diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
55 files changed, 467 insertions, 480 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix index ce29c5172a29..14c684d432c4 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix @@ -14,11 +14,11 @@ mkDerivation rec { pname = "kstars"; - version = "3.6.6"; + version = "3.6.7"; src = fetchurl { url = "mirror://kde/stable/kstars/kstars-${version}.tar.xz"; - sha256 = "sha256-Z4PatRvtIJBoeRDJJYkkBTOB/R+R7nGdDT38bfAShJQ="; + sha256 = "sha256-uEgzvhlHHpXyvi3Djfwg3GmYeZq+r48m7OJFIDARpe4="; }; nativeBuildInputs = [ extra-cmake-modules kdoctools ]; diff --git a/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix b/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix index db0411f1337a..255927d893d2 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitLab, pkg-config, meson, ninja +{ lib, stdenv, fetchFromGitLab, fetchpatch, pkg-config, meson, ninja, cmake , git, criterion, gtk3, libconfig, gnuplot, opencv, json-glib , fftwFloat, cfitsio, gsl, exiv2, librtprocess, wcslib, ffmpeg , libraw, libtiff, libpng, libjpeg, libheif, ffms, wrapGAppsHook @@ -6,17 +6,25 @@ stdenv.mkDerivation rec { pname = "siril"; - version = "1.0.6"; + version = "1.2.0"; src = fetchFromGitLab { owner = "free-astro"; - repo = pname; + repo = "siril"; rev = version; - sha256 = "sha256-KFCA3fUMVFHmh1BdKed5/dkq0EeYcmoWec97WX9ZHUc="; + hash = "sha256-lCoFQ7z6cZbyNPEm5s40DNdvTwFonHK3KCd8RniqQWs="; }; + patches = [ + (fetchpatch { + name = "siril-1.2-exiv2-0.28.patch"; + url = "https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-astronomy/siril/files/siril-1.2-exiv2-0.28.patch?id=002882203ad6a2b08ce035a18b95844a9f4b85d0"; + hash = "sha256-R1yslW6hzvJHKo0/IqBxkCuqcX6VrdRSz68gpAExxVE="; + }) + ]; + nativeBuildInputs = [ - meson ninja pkg-config git criterion wrapGAppsHook + meson ninja cmake pkg-config git criterion wrapGAppsHook ]; buildInputs = [ @@ -26,6 +34,7 @@ stdenv.mkDerivation rec { # Necessary because project uses default build dir for flatpaks/snaps dontUseMesonConfigure = true; + dontUseCmakeConfigure = true; configureScript = '' ${meson}/bin/meson --buildtype release nixbld . diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix index e2e1cda4c259..d656c39d0bc0 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix @@ -22,13 +22,13 @@ stdenv.mkDerivation rec { pname = "stellarium"; - version = "23.2"; + version = "23.3"; src = fetchFromGitHub { owner = "Stellarium"; repo = "stellarium"; rev = "v${version}"; - hash = "sha256-8Iheb/9wjf0u10ZQRkLMLNN2s7P++Fqcr26iatiKcTo="; + hash = "sha256-bYvGmYu9jMHk2IUICz2kCVh56Ymz8JHqurdWV+xEdJY="; }; patches = [ @@ -92,6 +92,6 @@ stdenv.mkDerivation rec { homepage = "https://stellarium.org/"; license = licenses.gpl2Plus; platforms = platforms.unix; - maintainers = with maintainers; [ ]; + maintainers = with maintainers; [ kilianar ]; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/bioawk/default.nix b/nixpkgs/pkgs/applications/science/biology/bioawk/default.nix new file mode 100644 index 000000000000..cfbb1a551fac --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bioawk/default.nix @@ -0,0 +1,50 @@ +{ lib +, stdenv +, fetchFromGitHub +, installShellFiles +, bison +, zlib +}: + +stdenv.mkDerivation { + pname = "bioawk"; + version = "unstable-2017-09-11"; + + src = fetchFromGitHub { + owner = "lh3"; + repo = "bioawk"; + rev = "fd40150b7c557da45e781a999d372abbc634cc21"; + hash = "sha256-WWgz96DPP83J45isWkMbgEvOlibq6WefK//ImV6+AU0="; + }; + + nativeBuildInputs = [ + bison + installShellFiles + ]; + + buildInputs = [ + zlib + ]; + + buildFlags = [ + "CC=${stdenv.cc.targetPrefix}cc" + ]; + + installPhase = '' + runHook preInstall + + install -Dm755 bioawk -t $out/bin + mv awk.1 bioawk.1 + installManPage bioawk.1 + + runHook postInstall + ''; + + meta = with lib; { + description = "BWK awk modified for biological data"; + homepage = "https://github.com/lh3/bioawk"; + license = licenses.hpnd; + maintainers = with maintainers; [ natsukium ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/blast/bin.nix b/nixpkgs/pkgs/applications/science/biology/blast/bin.nix index daae9c096144..48537a568e4b 100644 --- a/nixpkgs/pkgs/applications/science/biology/blast/bin.nix +++ b/nixpkgs/pkgs/applications/science/biology/blast/bin.nix @@ -13,20 +13,20 @@ }: let pname = "blast-bin"; - version = "2.13.0"; + version = "2.14.1"; srcs = rec { x86_64-linux = fetchurl { url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-linux.tar.gz"; - hash = "sha256-QPK3OdT++GoNI1NHyEpu2/hB2hqHYPQ/vNXFAVCwVEc="; + hash = "sha256-OO8MNOk6k0J9FlAGyCOhP+hirEIT6lL+rIInB8dQWEU="; }; aarch64-linux = fetchurl { - url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-arm-linux.tar.gz"; - hash = "sha256-vY8K66k7KunpBUjFsJTTb+ur5n1XmU0/mYxhZsi9ycs="; + url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-aarch64-linux.tar.gz"; + hash = "sha256-JlOyoxZQBbvUcHIMv5muTuGQgrh2uom3rzDurhHQ+FM="; }; x86_64-darwin = fetchurl { url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-macosx.tar.gz"; - hash = "sha256-Y0JlOUl9Ego6LTxTCNny3P5c1H3fApPXQm7Z6Zhq9RA="; + hash = "sha256-eMfuwMCD6VlDgeshLslDhYBBp0YOpL+6q/zSchR0bAs="; }; aarch64-darwin = x86_64-darwin; }; @@ -55,6 +55,7 @@ stdenv.mkDerivation { meta = with lib; { inherit (blast.meta) description homepage license; platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ]; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; maintainers = with maintainers; [ natsukium ]; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix index 954b704be0c6..e5c9c2864225 100644 --- a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "bowtie2"; - version = "2.5.1"; + version = "2.5.2"; src = fetchFromGitHub { owner = "BenLangmead"; repo = pname; rev = "v${version}"; - sha256 = "sha256-HaiZmWU6akHXJVWBmCvkG2E61NDrAP7UIxx9DNCEZqE="; + sha256 = "sha256-Bem4SHY/74suZPDbw/rwKMLBn3bRq5ooHbBoVnKuYk0="; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/biology/delly/default.nix b/nixpkgs/pkgs/applications/science/biology/delly/default.nix index 92eda1d1dd13..1c39d209c34e 100644 --- a/nixpkgs/pkgs/applications/science/biology/delly/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/delly/default.nix @@ -13,13 +13,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "delly"; - version = "1.1.6"; + version = "1.1.7"; src = fetchFromGitHub { owner = "dellytools"; repo = "delly"; rev = "v${finalAttrs.version}"; - hash = "sha256-/I//7MhsC/CcBeIJblzbjXp/yOSBm83KWJsrYpl6UJk="; + hash = "sha256-oBIY8s/ippf+Xw+3QzMwP0Esc/QpiT6yWeAnqpMix6s="; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix index 1281643fe794..78f226350f60 100644 --- a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix @@ -1,6 +1,7 @@ { lib , stdenv , cmake +, eigen , fetchFromGitHub , libcifpp , libmcfp @@ -8,24 +9,24 @@ }: let libcifpp' = libcifpp.overrideAttrs (oldAttrs: { - # dssp 4.3.1 requires specific version "5.1.0" of libcifpp - version = "5.1.0"; + # dssp 4.4.3 requires specific version "5.2.0" of libcifpp + version = "5.2.0"; src = fetchFromGitHub { inherit (oldAttrs.src) owner repo rev; - hash = "sha256-PUsi4T6huSqwaa6RnBP1Vj+0a1ePrvrHD0641Lkkc5s="; + hash = "sha256-Sj10j6HxUoUvQ66cd2B8CO7CVBRd7w9CTovxkwPDOvs="; }; }); in stdenv.mkDerivation (finalAttrs: { pname = "dssp"; - version = "4.4.2"; + version = "4.4.3"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = "dssp"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-Gic/rE/G24P5g4Uhf2lcvVa6i/4KGQzCpK4KlpjXcS0="; + hash = "sha256-zPmRR7sxVNErwabLqA5CNMO4K1qHdmC9FBPjcx91KuM="; }; nativeBuildInputs = [ @@ -33,6 +34,7 @@ stdenv.mkDerivation (finalAttrs: { ]; buildInputs = [ + eigen libcifpp' libmcfp zlib diff --git a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix index 2a4df9d21dba..243e067ddec3 100644 --- a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix @@ -1,12 +1,12 @@ { lib, stdenv, fetchurl }: stdenv.mkDerivation rec { - version = "3.3.2"; + version = "3.4"; pname = "hmmer"; src = fetchurl { url = "http://eddylab.org/software/hmmer/${pname}-${version}.tar.gz"; - sha256 = "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj"; + sha256 = "sha256-ynDZT9DPJxvXBjQjqrsRbULeUzEXNDqbJ6ZcF/8G+/M="; }; meta = with lib; { @@ -18,6 +18,7 @@ stdenv.mkDerivation rec { HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute. ''; homepage = "http://hmmer.org/"; + changelog = "https://github.com/EddyRivasLab/hmmer/blob/hmmer-${version}/release-notes/RELEASE-${version}.md"; license = licenses.gpl3; maintainers = [ maintainers.iimog ]; # at least SSE is *required* diff --git a/nixpkgs/pkgs/applications/science/biology/nest/default.nix b/nixpkgs/pkgs/applications/science/biology/nest/default.nix index 90fa69812473..5f0ad540f696 100644 --- a/nixpkgs/pkgs/applications/science/biology/nest/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/nest/default.nix @@ -20,13 +20,13 @@ stdenv.mkDerivation rec { pname = "nest"; - version = "3.5"; + version = "3.6"; src = fetchFromGitHub { owner = "nest"; repo = "nest-simulator"; rev = "v${version}"; - hash = "sha256-PPUIXlU6noJRAa/twNSKVxPgIvbWl0OillEJRDzt+4s="; + hash = "sha256-sXtF4JmHYoLp0t3o4KF6R2E0qLnKrzSPMXOxVJAm+sU="; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix index 5b08fbfd6704..6e5e4feb16fc 100644 --- a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { pname = "neuron"; - version = "8.2.2"; + version = "8.2.3"; # format is for pythonModule conversion format = "other"; @@ -83,7 +83,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://github.com/neuronsimulator/nrn/releases/download/${version}/full-src-package-${version}.tar.gz"; - sha256 = "sha256-orGeBxu3pu4AyAW5P1EGJv8G0dOUZcSOjpUaloqicZU="; + sha256 = "sha256-k8+71BRfh+a73sZho6v0QFRxVmrfx6jqrgaqammdtDI="; }; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix index 04ef7c2e062b..0a18c5f40fda 100644 --- a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "stacks"; - version = "2.62"; + version = "2.65"; src = fetchurl { url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz"; - sha256 = "sha256-7uhQVLC/AEPAPUdm3+vABoIwG4uhNy/EngjsrZjT0Ts="; + sha256 = "sha256-/9a9PWKVq5yJzEUfOF03zR1Hp3AZw9MF8xICoriV4uo="; }; buildInputs = [ zlib ]; @@ -15,5 +15,6 @@ stdenv.mkDerivation rec { homepage = "http://catchenlab.life.illinois.edu/stacks/"; maintainers = [ lib.maintainers.bzizou ]; license = lib.licenses.gpl3Plus; + platforms = lib.platforms.linux; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix index e626af56278f..946f4be60632 100644 --- a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix @@ -1,6 +1,5 @@ { lib , fetchFromGitHub -, fetchpatch , python3Packages , runtimeShell , bcftools @@ -16,37 +15,28 @@ let }; in python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "4.0.0"; + version = "4.1.0"; + pyproject = true; src = fetchFromGitHub { owner = "ACEnglish"; repo = "truvari"; rev = "v${version}"; - hash = "sha256-UJNMKEV5m2jFqnWvkVAtymkcE2TjPIXp7JqRZpMSqsE="; + hash = "sha256-HFVAv1TTL/nMjr62tQKhMdwh25P/y4nBGzSbxoJxMmo="; }; - patches = [ - (fetchpatch { - name = "fix-anno-trf-on-darwin.patch"; - url = "https://github.com/ACEnglish/truvari/commit/f9f36305e8eaa88f951562210e3672a4d4f71265.patch"; - hash = "sha256-7O9jTQDCC2b8hUBm0qJQCYMzTC9NFtn/E0dTHSfJALU="; - }) - (fetchpatch { - name = "fix-anno-grm-on-darwin.patch"; - url = "https://github.com/ACEnglish/truvari/commit/31416552008a506204ed4e2add55474f10392357.patch"; - hash = "sha256-42u0ewZU38GCoSfff+XQFv9hEFeO3WlJufTHcl6vkN4="; - }) - ]; - postPatch = '' - substituteInPlace setup.py \ - --replace "rich==" "rich>=" substituteInPlace truvari/utils.py \ --replace "/bin/bash" "${runtimeShell}" patchShebangs repo_utils/test_files ''; + nativeBuildInputs = [ + python3Packages.setuptools + ]; + propagatedBuildInputs = with python3Packages; [ + pywfa rich edlib pysam @@ -83,6 +73,7 @@ in python3Packages.buildPythonApplication rec { meta = with lib; { description = "Structural variant comparison tool for VCFs"; homepage = "https://github.com/ACEnglish/truvari"; + changelog = "https://github.com/ACEnglish/truvari/releases/tag/${src.rev}"; license = licenses.mit; maintainers = with maintainers; [ natsukium scalavision ]; longDescription = '' diff --git a/nixpkgs/pkgs/applications/science/chemistry/apbs/default.nix b/nixpkgs/pkgs/applications/science/chemistry/apbs/default.nix index 2a892dd56253..f4a2bab4243d 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/apbs/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/apbs/default.nix @@ -65,6 +65,10 @@ stdenv.mkDerivation (finalAttrs: { substituteInPlace CMakeLists.txt \ --replace "include(ImportFETK)" "" \ --replace 'import_fetk(''${FETK_VERSION})' "" + + # U was removed in python 3.11 because it had no effect + substituteInPlace tools/manip/inputgen.py \ + --replace '"rU"' '"r"' ''; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix index 29b983cde536..bb306fa322fe 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix @@ -1,15 +1,53 @@ -{ lib, stdenv, fetchFromGitHub, mpiCheckPhaseHook, python3, gfortran, blas, lapack -, fftw, libint, libvori, libxc, mpi, gsl, scalapack, openssh, makeWrapper -, libxsmm, spglib, which, pkg-config, plumed, zlib +{ lib +, stdenv +, fetchFromGitHub +, mpiCheckPhaseHook +, python3 +, gfortran +, blas +, lapack +, fftw +, libint +, libvori +, libxc +, mpi +, gsl +, scalapack +, openssh +, makeWrapper +, libxsmm +, spglib +, which +, pkg-config +, plumed +, zlib +, hdf5-fortran +, sirius +, libvdwxc +, spla +, spfft , enableElpa ? false , elpa -} : +, gpuBackend ? "none" +, cudaPackages +# gpuVersion needs to be set for both CUDA as well as ROCM hardware. +# gpuArch is only required for the ROCM stack. +# Change to a value suitable for your target GPU. +# For AMD values see https://github.com/cp2k/cp2k/blob/master/INSTALL.md#2v-rocmhip-support-for-amd-gpu +# and for Nvidia see https://github.com/cp2k/cp2k/blob/master/INSTALL.md#2i-cuda-optional-improved-performance-on-gpu-systems +, gpuVersion ? "Mi100" +, gpuArch ? "gfx908" +, rocmPackages +}: + +assert builtins.elem gpuBackend [ "none" "cuda" "rocm" ]; let cp2kVersion = "psmp"; arch = "Linux-x86-64-gfortran"; -in stdenv.mkDerivation rec { +in +stdenv.mkDerivation rec { pname = "cp2k"; version = "2023.2"; @@ -36,7 +74,22 @@ in stdenv.mkDerivation rec { lapack plumed zlib - ] ++ lib.optional enableElpa elpa; + hdf5-fortran + sirius + spla + spfft + libvdwxc + ] + ++ lib.optional enableElpa elpa + ++ lib.optional (gpuBackend == "cuda") cudaPackages.cudatoolkit + ++ lib.optional (gpuBackend == "rocm") [ + rocmPackages.clr + rocmPackages.rocm-core + rocmPackages.hipblas + rocmPackages.hipfft + rocmPackages.rocblas + ] + ; propagatedBuildInputs = [ mpi ]; propagatedUserEnvPkgs = [ mpi ]; @@ -46,7 +99,7 @@ in stdenv.mkDerivation rec { "VERSION=${cp2kVersion}" ]; - doCheck = true; + doCheck = gpuBackend == "none"; enableParallelBuilding = true; @@ -64,25 +117,46 @@ in stdenv.mkDerivation rec { FC = mpif90 LD = mpif90 AR = ar -r + ${lib.strings.optionalString (gpuBackend == "cuda") '' + OFFLOAD_CC = nvcc + OFFLOAD_FLAGS = -O3 -g -w --std=c++11 + OFFLOAD_TARGET = cuda + GPUVER = ${gpuVersion} + CXX = mpicxx + CXXFLAGS = -std=c++11 -fopenmp + ''} + ${lib.strings.optionalString (gpuBackend == "rocm") '' + GPUVER = ${gpuVersion} + OFFLOAD_CC = hipcc + OFFLOAD_FLAGS = -fopenmp -m64 -pthread -fPIC -D__GRID_HIP -O2 --offload-arch=${gpuArch} --rocm-path=${rocmPackages.rocm-core} + OFFLOAD_TARGET = hip + CXX = mpicxx + CXXFLAGS = -std=c++11 -fopenmp -D__HIP_PLATFORM_AMD__ + ''} DFLAGS = -D__FFTW3 -D__LIBXC -D__LIBINT -D__parallel -D__SCALAPACK \ -D__MPI_VERSION=3 -D__F2008 -D__LIBXSMM -D__SPGLIB \ -D__MAX_CONTR=4 -D__LIBVORI ${lib.optionalString enableElpa "-D__ELPA"} \ - -D__PLUMED2 - CFLAGS = -fopenmp + -D__PLUMED2 -D__HDF5 -D__GSL -D__SIRIUS -D__LIBVDWXC -D__SPFFT -D__SPLA \ + ${lib.strings.optionalString (gpuBackend == "cuda") "-D__OFFLOAD_CUDA -D__DBCSR_ACC"} \ + ${lib.strings.optionalString (gpuBackend == "rocm") "-D__OFFLOAD_HIP -D__DBCSR_ACC -D__NO_OFFLOAD_PW"} + CFLAGS = -fopenmp -I${lib.getDev hdf5-fortran}/include -I${lib.getDev gsl}/include FCFLAGS = \$(DFLAGS) -O2 -ffree-form -ffree-line-length-none \ -ftree-vectorize -funroll-loops -msse2 \ -std=f2008 \ -fopenmp -ftree-vectorize -funroll-loops \ - -I${libxc}/include -I${libxsmm}/include \ - -I${libint}/include ${lib.optionalString enableElpa "$(pkg-config --variable=fcflags elpa)"} + -I${lib.getDev libint}/include ${lib.optionalString enableElpa "$(pkg-config --variable=fcflags elpa)"} \ + -I${lib.getDev sirius}/include/sirius \ + -I${lib.getDev libxc}/include -I${lib.getDev libxsmm}/include LIBS = -lfftw3 -lfftw3_threads \ -lscalapack -lblas -llapack \ -lxcf03 -lxc -lxsmmf -lxsmm -lsymspg \ -lint2 -lstdc++ -lvori \ -lgomp -lpthread -lm \ -fopenmp ${lib.optionalString enableElpa "$(pkg-config --libs elpa)"} \ - -lz -ldl -lstdc++ ${lib.optionalString (mpi.pname == "openmpi") "$(mpicxx --showme:link)"} \ - -lplumed + -lz -ldl ${lib.optionalString (mpi.pname == "openmpi") "$(mpicxx --showme:link)"} \ + -lplumed -lhdf5_fortran -lhdf5_hl -lhdf5 -lgsl -lsirius -lspla -lspfft -lvdwxc \ + ${lib.strings.optionalString (gpuBackend == "cuda") "-lcudart -lnvrtc -lcuda -lcublas"} \ + ${lib.strings.optionalString (gpuBackend == "rocm") "-lamdhip64 -lhipfft -lhipblas -lrocblas"} LDFLAGS = \$(FCFLAGS) \$(LIBS) include ${plumed}/lib/plumed/src/lib/Plumed.inc EOF @@ -106,6 +180,7 @@ in stdenv.mkDerivation rec { mkdir -p $out/bin $out/share/cp2k cp exe/${arch}/* $out/bin + rm $out/bin/*_unittest.* for i in cp2k cp2k_shell graph; do wrapProgram $out/bin/$i.${cp2kVersion} \ diff --git a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix index e5807c6c108b..d6d371bf5054 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -21,10 +21,10 @@ in stdenv.mkDerivation rec { pname = "gwyddion"; - version = "2.61"; + version = "2.63"; src = fetchurl { url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz"; - sha256 = "sha256-rDhYVMDTH9mSu90HZAX8ap4HF//8fYhW/ozzJdIrUgo="; + sha256 = "sha256-FSs/Dbnr1shEw/W51DhUFPb61tM+0atc6wxY81EiTdM="; }; nativeBuildInputs = [ pkg-config file ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index 5745b87a777b..f80085278e0a 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.39"; + version = "16.1.41"; 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-${version}-binary.tar.gz"; - hash = "sha256-8M24VXMi7zHkTPNM5zd8nV4J0mXb3/MNIqqxfmlRt9M="; + hash = "sha256-91vPipS5FTqCl7BUSu47aApIfq2e8dD1SW/LEGQWWio="; }; patchPhase = '' diff --git a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix index 0f4d76c3f26b..5f08bebd47fc 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "23.4.0"; + version = "23.12.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "sha256-+jzGcuAcbXOwsyAL+Hr9Fas2vO2S8ZKSaZeCf/bnl7A="; + hash = "sha256-5ycOteXcdgZaeDl3WQ95H2lD0OnnobCbmnVlfYwVdeI="; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/mopac/default.nix b/nixpkgs/pkgs/applications/science/chemistry/mopac/default.nix index d2b2b558bb78..c0cdc4eff410 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/mopac/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/mopac/default.nix @@ -12,13 +12,13 @@ assert blas.isILP64 == lapack.isILP64; stdenv.mkDerivation rec { pname = "mopac"; - version = "22.0.6"; + version = "22.1.0"; src = fetchFromGitHub { owner = "openmopac"; repo = pname; rev = "v${version}"; - hash = "sha256-j4AP3tki+Ep9Pv+pDg8TwCiJvpF2j5npW3Kpat+7gGg="; + hash = "sha256-4jQ0WCHK07CXWUPj5Z1zSXObKxnitMj+FJQbLDiS2Dc="; }; nativeBuildInputs = [ gfortran cmake ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix b/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix index 2a17be9f8a92..062c61fa5c9e 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix @@ -54,13 +54,13 @@ let in stdenv.mkDerivation rec { pname = "nwchem"; - version = "7.2.0"; + version = "7.2.1"; src = fetchFromGitHub { owner = "nwchemgit"; repo = "nwchem"; rev = "v${version}-release"; - hash = "sha256-/biwHOSMGpdnYRGrGlDounKKLVaG2XkBgCmpE0IKR/Y="; + hash = "sha256-nnNTZ+c7VVGAqwOBMkBlW3rImNjs08Ne35XRkI3ssGo="; }; nativeBuildInputs = [ @@ -106,6 +106,9 @@ stdenv.mkDerivation rec { # Overwrite script, skipping the download echo -e '#!/bin/sh\n cd ga-${versionGA};autoreconf -ivf' > src/tools/get-tools-github + # /usr/bin/env bash fails in sandbox/Makefile setting + substituteInPlace src/config/makefile.h --replace '/usr/bin/env bash' "${stdenv.shell}" + patchShebangs ./ ''; @@ -169,7 +172,6 @@ stdenv.mkDerivation rec { cp -r $NWCHEM_TOP/src/data $out/share/nwchem/ cp -r $NWCHEM_TOP/src/basis/libraries $out/share/nwchem/data cp -r $NWCHEM_TOP/src/nwpw/libraryps $out/share/nwchem/data - cp -r $NWCHEM_TOP/QA $out/share/nwchem wrapProgram $out/bin/nwchem \ --set-default NWCHEM_BASIS_LIBRARY $out/share/nwchem/data/libraries/ @@ -196,7 +198,7 @@ stdenv.mkDerivation rec { runHook preInstallCheck # run a simple water test - mpirun -np 2 $out/bin/nwchem $out/share/nwchem/QA/tests/h2o/h2o.nw > h2o.out + mpirun -np 2 $out/bin/nwchem $NWCHEM_TOP/QA/tests/h2o/h2o.nw > h2o.out grep "Total SCF energy" h2o.out | grep 76.010538 runHook postInstallCheck diff --git a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix index 695d5502b5eb..42cf5ddc9511 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -43,14 +43,14 @@ let in stdenv.mkDerivation { pname = "openmolcas"; - version = "23.06"; + version = "23.10"; src = fetchFromGitLab { owner = "Molcas"; repo = "OpenMolcas"; # The tag keeps moving, fix a hash instead - rev = "1cda3772686cbf99a4af695929a12d563c795ca2"; # 2023-06-12 - sha256 = "sha256-DLRQsRy2jt8V8q2sKmv2hLuKCuMihp/+zcMY/3sg1Fk="; + rev = "c74317e68572d1da82fdce4210b005c2c1b1de53"; # 2023-09-25 + hash = "sha256-wBrASZ6YFsWsu/TreEZ6Q+VxNQwCwMpyPC8AOqmNxos="; }; patches = [ @@ -104,7 +104,7 @@ stdenv.mkDerivation { "-DTOOLS=ON" "-DHDF5=ON" "-DFDE=ON" - "-DEXTERNAL_LIBXC=${libxc}" + "-DEXTERNAL_LIBXC=${lib.getDev libxc}" "-DDMRG=ON" "-DNEVPT2=ON" "-DCMAKE_SKIP_BUILD_RPATH=ON" diff --git a/nixpkgs/pkgs/applications/science/chemistry/wxmacmolplt/default.nix b/nixpkgs/pkgs/applications/science/chemistry/wxmacmolplt/default.nix index 4e8dbb6f0768..13bcf2d1dc66 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/wxmacmolplt/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/wxmacmolplt/default.nix @@ -29,6 +29,8 @@ stdenv.mkDerivation rec { xorg.libX11.dev ]; + configureFlags = [ "LDFLAGS=-lGL" ]; + enableParallelBuilding = true; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/base.nix b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/base.nix new file mode 100644 index 000000000000..8ce75a6ce241 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/base.nix @@ -0,0 +1,58 @@ +{ lib +, cppzmq +, curl +, fetchFromGitHub +, glm +, gtkmm3 +, libarchive +, libepoxy +, libgit2 +, librsvg +, libuuid +, opencascade-occt +, pkg-config +, podofo +, sqlite +}: + +# This base is used in horizon-eda and python3Packages.horizon-eda +rec { + pname = "horizon-eda"; + version = "2.5.0"; + + src = fetchFromGitHub { + owner = "horizon-eda"; + repo = "horizon"; + rev = "v${version}"; + hash = "sha256-UcjbDJR6shyETpanNkRoH8LF8r6gFjsyNHVSCMHKqS8="; + }; + + nativeBuildInputs = [ + pkg-config + ]; + + buildInputs = [ + cppzmq + curl + glm + gtkmm3 + libarchive + libepoxy + libgit2 + librsvg + libuuid + opencascade-occt + podofo + sqlite + ]; + + CASROOT = opencascade-occt; + + meta = with lib; { + description = "A free EDA software to develop printed circuit boards"; + homepage = "https://horizon-eda.org"; + maintainers = with maintainers; [ guserav jue89 ]; + license = licenses.gpl3Plus; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix index c4c1e798dd51..1fbc92f06115 100644 --- a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix @@ -1,62 +1,33 @@ { stdenv , boost +, callPackage , coreutils -, cppzmq -, curl -, libepoxy -, fetchFromGitHub -, glm -, gtkmm3 -, lib -, libarchive -, libgit2 -, librsvg , libspnav -, libuuid -, opencascade-occt -, pkg-config -, podofo , python3 -, sqlite , wrapGAppsHook }: +let + base = callPackage ./base.nix { }; +in stdenv.mkDerivation rec { - pname = "horizon-eda"; - version = "2.5.0"; + inherit (base) pname version src meta CASROOT; - src = fetchFromGitHub { - owner = "horizon-eda"; - repo = "horizon"; - rev = "v${version}"; - sha256 = "sha256-UcjbDJR6shyETpanNkRoH8LF8r6gFjsyNHVSCMHKqS8="; + # provide base for python module + passthru = { + inherit base; }; - buildInputs = [ - cppzmq - curl - libepoxy - glm - gtkmm3 - libarchive - libgit2 - librsvg + buildInputs = base.buildInputs ++ [ libspnav - libuuid - opencascade-occt - podofo - python3 - sqlite ]; - nativeBuildInputs = [ + nativeBuildInputs = base.nativeBuildInputs ++ [ boost.dev - pkg-config wrapGAppsHook + python3 ]; - CASROOT = opencascade-occt; - installFlags = [ "INSTALL=${coreutils}/bin/install" "DESTDIR=$(out)" @@ -64,12 +35,4 @@ stdenv.mkDerivation rec { ]; enableParallelBuilding = true; - - meta = with lib; { - description = "A free EDA software to develop printed circuit boards"; - homepage = "https://horizon-eda.org"; - maintainers = with maintainers; [ guserav ]; - license = licenses.gpl3; - platforms = platforms.linux; - }; } diff --git a/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix b/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix index bd824ac28889..dfd679d4d531 100644 --- a/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix @@ -1,21 +1,22 @@ { stdenv, lib, fetchFromGitHub -, qtbase, qttools, cmake, wrapQtAppsHook +, qtbase, qttools, qtquickcontrols2, opencascade-occt, libGLU, libSM, freeimage, cmake, wrapQtAppsHook }: stdenv.mkDerivation rec { pname = "librepcb"; - version = "0.1.7"; + version = "1.0.0"; src = fetchFromGitHub { owner = pname; repo = pname; rev = version; - sha256 = "sha256-zqvvc3CHqdRWVUFt4BkH5Vq50/FKNvMNW2NvGyfWwFM="; + sha256 = "sha256-2o2Gue/RnDWxe8jk/Ehx9CM+B3ac5rEQn0H7yodUEZ8="; fetchSubmodules = true; }; - nativeBuildInputs = [ cmake qttools wrapQtAppsHook ]; + nativeBuildInputs = [ cmake qttools wrapQtAppsHook qtquickcontrols2 opencascade-occt libGLU ]; buildInputs = [ qtbase ]; + propagatedBuildInputs = [ libSM freeimage ]; meta = with lib; { description = "A free EDA software to develop printed circuit boards"; diff --git a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix index 94e0741f79a5..dc4991bf480b 100644 --- a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation rec { pname = "nvc"; - version = "1.10.3"; + version = "1.10.4"; src = fetchFromGitHub { owner = "nickg"; repo = "nvc"; rev = "r${version}"; - hash = "sha256-0KLya2B+gs7aoOvkQdHuJuQtCHLUeSYATToBfIDhm/c="; + hash = "sha256-f4VjSBoJnsGb8MHKegJDlomPG32DuTgFcyv1w0GxKvA="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/geometry/drgeo/default.nix b/nixpkgs/pkgs/applications/science/geometry/drgeo/default.nix deleted file mode 100644 index 0cc8bcb0fb38..000000000000 --- a/nixpkgs/pkgs/applications/science/geometry/drgeo/default.nix +++ /dev/null @@ -1,30 +0,0 @@ -{ lib, stdenv, fetchurl, libglade, gtk2, guile, libxml2, perl -, intltool, libtool, pkg-config }: - -stdenv.mkDerivation rec { - pname = "drgeo"; - version = "1.1.0"; - - hardeningDisable = [ "format" ]; - - src = fetchurl { - url = "mirror://sourceforge/ofset/${pname}-${version}.tar.gz"; - sha256 = "05i2czgzhpzi80xxghinvkyqx4ym0gm9f38fz53idjhigiivp4wc"; - }; - patches = [ ./struct.patch ]; - - nativeBuildInputs = [ pkg-config intltool ]; - buildInputs = [libglade gtk2 guile libxml2 - perl libtool ]; - - prebuild = '' - cp drgeo.desktop.in drgeo.desktop - ''; - - meta = with lib; { - description = "Interactive geometry program"; - homepage = "https://sourceforge.net/projects/ofset"; - license = licenses.gpl2; - platforms = platforms.linux; - }; -} diff --git a/nixpkgs/pkgs/applications/science/geometry/drgeo/struct.patch b/nixpkgs/pkgs/applications/science/geometry/drgeo/struct.patch deleted file mode 100644 index 7364cae5f58d..000000000000 --- a/nixpkgs/pkgs/applications/science/geometry/drgeo/struct.patch +++ /dev/null @@ -1,68 +0,0 @@ --- drgeo-1.1.0/debian/patches/00list -++ drgeo-1.1.0/debian/patches/00list -@ -7 +7 @@ - -07-fix_ftbfs-gcc-4.5.dpatch -nly in patch2: -nchanged: --- drgeo-1.1.0.orig/debian/patches/07-fix_ftbfs-gcc-4.5.dpatch -++ drgeo-1.1.0/debian/patches/07-fix_ftbfs-gcc-4.5.dpatch -@ -0,0 +1,58 @@ -#! /bin/sh /usr/share/dpatch/dpatch-run -## 07-fix_ftbfs-gcc-4.5.dpatch by Fabrice Coutadeur <fabric...@ubuntu.com> -## -## Description: fix FTBFS with gcc 4.5 with undefined reference to -## `drgeoDialogData' -## Author: Petr Gajdos <pgaj...@suse.cz> -## Origin: https://build.opensuse.org/package/files?package=drgeo&project=openSUSE%3A11.3%3AContrib - -...@dpatch@ -diff -urNad '--exclude=CVS' '--exclude=.svn' '--exclude=.git' '--exclude=.arch' '--exclude=.hg' '--exclude=_darcs' '--exclude=.bzr' drgeo-1.1.0~/geo/drgeo_dialog.cc drgeo-1.1.0/geo/drgeo_dialog.cc ---- drgeo-1.1.0~/geo/drgeo_dialog.cc 2003-10-27 10:17:25.000000000 +0000 -+++ drgeo-1.1.0/geo/drgeo_dialog.cc 2010-11-13 07:26:03.258908003 +0000 -@@ -38,12 +38,7 @@ - // Used in the style dialod callback, I know it's ugly, but so easy - static drgeoFigure *selected_figure; - --struct --{ -- drgeoPoint mouse; -- drgeoFigure *figure; --} --drgeoDialogData; -+DialogData drgeoDialogData; - - - static void drgeo_edit_dialog_cb (GtkWidget * dialog, -diff -urNad '--exclude=CVS' '--exclude=.svn' '--exclude=.git' '--exclude=.arch' '--exclude=.hg' '--exclude=_darcs' '--exclude=.bzr' drgeo-1.1.0~/geo/drgeo_dialog.h drgeo-1.1.0/geo/drgeo_dialog.h ---- drgeo-1.1.0~/geo/drgeo_dialog.h 2003-06-12 22:30:23.000000000 +0000 -+++ drgeo-1.1.0/geo/drgeo_dialog.h 2010-11-13 07:26:03.258908003 +0000 -@@ -34,4 +34,11 @@ - } - - #endif /* __cplusplus */ -+ -+typedef struct -+{ -+ drgeoPoint mouse; -+ drgeoFigure *figure; -+} DialogData; -+ - #endif -diff -urNad '--exclude=CVS' '--exclude=.svn' '--exclude=.git' '--exclude=.arch' '--exclude=.hg' '--exclude=_darcs' '--exclude=.bzr' drgeo-1.1.0~/geo/drgeo_figure.cc drgeo-1.1.0/geo/drgeo_figure.cc ---- drgeo-1.1.0~/geo/drgeo_figure.cc 2005-07-14 07:30:01.000000000 +0000 -+++ drgeo-1.1.0/geo/drgeo_figure.cc 2010-11-13 07:26:03.258908003 +0000 -@@ -48,12 +48,7 @@ - #include "drgeo_dialog.h" - #include "traite.h" - --extern struct --{ -- drgeoPoint mouse; -- drgeoFigure *figure; --} --drgeoDialogData; -+extern DialogData drgeoDialogData; - - typedef struct drgeoSearchValue - { diff --git a/nixpkgs/pkgs/applications/science/geometry/gama/default.nix b/nixpkgs/pkgs/applications/science/geometry/gama/default.nix index 728cbe62292d..790a9b2d216e 100644 --- a/nixpkgs/pkgs/applications/science/geometry/gama/default.nix +++ b/nixpkgs/pkgs/applications/science/geometry/gama/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, lib, expat, octave, libxml2, texinfo, zip }: stdenv.mkDerivation rec { pname = "gama"; - version = "2.25"; + version = "2.26"; src = fetchurl { url = "mirror://gnu/${pname}/${pname}-${version}.tar.gz"; - sha256 = "sha256-1j4fsPQEaftqmrdk6ZPWKSl7ywA/UPN8bdddGVlPxDQ="; + sha256 = "sha256-8zKPPpbp66tD2zMmcv2H5xeCSdDhUk0uYPhqwpGqx9Y="; }; buildInputs = [ expat ]; diff --git a/nixpkgs/pkgs/applications/science/logic/abc/default.nix b/nixpkgs/pkgs/applications/science/logic/abc/default.nix index 1062582d82c4..1d4a11bfb3f2 100644 --- a/nixpkgs/pkgs/applications/science/logic/abc/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/abc/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { pname = "abc-verifier"; - version = "unstable-2023-06-28"; + version = "unstable-2023-09-13"; src = fetchFromGitHub { owner = "yosyshq"; repo = "abc"; - rev = "bb64142b07794ee685494564471e67365a093710"; - hash = "sha256-Qkk61Lh84ervtehWskSB9GKh+JPB7mI1IuG32OSZMdg="; + rev = "daad9ede0137dc58487a0abc126253e671a85b14"; + hash = "sha256-5XeFYvdqT08xduFUDC5yK1jEOV1fYzyQD7N9ZmG3mpQ="; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix index ce084c1f4a73..bc8c6ae48587 100644 --- a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix @@ -1,47 +1,35 @@ -{ fetchFromGitHub, fetchpatch, lib, which, ocamlPackages }: +{ fetchurl, fetchpatch, lib, ocamlPackages }: let pname = "alt-ergo"; - version = "2.4.3"; + version = "2.5.2"; - configureScript = "ocaml unix.cma configure.ml"; - - src = fetchFromGitHub { - owner = "OCamlPro"; - repo = pname; - rev = "refs/tags/${version}"; - hash = "sha256-2XARGr8rLiPMOM0rBBoRv5tZvKYtkLkJctGqLYkMe7Q="; + src = fetchurl { + url = "https://github.com/OCamlPro/alt-ergo/releases/download/v${version}/alt-ergo-${version}.tbz"; + hash = "sha256-9GDBcBH49sheO5AjmDsznMEbw0JSrnSOcIIRN40/aJU="; }; in let alt-ergo-lib = ocamlPackages.buildDunePackage rec { pname = "alt-ergo-lib"; - inherit version src configureScript; - configureFlags = [ pname ]; - nativeBuildInputs = [ which ]; - buildInputs = with ocamlPackages; [ dune-configurator ]; - propagatedBuildInputs = with ocamlPackages; [ dune-build-info num ocplib-simplex seq stdlib-shims zarith ]; - preBuild = '' - substituteInPlace src/lib/util/version.ml --replace 'version="dev"' 'version="${version}"' - ''; + inherit version src; + buildInputs = with ocamlPackages; [ ppx_blob ]; + propagatedBuildInputs = with ocamlPackages; [ camlzip dolmen_loop dune-build-info fmt ocplib-simplex seq stdlib-shims zarith ]; }; in let alt-ergo-parsers = ocamlPackages.buildDunePackage rec { pname = "alt-ergo-parsers"; - inherit version src configureScript; - configureFlags = [ pname ]; - nativeBuildInputs = [ which ocamlPackages.menhir ]; - propagatedBuildInputs = [ alt-ergo-lib ] ++ (with ocamlPackages; [ camlzip psmt2-frontend ]); + inherit version src; + nativeBuildInputs = [ ocamlPackages.menhir ]; + propagatedBuildInputs = [ alt-ergo-lib ] ++ (with ocamlPackages; [ psmt2-frontend ]); }; in ocamlPackages.buildDunePackage { - inherit pname version src configureScript; - - configureFlags = [ pname ]; + inherit pname version src; - nativeBuildInputs = [ which ocamlPackages.menhir ]; - buildInputs = [ alt-ergo-parsers ocamlPackages.cmdliner ]; + nativeBuildInputs = [ ocamlPackages.menhir ]; + buildInputs = [ alt-ergo-parsers ] ++ (with ocamlPackages; [ cmdliner dune-site ]); meta = { description = "High-performance theorem prover and SMT solver"; diff --git a/nixpkgs/pkgs/applications/science/logic/beluga/default.nix b/nixpkgs/pkgs/applications/science/logic/beluga/default.nix index 3cb06c4e7b14..693be7f33886 100644 --- a/nixpkgs/pkgs/applications/science/logic/beluga/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/beluga/default.nix @@ -2,13 +2,13 @@ ocamlPackages.buildDunePackage rec { pname = "beluga"; - version = "1.1"; + version = "1.1.1"; src = fetchFromGitHub { owner = "Beluga-lang"; repo = "Beluga"; rev = "refs/tags/v${version}"; - hash = "sha256-0E7rmiLmQPfOAQ1qKiqxeLdqviVl+Thkl6KfOWkGZRc="; + hash = "sha256-l/C77czLtlLnpadVx4d9ve9jv/e11jsOgzrbXt+Zo5s="; }; duneVersion = "3"; diff --git a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix index a49aea8d40c8..9bfadc41f609 100644 --- a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cadical"; - version = "1.5.3"; + version = "1.8.0"; src = fetchFromGitHub { owner = "arminbiere"; repo = "cadical"; rev = "rel-${version}"; - sha256 = "sha256-3H/vowWfE1jfomYg2hOi3B3zjWa4CaLHAJXnoKWzskU="; + sha256 = "sha256-hY7+gTwBqQegbm5RjLKhM2vfBOjIRz797Z6wd6usj9s="; }; outputs = [ "out" "dev" "lib" ]; diff --git a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix index c5e263c319e6..0645fd29522f 100644 --- a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix @@ -8,13 +8,13 @@ stdenv.mkDerivation rec { pname = "cryptominisat"; - version = "5.11.12"; + version = "5.11.14"; src = fetchFromGitHub { owner = "msoos"; repo = "cryptominisat"; rev = version; - hash = "sha256-1AJx8gPf+qDpAp0p4cfCObKZDWKDAKdGopllr2ajpHw="; + hash = "sha256-p/sVinjEh078PGtJ6JBRA8EmrJVcchBs9L3bRZvCHuo="; }; buildInputs = [ python3 boost ]; diff --git a/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix index f056b3e433fb..66ba807c8dd8 100644 --- a/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix @@ -2,31 +2,42 @@ stdenv.mkDerivation rec { pname = "cryptoverif"; - version = "2.05"; + version = "2.07"; src = fetchurl { url = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${version}.tar.gz"; - sha256 = "sha256-F5eVN5ATYo9Ivpi2eYh96ktuTWUeoqgWMR4BqHu8EFs="; + hash = "sha256-GXXql4+JZ396BM6W2I3kN0u59xos7UCAtzR0IjMIETY="; }; - strictDeps = true; - - nativeBuildInputs = [ ocaml ]; - /* Fix up the frontend to load the 'default' cryptoverif library ** from under $out/libexec. By default, it expects to find the files ** in $CWD which doesn't work. */ - patchPhase = '' + postPatch = '' substituteInPlace ./src/syntax.ml \ --replace \"default\" \"$out/libexec/default\" ''; - buildPhase = "./build"; + strictDeps = true; + + nativeBuildInputs = [ ocaml ]; + + buildPhase = '' + runHook preBuild + + ./build + + runHook postBuild + ''; + installPhase = '' + runHook preInstall + mkdir -p $out/bin $out/libexec cp ./cryptoverif $out/bin cp ./default.cvl $out/libexec cp ./default.ocvl $out/libexec + + runHook postInstall ''; meta = { diff --git a/nixpkgs/pkgs/applications/science/logic/dafny/default.nix b/nixpkgs/pkgs/applications/science/logic/dafny/default.nix index 2b30d3aeeb45..7da1958af386 100644 --- a/nixpkgs/pkgs/applications/science/logic/dafny/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/dafny/default.nix @@ -8,28 +8,36 @@ buildDotnetModule rec { pname = "Dafny"; - version = "4.2.0"; + version = "4.3.0"; src = fetchFromGitHub { owner = "dafny-lang"; repo = "dafny"; rev = "v${version}"; - sha256 = "sha256-RSGaOgGf3m94t3SKnvSPqz0VHhWr6NmIMtGsmOynMaM="; + hash = "sha256-bnKaaqh1/921SRwnwqgYb31SJ8vguEBtzywPTz79S6I="; }; - postPatch = '' - cp ${writeScript "fake-gradlew-for-dafny" '' - mkdir -p build/libs/ - javac $(find -name "*.java" | grep "^./src/main") -d classes - jar cf build/libs/DafnyRuntime-${version}.jar -C classes dafny - ''} Source/DafnyRuntime/DafnyRuntimeJava/gradlew - - # Needed to fix - # "error NETSDK1129: The 'Publish' target is not supported without specifying a target framework. The current project targets multiple frameworks, you must specify the framework for the published application." - substituteInPlace Source/DafnyRuntime/DafnyRuntime.csproj \ - --replace TargetFrameworks TargetFramework \ - --replace "netstandard2.0;net452" net6.0 - ''; + postPatch = + # This version number seems to be hardcoded and didn't get updated with the + # version bump from 4.2.0 to 4.3.0. + let dafnyRuntimeJarVersion = "4.2.0"; + in '' + cp ${ + writeScript "fake-gradlew-for-dafny" '' + mkdir -p build/libs/ + javac $(find -name "*.java" | grep "^./src/main") -d classes + jar cf build/libs/DafnyRuntime-${dafnyRuntimeJarVersion}.jar -C classes dafny + ''} Source/DafnyRuntime/DafnyRuntimeJava/gradlew + + # Needed to fix + # "error NETSDK1129: The 'Publish' target is not supported without + # specifying a target framework. The current project targets multiple + # frameworks, you must specify the framework for the published + # application." + substituteInPlace Source/DafnyRuntime/DafnyRuntime.csproj \ + --replace TargetFrameworks TargetFramework \ + --replace "netstandard2.0;net452" net6.0 + ''; buildInputs = [ jdk11 ]; nugetDeps = ./deps.nix; diff --git a/nixpkgs/pkgs/applications/science/logic/easycrypt/default.nix b/nixpkgs/pkgs/applications/science/logic/easycrypt/default.nix index abd2b0cb2758..32243455ae5f 100644 --- a/nixpkgs/pkgs/applications/science/logic/easycrypt/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/easycrypt/default.nix @@ -1,25 +1,16 @@ -{ lib, stdenv, fetchFromGitHub, fetchpatch, ocamlPackages, why3 }: +{ lib, stdenv, fetchFromGitHub, ocamlPackages, why3 }: stdenv.mkDerivation rec { pname = "easycrypt"; - version = "2022.04"; + version = "2023.09"; src = fetchFromGitHub { owner = pname; repo = pname; rev = "r${version}"; - sha256 = "sha256:09rdwcj70lkamkhd895p284rfpz4bcnsf55mcimhiqncd2a21ml7"; + hash = "sha256-9xavU9jRisZekPqC87EyiLXtZCGu/9QeGzq6BJGt1+Y="; }; - patches = lib.lists.map fetchpatch [ - # Fix build with Why3 1.5 - { url = "https://github.com/EasyCrypt/easycrypt/commit/d226387432deb7f22738e1d5579346a2cbc9be7a.patch"; - hash = "sha256:1zvxij35fnr3h9b5wdl8ml17aqfx3a39rd4mgwmdvkapbg3pa4lm"; } - # Fix build with Why3 1.6 - { url = "https://github.com/EasyCrypt/easycrypt/commit/876f2ed50a0434afdf2fb20e7c50b8a3e26bb06e.patch"; - hash = "sha256-UycfLZWYHNsppb7qHSRaAF4Y0UnwoFueEG0wUcBUPYE="; } - ]; - nativeBuildInputs = with ocamlPackages; [ dune_3 findlib diff --git a/nixpkgs/pkgs/applications/science/logic/kissat/default.nix b/nixpkgs/pkgs/applications/science/logic/kissat/default.nix index 5f982508c8c6..2941952287be 100644 --- a/nixpkgs/pkgs/applications/science/logic/kissat/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/kissat/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { pname = "kissat"; - version = "3.1.0"; + version = "3.1.1"; src = fetchFromGitHub { owner = "arminbiere"; repo = "kissat"; rev = "rel-${version}"; - sha256 = "sha256-AFUVkkD+toOfVEvIKfz3ncEdABLRxs9yQ8aJx6Q0ETM="; + sha256 = "sha256-zK20/vhbVihrxmd52DjByDUO99pBAr8SlJtQpX5fmwY="; }; outputs = [ "out" "dev" "lib" ]; diff --git a/nixpkgs/pkgs/applications/science/logic/lean4/default.nix b/nixpkgs/pkgs/applications/science/logic/lean4/default.nix index 7509ca63c804..12465ad9087f 100644 --- a/nixpkgs/pkgs/applications/science/logic/lean4/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/lean4/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "lean4"; - version = "4.0.0"; + version = "4.1.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "lean4"; rev = "v${version}"; - hash = "sha256-3Ni+NiD0iSsOruUyRpBd+aC0TZNYfOLhwqCpPHPruPg="; + hash = "sha256-6qbCafG0bL5KxQt2gL6hV4PFDsEMM0UXfldeOOqxsaE="; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/logic/surelog/default.nix b/nixpkgs/pkgs/applications/science/logic/surelog/default.nix index d8c762de60c1..5c7be408bf4a 100644 --- a/nixpkgs/pkgs/applications/science/logic/surelog/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/surelog/default.nix @@ -11,17 +11,18 @@ , uhdm , antlr4 , capnproto +, nlohmann_json }: stdenv.mkDerivation (finalAttrs: { pname = "surelog"; - version = "1.73"; + version = "1.76"; src = fetchFromGitHub { owner = "chipsalliance"; repo = finalAttrs.pname; rev = "v${finalAttrs.version}"; - hash = "sha256-z47Eqs3fP53pbEb3s66CqMiO4UpEwox+fKakxtRBakQ="; + hash = "sha256-Vg9NZrgzFRVIsEbZQe8DItDhFOVG1XZoQWBrLzVNwLU="; fetchSubmodules = false; # we use all dependencies from nix }; @@ -43,6 +44,7 @@ stdenv.mkDerivation (finalAttrs: { uhdm capnproto antlr4.runtime.cpp + nlohmann_json ]; cmakeFlags = [ @@ -50,6 +52,7 @@ stdenv.mkDerivation (finalAttrs: { "-DSURELOG_USE_HOST_UHDM=On" "-DSURELOG_USE_HOST_GTEST=On" "-DSURELOG_USE_HOST_ANTLR=On" + "-DSURELOG_USE_HOST_JSON=On" "-DANTLR_JAR_LOCATION=${antlr4.jarLocation}" ]; diff --git a/nixpkgs/pkgs/applications/science/logic/uhdm/default.nix b/nixpkgs/pkgs/applications/science/logic/uhdm/default.nix index c1acd79dcab0..7312f989cb66 100644 --- a/nixpkgs/pkgs/applications/science/logic/uhdm/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/uhdm/default.nix @@ -9,13 +9,14 @@ stdenv.mkDerivation (finalAttrs: { pname = "UHDM"; - version = "1.73"; + # When updating this package, also consider updating science/logic/surelog + version = "1.76"; src = fetchFromGitHub { owner = "chipsalliance"; repo = finalAttrs.pname; rev = "v${finalAttrs.version}"; - hash = "sha256-VmRn51UrJTGEG4n2fi5kRv8khXakfGbqMtYPejsZCBI="; + hash = "sha256-Q/u5lvILYDT5iScES3CTPIm/B5apoOHXOQmCsZ73NlU="; fetchSubmodules = false; # we use all dependencies from nix }; diff --git a/nixpkgs/pkgs/applications/science/math/calc/default.nix b/nixpkgs/pkgs/applications/science/math/calc/default.nix index 0c70a6e03b2c..4cfc4fb182b8 100644 --- a/nixpkgs/pkgs/applications/science/math/calc/default.nix +++ b/nixpkgs/pkgs/applications/science/math/calc/default.nix @@ -10,14 +10,14 @@ stdenv.mkDerivation (finalAttrs: { pname = "calc"; - version = "2.14.3.5"; + version = "2.15.0.1"; src = fetchurl { urls = [ "https://github.com/lcn2/calc/releases/download/v${finalAttrs.version}/calc-${finalAttrs.version}.tar.bz2" "http://www.isthe.com/chongo/src/calc/calc-${finalAttrs.version}.tar.bz2" ]; - hash = "sha256-4eXs6NDfsJO5Vr9Mo2jC16hTRAyt++1s+Z/JrWDKwUk="; + hash = "sha256-u/mt9y4805IWYDdEHz94dPb4V+d4YVrrhzz8v3B+q24="; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/math/cntk/default.nix b/nixpkgs/pkgs/applications/science/math/cntk/default.nix deleted file mode 100644 index 91d208a56ede..000000000000 --- a/nixpkgs/pkgs/applications/science/math/cntk/default.nix +++ /dev/null @@ -1,134 +0,0 @@ -{ lib, stdenv, fetchFromGitHub, cmake -, fetchpatch -, openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi -, onebitSGDSupport ? false -, config -, cudaSupport ? config.cudaSupport, cudaPackages ? { }, addOpenGLRunpath, cudatoolkit, nvidia_x11 -, cudnnSupport ? cudaSupport -}: - -let - inherit (cudaPackages) cudatoolkit cudnn; -in - -assert cudnnSupport -> cudaSupport; -assert blas.implementation == "openblas" && lapack.implementation == "openblas"; - -let - # Old specific version required for CNTK. - cub = fetchFromGitHub { - owner = "NVlabs"; - repo = "cub"; - rev = "1.7.4"; - sha256 = "0ksd5n1lxqhm5l5cd2lps4cszhjkf6gmzahaycs7nxb06qci8c66"; - }; - -in stdenv.mkDerivation rec { - pname = "CNTK"; - version = "2.7"; - - src = fetchFromGitHub { - owner = "Microsoft"; - repo = "CNTK"; - rev = "v${version}"; - sha256 = "sha256-2rIrPJyvZhnM5EO6tNhF6ARTocfUHce4N0IZk/SZiaI="; - fetchSubmodules = true; - }; - - patches = [ - # Fix build with protobuf 3.18+ - # Remove with onnx submodule bump to 1.9+ - (fetchpatch { - url = "https://github.com/onnx/onnx/commit/d3bc82770474761571f950347560d62a35d519d7.patch"; - extraPrefix = "Source/CNTKv2LibraryDll/proto/onnx/onnx_repo/"; - stripLen = 1; - sha256 = "00raqj8wx30b06ky6cdp5vvc1mrzs7hglyi6h58hchw5lhrwkzxp"; - }) - ]; - - postPatch = '' - # Fix build with protobuf 3.18+ - substituteInPlace Source/CNTKv2LibraryDll/Serialization.cpp \ - --replace 'SetTotalBytesLimit(INT_MAX, INT_MAX)' \ - 'SetTotalBytesLimit(INT_MAX)' \ - --replace 'SetTotalBytesLimit(limit, limit)' \ - 'SetTotalBytesLimit(limit)' - ''; - - nativeBuildInputs = [ cmake ] ++ lib.optional cudaSupport addOpenGLRunpath; - - # Force OpenMPI to use g++ in PATH. - OMPI_CXX = "g++"; - - # Uses some deprecated tensorflow functions - env.NIX_CFLAGS_COMPILE = "-Wno-error=deprecated-declarations"; - - buildInputs = [ openblas opencv3 libzip boost protobuf mpi ] - ++ lib.optional cudaSupport cudatoolkit - ++ lib.optional cudnnSupport cudnn; - - configureFlags = [ - "--with-opencv=${opencv3}" - "--with-libzip=${libzip.dev}" - "--with-openblas=${openblas.dev}" - "--with-boost=${boost.dev}" - "--with-protobuf=${protobuf}" - "--with-mpi=${mpi}" - "--cuda=${if cudaSupport then "yes" else "no"}" - # FIXME - "--asgd=no" - ] ++ lib.optionals cudaSupport [ - "--with-cuda=${cudatoolkit}" - "--with-gdk-include=${cudatoolkit}/include" - "--with-gdk-nvml-lib=${nvidia_x11}/lib" - "--with-cub=${cub}" - ] ++ lib.optional onebitSGDSupport "--1bitsgd=yes"; - - configurePhase = '' - sed -i \ - -e 's,^GIT_STATUS=.*,GIT_STATUS=,' \ - -e 's,^GIT_COMMIT=.*,GIT_COMMIT=v${version},' \ - -e 's,^GIT_BRANCH=.*,GIT_BRANCH=v${version},' \ - -e 's,^BUILDER=.*,BUILDER=nixbld,' \ - -e 's,^BUILDMACHINE=.*,BUILDMACHINE=machine,' \ - -e 's,^BUILDPATH=.*,BUILDPATH=/homeless-shelter,' \ - -e '/git does not exist/d' \ - Tools/generate_build_info - - patchShebangs . - mkdir build - cd build - ${lib.optionalString cudnnSupport '' - mkdir cuda - ln -s ${cudnn}/include cuda - export configureFlags="$configureFlags --with-cudnn=$PWD" - ''} - - ../configure $configureFlags - ''; - - installPhase = '' - mkdir -p $out/bin - # Moving to make patchelf remove references later. - mv lib $out - cp bin/cntk $out/bin - ''; - - postFixup = lib.optionalString cudaSupport '' - for lib in $out/lib/*; do - addOpenGLRunpath "$lib" - done - ''; - - meta = with lib; { - homepage = "https://github.com/Microsoft/CNTK"; - description = "An open source deep-learning toolkit"; - license = if onebitSGDSupport then licenses.unfreeRedistributable else licenses.mit; - platforms = [ "x86_64-linux" ]; - maintainers = with maintainers; [ abbradar ]; - # Newer cub is included with cudatoolkit now and it breaks the build. - # https://github.com/Microsoft/CNTK/issues/3191 - # broken = cudaSupport; - broken = true; # at 2022-11-23 - }; -} diff --git a/nixpkgs/pkgs/applications/science/math/ginac/default.nix b/nixpkgs/pkgs/applications/science/math/ginac/default.nix index 057b242e609b..d9d12cbf388d 100644 --- a/nixpkgs/pkgs/applications/science/math/ginac/default.nix +++ b/nixpkgs/pkgs/applications/science/math/ginac/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "ginac"; - version = "1.8.6"; + version = "1.8.7"; src = fetchurl { url = "https://www.ginac.de/ginac-${version}.tar.bz2"; - sha256 = "sha256-ALMgsRFsrlt7QzZNv/t5EkcdFx9ITYJ2RgXXFYWNl1s="; + sha256 = "sha256-cf9PLYoA5vB86P7mm3bcweu7cnvmdgtYfB+7XM97Yeo="; }; propagatedBuildInputs = [ cln ]; diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix index f245e8745b4a..ade614c89b0f 100644 --- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -1,19 +1,20 @@ -{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, curl, wrapGAppsHook }: +{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, curl, wrapGAppsHook, desktopToDarwinBundle }: stdenv.mkDerivation (finalAttrs: { pname = "qalculate-gtk"; - version = "4.8.0"; + version = "4.8.1"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${finalAttrs.version}"; - sha256 = "sha256-GYy3Ot2vjXpCp89Rib3Ua0XeVGOOTejKcaqNZvPmxm0="; + sha256 = "sha256-bG0hui5GjHWHny/8Rq5sZGz3s5rYnYlpc+K8I/LwDto="; }; hardeningDisable = [ "format" ]; - nativeBuildInputs = [ intltool pkg-config autoreconfHook wrapGAppsHook ]; + nativeBuildInputs = [ intltool pkg-config autoreconfHook wrapGAppsHook ] + ++ lib.optionals stdenv.isDarwin [ desktopToDarwinBundle ]; buildInputs = [ libqalculate gtk3 curl ]; enableParallelBuilding = true; diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix index 34d2d98171eb..adc43b5f9dab 100644 --- a/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix +++ b/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "qalculate-qt"; - version = "4.8.0"; + version = "4.8.1"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-qt"; rev = "v${finalAttrs.version}"; - hash = "sha256-7VlaoiY+HgHCMZCegUdy2wpgfx3fKaViMtkdNRleHaA="; + hash = "sha256-hH+orU+5PmPcrhkLKCdsDhVCrD8Mvxp2RPTGSlsUP7Y="; }; nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ]; diff --git a/nixpkgs/pkgs/applications/science/math/sage/README.md b/nixpkgs/pkgs/applications/science/math/sage/README.md index c4de5da45dbf..35e8d0deeffb 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/README.md +++ b/nixpkgs/pkgs/applications/science/math/sage/README.md @@ -2,7 +2,7 @@ Sage is a pretty complex package that depends on many other complex packages and patches some of those. As a result, the sage nix package is also quite complex. -Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most importent ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package. +Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most important ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package. ## The sage build is broken diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix index 9fe07603fe7d..8064a965bd1f 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix @@ -110,6 +110,13 @@ stdenv.mkDerivation rec { url = "https://github.com/sagemath/sage/commit/d88bc3815c0901bfdeaa3e4a31107c084199f614.diff"; sha256 = "sha256-dXaEwk2wXxmx02sCw4Vu9mF0ZrydhFD4LRwNAiQsPgM="; }) + + # https://github.com/sagemath/sage/pull/36279, landed in 10.2.beta4 + (fetchpatch { + name = "matplotlib-3.8-upgrade.patch"; + url = "https://github.com/sagemath/sage/commit/0fcf88935908440930c5f79202155aca4ad57518.diff"; + sha256 = "sha256-mvqAHaTCXsxPv901L8HSTnrfghfXYdq0wfLoP/cYQZI="; + }) ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix index d8d5586e2193..f8beabaac1ff 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix @@ -78,6 +78,7 @@ , sphinx , sympy , typing-extensions +, nbclassic }: assert (!blas.isILP64) && (!lapack.isILP64); @@ -181,6 +182,8 @@ buildPythonPackage rec { sphinx sympy typing-extensions + + nbclassic ]; preBuild = '' diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix index 6dc630181be2..993bc26bba28 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix @@ -2,6 +2,7 @@ , lib , callPackage , fetchurl +, fetchpatch , makeWrapper , cmake , coreutils @@ -109,6 +110,18 @@ stdenv.mkDerivation rec { patches = [ ./sw_vers.patch + # glibc >=2.38 already has strlcat implemented. + # merged upstream, remove on next package bump. + (fetchpatch { + url = "https://github.com/root-project/root/commit/8fb0e35446ed67c9d56639b4708c8f05459b7f84.patch"; + hash = "sha256-7EabmYanqlQsYSQsi+S9eWs1v1pY6MncopL420Y3D4w="; + }) + ] ++ lib.optionals (python.pkgs.pythonAtLeast "3.11") [ + # Fix build against Python 3.11 + (fetchpatch { + url = "https://github.com/root-project/root/commit/484deb056dacf768aba4954073b41105c431bffc.patch"; + hash = "sha256-4qur2e3SxMIPgOg4IjlvuULR2BObuP7xdvs+LmNT2/s="; + }) ]; preConfigure = '' diff --git a/nixpkgs/pkgs/applications/science/misc/tulip/default.nix b/nixpkgs/pkgs/applications/science/misc/tulip/default.nix index a2d3f3d9a2aa..947cc2c7c3bb 100644 --- a/nixpkgs/pkgs/applications/science/misc/tulip/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/tulip/default.nix @@ -1,26 +1,32 @@ -{ fetchurl, lib, stdenv, libxml2, freetype, libGLU, libGL, glew -, qtbase, wrapQtAppsHook, python3 -, cmake, libjpeg }: +{ lib, stdenv, fetchurl, libxml2, freetype, libGLU, libGL, glew +, qtbase, wrapQtAppsHook, autoPatchelfHook, python3 +, cmake, libjpeg, llvmPackages }: stdenv.mkDerivation rec { pname = "tulip"; - version = "5.6.1"; + version = "5.7.2"; src = fetchurl { - url = "mirror://sourceforge/auber/${pname}-${version}_src.tar.gz"; - sha256 = "1fy3nvgxv3igwc1d23zailcgigj1d0f2kkh7a5j24c0dyqz5zxmw"; + url = "mirror://sourceforge/auber/tulip-${version}_src.tar.gz"; + hash = "sha256-b+XFCS6Ks+EpwxgYFzWdRomfCpHXmZHXnrQM+ZSLN/0="; }; - buildInputs = [ libxml2 freetype glew libGLU libGL libjpeg qtbase python3 ]; - nativeBuildInputs = [ cmake wrapQtAppsHook ]; + nativeBuildInputs = [ cmake wrapQtAppsHook ] + ++ lib.optionals stdenv.isLinux [ autoPatchelfHook ]; + + buildInputs = [ libxml2 freetype glew libjpeg qtbase python3 ] + ++ lib.optionals stdenv.isDarwin [ llvmPackages.openmp ] + ++ lib.optionals stdenv.isLinux [ libGLU libGL ]; qtWrapperArgs = [ ''--prefix PATH : ${lib.makeBinPath [ python3 ]}'' ]; + # error: format string is not a string literal (potentially insecure) + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-Wno-format-security"; + # FIXME: "make check" needs Docbook's DTD 4.4, among other things. doCheck = false; meta = { - broken = (stdenv.isLinux && stdenv.isAarch64); description = "A visualization framework for the analysis and visualization of relational data"; longDescription = @@ -36,6 +42,6 @@ stdenv.mkDerivation rec { license = lib.licenses.gpl3Plus; maintainers = [ ]; - platforms = lib.platforms.gnu ++ lib.platforms.linux; # arbitrary choice + platforms = lib.platforms.all; }; } diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index f6301ff6fce6..2ca47d812bbf 100644 --- a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -20,13 +20,17 @@ let in stdenv.mkDerivation rec { pname = "gromacs"; - version = "2023.2"; + version = "2023.3"; src = fetchurl { url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz"; - sha256 = "sha256-vOFIByfksruQBBO3XZmjJm81B4d9pPWy1JHfeY+fza4="; + sha256 = "sha256-Tsj40MevdrE/j9FtuOLBIOdJ3kOa6VVNn2U/gS140cs="; }; + patches = [ ./pkgconfig.patch ]; + + outputs = [ "out" "dev" "man" ]; + nativeBuildInputs = [ cmake ]; buildInputs = [ @@ -64,10 +68,8 @@ in stdenv.mkDerivation rec { ] ) ++ lib.optional enableCuda "-DGMX_GPU=CUDA"; - postFixup = '' - substituteInPlace "$out"/lib/pkgconfig/*.pc \ - --replace '=''${prefix}//' '=/' \ - --replace "$out/$out/" "$out/" + postInstall = '' + moveToOutput share/cmake $dev ''; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/pkgconfig.patch b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/pkgconfig.patch new file mode 100644 index 000000000000..6740d2312369 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/pkgconfig.patch @@ -0,0 +1,24 @@ +diff --git a/src/external/muparser/muparser.pc.in b/src/external/muparser/muparser.pc.in +index 646787cb53..9b97ad57f7 100644 +--- a/src/external/muparser/muparser.pc.in ++++ b/src/external/muparser/muparser.pc.in +@@ -1,7 +1,5 @@ +-prefix=@CMAKE_INSTALL_PREFIX@ +-exec_prefix=${prefix} +-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@ +-includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@ ++libdir=@CMAKE_INSTALL_FULL_LIBDIR@ ++includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@ + + Name: @PACKAGE_NAME@ + Description: Mathematical expressions parser library +diff --git a/src/gromacs/libgromacs.pc.cmakein b/src/gromacs/libgromacs.pc.cmakein +index ec1ed6684e..ca1105474a 100644 +--- a/src/gromacs/libgromacs.pc.cmakein ++++ b/src/gromacs/libgromacs.pc.cmakein +@@ -1,4 +1,4 @@ +-libdir=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@ ++libdir=@CMAKE_INSTALL_FULL_LIBDIR@ + + Name: libgromacs@GMX_LIBS_SUFFIX@ + Description: Gromacs library diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/lammps/default.nix index f11e9bdeeb13..7924d044c2ab 100644 --- a/nixpkgs/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -44,15 +44,16 @@ }: stdenv.mkDerivation (finalAttrs: { - # LAMMPS has weird versioning converted to ISO 8601 format - version = "2Aug2023"; + # LAMMPS has weird versioning convention. Updates should go smoothly with: + # nix-update --commit lammps --version-regex 'stable_(.*)' + version = "2Aug2023_update1"; pname = "lammps"; src = fetchFromGitHub { owner = "lammps"; repo = "lammps"; rev = "stable_${finalAttrs.version}"; - hash = "sha256-6T4YAa4iN3pJpODGPW+faR16xxyYYdkHLavtiPUbZ4o="; + hash = "sha256-Zmn87a726qdidBfyvJlYleYv9jqyFAakxjGrg3lipc0="; }; preConfigure = '' cd cmake diff --git a/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix b/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix index 41a0e00ae784..e63203a93f28 100644 --- a/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix @@ -1,14 +1,14 @@ -{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, pkg-config, libGL, libGLU, opencascade, libsForQt5, tbb, vtkWithQt5 }: +{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, pkg-config, libGL, libGLU, opencascade-occt, libsForQt5, tbb, vtkWithQt5 }: stdenv.mkDerivation rec { pname = "elmerfem"; - version = "unstable-2023-02-03"; + version = "unstable-2023-09-18"; src = fetchFromGitHub { owner = "elmercsc"; repo = pname; - rev = "39c8784b6e4543a6bf560b5d597e0eec1eb06343"; - hash = "sha256-yyxgFvlS+I4PouDL6eD4ZrXuONTDejCSYKq2AwQ0Iug="; + rev = "0fcced06f91c93f44557efd6a5f10b2da5c7066c"; + hash = "sha256-UuARDYW7D3a4dB6I86s2Ed5ecQxc+Y/es3YIeF2VyTc="; }; hardeningDisable = [ "format" ]; @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { libsForQt5.qwt libGL libGLU - opencascade + opencascade-occt tbb vtkWithQt5 ]; |