk -i inplace -f ${configAwkScript} $out/share/why3/why3.conf + mkdir -p $out/share/why3/ + why3 config --detect-provers -C $out/share/why3/why3.conf + awk -i inplace -f ${configAwkScript} $out/share/why3/why3.conf ''; installPhase = '' - mkdir -p $out/bin - makeWrapper ${why3}/bin/why3 $out/bin/why3 --add-flags "--extra-config $out/share/why3/why3.conf" + mkdir -p $out/bin + makeWrapper ${why3}/bin/why3 $out/bin/why3 --add-flags "--extra-config $out/share/why3/why3.conf" ''; } diff --git a/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix b/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix index 63a946365604..2829cb59340b 100644 --- a/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/workcraft/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "workcraft"; - version = "3.3.2"; + version = "3.3.5"; src = fetchurl { url = "https://github.com/workcraft/workcraft/releases/download/v${version}/workcraft-v${version}-linux.tar.gz"; - sha256 = "0v71x3fph2j3xrnysvkm7zsgnbxisfbdfgxzvzxxfdg59a6l3xid"; + sha256 = "sha256-KErKYK3mmjp5uNdGQnjzUUIEwXT5fqbAPUunH72Mtig="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/machine-learning/finalfusion-utils/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/finalfusion-utils/default.nix index 6655b415d2ab..4c04b3c07368 100644 --- a/nixpkgs/pkgs/applications/science/machine-learning/finalfusion-utils/default.nix +++ b/nixpkgs/pkgs/applications/science/machine-learning/finalfusion-utils/default.nix @@ -11,16 +11,16 @@ rustPlatform.buildRustPackage rec { pname = "finalfusion-utils"; - version = "0.12.0"; + version = "0.13.0"; src = fetchFromGitHub { owner = "finalfusion"; repo = pname; rev = version; - sha256 = "0gxcjrhfa86kz5qmdf5h278ydc3nc0nfj61brnykb723mg45jj41"; + sha256 = "sha256-ME0qDSFD8G492+7ex7VQWh9P76a+tOCo+SJ9n9ZIYUI="; }; - cargoSha256 = "0dj3xpinzzdfgy06wkp336sp1nyqk7nnvd3hwhyysripmz9apdgg"; + cargoSha256 = "sha256-/rLv2/bcVsmWw+ZfyumDcj0ptHPQBCCYR9O/lVlV+G0="; # Enables build against a generic BLAS. cargoBuildFlags = [ diff --git a/nixpkgs/pkgs/applications/science/machine-learning/nengo-gui/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/nengo-gui/default.nix new file mode 100644 index 000000000000..6380f25177cb --- /dev/null +++ b/nixpkgs/pkgs/applications/science/machine-learning/nengo-gui/default.nix @@ -0,0 +1,26 @@ +{ lib, fetchFromGitHub, python3Packages }: + +python3Packages.buildPythonPackage rec { + pname = "nengo-gui"; + version = "0.4.8"; + + src = fetchFromGitHub { + owner = "nengo"; + repo = "nengo-gui"; + rev = "v${version}"; + sha256 = "1awb0h2l6yifb77zah7a4qzxqvkk4ac5fynangalidr10sk9rzk3"; + }; + + propagatedBuildInputs = with python3Packages; [ nengo ]; + + # checks req missing: + # pyimgur + doCheck = false; + + meta = with lib; { + description = "Nengo interactive visualizer"; + homepage = "https://nengo.ai/"; + license = licenses.unfreeRedistributable; + maintainers = with maintainers; [ arjix ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/machine-learning/vowpal-wabbit/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/vowpal-wabbit/default.nix index d1523b571f4b..7ecbe09f5e18 100644 --- a/nixpkgs/pkgs/applications/science/machine-learning/vowpal-wabbit/default.nix +++ b/nixpkgs/pkgs/applications/science/machine-learning/vowpal-wabbit/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "vowpal-wabbit"; - version = "8.10.0"; + version = "8.11.0"; src = fetchFromGitHub { owner = "VowpalWabbit"; repo = "vowpal_wabbit"; rev = version; - sha256 = "1vxnwanflsx6zf8m9mrxms28ii7rl61xfxp3556y3iawmy11d6pl"; + sha256 = "sha256-F3la4n1ULMN2nktr+PVWFPl3V2RfCowR0ozL+dnbhgA="; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix index 827c817fd1a6..a8fdfe8571a6 100644 --- a/nixpkgs/pkgs/applications/science/math/R/default.nix +++ b/nixpkgs/pkgs/applications/science/math/R/default.nix @@ -1,9 +1,10 @@ { lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng , libtiff, ncurses, pango, pcre2, perl, readline, tcl, texLive, tk, xz, zlib , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack -, curl, Cocoa, Foundation, libobjc, libcxx, tzdata, fetchpatch +, curl, Cocoa, Foundation, libobjc, libcxx, tzdata , withRecommendedPackages ? true , enableStrictBarrier ? false +, enableMemoryProfiling ? false # R as of writing does not support outputting both .so and .a files; it outputs: # --enable-R-static-lib conflicts with --enable-R-shlib and will be ignored , static ? false @@ -13,11 +14,11 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation rec { pname = "R"; - version = "4.0.4"; + version = "4.1.1"; src = fetchurl { url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz"; - sha256 = "0bl098xcv8v316kqnf43v6gb4kcsv31ydqfm1f7qr824jzb2fgsj"; + sha256 = "0r6kpnxjbvb7gdfg4m1z8zc6xd225vw81wrnf05ps9ajawk06pji"; }; dontUseImakeConfigure = true; @@ -30,7 +31,7 @@ stdenv.mkDerivation rec { patches = [ ./no-usr-local-search-paths.patch - ./fix-failing-test.patch + ./skip-check-for-aarch64.patch ]; prePatch = lib.optionalString stdenv.isDarwin '' @@ -56,6 +57,7 @@ stdenv.mkDerivation rec { --with-libtiff --with-ICU ${lib.optionalString enableStrictBarrier "--enable-strict-barrier"} + ${lib.optionalString enableMemoryProfiling "--enable-memory-profiling"} ${if static then "--enable-R-static-lib" else "--enable-R-shlib"} AR=$(type -p ar) AWK=$(type -p gawk) diff --git a/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch b/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch deleted file mode 100644 index 5fb3b3b9c317..000000000000 --- a/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch +++ /dev/null @@ -1,25 +0,0 @@ -From e8f54bc562eb301d204b5f880614be58a2b39a2b Mon Sep 17 00:00:00 2001 -From: maechler <maechler@00db46b3-68df-0310-9c12-caf00c1e9a41> -Date: Mon, 30 Mar 2020 19:15:59 +0000 -Subject: [PATCH] no longer fail in norm() check for broken OpenBLAS Lapack - 3.9.0 - -git-svn-id: https://svn.r-project.org/R/trunk@78112 00db46b3-68df-0310-9c12-caf00c1e9a41 ---- - tests/reg-tests-1d.R | 3 ++- - 1 file changed, 2 insertions(+), 1 deletion(-) - -diff --git a/tests/reg-tests-1d.R b/tests/reg-tests-1d.R -index 6b7de765a95..fafd6911e7a 100644 ---- a/tests/reg-tests-1d.R -+++ b/tests/reg-tests-1d.R -@@ -3836,7 +3836,8 @@ stopifnot(is.na( norm(diag(c(1, NA)), "2") )) - ## norm(<matrix-w-NA>, "F") - (m <- cbind(0, c(NA, 0), 0:-1)) - nTypes <- eval(formals(base::norm)$type) # "O" "I" "F" "M" "2" --stopifnot(is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN -+print( # stopifnot( -- for now, as Lapack is still broken in some OpenBLAS -- FIXME -+ is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN - ## "F" gave non-NA with LAPACK 3.9.0, before our patch in R-devel and R-patched - - diff --git a/nixpkgs/pkgs/applications/science/math/R/skip-check-for-aarch64.patch b/nixpkgs/pkgs/applications/science/math/R/skip-check-for-aarch64.patch new file mode 100644 index 000000000000..8721bf6b422d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/R/skip-check-for-aarch64.patch @@ -0,0 +1,11 @@ +diff -ur a/src/library/stats/man/nls.Rd b/src/library/stats/man/nls.Rd +--- a/src/library/stats/man/nls.Rd 2021-05-21 19:15:02.000000000 -0300 ++++ b/src/library/stats/man/nls.Rd 2021-08-12 12:39:00.094758280 -0300 +@@ -287,7 +287,7 @@ + options(digits = 10) # more accuracy for 'trace' + ## IGNORE_RDIFF_BEGIN + try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where central diff. work here: +- (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral=TRUE), trace=TRUE)) ++ (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral=TRUE, warnOnly=TRUE), trace=TRUE)) + ## --> convergence tolerance 4.997e-8 (in 11 iter.) + ## IGNORE_RDIFF_END diff --git a/nixpkgs/pkgs/applications/science/math/colpack/default.nix b/nixpkgs/pkgs/applications/science/math/colpack/default.nix index f203852c9657..3cc9290a7626 100644 --- a/nixpkgs/pkgs/applications/science/math/colpack/default.nix +++ b/nixpkgs/pkgs/applications/science/math/colpack/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, autoconf, automake, libtool, gettext }: +{ lib, stdenv, fetchFromGitHub, autoreconfHook }: stdenv.mkDerivation rec { @@ -12,20 +12,32 @@ stdenv.mkDerivation rec { sha256 = "1p05vry940mrjp6236c0z83yizmw9pk6ly2lb7d8rpb7j9h03glr"; }; - buildInputs = [ autoconf automake gettext libtool ]; + nativeBuildInputs = [ autoreconfHook ]; - configurePhase = '' - autoreconf -vif - ./configure --prefix=$out --enable-openmp + configureFlags = [ + "--enable-openmp=${if stdenv.isLinux then "yes" else "no"}" + "--enable-examples=no" + ]; + + postInstall = '' + # Remove libtool archive + rm $out/lib/*.la + + # Remove compiled examples (Basic examples get compiled anyway) + rm -r $out/examples + + # Copy the example sources (Basic tree contains scripts and object files) + mkdir -p $out/share/ColPack/examples/Basic + cp SampleDrivers/Basic/*.cpp $out/share/ColPack/examples/Basic + cp -r SampleDrivers/Matrix* $out/share/ColPack/examples ''; meta = with lib; { description = "A package comprising of implementations of algorithms for vertex coloring and derivative computation"; homepage = "http://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities"; - license = licenses.lgpl3; - platforms = platforms.linux; + license = licenses.lgpl3Plus; + platforms = platforms.unix; maintainers = with maintainers; [ edwtjo ]; }; - } diff --git a/nixpkgs/pkgs/applications/science/math/ginac/default.nix b/nixpkgs/pkgs/applications/science/math/ginac/default.nix index 901b9a340fea..78b64d7f587a 100644 --- a/nixpkgs/pkgs/applications/science/math/ginac/default.nix +++ b/nixpkgs/pkgs/applications/science/math/ginac/default.nix @@ -1,30 +1,34 @@ { lib, stdenv, fetchurl, cln, pkg-config, readline, gmp, python3 }: stdenv.mkDerivation rec { - name = "ginac-1.8.0"; + pname = "ginac"; + version = "1.8.1"; src = fetchurl { - url = "${meta.homepage}/${name}.tar.bz2"; - sha256 = "0l9byzfxq3f9az5pcdldnl95ws8mpirkqky46f973mvxi5541d24"; + url = "https://www.ginac.de/ginac-${version}.tar.bz2"; + sha256 = "sha256-8WldvWsYcGHvP7pQdkjJ1tukOPczsFjBb5J4y9z14as="; }; propagatedBuildInputs = [ cln ]; - buildInputs = [ readline ] ++ lib.optional stdenv.isDarwin gmp; + buildInputs = [ readline ] + ++ lib.optional stdenv.isDarwin gmp; nativeBuildInputs = [ pkg-config python3 ]; strictDeps = true; - preConfigure = "patchShebangs ginsh"; + preConfigure = '' + patchShebangs ginsh + ''; configureFlags = [ "--disable-rpath" ]; meta = with lib; { description = "GiNaC is Not a CAS"; - homepage = "https://www.ginac.de/"; + homepage = "https://www.ginac.de/"; maintainers = with maintainers; [ lovek323 ]; license = licenses.gpl2; - platforms = platforms.all; + platforms = platforms.all; }; } diff --git a/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix b/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix index f944499af401..876222772e86 100644 --- a/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix +++ b/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix @@ -1,40 +1,45 @@ -{ lib, stdenv, fetchurl }: +{ lib, stdenv, fetchurl, cctools, fixDarwinDylibNames }: stdenv.mkDerivation rec { pname = "lp_solve"; - version = "5.5.2.5"; + version = "5.5.2.11"; src = fetchurl { url = "mirror://sourceforge/project/lpsolve/lpsolve/${version}/lp_solve_${version}_source.tar.gz"; - sha256 = "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"; + sha256 = "sha256-bUq/9cxqqpM66ObBeiJt8PwLZxxDj2lxXUHQn+gfkC8="; }; - patches = [ ./isnan.patch ]; - - buildCommand = '' - . $stdenv/setup - tar xvfz $src - ( - cd lp_solve* - eval patchPhase - ) - ( - cd lp_solve*/lpsolve55 - bash ccc - mkdir -pv $out/lib - find bin -type f -exec cp -v "{}" $out/lib \; - ) - ( - cd lp_solve*/lp_solve - bash ccc - mkdir -pv $out/bin - find bin -type f -exec cp -v "{}" $out/bin \; - ) - ( - mkdir -pv $out/include - cp -v lp_solve*/*.h $out/include - ) + nativeBuildInputs = lib.optionals stdenv.isDarwin [ + cctools + fixDarwinDylibNames + ]; + + dontConfigure = true; + + buildPhase = let + ccc = if stdenv.isDarwin then "ccc.osx" else "ccc"; + in '' + runHook preBuild + + (cd lpsolve55 && bash -x -e ${ccc}) + (cd lp_solve && bash -x -e ${ccc}) + + runHook postBuild + ''; + + installPhase = '' + runHook preInstall + + install -d -m755 $out/bin $out/lib $out/include/lpsolve + install -m755 lp_solve/bin/*/lp_solve -t $out/bin + install -m644 lpsolve55/bin/*/liblpsolve* -t $out/lib + install -m644 lp_*.h -t $out/include/lpsolve + + rm $out/lib/liblpsolve*.a + rm $out/include/lpsolve/lp_solveDLL.h # A Windows header + + runHook postInstall ''; meta = with lib; { @@ -44,6 +49,4 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ smironov ]; platforms = platforms.unix; }; - } - diff --git a/nixpkgs/pkgs/applications/science/math/lp_solve/isnan.patch b/nixpkgs/pkgs/applications/science/math/lp_solve/isnan.patch deleted file mode 100644 index bc1983d4423d..000000000000 --- a/nixpkgs/pkgs/applications/science/math/lp_solve/isnan.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff -u a/lp_lib.h b/lp_lib.h ---- a/lp_lib.h 2016-05-04 19:45:15.753143720 +0900 -+++ b/lp_lib.h 2016-05-04 19:53:59.536920722 +0900 -@@ -59,9 +59,6 @@ - # if defined _WIN32 && !defined __GNUC__ - # define isnan _isnan - # endif --#if defined NOISNAN --# define isnan(x) FALSE --#endif - - #define SETMASK(variable, mask) variable |= mask - #define CLEARMASK(variable, mask) variable &= ~(mask) diff --git a/nixpkgs/pkgs/applications/science/math/maxima/default.nix b/nixpkgs/pkgs/applications/science/math/maxima/default.nix index 01f086c92c75..2b82a8f81705 100644 --- a/nixpkgs/pkgs/applications/science/math/maxima/default.nix +++ b/nixpkgs/pkgs/applications/science/math/maxima/default.nix @@ -1,14 +1,16 @@ -{ lib, stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python, makeWrapper, autoreconfHook +{ lib, stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python3, makeWrapper, autoreconfHook , rlwrap ? null, tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false }: let name = "maxima"; - version = "5.44.0"; + version = "5.45.0"; + + lisp-compiler = if ecl-fasl then ecl else sbcl; searchPath = lib.makeBinPath - (lib.filter (x: x != null) [ sbcl ecl rlwrap tk gnuplot ]); + (lib.filter (x: x != null) [ lisp-compiler rlwrap tk gnuplot ]); in stdenv.mkDerivation ({ inherit version; @@ -16,14 +18,21 @@ stdenv.mkDerivation ({ src = fetchurl { url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz"; - sha256 = "1v6jr5s6hhj6r18gfk6hgxk2qd6z1dxkrjq9ss2z1y6sqi45wgyr"; + sha256 = "sha256-x2MfMmRIBc67e6/vOrUzHEus0sJ+OE/YgyO1A5pg0Ng="; }; - nativeBuildInputs = [ autoreconfHook ]; + nativeBuildInputs = [ + autoreconfHook + lisp-compiler + makeWrapper + python3 + texinfo + ]; + + strictDeps = true; - buildInputs = lib.filter (x: x != null) [ - sbcl ecl texinfo perl python makeWrapper - gnuplot # required in the test suite + checkInputs = [ + gnuplot ]; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/math/nasc/default.nix b/nixpkgs/pkgs/applications/science/math/nasc/default.nix index b55e4047fe47..431668f0c583 100644 --- a/nixpkgs/pkgs/applications/science/math/nasc/default.nix +++ b/nixpkgs/pkgs/applications/science/math/nasc/default.nix @@ -21,26 +21,16 @@ stdenv.mkDerivation rec { pname = "nasc"; - version = "0.7.5"; + version = "0.8.0"; src = fetchFromGitHub { owner = "parnold-x"; repo = pname; rev = version; - sha256 = "kSRc5RLkI6SBJirUYw6swZi8IJhaL3y74b2Zw8kh2XA="; + sha256 = "02b9a59a9fzsb6nn3ycwwbcbv04qfzm6x7csq2addpzx5wak6dd8"; fetchSubmodules = true; }; - patches = [ - # fix compilation with gcc10 - (fetchpatch { - url = "https://github.com/parnold-x/libqalculate/commit/4fa8f2cceada128ef19f82407226b2c230b780d5.patch"; - extraPrefix = "subprojects/libqalculate/"; - stripLen = "1"; - sha256 = "0kbff623zl0s6yx5avx068f2apwzxzvihjahja4qhlkqkhhzj9dm"; - }) - ]; - nativeBuildInputs = [ glib # post_install.py gtk3 # post_install.py diff --git a/nixpkgs/pkgs/applications/science/math/nauty/default.nix b/nixpkgs/pkgs/applications/science/math/nauty/default.nix index a941a6334508..c435c63ab2ef 100644 --- a/nixpkgs/pkgs/applications/science/math/nauty/default.nix +++ b/nixpkgs/pkgs/applications/science/math/nauty/default.nix @@ -6,7 +6,7 @@ stdenv.mkDerivation rec { pname = "nauty"; version = "27r1"; src = fetchurl { - url = "http://pallini.di.uniroma1.it/nauty${version}.tar.gz"; + url = "https://pallini.di.uniroma1.it/nauty${version}.tar.gz"; sha256 = "0xsfqfcknbd6g6wzpa5l7crmmk3bf3zjh37rhylq6b20dqcmvjkn"; }; outputs = [ "out" "dev" ]; @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { # I'm not sure if the filename will remain the same for future changelog or # if it will track changes to minor releases. Lets see. Better than nothing # in any case. - changelog = "http://pallini.di.uniroma1.it/changes24-27.txt"; - homepage = "http://pallini.di.uniroma1.it/"; + changelog = "https://pallini.di.uniroma1.it/changes24-27.txt"; + homepage = "https://pallini.di.uniroma1.it/"; }; } diff --git a/nixpkgs/pkgs/applications/science/math/polymake/default.nix b/nixpkgs/pkgs/applications/science/math/polymake/default.nix index b1abb31c7650..9566801479a3 100644 --- a/nixpkgs/pkgs/applications/science/math/polymake/default.nix +++ b/nixpkgs/pkgs/applications/science/math/polymake/default.nix @@ -1,27 +1,32 @@ { lib, stdenv, fetchurl -, ninja, libxml2, libxslt, readline, perl, gmp, mpfr, boost +, perl, gmp, mpfr, flint, boost , bliss, ppl, singular, cddlib, lrs, nauty -, ant, openjdk +, ninja, ant, openjdk , perlPackages , makeWrapper }: +# polymake compiles its own version of sympol and atint because we +# don't have those packages. other missing optional dependencies: +# javaview, libnormaliz, scip, soplex, jreality. + stdenv.mkDerivation rec { pname = "polymake"; - version = "3.2.rc4"; + version = "4.4"; src = fetchurl { - url = "https://polymake.org/lib/exe/fetch.php/download/polymake-3.2r4.tar.bz2"; - sha256 = "02jpkvy1cc6kc23vkn7nkndzr40fq1gkb3v257bwyi1h5d37fyqy"; + # "The minimal version is a packager friendly version which omits + # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality." + url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2"; + sha256 = "sha256-2nF5F2xznI77pl2TslrxA8HLpw4fmzVnPOM8N3kOwJE="; }; buildInputs = [ - libxml2 libxslt readline perl gmp mpfr boost + perl gmp mpfr flint boost bliss ppl singular cddlib lrs nauty openjdk - ] ++ - (with perlPackages; [ - XMLLibXML XMLLibXSLT XMLWriter TermReadLineGnu TermReadKey + ] ++ (with perlPackages; [ + JSON TermReadLineGnu TermReadKey XMLSAX ]); nativeBuildInputs = [ @@ -36,11 +41,11 @@ stdenv.mkDerivation rec { done ''; - meta = { + meta = with lib; { description = "Software for research in polyhedral geometry"; - license = lib.licenses.gpl2 ; - maintainers = [lib.maintainers.raskin]; - platforms = lib.platforms.linux; + license = licenses.gpl2Plus; + maintainers = teams.sage.members; + platforms = platforms.linux; homepage = "https://www.polymake.org/doku.php"; }; } diff --git a/nixpkgs/pkgs/applications/science/math/pynac/default.nix b/nixpkgs/pkgs/applications/science/math/pynac/default.nix index 138c97d73be1..88515b92beaf 100644 --- a/nixpkgs/pkgs/applications/science/math/pynac/default.nix +++ b/nixpkgs/pkgs/applications/science/math/pynac/default.nix @@ -1,4 +1,5 @@ { lib, stdenv +, fetchpatch , fetchFromGitHub , autoreconfHook , pkg-config @@ -20,6 +21,16 @@ stdenv.mkDerivation rec { sha256 = "sha256-ocR7emXtKs+Xe2f6dh4xEDAacgiolY8mtlLnWnNBS8A="; }; + patches = [ + # the patch below is included in sage 9.4 and should be included + # in a future pynac release. see https://trac.sagemath.org/ticket/28357 + (fetchpatch { + name = "realpartloop.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/realpartloop.patch?h=9.4.beta5"; + sha256 = "sha256-1nj0xtlFN5fZKEiRLD+tiW/ZtxMQre1ziEGA0OVUGE4="; + }) + ]; + buildInputs = [ flint gmp diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix index 7807ae613e8c..bc192fe4218b 100644 --- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "qalculate-gtk"; - version = "3.19.0"; + version = "3.20.1"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v"; + sha256 = "sha256-GTOdJ4dxR491WU6WM47xLHO7RGUGXkdHuQIDxJvVvFE="; }; hardeningDisable = [ "format" ]; diff --git a/nixpkgs/pkgs/applications/science/math/sage/default.nix b/nixpkgs/pkgs/applications/science/math/sage/default.nix index e39db4b1ac2d..b7821db1f9a7 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/default.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/default.nix @@ -38,8 +38,8 @@ let ]; language = "sagemath"; # just one 16x16 logo is available - logo32 = "${sage-src}/doc/common/themes/sage/static/sageicon.png"; - logo64 = "${sage-src}/doc/common/themes/sage/static/sageicon.png"; + logo32 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png"; + logo64 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png"; }; three = callPackage ./threejs-sage.nix { }; diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch index 0dbfba642e82..178cef3e54ea 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch @@ -1,8 +1,8 @@ diff --git a/src/sage/env.py b/src/sage/env.py -index 2908f5d04f..81dfd75c0d 100644 +index 95980cc2df..37107a30e1 100644 --- a/src/sage/env.py +++ b/src/sage/env.py -@@ -218,93 +218,12 @@ NTL_LIBDIR = var("NTL_LIBDIR") +@@ -227,93 +227,12 @@ OPENMP_CXXFLAGS = var("OPENMP_CXXFLAGS", "") SAGE_BANNER = var("SAGE_BANNER", "") SAGE_IMPORTALL = var("SAGE_IMPORTALL", "yes") @@ -51,10 +51,9 @@ index 2908f5d04f..81dfd75c0d 100644 - if sys.platform == 'cygwin': - # Later down we take the first matching DLL found, so search - # SAGE_LOCAL first so that it takes precedence -- search_directories = [ -- Path(SAGE_LOCAL) / 'bin', -- Path(sysconfig.get_config_var('BINDIR')), -- ] +- if SAGE_LOCAL: +- search_directories.append(Path(SAGE_LOCAL) / 'bin') +- search_directories.append(Path(sysconfig.get_config_var('BINDIR'))) - # Note: The following is not very robust, since if there are multible - # versions for the same library this just selects one more or less - # at arbitrary. However, practically speaking, on Cygwin, there @@ -66,14 +65,15 @@ index 2908f5d04f..81dfd75c0d 100644 - else: - ext = 'so' - -- search_directories = [Path(SAGE_LOCAL) / 'lib'] +- if SAGE_LOCAL: +- search_directories.append(Path(SAGE_LOCAL) / 'lib') - libdir = sysconfig.get_config_var('LIBDIR') - if libdir is not None: - libdir = Path(libdir) - search_directories.append(libdir) - - multiarchlib = sysconfig.get_config_var('MULTIARCH') -- if multiarchlib is not None: +- if multiarchlib is not None: - search_directories.append(libdir / multiarchlib), - - patterns = [f'lib{libname}.{ext}'] @@ -97,4 +97,4 @@ index 2908f5d04f..81dfd75c0d 100644 +GAP_SO = var("GAP_SO", '/default') # post process - if ' ' in DOT_SAGE: + if DOT_SAGE is not None and ' ' in DOT_SAGE: diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch deleted file mode 100644 index a91ee319b8f0..000000000000 --- a/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff --git a/src/sage/tests/cmdline.py b/src/sage/tests/cmdline.py -index 6e034dcb5a..8ec60ec72b 100644 ---- a/src/sage/tests/cmdline.py -+++ b/src/sage/tests/cmdline.py -@@ -660,8 +660,8 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False - sage: with open(input, 'w') as F: - ....: _ = F.write(s) - sage: L = ["sage", "--rst2ipynb", input, output] -- sage: test_executable(L) # optional - rst2ipynb -- ('', '', 0) -+ sage: test_executable(L)[2] # optional - rst2ipynb -+ 0 - sage: import json # optional - rst2ipynb - sage: d = json.load(open(output,'r')) # optional - rst2ipynb - sage: type(d) # optional - rst2ipynb -@@ -757,8 +757,6 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False - /// - 4 - }}} -- sage: err # py2 # optional -- sagenb -- '' - sage: ret # py2 # optional -- sagenb - 0 - diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix index 218ab920a872..3ba21cf6c8be 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix @@ -13,30 +13,52 @@ let # Fetch a diff between `base` and `rev` on sage's git server. # Used to fetch trac tickets by setting the `base` to the last release and the # `rev` to the last commit of the ticket. - fetchSageDiff = { base, name, rev, sha256, ...}@args: ( + fetchSageDiff = { base, name, rev, sha256, squashed ? false, ...}@args: ( fetchpatch ({ inherit name sha256; - # We used to use - # "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}" - # but the former way does not squash multiple patches together. - url = "https://github.com/sagemath/sage/compare/${base}...${rev}.diff"; + # There are three places to get changes from: + # + # 1) From Sage's Trac. Contains all release tags (like "9.4") and all developer + # branches (wip patches from tickets), but exports each commit as a separate + # patch, so merge commits can lead to conflicts. Used if squashed == false. + # + # 2) From GitHub's sagemath/sage repo. This lets us use a GH feature that allows + # us to choose between a .patch file, with one patch per commit, or a .diff file, + # which squashes all commits into a single diff. This is used if squashed == + # true. This repo has all release tags. However, it has no developer branches, so + # this option can't be used if a change wasn't yet shipped in a (possibly beta) + # release. + # + # 3) From GitHub's sagemath/sagetrac-mirror repo. Mirrors all developer branches, + # but has no release tags. The only use case not covered by 1 or 2 is when we need + # to apply a patch from an open ticket that contains merge commits. + # + # Item 3 could cover all use cases if the sagemath/sagetrack-mirror repo had + # release tags, but it requires a sha instead of a release number in "base", which + # is inconvenient. + urls = if squashed + then [ + "https://github.com/sagemath/sage/compare/${base}...${rev}.diff" + "https://github.com/sagemath/sagetrac-mirror/compare/${base}...${rev}.diff" + ] + else [ "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}" ]; # We don't care about sage's own build system (which builds all its dependencies). # Exclude build system changes to avoid conflicts. excludes = [ "build/*" ]; - } // builtins.removeAttrs args [ "rev" "base" "sha256" ]) + } // builtins.removeAttrs args [ "rev" "base" "sha256" "squashed" ]) ); in stdenv.mkDerivation rec { - version = "9.3"; + version = "9.4"; pname = "sage-src"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "sha256-l9DX8jcDdKA7GJ6xU+nBsmlZxrcZ9ZUAJju621ooBEo="; + sha256 = "sha256-jqkr4meG02KbTCMsGvyr1UbosS4ZuUJhPXU/InuS+9A="; }; # Patches needed because of particularities of nix or the way this is packaged. @@ -77,63 +99,16 @@ stdenv.mkDerivation rec { # be empty since dependencies update all the time. packageUpgradePatches = [ # After updating smypow to (https://trac.sagemath.org/ticket/3360) we can - # now set the cache dir to be withing the .sage directory. This is not + # now set the cache dir to be within the .sage directory. This is not # strictly necessary, but keeps us from littering in the user's HOME. ./patches/sympow-cache.patch - # ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests - ./patches/ignore-cmp-deprecation.patch - - # remove use of matplotlib function deprecated in 3.4 - # https://trac.sagemath.org/ticket/31827 - (fetchSageDiff { - base = "9.3"; - name = "remove-matplotlib-deprecated-function.patch"; - rev = "32b2bcaefddc4fa3d2aee6fa690ce1466cbb5948"; - sha256 = "sha256-SXcUGBMOoE9HpuBzgKC3P6cUmM5MiktXbe/7dVdrfWo="; - }) - - # pari 2.13 update - # https://trac.sagemath.org/ticket/30801 - # - # the last commit in that ticket is - # c78b1470fccd915e2fa93f95f2fefba6220fb1f7, but commits after - # 10a4531721d2700fd717e2b3a1364508ffd971c3 only deal with 32-bit - # and post-26635 breakage, none of which is relevant to us. since - # there are post-9.4.beta0 rebases after that, we just skip later - # commits. - (fetchSageDiff { - base = "9.3"; - name = "pari-2.13.1.patch"; - rev = "10a4531721d2700fd717e2b3a1364508ffd971c3"; - sha256 = "sha256-gffWKK9CMREaNOb5zb63iZUgON4FvsPrMQNqe+5ZU9E="; - }) - - # sympy 1.8 update - # https://trac.sagemath.org/ticket/31647 - (fetchSageDiff { - base = "9.4.beta0"; - name = "sympy-1.8.patch"; - rev = "fa864b36e15696450c36d54215b1e68183b29d25"; - sha256 = "sha256-fj/9QEZlVF0fw9NpWflkTuBSKpGjCE6b96ECBgdn77o="; - }) - - # sphinx 4 update - # https://trac.sagemath.org/ticket/31696 - (fetchSageDiff { - base = "9.4.beta3"; - name = "sphinx-4.patch"; - rev = "bc84af8c795b7da433d2000afc3626ee65ba28b8"; - sha256 = "sha256-5Kvs9jarC8xRIU1rdmvIWxQLC25ehiTLJpg5skh8WNM="; - }) - - # eclib 20210625 update - # https://trac.sagemath.org/ticket/31443 + # https://trac.sagemath.org/ticket/32305 (fetchSageDiff { - base = "9.4.beta3"; - name = "eclib-20210625.patch"; - rev = "789550ca04c94acfb1e803251538996a34962038"; - sha256 = "sha256-VlyEn5hg3joG8t/GwiRfq9TzJ54AoHxLolsNQ3shc2c="; + base = "9.4"; + name = "networkx-2.6-upgrade.patch"; + rev = "9808325853ba9eb035115e5b056305a1c9d362a0"; + sha256 = "sha256-gJSqycCtbAVr5qnVEbHFUvIuTOvaxFIeffpzd6nH4DE="; }) ]; diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix index f60cb64d2e8d..b9c98ed64d01 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix @@ -27,6 +27,7 @@ , linbox , m4ri , m4rie +, memory-allocator , libmpc , mpfi , ntl @@ -107,6 +108,7 @@ buildPythonPackage rec { lrcalc m4ri m4rie + memory-allocator mpfi ntl blas diff --git a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix index f9abdee2d148..5dea2c7653aa 100644 --- a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix +++ b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix @@ -39,8 +39,6 @@ stdenv.mkDerivation { xorg.libXxf86vm ]; - phases = [ "unpackPhase" "fixupPhase" "installPhase" ]; - fixupPhase = '' sed -i 's|\$(/bin/|$(|g' bin/scilab sed -i 's|/usr/bin/||g' bin/scilab diff --git a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix index 94e675d7dd44..2205e96383a4 100644 --- a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix +++ b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { pname = "wxmaxima"; - version = "21.02.0"; + version = "21.05.2"; src = fetchFromGitHub { owner = "wxMaxima-developers"; repo = "wxmaxima"; rev = "Version-${version}"; - sha256 = "sha256-5nvaaKsvSEs7QxOszjDK1Xkana2er1BCMZ83b1JZSqc="; + sha256 = "sha256-HPqdxGrPxe5FZNOimTpAP+c9VpDBkXu3Z1c1Aaf3+UA="; }; buildInputs = [ wxGTK maxima gnome.adwaita-icon-theme ]; diff --git a/nixpkgs/pkgs/applications/science/medicine/dcmtk/default.nix b/nixpkgs/pkgs/applications/science/medicine/dcmtk/default.nix index 8a06260ebc71..b6a9c161638a 100644 --- a/nixpkgs/pkgs/applications/science/medicine/dcmtk/default.nix +++ b/nixpkgs/pkgs/applications/science/medicine/dcmtk/default.nix @@ -26,6 +26,6 @@ stdenv.mkDerivation rec { homepage = "https://dicom.offis.de/dcmtk"; license = licenses.bsd3; maintainers = with maintainers; [ iimog ]; - platforms = platforms.linux; + platforms = with platforms; linux ++ darwin; }; } diff --git a/nixpkgs/pkgs/applications/science/misc/cwltool/default.nix b/nixpkgs/pkgs/applications/science/misc/cwltool/default.nix new file mode 100644 index 000000000000..21e3c47b323d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/cwltool/default.nix @@ -0,0 +1,41 @@ +{ lib +, python3Packages +}: + +python3Packages.buildPythonApplication rec { + pname = "cwltool"; + version = "3.1.20210628163208"; + + src = python3Packages.fetchPypi { + inherit pname version; + sha256 = "21b885f725420413d2f87eadc5e81c08a9c91beceda89b35d1a702ec4df47e52"; + }; + + postPatch = '' + substituteInPlace setup.py \ + --replace 'prov == 1.5.1' 'prov' + ''; + + propagatedBuildInputs = with python3Packages; [ + argcomplete + bagit + coloredlogs + mypy-extensions + prov + psutil + pydot + schema-salad + shellescape + typing-extensions + ]; + + doCheck = false; # hard to setup + pythonImportsCheck = [ "cwltool" ]; + + meta = with lib; { + homepage = "https://www.commonwl.org"; + license = with licenses; [ asl20 ]; + description = "Common Workflow Language reference implementation"; + maintainers = with maintainers; [ veprbl ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/combined/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/combined/default.nix new file mode 100644 index 000000000000..459a325111e2 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/combined/default.nix @@ -0,0 +1,30 @@ +{ stdenv, lib, openmodelica, symlinkJoin, gnumake, blas, lapack, makeWrapper }: +symlinkJoin { + name = "openmodelica-combined"; + paths = with openmodelica; [ + omcompiler + omsimulator + omplot + omparser + omedit + omlibrary + omshell + ]; + + buildInputs = [ gnumake makeWrapper ]; + + postBuild = '' + wrapProgram $out/bin/OMEdit \ + --prefix PATH : ${lib.makeBinPath [ gnumake stdenv.cc ]} \ + --prefix LIBRARY_PATH : "${lib.makeLibraryPath [ blas lapack ]}" \ + --set-default OPENMODELICALIBRARY "${openmodelica.omlibrary}/lib/omlibrary" + ''; + + meta = with lib; { + description = "An open-source Modelica-based modeling and simulation environment intended for industrial and academic usage"; + homepage = "https://openmodelica.org"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/default.nix index cab0fa5ff5c6..10fccfdf6da8 100644 --- a/nixpkgs/pkgs/applications/science/misc/openmodelica/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/default.nix @@ -1,53 +1,17 @@ -{lib, stdenv, fetchgit, fetchsvn, autoconf, automake, libtool, gfortran, clang, cmake, gnumake, -hwloc, jre, lapack, blas, hdf5, expat, ncurses, readline, qt4, webkitgtk, which, -lp_solve, omniorb, sqlite, libatomic_ops, pkg-config, file, gettext, flex, bison, -doxygen, boost, openscenegraph, gnome2, xorg, git, bash, gtk2, makeWrapper }: - -let - - fakegit = import ./fakegit.nix { inherit lib stdenv fetchgit fetchsvn bash; }; - -in - -stdenv.mkDerivation { - name = "openmodelica"; - - src = fetchgit (import ./src-main.nix); - - buildInputs = [autoconf cmake automake libtool gfortran clang gnumake - hwloc jre lapack blas hdf5 expat ncurses readline qt4 webkitgtk which - lp_solve omniorb sqlite libatomic_ops pkg-config file gettext flex bison - doxygen boost openscenegraph gnome2.gtkglext xorg.libXmu - git gtk2 makeWrapper]; - - hardeningDisable = [ "format" ]; - - patchPhase = '' - cp -fv ${fakegit}/bin/checkout-git.sh libraries/checkout-git.sh - cp -fv ${fakegit}/bin/checkout-svn.sh libraries/checkout-svn.sh - ''; - - configurePhase = '' - export NIX_LDFLAGS="$NIX_LDFLAGS -L${gfortran.cc.lib}/lib" - - autoconf - ./configure CC=${clang}/bin/clang CXX=${clang}/bin/clang++ --prefix=$out - ''; - - postFixup = '' - for e in $(cd $out/bin && ls); do - wrapProgram $out/bin/$e \ - --prefix PATH : "${gnumake}/bin" \ - --prefix LIBRARY_PATH : "${lib.makeLibraryPath [ lapack blas ]}" - done - ''; - - meta = with lib; { - description = "An open-source Modelica-based modeling and simulation environment"; - homepage = "https://openmodelica.org"; - license = licenses.gpl3; - maintainers = with maintainers; [ smironov ]; - platforms = platforms.linux; - broken = true; - }; -} +{ lib, newScope, libsForQt5, clangStdenv }: +lib.makeScope newScope (self: + let + callPackage = self.newScope { stdenv = clangStdenv; }; + callQtPackage = self.newScope (libsForQt5 // { stdenv = clangStdenv; }); + in + { + mkOpenModelicaDerivation = callPackage ./mkderivation { }; + omcompiler = callPackage ./omcompiler { }; + omplot = callQtPackage ./omplot { }; + omsimulator = callPackage ./omsimulator { }; + omparser = callPackage ./omparser { }; + omedit = callQtPackage ./omedit { }; + omlibrary = callPackage ./omlibrary { }; + omshell = callQtPackage ./omshell { }; + combined = callPackage ./combined { }; + }) diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/fakegit.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/fakegit.nix deleted file mode 100644 index 47cca7c74917..000000000000 --- a/nixpkgs/pkgs/applications/science/misc/openmodelica/fakegit.nix +++ /dev/null @@ -1,81 +0,0 @@ -{ lib, stdenv, fetchgit, fetchsvn, bash }: - -let - mkscript = path : text : '' - mkdir -pv `dirname ${path}` - cat > ${path} <<"EOF" - #!${bash}/bin/bash - ME=`basename ${path}` - ${text} - EOF - sed -i "s@%out@$out@g" ${path} - chmod +x ${path} - ''; - - hashname = r: let - rpl = lib.replaceChars [":" "/"] ["_" "_"]; - in - (rpl r.url) + "-" + (rpl r.rev); - -in - -stdenv.mkDerivation { - name = "fakegit"; - - buildCommand = '' - mkdir -pv $out/repos - ${lib.concatMapStrings - (r : '' - cp -r ${fetchgit r} $out/repos/${hashname r} - '' - ) (import ./src-libs-git.nix) - } - - ${mkscript "$out/bin/checkout-git.sh" '' - if test "$#" -ne 4; then - echo "Usage: $0 DESTINATION URL GITBRANCH HASH" - exit 1 - fi - DEST=$1 - URL=`echo $2 | tr :/ __` - GITBRANCH=$3 - REVISION=$4 - - L=`echo $REVISION | wc -c` - if expr $L '<' 10 >/dev/null; then - REVISION=refs/tags/$REVISION - fi - - REVISION=`echo $REVISION | tr :/ __` - - rm -rf $DEST - mkdir -pv $DEST - echo "FAKEGIT cp -r %out/repos/$URL-$REVISION $DEST" >&2 - cp -r %out/repos/$URL-$REVISION/* $DEST - chmod u+w -R $DEST - ''} - - ${lib.concatMapStrings - (r : '' - cp -r ${fetchsvn r} $out/repos/${hashname r} - '' - ) (import ./src-libs-svn.nix) - } - - ${mkscript "$out/bin/checkout-svn.sh" '' - if test "$#" -ne 3; then - echo "Usage: $0 DESTINATION URL REVISION" - exit 1 - fi - DEST=$1 - URL=`echo $2 | tr :/ __` - REVISION=`echo $4 | tr :/ __` - - rm -rf $DEST - mkdir -pv $DEST - echo "FAKE COPY %out/repos/$URL-$REVISION $DEST" - cp -r %out/repos/$URL-$REVISION/* $DEST - chmod u+w -R $DEST - ''} - ''; -} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/mkderivation/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/mkderivation/default.nix new file mode 100644 index 000000000000..94029fead48e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/mkderivation/default.nix @@ -0,0 +1,101 @@ +# mkOpenModelicaDerivation is an mkDerivation function for packages +# from OpenModelica suite. + +{ stdenv, lib, fetchgit, autoconf, automake, libtool, cmake, autoreconfHook, symlinkJoin }: +pkg: +let + inherit (builtins) hasAttr getAttr length elemAt; + inherit (lib) attrByPath concatStringsSep; + + + # A few helpers functions: + + # getAttrDef is just a getAttr with default fallback + getAttrDef = attr: default: x: attrByPath [ attr ] default x; + + # getAttr-like helper for optional append to string: + # "Hello" + appendByAttr "a" " " {a = "world";} = "Hello world" + # "Hello" + appendByAttr "a" " " {} = "Hello" + appendByAttr = attr: sep: x: if hasAttr attr x then sep + (getAttr attr x) else ""; + + # Are there any OM dependencies at all? + ifDeps = length pkg.omdeps != 0; + + # Dependencies of current OpenModelica-target joined in one file tree. + # Return the dep itself in case it is a single one. + joinedDeps = + if length pkg.omdeps == 1 + then elemAt pkg.omdeps 0 + else + symlinkJoin { + name = pkg.pname + "-omhome"; + paths = pkg.omdeps; + }; + + # Should we run ./configure for the target pkg? + omautoconf = getAttrDef "omautoconf" false pkg; + + # Name of the make target + omtarget = getAttrDef "omtarget" pkg.pname pkg; + + # Directory of target sources + omdir = getAttrDef "omdir" pkg.pname pkg; + + # Simple to to m4 configuration scripts + postPatch = lib.optionalString ifDeps '' + sed -i ''$(find -name omhome.m4) -e 's|if test ! -z "$USINGPRESETBUILDDIR"|if test ! -z "$USINGPRESETBUILDDIR" -a -z "$OMHOME"|' + '' + + appendByAttr "postPatch" "\n" pkg; + + # Update shebangs in the scripts before running configuration. + preAutoreconf = "patchShebangs --build common" + + appendByAttr "preAutoreconf" "\n" pkg; + + # Tell OpenModelica where built dependencies are located. + configureFlags = lib.optional ifDeps "--with-openmodelicahome=${joinedDeps}" ++ + getAttrDef "configureFlags" [ ] pkg; + + # Our own configurePhase that accounts for omautoconf + configurePhase = '' + runHook preConfigure + export configureFlags="''${configureFlags} --with-ombuilddir=$PWD/build --prefix=$prefix" + ./configure --no-recursion $configureFlags + ${lib.optionalString omautoconf "(cd ${omdir}; ./configure $configureFlags)"} + runHook postConfigure + ''; + + # Targets that we want to build ourselves: + deptargets = lib.forEach pkg.omdeps (dep: dep.omtarget); + + # ... so we ask openmodelica makefile to skip those targets. + preBuild = '' + for target in ${concatStringsSep " " deptargets}; do + touch ''${target}.skip; + done + '' + + appendByAttr "preBuild" "\n" pkg; + + makeFlags = "${omtarget}" + + appendByAttr "makeFlags" " " pkg; + + installFlags = "-i " + + appendByAttr "installFlags" " " pkg; + + +in +stdenv.mkDerivation (pkg // { + inherit omtarget postPatch preAutoreconf configureFlags configurePhase preBuild makeFlags installFlags; + + src = fetchgit (import ./src-main.nix); + version = "1.17.0"; + + nativeBuildInputs = getAttrDef "nativeBuildInputs" [ ] pkg + ++ [ autoconf automake libtool cmake autoreconfHook ]; + + buildInputs = getAttrDef "buildInputs" [ ] pkg + ++ lib.optional ifDeps joinedDeps; + + dontUseCmakeConfigure = true; + + hardeningDisable = [ "format" ]; +}) diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/mkderivation/src-main.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/mkderivation/src-main.nix new file mode 100644 index 000000000000..c31b23d2f948 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/mkderivation/src-main.nix @@ -0,0 +1,7 @@ +{ + url = "https://github.com/OpenModelica/OpenModelica/"; + rev = "08fd3f9144235f209a4ed7602bfadb32b1823628"; + sha256 = "0clgqk9ilnr43iyl5sdzwfzqpnw9amfy1npdgkpgm1wfnsvz6xrw"; + fetchSubmodules = true; +} +# Update with: nix run -f ./nixpkgs/default.nix nix-prefetch-git -c nix-prefetch-git 'https://github.com/OpenModelica/OpenModelica/' 'v1.17.0' --fetch-submodules diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix new file mode 100644 index 000000000000..b49c0f0f60ca --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix @@ -0,0 +1,63 @@ +{ stdenv +, lib +, gfortran +, flex +, bison +, jre8 +, blas +, lapack +, curl +, readline +, expat +, pkg-config +, buildPackages +, targetPackages +, libffi +, binutils +, mkOpenModelicaDerivation +}: +let + isCross = stdenv.buildPlatform != stdenv.hostPlatform; + nativeOMCompiler = buildPackages.openmodelica.omcompiler; +in +mkOpenModelicaDerivation ({ + pname = "omcompiler"; + omtarget = "omc"; + omdir = "OMCompiler"; + omdeps = [ ]; + omautoconf = true; + + nativeBuildInputs = [ + jre8 + gfortran + flex + bison + pkg-config + ] ++ lib.optional isCross nativeOMCompiler; + + buildInputs = [ targetPackages.stdenv.cc.cc blas lapack curl readline expat libffi binutils ]; + + postPatch = '' + sed -i -e '/^\s*AR=ar$/ s/ar/${stdenv.cc.targetPrefix}ar/ + /^\s*ar / s/ar /${stdenv.cc.targetPrefix}ar / + /^\s*ranlib/ s/ranlib /${stdenv.cc.targetPrefix}ranlib /' \ + $(find ./OMCompiler -name 'Makefile*') + ''; + + preFixup = '' + for entry in $(find $out -name libipopt.so); do + patchelf --shrink-rpath --allowed-rpath-prefixes /nix/store $entry + patchelf --set-rpath '$ORIGIN':"$(patchelf --print-rpath $entry)" $entry + done + ''; + + meta = with lib; { + description = "Modelica compiler from OpenModelica suite"; + homepage = "https://openmodelica.org"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.linux; + }; +} // lib.optionalAttrs isCross { + configureFlags = [ "--with-omc=${nativeOMCompiler}/bin/omc" ]; +}) diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omedit/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omedit/default.nix new file mode 100644 index 000000000000..b0cc530ba37b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omedit/default.nix @@ -0,0 +1,38 @@ +{ lib +, jre8 +, qmake +, qtbase +, qttools +, qtwebkit +, qtxmlpatterns +, binutils +, wrapQtAppsHook +, openmodelica +, mkOpenModelicaDerivation +}: +with openmodelica; +mkOpenModelicaDerivation rec { + pname = "omedit"; + omdir = "OMEdit"; + omdeps = [ omcompiler omplot omparser omsimulator ]; + omautoconf = true; + + nativeBuildInputs = [ jre8 qmake qtbase qttools wrapQtAppsHook ]; + + buildInputs = [ qtwebkit qtxmlpatterns binutils ]; + + postPatch = '' + sed -i ''$(find -name qmake.m4) -e '/^\s*LRELEASE=/ s|LRELEASE=.*$|LRELEASE=${lib.getDev qttools}/bin/lrelease|' + ''; + + dontUseQmakeConfigure = true; + QMAKESPEC = "linux-clang"; + + meta = with lib; { + description = "A Modelica connection editor for OpenModelica"; + homepage = "https://openmodelica.org"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix new file mode 100644 index 000000000000..006daf18812f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix @@ -0,0 +1,37 @@ +{ lib +, stdenv +, fetchgit +, bash +, pkg-config +, jre8 +, libuuid +, openmodelica +, mkOpenModelicaDerivation +}: +let + fakegit = import ./fakegit.nix { inherit lib stdenv fetchgit bash; }; +in +mkOpenModelicaDerivation { + pname = "omlibrary"; + omdir = "libraries"; + omtarget = "omlibrary-all"; + omdeps = [ openmodelica.omcompiler ]; + + postPatch = '' + patchShebangs --build libraries + cp -fv ${fakegit}/bin/checkout-git.sh libraries/checkout-git.sh + + # The EMOTH library is broken in OpenModelica 1.17.0 + # Let's remove it from targets. + sed -i -e '/^OTHER_LIBS=/ s/EMOTH //' libraries/Makefile.libs + ''; + + meta = with lib; { + description = "A collection of Modelica libraries to use with OpenModelica, +including Modelica Standard Library"; + homepage = "https://openmodelica.org"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/fakegit.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/fakegit.nix new file mode 100644 index 000000000000..fdbc79aae599 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/fakegit.nix @@ -0,0 +1,49 @@ +{ lib, stdenv, fetchgit, bash }: +let + mkscript = path: text: '' + mkdir -pv `dirname ${path}` + cat > ${path} <<"EOF" + #!${bash}/bin/bash + ME=$(basename ${path}) + ${text} + EOF + sed -i "s@%out@$out@g" ${path} + chmod +x ${path} + ''; + + hashname = r: + let + rpl = lib.replaceChars [ ":" "/" ] [ "_" "_" ]; + in + (rpl r.url) + "-" + (rpl r.rev); + +in +stdenv.mkDerivation { + name = "fakegit"; + + buildCommand = '' + mkdir -pv $out/repos + ${lib.concatMapStrings + (r: "cp -r ${fetchgit r} $out/repos/${hashname r}\n") + (import ./src-libs.nix)} + + ${mkscript "$out/bin/checkout-git.sh" '' + if test "$#" -ne 4; then + echo "Usage: $0 DESTINATION URL GITBRANCH HASH" + exit 1 + fi + DEST=$1 + URL=`echo $2 | tr :/ __` + GITBRANCH=$3 + REVISION=$4 + + REVISION=`echo $REVISION | tr :/ __` + + rm -rf $DEST + mkdir -pv $DEST + echo "FAKEGIT cp -r %out/repos/$URL-$REVISION $DEST" >&2 + cp -r %out/repos/$URL-$REVISION/* $DEST + chmod u+w -R $DEST + ''} + ''; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/src-libs.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/src-libs.nix new file mode 100644 index 000000000000..c91addf78040 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/src-libs.nix @@ -0,0 +1,83 @@ +[ + { url = "https://github.com/modelica-3rdparty/AdvancedNoise.git"; rev = "5ce57acd279dadd0d25b76a6b02d3f9e9d061246"; sha256 = "07jjbj0y6bak269md3xniqb5lgc33m92ar5qixqxj5yxdjaahfs2"; fetchSubmodules = true; } + { url = "https://github.com/RWTH-EBC/AixLib.git"; rev = "b00e01d911e2e54e148f24e36ee387a8b457d89c"; sha256 = "1sljddxkx208nill0975sz9b1xd701n97aia4wxihr140dgs4dgb"; fetchSubmodules = true; } + { url = "https://github.com/RWTH-EBC/AixLib.git"; rev = "v0.4.0"; sha256 = "0dw34mjq29n55xh51g1c9a9d0d8gbpn16gj309dfxn4v2hbnfvzx"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/AlgebraTestSuite.git"; rev = "b937e1a7f447138c59abec9b2092f84f16bf02e8"; sha256 = "0406inasx61dk7vcnziiyhxkna7g61a5hn0znnbxj817hz6q11zn"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/ApproxSpline.git"; rev = "28420f5c1a88c9cd069defbd8c05e4a78a090675"; sha256 = "07gpyi2brj5zpvrlsnflqjnhbrgxvpqbdshp8lp4lh9mnj5jv95d"; fetchSubmodules = true; } + { url = "https://github.com/OpenModelica/BioChem.git"; rev = "v1.0.2"; sha256 = "037bvj2lqrslg8k5r0rjgdzccslj9bj25b55k4g440vabm5p05qm"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/BondGraph.git"; rev = "20c23e60d12989bd4668ccac47659d82d39d29cc"; sha256 = "0yrkk708v4bvf423xb4zgpmnaj8qhq5primdg758ayddgli23wa9"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/BrineProp.git"; rev = "c2f564ae284726a2df6252a8561856691681572b"; sha256 = "01c2i2rlry7b4a6f2skkvzphcrfg5a2waxv4i7zgx5q275fg06i1"; fetchSubmodules = true; } + { url = "https://github.com/EDF-TREE/BuildSysPro.git"; rev = "v3.3.0"; sha256 = "1cvcany3q9p1xndarxa2d8mmqxdnqk22476q8l61nayz5qy25x61"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/BuildingControlLib.git"; rev = "v1.0.0"; sha256 = "0ckdxway0m755mbrl94k4458sijzgknlzsrf7xs5bjymxchm8r2m"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/BuildingSystems.git"; rev = "1e07bb475b921a4eedc6155c5310d1f9f3ef7550"; sha256 = "1xg831vqh6zw88cxxcb3sjgz44l7ygsgxddl05fp6xvz5sjpfcna"; fetchSubmodules = true; } + { url = "https://github.com/lbl-srg/modelica-buildings.git"; rev = "v6.0.0"; sha256 = "0rnnk1clji0myzr7adggki6knbl6v8381vwnqgiz8mkxbmzdwm4f"; fetchSubmodules = true; } + { url = "https://github.com/lbl-srg/modelica-buildings.git"; rev = "v7.0.0"; sha256 = "04n04pp4zvyg8n8h7h79c3wyk7lmn940mh7qzs0lv76g1ybypnlz"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/Chemical.git"; rev = "5645573fced862430b7b598b4d7ec1a39c7aa0fa"; sha256 = "1kh7kpmjfz55pb8553srlnrh8l00nw21xf5mjzh7nx9b1rndnmyg"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/DeployStructLib.git"; rev = "v1.0"; sha256 = "1k4zw9lnd0javw4zigxc15l58yf7xdz36b7808g65qxy89w6ksr2"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/DisHeatLib.git"; rev = "b11f53379c122870a52f2da9b1705d2c911cd21d"; sha256 = "1vm96a4z0b40r0nisxrrzyvan4yphjdkx4ad655phva2636xb5rr"; fetchSubmodules = true; } + { url = "https://github.com/AHaumer/DriveControl.git"; rev = "b7233fd97a92867bb4ec2c3647c7f7e888398644"; sha256 = "0nyp1n8wrkjzfypsmjjzac0g9p4wbc1cxxr040fj20bqdg9l3h1b"; 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sha256 = "0mg8jlvlwql2nsjiy7c3rdibv73bkfk149ac0450d5pc0hfn9mln"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/FailureModes.git"; rev = "v1.2.1"; sha256 = "1z8bwrld1rkydgssab5gnrd76frrbky8qxi1lvlaf2jidj6bzn1l"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/FaultTriggering.git"; rev = "v0.6.6"; sha256 = "0a08yyrbg4a49s0bgqgyds6pidx9xr47yspvl9bdak1mq34qibip"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/FeedDriveLibrary.git"; rev = "1.0.1"; sha256 = "15fi9dj6zgl0fr90cwxqjbpphj0dwrrmk74hf25j6zd85w2ycqdz"; fetchSubmodules = true; } + { url = "https://github.com/DLR-SR/FractionalOrder.git"; rev = "99918820e346c362c3ad52d782c8215e5deeac4c"; sha256 = "1pycss6fqh86frfdbdfffjhaz09fz1558f9azgckhf8drx6ry1qs"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/Greenhouses-Library.git"; rev = "89ae0e8097eb0751abce2013d304fa5f9c09b885"; sha256 = "1q77xj6aysqsn3d7kjmcq7dihbw18iqm35ifzdi75xgf3cgwla4f"; fetchSubmodules = true; } + { url = "https://github.com/christiankral/HanserModelica.git"; rev = "v1.1.0"; sha256 = "0zwkrhg2y42m18p4z51izrickiv1vikgz0z7fpjia4dbppckav8i"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/HelmholtzMedia.git"; rev = "3b4a4bca94d388744b2d045344ea2f9b0b4d405b"; sha256 = "17fzpan89075vb5vbhw5ylgxcdsmj2vjnmmka7cgzh06izb69nvh"; fetchSubmodules = true; } + { url = "https://github.com/ibpsa/modelica-ibpsa.git"; rev = "v3.0.0"; sha256 = "0xwgfndlw76zfmiiqadl85l9na9igsqlmfcawx526sdw2lhhgics"; fetchSubmodules = true; } + { url = "https://github.com/open-ideas/IDEAS.git"; rev = "v2.1.0"; sha256 = "0xp0zg6ib5536d5vl361lsn5w5faqdf6djhcmfxns629wjima8rn"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/IndustrialControlSystems.git"; rev = "v1.1.0"; sha256 = "1nvgx94iy1pws0768anrl7ssjlzslb5mbp21j7xvf6wpqfmj0npc"; fetchSubmodules = true; } + { url = "https://github.com/christiankral/KeyWordIO.git"; rev = "v0.9.0"; sha256 = "10kvj6zn2r6m3403ja8nkkxbfcchkz0pfk3g70ibr76zivxb5nim"; 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} + { url = "https://github.com/modelica/Modelica_Synchronous.git"; rev = "c8350276bfd945086962cf4150ba941b9c57ed13"; sha256 = "12ad7fpjy50ky3lvl65r9d5xvlzvw5yqdnbp4rsgl3qw7s3wrmja"; fetchSubmodules = true; } + { url = "https://github.com/jwindahlModelon/MultiPhaseMixtureMedia.git"; rev = "0bda0c58af6384f8e0edf7aa7520afb369af3e38"; sha256 = "11bqm69504bh4h05dxlwdmjfxwls06mr49cz47kl8jmrygkfi4i2"; fetchSubmodules = true; } + { url = "https://github.com/OpenIPSL/OpenIPSL.git"; rev = "v1.5.0"; sha256 = "09xrcz0rdxdy220ki5zyl7920y0a4lg24p0aibna4ad15vszhhwj"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/Optimisers.git"; rev = "e33c69edaad6dad8029167b0ca00533964a6fe37"; sha256 = "0hcxsrr2n4fzaxdjvgvqayz38kpfk86cclvg5pzcfmjc5bznb8bs"; fetchSubmodules = true; } + { url = "https://github.com/lochel/PNlib.git"; rev = "ab9b6b8527c0c78140365e7b105ae469d4954a64"; sha256 = "0y7bfbnvzv9bnz4v8wvmy42dji3cqpy5b2fmd2jj0rhlzs1infzh"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/PVSystems.git"; rev = "v0.6.2"; sha256 = "0vcgvdaqfbn46lpzk0kvsif3d55wf8yzhkbdpf5zv04kv7zw25w9"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/PhotoVoltaics.git"; rev = "v1.6.0"; sha256 = "0zqx77z217iln3vfxn2v3c2jl0jz5kgcd96ylvimjnwr30mxr09n"; fetchSubmodules = true; } + { url = "https://github.com/MarekMatejak/Physiolibrary.git"; rev = "v2.3.1"; sha256 = "0nxfw63m278gaff18zz29n2s1vk4kwdbv2qvbjmcq86fl1i5b3bg"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/Physiomodel.git"; rev = "v1.0.0"; sha256 = "1sdhv5qgjqv3zdq57pkkrh04ainwv9n5zqd8mb9a3ybjmwdjf6f9"; fetchSubmodules = true; } + { url = "https://github.com/dzimmer/PlanarMechanics.git"; rev = "55224a9e76de8aa7f708236bd4d7dee624ecba50"; sha256 = "0hf7vi44adss86x5ahk5if7bdjgw773d8mb3d8ianq12g8azycyd"; fetchSubmodules = true; } + { url = "https://github.com/PowerGrids/PowerGrids.git"; rev = "v1.0.0"; sha256 = "06bx8mqvmizhfwg99djdfgh2mblc4wzmg0zq4ilrp586jwfninmz"; fetchSubmodules = true; } + { url = "https://github.com/modelica/PowerSystems.git"; rev = "v1.0.0"; sha256 = "1xwhwich7gi6vl33zl2r78xdjklchgkjcnvww6390j20l1wjznkn"; fetchSubmodules = true; } + { url = "https://github.com/modelica/PowerSystems.git"; rev = "7369976265a9d7b62097340aba5e463c62cc5061"; sha256 = "1f0h148v2g057l6ixf646d8ymsx1jzqn14xlram8h62la2k6nmvw"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/RealTimeCoordinationLibrary.git"; rev = "v1.0.2"; sha256 = "0ch4la04hm059ii5wzph9gsbvqhnfqrvvpqi57qn27bm10c4la0m"; fetchSubmodules = true; } + { url = "https://github.com/casella/ScalableTestSuite.git"; rev = "v1.11.5"; sha256 = "0bhj1q9b8d29nrbr253zszy1w1yvyizvyr3law1pqjj6mhbqmg4i"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/Servomechanisms.git"; rev = "3bf82ba5d3f31b4a0ae05f99ae690037358e153e"; sha256 = "1swka7d58wkg5pqv59lqgfi7gv6rg5vra4j6r76pn9czx9ddal8w"; fetchSubmodules = true; } + { url = "https://github.com/SolarTherm/SolarTherm.git"; rev = "d80fc335d1fa5d1628c45c2e73204bcb8a614b21"; sha256 = "18d8cqlh0ic2yfcxzkz0ar9z19486z9x4sc7c9mpggxib28p39aa"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/Soltermica.git"; rev = "9f7224bd89335f95dffe1ccdaa094df5a3279fdf"; sha256 = "1bif3cnwjas6x7b8ahwkm7dbrqrfdqwwa26zmdc6zrpfncl3kqd0"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/SystemDynamics.git"; rev = "2f6bd9382c5aac2aff9148cd9113a418767734b6"; sha256 = "0ii2mj6ngwjir3gzyad8wsj86pvd6wzal91nz2y7gzwj1djchb3x"; fetchSubmodules = true; } + { url = "https://github.com/thom-marx/ThermalSeparation.git"; rev = "ffa0495ba829ecab105be4bfb3b7652625ec9c03"; sha256 = "1czm97bcrpp2jv0a0kd31a929wqlrlzdhdxvyy4w499dn20jzv1l"; fetchSubmodules = true; } + { url = "https://github.com/casella/ThermoPower.git"; rev = "82d21eba0d330005899dd50a6a0ceb7d09c4caeb"; sha256 = "0n83b40hjisy7lpnbz692947d2q3hw5hk4rak7fg0w5dbm4i719p"; fetchSubmodules = true; } + { url = "https://openmodelica.org/git/ThermoSysPro.git"; rev = "db81ae1b5a6a85f6c6c7693244cafa6087e18ff5"; sha256 = "12fsf0xxxc1ja6vmm9ff85f8j5sg1lb7w4g57s2w3fkf4d3a7d0c"; 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sha256 = "1w2iah8c5d8n01wmxydjk0rrcxh88g8yjy2zmv403azcccq7byzp"; fetchSubmodules = true; } + { url = "https://github.com/modelica-3rdparty/netCDF-DataReader.git"; rev = "v2.5.0"; sha256 = "1pd5xf5bgz010lryv8bj6lvlfqn9p184csiffwj8icx7rycnlcqb"; fetchSubmodules = true; } + { url = "https://github.com/joewa/open-bldc-modelica.git"; rev = "58a83b5b36f267613de4676c95163489b1ddc2e7"; sha256 = "0wf6dn64d2psv9b3xg5227vzpk109r3dqzi4m2wwhrilaxs3v004"; fetchSubmodules = true; } +] diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/update-src-libs.sh b/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/update-src-libs.sh new file mode 100755 index 000000000000..b8f2e95923b5 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omlibrary/update-src-libs.sh @@ -0,0 +1,39 @@ +#!/usr/bin/env nix-shell +#! nix-shell -i bash -p bash + +CWD=$PWD + +chko() { + ( + T=`mktemp -d` + trap "rm -rf $T" EXIT INT PIPE + cd $T + cat >check.nix <<EOF +with import <nixpkgs> {}; +fetchgit `cat $CWD/../mkderivation/src-main.nix` +EOF + nix-build check.nix + cat result/libraries/Makefile.libs + ) +} + +getsha256() { + URL=$(echo "$1" | sed 's/^"\(.*\)"$/\1/') + REV=$(echo "$2" | sed 's/^"\(.*\)"$/\1/') + SHA=$(nix run nixpkgs.nix-prefetch-git -c nix-prefetch-git --fetch-submodules "$URL" "$REV" 2>/dev/null | sed -n 's/.*"sha256": "\(.*\)",/\1/g p') + echo "{ url = $1; rev = $2; sha256 = \"$SHA\"; fetchSubmodules = true; }" +} + +OUT=src-libs.nix + +echo '[' > $OUT + +chko | +grep checkout-git.sh | +tr \' \" | +while read NM TGT URL BR REV ; do + echo Trying $TGT $URL $REV >&2 + getsha256 $URL $REV >> $OUT || exit 1 +done + +echo ']' >> $OUT diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omparser/Makefile.in.patch b/nixpkgs/pkgs/applications/science/misc/openmodelica/omparser/Makefile.in.patch new file mode 100644 index 000000000000..a8f04203a8c9 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omparser/Makefile.in.patch @@ -0,0 +1,22 @@ +--- a/Makefile.in ++++ b/Makefile.in +@@ -23,7 +23,7 @@ + omedit-testsuite: omedit-testsuite.skip + omedit-testsuite.skip: omedit.skip testsuite-depends + $(MAKE) -f $(defaultMakefileTarget) -C OMEdit/Testsuite +-omparser: omparser.skip ++omparser: build-dirs omparser.skip + omparser.skip: + test -f $@ || $(MAKE) -C OMParser OMBUILDDIR=@OMBUILDDIR@ "host_short=@host_short@" CC="@CC@" CXX="@CXX@" CFLAGS="@CFLAGS@" CPPFLAGS="@CPPFLAGS@" CXXFLAGS="@CXXFLAGS@" + omsimulator: omsimulator.skip +@@ -134,6 +134,10 @@ + INSTALL_JAVADIR = ${DESTDIR}${datadir}/omc/java + INSTALL_LOCALEDIR = ${DESTDIR}${datadir}/locale + ++build-dirs: ++ mkdir -p "@OMBUILDDIR@"/lib/@host_short@/omc ++ mkdir -p "@OMBUILDDIR@"/include/omc ++ + install-dirs: + @test ! "${DESTDIR}/@prefix@" -ef "@OMBUILDDIR@" || (echo Error: Install and build dirs are the same && false) + if [ "@APP@" = ".app" ]; then mkdir -p ${INSTALL_APPDIR}; fi diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omparser/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omparser/default.nix new file mode 100644 index 000000000000..fcf5acd29ee9 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omparser/default.nix @@ -0,0 +1,28 @@ +{ lib +, pkg-config +, jre8 +, libuuid +, openmodelica +, mkOpenModelicaDerivation +}: + +mkOpenModelicaDerivation rec { + pname = "omparser"; + omdir = "OMParser"; + omdeps = [ openmodelica.omcompiler ]; + + nativeBuildInputs = [ pkg-config ]; + + buildInputs = [ jre8 libuuid ]; + + patches = [ ./Makefile.in.patch ]; + + meta = with lib; { + description = "An antlr4-based parser of Modelica files from OpenModelica +suite"; + homepage = "https://openmodelica.org"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omplot/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omplot/default.nix new file mode 100644 index 000000000000..7edc4b6efb22 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omplot/default.nix @@ -0,0 +1,34 @@ +{ lib +, qtbase +, qttools +, qmake +, wrapQtAppsHook +, openmodelica +, mkOpenModelicaDerivation +}: + +mkOpenModelicaDerivation rec { + pname = "omplot"; + omdir = "OMPlot"; + omdeps = [ openmodelica.omcompiler ]; + omautoconf = true; + + nativeBuildInputs = [ qtbase qttools qmake wrapQtAppsHook ]; + + postPatch = '' + sed -i OMPlot/Makefile.in -e 's|bindir = @includedir@|includedir = @includedir@|' + sed -i OMPlot/OMPlot/OMPlotGUI/*.pro -e '/INCLUDEPATH +=/s|$| ../../qwt/src|' + sed -i ''$(find -name qmake.m4) -e '/^\s*LRELEASE=/ s|LRELEASE=.*$|LRELEASE=${lib.getDev qttools}/bin/lrelease|' + ''; + + dontUseQmakeConfigure = true; + QMAKESPEC = "linux-clang"; + + meta = with lib; { + description = "Plotting tool for OpenModelica-generated results files"; + homepage = "https://openmodelica.org"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omshell/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omshell/default.nix new file mode 100644 index 000000000000..2f8c5203c07a --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omshell/default.nix @@ -0,0 +1,40 @@ +{ lib, qttools, qmake, qtwebkit, wrapQtAppsHook, readline, openmodelica, mkOpenModelicaDerivation }: + +mkOpenModelicaDerivation rec { + pname = "omshell"; + omdir = "OMShell"; + omdeps = [ openmodelica.omcompiler ]; + omautoconf = true; + + nativeBuildInputs = [ qmake wrapQtAppsHook ]; + + buildInputs = [ readline qtwebkit ]; + + postPatch = with openmodelica; '' + sed -i ''$(find -name qmake.m4) -e '/^\s*LRELEASE=/ s|LRELEASE=.*$|LRELEASE=${lib.getDev qttools}/bin/lrelease|' + sed -i OMShell/OMShell/OMShellGUI/*.pro -e ' + s|\$\$\[QT_INSTALL_BINS\]/lrelease|${lib.getDev qttools}/bin/lrelease| + /^\s*OMCLIBS =/ s|\$\$(OMBUILDDIR)|${omcompiler}| + /^\s*OMCINC =/ s|\$\$(OMBUILDDIR)|${omcompiler}| + ' + sed -i OMShell/OMShell/OMShellGUI/OMShell.config.in -e ' + s|@OMBUILDDIR@|${omcompiler}| + s|@OPENMODELICAHOME@|${omcompiler}| + ' + sed -i OMShell/mosh/src/Makefile.in -e ' + /^CFLAGS =/ s|-I../../../build|-I${omcompiler}| + /^LIBS =/ s|-L@OMBUILDDIR@|-L${omcompiler}| + ' + ''; + + dontUseQmakeConfigure = true; + QMAKESPEC = "linux-clang"; + + meta = with lib; { + description = "Interactive OpenModelica session shell"; + homepage = "https://openmodelica.org"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix new file mode 100644 index 000000000000..448cdee6c263 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix @@ -0,0 +1,26 @@ +{ lib +, pkg-config +, boost +, readline +, libxml2 +, openmodelica +, mkOpenModelicaDerivation +}: + +mkOpenModelicaDerivation rec { + pname = "omsimulator"; + omdir = "OMSimulator"; + omdeps = [ openmodelica.omcompiler ]; + + nativeBuildInputs = [ pkg-config ]; + + buildInputs = [ readline libxml2 boost ]; + + meta = with lib; { + description = "The OpenModelica FMI & SSP-based co-simulation environment"; + homepage = "https://openmodelica.org"; + license = licenses.gpl3Only; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/src-libs-git.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/src-libs-git.nix deleted file mode 100644 index aae5ab321fbe..000000000000 --- a/nixpkgs/pkgs/applications/science/misc/openmodelica/src-libs-git.nix +++ /dev/null @@ -1,71 +0,0 @@ -[ -{ url = "https://github.com/modelica-3rdparty/ADGenKinetics.git"; rev = "42428db6e84bcde28543a3bba9bccee581309bb1"; sha256="14l005jwj1wz35gq8xlbzfz0bpsx99rs4q3dxkfh76yhnv1jh9h3"; } -{ url = "https://github.com/modelica-3rdparty/ADMSL.git"; rev = "ed0305603f86b46d9af03e7d37dcb8b6704915b4"; sha256="15b0nqxyh8444az56ydjn594jikdl1ina5wamabk3nzm1yx218cl"; } -{ url = "https://github.com/iea-annex60/modelica-annex60.git"; rev = "8015a01591bb24d219f57e7b69cdfcde66e39b47"; sha256="05k4pa007a6p628fq1xac0cfv8g8dnpy2bgy8h99rqpmlaa072z7"; 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} -{ url = "https://github.com/modelica-3rdparty/QCalc.git"; rev = "af6c34dda691a9bdf7ca1de10650974b2d5cecf5"; sha256="0p0zhl27cnr492byrzib0dyn7zp5yb7wcr0spv10ngm6j90cij6y"; } -{ url = "https://github.com/modelica-3rdparty/QSSFluidFlow.git"; rev = "d84a2c107132f2cd47ea3c3751238d69e4b1f64b"; sha256="02cdvv33pi0qlmg8n401s4cxf59l9b4ff4ixf7gwn4w4n1y9bw0g"; } -{ url = "https://github.com/modelica-3rdparty/RealTimeCoordinationLibrary.git"; rev = "655ac1a22aa6deb04ea8e3869dd0aa9fb9540754"; sha256="19crf8pl9vpqq3pq1rhcbl49kkmnm4jrzpwrpqp8qc6dj8096za4"; } -{ url = "https://github.com/modelica-3rdparty/ScalableTestSuite.git"; rev = "c6319908d45ac97ffb10e96cd42654bce36ffb97"; sha256="1g79d88bfmzcqvaghyyj86ajs38v0qnmjxbj8d53yp6nmgnaasx5"; } -{ url = "https://github.com/modelica-3rdparty/Servomechanisms.git"; rev = "22e1874ef9ad46156617817c67a4fb1238621bf5"; sha256="0nwb7apayk7ba9iv27yv67wi4b934dy57kkvn0acxy393jhd8jqd"; } -{ url = "https://openmodelica.org/git/SiemensPower.git"; rev = "73a3bfc6d2ddd72165bb0f3e7e9df48b643a5ed0"; sha256="0mvrkpkmr0bx2cvsb23syg7cs8k6a15vjf4n1hivdcigq4x8g2nc"; } -{ url = "https://openmodelica.org/git/SiemensPower.git"; rev = "5ef2e38b64ff481801c0db19d52f0bef21f85f77"; sha256="1llnpl2x1g28gari1rk34hdnnwf7a4fwwxlf7i18d8bl1vsrfaja"; } -{ url = "https://openmodelica.org/git/SiemensPower.git"; rev = "2bd9e367baaa8d44946897c3c3a32a4050ad2a2a"; sha256="1shm9blpn9m87ci6wwkinpmihr1fik9j0a0pj2nxy0cjrr2jzbn4"; } -{ url = "https://github.com/modelica-3rdparty/Spot.git"; rev = "2f74417f1681570900a1ed373dcbe4b42634ec7b"; sha256="0k5h2k6x98zvvsafpw7y16xs9d6lxz0csa0mlm4wwggaywadn255"; } -{ url = "https://github.com/modelica-3rdparty/SystemDynamics.git"; rev = "c58a26dc3e62a50e64fd336dc4aa499b2d5ad314"; sha256="0ra3a2vgqmry92kmm060gfa41mrpkgbs4swzl78ih3icawfzjz8q"; } -{ url = "https://github.com/modelica-3rdparty/ThermoPower.git"; rev = "e012268625dd1645fe5570cf31d64129d83a8192"; sha256="1rlkli48kc9hnkplgb0bjkb6ajn7agiw4yh9l5sfvlv7k7k2gc8l"; } -{ url = "https://openmodelica.org/git/ThermoSysPro.git"; rev = "d4f9c3ed35f7520f82439eb6e9f4057ae0f82b73"; sha256="0hxbn26g479qkr6rrglx9ljdxnpzd5ll1sf2v08skghrdjjb8jcx"; } -{ url = "https://openmodelica.org/git/ThermoSysPro.git"; rev = "51e7ea2d2e121ee640e7897335c294923f8eaeb0"; sha256="0l11mzjkaxndsqrnnr0z7qvk08svv229119qkm81yb53ich9wnyw"; } -{ url = "https://github.com/modelica/VehicleInterfaces.git"; rev = "ad956a35643d53e207ee126d67ea1f3f38337a39"; sha256="0g90cqwjpi06gn7vca5kqnz56im76s2hrdqjhsj2bl43rza8mhr0"; } -{ url = "https://github.com/modelica-3rdparty/WasteWater.git"; rev = "90ff44ac791ba5ed98444c8597efbd2a2af01cad"; sha256="1icrn0y389rhxmf6i0mnsfgw9v9j5innpkz3q069rfm2ji268b12"; } -{ url = "https://github.com/xogeny/XogenyTest.git"; rev = "9b98981e8ff0f440dd319d1a806e1fd2f0ab3436"; sha256="18glaxrlxfml26w7ljlf0yj3ah1fnhpbg01py28nplsgnrfwfwqj"; } -{ url = "https://github.com/modelica-3rdparty/msgpack-modelica.git"; rev = "6ce2ca600c4902038c0f20b43ed442f1ee204310"; sha256="01x5a9y11yf62sc0j2y49yxwm24imj2lfl3z5mwvi9038gwn0lkx"; } -{ url = "https://github.com/modelica-3rdparty/netCDF-DataReader.git"; rev = "3d2cc8272abfbc4b667d8868f851bf3e11c6f00e"; sha256="194810a4rn0flxgirrlnxsbxarnm97309dkp1w7nva9zv1q3wj7h"; } -{ url = "https://github.com/joewa/open-bldc-modelica.git"; rev = "7817cd703b88fc1f433269d32c31e75eb50a21c6"; sha256="1plkxkx51f9yi99ysarmx2ymldizvyr0m66k996y5lj5h81jv8a8"; } -] diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/src-libs-svn.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/src-libs-svn.nix deleted file mode 100644 index 244da64fb4e6..000000000000 --- a/nixpkgs/pkgs/applications/science/misc/openmodelica/src-libs-svn.nix +++ /dev/null @@ -1,5 +0,0 @@ -[ -{ url = "https://svn.modelica.org/projects/Modelica_ElectricalSystems/InstantaneousSymmetricalComponents"; rev = "7978"; sha256="0f100c7bz4ai3ryhpkbbszw8z6mykvg40p03ic92n2qq58wjk37z"; } -{ url = "https://svn.modelica.org/projects/Modelica_EmbeddedSystems/trunk/Modelica_StateGraph2"; rev = "8121"; sha256="1cys57nc1yzkr5admc139qs5pa48rj3g69pb3j3s9xcmpd483hzp"; } -{ url = "https://svn.modelica.org/projects/Modelica_ElectricalSystems/Modelica_PowerFlow/trunk"; rev = "3174"; sha256="0yviw1b8psn8vfyl4q1naylak3lcqi2q1bqplqg3gg9iw4aiymxl"; } -] diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/src-main.nix b/nixpkgs/pkgs/applications/science/misc/openmodelica/src-main.nix deleted file mode 100644 index 99e82259bfe6..000000000000 --- a/nixpkgs/pkgs/applications/science/misc/openmodelica/src-main.nix +++ /dev/null @@ -1,6 +0,0 @@ -{ - url = "https://openmodelica.org/git-readonly/OpenModelica.git"; - fetchSubmodules = true; - rev = "8c5d48eb31a638d5220621b20377bfe6f9e9535e"; - sha256 = "0i5cznkh4wwayjqms14f3phizqm493nrr1yjgs9747nfw7vnwsff"; -} diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/update-src-libs-git.sh b/nixpkgs/pkgs/applications/science/misc/openmodelica/update-src-libs-git.sh deleted file mode 100755 index 481a89796415..000000000000 --- a/nixpkgs/pkgs/applications/science/misc/openmodelica/update-src-libs-git.sh +++ /dev/null @@ -1,64 +0,0 @@ -#!/bin/sh - -CWD=`pwd` - -chko() { ( -T=`mktemp -d` -trap "rm -rf $T" EXIT INT PIPE -cd $T -cat >check.nix <<EOF -with import <nixpkgs> {}; -fetchgit `cat $CWD/src-main.nix` -EOF -nix-build check.nix -cat result/libraries/Makefile.libs -) } - -getsha256() { ( -T=`mktemp -d` -trap "rm -rf $T" EXIT INT PIPE -cd $T - -L=`echo $2 | wc -c` -if expr $L '<' 10 >/dev/null; then -T=`echo $2 | sed 's@"\(.*\)"@"refs/tags/\1"@'` -cat >check.nix <<EOF -with import <nixpkgs> {}; -fetchgit { - url = $1; - rev = $T; - sha256 = "0000000000000000000000000000000000000000000000000000"; -} -EOF -SHA=`nix-build check.nix 2>&1 | sed -n 's/.*instead has ‘\(.*\)’.*/\1/g p'` -echo "{ url = $1; rev = $T; sha256=\"$SHA\"; }" -else -cat >check.nix <<EOF -with import <nixpkgs> {}; -fetchgit { - url = $1; - rev = $2; - sha256 = "0000000000000000000000000000000000000000000000000000"; -} -EOF -SHA=`nix-build check.nix 2>&1 | sed -n 's/.*instead has ‘\(.*\)’.*/\1/g p'` -echo "{ url = $1; rev = $2; sha256=\"$SHA\"; }" -fi - -# nix-build check.nix -) } - -OUT=src-libs-git.nix - -echo '[' > $OUT - -chko | -grep checkout-git.sh | -tr \' \" | -while read NM TGT URL BR REV ; do - echo Trying $TGT $URL $REV >&2 - getsha256 $URL $REV >> $OUT || exit 1 -done - -echo ']' >> $OUT - diff --git a/nixpkgs/pkgs/applications/science/misc/openmodelica/update-src-libs-svn.sh b/nixpkgs/pkgs/applications/science/misc/openmodelica/update-src-libs-svn.sh deleted file mode 100755 index 972bc7d61f13..000000000000 --- a/nixpkgs/pkgs/applications/science/misc/openmodelica/update-src-libs-svn.sh +++ /dev/null @@ -1,50 +0,0 @@ -#!/bin/sh - -CWD=`pwd` - -chko() { ( -T=`mktemp -d` -trap "rm -rf $T" EXIT INT PIPE -cd $T -cat >check.nix <<EOF -with import <nixpkgs> {}; -fetchgit `cat $CWD/src-main.nix` -EOF -nix-build check.nix -cat result/libraries/Makefile.libs -) } - -getsha256() { ( -T=`mktemp -d` -trap "rm -rf $T" EXIT INT PIPE -cd $T - -L=`echo $2 | wc -c` -cat >check.nix <<EOF -with import <nixpkgs> {}; -fetchsvn { - url = $1; - rev = $2; - sha256 = "0000000000000000000000000000000000000000000000000000"; -} -EOF -SHA=`nix-build check.nix 2>&1 | sed -n 's/.*instead has ‘\(.*\)’.*/\1/g p'` -echo "{ url = $1; rev = $2; sha256=\"$SHA\"; }" - -# nix-build check.nix -) } - -OUT=src-libs-svn.nix - -echo '[' > $OUT - -chko | -grep checkout-svn.sh | -tr \' \" | -while read NM TGT URL REV ; do - echo Trying $TGT $URL $REV >&2 - getsha256 $URL $REV >> $OUT || exit 1 -done - -echo ']' >> $OUT - diff --git a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix index 419323cfa31f..4ff751ff8d18 100644 --- a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix @@ -2,7 +2,7 @@ python3Packages.buildPythonApplication rec { pname = "snakemake"; - version = "6.6.1"; + version = "6.7.0"; propagatedBuildInputs = with python3Packages; [ appdirs @@ -31,7 +31,7 @@ python3Packages.buildPythonApplication rec { src = python3Packages.fetchPypi { inherit pname version; - sha256 = "91637a801342f3bc349c033b284fef7c0201b4e5e29d5650cb6c7f69096d4184"; + sha256 = "6f53d54044c5d1718c7858f45286beeffb220c794fe5f602a5c20bf0caf8ec07"; }; doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json diff --git a/nixpkgs/pkgs/applications/science/physics/quantomatic/default.nix b/nixpkgs/pkgs/applications/science/physics/quantomatic/default.nix index c1400869a258..8c33a8ae6b1a 100644 --- a/nixpkgs/pkgs/applications/science/physics/quantomatic/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/quantomatic/default.nix @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ makeWrapper ]; buildInputs = [ jre ]; - phases = [ "installPhase" ]; + dontUnpack = true; installPhase = '' mkdir -p $out/libexec/quantomatic diff --git a/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix b/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix index ba519cc2d032..eb718be12e4a 100644 --- a/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { sha256 = "1iwa17s8ipj6a2b8zss5csb1k5y9s5js38syvq932rxcinbyjsl4"; }; - postPatch = lib.optional (stdenv.hostPlatform.libc == "glibc") '' + postPatch = lib.optionalString (stdenv.hostPlatform.libc == "glibc") '' sed -ie '/sys\/sysctl.h/d' ATOOLS/Org/Run_Parameter.C ''; diff --git a/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix b/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix index 5ae56528f964..85e20f38b668 100644 --- a/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix @@ -9,8 +9,6 @@ mkDerivation rec { sha256 = "02x3r9iv3ndwxa65mxn9m5dlhcrnjiq7cffi6rmb456gs3v3dnav"; }; - enableParallelBuilding = true; - nativeBuildInputs = [ qmake ]; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/programming/plm/default.nix b/nixpkgs/pkgs/applications/science/programming/plm/default.nix index e56282b68631..ca8e87a05533 100644 --- a/nixpkgs/pkgs/applications/science/programming/plm/default.nix +++ b/nixpkgs/pkgs/applications/science/programming/plm/default.nix @@ -1,37 +1,39 @@ -{lib, stdenv, fetchurl, makeWrapper, jre, gcc, valgrind}: +{ lib, stdenv, fetchurl, makeWrapper, jre, gcc, valgrind }: # gcc and valgrind are not strict dependencies, they could be made # optional. They are here because plm can only help you learn C if you # have them installed. stdenv.mkDerivation rec { - major = "2"; - minor = "5"; - version = "${major}-${minor}"; pname = "plm"; + version = "2.9.3"; src = fetchurl { - url = "http://webloria.loria.fr/~quinson/Teaching/PLM/plm-${major}_${minor}.jar"; - sha256 = "0m17cxa3nxi2cbswqvlfzp0mlfi3wrkw8ry2xhkxy6aqzm2mlgcc"; + url = "https://github.com/BuggleInc/PLM/releases/download/v${version}/plm-${version}.jar"; + sha256 = "0i9ghx9pm3kpn9x9n1hl10zdr36v5mv3drx8lvhsqwhlsvz42p5i"; name = "${pname}-${version}.jar"; }; nativeBuildInputs = [ makeWrapper ]; buildInputs = [ jre gcc valgrind ]; - phases = [ "installPhase" ]; + dontUnpack = true; installPhase = '' + runHook preInstall + mkdir -p "$prefix/bin" makeWrapper ${jre}/bin/java $out/bin/plm \ --add-flags "-jar $src" \ --prefix PATH : "$PATH" + + runHook postInstall ''; meta = with lib; { description = "Free cross-platform programming exerciser"; + homepage = "http://people.irisa.fr/Martin.Quinson/Teaching/PLM/"; license = licenses.gpl3; maintainers = [ ]; platforms = lib.platforms.all; - broken = true; }; } diff --git a/nixpkgs/pkgs/applications/science/robotics/apmplanner2/default.nix b/nixpkgs/pkgs/applications/science/robotics/apmplanner2/default.nix index 0f5e7e6daa85..b65c23521395 100644 --- a/nixpkgs/pkgs/applications/science/robotics/apmplanner2/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/apmplanner2/default.nix @@ -30,8 +30,6 @@ mkDerivation rec { --replace /usr $out ''; - enableParallelBuilding = true; - meta = { description = "Ground station software for autonomous vehicles"; longDescription = '' diff --git a/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix b/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix index ba0c2530849a..4f83f957dbf7 100644 --- a/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix @@ -3,11 +3,11 @@ buildPythonApplication rec { pname = "MAVProxy"; - version = "1.8.39"; + version = "1.8.40"; src = fetchPypi { inherit pname version; - sha256 = "sha256-1RXuAiz9i5ZnLtDGQ+o3DNgWJ2FDJGIoelmlDmEzrts="; + sha256 = "cad317e2e879f1f7cb59af078788aaf0d09cd761ecd91ad091adf7ac6cc1bcdb"; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/nixpkgs/pkgs/applications/science/robotics/qgroundcontrol/default.nix index 1b9304d49e71..2759723841cc 100644 --- a/nixpkgs/pkgs/applications/science/robotics/qgroundcontrol/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/qgroundcontrol/default.nix @@ -17,7 +17,6 @@ mkDerivation rec { gstreamer gst-plugins-base gst-plugins-good gst-plugins-bad wayland ]; - enableParallelBuilding = true; buildInputs = [ SDL2 ] ++ gstInputs ++ qtInputs; nativeBuildInputs = [ pkg-config qmake qttools ]; |