diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
29 files changed, 257 insertions, 183 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/kalign/default.nix b/nixpkgs/pkgs/applications/science/biology/kalign/default.nix index b28c640cb7aa..3ca83978d969 100644 --- a/nixpkgs/pkgs/applications/science/biology/kalign/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/kalign/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "kalign"; - version = "3.3.5"; + version = "3.4.0"; src = fetchFromGitHub { owner = "TimoLassmann"; repo = "kalign"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-QufTiaiRcNOnLhOO4cnOE9bNcj9mlCg/ERFIHJB8KOU="; + hash = "sha256-QcFNaCTqj6CFiOzQ6ezfBL0mu8PDU11hyNdkcsLOPzA="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix index 7cf1560d2492..607b1ee51cc5 100644 --- a/nixpkgs/pkgs/applications/science/biology/last/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1499"; + version = "1518"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-uofXtGGDloM1FxW0PYKKwfDOPlAJiapGVKwd1clFzp8="; + hash = "sha256-a6i5BfJhVHkXTLd7SVFxISEB+Kwl7BhjUUkF8ItMOak="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/poretools/default.nix b/nixpkgs/pkgs/applications/science/biology/poretools/default.nix index efbedf9a121a..47ffd507efda 100644 --- a/nixpkgs/pkgs/applications/science/biology/poretools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/poretools/default.nix @@ -11,12 +11,13 @@ python2Packages.buildPythonPackage rec { sha256 = "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"; }; - propagatedBuildInputs = [python2Packages.h5py python2Packages.matplotlib python2Packages.seaborn python2Packages.pandas]; + 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]; + maintainers = [ lib.maintainers.rybern ]; + broken = true; # Build error: h5py-3.9.0 not supported for interpreter python2.7 }; } diff --git a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix index 9730601e4e7d..ad6c0d9e5a4c 100644 --- a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix @@ -1,4 +1,4 @@ -{lib, stdenv, fetchFromGitHub, cmake, zlib, python2}: +{lib, stdenv, fetchFromGitHub, fetchpatch, cmake, boost, zlib, python2}: stdenv.mkDerivation rec { pname = "strelka"; @@ -11,8 +11,28 @@ stdenv.mkDerivation rec { sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf"; }; + patches = [ + # Pull pending fix for gcc-12: + # https://github.com/Illumina/strelka/pull/204 + (fetchpatch { + name = "limits.patch"; + url = "https://github.com/Illumina/strelka/commit/98272cd345c6e4c672e6a5b7721204fcac0502d6.patch"; + hash = "sha256-psBiuN32nvwZ+QX51JQjIdRhEE3k7PfwbkD10ckqvZk="; + }) + ]; + + postPatch = '' + substituteInPlace src/cmake/boost.cmake \ + --replace "1.58.0" "${boost.version}" \ + --replace "Boost_USE_STATIC_LIBS ON" "Boost_USE_STATIC_LIBS OFF" + ''; + nativeBuildInputs = [ cmake ]; - buildInputs = [ zlib python2 ]; + buildInputs = [ boost zlib python2 ]; + + cmakeFlags = [ + "-DCMAKE_CXX_STANDARD=14" + ]; env.NIX_CFLAGS_COMPILE = toString [ "-Wno-error=maybe-uninitialized" @@ -37,7 +57,7 @@ stdenv.mkDerivation rec { license = licenses.gpl3; homepage = "https://github.com/Illumina/strelka"; maintainers = with maintainers; [ jbedo ]; - platforms = [ "x86_64-linux" ]; + platforms = platforms.linux; }; } diff --git a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix index 5794d7077af9..59ff285c1537 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -68,7 +68,6 @@ stdenv.mkDerivation rec { license = lib.licenses.gpl2; platforms = with lib.platforms; linux ++ darwin; maintainers = [ lib.maintainers.cge ]; - # never built on aarch64-darwin since first introduction in nixpkgs - broken = stdenv.isDarwin && stdenv.isAarch64; + broken = true; # Build error: h5py-3.9.0 not supported for interpreter python2.7 }; } diff --git a/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix index 9933d0d8c727..4c4482919772 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/quantum-espresso/default.nix @@ -1,41 +1,119 @@ { lib , stdenv , fetchFromGitLab +, fetchFromGitHub +, fetchurl +, git +, cmake +, gnum4 , gfortran +, pkg-config , fftw , blas , lapack -, useMpi ? false +, scalapack +, wannier90 +, hdf5 +, libmbd +, libxc +, enableMpi ? true , mpi }: +assert ! blas.isILP64; +assert ! lapack.isILP64; + +let + # "rev"s must exactly match the git submodule commits in the QE repo + gitSubmodules = { + devxlib = fetchFromGitLab { + group = "max-centre"; + owner = "components"; + repo = "devicexlib"; + rev = "a6b89ef77b1ceda48e967921f1f5488d2df9226d"; + hash = "sha256-p3fRplVG4YSN6ILNlOwf+aSEhpTJPXqiS1+wnzWVA2U="; + }; + + pw2qmcpack = fetchFromGitHub { + owner = "QMCPACK"; + repo = "pw2qmcpack"; + rev = "f72ab25fa4ea755c1b4b230ae8074b47d5509c70"; + hash = "sha256-K1Z90xexsUvk4SdEb8FGryRal0GAFoLz3j1h/RT2nYw="; + }; + }; + +in stdenv.mkDerivation rec { - version = "6.6"; + version = "7.2"; pname = "quantum-espresso"; src = fetchFromGitLab { owner = "QEF"; repo = "q-e"; rev = "qe-${version}"; - sha256 = "1mkfmw0fq1dabplzdn6v1abhw0ds55gzlvbx3a9brv493whk21yp"; + hash = "sha256-0q0QWX4BVjVHjcbKOBpjbBADuL+2S5LAALyrxmjVs4c="; }; - passthru = { - inherit mpi; - }; + # add git submodules manually and fix pkg-config file + prePatch = '' + chmod -R +rwx external/ + + substituteInPlace external/devxlib.cmake \ + --replace "qe_git_submodule_update(external/devxlib)" "" + substituteInPlace external/CMakeLists.txt \ + --replace "qe_git_submodule_update(external/pw2qmcpack)" "" \ + --replace "qe_git_submodule_update(external/d3q)" "" \ + --replace "qe_git_submodule_update(external/qe-gipaw)" "" - preConfigure = '' - patchShebangs configure + ${builtins.toString (builtins.attrValues + (builtins.mapAttrs + (name: val: '' + cp -r ${val}/* external/${name}/. + chmod -R +rwx external/${name} + '') + gitSubmodules + ) + )} + + substituteInPlace cmake/quantum_espresso.pc.in \ + --replace 'libdir="''${prefix}/@CMAKE_INSTALL_LIBDIR@"' 'libdir="@CMAKE_INSTALL_FULL_LIBDIR@"' ''; - nativeBuildInputs = [ gfortran ]; + passthru = { inherit mpi; }; + + nativeBuildInputs = [ + cmake + gfortran + git + pkg-config + ]; - buildInputs = [ fftw blas lapack ] - ++ (lib.optionals useMpi [ mpi ]); + buildInputs = [ + fftw + blas + lapack + wannier90 + libmbd + libxc + hdf5 + ] ++ lib.optional enableMpi scalapack; - configureFlags = if useMpi then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ]; + propagatedBuildInputs = lib.optional enableMpi mpi; + propagatedUserEnvPkgs = lib.optional enableMpi mpi; - makeFlags = [ "all" ]; + cmakeFlags = [ + "-DBUILD_SHARED_LIBS=ON" + "-DWANNIER90_ROOT=${wannier90}" + "-DMBD_ROOT=${libmbd}" + "-DQE_ENABLE_OPENMP=ON" + "-DQE_ENABLE_LIBXC=ON" + "-DQE_ENABLE_HDF5=ON" + "-DQE_ENABLE_PLUGINS=pw2qmcpack" + ] ++ lib.optionals enableMpi [ + "-DQE_ENABLE_MPI=ON" + "-DQE_ENABLE_MPI_MODULE=ON" + "-DQE_ENABLE_SCALAPACK=ON" + ]; meta = with lib; { description = "Electronic-structure calculations and materials modeling at the nanoscale"; diff --git a/nixpkgs/pkgs/applications/science/electronics/csxcad/default.nix b/nixpkgs/pkgs/applications/science/electronics/csxcad/default.nix index f6b0ff93fff5..abdb0716f370 100644 --- a/nixpkgs/pkgs/applications/science/electronics/csxcad/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/csxcad/default.nix @@ -13,13 +13,13 @@ stdenv.mkDerivation rec { pname = "csxcad"; - version = "unstable-2022-05-18"; + version = "0.6.3"; src = fetchFromGitHub { owner = "thliebig"; repo = "CSXCAD"; - rev = "cd9decb4d9cebe3c8bf115e2c0ee73f730f22da1"; - sha256 = "1604amhvp7dm8ych7gwzxwawqvb9hpjglk5ffd4qm0y3k6r89arn"; + rev = "v${version}"; + sha256 = "sha256-SSV5ulx3rCJg99I/oOQbqe+gOSs+BfcCo6UkWHVhnSs="; }; patches = [./searchPath.patch ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/flatcam/shapely-library-paths.patch b/nixpkgs/pkgs/applications/science/electronics/flatcam/shapely-library-paths.patch deleted file mode 100644 index d095eada9d6e..000000000000 --- a/nixpkgs/pkgs/applications/science/electronics/flatcam/shapely-library-paths.patch +++ /dev/null @@ -1,31 +0,0 @@ -diff --git a/shapely/geos.py b/shapely/geos.py -index 88c5f53..1ccd6e4 100644 ---- a/shapely/geos.py -+++ b/shapely/geos.py -@@ -96,6 +96,7 @@ if sys.platform.startswith('linux'): - alt_paths = [ - 'libgeos_c.so.1', - 'libgeos_c.so', -+ '@libgeos_c@', - ] - _lgeos = load_dll('geos_c', fallbacks=alt_paths) - -@@ -160,6 +161,7 @@ elif sys.platform == 'darwin': - "/usr/local/lib/libgeos_c.dylib", - # homebrew Apple Silicon - "/opt/homebrew/lib/libgeos_c.dylib", -+ "@libgeos_c@", - ] - _lgeos = load_dll('geos_c', fallbacks=alt_paths) - -diff --git a/tests/test_dlls.py b/tests/test_dlls.py -index c71da8e..c36262c 100644 ---- a/tests/test_dlls.py -+++ b/tests/test_dlls.py -@@ -18,4 +18,5 @@ class LoadingTestCase(unittest.TestCase): - '/opt/homebrew/lib/libgeos_c.dylib', # homebrew (macOS) - os.path.join(sys.prefix, "lib", "libgeos_c.so"), # anaconda (Linux) - 'libgeos_c.so.1', -- 'libgeos_c.so']) -+ 'libgeos_c.so', -+ '@libgeos_c@']) diff --git a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix index dc4991bf480b..284a0b15830b 100644 --- a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation rec { pname = "nvc"; - version = "1.10.4"; + version = "1.11.0"; src = fetchFromGitHub { owner = "nickg"; repo = "nvc"; rev = "r${version}"; - hash = "sha256-f4VjSBoJnsGb8MHKegJDlomPG32DuTgFcyv1w0GxKvA="; + hash = "sha256-95vIyBQ38SGpI+gnDqK1MRRzOT6uiYjDr1c//folqZ8="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/electronics/openems/default.nix b/nixpkgs/pkgs/applications/science/electronics/openems/default.nix index 083f01a42881..864b120993d9 100644 --- a/nixpkgs/pkgs/applications/science/electronics/openems/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/openems/default.nix @@ -18,15 +18,15 @@ , hyp2mat }: -stdenv.mkDerivation { +stdenv.mkDerivation rec { pname = "openems"; - version = "unstable-2020-02-15"; + version = "0.0.36"; src = fetchFromGitHub { owner = "thliebig"; repo = "openEMS"; - rev = "ba793ac84e2f78f254d6d690bb5a4c626326bbfd"; - sha256 = "1dca6b6ccy771irxzsj075zvpa3dlzv4mjb8xyg9d889dqlgyl45"; + rev = "v${version}"; + sha256 = "sha256-wdH+Zw7G2ZigzBMX8p3GKdFVx/AhbTNL+P3w+YjI/dc="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix index 0645fd29522f..a028803db139 100644 --- a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix @@ -8,13 +8,13 @@ stdenv.mkDerivation rec { pname = "cryptominisat"; - version = "5.11.14"; + version = "5.11.15"; src = fetchFromGitHub { owner = "msoos"; repo = "cryptominisat"; rev = version; - hash = "sha256-p/sVinjEh078PGtJ6JBRA8EmrJVcchBs9L3bRZvCHuo="; + hash = "sha256-OenuIPo5U0+egWMpxfaKWPLbO5YRQJSXLYptih+ZQQ0="; }; buildInputs = [ python3 boost ]; diff --git a/nixpkgs/pkgs/applications/science/logic/eprover/default.nix b/nixpkgs/pkgs/applications/science/logic/eprover/default.nix index ec1fc6b11d25..d4a8b7a6b2e8 100644 --- a/nixpkgs/pkgs/applications/science/logic/eprover/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/eprover/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "eprover"; - version = "3.0"; + version = "3.0.03"; src = fetchurl { url = "https://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_${version}/E.tgz"; - hash = "sha256-gBgDC+GH948JMsjzo/SOpWDzJXu0g58YX1VW28PeorI="; + hash = "sha256-cS5zUe2N9Kd9uzbNpeBtvLbgUN0c3N3tGcYczK3KsdQ="; }; buildInputs = [ which ]; diff --git a/nixpkgs/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix b/nixpkgs/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix index 7587c4638c18..d9b8dd5cf28f 100644 --- a/nixpkgs/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix +++ b/nixpkgs/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "isabelle-linter"; - version = "1.2.1"; + version = "2023-1.0.0"; src = fetchFromGitHub { owner = "isabelle-prover"; repo = "isabelle-linter"; - rev = "Isabelle2022-v${version}"; - sha256 = "sha256-qlojNCsm3/49TtAVq6J31BbQipdIoDcn71pBotZyquY="; + rev = "Isabelle2023-v1.0.0"; + sha256 = "sha256-q9+qN94NaTzvhbcNQj7yH/VVfs1QgCH8OU8HW+5+s9U="; }; nativeBuildInputs = [ isabelle ]; diff --git a/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix b/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix index 2cb96bbc0a37..edc4483bcfa9 100644 --- a/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix @@ -46,7 +46,7 @@ let }; in stdenv.mkDerivation (finalAttrs: rec { pname = "isabelle"; - version = "2022"; + version = "2023"; dirname = "Isabelle${version}"; @@ -56,18 +56,18 @@ in stdenv.mkDerivation (finalAttrs: rec { fetchurl { url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_macos.tar.gz"; - sha256 = "0b84rx9b7b5y8m1sg7xdp17j6yngd2dkx6v5bkd8h7ly102lai18"; + sha256 = "sha256-0VSW2SrHNI3/k4cCCZ724ruXaq7W1NCPsLrXFZ9l1/Q="; } else if stdenv.hostPlatform.isx86 then fetchurl { url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_linux.tar.gz"; - sha256 = "1ih4gykkp1an43qdgc5xzyvf30fhs0dah3y0a5ksbmvmjsfnxyp7"; + sha256 = "sha256-Go4ZCsDz5gJ7uWG5VLrNJOddMPX18G99FAadpX53Rqg="; } else fetchurl { url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_linux_arm.tar.gz"; - hash = "sha256-qI/BR/KZwLjnkO5q/yYeW4lN4xyUe78VOM2INC/Z/io="; + hash = "sha256-Tzxxs0gKw6vymbaXIzH8tK5VgUrpOIp9vcWQ/zxnRCc="; }; nativeBuildInputs = [ java ]; @@ -134,8 +134,7 @@ in stdenv.mkDerivation (finalAttrs: rec { substituteInPlace src/Tools/Setup/src/Environment.java \ --replace 'cmd.add("/usr/bin/env");' "" \ - --replace 'cmd.add("bash");' "cmd.add(\"$SHELL\");" \ - --replace 'private static read_file(path: Path): String =' 'private static String read_file(Path path) throws IOException' + --replace 'cmd.add("bash");' "cmd.add(\"$SHELL\");" substituteInPlace src/Pure/General/sha1.ML \ --replace '"$ML_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so")' '"${sha1}/lib/libsha1.so"' diff --git a/nixpkgs/pkgs/applications/science/logic/naproche/default.nix b/nixpkgs/pkgs/applications/science/logic/naproche/default.nix index ecc347080081..f6743745a7b6 100644 --- a/nixpkgs/pkgs/applications/science/logic/naproche/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/naproche/default.nix @@ -2,13 +2,13 @@ with haskellPackages; mkDerivation { pname = "Naproche-SAD"; - version = "2022-10-24"; + version = "unstable-2023-07-11"; src = fetchFromGitHub { owner = "naproche"; repo = "naproche"; - rev = "c8c4ca2d5fdb92bf17e0e54c99bd2a9691255d80"; - sha256 = "0xvh6kkl5k5ygp2nrbq3k0snvzczbmcp1yrwdkah3fzhf9i3yykx"; + rev = "4c399d49a86987369bec6e1ac5ae3739cd6db0a8"; + sha256 = "sha256-Ji6yxbDEcwuYAzIZwK5sHNltK1WBFBfpyoEtoID/U4k="; }; isExecutable = true; diff --git a/nixpkgs/pkgs/applications/science/logic/z3/default.nix b/nixpkgs/pkgs/applications/science/logic/z3/default.nix index 6165cfe8bd22..26848e1397aa 100644 --- a/nixpkgs/pkgs/applications/science/logic/z3/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/z3/default.nix @@ -24,7 +24,7 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: inherit version sha256 patches; src = fetchFromGitHub { owner = "Z3Prover"; - repo = pname; + repo = "z3"; rev = "${tag}-${version}"; sha256 = sha256; }; diff --git a/nixpkgs/pkgs/applications/science/math/caffe/default.nix b/nixpkgs/pkgs/applications/science/math/caffe/default.nix index 42c160393595..6595f0b846dd 100644 --- a/nixpkgs/pkgs/applications/science/math/caffe/default.nix +++ b/nixpkgs/pkgs/applications/science/math/caffe/default.nix @@ -26,24 +26,17 @@ let # The default for cudatoolkit 10.1 is CUDNN 8.0.5, the last version to support CUDA 10.1. # However, this caffe does not build with CUDNN 8.x, so we use CUDNN 7.6.5 instead. # Earlier versions of cudatoolkit use pre-8.x CUDNN, so we use the default. - cudnn = if lib.versionOlder cudatoolkit.version "10.1" - then cudaPackages.cudnn - else cudaPackages.cudnn_7_6; -in - -assert leveldbSupport -> (leveldb != null && snappy != null); -assert cudnnSupport -> cudaSupport; -assert ncclSupport -> cudaSupport; -assert pythonSupport -> (python != null && numpy != null); + hasCudnn = + if lib.versionOlder cudatoolkit.version "10.1" + then cudaPackages ? cudnn + else cudaPackages ? cudnn_7_6; -let toggle = bool: if bool then "ON" else "OFF"; test_model_weights = fetchurl { url = "http://dl.caffe.berkeleyvision.org/bvlc_reference_caffenet.caffemodel"; sha256 = "472d4a06035497b180636d8a82667129960371375bd10fcb6df5c6c7631f25e0"; }; - in stdenv.mkDerivation rec { @@ -74,7 +67,8 @@ stdenv.mkDerivation rec { buildInputs = [ boost gflags glog protobuf hdf5-cpp opencv4 blas ] ++ lib.optional cudaSupport cudatoolkit - ++ lib.optional cudnnSupport cudnn + ++ lib.optional (lib.versionOlder cudatoolkit.version "10.1" && hasCudnn) cudaPackages.cudnn + ++ lib.optional (lib.versionAtLeast cudatoolkit.version "10.1" && hasCudnn) cudaPackages.cudnn_7_6 ++ lib.optional lmdbSupport lmdb ++ lib.optional ncclSupport nccl ++ lib.optionals leveldbSupport [ leveldb snappy ] @@ -154,7 +148,14 @@ stdenv.mkDerivation rec { ''; homepage = "http://caffe.berkeleyvision.org/"; maintainers = with maintainers; [ ]; - broken = (pythonSupport && (python.isPy310)) || cudaSupport; + broken = + (pythonSupport && (python.isPy310)) + || cudaSupport + || !(leveldbSupport -> (leveldb != null && snappy != null)) + || !(cudnnSupport -> (hasCudnn && cudaSupport)) + || !(ncclSupport -> cudaSupport) + || !(pythonSupport -> (python != null && numpy != null)) + ; license = licenses.bsd2; platforms = platforms.linux ++ platforms.darwin; }; diff --git a/nixpkgs/pkgs/applications/science/math/calc/default.nix b/nixpkgs/pkgs/applications/science/math/calc/default.nix index 86ec445d9b3e..0f8982eac5b9 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 = "2.15.0.1"; + version = "2.15.0.2"; 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-u/mt9y4805IWYDdEHz94dPb4V+d4YVrrhzz8v3B+q24="; + hash = "sha256-dPEj32SiR7RhI9fBa9ny9+EEuuiXS2WswRcDVuOMJXc="; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/math/cbc/default.nix b/nixpkgs/pkgs/applications/science/math/cbc/default.nix index 1909e4bb1d04..fb92b1cc98fb 100644 --- a/nixpkgs/pkgs/applications/science/math/cbc/default.nix +++ b/nixpkgs/pkgs/applications/science/math/cbc/default.nix @@ -13,7 +13,8 @@ stdenv.mkDerivation rec { }; # or-tools has a hard dependency on Cbc static libraries, so we build both - configureFlags = [ "-C" "--enable-static" ]; + configureFlags = [ "-C" "--enable-static" ] + ++ lib.optionals stdenv.cc.isClang [ "CXXFLAGS=-std=c++14" ]; enableParallelBuilding = true; diff --git a/nixpkgs/pkgs/applications/science/math/clp/default.nix b/nixpkgs/pkgs/applications/science/math/clp/default.nix index 52a74ff3979c..4cfff4702e69 100644 --- a/nixpkgs/pkgs/applications/science/math/clp/default.nix +++ b/nixpkgs/pkgs/applications/science/math/clp/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { license = licenses.epl20; homepage = "https://github.com/coin-or/Clp"; description = "An open-source linear programming solver written in C++"; - platforms = platforms.darwin ++ [ "x86_64-linux" ]; + platforms = platforms.darwin ++ platforms.linux; maintainers = [ maintainers.vbgl ]; }; } diff --git a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix index 1e80d9a06eba..a2743b163247 100644 --- a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix +++ b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2023-11-17"; + version = "unstable-2023-12-12"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "b0d822f10243ad5b1c88efb5a82b43a0bbf1bfbc"; - hash = "sha256-eJ/EmzV5UZGxwZNIna/XXkYY+vkLc610KcywBFPRfyM="; + rev = "bec2c9bd0750ec7970f6c701e619565c9d348e84"; + hash = "sha256-+VohU8mkFjZ0zhjmri0KY1kTzPLn2q5Au4nEBdXcR+8="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix index ade614c89b0f..0c859fd95bea 100644 --- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "qalculate-gtk"; - version = "4.8.1"; + version = "4.9.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${finalAttrs.version}"; - sha256 = "sha256-bG0hui5GjHWHny/8Rq5sZGz3s5rYnYlpc+K8I/LwDto="; + hash = "sha256-rQxOOxM4TazkDs/H3KEPbdo6WBl0ptyAlZwv8nnGMss="; }; hardeningDisable = [ "format" ]; @@ -23,6 +23,7 @@ stdenv.mkDerivation (finalAttrs: { homepage = "http://qalculate.github.io"; maintainers = with maintainers; [ gebner doronbehar alyaeanyx ]; license = licenses.gpl2Plus; + mainProgram = "qalculate-gtk"; platforms = platforms.all; }; }) diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix index adc43b5f9dab..9932c7c2dcd9 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 = "4.8.1"; + version = "4.9.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-qt"; rev = "v${finalAttrs.version}"; - hash = "sha256-hH+orU+5PmPcrhkLKCdsDhVCrD8Mvxp2RPTGSlsUP7Y="; + hash = "sha256-Ac8RRxLheaenlR7JqKzfBpPxsq7PHfE9qXFf3Vx4GSg="; }; nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ]; @@ -31,6 +31,7 @@ stdenv.mkDerivation (finalAttrs: { homepage = "http://qalculate.github.io"; maintainers = with maintainers; [ _4825764518 ]; license = licenses.gpl2Plus; + mainProgram = "qalculate-qt"; platforms = platforms.unix; }; }) diff --git a/nixpkgs/pkgs/applications/science/math/yacas/fix-test-script.patch b/nixpkgs/pkgs/applications/science/math/yacas/fix-test-script.patch deleted file mode 100644 index da85f0dc0e1b..000000000000 --- a/nixpkgs/pkgs/applications/science/math/yacas/fix-test-script.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git i/tests/test-yacas w/tests/test-yacas -index b375d78b..0e3a616b 100755 ---- i/tests/test-yacas -+++ w/tests/test-yacas -@@ -35,9 +35,9 @@ FAILED_TESTS="" # list of failed tests - FAILURES=0 # number of failed tests - TOTALTESTS=0 # total number of tests - --TESTFILE=/tmp/test-yacas.$$ --TIMEFILE=/tmp/time-yacas.$$ --VERSIONF=/tmp/version-yacas-$$.ys -+TESTFILE="$(mktemp -t test-yacas.XXX)" -+TIMEFILE="$(mktemp -t time-yacas.XXX)" -+VERSIONF="$(mktemp -t version-yacas-XXX.ys)" - LOGFILE=yacas-logfile.txt - echo "Print(Version());" > $VERSIONF - VERSION=`$CMD $VERSIONF` -@@ -69,7 +69,7 @@ for scr in $SCRIPTS; do - # fi - echo "Running $scr" - if [ -f $TESTFILE ]; then rm $TESTFILE ; fi -- /bin/bash -c "time -p ($CMD $f || echo \"Error: exit status $?\") | tee $TESTFILE" \ -+ bash -c "time -p ($CMD $f || echo \"Error: exit status $?\") | tee $TESTFILE" \ - 2> $TIMEFILE \ - || (echo "Error -- User interrupt" > $TESTFILE) - # cat $TIMEFILE diff --git a/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix b/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix index cdc083a467d8..f61fe5b01857 100644 --- a/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix +++ b/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix @@ -1,8 +1,11 @@ { lib -, stdenv +, buildFHSEnv , fetchFromGitHub -, scons +, ocl-icd , openssl +, scons +, stdenv +, extraPkgs ? [ ] }: let version = "8.1.18"; @@ -14,57 +17,64 @@ let hash = "sha256-G0rknVmZiyC4sRTOowFjf7EQ5peGf+HLPPcLWXXFlX4="; }; - fah-web-client-bastetSrc = fetchFromGitHub { - owner = "foldingathome"; - repo = "fah-web-client-bastet"; - rev = "v${version}"; - hash = lib.fakeHash; - }; -in -stdenv.mkDerivation { - pname = "fah-client"; - inherit version; - - src = fetchFromGitHub { - owner = "FoldingAtHome"; - repo = "fah-client-bastet"; - rev = "v${version}"; - hash = "sha256-IgT/5NqCwN8N8OObjtASuT4IRb2EN4bdixxUdjiyddI="; - }; + fah-client = stdenv.mkDerivation { + pname = "fah-client"; + inherit version; - nativeBuildInputs = [ scons ]; + src = fetchFromGitHub { + owner = "FoldingAtHome"; + repo = "fah-client-bastet"; + rev = "v${version}"; + hash = "sha256-IgT/5NqCwN8N8OObjtASuT4IRb2EN4bdixxUdjiyddI="; + }; - buildInputs = [ openssl ]; + nativeBuildInputs = [ scons ]; - postUnpack = '' - export CBANG_HOME=$NIX_BUILD_TOP/cbang + buildInputs = [ openssl ]; - cp -r --no-preserve=mode ${cbangSrc} $CBANG_HOME - ''; + postUnpack = '' + export CBANG_HOME=$NIX_BUILD_TOP/cbang - preBuild = '' - scons -C $CBANG_HOME - ''; + cp -r --no-preserve=mode ${cbangSrc} $CBANG_HOME + ''; + + preBuild = '' + scons -C $CBANG_HOME + ''; + + installPhase = '' + runHook preInstall + + mkdir -p $out/{bin,share/applications,share/feh-client} - installPhase = '' - runHook preInstall + cp fah-client $out/bin/fah-client - mkdir -p $out/{bin,share/applications,share/feh-client} + cp install/lin/fah-client.desktop $out/share/applications/ + cp -r images $out/share/feh-client/ - cp fah-client $out/bin/fah-client + sed -e "s|Icon=.*|Icon=$out/share/feh-client/images/fahlogo.png|g" -i $out/share/applications/fah-client.desktop + + runHook postInstall + ''; + + }; +in +buildFHSEnv { + name = fah-client.name; - cp install/lin/fah-client.desktop $out/share/applications/ - cp -r images $out/share/feh-client/ + targetPkgs = _: [ fah-client ocl-icd ] ++ extraPkgs; - sed -e "s|Icon=.*|Icon=$out/share/feh-client/images/fahlogo.png|g" -i $out/share/applications/fah-client.desktop + runScript = "/bin/fah-client"; - runHook postInstall + extraInstallCommands = '' + mv $out/bin/$name $out/bin/fah-client ''; meta = { description = "Folding@home client"; homepage = "https://foldingathome.org/"; license = lib.licenses.gpl3; + mainProgram = "fah-client"; maintainers = [ lib.maintainers.zimbatm ]; platforms = [ "x86_64-linux" ]; }; diff --git a/nixpkgs/pkgs/applications/science/misc/root/5.nix b/nixpkgs/pkgs/applications/science/misc/root/5.nix index 2d830e3d1016..dfe7b5eca97f 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/5.nix +++ b/nixpkgs/pkgs/applications/science/misc/root/5.nix @@ -155,7 +155,7 @@ stdenv.mkDerivation rec { homepage = "https://root.cern.ch/"; description = "A data analysis framework"; platforms = platforms.unix; - broken = !stdenv.isx86_64; + broken = !stdenv.isx86_64 || stdenv.cc.isClang or false; maintainers = with maintainers; [ veprbl ]; license = licenses.lgpl21; }; diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix index 3f3b64069bb1..24844eb621ec 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix @@ -58,7 +58,7 @@ stdenv.mkDerivation rec { pname = "root"; - version = "6.28.08"; + version = "6.28.10"; passthru = { tests = import ./tests { inherit callPackage; }; @@ -66,7 +66,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://root.cern.ch/download/root_v${version}.source.tar.gz"; - hash = "sha256-o+ZLTAH4fNm75X5h75a0FibkmwRGCVBw1B2b+6NSaGI="; + hash = "sha256-adb962B+ayC9AsdX+mIXAkwLYTLB6bHf9Nhdmiu35R4="; }; nativeBuildInputs = [ makeWrapper cmake pkg-config git ]; diff --git a/nixpkgs/pkgs/applications/science/misc/toil/default.nix b/nixpkgs/pkgs/applications/science/misc/toil/default.nix index 7fc070f4f9f7..9142676fff48 100644 --- a/nixpkgs/pkgs/applications/science/misc/toil/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/toil/default.nix @@ -6,21 +6,16 @@ python3.pkgs.buildPythonApplication rec { pname = "toil"; - version = "5.7.1"; + version = "5.12.0"; format = "setuptools"; src = fetchFromGitHub { owner = "DataBiosphere"; repo = pname; rev = "refs/tags/releases/${version}"; - hash = "sha256-m+XvNyzd0ly2YqKhgxezgGaCXLs3CmupJMnp5RIZqNI="; + hash = "sha256-cTpbQo9tPZifUO59vbnIa3XUinFJ2/5Slfe4yszglFM="; }; - postPatch = '' - substituteInPlace requirements.txt \ - --replace "docker>=3.7.2, <6" "docker" - ''; - propagatedBuildInputs = with python3.pkgs; [ addict dill @@ -42,7 +37,6 @@ python3.pkgs.buildPythonApplication rec { boto botocore flask - mypy-boto3-s3 pytestCheckHook stubserver ]); @@ -63,6 +57,10 @@ python3.pkgs.buildPythonApplication rec { "src/toil/test/src" "src/toil/test/wdl" "src/toil/test/utils/utilsTest.py" + "src/toil/test/cwl/cwlTest.py" + "src/toil/test/lib/test_ec2.py" + "src/toil/test/lib/aws/test_iam.py" + "src/toil/test/lib/aws/test_s3.py" ]; disabledTests = [ diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index e669562c9cc7..1daeeb81410a 100644 --- a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -1,4 +1,14 @@ -{ lib, stdenv, fetchurl, cmake, hwloc, fftw, perl, blas, lapack, mpi, cudatoolkit +{ lib +, stdenv +, fetchurl +, cmake +, hwloc +, fftw +, perl +, blas +, lapack +, mpi +, cudaPackages , plumed , singlePrec ? true , config @@ -9,6 +19,8 @@ }: let + inherit (cudaPackages.cudaFlags) cudaCapabilities dropDot; + # Select reasonable defaults for all major platforms # The possible values are defined in CMakeLists.txt: # AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 @@ -52,7 +64,7 @@ in stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ] ++ lib.optional enablePlumed plumed - ; + ++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ]; buildInputs = [ fftw @@ -61,13 +73,17 @@ in stdenv.mkDerivation rec { blas lapack ] ++ lib.optional enableMpi mpi - ++ lib.optional enableCuda cudatoolkit - ; + ++ lib.optionals enableCuda [ + cudaPackages.cuda_cudart + cudaPackages.libcufft + cudaPackages.cuda_profiler_api + ]; propagatedBuildInputs = lib.optional enableMpi mpi; propagatedUserEnvPkgs = lib.optional enableMpi mpi; cmakeFlags = [ + (lib.cmakeBool "GMX_HWLOC" true) "-DGMX_SIMD:STRING=${SIMD cpuAcceleration}" "-DGMX_OPENMP:BOOL=TRUE" "-DBUILD_SHARED_LIBS=ON" @@ -87,7 +103,13 @@ in stdenv.mkDerivation rec { else [ "-DGMX_MPI:BOOL=FALSE" ] - ) ++ lib.optional enableCuda "-DGMX_GPU=CUDA"; + ) ++ lib.optionals enableCuda [ + "-DGMX_GPU=CUDA" + (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" (builtins.concatStringsSep ";" (map dropDot cudaCapabilities))) + + # Gromacs seems to ignore and override the normal variables, so we add this ad hoc: + (lib.cmakeFeature "GMX_CUDA_TARGET_COMPUTE" (builtins.concatStringsSep ";" (map dropDot cudaCapabilities))) + ]; postInstall = '' moveToOutput share/cmake $dev |