diff options
Diffstat (limited to 'pkgs/applications/science')
182 files changed, 503 insertions, 506 deletions
diff --git a/pkgs/applications/science/astronomy/astrolabe-generator/default.nix b/pkgs/applications/science/astronomy/astrolabe-generator/default.nix index c58b09889772d..603fb8087266f 100644 --- a/pkgs/applications/science/astronomy/astrolabe-generator/default.nix +++ b/pkgs/applications/science/astronomy/astrolabe-generator/default.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { meta = with lib;{ homepage = "https://www.astrolabeproject.com"; - description = "A Java-based tool for generating EPS files for constructing astrolabes and related tools"; + description = "Java-based tool for generating EPS files for constructing astrolabes and related tools"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.gpl3; maintainers = [ ]; diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index c7a1391c3007b..c4b932f6dbae8 100644 --- a/pkgs/applications/science/biology/ants/default.nix +++ b/pkgs/applications/science/biology/ants/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "ANTs"; - version = "2.5.1"; + version = "2.5.2"; src = fetchFromGitHub { owner = "ANTsX"; repo = "ANTs"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-q252KC6SKUN5JaQWAcsVmDprVkLXDvkYzNhC7yHJNpk="; + hash = "sha256-crvLxUP/uM0u1oakxcpsiULAKUo+86hGATs/kHNseaw="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix index 76780298120ed..19df156ae17cc 100644 --- a/pkgs/applications/science/biology/bedtools/default.nix +++ b/pkgs/applications/science/biology/bedtools/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} install"; meta = with lib; { - description = "A powerful toolset for genome arithmetic"; + description = "Powerful toolset for genome arithmetic"; license = licenses.gpl2; homepage = "https://bedtools.readthedocs.io/en/latest/"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/bftools/default.nix b/pkgs/applications/science/biology/bftools/default.nix index a8bb739bbed85..6b8a7fd96d099 100644 --- a/pkgs/applications/science/biology/bftools/default.nix +++ b/pkgs/applications/science/biology/bftools/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ makeWrapper ]; meta = with lib; { - description = "A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included"; + description = "Bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.gpl2; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/bowtie/default.nix b/pkgs/applications/science/biology/bowtie/default.nix index bec263a2d9315..2009788ead6a5 100644 --- a/pkgs/applications/science/biology/bowtie/default.nix +++ b/pkgs/applications/science/biology/bowtie/default.nix @@ -36,7 +36,7 @@ stdenv.mkDerivation rec { installFlags = [ "prefix=$(out)" ]; meta = with lib; { - description = "An ultrafast memory-efficient short read aligner"; + description = "Ultrafast memory-efficient short read aligner"; license = licenses.artistic2; homepage = "https://bowtie-bio.sourceforge.net"; maintainers = with maintainers; [ prusnak ]; diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix index dbcecb7ac3fba..576b46288c885 100644 --- a/pkgs/applications/science/biology/bowtie2/default.nix +++ b/pkgs/applications/science/biology/bowtie2/default.nix @@ -12,14 +12,14 @@ stdenv.mkDerivation (finalAttrs: { pname = "bowtie2"; - version = "2.5.3"; + version = "2.5.4"; src = fetchFromGitHub { owner = "BenLangmead"; repo = "bowtie2"; rev = "refs/tags/v${finalAttrs.version}"; fetchSubmodules = true; - hash = "sha256-vjJRA9KFfJChxxg2wxBkwsnDw7fx5SNH3JhRXQw+7XA="; + hash = "sha256-ZbmVOItfAgKdsMrvQIXgKiPtoQJZYfGblCGDoNPjvTU="; }; # because of this flag, gcc on aarch64 cannot find the Threads @@ -51,7 +51,7 @@ stdenv.mkDerivation (finalAttrs: { }; meta = with lib; { - description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; + description = "Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; license = licenses.gpl3Plus; homepage = "http://bowtie-bio.sf.net/bowtie2"; changelog = "https://github.com/BenLangmead/bowtie2/releases/tag/${finalAttrs.src.rev}"; diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix index 8c883e2617bfa..c70eba475d233 100644 --- a/pkgs/applications/science/biology/bwa/default.nix +++ b/pkgs/applications/science/biology/bwa/default.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation { ''; meta = with lib; { - description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome"; + description = "Software package for mapping low-divergent sequences against a large reference genome, such as the human genome"; mainProgram = "bwa"; license = licenses.gpl3Plus; homepage = "https://bio-bwa.sourceforge.net/"; diff --git a/pkgs/applications/science/biology/emboss/default.nix b/pkgs/applications/science/biology/emboss/default.nix index d590a5da8a674..90fe611209f5d 100644 --- a/pkgs/applications/science/biology/emboss/default.nix +++ b/pkgs/applications/science/biology/emboss/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "The European Molecular Biology Open Software Suite"; + description = "European Molecular Biology Open Software Suite"; longDescription = ''EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community, including libraries. The software automatically copes with diff --git a/pkgs/applications/science/biology/gatk/default.nix b/pkgs/applications/science/biology/gatk/default.nix index 9884e3a771111..41623bf640dda 100644 --- a/pkgs/applications/science/biology/gatk/default.nix +++ b/pkgs/applications/science/biology/gatk/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://gatk.broadinstitute.org/hc/en-us"; - description = "A wide variety of tools with a primary focus on variant discovery and genotyping." ; + description = "Wide variety of tools with a primary focus on variant discovery and genotyping." ; license = licenses.asl20; sourceProvenance = with lib.sourceTypes; [ binaryBytecode ] ; maintainers = with maintainers; [ apraga ]; diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 219792326b685..0c74b65c98a26 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://www.broadinstitute.org/igv/"; - description = "A visualization tool for interactive exploration of genomic datasets"; + description = "Visualization tool for interactive exploration of genomic datasets"; license = licenses.mit; platforms = platforms.unix; maintainers = [ maintainers.mimame ]; diff --git a/pkgs/applications/science/biology/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index c1025d0b1919a..395e5b5dcd9ab 100644 --- a/pkgs/applications/science/biology/jbrowse/default.nix +++ b/pkgs/applications/science/biology/jbrowse/default.nix @@ -2,11 +2,11 @@ let pname = "jbrowse"; - version = "2.11.1"; + version = "2.11.2"; src = fetchurl { url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage"; - sha256 = "sha256-/1QNpoJy4u2sSw6907UQpdYX9aFWp31BxsYVTQoDpi4="; + sha256 = "sha256-7kZsK3vYgxubgtoIG1dByHgEBOlh9GUq+i3u/1eo0/o="; }; appimageContents = appimageTools.extractType2 { @@ -28,7 +28,7 @@ appimageTools.wrapType2 { ''; meta = with lib; { - description = "The next-generation genome browser"; + description = "Next-generation genome browser"; mainProgram = "jbrowse-desktop"; homepage = "https://jbrowse.org/jb2/"; license = licenses.asl20; diff --git a/pkgs/applications/science/biology/kalign/default.nix b/pkgs/applications/science/biology/kalign/default.nix index f26b679f799db..55df8d875bbd5 100644 --- a/pkgs/applications/science/biology/kalign/default.nix +++ b/pkgs/applications/science/biology/kalign/default.nix @@ -36,7 +36,7 @@ stdenv.mkDerivation (finalAttrs: { doCheck = true; meta = { - description = "A fast multiple sequence alignment program"; + description = "Fast multiple sequence alignment program"; mainProgram = "kalign"; homepage = "https://github.com/TimoLassmann/kalign"; changelog = "https://github.com/TimoLassmann/kalign/releases/tag/${finalAttrs.src.rev}"; diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix index b6e4661ccfd61..56cfa5168a486 100644 --- a/pkgs/applications/science/biology/kent/default.nix +++ b/pkgs/applications/science/biology/kent/default.nix @@ -13,13 +13,13 @@ }: stdenv.mkDerivation rec { pname = "kent"; - version = "446"; + version = "466"; src = fetchFromGitHub { owner = "ucscGenomeBrowser"; repo = pname; rev = "v${version}_base"; - hash = "sha256-d8gcoyMwINdHoD6xaNKt4rCKrKir99+i4KIzJ2YnxRw="; + hash = "sha256-zoDZ+8G0SHKfWmkXBqp+WSjQXtmkcTIZjrjPhUIJw1c="; }; buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 85fb1ca80ac65..700b2cf3b4548 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1543"; + version = "1544"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-APHPv7Q64JITfHsvjCThZ6hvGHerk6wjOm32KdTv4k8="; + hash = "sha256-jxNudfUvSqV1QUzdvG8LWtL977oho9QuOQImmwbQiIM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/megahit/default.nix b/pkgs/applications/science/biology/megahit/default.nix index 5fa9420bc87cb..185f763c2fb8c 100644 --- a/pkgs/applications/science/biology/megahit/default.nix +++ b/pkgs/applications/science/biology/megahit/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { "-DSTATIC_BUILD=ON" ]; meta = with lib; { - description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"; + description = "Ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"; license = licenses.gpl3; homepage = "https://github.com/voutcn/megahit"; maintainers = with maintainers; [ luispedro ]; diff --git a/pkgs/applications/science/biology/messer-slim/default.nix b/pkgs/applications/science/biology/messer-slim/default.nix index af3856f041674..3812e9980cdfe 100644 --- a/pkgs/applications/science/biology/messer-slim/default.nix +++ b/pkgs/applications/science/biology/messer-slim/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { "-DCMAKE_RANLIB=${gcc-unwrapped}/bin/gcc-ranlib" ]; meta = { - description = "An evolutionary simulation framework"; + description = "Evolutionary simulation framework"; homepage = "https://messerlab.org/slim/"; license = with lib.licenses; [ gpl3 ]; maintainers = with lib.maintainers; [ bzizou ]; diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index 923d72f7fb387..5597b5504678d 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A versatile pairwise aligner for genomic and spliced nucleotide sequences"; + description = "Versatile pairwise aligner for genomic and spliced nucleotide sequences"; mainProgram = "minimap2"; homepage = "https://lh3.github.io/minimap2"; license = licenses.mit; diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index 6e5e4feb16fc6..ef79fb11a824d 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -1,6 +1,6 @@ { lib , stdenv -, fetchurl +, fetchFromGitHub , readline , xorg , mpi @@ -17,11 +17,13 @@ , useCore ? false , useRx3d ? false }: - - -stdenv.mkDerivation rec { +let + inherit (lib.lists) optionals; + inherit (lib.strings) cmakeBool; +in +stdenv.mkDerivation (finalAttrs: { pname = "neuron"; - version = "8.2.3"; + version = "8.2.4"; # format is for pythonModule conversion format = "other"; @@ -31,10 +33,10 @@ stdenv.mkDerivation rec { bison flex git - ] ++ lib.optionals useCore [ perl gsl ] - ++ lib.optionals stdenv.isDarwin [ xcbuild ]; + ] ++ optionals useCore [ perl gsl ] + ++ optionals stdenv.isDarwin [ xcbuild ]; - buildInputs = lib.optionals useIv [ + buildInputs = optionals useIv [ xorg.libX11.dev xorg.libXcomposite.dev xorg.libXext.dev @@ -47,28 +49,29 @@ stdenv.mkDerivation rec { python3.pkgs.setuptools python3.pkgs.scikit-build python3.pkgs.matplotlib - ] ++ lib.optionals useMpi [ + ] ++ optionals useMpi [ mpi - ] ++ lib.optionals useMpi [ + ] ++ optionals useMpi [ python3.pkgs.mpi4py - ] ++ lib.optionals useRx3d [ - python3.pkgs.cython + ] ++ optionals useRx3d [ + python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.4 python3.pkgs.numpy ]; - patches = [ ./neuron_darwin_rpath.patch ]; - # Patch build shells for cmake (bin, src, cmake) and submodules (external) postPatch = '' patchShebangs ./bin ./src ./external ./cmake - sed -e 's#DESTDIR =#DESTDIR = '"$out"'#' -i external/coreneuron/extra/nrnivmodl_core_makefile.in + substituteInPlace external/coreneuron/extra/nrnivmodl_core_makefile.in \ + --replace-fail \ + "DESTDIR =" \ + "DESTDIR = $out" ''; cmakeFlags = [ - "-DNRN_ENABLE_INTERVIEWS=${if useIv then "ON" else "OFF"}" - "-DNRN_ENABLE_MPI=${if useMpi then "ON" else "OFF"}" - "-DNRN_ENABLE_CORENEURON=${if useCore then "ON" else "OFF"}" - "-DNRN_ENABLE_RX3D=${if useRx3d then "ON" else "OFF"}" + (cmakeBool "NRN_ENABLE_INTERVIEWS" useIv) + (cmakeBool "NRN_ENABLE_MPI" useMpi) + (cmakeBool "NRN_ENABLE_CORENEURON" useCore) + (cmakeBool "NRN_ENABLE_RX3D" useRx3d) ]; postInstall = '' @@ -81,9 +84,12 @@ stdenv.mkDerivation rec { done ''; - src = fetchurl { - url = "https://github.com/neuronsimulator/nrn/releases/download/${version}/full-src-package-${version}.tar.gz"; - sha256 = "sha256-k8+71BRfh+a73sZho6v0QFRxVmrfx6jqrgaqammdtDI="; + src = fetchFromGitHub { + owner = "neuronsimulator"; + repo = "nrn"; + rev = finalAttrs.version; + fetchSubmodules = true; + hash = "sha256-KsULc+LHoWmrkGYebpoUot6DhStKidbLQf5a3S+pi4s="; }; meta = with lib; { @@ -101,4 +107,4 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ adev davidcromp ]; platforms = platforms.all; }; -} +}) diff --git a/pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch b/pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch deleted file mode 100644 index 1b0fa2670782a..0000000000000 --- a/pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/src/nrnpython/setup.py.in -+++ b/src/nrnpython/setup.py.in -@@ -124,7 +124,7 @@ libdirs = [destdir + get_escaped_path("@NRN_LIBDIR@"), - rpath_prefix_flag='-Wl,-R' - extra_link_args = [@NRN_LINK_FLAGS_COMMA_SEPARATED_STRINGS@] - @MAC_DARWIN_FALSE@extra_link_args += [rpath_prefix_flag+lib_path for lib_path in libdirs] --@MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,@loader_path/../../") -+@MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,@loader_path/../../../") - @MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,%s" % ivlibdir) - - # as neuron module will be built during make, add build/lib diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix index d602395b87572..56e1852213961 100644 --- a/pkgs/applications/science/biology/platypus/default.nix +++ b/pkgs/applications/science/biology/platypus/default.nix @@ -30,7 +30,7 @@ in stdenv.mkDerivation { ''; meta = with lib; { - description = "The Platypus variant caller"; + description = "Platypus variant caller"; license = licenses.gpl3; homepage = "https://github.com/andyrimmer/Platypus"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/plink-ng/default.nix b/pkgs/applications/science/biology/plink-ng/default.nix index 0e65bed4cf3e4..b91655ac8fdac 100644 --- a/pkgs/applications/science/biology/plink-ng/default.nix +++ b/pkgs/applications/science/biology/plink-ng/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { meta = { broken = (stdenv.isLinux && stdenv.isAarch64); - description = "A comprehensive update to the PLINK association analysis toolset"; + description = "Comprehensive update to the PLINK association analysis toolset"; mainProgram = "plink"; homepage = "https://www.cog-genomics.org/plink2"; license = lib.licenses.gpl3; diff --git a/pkgs/applications/science/biology/poretools/default.nix b/pkgs/applications/science/biology/poretools/default.nix deleted file mode 100644 index 47ffd507efdaf..0000000000000 --- a/pkgs/applications/science/biology/poretools/default.nix +++ /dev/null @@ -1,23 +0,0 @@ -{ lib, python2Packages, fetchFromGitHub }: - -python2Packages.buildPythonPackage rec { - pname = "poretools"; - version = "unstable-2016-07-10"; - - src = fetchFromGitHub { - repo = pname; - owner = "arq5x"; - rev = "e426b1f09e86ac259a00c261c79df91510777407"; - sha256 = "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"; - }; - - propagatedBuildInputs = [ python2Packages.h5py python2Packages.matplotlib python2Packages.seaborn python2Packages.pandas ]; - - meta = { - description = "a toolkit for working with nanopore sequencing data from Oxford Nanopore"; - license = lib.licenses.mit; - homepage = "https://poretools.readthedocs.io/en/latest/"; - maintainers = [ lib.maintainers.rybern ]; - broken = true; # Build error: h5py-3.9.0 not supported for interpreter python2.7 - }; -} diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix index 0cc20b0635036..94ccafd36d00c 100644 --- a/pkgs/applications/science/biology/raxml/default.nix +++ b/pkgs/applications/science/biology/raxml/default.nix @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies"; + description = "Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies"; license = licenses.gpl3; homepage = "https://sco.h-its.org/exelixis/web/software/raxml/"; maintainers = [ maintainers.unode ]; diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix deleted file mode 100644 index 0b0491a71aaef..0000000000000 --- a/pkgs/applications/science/biology/spades/default.nix +++ /dev/null @@ -1,32 +0,0 @@ -{ lib, stdenv, fetchurl, zlib, bzip2, cmake, python3 }: - -stdenv.mkDerivation rec { - pname = "SPAdes"; - version = "3.15.5"; - - src = fetchurl { - url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o="; - }; - - nativeBuildInputs = [ cmake ]; - - buildInputs = [ zlib bzip2 python3 ]; - - doCheck = true; - - sourceRoot = "${pname}-${version}/src"; - - env.CXXFLAGS = toString [ - # GCC 13: error: 'uint32_t' does not name a type - "-include cstdint" - ]; - - meta = with lib; { - description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"; - license = licenses.gpl2Only; - homepage = "http://cab.spbu.ru/software/spades/"; - platforms = [ "x86_64-linux" "x86_64-darwin" ]; - maintainers = [ maintainers.bzizou ]; - }; -} diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix index a36157ed5d169..62c21a23eb66a 100644 --- a/pkgs/applications/science/biology/sratoolkit/default.nix +++ b/pkgs/applications/science/biology/sratoolkit/default.nix @@ -48,8 +48,8 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://github.com/ncbi/sra-tools"; - description = "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives."; - license = licenses.publicDomain; + description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives"; + license = licenses.ncbiPd; maintainers = with maintainers; [ thyol ]; platforms = [ "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/applications/science/biology/tandem-aligner/default.nix index 0b3f2520d82be..d44489debbb62 100644 --- a/pkgs/applications/science/biology/tandem-aligner/default.nix +++ b/pkgs/applications/science/biology/tandem-aligner/default.nix @@ -56,7 +56,7 @@ stdenv.mkDerivation (finalAttrs: { ''; meta = { - description = "A parameter-free algorithm for sequence alignment"; + description = "Parameter-free algorithm for sequence alignment"; homepage = "https://github.com/seryrzu/tandem_aligner"; changelog = "https://github.com/seryrzu/tandem_aligner/releases/tag/v${finalAttrs.version}"; license = lib.licenses.bsd3; diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix index b27a63a2135ae..b2ef121caa9a2 100644 --- a/pkgs/applications/science/biology/trimal/default.nix +++ b/pkgs/applications/science/biology/trimal/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment"; + description = "Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment"; license = licenses.gpl3; platforms = platforms.linux; homepage = "http://trimal.cgenomics.org"; diff --git a/pkgs/applications/science/biology/trimmomatic/default.nix b/pkgs/applications/science/biology/trimmomatic/default.nix index db19278eaa479..111a4dda9e9df 100644 --- a/pkgs/applications/science/biology/trimmomatic/default.nix +++ b/pkgs/applications/science/biology/trimmomatic/default.nix @@ -54,7 +54,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { changelog = "https://github.com/usadellab/Trimmomatic/blob/main/versionHistory.txt"; - description = "A flexible read trimming tool for Illumina NGS data"; + description = "Flexible read trimming tool for Illumina NGS data"; longDescription = '' Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data: adapter trimming, quality trimming, diff --git a/pkgs/applications/science/biology/vcftools/default.nix b/pkgs/applications/science/biology/vcftools/default.nix index a4ec84d4d5060..644c7eb2bd37b 100644 --- a/pkgs/applications/science/biology/vcftools/default.nix +++ b/pkgs/applications/science/biology/vcftools/default.nix @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { buildInputs = [ zlib perl ]; meta = with lib; { - description = "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project"; + description = "Set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project"; license = licenses.lgpl3; platforms = platforms.linux; homepage = "https://vcftools.github.io/index.html"; diff --git a/pkgs/applications/science/biology/xenomapper/default.nix b/pkgs/applications/science/biology/xenomapper/default.nix index 194db966915e1..98ee7c2819bec 100644 --- a/pkgs/applications/science/biology/xenomapper/default.nix +++ b/pkgs/applications/science/biology/xenomapper/default.nix @@ -15,7 +15,7 @@ python3.pkgs.buildPythonApplication rec { meta = with lib; { homepage = "https://github.com/genomematt/xenomapper"; - description = "A utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins"; + description = "Utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins"; license = licenses.gpl3; platforms = platforms.all; maintainers = [ maintainers.jbedo ]; diff --git a/pkgs/applications/science/chemistry/element/default.nix b/pkgs/applications/science/chemistry/element/default.nix index c3c4a0fe582ed..cc80cb058d92c 100644 --- a/pkgs/applications/science/chemistry/element/default.nix +++ b/pkgs/applications/science/chemistry/element/default.nix @@ -14,7 +14,7 @@ buildGoModule rec { vendorHash = "sha256-A4g2rQTaYrA4/0rqldUv7iuibzNINEvx9StUnaN2/Yg="; meta = with lib; { - description = "The periodic table on the command line"; + description = "Periodic table on the command line"; mainProgram = "element"; homepage = "https://github.com/gennaro-tedesco/element"; license = licenses.asl20; diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index a4b1cd943e1bb..c379e432bdeb2 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -16,10 +16,10 @@ stdenv.mkDerivation rec { pname = "gwyddion"; - version = "2.65"; + version = "2.66"; src = fetchurl { url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz"; - sha256 = "sha256-kRX7CoPJY8YkYNode5g0OCyWmL+5sM8puCmk9ZE2nqM="; + sha256 = "sha256-N3vtzSsNjRM6MpaG2p9fkYB/8dR5N/mZEZXx6GN5LVI="; }; nativeBuildInputs = [ pkg-config file ]; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index bafbeb3529c69..cba6a40b59923 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.2.15"; + version = "16.2.17"; 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-${version}-binary.tar.gz"; - hash = "sha256-zPHh5IFdttliPc0SCgkM/3UQmS4eT2rfi5HqpFjY5hA="; + hash = "sha256-1iBLLfaoztbphhrG3NVWH+PVSbCZd+HQqvCYF3H9S/E="; }; patchPhase = '' @@ -52,7 +52,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with lib; { - description = "A Java 3D viewer for chemical structures"; + description = "Java 3D viewer for chemical structures"; mainProgram = "jmol"; homepage = "https://sourceforge.net/projects/jmol"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index 090c252bb82ce..4228e818e4887 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -39,7 +39,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "A chemical modelling, analysis and structure drawing program"; + description = "Chemical modelling, analysis and structure drawing program"; homepage = "https://chemaxon.com/products/marvin"; maintainers = with maintainers; [ fusion809 ]; license = licenses.unfree; diff --git a/pkgs/applications/science/chemistry/openmolcas/default.nix b/pkgs/applications/science/chemistry/openmolcas/default.nix index 8ad9794739559..d500e78b24820 100644 --- a/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -43,13 +43,13 @@ let in stdenv.mkDerivation rec { pname = "openmolcas"; - version = "24.02"; + version = "24.06"; src = fetchFromGitLab { owner = "Molcas"; repo = "OpenMolcas"; rev = "v${version}"; - hash = "sha256-4Ek0cnaRfLEbj1Nj31rRp9b2sois4rIFTcpOUq9h2mw="; + hash = "sha256-/y6vEvA1Zf+p7Z0WpcN4P5voLN8MmfbKz1FuthgVQp0="; }; patches = [ diff --git a/pkgs/applications/science/chemistry/siesta/default.nix b/pkgs/applications/science/chemistry/siesta/default.nix index 02586dea2e297..2ec4d37f73ed2 100644 --- a/pkgs/applications/science/chemistry/siesta/default.nix +++ b/pkgs/applications/science/chemistry/siesta/default.nix @@ -63,7 +63,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A first-principles materials simulation code using DFT"; + description = "First-principles materials simulation code using DFT"; mainProgram = "siesta"; longDescription = '' SIESTA is both a method and its computer program diff --git a/pkgs/applications/science/computer-architecture/accelergy/default.nix b/pkgs/applications/science/computer-architecture/accelergy/default.nix index ec702d2b2906e..9eb6f341b714d 100644 --- a/pkgs/applications/science/computer-architecture/accelergy/default.nix +++ b/pkgs/applications/science/computer-architecture/accelergy/default.nix @@ -19,7 +19,7 @@ python3Packages.buildPythonApplication rec { ]; meta = with lib; { - description = "An architecture-level energy/area estimator for accelerator designs"; + description = "Architecture-level energy/area estimator for accelerator designs"; license = licenses.mit; homepage = "https://accelergy.mit.edu/"; maintainers = with maintainers; [ gdinh ]; diff --git a/pkgs/applications/science/electronics/csxcad/default.nix b/pkgs/applications/science/electronics/csxcad/default.nix index 83ee992f4b28a..bc1f4287c1158 100644 --- a/pkgs/applications/science/electronics/csxcad/default.nix +++ b/pkgs/applications/science/electronics/csxcad/default.nix @@ -38,7 +38,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; meta = with lib; { - description = "A C++ library to describe geometrical objects"; + description = "C++ library to describe geometrical objects"; homepage = "https://github.com/thliebig/CSXCAD"; license = licenses.lgpl3; maintainers = with maintainers; [ matthuszagh ]; diff --git a/pkgs/applications/science/electronics/degate/default.nix b/pkgs/applications/science/electronics/degate/default.nix index 30ded5d1354f6..580d452f333df 100644 --- a/pkgs/applications/science/electronics/degate/default.nix +++ b/pkgs/applications/science/electronics/degate/default.nix @@ -66,7 +66,7 @@ in stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A modern and open-source cross-platform software for chips reverse engineering"; + description = "Modern and open-source cross-platform software for chips reverse engineering"; mainProgram = "Degate"; homepage = "https://degate.readthedocs.io/"; license = licenses.gpl3; diff --git a/pkgs/applications/science/electronics/dsview/default.nix b/pkgs/applications/science/electronics/dsview/default.nix index 2818379afc38b..5d6c83f5dfaa1 100644 --- a/pkgs/applications/science/electronics/dsview/default.nix +++ b/pkgs/applications/science/electronics/dsview/default.nix @@ -1,18 +1,18 @@ { stdenv, lib, fetchFromGitHub, pkg-config, cmake, wrapQtAppsHook -, libzip, boost, fftw, qtbase, qtwayland, qtsvg, libusb1 +, libzip, boost, fftw, libusb1, qtbase, qtsvg, qtwayland , python3, desktopToDarwinBundle }: stdenv.mkDerivation rec { pname = "dsview"; - version = "1.3.1"; + version = "1.3.2"; src = fetchFromGitHub { owner = "DreamSourceLab"; repo = "DSView"; rev = "v${version}"; - sha256 = "sha256-LwrlB+Nwq34YjwGmnbUWS3W//ZHr8Do2Wf2te+2oBeI="; + sha256 = "sha256-d/TfCuJzAM0WObOiBhgfsTirlvdROrlCm+oL1cqUrIs="; }; patches = [ @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { ] ++ lib.optional stdenv.isLinux qtwayland; meta = with lib; { - description = "A GUI program for supporting various instruments from DreamSourceLab, including logic analyzer, oscilloscope, etc"; + description = "GUI program for supporting various instruments from DreamSourceLab, including logic analyzer, oscilloscope, etc"; mainProgram = "DSView"; homepage = "https://www.dreamsourcelab.com/"; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/electronics/dwfv/default.nix b/pkgs/applications/science/electronics/dwfv/default.nix index 2d88e2647dfd7..415cc29812d3d 100644 --- a/pkgs/applications/science/electronics/dwfv/default.nix +++ b/pkgs/applications/science/electronics/dwfv/default.nix @@ -12,7 +12,7 @@ rustPlatform.buildRustPackage rec { cargoSha256 = "1z51yx3psdxdzmwny0rzlch5hjx2pssll73q79qij2bc7wgyjscy"; meta = with lib; { - description = "A simple digital waveform viewer with vi-like key bindings"; + description = "Simple digital waveform viewer with vi-like key bindings"; mainProgram = "dwfv"; homepage = "https://github.com/psurply/dwfv"; license = licenses.mit; diff --git a/pkgs/applications/science/electronics/flopoco/default.nix b/pkgs/applications/science/electronics/flopoco/default.nix index 7ce1087209e2c..2da80512e2b2c 100644 --- a/pkgs/applications/science/electronics/flopoco/default.nix +++ b/pkgs/applications/science/electronics/flopoco/default.nix @@ -84,7 +84,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "The FloPoCo arithmetic core generator"; + description = "FloPoCo arithmetic core generator"; homepage = "https://flopoco.org/"; license = licenses.unfree; platforms = platforms.unix; diff --git a/pkgs/applications/science/electronics/fped/default.nix b/pkgs/applications/science/electronics/fped/default.nix index 6d10426b298a5..edfe34c0e25e8 100644 --- a/pkgs/applications/science/electronics/fped/default.nix +++ b/pkgs/applications/science/electronics/fped/default.nix @@ -40,7 +40,7 @@ stdenv.mkDerivation { ]; meta = { - description = "An editor that allows the interactive creation of footprints electronic components"; + description = "Editor that allows the interactive creation of footprints electronic components"; mainProgram = "fped"; homepage = "http://projects.qi-hardware.com/index.php/p/fped/"; license = licenses.gpl2; diff --git a/pkgs/applications/science/electronics/fritzing/default.nix b/pkgs/applications/science/electronics/fritzing/default.nix index 955edb9b59ae2..9eb7b50445020 100644 --- a/pkgs/applications/science/electronics/fritzing/default.nix +++ b/pkgs/applications/science/electronics/fritzing/default.nix @@ -109,7 +109,7 @@ stdenv.mkDerivation { ''; meta = with lib; { - description = "An open source prototyping tool for Arduino-based projects"; + description = "Open source prototyping tool for Arduino-based projects"; homepage = "https://fritzing.org/"; license = with licenses; [ gpl3 cc-by-sa-30 ]; maintainers = with maintainers; [ robberer muscaln ]; diff --git a/pkgs/applications/science/electronics/gerbv/default.nix b/pkgs/applications/science/electronics/gerbv/default.nix index 5f178e08280a9..c4c46b5507994 100644 --- a/pkgs/applications/science/electronics/gerbv/default.nix +++ b/pkgs/applications/science/electronics/gerbv/default.nix @@ -45,7 +45,7 @@ stdenv.mkDerivation rec { ]; meta = with lib; { - description = "A Gerber (RS-274X) viewer"; + description = "Gerber (RS-274X) viewer"; mainProgram = "gerbv"; homepage = "https://gerbv.github.io/"; changelog = "https://github.com/gerbv/gerbv/releases/tag/v${version}"; diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index 3e0f3613ba903..d28a5cf809065 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -16,11 +16,11 @@ stdenv.mkDerivation rec { pname = "gtkwave"; - version = "3.3.119"; + version = "3.3.120"; src = fetchurl { url = "mirror://sourceforge/gtkwave/${pname}-gtk3-${version}.tar.gz"; - sha256 = "sha256-6rPgnnZBEVwHhIv7MPfdDDu+K4y+RQF+leB327pqwDg="; + sha256 = "sha256-XalIY/suXYjMAZ4r/cZ2AiOYETiUtYXYZOEcqDQbJNg="; }; nativeBuildInputs = [ pkg-config wrapGAppsHook3 ]; diff --git a/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix b/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix index 4c3692266a5c4..c193352eb4559 100644 --- a/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix +++ b/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix @@ -143,7 +143,7 @@ in stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A comprehensive reverse engineering and manipulation framework for gate-level netlists"; + description = "Comprehensive reverse engineering and manipulation framework for gate-level netlists"; mainProgram = "hal"; homepage = "https://github.com/emsec/hal"; license = licenses.mit; diff --git a/pkgs/applications/science/electronics/horizon-eda/base.nix b/pkgs/applications/science/electronics/horizon-eda/base.nix index 2a37c0265dc37..0292ee493a829 100644 --- a/pkgs/applications/science/electronics/horizon-eda/base.nix +++ b/pkgs/applications/science/electronics/horizon-eda/base.nix @@ -51,7 +51,7 @@ rec { CASROOT = opencascade-occt; meta = with lib; { - description = "A free EDA software to develop printed circuit boards"; + description = "Free EDA software to develop printed circuit boards"; homepage = "https://horizon-eda.org"; maintainers = with maintainers; [ guserav jue89 ]; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/electronics/kicad/addons/kikit.nix b/pkgs/applications/science/electronics/kicad/addons/kikit.nix index 6e5fc5ad96781..b6d3cf3e72054 100644 --- a/pkgs/applications/science/electronics/kicad/addons/kikit.nix +++ b/pkgs/applications/science/electronics/kicad/addons/kikit.nix @@ -24,7 +24,7 @@ let "kikit-library" = { makeTarget = "pcm-lib"; resultZip = "pcm-kikit-lib.zip"; - description = "KiKit uses these symbols and footprints to annotate your boards (e.g., to place a tab in a panel)."; + description = "KiKit uses these symbols and footprints to annotate your boards (e.g., to place a tab in a panel)"; }; }; targetSpec = targetSpecs.${addonName}; diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix index 4c55703edccf4..b3ddbd5b604fe 100644 --- a/pkgs/applications/science/electronics/kicad/versions.nix +++ b/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,23 +3,23 @@ { "kicad" = { kicadVersion = { - version = "8.0.2"; + version = "8.0.3"; src = { - rev = "55a4d4f5e2f54be6ccf74a8919d04684c9df4c50"; - sha256 = "069ycii9zvdxwxd73afd6bp975r1555yvifi9zdb77qyvn0d9nr9"; + rev = "8ba5ba46af8502ea7a7d2a9754363167c2742399"; + sha256 = "0hafvcjjwylgcpgyyasmb2q210k82wvcswvgjvwwh76bwshwcpwa"; }; }; libVersion = { - version = "8.0.2"; + version = "8.0.3"; libSources = { - symbols.rev = "099ac0c8ac402a685fde00b1369e34a116e29661"; - symbols.sha256 = "0w333f89yw2m0zlpkg0k6hfwlj10snm8laihdjnsb22asyz4pbhn"; - templates.rev = "2e2da58e02707d327d59d4101c401a82dc9a26f6"; - templates.sha256 = "073a6cyvzzy0vmkj3ip4ziq7b7pcizs70nm5acw838dxghjfyv3v"; - footprints.rev = "e8c30550cde4945cbe1bf30cccf0b3c1e2bda6c6"; - footprints.sha256 = "10j8qjljc1fv8k4zp3zn0da33g57hn6pgrgmbgp18dsa539xvxcz"; - packages3d.rev = "249f7947587529026e1676cd70c8d7493a8d8162"; - packages3d.sha256 = "04gvfb54jhnww2qwrxc27wpyrvmjasdc4xhr0ridl7dglh4qcp35"; + symbols.rev = "2bc103c46a8daacbba2cded8b9f095b330ba928d"; + symbols.sha256 = "1za0spq09bbj7xwfwr1abmwjnqfd3zx0crayaz7915ja0ifi75hd"; + templates.rev = "0f57b59d365d1f8b8fdd0745e10beb035e88ba37"; + templates.sha256 = "03idwrk3vj9h2az8j8lqpbdbnfxdbkzh4db68kq3644yj3cnlcza"; + footprints.rev = "539ffd8c0898ad8c8c51c2ab85ba56bfd77271c7"; + footprints.sha256 = "0ik4hjl5m65wnpaymg58zbvsfvchhyq5x3psvj6005mgv2hrican"; + packages3d.rev = "3172a1cc0931c1734efad68623374d5277f8ab60"; + packages3d.sha256 = "1yjlg7cxwhlzcdbxjqyqamr140sz8gvzi63k2401mhdbh88c9kii"; }; }; }; diff --git a/pkgs/applications/science/electronics/librepcb/default.nix b/pkgs/applications/science/electronics/librepcb/default.nix index 67bc014646e09..cff52d67dc477 100644 --- a/pkgs/applications/science/electronics/librepcb/default.nix +++ b/pkgs/applications/science/electronics/librepcb/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { buildInputs = [ qtbase ]; meta = with lib; { - description = "A free EDA software to develop printed circuit boards"; + description = "Free EDA software to develop printed circuit boards"; homepage = "https://librepcb.org/"; maintainers = with maintainers; [ luz thoughtpolice ]; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix index 5fc4b0036f9fb..0be742f76e3c6 100644 --- a/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -13,11 +13,11 @@ stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.465"; + version = "8.3.483"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-cb9A8rpjD3x3fJo+xexlyzn+/3M5iUJmSoBraom9zd8="; + sha256 = "sha256-JyawlH/zUTJ7fGf63zHvZ3q8AYRwFELwh+63RN9IkBA="; }; nativeBuildInputs = [ python3 ]; diff --git a/pkgs/applications/science/electronics/simulide/default.nix b/pkgs/applications/science/electronics/simulide/default.nix index 9053bcfe58e50..717f7b57de74c 100644 --- a/pkgs/applications/science/electronics/simulide/default.nix +++ b/pkgs/applications/science/electronics/simulide/default.nix @@ -71,7 +71,7 @@ let ''; meta = { - description = "A simple real time electronic circuit simulator"; + description = "Simple real time electronic circuit simulator"; longDescription = '' SimulIDE is a simple real time electronic circuit simulator, intended for hobbyist or students to learn and experiment with analog and digital electronic circuits and microcontrollers. diff --git a/pkgs/applications/science/electronics/systemc/default.nix b/pkgs/applications/science/electronics/systemc/default.nix index 4e14d08e63bfa..8e47ef9606566 100644 --- a/pkgs/applications/science/electronics/systemc/default.nix +++ b/pkgs/applications/science/electronics/systemc/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "systemc"; - version = "2.3.4"; + version = "3.0.0"; src = fetchFromGitHub { owner = "accellera-official"; repo = pname; rev = version; - sha256 = "0sj8wlkp68cjhmkd9c9lvm3lk3sckczpz7w9vby64inc1f9fnf0b"; + sha256 = "sha256-qeQUrPhD+Gb1lResM7NZzO/vEgJd3NE6lbnM380VVa0="; }; nativeBuildInputs = [ cmake ]; @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { doCheck = stdenv.buildPlatform.canExecute stdenv.hostPlatform; meta = with lib; { - description = "The language for System-level design, modeling and verification"; + description = "Language for System-level design, modeling and verification"; homepage = "https://systemc.org/"; license = licenses.asl20; platforms = platforms.unix; diff --git a/pkgs/applications/science/geometry/antiprism/default.nix b/pkgs/applications/science/geometry/antiprism/default.nix index 79688e05fb807..62ffc099dc6cd 100644 --- a/pkgs/applications/science/geometry/antiprism/default.nix +++ b/pkgs/applications/science/geometry/antiprism/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://www.antiprism.com"; - description = "A collection of programs for generating, manipulating, transforming and viewing polyhedra"; + description = "Collection of programs for generating, manipulating, transforming and viewing polyhedra"; license = with licenses; [ mit ]; maintainers = with maintainers; [ AndersonTorres ]; }; diff --git a/pkgs/applications/science/logic/abc/default.nix b/pkgs/applications/science/logic/abc/default.nix index 1685bb7aba33c..a71122c5465c5 100644 --- a/pkgs/applications/science/logic/abc/default.nix +++ b/pkgs/applications/science/logic/abc/default.nix @@ -29,7 +29,7 @@ stdenv.mkDerivation (finalAttrs: { passthru.rev = finalAttrs.src.rev; meta = with lib; { - description = "A tool for squential logic synthesis and formal verification"; + description = "Tool for squential logic synthesis and formal verification"; homepage = "https://people.eecs.berkeley.edu/~alanmi/abc"; license = licenses.mit; maintainers = with maintainers; [ thoughtpolice Luflosi ]; diff --git a/pkgs/applications/science/logic/acgtk/default.nix b/pkgs/applications/science/logic/acgtk/default.nix index 3fa4111668ebc..37c7b527a9134 100644 --- a/pkgs/applications/science/logic/acgtk/default.nix +++ b/pkgs/applications/science/logic/acgtk/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation { meta = with lib; { homepage = "https://acg.loria.fr/"; - description = "A toolkit for developing ACG signatures and lexicon"; + description = "Toolkit for developing ACG signatures and lexicon"; license = licenses.cecill20; inherit (ocamlPackages.ocaml.meta) platforms; maintainers = [ maintainers.jirkamarsik ]; diff --git a/pkgs/applications/science/logic/beluga/default.nix b/pkgs/applications/science/logic/beluga/default.nix index 693be7f338866..b1497e2b1dcbe 100644 --- a/pkgs/applications/science/logic/beluga/default.nix +++ b/pkgs/applications/science/logic/beluga/default.nix @@ -33,7 +33,7 @@ ocamlPackages.buildDunePackage rec { ''; meta = with lib; { - description = "A functional language for reasoning about formal systems"; + description = "Functional language for reasoning about formal systems"; homepage = "https://complogic.cs.mcgill.ca/beluga"; changelog = "https://github.com/Beluga-lang/Beluga/releases/tag/v${version}"; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/logic/bitwuzla/default.nix b/pkgs/applications/science/logic/bitwuzla/default.nix index 1fa78849db6e8..c1eb751fb1a57 100644 --- a/pkgs/applications/science/logic/bitwuzla/default.nix +++ b/pkgs/applications/science/logic/bitwuzla/default.nix @@ -1,6 +1,5 @@ { stdenv , fetchFromGitHub -, fetchpatch , lib , python3 , meson @@ -18,24 +17,15 @@ stdenv.mkDerivation (finalAttrs: { pname = "bitwuzla"; - version = "0.4.0"; + version = "0.5.0"; src = fetchFromGitHub { owner = "bitwuzla"; repo = "bitwuzla"; rev = finalAttrs.version; - hash = "sha256-ZEdV4ml1LwrYwscgOcL2gLx/ijPYqRktXMQH/Njh8OI="; + hash = "sha256-/izxmN+zlrXsY6g6TRC1QqsLqltvrmZquXRd6h8RLRc="; }; - patches = [ - # fix parser on aarch64 - # remove on next release - (fetchpatch { - url = "https://github.com/bitwuzla/bitwuzla/commit/4d914aa5ec34076c37749f0cf6dce976ea510386.patch"; - hash = "sha256-gp+HEamOySjPXCC39tt5DIMdQqEew26a+M15sNdCmTM="; - }) - ]; - strictDeps = true; nativeBuildInputs = [ meson pkg-config git ninja ]; @@ -62,7 +52,7 @@ stdenv.mkDerivation (finalAttrs: { doCheck = stdenv.hostPlatform.isLinux; meta = { - description = "A SMT solver for fixed-size bit-vectors, floating-point arithmetic, arrays, and uninterpreted functions"; + description = "SMT solver for fixed-size bit-vectors, floating-point arithmetic, arrays, and uninterpreted functions"; mainProgram = "bitwuzla"; homepage = "https://bitwuzla.github.io"; license = lib.licenses.mit; diff --git a/pkgs/applications/science/logic/boolector/default.nix b/pkgs/applications/science/logic/boolector/default.nix index d23db163aeb64..1fd6bf7dc5431 100644 --- a/pkgs/applications/science/logic/boolector/default.nix +++ b/pkgs/applications/science/logic/boolector/default.nix @@ -58,7 +58,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "An extremely fast SMT solver for bit-vectors and arrays"; + description = "Extremely fast SMT solver for bit-vectors and arrays"; homepage = "https://boolector.github.io"; license = licenses.mit; platforms = with platforms; linux ++ darwin; diff --git a/pkgs/applications/science/logic/btor2tools/default.nix b/pkgs/applications/science/logic/btor2tools/default.nix index ce73ea636f295..a66637150bdfd 100644 --- a/pkgs/applications/science/logic/btor2tools/default.nix +++ b/pkgs/applications/science/logic/btor2tools/default.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { ]; meta = with lib; { - description = "A generic parser and tool package for the BTOR2 format"; + description = "Generic parser and tool package for the BTOR2 format"; homepage = "https://github.com/Boolector/btor2tools"; license = licenses.mit; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/cbmc/0001-Do-not-download-sources-in-cmake.patch b/pkgs/applications/science/logic/cbmc/0001-Do-not-download-sources-in-cmake.patch index 181214093ef8a..c209ed059e44f 100644 --- a/pkgs/applications/science/logic/cbmc/0001-Do-not-download-sources-in-cmake.patch +++ b/pkgs/applications/science/logic/cbmc/0001-Do-not-download-sources-in-cmake.patch @@ -1,4 +1,4 @@ -From 206084d2e08198b0b5b67733c407bd3fb74affb1 Mon Sep 17 00:00:00 2001 +From 714f5ebe9ade721abdccf58edfcddba52465cb8d Mon Sep 17 00:00:00 2001 From: Jiajie Chen <c@jia.je> Date: Sun, 2 Jul 2023 22:43:27 +0800 Subject: [PATCH] Do not download sources in cmake @@ -8,7 +8,7 @@ Subject: [PATCH] Do not download sources in cmake 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/src/solvers/CMakeLists.txt b/src/solvers/CMakeLists.txt -index 8bfcf4d13c..6ba858a461 100644 +index daa0853a57..4bcbbdaa47 100644 --- a/src/solvers/CMakeLists.txt +++ b/src/solvers/CMakeLists.txt @@ -123,16 +123,6 @@ foreach(SOLVER ${sat_impl}) @@ -16,11 +16,11 @@ index 8bfcf4d13c..6ba858a461 100644 message(STATUS "Building solvers with cadical") - download_project(PROJ cadical -- URL https://github.com/arminbiere/cadical/archive/rel-1.5.3.tar.gz -- PATCH_COMMAND patch -p1 -i ${CBMC_SOURCE_DIR}/../scripts/cadical-1.5.3-patch +- URL https://github.com/arminbiere/cadical/archive/rel-1.7.2.tar.gz +- PATCH_COMMAND patch -p1 -i ${CBMC_SOURCE_DIR}/../scripts/cadical-1.7.2-patch - COMMAND cmake -E copy ${CBMC_SOURCE_DIR}/../scripts/cadical_CMakeLists.txt CMakeLists.txt - COMMAND ./configure -- URL_MD5 265b1a715000ed3c5b6de36ddd1278a0 +- URL_MD5 be646831a017f81b300664e58deba1b5 - ) - - add_subdirectory(${cadical_SOURCE_DIR} ${cadical_BINARY_DIR}) @@ -32,10 +32,10 @@ index 8bfcf4d13c..6ba858a461 100644 target_include_directories(solvers PUBLIC ${cadical_SOURCE_DIR}/src -+ ${cadical_INCLUDE_DIR} ++ ${cadical_INCLUDE_DIR} ) target_link_libraries(solvers cadical) -- -2.40.1 +2.42.0 diff --git a/pkgs/applications/science/logic/cbmc/default.nix b/pkgs/applications/science/logic/cbmc/default.nix index 6a878735bb3d9..0a81b2a09ef1d 100644 --- a/pkgs/applications/science/logic/cbmc/default.nix +++ b/pkgs/applications/science/logic/cbmc/default.nix @@ -13,13 +13,13 @@ stdenv.mkDerivation rec { pname = "cbmc"; - version = "5.91.0"; + version = "6.0.0"; src = fetchFromGitHub { owner = "diffblue"; repo = pname; rev = "${pname}-${version}"; - sha256 = "sha256-7DzhGEDS9T6WIjGoxOw9Gf/q+tYNFJDPbQUBV3tbn/I="; + sha256 = "sha256-mPRkkKN7Hz9Qi6a3fEwVFh7a9OaBFcksNw9qwNOarao="; }; nativeBuildInputs = [ @@ -82,7 +82,7 @@ stdenv.mkDerivation rec { license = licenses.bsdOriginal; maintainers = with maintainers; [ jiegec ]; platforms = platforms.unix; - # https://github.com/diffblue/cbmc/issues/7423 - broken = stdenv.isLinux && stdenv.isAarch64; + # error: no member named 'aligned_alloc' in the global namespace + broken = stdenv.isDarwin && stdenv.isx86_64; }; } diff --git a/pkgs/applications/science/logic/cedille/default.nix b/pkgs/applications/science/logic/cedille/default.nix index fe12d5995a6f9..1ac3ff3fe310a 100644 --- a/pkgs/applications/science/logic/cedille/default.nix +++ b/pkgs/applications/science/logic/cedille/default.nix @@ -46,7 +46,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "An interactive theorem-prover and dependently typed programming language, based on extrinsic (aka Curry-style) type theory"; + description = "Interactive theorem-prover and dependently typed programming language, based on extrinsic (aka Curry-style) type theory"; homepage = "https://cedille.github.io/"; license = licenses.mit; maintainers = with maintainers; [ mpickering ]; diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 68b424b32fb4a..af672d500fa6a 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -58,6 +58,7 @@ let "8.18.0".sha256 = "sha256-WhiBs4nzPHQ0R24xAdM49kmxSCPOxiOVMA1iiMYunz4="; "8.19.0".sha256 = "sha256-ixsYCvCXpBHqJ71hLQklphlwoOO3i/6w2PJjllKqf9k="; "8.19.1".sha256 = "sha256-kmZ8Uk8jpzjOd67aAPp3C+vU2oNaBw9pr7+Uixcgg94="; + "8.19.2".sha256 = "sha256-q+i07JsMZp83Gqav6v1jxsgPLN7sPvp5/oszVnavmz0="; }; releaseRev = v: "V${v}"; fetched = import ../../../../build-support/coq/meta-fetch/default.nix diff --git a/pkgs/applications/science/logic/cryptominisat/default.nix b/pkgs/applications/science/logic/cryptominisat/default.nix index 4040cdb797290..7c2ee23d36cb8 100644 --- a/pkgs/applications/science/logic/cryptominisat/default.nix +++ b/pkgs/applications/science/logic/cryptominisat/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "An advanced SAT Solver"; + description = "Advanced SAT Solver"; mainProgram = "cryptominisat5"; homepage = "https://github.com/msoos/cryptominisat"; license = licenses.mit; diff --git a/pkgs/applications/science/logic/cryptoverif/default.nix b/pkgs/applications/science/logic/cryptoverif/default.nix index 4b74cdd518ca2..7c95c21c2ccf3 100644 --- a/pkgs/applications/science/logic/cryptoverif/default.nix +++ b/pkgs/applications/science/logic/cryptoverif/default.nix @@ -1,12 +1,12 @@ { lib, stdenv, fetchurl, ocaml }: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "cryptoverif"; - version = "2.08pl1"; + version = "2.09"; src = fetchurl { - url = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${version}.tar.gz"; - hash = "sha256-rmORSZuhds9W2WpNgYf4AJM2jgEUPoJit4G64qLqj5w="; + url = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${finalAttrs.version}.tar.gz"; + hash = "sha256-FJlPZgTUZ+6HzhG/B0dOiVIjDvoCnF6yg2E9UriSojw="; }; /* Fix up the frontend to load the 'default' cryptoverif library @@ -48,4 +48,4 @@ stdenv.mkDerivation rec { platforms = lib.platforms.unix; maintainers = [ lib.maintainers.thoughtpolice ]; }; -} +}) diff --git a/pkgs/applications/science/logic/cubicle/default.nix b/pkgs/applications/science/logic/cubicle/default.nix index 03409e68ea336..2af9e6e926492 100644 --- a/pkgs/applications/science/logic/cubicle/default.nix +++ b/pkgs/applications/science/logic/cubicle/default.nix @@ -36,7 +36,7 @@ stdenv.mkDerivation rec { }; meta = with lib; { - description = "An open source model checker for verifying safety properties of array-based systems"; + description = "Open source model checker for verifying safety properties of array-based systems"; mainProgram = "cubicle"; homepage = "https://cubicle.lri.fr/"; license = licenses.asl20; diff --git a/pkgs/applications/science/logic/cvc3/default.nix b/pkgs/applications/science/logic/cvc3/default.nix index bec5a89cc691b..8b78b86cbb073 100644 --- a/pkgs/applications/science/logic/cvc3/default.nix +++ b/pkgs/applications/science/logic/cvc3/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A prover for satisfiability modulo theory (SMT)"; + description = "Prover for satisfiability modulo theory (SMT)"; mainProgram = "cvc3"; maintainers = with maintainers; [ raskin ]; diff --git a/pkgs/applications/science/logic/cvc4/default.nix b/pkgs/applications/science/logic/cvc4/default.nix index ac45db8cb3127..2dc12b7ab7234 100644 --- a/pkgs/applications/science/logic/cvc4/default.nix +++ b/pkgs/applications/science/logic/cvc4/default.nix @@ -39,7 +39,7 @@ stdenv.mkDerivation rec { cmakeBuildType = "Production"; meta = with lib; { - description = "A high-performance theorem prover and SMT solver"; + description = "High-performance theorem prover and SMT solver"; mainProgram = "cvc4"; homepage = "http://cvc4.cs.stanford.edu/web/"; license = licenses.gpl3; diff --git a/pkgs/applications/science/logic/cvc5/default.nix b/pkgs/applications/science/logic/cvc5/default.nix index d34b293372968..93a05e97ff9e1 100644 --- a/pkgs/applications/science/logic/cvc5/default.nix +++ b/pkgs/applications/science/logic/cvc5/default.nix @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { ]; meta = with lib; { - description = "A high-performance theorem prover and SMT solver"; + description = "High-performance theorem prover and SMT solver"; mainProgram = "cvc5"; homepage = "https://cvc5.github.io"; license = licenses.gpl3Only; diff --git a/pkgs/applications/science/logic/dafny/default.nix b/pkgs/applications/science/logic/dafny/default.nix index acf4f05000bf1..f85e6cf22879d 100644 --- a/pkgs/applications/science/logic/dafny/default.nix +++ b/pkgs/applications/science/logic/dafny/default.nix @@ -56,7 +56,7 @@ buildDotnetModule rec { ''; meta = with lib; { - description = "A programming language with built-in specification constructs"; + description = "Programming language with built-in specification constructs"; homepage = "https://research.microsoft.com/dafny"; maintainers = with maintainers; [ layus ]; license = licenses.mit; diff --git a/pkgs/applications/science/logic/drat-trim/default.nix b/pkgs/applications/science/logic/drat-trim/default.nix index 78d810e19be23..fb8468f4fbda6 100644 --- a/pkgs/applications/science/logic/drat-trim/default.nix +++ b/pkgs/applications/science/logic/drat-trim/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation { ''; meta = with lib; { - description = "A proof checker for unSAT proofs"; + description = "Proof checker for unSAT proofs"; longDescription = '' DRAT-trim is a satisfiability proof checking and trimming utility designed to validate proofs for all known satisfiability diff --git a/pkgs/applications/science/logic/egglog/default.nix b/pkgs/applications/science/logic/egglog/default.nix index 8b94c449c6be2..f730d0ec55eaf 100644 --- a/pkgs/applications/science/logic/egglog/default.nix +++ b/pkgs/applications/science/logic/egglog/default.nix @@ -24,7 +24,7 @@ rustPlatform.buildRustPackage { }; meta = with lib; { - description = "A fixpoint reasoning system that unifies Datalog and equality saturation"; + description = "Fixpoint reasoning system that unifies Datalog and equality saturation"; mainProgram = "egglog"; homepage = "https://github.com/egraphs-good/egglog"; license = licenses.mit; diff --git a/pkgs/applications/science/logic/fast-downward/default.nix b/pkgs/applications/science/logic/fast-downward/default.nix index 77b538d1cbd86..c18a610467470 100644 --- a/pkgs/applications/science/logic/fast-downward/default.nix +++ b/pkgs/applications/science/logic/fast-downward/default.nix @@ -58,7 +58,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A domain-independent planning system"; + description = "Domain-independent planning system"; mainProgram = "fast-downward"; homepage = "https://www.fast-downward.org/"; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/logic/hol_light/default.nix b/pkgs/applications/science/logic/hol_light/default.nix index 813397ba01f93..0e3dee4b0c0ad 100644 --- a/pkgs/applications/science/logic/hol_light/default.nix +++ b/pkgs/applications/science/logic/hol_light/default.nix @@ -1,8 +1,12 @@ -{ lib, stdenv, runtimeShell, fetchFromGitHub, fetchpatch, ocaml, findlib, num, camlp5, camlp-streams }: +{ lib, stdenv, runtimeShell, fetchFromGitHub, fetchpatch, ocaml, findlib, num, zarith, camlp5, camlp-streams }: let + use_zarith = lib.versionAtLeast ocaml.version "4.14"; load_num = - lib.optionalString (num != null) '' + if use_zarith then '' + -I ${zarith}/lib/ocaml/${ocaml.version}/site-lib/zarith \ + -I ${zarith}/lib/ocaml/${ocaml.version}/site-lib/stublibs \ + '' else lib.optionalString (num != null) '' -I ${num}/lib/ocaml/${ocaml.version}/site-lib/num \ -I ${num}/lib/ocaml/${ocaml.version}/site-lib/top-num \ -I ${num}/lib/ocaml/${ocaml.version}/site-lib/stublibs \ @@ -22,18 +26,15 @@ let ''; in -lib.throwIf (lib.versionAtLeast ocaml.version "5.0") - "hol_light is not available for OCaml ${ocaml.version}" - stdenv.mkDerivation { pname = "hol_light"; - version = "unstable-2023-11-03"; + version = "unstable-2024-05-10"; src = fetchFromGitHub { owner = "jrh13"; repo = "hol-light"; - rev = "dcd765c6032f52a0c0bf21fce5da4794a823e880"; - hash = "sha256-k2RBNDo4tc3eobKB84Y2xr0UQJvef0hv6jyFCaDCQFM="; + rev = "d8366986e22555c4e4c8ff49667d646d15c35f14"; + hash = "sha256-dN9X7yQlFof759I5lxxL4DxDe8V3XAhCRaryO9NabY4="; }; patches = [ @@ -46,7 +47,10 @@ stdenv.mkDerivation { strictDeps = true; nativeBuildInputs = [ ocaml findlib camlp5 ]; - propagatedBuildInputs = [ camlp-streams num ]; + propagatedBuildInputs = [ + camlp-streams + (if use_zarith then zarith else num) + ]; installPhase = '' mkdir -p "$out/lib/hol_light" "$out/bin" diff --git a/pkgs/applications/science/logic/iprover/default.nix b/pkgs/applications/science/logic/iprover/default.nix index 77e5919c0eee1..ad21323ec3e13 100644 --- a/pkgs/applications/science/logic/iprover/default.nix +++ b/pkgs/applications/science/logic/iprover/default.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "An automated first-order logic theorem prover"; + description = "Automated first-order logic theorem prover"; homepage = "http://www.cs.man.ac.uk/~korovink/iprover/"; maintainers = with maintainers; [ raskin gebner ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix b/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix index d9b8dd5cf28f6..91bf5ba32b68e 100644 --- a/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix +++ b/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "Linter component for Isabelle."; + description = "Linter component for Isabelle"; homepage = "https://github.com/isabelle-prover/isabelle-linter"; maintainers = with maintainers; [ jvanbruegge ]; license = licenses.mit; diff --git a/pkgs/applications/science/logic/kissat/default.nix b/pkgs/applications/science/logic/kissat/default.nix index 65bcebdc6b1a1..9a34409730fee 100644 --- a/pkgs/applications/science/logic/kissat/default.nix +++ b/pkgs/applications/science/logic/kissat/default.nix @@ -39,7 +39,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A 'keep it simple and clean bare metal SAT solver' written in C"; + description = "'keep it simple and clean bare metal SAT solver' written in C"; mainProgram = "kissat"; longDescription = '' Kissat is a "keep it simple and clean bare metal SAT solver" written in C. diff --git a/pkgs/applications/science/logic/klee/default.nix b/pkgs/applications/science/logic/klee/default.nix index 4f17558b340e4..fb02c6d40b9dc 100644 --- a/pkgs/applications/science/logic/klee/default.nix +++ b/pkgs/applications/science/logic/klee/default.nix @@ -1,10 +1,8 @@ { lib -, stdenv +, llvmPackages , callPackage , fetchFromGitHub , cmake -, clang -, llvm , python3 , z3 , stp @@ -13,6 +11,7 @@ , sqlite , gtest , lit +, nix-update-script # Build KLEE in debug mode. Defaults to false. , debug ? false @@ -30,19 +29,35 @@ # Enable runtime asserts. Default false. , runtimeAsserts ? false -# Extra klee-uclibc config. +# Klee uclibc. Defaults to the bundled version. +, kleeuClibc ? null + +# Extra klee-uclibc config for the default klee-uclibc. , extraKleeuClibcConfig ? {} }: +# Klee supports these LLVM versions. +let + llvmVersion = llvmPackages.llvm.version; + inherit (lib.strings) versionAtLeast versionOlder; +in +assert versionAtLeast llvmVersion "11" && versionOlder llvmVersion "17"; + let + # The chosen version of klee-uclibc. + chosenKleeuClibc = + if kleeuClibc == null then + callPackage ./klee-uclibc.nix { + llvmPackages = llvmPackages; + inherit extraKleeuClibcConfig debugRuntime runtimeAsserts; + } + else + kleeuClibc; + # Python used for KLEE tests. kleePython = python3.withPackages (ps: with ps; [ tabulate ]); - - # The klee-uclibc derivation. - kleeuClibc = callPackage ./klee-uclibc.nix { - inherit stdenv clang llvm extraKleeuClibcConfig debugRuntime runtimeAsserts; - }; -in stdenv.mkDerivation rec { +in +llvmPackages.stdenv.mkDerivation rec { pname = "klee"; version = "3.1"; @@ -54,14 +69,16 @@ in stdenv.mkDerivation rec { }; nativeBuildInputs = [ cmake ]; + buildInputs = [ + llvmPackages.llvm cryptominisat gperftools - llvm sqlite stp z3 ]; + nativeCheckInputs = [ gtest @@ -77,10 +94,10 @@ in stdenv.mkDerivation rec { onOff = val: if val then "ON" else "OFF"; in [ "-DKLEE_RUNTIME_BUILD_TYPE=${if debugRuntime then "Debug" else "Release"}" - "-DLLVMCC=${clang}/bin/clang" - "-DLLVMCXX=${clang}/bin/clang++" + "-DLLVMCC=${llvmPackages.clang}/bin/clang" + "-DLLVMCXX=${llvmPackages.clang}/bin/clang++" "-DKLEE_ENABLE_TIMESTAMP=${onOff false}" - "-DKLEE_UCLIBC_PATH=${kleeuClibc}" + "-DKLEE_UCLIBC_PATH=${chosenKleeuClibc}" "-DENABLE_KLEE_ASSERTS=${onOff asserts}" "-DENABLE_POSIX_RUNTIME=${onOff true}" "-DENABLE_UNIT_TESTS=${onOff true}" @@ -94,21 +111,26 @@ in stdenv.mkDerivation rec { env.NIX_CFLAGS_COMPILE = toString ["-Wno-macro-redefined"]; prePatch = '' - patchShebangs . + patchShebangs --build . ''; # https://github.com/klee/klee/issues/1690 hardeningDisable = [ "fortify" ]; + enableParallelBuilding = true; doCheck = true; passthru = { - # Let the user depend on `klee.uclibc` for klee-uclibc - uclibc = kleeuClibc; + updateScript = nix-update-script { + extraArgs = [ "--version-regex" "v(\d\.\d)" ]; + }; + # Let the user access the chosen uClibc outside the derivation. + uclibc = chosenKleeuClibc; }; meta = with lib; { - description = "A symbolic virtual machine built on top of LLVM"; + mainProgram = "klee"; + description = "Symbolic virtual machine built on top of LLVM"; longDescription = '' KLEE is a symbolic virtual machine built on top of the LLVM compiler infrastructure. Currently, there are two primary components: @@ -128,7 +150,7 @@ in stdenv.mkDerivation rec { that matches a computed test input, including setting up files, pipes, environment variables, and passing command line arguments. ''; - homepage = "https://klee.github.io/"; + homepage = "https://klee.github.io"; license = licenses.ncsa; platforms = [ "x86_64-linux" ]; maintainers = with maintainers; [ numinit ]; diff --git a/pkgs/applications/science/logic/klee/klee-uclibc.nix b/pkgs/applications/science/logic/klee/klee-uclibc.nix index a8e459a6bdaee..c87a881e75336 100644 --- a/pkgs/applications/science/logic/klee/klee-uclibc.nix +++ b/pkgs/applications/science/logic/klee/klee-uclibc.nix @@ -1,13 +1,12 @@ { lib -, stdenv +, llvmPackages , fetchurl , fetchFromGitHub -, which , linuxHeaders -, clang -, llvm , python3 , curl +, which +, nix-update-script , debugRuntime ? true , runtimeAsserts ? false , extraKleeuClibcConfig ? {} @@ -24,21 +23,22 @@ let "RUNTIME_PREFIX" = "/"; "DEVEL_PREFIX" = "/"; }); -in stdenv.mkDerivation rec { +in +llvmPackages.stdenv.mkDerivation rec { pname = "klee-uclibc"; version = "1.4"; src = fetchFromGitHub { owner = "klee"; repo = "klee-uclibc"; rev = "klee_uclibc_v${version}"; - sha256 = "sha256-sogQK5Ed0k5tf4rrYwCKT4YRKyEovgT25p0BhGvJ1ok="; + hash = "sha256-sogQK5Ed0k5tf4rrYwCKT4YRKyEovgT25p0BhGvJ1ok="; }; nativeBuildInputs = [ - clang - curl - llvm + llvmPackages.clang + llvmPackages.llvm python3 + curl which ]; @@ -47,11 +47,11 @@ in stdenv.mkDerivation rec { # HACK: needed for cross-compile. # See https://www.mail-archive.com/klee-dev@imperial.ac.uk/msg03141.html - KLEE_CFLAGS = "-idirafter ${clang}/resource-root/include"; + KLEE_CFLAGS = "-idirafter ${llvmPackages.clang}/resource-root/include"; prePatch = '' - patchShebangs ./configure - patchShebangs ./extra + patchShebangs --build ./configure + patchShebangs --build ./extra ''; # klee-uclibc configure does not support --prefix, so we override configurePhase entirely @@ -88,13 +88,19 @@ in stdenv.mkDerivation rec { makeFlags = ["HAVE_DOT_CONFIG=y"]; + enableParallelBuilding = true; + + passthru.updateScript = nix-update-script { + extraArgs = [ "--version-regex" "v(\d\.\d)" ]; + }; + meta = with lib; { - description = "A modified version of uClibc for KLEE."; + description = "Modified version of uClibc for KLEE"; longDescription = '' klee-uclibc is a bitcode build of uClibc meant for compatibility with the KLEE symbolic virtual machine. ''; - homepage = "https://klee.github.io/"; + homepage = "https://github.com/klee/klee-uclibc"; license = licenses.lgpl3; maintainers = with maintainers; [ numinit ]; }; diff --git a/pkgs/applications/science/logic/lean4/default.nix b/pkgs/applications/science/logic/lean4/default.nix index ac41b03643dc7..2ec05098f4078 100644 --- a/pkgs/applications/science/logic/lean4/default.nix +++ b/pkgs/applications/science/logic/lean4/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "lean4"; - version = "4.7.0"; + version = "4.8.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "lean4"; rev = "v${finalAttrs.version}"; - hash = "sha256-jHY8BhDotfGcMS0Xzl5iawqCaug3dDEKuD5Y1WcM06I="; + hash = "sha256-R75RrAQb/tRTtMvy/ddLl1KQaA7V71nocvjIS9geMrg="; }; postPatch = '' diff --git a/pkgs/applications/science/logic/leo2/default.nix b/pkgs/applications/science/logic/leo2/default.nix index dcf2d5b7c33c3..7fdc37c4db4e3 100644 --- a/pkgs/applications/science/logic/leo2/default.nix +++ b/pkgs/applications/science/logic/leo2/default.nix @@ -44,7 +44,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A high-performance typed higher order prover"; + description = "High-performance typed higher order prover"; mainProgram = "leo"; maintainers = [ maintainers.raskin ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/leo3/binary.nix b/pkgs/applications/science/logic/leo3/binary.nix index 0cdf8a4dc2103..e8af3fdaab1a3 100644 --- a/pkgs/applications/science/logic/leo3/binary.nix +++ b/pkgs/applications/science/logic/leo3/binary.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "An automated theorem prover for classical higher-order logic with choice"; + description = "Automated theorem prover for classical higher-order logic with choice"; mainProgram = "leo3"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.bsd3; diff --git a/pkgs/applications/science/logic/mcrl2/default.nix b/pkgs/applications/science/logic/mcrl2/default.nix index 854c2c16f5acf..c26e5f2e761f6 100644 --- a/pkgs/applications/science/logic/mcrl2/default.nix +++ b/pkgs/applications/science/logic/mcrl2/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { meta = with lib; { broken = stdenv.isDarwin; - description = "A toolset for model-checking concurrent systems and protocols"; + description = "Toolset for model-checking concurrent systems and protocols"; longDescription = '' A formal specification language with an associated toolset, that can be used for modelling, validation and verification of diff --git a/pkgs/applications/science/logic/nusmv/default.nix b/pkgs/applications/science/logic/nusmv/default.nix index d3e3dc998cc0e..d7ecbc7cd8874 100644 --- a/pkgs/applications/science/logic/nusmv/default.nix +++ b/pkgs/applications/science/logic/nusmv/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A new symbolic model checker for the analysis of synchronous finite-state and infinite-state systems"; + description = "New symbolic model checker for the analysis of synchronous finite-state and infinite-state systems"; homepage = "https://nuxmv.fbk.eu/pmwiki.php"; maintainers = with maintainers; [ mgttlinger ]; sourceProvenance = with sourceTypes; [ binaryNativeCode ]; diff --git a/pkgs/applications/science/logic/opensmt/default.nix b/pkgs/applications/science/logic/opensmt/default.nix index 4a5f453f35478..1a031e8d1e1dd 100644 --- a/pkgs/applications/science/logic/opensmt/default.nix +++ b/pkgs/applications/science/logic/opensmt/default.nix @@ -6,13 +6,13 @@ stdenv.mkDerivation rec { pname = "opensmt"; - version = "2.6.0"; + version = "2.7.0"; src = fetchFromGitHub { owner = "usi-verification-and-security"; repo = "opensmt"; rev = "v${version}"; - sha256 = "sha256-glIiyPSkLG7sGYw5ujfl47GuDuPIPdP+UybA1vSn0Uw="; + sha256 = "sha256-zhNNnwc41B4sNq50kPub29EYhqV+FoDKRD/CLHnVyZw="; }; nativeBuildInputs = [ cmake bison flex ]; @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { meta = with lib; { broken = (stdenv.isLinux && stdenv.isAarch64); - description = "A satisfiability modulo theory (SMT) solver"; + description = "Satisfiability modulo theory (SMT) solver"; mainProgram = "opensmt"; maintainers = [ maintainers.raskin ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/logic/ott/default.nix b/pkgs/applications/science/logic/ott/default.nix index b8197aaa41230..73de6373e8f05 100644 --- a/pkgs/applications/science/logic/ott/default.nix +++ b/pkgs/applications/science/logic/ott/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "A tool for the working semanticist"; + description = "Tool for the working semanticist"; mainProgram = "ott"; longDescription = '' Ott is a tool for writing definitions of programming languages and diff --git a/pkgs/applications/science/logic/petrinizer/default.nix b/pkgs/applications/science/logic/petrinizer/default.nix deleted file mode 100644 index 9fd20e3ed4afd..0000000000000 --- a/pkgs/applications/science/logic/petrinizer/default.nix +++ /dev/null @@ -1,31 +0,0 @@ -{ mkDerivation -, async, base, bytestring, containers, fetchFromGitLab, mtl -, parallel-io, parsec, lib, stm, transformers, sbv_7_13}: - -mkDerivation rec { - pname = "petrinizer"; - version = "0.9.1.1"; - - src = fetchFromGitLab { - domain = "gitlab.lrz.de"; - owner = "i7"; - repo = pname; - rev = version; - sha256 = "1n7fzm96gq5rxm2f8w8sr1yzm1zcxpf0b473c6xnhsgqsis5j4xw"; - }; - - isLibrary = false; - isExecutable = true; - executableHaskellDepends = [ - async base bytestring containers mtl parallel-io parsec sbv_7_13 stm - transformers - ]; - description = "Safety and Liveness Analysis of Petri Nets with SMT solvers"; - license = lib.licenses.gpl3; - maintainers = with lib.maintainers; [ raskin ]; - inherit (sbv_7_13.meta) platforms; - - # dependency sbv no longer builds - hydraPlatforms = lib.platforms.none; - broken = true; -} diff --git a/pkgs/applications/science/logic/prooftree/default.nix b/pkgs/applications/science/logic/prooftree/default.nix index d0d95818ff93b..bb20477fd1788 100644 --- a/pkgs/applications/science/logic/prooftree/default.nix +++ b/pkgs/applications/science/logic/prooftree/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "prooftree"; - version = "0.13"; + version = "0.14"; src = fetchurl { url = "https://askra.de/software/prooftree/releases/prooftree-${version}.tar.gz"; - sha256 = "0z1z4wqbqwgppkh2bm89fgy07a0y2m6g4lvcyzs09sm1ysklk2dh"; + sha256 = "sha256-nekV2UnjibOk4h0jZ1jV7W5pE/hXWb3fUoLTJb3Jzc0="; }; strictDeps = true; @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { prefixKey = "--prefix "; meta = with lib; { - description = "A program for proof-tree visualization"; + description = "Program for proof-tree visualization"; mainProgram = "prooftree"; longDescription = '' Prooftree is a program for proof-tree visualization during interactive diff --git a/pkgs/applications/science/logic/redprl/default.nix b/pkgs/applications/science/logic/redprl/default.nix index 2749730f9d667..03117d4e03285 100644 --- a/pkgs/applications/science/logic/redprl/default.nix +++ b/pkgs/applications/science/logic/redprl/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation { ''; meta = with lib; { - description = "A proof assistant for Nominal Computational Type Theory"; + description = "Proof assistant for Nominal Computational Type Theory"; mainProgram = "redprl"; homepage = "http://www.redprl.org/"; license = licenses.mit; diff --git a/pkgs/applications/science/logic/sharpsat-td/default.nix b/pkgs/applications/science/logic/sharpsat-td/default.nix index 2f2128d542f1b..4c5e22ba9b4f2 100644 --- a/pkgs/applications/science/logic/sharpsat-td/default.nix +++ b/pkgs/applications/science/logic/sharpsat-td/default.nix @@ -73,7 +73,7 @@ in stdenv.mkDerivation rec { ''; meta = { - description = "A fast solver for the #SAT model counting problem"; + description = "Fast solver for the #SAT model counting problem"; homepage = "https://github.com/Laakeri/sharpsat-td"; license = with lib.licenses; [ mit asl20 ]; maintainers = with lib.maintainers; [ ris ]; diff --git a/pkgs/applications/science/logic/symbiyosys/default.nix b/pkgs/applications/science/logic/symbiyosys/default.nix index 19c021684b3ff..c3df8340d20c8 100644 --- a/pkgs/applications/science/logic/symbiyosys/default.nix +++ b/pkgs/applications/science/logic/symbiyosys/default.nix @@ -55,7 +55,7 @@ stdenv.mkDerivation { description = "Tooling for Yosys-based verification flows"; homepage = "https://symbiyosys.readthedocs.io/"; license = lib.licenses.isc; - maintainers = with lib.maintainers; [ thoughtpolice emily ]; + maintainers = with lib.maintainers; [ thoughtpolice ]; mainProgram = "sby"; platforms = lib.platforms.all; }; diff --git a/pkgs/applications/science/logic/tlaplus/default.nix b/pkgs/applications/science/logic/tlaplus/default.nix index 2d2542a607a53..f478bf204d4f3 100644 --- a/pkgs/applications/science/logic/tlaplus/default.nix +++ b/pkgs/applications/science/logic/tlaplus/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "An algorithm specification language with model checking tools"; + description = "Algorithm specification language with model checking tools"; homepage = "http://lamport.azurewebsites.net/tla/tla.html"; sourceProvenance = with lib.sourceTypes; [ binaryBytecode ]; license = lib.licenses.mit; diff --git a/pkgs/applications/science/logic/tlaplus/tlaplus18.nix b/pkgs/applications/science/logic/tlaplus/tlaplus18.nix index 4f34846a89276..2bd0f4b835647 100644 --- a/pkgs/applications/science/logic/tlaplus/tlaplus18.nix +++ b/pkgs/applications/science/logic/tlaplus/tlaplus18.nix @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "An algorithm specification language with model checking tools"; + description = "Algorithm specification language with model checking tools"; homepage = "http://lamport.azurewebsites.net/tla/tla.html"; sourceProvenance = with lib.sourceTypes; [ binaryBytecode ]; license = lib.licenses.mit; diff --git a/pkgs/applications/science/logic/vampire/default.nix b/pkgs/applications/science/logic/vampire/default.nix index 62427e2ee4554..e86f22613ad47 100644 --- a/pkgs/applications/science/logic/vampire/default.nix +++ b/pkgs/applications/science/logic/vampire/default.nix @@ -46,7 +46,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://vprover.github.io/"; - description = "The Vampire Theorem Prover"; + description = "Vampire Theorem Prover"; mainProgram = "vampire"; platforms = platforms.unix; license = licenses.bsd3; diff --git a/pkgs/applications/science/logic/verit/default.nix b/pkgs/applications/science/logic/verit/default.nix index 6c0d1061dcab9..65878ba43df93 100644 --- a/pkgs/applications/science/logic/verit/default.nix +++ b/pkgs/applications/science/logic/verit/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation { ''; meta = with lib; { - description = "An open, trustable and efficient SMT-solver"; + description = "Open, trustable and efficient SMT-solver"; homepage = "https://verit.loria.fr/"; license = licenses.bsd3; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix index 42256ae70aa69..ac9475417dbdd 100644 --- a/pkgs/applications/science/logic/why3/default.nix +++ b/pkgs/applications/science/logic/why3/default.nix @@ -67,7 +67,7 @@ stdenv.mkDerivation rec { passthru.withProvers = callPackage ./with-provers.nix {}; meta = with lib; { - description = "A platform for deductive program verification"; + description = "Platform for deductive program verification"; homepage = "https://why3.lri.fr/"; license = licenses.lgpl21; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix index b97245cab4768..de80cd725653f 100644 --- a/pkgs/applications/science/logic/yices/default.nix +++ b/pkgs/applications/science/logic/yices/default.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { doCheck = true; meta = with lib; { - description = "A high-performance theorem prover and SMT solver"; + description = "High-performance theorem prover and SMT solver"; homepage = "https://yices.csl.sri.com"; license = licenses.gpl3; platforms = with platforms; linux ++ darwin; diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index f35da4a732b09..2db1fc95f7974 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -78,7 +78,7 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: ++ optional ocamlBindings "ocaml"; meta = with lib; { - description = "A high-performance theorem prover and SMT solver"; + description = "High-performance theorem prover and SMT solver"; mainProgram = "z3"; homepage = "https://github.com/Z3Prover/z3"; changelog = "https://github.com/Z3Prover/z3/releases/tag/z3-${version}"; diff --git a/pkgs/applications/science/machine-learning/labelimg/default.nix b/pkgs/applications/science/machine-learning/labelimg/default.nix index 21174305b9e3e..b610920955904 100644 --- a/pkgs/applications/science/machine-learning/labelimg/default.nix +++ b/pkgs/applications/science/machine-learning/labelimg/default.nix @@ -41,7 +41,7 @@ python3Packages.buildPythonApplication rec { makeWrapperArgs+=("''${qtWrapperArgs[@]}") ''; meta = with lib; { - description = "A graphical image annotation tool and label object bounding boxes in images"; + description = "Graphical image annotation tool and label object bounding boxes in images"; mainProgram = "labelImg"; homepage = "https://github.com/tzutalin/labelImg"; license = licenses.mit; diff --git a/pkgs/applications/science/machine-learning/shogun/default.nix b/pkgs/applications/science/machine-learning/shogun/default.nix index d25bc06385ea9..1e317fdec03e3 100644 --- a/pkgs/applications/science/machine-learning/shogun/default.nix +++ b/pkgs/applications/science/machine-learning/shogun/default.nix @@ -200,7 +200,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A toolbox which offers a wide range of efficient and unified machine learning methods"; + description = "Toolbox which offers a wide range of efficient and unified machine learning methods"; homepage = "http://shogun-toolbox.org/"; license = if withSvmLight then licenses.unfree else licenses.gpl3Plus; maintainers = with maintainers; [ edwtjo smancill ]; diff --git a/pkgs/applications/science/math/4ti2/default.nix b/pkgs/applications/science/math/4ti2/default.nix index 9424612c7587a..940e2e45d5acf 100644 --- a/pkgs/applications/science/math/4ti2/default.nix +++ b/pkgs/applications/science/math/4ti2/default.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec{ meta = with lib;{ homepage = "https://4ti2.github.io/"; - description = "A software package for algebraic, geometric and combinatorial problems on linear spaces"; + description = "Software package for algebraic, geometric and combinatorial problems on linear spaces"; license = with licenses; [ gpl2Plus ]; maintainers = with maintainers; [ AndersonTorres ]; platforms = platforms.all; diff --git a/pkgs/applications/science/math/LiE/default.nix b/pkgs/applications/science/math/LiE/default.nix index 7eb9edbb3b192..dbc66fe2a05fe 100644 --- a/pkgs/applications/science/math/LiE/default.nix +++ b/pkgs/applications/science/math/LiE/default.nix @@ -8,7 +8,7 @@ stdenv.mkDerivation { pname = "lie"; meta = { - description = "A Computer algebra package for Lie group computations"; + description = "Computer algebra package for Lie group computations"; mainProgram = "lie"; homepage = "http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/"; license = lib.licenses.lgpl3; # see the website diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index 5ceb413a24211..b6fac3cca9e5a 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, fetchpatch, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng +{ lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng , libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texliveSmall, tk, xz, zlib , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack , curl, Cocoa, Foundation, libobjc, libcxx, tzdata @@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation (finalAttrs: { pname = "R"; - version = "4.3.3"; + version = "4.4.1"; src = let inherit (finalAttrs) pname version; in fetchurl { url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-gIUSMTk7hb84d+6eObKC51Dthkxexgy9aObhOfBSAzA="; + sha256 = "sha256-tMtnXequtymdOyZdIYzeQ/GSlRzluJt7saUUijay2U0="; }; outputs = [ "out" "tex" ]; @@ -37,12 +37,6 @@ stdenv.mkDerivation (finalAttrs: { patches = [ ./no-usr-local-search-paths.patch - (fetchpatch { - # https://hiddenlayer.com/research/r-bitrary-code-execution/ - name = "CVE-2024-27322.patch"; - url = "https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7.patch"; - hash = "sha256-CH2mMmie9E96JeGSC7UGm7/roUNhK5xv6HO53N2ixEI="; - }) ]; # Test of the examples for package 'tcltk' fails in Darwin sandbox. See: diff --git a/pkgs/applications/science/math/bliss/default.nix b/pkgs/applications/science/math/bliss/default.nix index 33969c705d05d..5673fcc34d959 100644 --- a/pkgs/applications/science/math/bliss/default.nix +++ b/pkgs/applications/science/math/bliss/default.nix @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "An open source tool for computing automorphism groups and canonical forms of graphs. It has both a command line user interface as well as C++ and C programming language APIs"; + description = "Open source tool for computing automorphism groups and canonical forms of graphs. It has both a command line user interface as well as C++ and C programming language APIs"; mainProgram = "bliss"; homepage = "http://www.tcs.hut.fi/Software/bliss/"; license = licenses.lgpl3; diff --git a/pkgs/applications/science/math/cbc/default.nix b/pkgs/applications/science/math/cbc/default.nix index fb92b1cc98fbb..aa979a78cb485 100644 --- a/pkgs/applications/science/math/cbc/default.nix +++ b/pkgs/applications/science/math/cbc/default.nix @@ -29,6 +29,6 @@ stdenv.mkDerivation rec { license = lib.licenses.epl10; maintainers = [ lib.maintainers.eelco ]; platforms = lib.platforms.linux ++ lib.platforms.darwin; - description = "A mixed integer programming solver"; + description = "Mixed integer programming solver"; }; } diff --git a/pkgs/applications/science/math/clp/default.nix b/pkgs/applications/science/math/clp/default.nix index 06032b4a3182e..f1c2c53638adf 100644 --- a/pkgs/applications/science/math/clp/default.nix +++ b/pkgs/applications/science/math/clp/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { meta = with lib; { license = licenses.epl20; homepage = "https://github.com/coin-or/Clp"; - description = "An open-source linear programming solver written in C++"; + description = "Open-source linear programming solver written in C++"; mainProgram = "clp"; platforms = platforms.darwin ++ platforms.linux; maintainers = [ maintainers.vbgl ]; diff --git a/pkgs/applications/science/math/colpack/default.nix b/pkgs/applications/science/math/colpack/default.nix index d5ab38ff75149..768366cc5d7a5 100644 --- a/pkgs/applications/science/math/colpack/default.nix +++ b/pkgs/applications/science/math/colpack/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A package comprising of implementations of algorithms for + description = "Package comprising of implementations of algorithms for vertex coloring and derivative computation"; homepage = "https://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities"; license = licenses.lgpl3Plus; diff --git a/pkgs/applications/science/math/csdp/default.nix b/pkgs/applications/science/math/csdp/default.nix index 6ce03008d3a98..c0f863a6d26b5 100644 --- a/pkgs/applications/science/math/csdp/default.nix +++ b/pkgs/applications/science/math/csdp/default.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { homepage = "https://projects.coin-or.org/Csdp"; license = lib.licenses.cpl10; maintainers = [ lib.maintainers.roconnor ]; - description = "A C Library for Semidefinite Programming"; + description = "C Library for Semidefinite Programming"; platforms = lib.platforms.unix; }; } diff --git a/pkgs/applications/science/math/dap/default.nix b/pkgs/applications/science/math/dap/default.nix index ed3290f6c27d8..40ce12f66ebd0 100644 --- a/pkgs/applications/science/math/dap/default.nix +++ b/pkgs/applications/science/math/dap/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://www.gnu.org/software/dap"; - description = "A small statistics and graphics package based on C"; + description = "Small statistics and graphics package based on C"; longDescription = '' Dap is a small statistics and graphics package based on C. Version 3.0 and later of Dap can read SBS programs (based on the utterly famous, industry diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index 1ebb93e516305..a120de87b9ff1 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "0-unstable-2024-05-18"; + version = "3.27-unstable-2024-06-20"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "e5fc4a44797549da9d8994203547da63002b3700"; - hash = "sha256-pX8rRIrOq0fQvzVrvAh47ZBzdkS6ZKuXTQ9joa/XJgg="; + rev = "c3e3da104dbef888c3e52659134d5e9bdc12764d"; + hash = "sha256-fqCphnRQw79v7ZTCZU9ucm/R7BKY7yCZYDSnxD7uRS8="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/pkgs/applications/science/math/form/default.nix b/pkgs/applications/science/math/form/default.nix index c56ee432bdae0..3c5569f116d81 100644 --- a/pkgs/applications/science/math/form/default.nix +++ b/pkgs/applications/science/math/form/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation { buildInputs = [ gmp zlib ]; meta = with lib; { - description = "The FORM project for symbolic manipulation of very big expressions"; + description = "FORM project for symbolic manipulation of very big expressions"; homepage = "https://www.nikhef.nl/~form/"; license = licenses.gpl3; maintainers = [ maintainers.veprbl ]; diff --git a/pkgs/applications/science/math/fricas/default.nix b/pkgs/applications/science/math/fricas/default.nix index 355238ace15ce..9f0b87f011a10 100644 --- a/pkgs/applications/science/math/fricas/default.nix +++ b/pkgs/applications/science/math/fricas/default.nix @@ -1,21 +1,28 @@ -{ lib, stdenv, fetchurl, sbcl, libX11, libXpm, libICE, libSM, libXt, libXau, libXdmcp }: +{ lib, stdenv, fetchFromGitHub, sbcl, libX11, libXpm, libICE, libSM, libXt, libXau, libXdmcp }: stdenv.mkDerivation rec { pname = "fricas"; - version = "1.3.9"; + version = "1.3.10"; - src = fetchurl { - url = "mirror://sourceforge/fricas/fricas/${version}/fricas-${version}-full.tar.bz2"; - sha256 = "sha256-5RPcffM0GN0l6r8IgHJlwdxwwp2y4kIdJ5M3JnGZCzc="; + src = fetchFromGitHub { + owner = "fricas"; + repo = "fricas"; + rev = version; + sha256 = "sha256-T1xDndDnHq/hmhTWWO3Eu0733u8+C8sJMCF6pbLU2GI="; }; buildInputs = [ sbcl libX11 libXpm libICE libSM libXt libXau libXdmcp ]; + # Remove when updating to next version + configurePhase = '' + ./configure --prefix=$out --with-lisp='sbcl --dynamic-space-size 3072' + ''; + dontStrip = true; meta = { - homepage = "https://fricas.sourceforge.net/"; - description = "An advanced computer algebra system"; + homepage = "https://fricas.github.io"; + description = "Advanced computer algebra system"; license = lib.licenses.bsd3; platforms = lib.platforms.linux; diff --git a/pkgs/applications/science/math/getdp/default.nix b/pkgs/applications/science/math/getdp/default.nix index 5df35cce8e231..8accf9d76725a 100644 --- a/pkgs/applications/science/math/getdp/default.nix +++ b/pkgs/applications/science/math/getdp/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { cmakeFlags = lib.optional mpiSupport "-DENABLE_MPI=1"; meta = with lib; { - description = "A General Environment for the Treatment of Discrete Problems"; + description = "General Environment for the Treatment of Discrete Problems"; mainProgram = "getdp"; longDescription = '' GetDP is a free finite element solver using mixed elements to discretize diff --git a/pkgs/applications/science/math/gfan/default.nix b/pkgs/applications/science/math/gfan/default.nix index 8fa6da16e336b..ee1fce783d265 100644 --- a/pkgs/applications/science/math/gfan/default.nix +++ b/pkgs/applications/science/math/gfan/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { buildInputs = [ gmp mpir cddlib ]; meta = { - description = "A software package for computing Gröbner fans and tropical varieties"; + description = "Software package for computing Gröbner fans and tropical varieties"; license = lib.licenses.gpl2 ; maintainers = [lib.maintainers.raskin]; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix index 0dc12b6dcb050..834ae7b3d61f3 100644 --- a/pkgs/applications/science/math/giac/default.nix +++ b/pkgs/applications/science/math/giac/default.nix @@ -125,7 +125,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A free computer algebra system (CAS)"; + description = "Free computer algebra system (CAS)"; homepage = "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html"; license = licenses.gpl3Plus; platforms = platforms.linux ++ (optionals (!enableGUI) platforms.darwin); diff --git a/pkgs/applications/science/math/glsurf/default.nix b/pkgs/applications/science/math/glsurf/default.nix index d2ebba75638b9..38caee5805b43 100644 --- a/pkgs/applications/science/math/glsurf/default.nix +++ b/pkgs/applications/science/math/glsurf/default.nix @@ -65,7 +65,7 @@ stdenv.mkDerivation rec { meta = { homepage = "https://raffalli.eu/~christophe/glsurf/"; - description = "A program to draw implicit surfaces and curves"; + description = "Program to draw implicit surfaces and curves"; mainProgram = "glsurf"; license = lib.licenses.gpl2Plus; platforms = lib.platforms.all; diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index 57b20fe12d7c2..3e88e7f94bbe6 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -7,11 +7,11 @@ assert enablePython -> (python != null); stdenv.mkDerivation rec { pname = "gmsh"; - version = "4.12.2"; + version = "4.13.1"; src = fetchurl { url = "https://gmsh.info/src/gmsh-${version}-source.tgz"; - hash = "sha256-E+CdnKgQLlxAFx1u4VDGaHQrmMOmylf4N/e2Th4q9I8="; + hash = "sha256-d5chRfQxcmAm1QWWpqRPs8HJXCElUhjWaVWAa4btvo0="; }; buildInputs = [ @@ -50,7 +50,7 @@ stdenv.mkDerivation rec { doCheck = true; meta = { - description = "A three-dimensional finite element mesh generator"; + description = "Three-dimensional finite element mesh generator"; mainProgram = "gmsh"; homepage = "https://gmsh.info/"; license = lib.licenses.gpl2Plus; diff --git a/pkgs/applications/science/math/gretl/default.nix b/pkgs/applications/science/math/gretl/default.nix index 552639de6c532..dc2c62b8ad64c 100644 --- a/pkgs/applications/science/math/gretl/default.nix +++ b/pkgs/applications/science/math/gretl/default.nix @@ -19,11 +19,11 @@ stdenv.mkDerivation (finalAttrs: { pname = "gretl"; - version = "2024a"; + version = "2024b"; src = fetchurl { url = "mirror://sourceforge/gretl/gretl-${finalAttrs.version}.tar.xz"; - hash = "sha256-6ha0d/n75Xf0hZM0GRHLOnM274P1h2MerB/8SHWTh+o="; + hash = "sha256-mkmOmKO2tiAysZhwC8kNuCXNml8NdFPfaNFykdxYFAY="; }; buildInputs = [ @@ -54,7 +54,7 @@ stdenv.mkDerivation (finalAttrs: { enableParallelInstalling = false; meta = { - description = "A software package for econometric analysis"; + description = "Software package for econometric analysis"; homepage = "https://gretl.sourceforge.net"; license = lib.licenses.gpl3; longDescription = '' diff --git a/pkgs/applications/science/math/labplot/default.nix b/pkgs/applications/science/math/labplot/default.nix index 8bb667e1a8fac..0aeb232dd0313 100644 --- a/pkgs/applications/science/math/labplot/default.nix +++ b/pkgs/applications/science/math/labplot/default.nix @@ -1,5 +1,6 @@ { lib , stdenv +, fetchpatch , fetchurl , cmake , extra-cmake-modules @@ -54,6 +55,14 @@ stdenv.mkDerivation rec { "-DENABLE_VECTOR_BLF=OFF" ]; + patches = [ + (fetchpatch { + name = "matio-fix-compilation-for-latest-version-1.5.27.patch"; + url = "https://github.com/KDE/labplot/commit/d6142308ffa492d9f7cea00fad3b4cd1babfd00c.patch"; + hash = "sha256-qD5jj6GxBKbQezKJb1Z8HnwFO84WJBGQDawS/6o/wHE="; + }) + ]; + nativeBuildInputs = [ cmake extra-cmake-modules diff --git a/pkgs/applications/science/math/lp_solve/default.nix b/pkgs/applications/science/math/lp_solve/default.nix index fdabc8896a582..773f1f3c089e4 100644 --- a/pkgs/applications/science/math/lp_solve/default.nix +++ b/pkgs/applications/science/math/lp_solve/default.nix @@ -58,7 +58,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A Mixed Integer Linear Programming (MILP) solver"; + description = "Mixed Integer Linear Programming (MILP) solver"; mainProgram = "lp_solve"; homepage = "https://lpsolve.sourceforge.net"; license = licenses.gpl2Plus; diff --git a/pkgs/applications/science/math/mathmod/default.nix b/pkgs/applications/science/math/mathmod/default.nix new file mode 100644 index 0000000000000..dd85d06784922 --- /dev/null +++ b/pkgs/applications/science/math/mathmod/default.nix @@ -0,0 +1,34 @@ +{ lib +, mkDerivation +, fetchFromGitHub +, qmake +}: + +mkDerivation { + pname = "mathmod"; + version = "11.1-unstable-2024-01-26"; + + src = fetchFromGitHub { + owner = "parisolab"; + repo = "mathmod"; + rev = "24d03a04c17363520ae7cf077e72a7b8684eb6fd"; + hash = "sha256-HiqHssPGqYEVZWchZRj4rFPc+xNVZk1ryl5qvFC2BmQ="; + }; + + patches = [ ./fix-paths.patch ]; + + postPatch = '' + substituteInPlace MathMod.pro --subst-var out + ''; + + nativeBuildInputs = [ qmake ]; + + meta = { + description = "Mathematical modelling software"; + homepage = "https://github.com/parisolab/mathmod"; + license = lib.licenses.gpl2Plus; + mainProgram = "MathMod"; + maintainers = with lib.maintainers; [ tomasajt ]; + platforms = lib.platforms.unix; + }; +} diff --git a/pkgs/applications/science/math/mathmod/fix-paths.patch b/pkgs/applications/science/math/mathmod/fix-paths.patch new file mode 100644 index 0000000000000..b65b107882ee6 --- /dev/null +++ b/pkgs/applications/science/math/mathmod/fix-paths.patch @@ -0,0 +1,14 @@ +diff --git a/MathMod.pro b/MathMod.pro +index 2e2fbf1..bb8f8bd 100644 +--- a/MathMod.pro ++++ b/MathMod.pro +@@ -63,7 +63,5 @@ OTHER_FILES += \ + mathmodcollection.js \ + mathmodconfig.js + # install +-target.path = $TARGET +-sources.files = $$SOURCES $$HEADERS $$RESOURCES $$FORMS mathmod.pro +-sources.path = $TARGET +-INSTALLS += target sources ++target.path = @out@/bin ++INSTALLS += target diff --git a/pkgs/applications/science/math/msieve/default.nix b/pkgs/applications/science/math/msieve/default.nix index 1de6d416a0e64..bda3e5b3a040a 100644 --- a/pkgs/applications/science/math/msieve/default.nix +++ b/pkgs/applications/science/math/msieve/default.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "A C library implementing a suite of algorithms to factor large integers"; + description = "C library implementing a suite of algorithms to factor large integers"; mainProgram = "msieve"; license = lib.licenses.publicDomain; homepage = "http://msieve.sourceforge.net/"; diff --git a/pkgs/applications/science/math/nota/default.nix b/pkgs/applications/science/math/nota/default.nix index 810d7d6d72bcb..eae11806d7254 100644 --- a/pkgs/applications/science/math/nota/default.nix +++ b/pkgs/applications/science/math/nota/default.nix @@ -33,7 +33,7 @@ mkDerivation rec { time ]; - description = "The most beautiful command line calculator"; + description = "Most beautiful command line calculator"; homepage = "https://kary.us/nota"; license = lib.licenses.mpl20; maintainers = with lib.maintainers; [ dtzWill ]; diff --git a/pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch b/pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch deleted file mode 100644 index 0bc29b9aab5f4..0000000000000 --- a/pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/ion/src/simulator/linux/Makefile b/ion/src/simulator/linux/Makefile -index ca7da03fa..b05bba115 100644 ---- a/ion/src/simulator/linux/Makefile -+++ b/ion/src/simulator/linux/Makefile -@@ -28,7 +28,6 @@ ion_src += $(addprefix ion/src/simulator/shared/, \ - collect_registers.cpp \ - haptics.cpp \ - journal.cpp \ -- platform_action_modifier_ctrl.cpp \ - state_file.cpp \ - ) - diff --git a/pkgs/applications/science/math/numworks-epsilon/default.nix b/pkgs/applications/science/math/numworks-epsilon/default.nix index a90ebc67b65b8..98d5d0d4560ad 100644 --- a/pkgs/applications/science/math/numworks-epsilon/default.nix +++ b/pkgs/applications/science/math/numworks-epsilon/default.nix @@ -9,17 +9,18 @@ , imagemagick , gcc-arm-embedded , pkg-config +, python3Packages }: stdenv.mkDerivation rec { pname = "numworks-epsilon"; - version = "15.5.0"; + version = "22.2.0"; src = fetchFromGitHub { owner = "numworks"; repo = "epsilon"; rev = version; - sha256 = "fPBO3FzZ4k5OxG+Ifc6R/au4Te974HNKAEdHz+aFdSg="; + hash = "sha256-E2WaXTn8+Ky9kdZxvQmEt63Ggo6Ns0fZ0Za+rQGIMSg="; }; nativeBuildInputs = [ pkg-config ]; @@ -31,18 +32,13 @@ stdenv.mkDerivation rec { python3 imagemagick gcc-arm-embedded + python3Packages.lz4 ]; makeFlags = [ "PLATFORM=simulator" ]; - patches = [ - # Remove make rule Introduced in cba596dde7 - # which causes it to not build with nix - ./0001-ion-linux-makerules.patch - ]; - installPhase = '' runHook preInstall diff --git a/pkgs/applications/science/math/palp/default.nix b/pkgs/applications/science/math/palp/default.nix index 2fe77aa14a650..a3b54b78f99bc 100644 --- a/pkgs/applications/science/math/palp/default.nix +++ b/pkgs/applications/science/math/palp/default.nix @@ -55,7 +55,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A Package for Analyzing Lattice Polytopes"; + description = "Package for Analyzing Lattice Polytopes"; longDescription = '' A Package for Analyzing Lattice Polytopes (PALP) is a set of C programs for calculations with lattice polytopes and applications to diff --git a/pkgs/applications/science/math/pari/gp2c.nix b/pkgs/applications/science/math/pari/gp2c.nix index 512aaba78d54b..c99c2fed2bd16 100644 --- a/pkgs/applications/science/math/pari/gp2c.nix +++ b/pkgs/applications/science/math/pari/gp2c.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "http://pari.math.u-bordeaux.fr/"; - description = "A compiler to translate GP scripts to PARI programs"; + description = "Compiler to translate GP scripts to PARI programs"; downloadPage = "http://pari.math.u-bordeaux.fr/download.html"; inherit (pari.meta) license maintainers platforms broken; }; diff --git a/pkgs/applications/science/math/perseus/default.nix b/pkgs/applications/science/math/perseus/default.nix index 9a37eeac66daa..63836b7dc76ec 100644 --- a/pkgs/applications/science/math/perseus/default.nix +++ b/pkgs/applications/science/math/perseus/default.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation { ''; meta = { - description = "The Persistent Homology Software"; + description = "Persistent Homology Software"; mainProgram = "perseus"; longDescription = '' Persistent homology - or simply, persistence - is an algebraic diff --git a/pkgs/applications/science/math/programmer-calculator/default.nix b/pkgs/applications/science/math/programmer-calculator/default.nix index 9cb220ceca6a5..cc418feb763dd 100644 --- a/pkgs/applications/science/math/programmer-calculator/default.nix +++ b/pkgs/applications/science/math/programmer-calculator/default.nix @@ -20,7 +20,7 @@ gccStdenv.mkDerivation rec { ''; meta = with lib; { - description = "A terminal calculator for programmers"; + description = "Terminal calculator for programmers"; mainProgram = "pcalc"; longDescription = '' Terminal calculator made for programmers working with multiple number diff --git a/pkgs/applications/science/math/pspp/default.nix b/pkgs/applications/science/math/pspp/default.nix index 420b495e736e6..100cb5b9bc056 100644 --- a/pkgs/applications/science/math/pspp/default.nix +++ b/pkgs/applications/science/math/pspp/default.nix @@ -38,7 +38,7 @@ stdenv.mkDerivation rec { meta = { homepage = "https://www.gnu.org/software/pspp/"; - description = "A free replacement for SPSS, a program for statistical analysis of sampled data"; + description = "Free replacement for SPSS, a program for statistical analysis of sampled data"; license = lib.licenses.gpl3Plus; longDescription = '' diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index ab11d833f70c5..e4fc506516fdd 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation (finalAttrs: { enableParallelBuilding = true; meta = with lib; { - description = "The ultimate desktop calculator"; + description = "Ultimate desktop calculator"; homepage = "http://qalculate.github.io"; maintainers = with maintainers; [ gebner doronbehar alyaeanyx ]; license = licenses.gpl2Plus; diff --git a/pkgs/applications/science/math/qalculate-qt/default.nix b/pkgs/applications/science/math/qalculate-qt/default.nix index a830c7ddd00ec..3c4e19d56ebd7 100644 --- a/pkgs/applications/science/math/qalculate-qt/default.nix +++ b/pkgs/applications/science/math/qalculate-qt/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation (finalAttrs: { ''; meta = with lib; { - description = "The ultimate desktop calculator"; + description = "Ultimate desktop calculator"; homepage = "http://qalculate.github.io"; maintainers = with maintainers; [ _4825764518 ]; license = licenses.gpl2Plus; diff --git a/pkgs/applications/science/math/ratpoints/default.nix b/pkgs/applications/science/math/ratpoints/default.nix index 69b972fe97907..f2aa1aac26079 100644 --- a/pkgs/applications/science/math/ratpoints/default.nix +++ b/pkgs/applications/science/math/ratpoints/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { preInstall = ''mkdir -p "$out"/{bin,share,lib,include}''; meta = { - description = "A program to find rational points on hyperelliptic curves"; + description = "Program to find rational points on hyperelliptic curves"; mainProgram = "ratpoints"; license = lib.licenses.gpl2Plus; maintainers = [lib.maintainers.raskin]; diff --git a/pkgs/applications/science/math/ripser/default.nix b/pkgs/applications/science/math/ripser/default.nix index 83cf6bc51aa40..3f536f25aa115 100644 --- a/pkgs/applications/science/math/ripser/default.nix +++ b/pkgs/applications/science/math/ripser/default.nix @@ -49,7 +49,7 @@ stdenv.mkDerivation { ''; meta = { - description = "A lean C++ code for the computation of Vietoris–Rips persistence barcodes"; + description = "Lean C++ code for the computation of Vietoris–Rips persistence barcodes"; mainProgram = "ripser"; homepage = "https://github.com/Ripser/ripser"; license = lib.licenses.lgpl3; diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index b1c9c62a5748b..de0c2e3b1e20e 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -61,12 +61,19 @@ stdenv.mkDerivation rec { hash = "sha256-uCXchYx26DdxTjR1k2748KCEHPnekKS2fAM7SpyhNvM="; }) - # https://github.com/sagemath/sage/pull/37763 + # https://github.com/sagemath/sage/pull/37763, landed in 10.4.beta2 (fetchpatch { name = "scipy-fault-tolerance.patch"; - url = "https://github.com/sagemath/sage/commit/547d502ed56f9fd44eb5d9b4ee0824746c60fef7.diff"; + url = "https://github.com/sagemath/sage/commit/551139c09f26a5da96b1187c3f0dd17b8d80ef84.diff"; hash = "sha256-PR4przrZ3ieHaW2nSY7l7VhNfrUupu9yCIrXpeyoAgg="; }) + + # first two commits from https://github.com/sagemath/sage/pull/38100 + (fetchpatch { + name = "sphinx-7.3-update.patch"; + url = "https://github.com/sagemath/sage/compare/10.4.beta7...d2932e142991b442a3eee5dc4f8949e3f7e6fe5c.patch"; + hash = "sha256-g6w0ImE0d2ocKnbGMQikcz9eI9r3/gESlA1NrQfGimk="; + }) ]; # Patches needed because of package updates. We could just pin the versions of diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix index 5e2191486bf08..cbf593398ac44 100644 --- a/pkgs/applications/science/math/sage/sagedoc.nix +++ b/pkgs/applications/science/math/sage/sagedoc.nix @@ -24,10 +24,6 @@ stdenv.mkDerivation rec { export HOME="$TMPDIR/sage_home" mkdir -p "$HOME" - # adapted from src/doc/Makefile (doc-src target), which tries to call Sage from PATH - mkdir -p $SAGE_DOC_SRC_OVERRIDE/en/reference/repl - ${sage-with-env}/bin/sage -advanced > $SAGE_DOC_SRC_OVERRIDE/en/reference/repl/options.txt - # needed to link them in the sage docs using intersphinx export PPLPY_DOCS=${python3.pkgs.pplpy.doc}/share/doc/pplpy diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index d079134aec76d..d1b17eccee23b 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -156,7 +156,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with lib; { - description = "A CAS for polynomial computations"; + description = "CAS for polynomial computations"; maintainers = teams.sage.members; # 32 bit x86 fails with some link error: `undefined reference to `__divmoddi4@GCC_7.0.0'` # https://www.singular.uni-kl.de:8002/trac/ticket/837 diff --git a/pkgs/applications/science/math/speedcrunch/default.nix b/pkgs/applications/science/math/speedcrunch/default.nix index a77474b86ffaa..021c1bedc348a 100644 --- a/pkgs/applications/science/math/speedcrunch/default.nix +++ b/pkgs/applications/science/math/speedcrunch/default.nix @@ -22,7 +22,7 @@ mkDerivation rec { meta = with lib; { homepage = "http://speedcrunch.org"; license = licenses.gpl2Plus; - description = "A fast power user calculator"; + description = "Fast power user calculator"; mainProgram = "speedcrunch"; longDescription = '' SpeedCrunch is a fast, high precision and powerful desktop calculator. diff --git a/pkgs/applications/science/math/symmetrica/default.nix b/pkgs/applications/science/math/symmetrica/default.nix index eea34fb778850..d6ec352d32a2f 100644 --- a/pkgs/applications/science/math/symmetrica/default.nix +++ b/pkgs/applications/science/math/symmetrica/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = with lib; { - description = "A collection of routines for representation theory and combinatorics"; + description = "Collection of routines for representation theory and combinatorics"; license = licenses.isc; maintainers = teams.sage.members; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/zegrapher/default.nix b/pkgs/applications/science/math/zegrapher/default.nix index 2beaf5757a550..ffe337efd7db5 100644 --- a/pkgs/applications/science/math/zegrapher/default.nix +++ b/pkgs/applications/science/math/zegrapher/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://zegrapher.com/"; - description = "An open source math plotter"; + description = "Open source math plotter"; mainProgram = "ZeGrapher"; longDescription = '' An open source, free and easy to use math plotter. It can plot functions, diff --git a/pkgs/applications/science/medicine/xmedcon/default.nix b/pkgs/applications/science/medicine/xmedcon/default.nix index e5c5bf68d53a7..1f0686cc0dad0 100644 --- a/pkgs/applications/science/medicine/xmedcon/default.nix +++ b/pkgs/applications/science/medicine/xmedcon/default.nix @@ -11,11 +11,11 @@ stdenv.mkDerivation rec { pname = "xmedcon"; - version = "0.23.0"; + version = "0.24.0"; src = fetchurl { url = "mirror://sourceforge/${pname}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-g1CRJDokLDzB+1YIuVQNByBLx01CI47EwGeluqVDujk="; + sha256 = "sha256-9NAAXGEVgpVPS7MB8FubnYUpkihE3lET/gep8QfPhB0="; }; buildInputs = [ @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkg-config wrapGAppsHook3 ]; meta = with lib; { - description = "An open source toolkit for medical image conversion "; + description = "Open source toolkit for medical image conversion "; homepage = "https://xmedcon.sourceforge.net/"; license = licenses.lgpl2Plus; maintainers = with maintainers; [ arianvp flokli ]; diff --git a/pkgs/applications/science/misc/bada-bib/default.nix b/pkgs/applications/science/misc/bada-bib/default.nix index 1895315325747..83abd40030ee5 100644 --- a/pkgs/applications/science/misc/bada-bib/default.nix +++ b/pkgs/applications/science/misc/bada-bib/default.nix @@ -74,7 +74,7 @@ python3Packages.buildPythonApplication rec { meta = with lib; { homepage = "https://github.com/RogerCrocker/BadaBib"; - description = "A simple BibTeX Viewer and Editor"; + description = "Simple BibTeX Viewer and Editor"; mainProgram = "badabib"; maintainers = [ maintainers.Cogitri ]; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix index 6a0aafad3e914..68134a99a2035 100644 --- a/pkgs/applications/science/misc/boinc/default.nix +++ b/pkgs/applications/science/misc/boinc/default.nix @@ -27,14 +27,14 @@ stdenv.mkDerivation rec { pname = "boinc"; - version = "8.0.1"; + version = "8.0.3"; src = fetchFromGitHub { name = "${pname}-${version}-src"; owner = "BOINC"; repo = "boinc"; rev = "client_release/${lib.versions.majorMinor version}/${version}"; - hash = "sha256-pjk9+VRWrFIoHolIEEWlRx89hifLNeFtIi34F1OBD38="; + hash = "sha256-kkEEJp7NTpHwbo03BGjjJAraFQIJcoNyV+oDsCZlzPQ="; }; nativeBuildInputs = [ libtool automake autoconf m4 pkg-config ]; diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix index 7919dfd176828..ab43eac8bffb0 100644 --- a/pkgs/applications/science/misc/cwltool/default.nix +++ b/pkgs/applications/science/misc/cwltool/default.nix @@ -7,14 +7,14 @@ python3.pkgs.buildPythonApplication rec { pname = "cwltool"; - version = "3.1.20240404144621"; + version = "3.1.20240508115724"; pyproject = true; src = fetchFromGitHub { owner = "common-workflow-language"; repo = "cwltool"; rev = "refs/tags/${version}"; - hash = "sha256-atpXkMIQ60POuUk99uiiuCoRXt4Seg11g/eHCeTDe+Q="; + hash = "sha256-hBP/8PIqvs820UsxrRuyMVIWgQGFVcMHCUToxhcupTk="; }; postPatch = '' @@ -24,7 +24,6 @@ python3.pkgs.buildPythonApplication rec { --replace '"schema-salad >= 8.4.20230426093816, < 9",' "" \ --replace "PYTEST_RUNNER + " "" substituteInPlace pyproject.toml \ - --replace "mypy==1.8.0" "mypy" \ --replace "ruamel.yaml>=0.16.0,<0.18" "ruamel.yaml" ''; diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix index 1d42600d9770d..392a529f0dedd 100644 --- a/pkgs/applications/science/misc/cytoscape/default.nix +++ b/pkgs/applications/science/misc/cytoscape/default.nix @@ -36,7 +36,7 @@ stdenv.mkDerivation rec { meta = { homepage = "http://www.cytoscape.org"; - description = "A general platform for complex network analysis and visualization"; + description = "General platform for complex network analysis and visualization"; mainProgram = "cytoscape"; license = lib.licenses.lgpl21; maintainers = [lib.maintainers.mimame]; diff --git a/pkgs/applications/science/misc/gephi/default.nix b/pkgs/applications/science/misc/gephi/default.nix index ab8134daf3aea..77b6584412a5a 100644 --- a/pkgs/applications/science/misc/gephi/default.nix +++ b/pkgs/applications/science/misc/gephi/default.nix @@ -36,7 +36,7 @@ mavenJdk11.buildMavenPackage rec { ''; meta = with lib; { - description = "A platform for visualizing and manipulating large graphs"; + description = "Platform for visualizing and manipulating large graphs"; mainProgram = "gephi"; homepage = "https://gephi.org"; sourceProvenance = with sourceTypes; [ diff --git a/pkgs/applications/science/misc/graphia/default.nix b/pkgs/applications/science/misc/graphia/default.nix index b24d5375ef9b8..a5055220e95fb 100644 --- a/pkgs/applications/science/misc/graphia/default.nix +++ b/pkgs/applications/science/misc/graphia/default.nix @@ -47,7 +47,7 @@ stdenv.mkDerivation rec { meta = with lib; { # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/graphia.x86_64-darwin broken = (stdenv.isLinux && stdenv.isAarch64) || stdenv.isDarwin; - description = "A visualisation tool for the creation and analysis of graphs."; + description = "Visualisation tool for the creation and analysis of graphs"; homepage = "https://graphia.app"; license = licenses.gpl3Only; mainProgram = "Graphia"; diff --git a/pkgs/applications/science/misc/netlogo/default.nix b/pkgs/applications/science/misc/netlogo/default.nix index 13c3c36f90ae6..20d001d8dba23 100644 --- a/pkgs/applications/science/misc/netlogo/default.nix +++ b/pkgs/applications/science/misc/netlogo/default.nix @@ -45,7 +45,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A multi-agent programmable modeling environment"; + description = "Multi-agent programmable modeling environment"; mainProgram = "netlogo"; longDescription = '' NetLogo is a multi-agent programmable modeling environment. It is used by diff --git a/pkgs/applications/science/misc/openmodelica/combined/default.nix b/pkgs/applications/science/misc/openmodelica/combined/default.nix index bc6bc96202152..8d937dddac547 100644 --- a/pkgs/applications/science/misc/openmodelica/combined/default.nix +++ b/pkgs/applications/science/misc/openmodelica/combined/default.nix @@ -21,7 +21,7 @@ symlinkJoin { ''; meta = with lib; { - description = "An open-source Modelica-based modeling and simulation environment intended for industrial and academic usage"; + description = "Open-source Modelica-based modeling and simulation environment intended for industrial and academic usage"; homepage = "https://openmodelica.org"; license = licenses.gpl3Only; maintainers = with maintainers; [ balodja smironov ]; diff --git a/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix b/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix index 360fea56fedfb..82b9f8e36fe1d 100644 --- a/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix +++ b/pkgs/applications/science/misc/openmodelica/omcompiler/default.nix @@ -44,6 +44,11 @@ mkOpenModelicaDerivation ({ $(find ./OMCompiler -name 'Makefile*') ''; + env.CFLAGS = toString [ + "-Wno-error=dynamic-exception-spec" + "-Wno-error=implicit-function-declaration" + ]; + preFixup = '' for entry in $(find $out -name libipopt.so); do patchelf --shrink-rpath --allowed-rpath-prefixes "$NIX_STORE" "$entry" diff --git a/pkgs/applications/science/misc/openmodelica/omedit/default.nix b/pkgs/applications/science/misc/openmodelica/omedit/default.nix index 57863482fef65..731d64c41755b 100644 --- a/pkgs/applications/science/misc/openmodelica/omedit/default.nix +++ b/pkgs/applications/science/misc/openmodelica/omedit/default.nix @@ -30,7 +30,7 @@ mkOpenModelicaDerivation rec { QMAKESPEC = "linux-clang"; meta = with lib; { - description = "A Modelica connection editor for OpenModelica"; + description = "Modelica connection editor for OpenModelica"; homepage = "https://openmodelica.org"; license = licenses.gpl3Only; maintainers = with maintainers; [ balodja smironov ]; diff --git a/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix b/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix index 6821e33d1a629..dee5aacf66655 100644 --- a/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix +++ b/pkgs/applications/science/misc/openmodelica/omlibrary/default.nix @@ -24,7 +24,7 @@ mkOpenModelicaDerivation { ''; meta = with lib; { - description = "A collection of Modelica libraries to use with OpenModelica, + description = "Collection of Modelica libraries to use with OpenModelica, including Modelica Standard Library"; homepage = "https://openmodelica.org"; license = licenses.gpl3Only; diff --git a/pkgs/applications/science/misc/openmodelica/omparser/default.nix b/pkgs/applications/science/misc/openmodelica/omparser/default.nix index cbf8f2255e76c..03030de2cf486 100644 --- a/pkgs/applications/science/misc/openmodelica/omparser/default.nix +++ b/pkgs/applications/science/misc/openmodelica/omparser/default.nix @@ -18,7 +18,7 @@ mkOpenModelicaDerivation rec { patches = [ ./Makefile.in.patch ]; meta = with lib; { - description = "An antlr4-based parser of Modelica files from OpenModelica + description = "Antlr4-based parser of Modelica files from OpenModelica suite"; homepage = "https://openmodelica.org"; license = licenses.gpl3Only; diff --git a/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix b/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix index d91d427a07703..9e28e3f21f26d 100644 --- a/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix +++ b/pkgs/applications/science/misc/openmodelica/omsimulator/default.nix @@ -5,6 +5,7 @@ , libxml2 , openmodelica , mkOpenModelicaDerivation +, fetchpatch }: mkOpenModelicaDerivation rec { @@ -12,12 +13,25 @@ mkOpenModelicaDerivation rec { omdir = "OMSimulator"; omdeps = [ openmodelica.omcompiler ]; + patches = [ + (fetchpatch { + url = "https://github.com/OpenModelica/OMSimulator/commit/5ef06e251d639a0224adc205cdbfa1f99bf9a956.patch"; + stripLen = 1; + extraPrefix = "OMSimulator/"; + hash = "sha256-hLsS6TNEjddm2o2Optnf8n6hh14up9bWJBoztNmisH0="; + }) + ]; + nativeBuildInputs = [ pkg-config ]; buildInputs = [ readline libxml2 boost ]; + env.CFLAGS = toString [ + "-Wno-error=implicit-function-declaration" + ]; + meta = with lib; { - description = "The OpenModelica FMI & SSP-based co-simulation environment"; + description = "OpenModelica FMI & SSP-based co-simulation environment"; homepage = "https://openmodelica.org"; license = licenses.gpl3Only; maintainers = with maintainers; [ balodja smironov ]; diff --git a/pkgs/applications/science/misc/openmvg/default.nix b/pkgs/applications/science/misc/openmvg/default.nix index 5cf4dc4377521..f622f87d2e412 100644 --- a/pkgs/applications/science/misc/openmvg/default.nix +++ b/pkgs/applications/science/misc/openmvg/default.nix @@ -74,7 +74,7 @@ stdenv.mkDerivation rec { meta = { broken = stdenv.isDarwin && stdenv.isx86_64; - description = "A library for computer-vision scientists and targeted for the Multiple View Geometry community"; + description = "Library for computer-vision scientists and targeted for the Multiple View Geometry community"; homepage = "https://openmvg.readthedocs.io/en/latest/"; license = lib.licenses.mpl20; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/misc/openrefine/default.nix b/pkgs/applications/science/misc/openrefine/default.nix index 9f2ef0f29b31f..b94f23671024b 100644 --- a/pkgs/applications/science/misc/openrefine/default.nix +++ b/pkgs/applications/science/misc/openrefine/default.nix @@ -15,12 +15,12 @@ let inherit jdk; }; - version = "3.7.9"; + version = "3.8.1"; src = fetchFromGitHub { owner = "openrefine"; repo = "openrefine"; rev = version; - hash = "sha256-wtg0BOGr/aJPZeFQbJSBHtTVfpcSCSHP++8AnpS8pgQ="; + hash = "sha256-MnFwFJdKIU7D8GQgnDvCO+P8r8h1Se/wmbt/Z3EX+3Q="; }; npmPkg = buildNpmPackage { @@ -29,7 +29,7 @@ let pname = "openrefine-npm"; sourceRoot = "${src.name}/main/webapp"; - npmDepsHash = "sha256-8GhcL4tohQ5u2HeYN6JyTMMobUOqAL8ETCLiP1SoDSk="; + npmDepsHash = "sha256-u9qledNFqGgMmOIsm2T8w3UoaLbb7WtksUw6xLoRgU8="; # package.json doesn't supply a version, which npm doesn't like - fix this. # directly referencing jq because buildNpmPackage doesn't pass @@ -55,20 +55,14 @@ in maven'.buildMavenPackage { postPatch = '' cp -r ${npmPkg} main/webapp/modules/core/3rdparty ''; - mvnParameters = "-DskipTests=true -pl !packaging"; - mvnHash = "sha256-MqE+iloqzBav6E3/rf1LP5BlKhW/FBIt6+6U+S8UJWA="; + mvnParameters = "-pl !packaging"; + mvnHash = "sha256-0qsKUMV9M0ZaddR5ust8VikSrsutdxVNNezKqR+F/6M="; nativeBuildInputs = [ makeWrapper ]; - installPhase = let - gitProperties = writeText "git.properties" (builtins.toJSON { - "git.build.version" = version; - "git.branch" = "none"; - "git.build.time" = "1970-01-01T00:00:00+0000"; - "git.commit.id.abbrev" = "none"; - "git.commit.id.describe" = "none"; - }); - in '' + doCheck = false; + + installPhase = '' mkdir -p $out/lib/server/target/lib cp -r server/target/lib/* $out/lib/server/target/lib/ cp server/target/openrefine-*-server.jar $out/lib/server/target/lib/ @@ -85,8 +79,6 @@ in maven'.buildMavenPackage { done ) - cp ${gitProperties} $out/lib/webapp/WEB-INF/classes/git.properties - mkdir -p $out/etc cp refine.ini $out/etc/ diff --git a/pkgs/applications/science/misc/reason-shell/default.nix b/pkgs/applications/science/misc/reason-shell/default.nix index 848f31abe4c6b..5491593cc7f70 100644 --- a/pkgs/applications/science/misc/reason-shell/default.nix +++ b/pkgs/applications/science/misc/reason-shell/default.nix @@ -31,7 +31,7 @@ rustPlatform.buildRustPackage rec { ]; meta = with lib; { - description = "A shell for research papers"; + description = "Shell for research papers"; mainProgram = "reason"; homepage = "https://github.com/jaywonchung/reason"; changelog = "https://github.com/jaywonchung/reason/releases/tag/${src.rev}"; diff --git a/pkgs/applications/science/misc/root/5.nix b/pkgs/applications/science/misc/root/5.nix index dfe7b5eca97f3..80f2df0688da3 100644 --- a/pkgs/applications/science/misc/root/5.nix +++ b/pkgs/applications/science/misc/root/5.nix @@ -153,7 +153,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://root.cern.ch/"; - description = "A data analysis framework"; + description = "Data analysis framework"; platforms = platforms.unix; broken = !stdenv.isx86_64 || stdenv.cc.isClang or false; maintainers = with maintainers; [ veprbl ]; diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index afc048cc41ef6..ded47a661a21a 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -3,7 +3,6 @@ , callPackage , fetchgit , fetchurl -, fetchpatch , makeWrapper , cmake , coreutils @@ -25,7 +24,7 @@ , libGL , libxcrypt , libxml2 -, llvm_13 +, llvm_16 , lsof , lz4 , xz @@ -41,7 +40,6 @@ , xxHash , zlib , zstd -, libAfterImage , giflib , libjpeg , libtiff @@ -58,7 +56,7 @@ stdenv.mkDerivation rec { pname = "root"; - version = "6.30.06"; + version = "6.32.00"; passthru = { tests = import ./tests { inherit callPackage; }; @@ -66,13 +64,13 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://root.cern.ch/download/root_v${version}.source.tar.gz"; - hash = "sha256-MA237RtnjtL7ljXKZ1khoZRcfCED2oQAM7STCR9VcAw="; + hash = "sha256-EvIDaBpZBBxHTOlSN2Hm8OiGGzvueN9feZqNtVGJ5dI="; }; clad_src = fetchgit { url = "https://github.com/vgvassilev/clad"; - rev = "refs/tags/v1.4"; # Make sure that this is the same tag as in the ROOT build files! - hash = "sha256-OI9PaS7kQ/ewD5Soe3gG5FZdlR6qG6Y3mfHwi5dj1sI="; + rev = "refs/tags/v1.5"; # Make sure that this is the same tag as in the ROOT build files! + hash = "sha256-s0DbHfLthv51ZICnTd30O4qG/DyZPk5tADeu3bBRoOw="; }; nativeBuildInputs = [ makeWrapper cmake pkg-config git ]; @@ -90,7 +88,7 @@ stdenv.mkDerivation rec { lapack libxcrypt libxml2 - llvm_13 + llvm_16 lz4 xz gsl @@ -98,7 +96,6 @@ stdenv.mkDerivation rec { openblas openssl xxHash - libAfterImage giflib libjpeg libtiff @@ -116,17 +113,6 @@ stdenv.mkDerivation rec { patches = [ ./sw_vers.patch - - # compatibility with recent XRootD - # https://github.com/root-project/root/pull/13752 - (fetchpatch { - url = "https://github.com/root-project/root/commit/3d3cda6c520791282298782189cdb8ca07ace4b9.diff"; - hash = "sha256-O3aXzrOEQiPjZgbAj9TL6Wt/adN1kKFwjooeaFRyT4I="; - }) - (fetchpatch { - url = "https://github.com/root-project/root/commit/6e7798e62dbed1ffa8b91a180fa5a080b7c04ba3.diff"; - hash = "sha256-47/J631DBnVlvM1Pm9iicKXDKAqN8v9hjAstQuHmH8Q="; - }) ]; preConfigure = '' @@ -142,18 +128,13 @@ stdenv.mkDerivation rec { # This should probably be fixed upstream with a flag to disable the # connectivity check! substituteInPlace CMakeLists.txt \ - --replace 'if(NO_CONNECTION)' 'if(FALSE)' - substituteInPlace interpreter/cling/tools/plugins/CMakeLists.txt \ - --replace 'if(NOT DEFINED NO_CONNECTION OR NOT NO_CONNECTION)' 'if(TRUE)' + --replace 'if(clad AND NO_CONNECTION)' 'if(FALSE)' # Make sure that clad is not downloaded when building substituteInPlace interpreter/cling/tools/plugins/clad/CMakeLists.txt \ --replace 'UPDATE_COMMAND ""' 'SOURCE_DIR ${clad_src} DOWNLOAD_COMMAND "" UPDATE_COMMAND ""' # Make sure that clad is finding the right llvm version substituteInPlace interpreter/cling/tools/plugins/clad/CMakeLists.txt \ - --replace '-DLLVM_DIR=''${LLVM_BINARY_DIR}' '-DLLVM_DIR=${llvm_13.dev}/lib/cmake/llvm' - # Fix that will also be upstream in ROOT 6.32. TODO: remove it when updating to 6.32 - substituteInPlace interpreter/cling/tools/plugins/clad/CMakeLists.txt \ - --replace 'set(_CLAD_LIBRARY_PATH ''${clad_install_dir}/plugins/lib)' 'set(_CLAD_LIBRARY_PATH ''${CMAKE_CURRENT_BINARY_DIR}/clad-prefix/src/clad-build/lib''${LLVM_LIBDIR_SUFFIX})' + --replace '-DLLVM_DIR=''${LLVM_BINARY_DIR}' '-DLLVM_DIR=${llvm_16.dev}/lib/cmake/llvm' substituteInPlace interpreter/llvm-project/clang/tools/driver/CMakeLists.txt \ --replace 'add_clang_symlink(''${link} clang)' "" @@ -197,9 +178,6 @@ stdenv.mkDerivation rec { "-Druntime_cxxmodules=OFF" ]; - # suppress warnings from compilation of the vendored clang to avoid running into log limits on the Hydra - NIX_CFLAGS_COMPILE = lib.optionals stdenv.cc.isGNU [ "-Wno-shadow" "-Wno-maybe-uninitialized" ]; - postInstall = '' for prog in rootbrowse rootcp rooteventselector rootls rootmkdir rootmv rootprint rootrm rootslimtree; do wrapProgram "$out/bin/$prog" \ @@ -257,7 +235,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://root.cern/"; - description = "A data analysis framework"; + description = "Data analysis framework"; platforms = platforms.unix; maintainers = [ maintainers.guitargeek maintainers.veprbl ]; license = licenses.lgpl21; diff --git a/pkgs/applications/science/misc/sasview/xhtml2pdf.nix b/pkgs/applications/science/misc/sasview/xhtml2pdf.nix index 41d15e2f1babc..b7ace57d74afc 100644 --- a/pkgs/applications/science/misc/sasview/xhtml2pdf.nix +++ b/pkgs/applications/science/misc/sasview/xhtml2pdf.nix @@ -25,7 +25,7 @@ buildPythonPackage rec { }; meta = { - description = "A pdf converter for the ReportLab Toolkit"; + description = "Pdf converter for the ReportLab Toolkit"; homepage = "https://github.com/xhtml2pdf/xhtml2pdf"; license = lib.licenses.asl20; maintainers = with lib.maintainers; [ rprospero ]; diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index 1a171f2c7db5d..7f0e70c642134 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -6,14 +6,14 @@ python3.pkgs.buildPythonApplication rec { pname = "snakemake"; - version = "8.11.4"; + version = "8.14.0"; format = "setuptools"; src = fetchFromGitHub { owner = "snakemake"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-nfPA2sQCeRc12A4rrlo17UPpiB8plKYbiumZjS7Yhz8="; + hash = "sha256-6oguN4u4OUDXpDsbueSBNwtWgLCaKmgq3w/d/MsMh7Y="; # https://github.com/python-versioneer/python-versioneer/issues/217 postFetch = '' sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#' diff --git a/pkgs/applications/science/misc/tulip/default.nix b/pkgs/applications/science/misc/tulip/default.nix index 02b5ad0c0458d..9808a572836d8 100644 --- a/pkgs/applications/science/misc/tulip/default.nix +++ b/pkgs/applications/science/misc/tulip/default.nix @@ -4,11 +4,11 @@ stdenv.mkDerivation rec { pname = "tulip"; - version = "5.7.3"; + version = "5.7.4"; src = fetchurl { url = "mirror://sourceforge/auber/tulip-${version}_src.tar.gz"; - hash = "sha256-arpC+FsDYGMf47phtSzyjjvDg/UYZS+akOe5CYfajdU="; + hash = "sha256-7z21WkPi1v2AGishDmXZPAedMjgXPRnpUiHTzEnc5LY="; }; nativeBuildInputs = [ cmake wrapQtAppsHook ] @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { doCheck = false; meta = { - description = "A visualization framework for the analysis and visualization of relational data"; + description = "Visualization framework for the analysis and visualization of relational data"; longDescription = '' Tulip is an information visualization framework dedicated to the diff --git a/pkgs/applications/science/molecular-dynamics/raspa/default.nix b/pkgs/applications/science/molecular-dynamics/raspa/default.nix index 149db0504bf1f..8fd395f9174d3 100644 --- a/pkgs/applications/science/molecular-dynamics/raspa/default.nix +++ b/pkgs/applications/science/molecular-dynamics/raspa/default.nix @@ -69,7 +69,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A general purpose classical molecular simulation package"; + description = "General purpose classical molecular simulation package"; homepage = "https://iraspa.org/raspa/"; license = licenses.mit; platforms = platforms.all; diff --git a/pkgs/applications/science/networking/sumo/default.nix b/pkgs/applications/science/networking/sumo/default.nix index 956691582bda3..6f5be3df816eb 100644 --- a/pkgs/applications/science/networking/sumo/default.nix +++ b/pkgs/applications/science/networking/sumo/default.nix @@ -5,13 +5,13 @@ stdenv.mkDerivation rec { pname = "sumo"; - version = "1.19.0"; + version = "1.20.0"; src = fetchFromGitHub { owner = "eclipse"; repo = "sumo"; rev = "v${lib.replaceStrings ["."] ["_"] version}"; - sha256 = "sha256-uB7Gy0uX3LsZDeeITyjl7DN76TFJQKgsQs4RoDVfSmY="; + sha256 = "sha256-y/bkdDWrb1KB0EOVSJPfPVYHGp/zQ2+Shb6eLsFQRNQ="; fetchSubmodules = true; }; @@ -54,7 +54,7 @@ stdenv.mkDerivation rec { ]); meta = with lib; { - description = "The SUMO traffic simulator"; + description = "SUMO traffic simulator"; longDescription = '' Eclipse SUMO is an open source, highly portable, microscopic and continuous traffic simulation package diff --git a/pkgs/applications/science/physics/dawn/default.nix b/pkgs/applications/science/physics/dawn/default.nix index c174d4c0720f7..a32311baca935 100644 --- a/pkgs/applications/science/physics/dawn/default.nix +++ b/pkgs/applications/science/physics/dawn/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A vectorized 3D PostScript processor with analytical hidden line/surface removal"; + description = "Vectorized 3D PostScript processor with analytical hidden line/surface removal"; license = licenses.unfree; homepage = "https://geant4.kek.jp/~tanaka/DAWN/About_DAWN.html"; platforms = platforms.unix; diff --git a/pkgs/applications/science/physics/dawncut/default.nix b/pkgs/applications/science/physics/dawncut/default.nix index 5c17837d2e952..2c1b987848810 100644 --- a/pkgs/applications/science/physics/dawncut/default.nix +++ b/pkgs/applications/science/physics/dawncut/default.nix @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A tool to generate a 3D scene data clipped with an arbitrary plane"; + description = "Tool to generate a 3D scene data clipped with an arbitrary plane"; license = licenses.unfree; homepage = "https://geant4.kek.jp/~tanaka/DAWN/About_DAWNCUT.html"; platforms = platforms.unix; diff --git a/pkgs/applications/science/physics/elmerfem/default.nix b/pkgs/applications/science/physics/elmerfem/default.nix index c3720602d08d2..4b19bc4b17b48 100644 --- a/pkgs/applications/science/physics/elmerfem/default.nix +++ b/pkgs/applications/science/physics/elmerfem/default.nix @@ -73,7 +73,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://elmerfem.org"; - description = "A finite element software for multiphysical problems"; + description = "Finite element software for multiphysical problems"; platforms = platforms.unix; maintainers = with maintainers; [ wulfsta broke ]; license = licenses.lgpl21; diff --git a/pkgs/applications/science/physics/nnpdf/default.nix b/pkgs/applications/science/physics/nnpdf/default.nix index d0104095f39a8..a4762323dcf95 100644 --- a/pkgs/applications/science/physics/nnpdf/default.nix +++ b/pkgs/applications/science/physics/nnpdf/default.nix @@ -54,7 +54,7 @@ stdenv.mkDerivation rec { ]; meta = with lib; { - description = "An open-source machine learning framework for global analyses of parton distributions"; + description = "Open-source machine learning framework for global analyses of parton distributions"; mainProgram = "evolven3fit"; homepage = "https://docs.nnpdf.science/"; license = licenses.gpl3Only; diff --git a/pkgs/applications/science/physics/professor/default.nix b/pkgs/applications/science/physics/professor/default.nix index 6d52951ee9c9b..1c6c21c52fef8 100644 --- a/pkgs/applications/science/physics/professor/default.nix +++ b/pkgs/applications/science/physics/professor/default.nix @@ -1,23 +1,51 @@ -{ lib, stdenv, fetchurl, eigen, makeWrapper, python3 }: +{ lib +, stdenv +, fetchFromGitLab +, eigen +, makeWrapper +, python3 +}: stdenv.mkDerivation rec { pname = "professor"; - version = "2.3.3"; + version = "2.4.2"; - src = fetchurl { - name = "Professor-${version}.tar.gz"; - url = "https://professor.hepforge.org/downloads/?f=Professor-${version}.tar.gz"; - sha256 = "17q026r2fpfxzf74d1013ksy3a9m57rcr2q164n9x02ci40bmib0"; + src = fetchFromGitLab { + owner = "hepcedar"; + repo = "professor"; + rev = "refs/tags/professor-2.4.2"; + hash = "sha256-z2Ub7SUTz4Hj3ajnzOV/QXZ+cH2v6zJv9UZM2M2y1Hg="; + # workaround unpacking to case-sensitive filesystems + postFetch = '' + rm -rf $out/[Dd]ocker + ''; }; - postPatch = lib.optionalString stdenv.isDarwin '' + postPatch = '' substituteInPlace Makefile \ - --replace '-shared -o' '-shared -install_name "$(out)/$@" -o' + --replace-fail 'pip install ' 'pip install --prefix $(out) ' + '' + lib.optionalString stdenv.isDarwin '' + substituteInPlace Makefile \ + --replace-fail '-shared -o' '-shared -install_name "$(out)/$@" -o' ''; - nativeBuildInputs = [ python3.pkgs.cython makeWrapper ]; - buildInputs = [ python3 eigen ]; - propagatedBuildInputs = with python3.pkgs; [ iminuit numpy matplotlib yoda ]; + nativeBuildInputs = [ + python3.pkgs.cython + python3.pkgs.pip + python3.pkgs.setuptools + python3.pkgs.wheel + makeWrapper + ]; + buildInputs = [ + python3 + eigen + ]; + propagatedBuildInputs = with python3.pkgs; [ + iminuit + numpy + matplotlib + yoda + ]; CPPFLAGS = [ "-I${eigen}/include/eigen3" ]; PREFIX = placeholder "out"; @@ -32,9 +60,9 @@ stdenv.mkDerivation rec { installCheckTarget = "check"; meta = with lib; { - description = "A tuning tool for Monte Carlo event generators"; + description = "Tuning tool for Monte Carlo event generators"; homepage = "https://professor.hepforge.org/"; - license = licenses.unfree; # no license specified + license = licenses.gpl3Only; maintainers = [ maintainers.veprbl ]; platforms = platforms.unix; }; diff --git a/pkgs/applications/science/physics/quantomatic/default.nix b/pkgs/applications/science/physics/quantomatic/default.nix index caff65f1d71b6..05011313bccea 100644 --- a/pkgs/applications/science/physics/quantomatic/default.nix +++ b/pkgs/applications/science/physics/quantomatic/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A piece of software for reasoning about monoidal theories; in particular, quantum information processing"; + description = "Piece of software for reasoning about monoidal theories; in particular, quantum information processing"; mainProgram = "quantomatic"; license = licenses.gpl3; homepage = "https://quantomatic.github.io/"; diff --git a/pkgs/applications/science/physics/sacrifice/default.nix b/pkgs/applications/science/physics/sacrifice/default.nix index 352b65dc700c0..dbe2365371393 100644 --- a/pkgs/applications/science/physics/sacrifice/default.nix +++ b/pkgs/applications/science/physics/sacrifice/default.nix @@ -39,7 +39,7 @@ stdenv.mkDerivation { enableParallelBuilding = true; meta = { - description = "A standalone contribution to AGILe for steering Pythia 8"; + description = "Standalone contribution to AGILe for steering Pythia 8"; mainProgram = "run-pythia"; license = lib.licenses.gpl2; homepage = "https://agile.hepforge.org/trac/wiki/Sacrifice"; diff --git a/pkgs/applications/science/physics/xfitter/default.nix b/pkgs/applications/science/physics/xfitter/default.nix index 77b57e08e2bbe..8a92c85a13830 100644 --- a/pkgs/applications/science/physics/xfitter/default.nix +++ b/pkgs/applications/science/physics/xfitter/default.nix @@ -55,7 +55,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "The xFitter project is an open source QCD fit framework ready to extract PDFs and assess the impact of new data"; + description = "XFitter project is an open source QCD fit framework ready to extract PDFs and assess the impact of new data"; license = licenses.gpl3; homepage = "https://www.xfitter.org/xFitter"; platforms = platforms.unix; diff --git a/pkgs/applications/science/physics/xflr5/default.nix b/pkgs/applications/science/physics/xflr5/default.nix index 497be8fcbaa9e..3090bcbfecd46 100644 --- a/pkgs/applications/science/physics/xflr5/default.nix +++ b/pkgs/applications/science/physics/xflr5/default.nix @@ -14,7 +14,7 @@ mkDerivation rec { nativeBuildInputs = [ qmake ]; meta = with lib; { - description = "An analysis tool for airfoils, wings and planes"; + description = "Analysis tool for airfoils, wings and planes"; mainProgram = "xflr5"; homepage = "https://sourceforge.net/projects/xflr5/"; license = licenses.gpl3; diff --git a/pkgs/applications/science/programming/fdr/default.nix b/pkgs/applications/science/programming/fdr/default.nix index f7b12342a6659..2237d9528701e 100644 --- a/pkgs/applications/science/programming/fdr/default.nix +++ b/pkgs/applications/science/programming/fdr/default.nix @@ -61,7 +61,7 @@ stdenv.mkDerivation { meta = with lib; { homepage = "https://cocotec.io/fdr/"; - description = "The CSP refinement checker"; + description = "CSP refinement checker"; license = licenses.unfreeRedistributable; sourceProvenance = with sourceTypes; [ binaryNativeCode ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/robotics/betaflight-configurator/default.nix b/pkgs/applications/science/robotics/betaflight-configurator/default.nix index 84f94102da136..a6cfb99d492b1 100644 --- a/pkgs/applications/science/robotics/betaflight-configurator/default.nix +++ b/pkgs/applications/science/robotics/betaflight-configurator/default.nix @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "The Betaflight flight control system configuration tool"; + description = "Betaflight flight control system configuration tool"; mainProgram = "betaflight-configurator"; longDescription = '' A crossplatform configuration tool for the Betaflight flight control system. diff --git a/pkgs/applications/science/robotics/emuflight-configurator/default.nix b/pkgs/applications/science/robotics/emuflight-configurator/default.nix index 62592b0cc3fc9..9669d48e744e0 100644 --- a/pkgs/applications/science/robotics/emuflight-configurator/default.nix +++ b/pkgs/applications/science/robotics/emuflight-configurator/default.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { ]; meta = with lib; { - description = "The Emuflight flight control system configuration tool"; + description = "Emuflight flight control system configuration tool"; mainProgram = "emuflight-configurator"; longDescription = '' A crossplatform configuration tool for the Emuflight flight control system. diff --git a/pkgs/applications/science/robotics/inav-configurator/default.nix b/pkgs/applications/science/robotics/inav-configurator/default.nix index 1a6f5951ed348..364f5185d00a8 100644 --- a/pkgs/applications/science/robotics/inav-configurator/default.nix +++ b/pkgs/applications/science/robotics/inav-configurator/default.nix @@ -43,7 +43,7 @@ stdenv.mkDerivation rec { }; meta = with lib; { - description = "The iNav flight control system configuration tool"; + description = "INav flight control system configuration tool"; mainProgram = "inav-configurator"; longDescription = '' A crossplatform configuration tool for the iNav flight control system. diff --git a/pkgs/applications/science/robotics/mission-planner/default.nix b/pkgs/applications/science/robotics/mission-planner/default.nix index f6e7e5f114fa7..0e60cb1fc2604 100644 --- a/pkgs/applications/science/robotics/mission-planner/default.nix +++ b/pkgs/applications/science/robotics/mission-planner/default.nix @@ -45,7 +45,7 @@ in stdenv.mkDerivation rec { ''; meta = with lib; { - description = "An ArduPilot ground station"; + description = "ArduPilot ground station"; mainProgram = "mission-planner"; longDescription = '' Full-featured ground station application for the ArduPilot open source diff --git a/pkgs/applications/science/robotics/mujoco/default.nix b/pkgs/applications/science/robotics/mujoco/default.nix index 76c18a788c30d..d4a7a961d3984 100644 --- a/pkgs/applications/science/robotics/mujoco/default.nix +++ b/pkgs/applications/science/robotics/mujoco/default.nix @@ -11,7 +11,7 @@ let pin = { - + # TODO: Check the following file and ensure the dependencies are up-to-date # See https://github.com/google-deepmind/mujoco/blob/<VERSION>/cmake/MujocoDependencies.cmake#L17-L64 abseil-cpp = fetchFromGitHub { owner = "abseil"; @@ -129,7 +129,7 @@ let in stdenv.mkDerivation rec { pname = "mujoco"; - version = "3.1.5"; + version = "3.1.6"; # Bumping version? Make sure to look though the MuJoCo's commit # history for bumped dependency pins! @@ -137,7 +137,7 @@ in stdenv.mkDerivation rec { owner = "google-deepmind"; repo = "mujoco"; rev = "refs/tags/${version}"; - hash = "sha256-XKN489oexHf2/Gv0MVxXUzqyeJJTJXV99+fNi8shdsg="; + hash = "sha256-64zUplr1E5WSb5RpTW9La1zKVT67a1VrftiUqc2SHlU="; }; patches = [ ./mujoco-system-deps-dont-fetch.patch ]; @@ -177,12 +177,16 @@ in stdenv.mkDerivation rec { passthru.pin = { inherit (pin) lodepng eigen3 abseil-cpp; }; - meta = with lib; { - description = "Multi-Joint dynamics with Contact. A general purpose physics simulator."; + meta = { + description = "Multi-Joint dynamics with Contact. A general purpose physics simulator"; homepage = "https://mujoco.org/"; changelog = "https://github.com/google-deepmind/mujoco/releases/tag/${version}"; - license = licenses.asl20; - maintainers = with maintainers; [ samuela tmplt ]; + license = lib.licenses.asl20; + maintainers = with lib.maintainers; [ + GaetanLepage + samuela + tmplt + ]; broken = stdenv.isDarwin; }; } |