diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
23 files changed, 184 insertions, 142 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix index c4721c490cce..ce29c5172a29 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 = "3.6.4"; + version = "3.6.6"; src = fetchurl { url = "mirror://kde/stable/kstars/kstars-${version}.tar.xz"; - sha256 = "sha256-9MJqJVgSZVBzlLv08Z6i8yO4YV1exsD5+yLJjqIGD20="; + sha256 = "sha256-Z4PatRvtIJBoeRDJJYkkBTOB/R+R7nGdDT38bfAShJQ="; }; nativeBuildInputs = [ extra-cmake-modules kdoctools ]; diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix index 00b36de28089..e2e1cda4c259 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix @@ -11,13 +11,13 @@ , qtpositioning , qtmultimedia , qtserialport -, qttranslations , qtwayland , qtwebengine , calcmysky , qxlsx , indilib , libnova +, qttools }: stdenv.mkDerivation rec { @@ -52,6 +52,7 @@ stdenv.mkDerivation rec { perl wrapGAppsHook wrapQtAppsHook + qttools ]; buildInputs = [ @@ -60,7 +61,6 @@ stdenv.mkDerivation rec { qtpositioning qtmultimedia qtserialport - qttranslations qtwebengine calcmysky qxlsx diff --git a/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix b/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix index abf9cfba45fd..37a8a58a92e1 100644 --- a/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation rec { pname = "iqtree"; - version = "2.2.2.6"; + version = "2.2.2.7"; src = fetchFromGitHub { owner = "iqtree"; repo = "iqtree2"; rev = "v${version}"; - hash = "sha256-dce7JOPZaosRP99/xRfz88EwXR9nYXK6Z4t2i5Uje1w="; + hash = "sha256-XyjVo5TYMoB+ZOAGc4ivYqFGnEO1M7mhxXrG45TP44Y="; fetchSubmodules = true; }; diff --git a/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix b/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix index 38333cbc9988..e1722a7086d8 100644 --- a/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation rec { pname = "sambamba"; - version = "1.0.0"; + version = "1.0.1"; src = fetchFromGitHub { owner = "biod"; repo = "sambamba"; rev = "v${version}"; - sha256 = "sha256-HwAzsbT71Q35Io6H7Hzs4RTatpRpdHqV0cwPYAlsf6c="; + sha256 = "sha256-3O9bHGpMuCgdR2Wm7Dv1VUjMT1QTn8K1hdwgjvwhFDw="; fetchSubmodules = true; }; diff --git a/nixpkgs/pkgs/applications/science/biology/sratoolkit/default.nix b/nixpkgs/pkgs/applications/science/biology/sratoolkit/default.nix index 8a1bb5376eaf..a36157ed5d16 100644 --- a/nixpkgs/pkgs/applications/science/biology/sratoolkit/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/sratoolkit/default.nix @@ -40,7 +40,7 @@ stdenv.mkDerivation rec { stdenv.cc.cc.lib ]; - sourceRoot = "./sratoolkit.${version}-ubuntu64/bin"; + sourceRoot = "sratoolkit.${version}-ubuntu64/bin"; installPhase = '' find -L . -executable -type f -! -name "*remote-fuser*" -exec install -m755 -D {} $out/bin/{} \; diff --git a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix index 5defaafa3cd0..29b983cde536 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, python3, gfortran, blas, lapack +{ lib, stdenv, fetchFromGitHub, mpiCheckPhaseHook, python3, gfortran, blas, lapack , fftw, libint, libvori, libxc, mpi, gsl, scalapack, openssh, makeWrapper , libxsmm, spglib, which, pkg-config, plumed, zlib , enableElpa ? false @@ -88,14 +88,18 @@ in stdenv.mkDerivation rec { EOF ''; + nativeCheckInputs = [ + mpiCheckPhaseHook + openssh + ]; + checkPhase = '' - export OMP_NUM_THREADS=1 + runHook preCheck - export HYDRA_IFACE=lo # Fix to make mpich run in a sandbox - export OMPI_MCA_rmaps_base_oversubscribe=1 export CP2K_DATA_DIR=data - mpirun -np 2 exe/${arch}/libcp2k_unittest.${cp2kVersion} + + runHook postCheck ''; installPhase = '' diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index e4ffb94eeba7..1b77cef6b809 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.33"; + version = "16.1.35"; pname = "jmol"; src = let baseVersion = "${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-vOFGmLsCQNYRBMuDRVrdjWE6/MxY7IucB1OpV4cdZrs="; + hash = "sha256-r1ydAwAdXl5RRj64W0j8L7XbgnC7VOYjFNE019BcbpY="; }; patchPhase = '' diff --git a/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix b/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix index 82daf5f85e74..2a17be9f8a92 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix @@ -3,6 +3,7 @@ , pkgs , fetchFromGitHub , fetchurl +, mpiCheckPhaseHook , which , openssh , gcc @@ -190,16 +191,15 @@ stdenv.mkDerivation rec { doCheck = false; doInstallCheck = true; + nativeCheckInputs = [ mpiCheckPhaseHook ]; installCheckPhase = '' - export OMP_NUM_THREADS=1 - - # Fix to make mpich run in a sandbox - export HYDRA_IFACE=lo - export OMPI_MCA_rmaps_base_oversubscribe=1 + runHook preInstallCheck # run a simple water test mpirun -np 2 $out/bin/nwchem $out/share/nwchem/QA/tests/h2o/h2o.nw > h2o.out grep "Total SCF energy" h2o.out | grep 76.010538 + + runHook postInstallCheck ''; passthru = { inherit mpi; }; diff --git a/nixpkgs/pkgs/applications/science/electronics/dataexplorer/default.nix b/nixpkgs/pkgs/applications/science/electronics/dataexplorer/default.nix index 596978fc9280..128a5f62eeaa 100644 --- a/nixpkgs/pkgs/applications/science/electronics/dataexplorer/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/dataexplorer/default.nix @@ -8,11 +8,11 @@ stdenv.mkDerivation rec { pname = "dataexplorer"; - version = "3.7.9"; + version = "3.8.0"; src = fetchurl { url = "mirror://savannah/dataexplorer/dataexplorer-${version}-src.tar.gz"; - sha256 = "sha256-CdIWAde7mytXP9U1PfI9d/rFK7Agy5biIq5tMTW9RD4="; + sha256 = "sha256-ZluT/jCjcOrlh2nqe0j56shmtGqfm11BCnsp6mWDXkQ="; }; nativeBuildInputs = [ ant makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/flatcam/default.nix b/nixpkgs/pkgs/applications/science/electronics/flatcam/default.nix index 338823bbf386..169130b41010 100644 --- a/nixpkgs/pkgs/applications/science/electronics/flatcam/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/flatcam/default.nix @@ -13,13 +13,16 @@ let packageOverrides = self: super: { shapely = super.shapely.overridePythonAttrs (old: rec { version = "1.8.4"; + src = fetchPypi { pname = "Shapely"; inherit version; hash = "sha256-oZXlHKr6IYKR8suqP+9p/TNTyT7EtlsqRyLEz0DDGYw="; }; + # Environment variable used in shapely/_buildcfg.py GEOS_LIBRARY_PATH = "${geos}/lib/libgeos_c${stdenv.hostPlatform.extensions.sharedLibrary}"; + patches = [ # Patch to search form GOES .so/.dylib files in a Nix-aware way (substituteAll { @@ -28,6 +31,11 @@ let libc = lib.optionalString (!stdenv.isDarwin) "${stdenv.cc.libc}/lib/libc${stdenv.hostPlatform.extensions.sharedLibrary}.6"; }) ]; + + postPatch = '' + substituteInPlace pyproject.toml \ + --replace 'setuptools<64' 'setuptools' + ''; }); }; }; diff --git a/nixpkgs/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix b/nixpkgs/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix index 5ee77fce963a..2b74a7de24e5 100644 --- a/nixpkgs/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix @@ -1,75 +1,71 @@ { lib , stdenv +, boost +, cmake , fetchFromGitHub , fetchpatch -, cmake +, graphviz +, igraph +, llvmPackages , ninja , pkg-config , python3Packages -, boost -, rapidjson , qtbase , qtsvg -, igraph +, quazip +, rapidjson , spdlog +, suitesparse , wrapQtAppsHook -, graphviz -, llvmPackages , z3 -, fmt_8 -, suitesparse }: let - igraph' = igraph.overrideAttrs (old: rec { + # hal doesn't work with igraph 0.10.x yet https://github.com/emsec/hal/pull/487 + igraph' = igraph.overrideAttrs (final: prev: { version = "0.9.10"; src = fetchFromGitHub { owner = "igraph"; - repo = "igraph"; - rev = version; + repo = final.pname; + rev = final.version; hash = "sha256-prDadHsNhDRkNp1i0niKIYxE0g85Zs0ngvUy6uK8evk="; }; - postPatch = old.postPatch + lib.optionalString stdenv.isAarch64 '' + patches = (prev.patches or []) ++ [ + # needed by clang + (fetchpatch { + name = "libxml2-2.11-compat.patch"; + url = "https://github.com/igraph/igraph/commit/5ad464be5ae2f6ebb69c97cb0140c800cc8d97d6.patch"; + hash = "sha256-adU5SctH+H54UaAmr5BZInytD3wjUzLtQbCwngAWs4o="; + }) + ]; + postPatch = prev.postPatch + lib.optionalString stdenv.isAarch64 '' # https://github.com/igraph/igraph/issues/1694 substituteInPlace tests/CMakeLists.txt \ --replace "igraph_scg_grouping3" "" \ --replace "igraph_scg_semiprojectors2" "" ''; - buildInputs = old.buildInputs ++ [ suitesparse ]; - cmakeFlags = old.cmakeFlags ++ [ "-DIGRAPH_USE_INTERNAL_CXSPARSE=OFF" ]; + # general options brought back from the old 0.9.x package + buildInputs = prev.buildInputs ++ [ suitesparse ]; + cmakeFlags = prev.cmakeFlags ++ [ "-DIGRAPH_USE_INTERNAL_CXSPARSE=OFF" ]; }); - # no stable hal release yet with recent spdlog/fmt support, remove - # once 4.0.0 is released - see https://github.com/emsec/hal/issues/452 - spdlog' = spdlog.override { - fmt_9 = fmt_8.overrideAttrs (_: rec { - version = "8.0.1"; - src = fetchFromGitHub { - owner = "fmtlib"; - repo = "fmt"; - rev = version; - sha256 = "1mnvxqsan034d2jiqnw2yvkljl7lwvhakmj5bscwp1fpkn655bbw"; - }; - }); - }; + in stdenv.mkDerivation rec { - version = "3.3.0"; + version = "4.2.0"; pname = "hal-hardware-analyzer"; src = fetchFromGitHub { owner = "emsec"; repo = "hal"; rev = "v${version}"; - sha256 = "sha256-uNpELHhSAVRJL/4iypvnl3nX45SqB419r37lthd2WmQ="; + sha256 = "sha256-Yl86AClE3vWygqj1omCOXX8koJK2SjTkMZFReRThez0="; }; patches = [ (fetchpatch { - # Fix build with python 3.10 - # https://github.com/emsec/hal/pull/463 - name = "hal-fix-python-3.10.patch"; - url = "https://github.com/emsec/hal/commit/f695f55cb2209676ef76366185b7c419417fbbc9.patch"; - sha256 = "sha256-HsCdG3tPllUsLw6kQtGaaEGkEHqZPSC2v9k6ycO2I/8="; - includes = [ "plugins/gui/src/python/python_context.cpp" ]; + name = "cmake-add-no-vendored-options.patch"; + # https://github.com/emsec/hal/pull/529 + url = "https://github.com/emsec/hal/commit/37d5c1a0eacb25de57cc552c13e74f559a5aa6e8.patch"; + hash = "sha256-a30VjDt4roJOTntisixqnH17wwCgWc4VWeh1+RgqFuY="; }) ]; @@ -77,14 +73,30 @@ in stdenv.mkDerivation rec { # copies them in full to the output, bloating the package postPatch = '' shopt -s extglob - rm -rf deps/!(sanitizers-cmake)/* + rm -rf deps/!(abc|sanitizers-cmake|subprocess)/* shopt -u extglob ''; - nativeBuildInputs = [ cmake ninja pkg-config ]; - buildInputs = [ qtbase qtsvg boost rapidjson igraph' spdlog' graphviz wrapQtAppsHook z3 ] - ++ (with python3Packages; [ python pybind11 ]) - ++ lib.optional stdenv.cc.isClang llvmPackages.openmp; + nativeBuildInputs = [ + cmake + ninja + pkg-config + wrapQtAppsHook + ]; + buildInputs = [ + qtbase + qtsvg + boost + rapidjson + igraph' + spdlog + graphviz + z3 + quazip + ] + ++ (with python3Packages; [ python pybind11 ]) + ++ lib.optional stdenv.cc.isClang llvmPackages.openmp + ; cmakeFlags = with lib.versions; [ "-DHAL_VERSION_RETURN=${version}" @@ -96,12 +108,23 @@ in stdenv.mkDerivation rec { "-DHAL_VERSION_DIRTY=false" "-DHAL_VERSION_BROKEN=false" "-DENABLE_INSTALL_LDCONFIG=off" + "-DUSE_VENDORED_PYBIND11=off" + "-DUSE_VENDORED_SPDLOG=off" + "-DUSE_VENDORED_QUAZIP=off" + "-DUSE_VENDORED_IGRAPH=off" "-DBUILD_ALL_PLUGINS=on" ]; # needed for macos build - this is why we use wrapQtAppsHook instead of # the qt mkDerivation - the latter forcibly overrides this. cmakeBuildType = "MinSizeRel"; + # some plugins depend on other plugins and need to be able to load them + postFixup = lib.optionalString stdenv.isLinux '' + find $out/lib/hal_plugins -name '*.so*' | while read -r f ; do + patchelf --set-rpath "$(patchelf --print-rpath "$f"):$out/lib/hal_plugins" "$f" + done + ''; + meta = with lib; { description = "A comprehensive reverse engineering and manipulation framework for gate-level netlists"; homepage = "https://github.com/emsec/hal"; diff --git a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix index 15157b11f29d..dde8f05d6239 100644 --- a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation rec { pname = "nvc"; - version = "1.10.1"; + version = "1.10.2"; src = fetchFromGitHub { owner = "nickg"; repo = "nvc"; rev = "r${version}"; - hash = "sha256-7Kw9irZltNE8VRnIvVX786/u0QQtmRhV8pzpba0h1JY="; + hash = "sha256-sAr51+8hFnpIq0jDd8dB5uiy00N09ufkFgWkFtW7ErU="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix b/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix index 9da94aa609be..0ce67ec4dbb1 100644 --- a/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix @@ -18,13 +18,13 @@ stdenv.mkDerivation rec { pname = "qucs-s"; - version = "1.1.0"; + version = "2.0.0"; src = fetchFromGitHub { owner = "ra3xdh"; repo = "qucs_s"; rev = version; - sha256 = "sha256-cQ9UNCTwRW61dOQYJX0mPNtCTk0qXKx8VQ6BIXl6Fa8="; + sha256 = "sha256-9/1sgxFqn9d9zlwrzjQosFO3m+2lC83qVcCtzfqY5XY="; }; nativeBuildInputs = [ flex bison wrapQtAppsHook cmake ]; @@ -48,7 +48,7 @@ stdenv.mkDerivation rec { ''; homepage = "https://ra3xdh.github.io/"; license = licenses.gpl2Plus; - maintainers = with maintainers; [ mazurel ]; + maintainers = with maintainers; [ mazurel kashw2 ]; platforms = with platforms; linux; }; } diff --git a/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix b/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix index 4709065e45bd..aee1d25a04cc 100644 --- a/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix @@ -56,7 +56,7 @@ stdenv.mkDerivation rec { srcs = [ xyce_src regression_src ]; - sourceRoot = "./${xyce_src.name}"; + sourceRoot = xyce_src.name; preConfigure = "./bootstrap"; diff --git a/nixpkgs/pkgs/applications/science/logic/egglog/default.nix b/nixpkgs/pkgs/applications/science/logic/egglog/default.nix index c74594df28fd..c2e46c6801b2 100644 --- a/nixpkgs/pkgs/applications/science/logic/egglog/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/egglog/default.nix @@ -5,13 +5,13 @@ rustPlatform.buildRustPackage { pname = "egglog"; - version = "unstable-2023-08-19"; + version = "unstable-2023-08-23"; src = fetchFromGitHub { owner = "egraphs-good"; repo = "egglog"; - rev = "a4768b1751b72292b0e79e6e442d54ab270748fb"; - hash = "sha256-WTdMhtdPvBtS6WAS3S4dui/8ospJ7nkeRhLce2zY8KE="; + rev = "9e530381961a59524f2bbacd89973575b4e036d8"; + hash = "sha256-xzfa1Z7ibSO4D5zpprC7heaswA7Be5Qmb81XoDwANqw="; }; cargoLock = { diff --git a/nixpkgs/pkgs/applications/science/logic/ekrhyper/default.nix b/nixpkgs/pkgs/applications/science/logic/ekrhyper/default.nix index 187cbc9a92ae..4a5124b23582 100644 --- a/nixpkgs/pkgs/applications/science/logic/ekrhyper/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/ekrhyper/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { strictDeps = true; nativeBuildInputs = [ ocaml perl ]; - setSourceRoot = "export sourceRoot=$(echo */ekrh/src/)"; + setSourceRoot = "export sourceRoot=$(echo */ekrh/src)"; preInstall = "export INSTALLDIR=$out"; postInstall = ''for i in "$out/casc"/*; do ln -s "$i" "$out/bin/ekrh-casc-$(basename $i)"; done ''; diff --git a/nixpkgs/pkgs/applications/science/logic/tamarin-prover/default.nix b/nixpkgs/pkgs/applications/science/logic/tamarin-prover/default.nix index d5d6512c734a..09ef2d7d4637 100644 --- a/nixpkgs/pkgs/applications/science/logic/tamarin-prover/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/tamarin-prover/default.nix @@ -4,12 +4,12 @@ }: let - version = "1.6.1"; + version = "1.8.0"; src = fetchFromGitHub { owner = "tamarin-prover"; repo = "tamarin-prover"; rev = version; - sha256 = "sha256:0cz1v7k4d0im749ag632nc34n91b51b0pq4z05rzw1p59a5lza92"; + sha256 = "sha256-ujnaUdbjqajmkphOS4Fs4QBCRGX4JZkQ2p1X2jripww="; }; # tamarin has its own dependencies, but they're kept inside the repo, @@ -51,6 +51,7 @@ let doHaddock = false; # broken libraryHaskellDepends = (with haskellPackages; [ aeson aeson-pretty parallel uniplate + regex-pcre-builtin regex-posix split ]) ++ [ tamarin-prover-utils tamarin-prover-term ]; }); @@ -62,31 +63,37 @@ let ]) ++ [ tamarin-prover-theory ]; }); + tamarin-prover-accountability = mkDerivation (common "tamarin-prover-accountability" (src + "/lib/accountability") // { + postPatch = "cp --remove-destination ${src}/LICENSE ."; + doHaddock = false; # broken + libraryHaskellDepends = (with haskellPackages; [ + raw-strings-qq + ]) ++ [ + tamarin-prover-utils + tamarin-prover-term + tamarin-prover-theory + ]; + }); + + tamarin-prover-export = mkDerivation (common "tamarin-prover-export" (src + "/lib/export") // { + postPatch = "cp --remove-destination ${src}/LICENSE ."; + doHaddock = false; # broken + libraryHaskellDepends = (with haskellPackages; [ + HStringTemplate + ]) ++ [ + tamarin-prover-utils + tamarin-prover-term + tamarin-prover-theory + tamarin-prover-sapic + ]; + }); + in mkDerivation (common "tamarin-prover" src // { isLibrary = false; isExecutable = true; - patches = [ - # Backport unreleased patch allowing maude 3.2.1 - (fetchpatch { - name = "tamarin-prover-allow-maude-3.2.1.patch"; - url = "https://github.com/tamarin-prover/tamarin-prover/commit/bfcf56909479e154a203f0eeefa767f4d91b600d.patch"; - sha256 = "1zjqzyxwnfp7z3h3li8jrxn9732dx6lyq9q3w2dsphmxbzrs64dg"; - }) - # Backport unreleased patch allowing maude 3.2.2 - (fetchpatch { - name = "tamarin-prover-allow-maude-3.2.2.patch"; - url = "https://github.com/tamarin-prover/tamarin-prover/commit/df1aa9fc4fcc72b6cf0bed0f71844efe3d8ad238.patch"; - sha256 = "1bkwvyyz5d660jjh08z8wq9c3l40s0rxd2nsbn20xnl2nynyvqpy"; - }) - # Backport proposed patch allowing maude 3.3 and 3.3.1 - (fetchpatch { - name = "tamarin-prover-allow-maude-3.3.patch"; - url = "https://github.com/tamarin-prover/tamarin-prover/pull/544/commits/d0313b1a1bac7c92130773f7ccdd890f8aec286d.patch"; - sha256 = "1jhlz8vp9a3aahyhj24yjcv4l1389y9kg878yfnq0rkkgvk0m681"; - }) - ]; + patches = [ ]; # strip out unneeded deps manually doHaddock = false; @@ -118,6 +125,8 @@ mkDerivation (common "tamarin-prover" src // { resourcet shakespeare threads wai warp yesod-core yesod-static ]) ++ [ tamarin-prover-utils tamarin-prover-sapic + tamarin-prover-accountability + tamarin-prover-export tamarin-prover-term tamarin-prover-theory ]; diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix index 970f5517c21f..405561510be0 100644 --- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -1,20 +1,20 @@ -{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, wrapGAppsHook }: +{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, curl, wrapGAppsHook }: stdenv.mkDerivation rec { pname = "qalculate-gtk"; - version = "4.7.0"; + version = "4.8.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "sha256-Fbi+vZEyXhUZQjWUX01IXd6G1cthfiuztdbisNQ/VZU="; + sha256 = "sha256-GYy3Ot2vjXpCp89Rib3Ua0XeVGOOTejKcaqNZvPmxm0="; }; hardeningDisable = [ "format" ]; nativeBuildInputs = [ intltool pkg-config autoreconfHook wrapGAppsHook ]; - buildInputs = [ libqalculate gtk3 ]; + buildInputs = [ libqalculate gtk3 curl ]; enableParallelBuilding = true; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix index abe65e413690..be9dd27695f7 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 rec { pname = "qalculate-qt"; - version = "4.7.0"; + version = "4.8.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-qt"; rev = "v${version}"; - hash = "sha256-fMchJgxuOO2e7cOHLako26c9gsWvQY2MTRVD3JWGSAU="; + hash = "sha256-7VlaoiY+HgHCMZCegUdy2wpgfx3fKaViMtkdNRleHaA="; }; nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ]; diff --git a/nixpkgs/pkgs/applications/science/misc/golly/default.nix b/nixpkgs/pkgs/applications/science/misc/golly/default.nix index 7d91c76579f9..52b05cbb7e9b 100644 --- a/nixpkgs/pkgs/applications/science/misc/golly/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/golly/default.nix @@ -1,10 +1,10 @@ {lib, stdenv, fetchurl, wxGTK, perl, python3, zlib, libGLU, libGL, libX11, SDL2}: stdenv.mkDerivation rec { pname = "golly"; - version = "4.1"; + version = "4.2"; src = fetchurl { - sha256 = "1j30dpzy6wh8fv1j2750hzc6wb0nhk83knl9fapccxgxw9n5lrbc"; + hash = "sha256-VpEoqSPaZMP/AGIYZAbk5R/f8Crqvx8pKYN1O9Bl6V0="; url="mirror://sourceforge/project/golly/golly/golly-${version}/golly-${version}-src.tar.gz"; }; @@ -13,13 +13,10 @@ stdenv.mkDerivation rec { ]; setSourceRoot = '' - sourceRoot=$(echo */gui-wx/) + sourceRoot=$(echo */gui-wx) ''; postPatch = '' - sed -e '/gollydir =/agollydir += "/../share/golly/";' -i wxgolly.cpp - grep share/golly wxgolly.cpp - sed -e 's@PYTHON_SHLIB@${python3}/lib/libpython3.so@' -i wxprefs.cpp sed -e 's@PERL_SHLIB@'"$(find "${perl}/lib/" -name libperl.so)"'@' -i wxprefs.cpp ! grep _SHLIB *.cpp @@ -31,6 +28,7 @@ stdenv.mkDerivation rec { makeFlags=[ "-f" "makefile-gtk" "ENABLE_SOUND=1" "ENABLE_PERL=1" + "GOLLYDIR=${placeholder "out"}/share/golly" ]; installPhase = '' diff --git a/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix b/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix index 43b04ba1eedd..b3337b7f55c8 100644 --- a/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix @@ -4,11 +4,11 @@ buildPythonApplication rec { pname = "MAVProxy"; - version = "1.8.62"; + version = "1.8.66"; src = fetchPypi { inherit pname version; - sha256 = "sha256-XypOQNETmxg9DYcuCGkXH9/LwCq+pR23KbNfP0mfs3I="; + hash = "sha256-tIwXiDHEmFHF5Jdv25hPkzEqAdig+i5h4fW6SGIrZDM="; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix b/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix index 4af3d6899fa9..c4f84e158399 100644 --- a/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix @@ -9,18 +9,18 @@ }: let - # See https://github.com/deepmind/mujoco/blob/573d331b69845c5d651b70f5d1b0f3a0d2a3a233/cmake/MujocoDependencies.cmake#L21-L59 + # See https://github.com/deepmind/mujoco/blob/c9246e1f5006379d599e0bcddf159a8616d31441/cmake/MujocoDependencies.cmake#L17-L55 abseil-cpp = fetchFromGitHub { owner = "abseil"; repo = "abseil-cpp"; - rev = "8c0b94e793a66495e0b1f34a5eb26bd7dc672db0"; - hash = "sha256-Od1FZOOWEXVQsnZBwGjDIExi6LdYtomyL0STR44SsG8="; + rev = "c2435f8342c2d0ed8101cb43adfd605fdc52dca2"; + hash = "sha256-PLoI7ix+reUqkZ947kWzls8lujYqWXk9A9a55UcfahI="; }; benchmark = fetchFromGitHub { owner = "google"; repo = "benchmark"; - rev = "d845b7b3a27d54ad96280a29d61fa8988d4fddcf"; - hash = "sha256-XTnTM1k6xMGXUws/fKdJUbpCPcc4U0IelL6BPEEnpEQ="; + rev = "2dd015dfef425c866d9a43f2c67d8b52d709acb6"; + hash = "sha256-pUW9YVaujs/y00/SiPqDgK4wvVsaM7QUp/65k0t7Yr0="; }; ccd = fetchFromGitHub { owner = "danfis"; @@ -31,14 +31,14 @@ let eigen3 = fetchFromGitLab { owner = "libeigen"; repo = "eigen"; - rev = "3bb6a48d8c171cf20b5f8e48bfb4e424fbd4f79e"; - hash = "sha256-k71DoEsx8JpC9AlQ0cCRI0fWMIWFBFL/Yscx+2iBtNM="; + rev = "211c5dfc6741a5570ad007983c113ef4d144f9f3"; + hash = "sha256-oT/h8QkL0vwaflh46Zsnu9Db1b65AP6p//nAga8M5jI="; }; googletest = fetchFromGitHub { owner = "google"; repo = "googletest"; - rev = "58d77fa8070e8cec2dc1ed015d66b454c8d78850"; - hash = "sha256-W+OxRTVtemt2esw4P7IyGWXOonUN5ZuscjvzqkYvZbM="; + rev = "b796f7d44681514f58a683a3a71ff17c94edb0c1"; + hash = "sha256-LVLEn+e7c8013pwiLzJiiIObyrlbBHYaioO/SWbItPQ="; }; lodepng = fetchFromGitHub { owner = "lvandeve"; @@ -49,8 +49,8 @@ let qhull = fetchFromGitHub { owner = "qhull"; repo = "qhull"; - rev = "3df027b91202cf179f3fba3c46eebe65bbac3790"; - hash = "sha256-aHO5n9Y35C7/zb3surfMyjyMjo109DoZnkozhiAKpYQ="; + rev = "0c8fc90d2037588024d9964515c1e684f6007ecc"; + hash = "sha256-Ptzxad3ewmKJbbcmrBT+os4b4SR976zlCG9F0nq0x94="; }; tinyobjloader = fetchFromGitHub { owner = "tinyobjloader"; @@ -61,12 +61,12 @@ let tinyxml2 = fetchFromGitHub { owner = "leethomason"; repo = "tinyxml2"; - rev = "1dee28e51f9175a31955b9791c74c430fe13dc82"; - hash = "sha256-AQQOctXi7sWIH/VOeSUClX6hlm1raEQUOp+VoPjLM14="; + rev = "9a89766acc42ddfa9e7133c7d81a5bda108a0ade"; + hash = "sha256-YGAe4+Ttv/xeou+9FoJjmQCKgzupTYdDhd+gzvtz/88="; }; - # See https://github.com/deepmind/mujoco/blob/573d331b69845c5d651b70f5d1b0f3a0d2a3a233/simulate/cmake/SimulateDependencies.cmake#L32-L35 - glfw = fetchFromGitHub { + # See https://github.com/deepmind/mujoco/blob/c9246e1f5006379d599e0bcddf159a8616d31441/simulate/cmake/SimulateDependencies.cmake#L32-L35 + glfw3 = fetchFromGitHub { owner = "glfw"; repo = "glfw"; rev = "7482de6071d21db77a7236155da44c172a7f6c9e"; @@ -75,13 +75,13 @@ let in stdenv.mkDerivation rec { pname = "mujoco"; - version = "2.3.0"; + version = "2.3.7"; src = fetchFromGitHub { owner = "deepmind"; repo = pname; rev = version; - hash = "sha256-FxMaXl7yfUAyY6LE1sxaw226dBtp1DOCWNnROp0WX2I="; + hash = "sha256-LgpA+iPGqciHuWBSD6/7yvZ7p+vo48ZYKjjrDZSnAwE="; }; patches = [ ./dependencies.patch ]; @@ -105,7 +105,7 @@ stdenv.mkDerivation rec { ln -s ${benchmark} build/_deps/benchmark-src ln -s ${ccd} build/_deps/ccd-src ln -s ${eigen3} build/_deps/eigen3-src - ln -s ${glfw} build/_deps/glfw-src + ln -s ${glfw3} build/_deps/glfw3-src ln -s ${googletest} build/_deps/googletest-src ln -s ${lodepng} build/_deps/lodepng-src ln -s ${qhull} build/_deps/qhull-src diff --git a/nixpkgs/pkgs/applications/science/robotics/mujoco/dependencies.patch b/nixpkgs/pkgs/applications/science/robotics/mujoco/dependencies.patch index 5ddbaaab5329..f7dcc06a9e05 100644 --- a/nixpkgs/pkgs/applications/science/robotics/mujoco/dependencies.patch +++ b/nixpkgs/pkgs/applications/science/robotics/mujoco/dependencies.patch @@ -1,8 +1,8 @@ diff --git a/cmake/MujocoDependencies.cmake b/cmake/MujocoDependencies.cmake -index 99e4a7a..cf9a901 100644 +index 3e322ea..980aace 100644 --- a/cmake/MujocoDependencies.cmake +++ b/cmake/MujocoDependencies.cmake -@@ -82,8 +82,6 @@ set(BUILD_SHARED_LIBS +@@ -87,8 +87,6 @@ set(BUILD_SHARED_LIBS if(NOT TARGET lodepng) FetchContent_Declare( lodepng @@ -11,7 +11,7 @@ index 99e4a7a..cf9a901 100644 ) FetchContent_GetProperties(lodepng) -@@ -111,10 +109,6 @@ findorfetch( +@@ -127,10 +125,6 @@ findorfetch( qhull LIBRARY_NAME qhull @@ -21,8 +21,8 @@ index 99e4a7a..cf9a901 100644 - ${MUJOCO_DEP_VERSION_qhull} TARGETS qhull - # TODO(fraromano) Remove when https://github.com/qhull/qhull/pull/112 is merged. -@@ -146,10 +140,6 @@ findorfetch( + EXCLUDE_FROM_ALL +@@ -151,10 +145,6 @@ findorfetch( tinyxml2 LIBRARY_NAME tinyxml2 @@ -33,7 +33,7 @@ index 99e4a7a..cf9a901 100644 TARGETS tinyxml2 EXCLUDE_FROM_ALL -@@ -164,10 +154,6 @@ findorfetch( +@@ -169,10 +159,6 @@ findorfetch( tinyobjloader LIBRARY_NAME tinyobjloader @@ -44,7 +44,7 @@ index 99e4a7a..cf9a901 100644 TARGETS tinyobjloader EXCLUDE_FROM_ALL -@@ -182,10 +168,6 @@ findorfetch( +@@ -187,10 +173,6 @@ findorfetch( ccd LIBRARY_NAME ccd @@ -55,7 +55,7 @@ index 99e4a7a..cf9a901 100644 TARGETS ccd EXCLUDE_FROM_ALL -@@ -222,10 +204,6 @@ if(MUJOCO_BUILD_TESTS) +@@ -227,10 +209,6 @@ if(MUJOCO_BUILD_TESTS) absl LIBRARY_NAME abseil-cpp @@ -66,7 +66,7 @@ index 99e4a7a..cf9a901 100644 TARGETS absl::core_headers EXCLUDE_FROM_ALL -@@ -249,10 +227,6 @@ if(MUJOCO_BUILD_TESTS) +@@ -254,10 +232,6 @@ if(MUJOCO_BUILD_TESTS) GTest LIBRARY_NAME googletest @@ -77,7 +77,7 @@ index 99e4a7a..cf9a901 100644 TARGETS gtest gmock -@@ -283,10 +257,6 @@ if(MUJOCO_BUILD_TESTS) +@@ -288,10 +262,6 @@ if(MUJOCO_BUILD_TESTS) benchmark LIBRARY_NAME benchmark @@ -88,7 +88,7 @@ index 99e4a7a..cf9a901 100644 TARGETS benchmark::benchmark benchmark::benchmark_main -@@ -303,8 +273,6 @@ if(MUJOCO_TEST_PYTHON_UTIL) +@@ -308,8 +278,6 @@ if(MUJOCO_TEST_PYTHON_UTIL) FetchContent_Declare( Eigen3 @@ -98,17 +98,17 @@ index 99e4a7a..cf9a901 100644 FetchContent_GetProperties(Eigen3) diff --git a/simulate/cmake/SimulateDependencies.cmake b/simulate/cmake/SimulateDependencies.cmake -index 6616d6f..5d5a889 100644 +index fa539c2..5985d5a 100644 --- a/simulate/cmake/SimulateDependencies.cmake +++ b/simulate/cmake/SimulateDependencies.cmake @@ -81,10 +81,6 @@ findorfetch( - glfw + glfw3 LIBRARY_NAME - glfw + glfw3 - GIT_REPO - https://github.com/glfw/glfw.git - GIT_TAG -- ${MUJOCO_DEP_VERSION_glfw} +- ${MUJOCO_DEP_VERSION_glfw3} TARGETS glfw EXCLUDE_FROM_ALL |