push sheeet

pkgs/applications/science/astronomy/calcmysky/default.nix

@@ -0,0 +1,48 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  wrapQtAppsHook,
+  glm,
+  eigen,
+  qtbase,
+  stellarium,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "calcmysky";
+  version = "0.3.5";
+
+  src = fetchFromGitHub {
+    owner = "10110111";
+    repo = "CalcMySky";
+    tag = "v${version}";
+    hash = "sha256-++011c4/IFf/5GKmFostTnxgfEdw3/GJf0e5frscCQ4=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+  buildInputs = [
+    glm
+    eigen
+    qtbase
+  ];
+
+  cmakeFlags = [ "-DQT_VERSION=6" ];
+
+  doCheck = true;
+
+  passthru.tests = {
+    inherit stellarium;
+  };
+
+  meta = with lib; {
+    description = "Simulator of light scattering by planetary atmospheres";
+    homepage = "https://github.com/10110111/CalcMySky";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ nickcao ];
+  };
+}

pkgs/applications/science/astronomy/celestia/default.nix

@@ -0,0 +1,78 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch2,
+  pkg-config,
+  libglut,
+  gtk2,
+  gtkglext,
+  libjpeg_turbo,
+  libtheora,
+  libXmu,
+  lua,
+  libGLU,
+  libGL,
+  perl,
+  autoreconfHook,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "celestia";
+  version = "1.6.4";
+
+  src = fetchFromGitHub {
+    owner = "CelestiaProject";
+    repo = "Celestia";
+    rev = version;
+    sha256 = "sha256-MkElGo1ZR0ImW/526QlDE1ePd+VOQxwkX7l+0WyZ6Vs=";
+  };
+
+  patches = [
+    (fetchpatch2 {
+      url = "https://github.com/CelestiaProject/Celestia/commit/94894bed3bf98d41c5097e7829d491d8ff8d4a62.patch?full_index=1";
+      hash = "sha256-hEZ6BhSEx6Qm+fLisc63xSCDT6GX92AHD0BuldOhzFk=";
+    })
+  ];
+
+  postPatch = ''
+    substituteInPlace configure.ac \
+      --replace-fail "dnl AM_GNU_GETTEXT_VERSION([0.15])" "AM_GNU_GETTEXT_VERSION([0.15])"
+  '';
+
+  nativeBuildInputs = [
+    pkg-config
+    autoreconfHook
+  ];
+  buildInputs = [
+    libglut
+    gtk2
+    gtkglext
+    lua
+    perl
+    libjpeg_turbo
+    libtheora
+    libXmu
+    libGLU
+    libGL
+  ];
+
+  configureFlags = [
+    "--with-gtk"
+    "--with-lua=${lua}"
+  ];
+
+  enableParallelBuilding = true;
+
+  meta = {
+    homepage = "https://celestiaproject.space/";
+    description = "Real-time 3D simulation of space";
+    mainProgram = "celestia";
+    changelog = "https://github.com/CelestiaProject/Celestia/releases/tag/${version}";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [
+      returntoreality
+    ];
+    platforms = lib.platforms.linux;
+  };
+}

pkgs/applications/science/astronomy/stellarium/default.nix

@@ -0,0 +1,119 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  perl,
+  wrapGAppsHook3,
+  wrapQtAppsHook,
+  qtbase,
+  qtcharts,
+  qtpositioning,
+  qtmultimedia,
+  qtserialport,
+  qtwayland,
+  qtwebengine,
+  calcmysky,
+  qxlsx,
+  indilib,
+  libnova,
+  qttools,
+  exiv2,
+  nlopt,
+  testers,
+  xvfb-run,
+  gitUpdater,
+  md4c,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "stellarium";
+  version = "25.2";
+
+  src = fetchFromGitHub {
+    owner = "Stellarium";
+    repo = "stellarium";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-2QK9dHflCdmDrRXEHCBpuJR73jsMz9D9lJNa1pbfrTs=";
+  };
+
+  postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
+    substituteInPlace CMakeLists.txt \
+      --replace-fail 'SET(CMAKE_INSTALL_PREFIX "''${PROJECT_BINARY_DIR}/Stellarium.app/Contents")' \
+                'SET(CMAKE_INSTALL_PREFIX "${placeholder "out"}/Applications/Stellarium.app/Contents")'
+    substituteInPlace src/CMakeLists.txt \
+      --replace-fail "\''${_qt_bin_dir}/../" "${qtmultimedia}/lib/qt-6/"
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    perl
+    wrapGAppsHook3
+    wrapQtAppsHook
+    qttools
+  ];
+
+  buildInputs = [
+    qtbase
+    qtcharts
+    qtpositioning
+    qtmultimedia
+    qtserialport
+    qtwebengine
+    calcmysky
+    qxlsx
+    indilib
+    libnova
+    exiv2
+    md4c
+    nlopt
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isLinux [
+    qtwayland
+  ];
+
+  preConfigure = ''
+    export SOURCE_DATE_EPOCH=$(date -d 20${lib.versions.major finalAttrs.version}0101 +%s)
+  ''
+  + lib.optionalString stdenv.hostPlatform.isDarwin ''
+    export LC_ALL=en_US.UTF-8
+  '';
+
+  # fatal error: 'QtSerialPort/QSerialPortInfo' file not found
+  env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.hostPlatform.isDarwin "-F${qtserialport}/lib";
+
+  dontWrapGApps = true;
+
+  postInstall = lib.optionalString stdenv.hostPlatform.isDarwin ''
+    makeWrapper $out/Applications/Stellarium.app/Contents/MacOS/Stellarium $out/bin/stellarium
+  '';
+
+  preFixup = ''
+    qtWrapperArgs+=("''${gappsWrapperArgs[@]}")
+  '';
+
+  passthru = {
+    tests.version = testers.testVersion {
+      package = finalAttrs.finalPackage;
+      command = ''
+        # Create a temporary home directory because stellarium aborts with an
+        # error if it can't write some configuration files.
+        tmpdir=$(mktemp -d)
+
+        # stellarium can't be run in headless mode, therefore we need xvfb-run.
+        HOME="$tmpdir" ${lib.getExe xvfb-run} stellarium --version
+      '';
+    };
+    updateScript = gitUpdater { rev-prefix = "v"; };
+  };
+
+  meta = {
+    description = "Free open-source planetarium";
+    mainProgram = "stellarium";
+    homepage = "https://stellarium.org/";
+    license = lib.licenses.gpl2Plus;
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [ kilianar ];
+    broken = stdenv.hostPlatform.isDarwin;
+  };
+})

pkgs/applications/science/biology/cd-hit/default.nix

@@ -0,0 +1,54 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  makeWrapper,
+  zlib,
+  perl,
+  perlPackages,
+  openmp,
+}:
+
+stdenv.mkDerivation rec {
+  version = "4.8.1";
+  pname = "cd-hit";
+
+  src = fetchFromGitHub {
+    owner = "weizhongli";
+    repo = "cdhit";
+    rev = "V${version}";
+    sha256 = "032nva6iiwmw59gjipm1mv0xlcckhxsf45mc2qbnv19lbis0q22i";
+  };
+
+  propagatedBuildInputs = [
+    perl
+    perlPackages.TextNSP
+    perlPackages.ImageMagick
+  ];
+
+  nativeBuildInputs = [
+    zlib
+    makeWrapper
+  ];
+  buildInputs = lib.optional stdenv.cc.isClang openmp;
+
+  makeFlags = [
+    "CC=${stdenv.cc.targetPrefix}c++" # remove once https://github.com/weizhongli/cdhit/pull/114 is merged
+    "PREFIX=$(out)/bin"
+  ];
+
+  preInstall = "mkdir -p $out/bin";
+
+  postFixup = ''
+    wrapProgram $out/bin/FET.pl --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/plot_2d.pl --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/clstr_list_sort.pl --prefix PERL5LIB : $PERL5LIB
+  '';
+  meta = with lib; {
+    description = "Clustering and comparing protein or nucleotide sequences";
+    homepage = "http://weizhongli-lab.org/cd-hit/";
+    license = licenses.gpl2;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.unix;
+  };
+}

pkgs/applications/science/biology/hh-suite/default.nix

@@ -0,0 +1,51 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  cmake,
+  xxd,
+  enableMpi ? false,
+  mpi,
+  openmp,
+}:
+stdenv.mkDerivation rec {
+  pname = "hh-suite";
+  version = "3.3.0";
+
+  src = fetchFromGitHub {
+    owner = "soedinglab";
+    repo = "hh-suite";
+    rev = "v${version}";
+    hash = "sha256-kjNqJddioCZoh/cZL3YNplweIGopWIGzCYQOnKDqZmw=";
+  };
+
+  patches = [
+    # Should be removable as soon as this upstream PR is merged: https://github.com/soedinglab/hh-suite/pull/357
+    (fetchpatch {
+      name = "fix-gcc13-build-issues.patch";
+      url = "https://github.com/soedinglab/hh-suite/commit/cec47cba5dcd580e668b1ee507c9282fbdc8e7d7.patch";
+      hash = "sha256-Msdmj9l8voPYXK0SSwUA6mEbFLBhTjjE/Kjp0VL4Kf4=";
+    })
+  ];
+
+  nativeBuildInputs = [
+    cmake
+    xxd
+  ];
+  cmakeFlags =
+    lib.optional stdenv.hostPlatform.isx86 "-DHAVE_SSE2=1"
+    ++ lib.optional stdenv.hostPlatform.isAarch "-DHAVE_ARM8=1"
+    ++ lib.optional stdenv.hostPlatform.avx2Support "-DHAVE_AVX2=1"
+    ++ lib.optional stdenv.hostPlatform.sse4_1Support "-DHAVE_SSE4_1=1";
+
+  buildInputs = lib.optional stdenv.cc.isClang openmp ++ lib.optional enableMpi mpi;
+
+  meta = with lib; {
+    description = "Remote protein homology detection suite";
+    homepage = "https://github.com/soedinglab/hh-suite";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+}

pkgs/applications/science/biology/minc-tools/default.nix

@@ -0,0 +1,69 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  makeWrapper,
+  flex,
+  bison,
+  perl,
+  TextFormat,
+  libminc,
+  libjpeg,
+  nifticlib,
+  zlib,
+}:
+
+stdenv.mkDerivation {
+  pname = "minc-tools";
+  version = "2.3.06-unstable-2023-08-12";
+
+  src = fetchFromGitHub {
+    owner = "BIC-MNI";
+    repo = "minc-tools";
+    rev = "c86a767dbb63aaa05ee981306fa09f6133bde427";
+    hash = "sha256-PLNcuDU0ht1PcjloDhrPzpOpE42gbhPP3rfHtP7WnM4=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    flex
+    bison
+    makeWrapper
+  ];
+
+  buildInputs = [
+    libminc
+    libjpeg
+    nifticlib
+    zlib
+  ];
+
+  propagatedBuildInputs = [
+    perl
+    TextFormat
+  ];
+
+  cmakeFlags = [
+    "-DLIBMINC_DIR=${libminc}/lib/cmake"
+    "-DZNZ_INCLUDE_DIR=${nifticlib}/include/nifti"
+    "-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti"
+  ];
+
+  env.NIX_CFLAGS_COMPILE = "-D_FillValue=NC_FillValue";
+
+  postFixup = ''
+    for prog in minccomplete minchistory mincpik; do
+      wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB
+    done
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/BIC-MNI/minc-tools";
+    description = "Command-line utilities for working with MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license = licenses.free;
+    broken = stdenv.hostPlatform.isDarwin;
+  };
+}

pkgs/applications/science/chemistry/autodock-vina/default.nix

@@ -0,0 +1,60 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  boost186,
+  glibc,
+}:
+let
+  boost' = boost186.override {
+    enableShared = false;
+  };
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "autodock-vina";
+  version = "1.2.7";
+
+  src = fetchFromGitHub {
+    owner = "ccsb-scripps";
+    repo = "autodock-vina";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-AQJl/EUAkdIQJZSN27sbjG7dYbQxeEb8Pd+p2kKRnvA=";
+  };
+
+  sourceRoot = "${finalAttrs.src.name}/build/${
+    if stdenv.hostPlatform.isDarwin then "mac" else "linux"
+  }/release";
+
+  buildInputs = [
+    boost'
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isLinux [
+    glibc.static
+  ];
+
+  makeFlags = [
+    "GPP=${stdenv.cc.targetPrefix}c++"
+    "BASE=${boost'}"
+    "BOOST_INCLUDE=${lib.getDev boost'}/include"
+  ];
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm755 vina vina_split -t $out/bin/
+
+    runHook postInstall
+  '';
+
+  passthru.boost = boost';
+
+  meta = with lib; {
+    description = "One of the fastest and most widely used open-source docking engines";
+    homepage = "https://vina.scripps.edu/";
+    changelog = "https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v${finalAttrs.version}";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+    mainProgram = "vina";
+  };
+})

pkgs/applications/science/chemistry/autodock-vina/python-bindings.nix

@@ -0,0 +1,65 @@
+{
+  lib,
+  buildPythonPackage,
+  autodock-vina,
+  swig,
+  setuptools,
+  numpy,
+}:
+
+let
+  inherit (autodock-vina) boost;
+in
+
+buildPythonPackage {
+  inherit (autodock-vina)
+    pname
+    version
+    src
+    meta
+    ;
+
+  format = "pyproject";
+
+  sourceRoot = "${autodock-vina.src.name}/build/python";
+
+  postPatch = ''
+    # wildcards are not allowed
+    # https://github.com/ccsb-scripps/AutoDock-Vina/issues/176
+    substituteInPlace setup.py \
+      --replace "python_requires='>=3.5.*'" "python_requires='>=3.5'"
+
+    # setupPyBuildFlags are not applied with `format = "pyproject"`
+    substituteInPlace setup.py \
+      --replace "= locate_boost()" "= '${lib.getDev boost}/include', '${boost}/lib'"
+
+    # this line attempts to delete the source code
+    substituteInPlace setup.py \
+      --replace "shutil.rmtree('src')" "..."
+
+    # np.int is deprecated
+    # https://github.com/ccsb-scripps/AutoDock-Vina/pull/167 and so on
+    substituteInPlace vina/vina.py \
+      --replace "np.int" "int"
+  '';
+
+  nativeBuildInputs = [
+    setuptools
+    swig
+  ];
+
+  buildInputs = [
+    boost
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+  ];
+
+  # upstream has no tests
+  doCheck = false;
+
+  pythonImportsCheck = [
+    "vina"
+  ];
+}

pkgs/applications/science/chemistry/avogadro2/default.nix

@@ -0,0 +1,65 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  eigen,
+  avogadrolibs,
+  molequeue,
+  hdf5,
+  openbabel,
+  qttools,
+  wrapQtAppsHook,
+  mesa,
+}:
+
+let
+  avogadroI18N = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "avogadro-i18n";
+    tag = "1.101.0";
+    hash = "sha256-3qFx/rc5xqfrLq3Kr5b/Rid2LR/gfP6uqhhATyQL6Y8=";
+  };
+
+in
+stdenv.mkDerivation rec {
+  pname = "avogadro2";
+  version = "1.101.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "avogadroapp";
+    rev = version;
+    hash = "sha256-F8to1DyeyyhsivkXDB/KH10/7teVnsoSU/ZHIsNISqc=";
+  };
+
+  postUnpack = ''
+    cp -r ${avogadroI18N} avogadro-i18n
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    avogadrolibs
+    molequeue
+    eigen
+    hdf5
+    qttools
+  ];
+
+  propagatedBuildInputs = [ openbabel ];
+
+  qtWrapperArgs = [ "--prefix PATH : ${lib.getBin openbabel}/bin" ];
+
+  meta = with lib; {
+    description = "Molecule editor and visualizer";
+    mainProgram = "avogadro2";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/avogadroapp";
+    inherit (mesa.meta) platforms;
+    license = licenses.bsd3;
+  };
+}

pkgs/applications/science/chemistry/nwchem/default.nix

@@ -0,0 +1,234 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchurl,
+  mpiCheckPhaseHook,
+  which,
+  openssh,
+  gcc,
+  gfortran,
+  perl,
+  mpi,
+  blas,
+  lapack,
+  python3,
+  tcsh,
+  automake,
+  autoconf,
+  libtool,
+  makeWrapper,
+}:
+
+assert blas.isILP64 == lapack.isILP64;
+
+let
+  versionGA = "5.8.2"; # Fixed by nwchem
+
+  gaSrc = fetchFromGitHub {
+    owner = "GlobalArrays";
+    repo = "ga";
+    rev = "v${versionGA}";
+    hash = "sha256-2ffQIg9topqKX7ygnWaa/UunL9d0Lj9qr9xucsjLuoY=";
+  };
+
+  dftd3Src = fetchurl {
+    url = "https://www.chemie.uni-bonn.de/grimme/software/dft-d3/dftd3.tgz";
+    hash = "sha256-2Xz5dY9hqoH9hUJUSPv0pujOB8EukjZzmDGjrzKID1k=";
+  };
+
+  versionLibxc = "6.1.0";
+  libxcSrc = fetchurl {
+    url = "https://gitlab.com/libxc/libxc/-/archive/${versionLibxc}/libxc-${versionLibxc}.tar.gz";
+    hash = "sha256-9ZN0X6R+v7ndxGeqr9wvoSdfDXJQxpLOl2E4mpDdjq8=";
+  };
+
+  plumedSrc = fetchFromGitHub {
+    owner = "edoapra";
+    repo = "plumed2";
+    rev = "88f06db71173e7893713a582e5ada7193e8ae1c9";
+    hash = "sha256-p5XNxHcE/QkJ5WdQH/xPp2EyrqCNjA/w/e1R2fkwYts=";
+  };
+
+in
+stdenv.mkDerivation rec {
+  pname = "nwchem";
+  version = "7.2.3";
+
+  src = fetchFromGitHub {
+    owner = "nwchemgit";
+    repo = "nwchem";
+    rev = "v${version}-release";
+    hash = "sha256-2qc4kLb/WmUJuJGonIyS7pgCfyt8yXdcpDAKU0RMY58=";
+  };
+
+  outputs = [
+    "out"
+    "dev"
+  ];
+
+  nativeBuildInputs = [
+    perl
+    automake
+    autoconf
+    libtool
+    makeWrapper
+    gfortran
+    which
+  ];
+  buildInputs = [
+    tcsh
+    openssh
+    blas
+    lapack
+    python3
+  ];
+  propagatedBuildInputs = [ mpi ];
+  propagatedUserEnvPkgs = [ mpi ];
+
+  postUnpack = ''
+    # These run 'configure' in source tree and
+    # require a writable directory
+    cp -r ${gaSrc}/ source/src/tools/ga-${versionGA}
+    chmod -R u+w source/src/tools/ga-${versionGA}
+
+    cp -r ${plumedSrc} source/src/libext/plumed/plumed2
+    chmod -R u+w source/src/libext/plumed/plumed2
+
+    # Provide tarball in expected location
+    ln -s ${dftd3Src} source/src/nwpw/nwpwlib/nwpwxc/dftd3.tgz
+    ln -s ${libxcSrc} source/src/libext/libxc/libxc-${versionLibxc}.tar.gz
+  '';
+
+  postPatch = ''
+    find -type f -executable -exec sed -i "s:/bin/csh:${tcsh}/bin/tcsh:" \{} \;
+    find -type f -name "GNUmakefile" -exec sed -i "s:/usr/bin/gcc:${gcc}/bin/gcc:" \{} \;
+    find -type f -name "GNUmakefile" -exec sed -i "s:/bin/rm:rm:" \{} \;
+    find -type f -executable -exec sed -i "s:/bin/rm:rm:" \{} \;
+    find -type f -name "makelib.h" -exec sed -i "s:/bin/rm:rm:" \{} \;
+
+    # 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 ./
+  '';
+
+  # There is no configure script. Instead the build is controlled via
+  # environment variables passed to the Makefile
+  configurePhase = ''
+    runHook preConfigure
+
+    # config parameters
+    export NWCHEM_TARGET="LINUX64"
+
+    export ARMCI_NETWORK="MPI-PR"
+    export USE_MPI="y"
+    export USE_MPIF="y"
+
+    export NWCHEM_MODULES="all python"
+
+    export USE_PYTHONCONFIG="y"
+    export USE_PYTHON64="n"
+    export PYTHONLIBTYPE="so"
+    export PYTHONHOME="${python3}"
+    export PYTHONVERSION=${lib.versions.majorMinor python3.version}
+
+    export BLASOPT="-L${blas}/lib -lblas"
+    export LAPACK_LIB="-L${lapack}/lib -llapack"
+    export BLAS_SIZE=${if blas.isILP64 then "8" else "4"}
+
+    # extra TCE related options
+    export MRCC_METHODS="y"
+    export EACCSD="y"
+    export IPCCSD="y"
+
+    export CCSDTQ="y"
+
+    export NWCHEM_TOP="$(pwd)"
+
+    runHook postConfigure
+  '';
+
+  # Required for build with gcc-14
+  env.NIX_CFLAGS_COMPILE = "-Wno-error=implicit-int";
+
+  enableParallelBuilding = true;
+
+  preBuild = ''
+    ln -s ${gaSrc} src/tools/ga-${versionGA}.tar.gz
+    cd src
+    make nwchem_config
+    ${lib.optionalString (!blas.isILP64) "make 64_to_32"}
+  '';
+
+  postBuild = ''
+    cd $NWCHEM_TOP/src/util
+    make version
+    make
+    cd $NWCHEM_TOP/src
+    make link
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin $out/share/nwchem
+
+    cp $NWCHEM_TOP/bin/LINUX64/nwchem $out/bin/nwchem
+    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
+
+    wrapProgram $out/bin/nwchem \
+      --set-default NWCHEM_BASIS_LIBRARY $out/share/nwchem/data/libraries/
+
+    cat > $out/share/nwchem/nwchemrc << EOF
+    nwchem_basis_library $out/share/nwchem/data/libraries/
+    nwchem_nwpw_library $out/share/nwchem//data/libraryps/
+    ffield amber
+    amber_1 $out/share/nwchem/data/amber_s/
+    amber_2 $out/share/nwchem/data/amber_q/
+    amber_3 $out/share/nwchem/data/amber_x/
+    amber_4 $out/share/nwchem/data/amber_u/
+    spce    $out/share/nwchem/data/solvents/spce.rst
+    charmm_s $out/share/nwchem/data/charmm_s/
+    charmm_x $out/share/nwchem/data/charmm_x/
+    EOF
+
+    runHook postInstall
+  '';
+
+  doCheck = false;
+
+  doInstallCheck = true;
+  nativeInstallCheckInputs = [ mpiCheckPhaseHook ];
+  installCheckPhase = ''
+    runHook preInstallCheck
+
+    # run a simple water test
+    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
+  '';
+
+  passthru = { inherit mpi; };
+
+  meta = with lib; {
+    description = "Open Source High-Performance Computational Chemistry";
+    mainProgram = "nwchem";
+    platforms = [
+      "x86_64-linux"
+      "aarch64-linux"
+    ];
+    maintainers = with maintainers; [
+      sheepforce
+      markuskowa
+    ];
+    homepage = "https://nwchemgit.github.io";
+    license = licenses.ecl20;
+  };
+}

pkgs/applications/science/chemistry/quantum-espresso/default.nix

@@ -0,0 +1,139 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitLab,
+  fetchFromGitHub,
+  git,
+  cmake,
+  gfortran,
+  pkg-config,
+  fftw,
+  blas,
+  lapack,
+  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 = "7.4.1";
+  pname = "quantum-espresso";
+
+  src = fetchFromGitLab {
+    owner = "QEF";
+    repo = "q-e";
+    rev = "qe-${version}";
+    hash = "sha256-o1CjIuJCTtIud4zeHROksK1Ub9RL/OB8GecAQOIGf1s=";
+  };
+
+  # 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)" ""
+
+    ${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@"'
+  '';
+
+  patches = [
+    # this patch reverts commit 5fb5a679, which enforced static library builds.
+    ./findLibxc.patch
+  ];
+
+  passthru = { inherit mpi; };
+
+  nativeBuildInputs = [
+    cmake
+    gfortran
+    git
+    pkg-config
+  ];
+
+  buildInputs = [
+    fftw
+    blas
+    lapack
+    wannier90
+    libmbd
+    libxc
+    hdf5
+  ]
+  ++ lib.optional enableMpi scalapack;
+
+  propagatedBuildInputs = lib.optional enableMpi mpi;
+  propagatedUserEnvPkgs = lib.optional enableMpi mpi;
+
+  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";
+    longDescription = ''
+      Quantum ESPRESSO is an integrated suite of Open-Source computer codes for
+      electronic-structure calculations and materials modeling at the
+      nanoscale. It is based on density-functional theory, plane waves, and
+      pseudopotentials.
+    '';
+    homepage = "https://www.quantum-espresso.org/";
+    license = licenses.gpl2;
+    platforms = [
+      "x86_64-linux"
+      "x86_64-darwin"
+    ];
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/applications/science/chemistry/quantum-espresso/findLibxc.patch

@@ -0,0 +1,70 @@
+diff --git a/cmake/FindLibxc.cmake b/cmake/FindLibxc.cmake
+index 011a36b77..226f38051 100644
+--- a/cmake/FindLibxc.cmake
++++ b/cmake/FindLibxc.cmake
+@@ -1,45 +1,50 @@
+-include(FindPackageHandleStandardArgs)
+-find_package(PkgConfig REQUIRED)
+-
+ pkg_search_module(_LIBXC libxc>=${Libxc_FIND_VERSION})
+
+-find_library(LIBXC_LIBRARIES NAMES libxc.a
++find_library(LIBXC_LIBRARIES NAMES xc
+   PATH_SUFFIXES lib
+   HINTS
+-  ${LIBXC_ROOT}
+   ENV EBROOTLIBXC
+   ENV LIBXCROOT
+   ${_LIBXC_LIBRARY_DIRS}
+   DOC "libxc libraries list")
+
+-find_library(LIBXC_LIBRARIES_F03 NAMES libxcf03.a
++find_library(LIBXC_LIBRARIES_F90 NAMES xcf90
+   PATH_SUFFIXES lib
+   HINTS
+-  ${LIBXC_ROOT}
+   ENV EBROOTLIBXC
+   ENV LIBXCROOT
+   ${_LIBXC_LIBRARY_DIRS}
+   DOC "libxc libraries list")
+
++find_library(LIBXC_LIBRARIES_F03 NAMES xcf03
++  PATH_SUFFIXES lib
++  HINTS
++  ENV EBROOTLIBXC
++  ENV LIBXCROOT
++  ${_LIBXC_LIBRARY_DIRS})
+ find_path(LIBXC_INCLUDE_DIR NAMES xc.h
+   PATH_SUFFIXES inc include
+   HINTS
+-  ${LIBXC_ROOT}
+   ${_LIBXC_INCLUDE_DIRS}
+   ENV EBROOTLIBXC
+   ENV LIBXCROOT)
+
++find_path(LIBXC_INCLUDE_DIR_F90 NAMES xc_f90_lib_m.mod
++  PATH_SUFFIXES inc include
++  HINTS
++  ${_LIBXC_INCLUDE_DIRS}
++  ENV EBROOTLIBXC
++  ENV LIBXCROOT)
+ find_path(LIBXC_INCLUDE_DIR_F03 NAMES xc_f03_lib_m.mod
+   PATH_SUFFIXES inc include
+   HINTS
+-  ${LIBXC_ROOT}
+   ${_LIBXC_INCLUDE_DIRS}
+   ENV EBROOTLIBXC
+   ENV LIBXCROOT)
+
+ find_package_handle_standard_args(Libxc DEFAULT_MSG LIBXC_LIBRARIES LIBXC_INCLUDE_DIR)
+
+-if (${Libxc_FOUND} AND LIBXC_LIBRARIES_F03 AND LIBXC_INCLUDE_DIR_F03)
++if (${Libxc_FOUND} AND LIBXC_LIBRARIES_F90 AND LIBXC_LIBRARIES_F03 AND LIBXC_INCLUDE_DIR_F90 AND LIBXC_INCLUDE_DIR_F03)
+   if(_LIBXC_VERSION)
+     set(Libxc_VERSION ${_LIBXC_VERSION})
+   else()
+@@ -53,4 +58,3 @@ if (${Libxc_FOUND} AND LIBXC_LIBRARIES_F03 AND LIBXC_INCLUDE_DIR_F03)
+ else()
+   unset(Libxc_FOUND)
+ endif()
+-

pkgs/applications/science/chemistry/siesta/default.nix

@@ -0,0 +1,107 @@
+{
+  lib,
+  stdenv,
+  gfortran,
+  blas,
+  lapack,
+  scalapack,
+  useMpi ? false,
+  mpi,
+  fetchFromGitLab,
+  cmake,
+  pkg-config,
+  readline,
+  ninja,
+  elpa,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "siesta";
+  version = "5.2.2";
+
+  src = fetchFromGitLab {
+    owner = "siesta-project";
+    repo = "siesta";
+    tag = finalAttrs.version;
+    hash = "sha256-pud8RlJAT+0TwyPRsbf5D/8FfLjZvPYPf84Xb7UH6os=";
+    fetchSubmodules = true;
+  };
+
+  passthru = {
+    inherit mpi;
+  };
+
+  nativeBuildInputs = [
+    ninja
+    gfortran
+    cmake
+    pkg-config
+  ];
+
+  buildInputs = [
+    blas
+    lapack
+    readline
+    elpa
+  ]
+  ++ lib.optionals useMpi [
+    mpi
+    scalapack
+  ];
+
+  NIX_LDFLAGS = "-lm";
+
+  cmakeFlags = [
+    "-DCMAKE_POLICY_VERSION_MINIMUM=3.5"
+    "-DCMAKE_INSTALL_INCLUDEDIR=include"
+    "-DCMAKE_INSTALL_LIBDIR=lib"
+  ];
+
+  enableParallelBuilding = false; # Started making trouble with gcc-11
+
+  preBuild = ''
+    # See https://gitlab.com/siesta-project/siesta/-/commit/a10bf1628e7141ba263841889c3503c263de1582
+    # This may be fixed in the next release.
+    makeFlagsArray=(
+        FFLAGS="-fallow-argument-mismatch"
+    )
+  ''
+  + (
+    if useMpi then
+      ''
+        makeFlagsArray+=(
+            CC="mpicc" FC="mpifort"
+            FPPFLAGS="-DMPI" MPI_INTERFACE="libmpi_f90.a" MPI_INCLUDE="."
+            COMP_LIBS="" LIBS="-lblas -llapack -lscalapack"
+        );
+      ''
+    else
+      ''
+        makeFlagsArray+=(
+          COMP_LIBS="" LIBS="-lblas -llapack"
+        );
+      ''
+  );
+
+  meta = {
+    description = "First-principles materials simulation code using DFT";
+    mainProgram = "siesta";
+    longDescription = ''
+      SIESTA is both a method and its computer program
+      implementation, to perform efficient electronic structure
+      calculations and ab initio molecular dynamics simulations of
+      molecules and solids. SIESTA's efficiency stems from the use
+      of strictly localized basis sets and from the implementation
+      of linear-scaling algorithms which can be applied to suitable
+      systems. A very important feature of the code is that its
+      accuracy and cost can be tuned in a wide range, from quick
+      exploratory calculations to highly accurate simulations
+      matching the quality of other approaches, such as plane-wave
+      and all-electron methods.
+    '';
+    homepage = "https://siesta-project.org/siesta/";
+    license = lib.licenses.gpl2;
+    platforms = [ "x86_64-linux" ];
+    maintainers = [ lib.maintainers.costrouc ];
+  };
+})

pkgs/applications/science/computer-architecture/qtrvsim/default.nix

@@ -0,0 +1,40 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  wrapQtAppsHook,
+  qtbase,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "QtRVSim";
+  version = "0.9.8";
+
+  src = fetchFromGitHub {
+    owner = "cvut";
+    repo = "qtrvsim";
+    tag = "v${version}";
+    sha256 = "sha256-+EpPDA2+mBTdQjq6i9TN11yeXqvJA28JtmdNihM1a/U=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [ qtbase ];
+
+  meta = with lib; {
+    description = "RISC-V CPU simulator for education purposes";
+    longDescription = ''
+      RISC-V CPU simulator for education purposes with pipeline and cache visualization.
+      Developed at FEE CTU for computer architecture classes.
+    '';
+    homepage = "https://github.com/cvut/qtrvsim";
+    license = licenses.gpl3Plus;
+    platforms = platforms.linux ++ platforms.darwin;
+    maintainers = with maintainers; [ jdupak ];
+    mainProgram = "qtrvsim_gui";
+  };
+}

pkgs/applications/science/electronics/bitscope/common.nix

@@ -0,0 +1,83 @@
+{
+  atk,
+  buildFHSEnv,
+  cairo,
+  dpkg,
+  gdk-pixbuf,
+  glib,
+  gtk2-x11,
+  makeWrapper,
+  pango,
+  lib,
+  stdenv,
+  xorg,
+}:
+
+{
+  src,
+  toolName,
+  version,
+  ...
+}@attrs:
+let
+  wrapBinary = libPaths: binaryName: ''
+    wrapProgram "$out/bin/${binaryName}" \
+      --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath libPaths}"
+  '';
+  pkg = stdenv.mkDerivation rec {
+    inherit (attrs) version src;
+
+    name = "${toolName}-${version}";
+
+    meta =
+      with lib;
+      {
+        homepage = "http://bitscope.com/software/";
+        sourceProvenance = with sourceTypes; [ binaryNativeCode ];
+        license = licenses.unfree;
+        platforms = [ "x86_64-linux" ];
+        maintainers = with maintainers; [
+          vidbina
+        ];
+      }
+      // (attrs.meta or { });
+
+    nativeBuildInputs = [
+      makeWrapper
+      dpkg
+    ];
+
+    libs =
+      attrs.libs or [
+        atk
+        cairo
+        gdk-pixbuf
+        glib
+        gtk2-x11
+        pango
+        xorg.libX11
+      ];
+
+    dontBuild = true;
+
+    unpackPhase =
+      attrs.unpackPhase or ''
+        dpkg-deb -x ${attrs.src} ./
+      '';
+
+    installPhase =
+      attrs.installPhase or ''
+        mkdir -p "$out/bin"
+        cp -a usr/* "$out/"
+        ${(wrapBinary libs) attrs.toolName}
+      '';
+  };
+in
+buildFHSEnv {
+  pname = attrs.toolName;
+  inherit (attrs) version;
+  runScript = "${pkg.outPath}/bin/${attrs.toolName}";
+}
+// {
+  inherit (pkg) meta name;
+}

pkgs/applications/science/electronics/bitscope/packages.nix

@@ -0,0 +1,164 @@
+{
+  callPackage,
+  fetchurl,
+}:
+
+let
+  mkBitscope = callPackage (import ./common.nix) { };
+in
+{
+  chart =
+    let
+      toolName = "bitscope-chart";
+      version = "2.0.FK22M";
+    in
+    mkBitscope {
+      inherit toolName version;
+
+      meta = {
+        description = "Multi-channel waveform data acquisition and chart recording application";
+        homepage = "http://bitscope.com/software/chart/";
+      };
+
+      src = fetchurl {
+        url = "http://bitscope.com/download/files/${toolName}_${version}_amd64.deb";
+        sha256 = "08mc82pjamyyyhh15sagsv0sc7yx5v5n54bg60fpj7v41wdwrzxw";
+      };
+    };
+
+  console =
+    let
+      toolName = "bitscope-console";
+      version = "1.0.FK29A";
+    in
+    mkBitscope {
+      # NOTE: this is meant as a demo by BitScope
+      inherit toolName version;
+
+      meta = {
+        description = "Demonstrative communications program designed to make it easy to talk to any model BitScope";
+      };
+
+      src = fetchurl {
+        url = "http://bitscope.com/download/files/${toolName}_${version}_amd64.deb";
+        sha256 = "00b4gxwz7w6pmfrcz14326b24kl44hp0gzzqcqxwi5vws3f0y49d";
+      };
+    };
+
+  display =
+    let
+      toolName = "bitscope-display";
+      version = "1.0.EC17A";
+    in
+    mkBitscope {
+      inherit toolName version;
+
+      meta = {
+        description = "Display diagnostic application for BitScope";
+        homepage = "http://bitscope.com/software/display/";
+      };
+
+      src = fetchurl {
+        url = "http://bitscope.com/download/files/${toolName}_${version}_amd64.deb";
+        sha256 = "05xr5mnka1v3ibcasg74kmj6nlv1nmn3lca1wv77whkq85cmz0s1";
+      };
+    };
+
+  dso =
+    let
+      toolName = "bitscope-dso";
+      version = "2.8.FE22H";
+    in
+    mkBitscope {
+      inherit toolName version;
+
+      meta = {
+        description = "Test and measurement software for BitScope";
+        homepage = "http://bitscope.com/software/dso/";
+      };
+
+      src = fetchurl {
+        url = "http://bitscope.com/download/files/${toolName}_${version}_amd64.deb";
+        sha256 = "0fc6crfkprj78dxxhvhbn1dx1db5chm0cpwlqpqv8sz6whp12mcj";
+      };
+    };
+
+  logic =
+    let
+      toolName = "bitscope-logic";
+      version = "1.2.FC20C";
+    in
+    mkBitscope {
+      inherit toolName version;
+
+      meta = {
+        description = "Mixed signal logic timing and serial protocol analysis software for BitScope";
+        homepage = "http://bitscope.com/software/logic/";
+      };
+
+      src = fetchurl {
+        url = "http://bitscope.com/download/files/${toolName}_${version}_amd64.deb";
+        sha256 = "0lkb7z9gfkiyxdwh4dq1zxfls8gzdw0na1vrrbgnxfg3klv4xns3";
+      };
+    };
+
+  meter =
+    let
+      toolName = "bitscope-meter";
+      version = "2.0.FK22G";
+    in
+    mkBitscope {
+      inherit toolName version;
+
+      meta = {
+        description = "Automated oscilloscope, voltmeter and frequency meter for BitScope";
+        homepage = "http://bitscope.com/software/logic/";
+      };
+
+      src = fetchurl {
+        url = "http://bitscope.com/download/files/${toolName}_${version}_amd64.deb";
+        sha256 = "0nirbci6ymhk4h4bck2s4wbsl5r9yndk2jvvv72zwkg21248mnbp";
+      };
+    };
+
+  proto =
+    let
+      toolName = "bitscope-proto";
+      version = "0.9.FG13B";
+    in
+    mkBitscope {
+      inherit toolName version;
+      # NOTE: this is meant as a demo by BitScope
+      # NOTE: clicking on logo produces error
+      # TApplication.HandleException Executable not found: "http://bitscope.com/blog/DK/?p=DK15A"
+
+      meta = {
+        description = "Demonstrative prototype oscilloscope built using the BitScope Library";
+        homepage = "http://bitscope.com/blog/DK/?p=DK15A";
+      };
+
+      src = fetchurl {
+        url = "http://bitscope.com/download/files/${toolName}_${version}_amd64.deb";
+        sha256 = "1ybjfbh3narn29ll4nci4b7rnxy0hj3wdfm4v8c6pjr8pfvv9spy";
+      };
+    };
+
+  server =
+    let
+      toolName = "bitscope-server";
+      version = "1.0.FK26A";
+    in
+    mkBitscope {
+      inherit toolName version;
+
+      meta = {
+        description = "Remote access server solution for any BitScope";
+        homepage = "http://bitscope.com/software/server/";
+      };
+
+      src = fetchurl {
+        url = "http://bitscope.com/download/files/${toolName}_${version}_amd64.deb";
+        sha256 = "1079n7msq6ks0n4aasx40rd4q99w8j9hcsaci71nd2im2jvjpw9a";
+      };
+    };
+}

pkgs/applications/science/electronics/caneda/default.nix

@@ -0,0 +1,39 @@
+{
+  mkDerivation,
+  lib,
+  fetchFromGitHub,
+  cmake,
+  qtbase,
+  qttools,
+  qtsvg,
+  qwt6_1,
+}:
+
+mkDerivation rec {
+  pname = "caneda";
+  version = "0.4.0";
+
+  src = fetchFromGitHub {
+    owner = "Caneda";
+    repo = "Caneda";
+    rev = version;
+    sha256 = "sha256-oE0cdOwufc7CHEFr3YU8stjg1hBGs4bemhXpNTCTpDQ=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [
+    qtbase
+    qttools
+    qtsvg
+    qwt6_1
+  ];
+
+  meta = {
+    description = "Open source EDA software focused on easy of use and portability";
+    mainProgram = "caneda";
+    homepage = "http://caneda.org";
+    license = lib.licenses.gpl2Plus;
+    maintainers = [ ];
+    platforms = with lib.platforms; linux;
+  };
+}

pkgs/applications/science/electronics/degate/default.nix

@@ -0,0 +1,78 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  cmake,
+  boost183,
+  qtbase,
+  qtimageformats,
+  qttools,
+  wrapQtAppsHook,
+}:
+
+let
+  boost_static = boost183.override { enableStatic = true; };
+
+in
+stdenv.mkDerivation rec {
+  pname = "degate";
+  version = "2.0.0";
+
+  src = fetchFromGitHub {
+    owner = "DegateCommunity";
+    repo = "Degate";
+    tag = "v${version}";
+    hash = "sha256-INoA3Z6ya03ZMn6E+nOCkXZLoxoo2WgPDw9v5miI09A=";
+  };
+
+  patches = [
+    # bump bundled catch2 to avoid incompatibility with modern glibc
+    (fetchpatch {
+      name = "catch2-2.13.9.patch";
+      url = "https://github.com/DegateCommunity/Degate/commit/06346dde4312cbb867854899eacf58679d6ac7e2.patch";
+      includes = [ "tests/catch2/catch.hpp" ];
+      hash = "sha256-SbSA813QI8RRVy1lvAOGMGAC2KUQKjwYR2imqX40pvU=";
+    })
+  ];
+
+  postPatch = ''
+    sed -i -E '/(_OUTPUT_DIRECTORY|DESTINATION)/s|\bout/||g' CMakeLists.txt
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    qttools
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    boost_static
+    qtbase
+  ];
+
+  doCheck = true;
+  checkPhase = ''
+    runHook preCheck
+
+    (
+      cd tests/out/bin
+
+      # provide qtimageformats plugin to allow tests to read tiff files
+      export QT_PLUGIN_PATH="${qtimageformats}/${qtbase.qtPluginPrefix}"
+
+      ./DegateTests
+    )
+
+    runHook postCheck
+  '';
+
+  meta = with lib; {
+    description = "Modern and open-source cross-platform software for chips reverse engineering";
+    mainProgram = "Degate";
+    homepage = "https://degate.readthedocs.io/";
+    license = licenses.gpl3;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ ris ];
+  };
+}

pkgs/applications/science/electronics/dsview/default.nix

@@ -0,0 +1,70 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  pkg-config,
+  cmake,
+  wrapQtAppsHook,
+  libzip,
+  boost,
+  fftw,
+  libusb1,
+  qtbase,
+  qtsvg,
+  qtwayland,
+  python3,
+  desktopToDarwinBundle,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "dsview";
+
+  version = "1.3.2";
+
+  src = fetchFromGitHub {
+    owner = "DreamSourceLab";
+    repo = "DSView";
+    rev = "v${finalAttrs.version}";
+    sha256 = "sha256-d/TfCuJzAM0WObOiBhgfsTirlvdROrlCm+oL1cqUrIs=";
+  };
+
+  patches = [
+    # Fix absolute install paths
+    ./install.patch
+  ];
+
+  # /build/source/libsigrok4DSL/strutil.c:343:19: error: implicit declaration of function 'strcasecmp'; did you mean 'g_strcasecmp'? []
+  env.NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration";
+
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+    wrapQtAppsHook
+  ]
+  ++ lib.optional stdenv.hostPlatform.isDarwin desktopToDarwinBundle;
+
+  buildInputs = [
+    boost
+    fftw
+    qtbase
+    qtsvg
+    libusb1
+    libzip
+    python3
+  ]
+  ++ lib.optional stdenv.hostPlatform.isLinux qtwayland;
+
+  doInstallCheck = true;
+
+  meta = {
+    description = "GUI program for supporting various instruments from DreamSourceLab, including logic analyzer, oscilloscope, etc";
+    mainProgram = "DSView";
+    homepage = "https://www.dreamsourcelab.com/";
+    license = lib.licenses.gpl3Plus;
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [
+      bachp
+      carlossless
+    ];
+  };
+})

pkgs/applications/science/electronics/dsview/install.patch

@@ -0,0 +1,23 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index eb9be42..220817c 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -662,16 +662,8 @@ install(FILES DSView/icons/logo.svg DESTINATION share/icons/hicolor/scalable/app
+ install(FILES DSView/icons/logo.svg DESTINATION share/pixmaps RENAME dsview.svg)
+ 
+ if(CMAKE_SYSTEM_NAME MATCHES "Linux")	
+-	install(FILES DSView/DSView.desktop DESTINATION /usr/share/applications RENAME dsview.desktop)
+-	
+-	if(IS_DIRECTORY /usr/lib/udev/rules.d)
+-		install(FILES DSView/DreamSourceLab.rules DESTINATION /usr/lib/udev/rules.d RENAME 60-dreamsourcelab.rules)
+-	elseif(IS_DIRECTORY /lib/udev/rules.d)
+-		install(FILES DSView/DreamSourceLab.rules DESTINATION /lib/udev/rules.d RENAME 60-dreamsourcelab.rules)
+-	elseif(IS_DIRECTORY /etc/udev/rules.d)
+-		install(FILES DSView/DreamSourceLab.rules DESTINATION /etc/udev/rules.d RENAME 60-dreamsourcelab.rules)
+-	endif()
+-
++	install(FILES DSView/DreamSourceLab.rules DESTINATION etc/udev/rules.d RENAME 60-dreamsourcelab.rules)
+ endif()
++install(FILES DSView/DSView.desktop DESTINATION share/applications RENAME dsview.desktop)
+ 
+ install(FILES NEWS25 DESTINATION share/DSView RENAME NEWS25)

pkgs/applications/science/electronics/eagle/eagle.nix

@@ -0,0 +1,136 @@
+{
+  lib,
+  stdenv,
+  mkDerivation,
+  fetchurl,
+  makeDesktopItem,
+  libXrender,
+  libXrandr,
+  libXcursor,
+  libX11,
+  libXext,
+  libXi,
+  libxcb,
+  libGL,
+  glib,
+  nss,
+  nspr,
+  expat,
+  alsa-lib,
+  qtbase,
+  qtdeclarative,
+  qtsvg,
+  qtlocation,
+  qtwebchannel,
+  qtwebengine,
+}:
+
+let
+  libPath = lib.makeLibraryPath [
+    libXrender
+    libXrandr
+    libXcursor
+    libX11
+    libXext
+    libXi
+    libxcb
+    libGL
+    glib
+    nss
+    nspr
+    expat
+    alsa-lib
+    qtbase
+    qtdeclarative
+    qtsvg
+    qtlocation
+    qtwebchannel
+    qtwebengine
+  ];
+in
+mkDerivation rec {
+  pname = "eagle";
+  version = "9.6.2";
+
+  src = fetchurl {
+    url = "https://eagle-updates.circuits.io/downloads/${
+      builtins.replaceStrings [ "." ] [ "_" ] version
+    }/Autodesk_EAGLE_${version}_English_Linux_64bit.tar.gz";
+    sha256 = "18syygnskl286kn8aqfzzdsyzq59d2w19y1h1ynyxsnrvkyv71h0";
+  };
+
+  desktopItem = makeDesktopItem {
+    name = "eagle";
+    exec = "eagle";
+    icon = "eagle";
+    comment = "Schematic capture and PCB layout";
+    desktopName = "Eagle";
+    genericName = "Schematic editor";
+    categories = [ "Development" ];
+  };
+
+  buildInputs = [
+    libXrender
+    libXrandr
+    libXcursor
+    libX11
+    libXext
+    libXi
+    libxcb
+    libGL
+    glib
+    nss
+    nspr
+    expat
+    alsa-lib
+    qtbase
+    qtdeclarative
+    qtsvg
+    qtlocation
+    qtwebchannel
+    qtwebengine
+  ];
+
+  installPhase = ''
+    # Extract eagle tarball
+    mkdir "$out"
+    tar -xzf "$src" -C "$out"
+
+    # Install manpage
+    mkdir -p "$out"/share/man/man1
+    ln -s "$out"/eagle-${version}/doc/eagle.1 "$out"/share/man/man1/eagle.1
+
+    patchelf \
+      --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
+      --set-rpath "${libPath}:$out/eagle-${version}/lib:${lib.getLib stdenv.cc.cc}/lib" \
+      "$out"/eagle-${version}/eagle
+
+    mkdir -p "$out"/bin
+    ln -s "$out"/eagle-${version}/eagle "$out"/bin/eagle
+
+    # Remove bundled libraries that are available in nixpkgs
+    # TODO: There still may be unused bundled libraries
+    rm "$out"/eagle-${version}/lib/libQt5*.so.5
+    rm "$out"/eagle-${version}/lib/{libxcb-*.so.*,libX*.so.*,libxshmfence.so.1}
+    rm "$out"/eagle-${version}/lib/{libEGL.so.1,libglapi.so.0,libgbm.so.1}
+
+    # No longer needed (we don't use the bundled Qt libraries)
+    rm -r "$out"/eagle-${version}/libexec
+    rm -r "$out"/eagle-${version}/plugins
+
+    # Make desktop item
+    mkdir -p "$out"/share/applications
+    cp "$desktopItem"/share/applications/* "$out"/share/applications/
+    mkdir -p "$out"/share/pixmaps
+    ln -s "$out/eagle-${version}/bin/eagle-logo.png" "$out"/share/pixmaps/eagle.png
+  '';
+
+  meta = with lib; {
+    description = "Schematic editor and PCB layout tool from Autodesk (formerly CadSoft)";
+    homepage = "https://www.autodesk.com/products/eagle/overview";
+    sourceProvenance = with sourceTypes; [ binaryNativeCode ];
+    license = licenses.unfree;
+    platforms = [ "x86_64-linux" ];
+    maintainers = [ ];
+  };
+}

pkgs/applications/science/electronics/eagle/eagle7_fixer.c

@@ -0,0 +1,134 @@
+/*
+ * LD_PRELOAD trick to make Eagle (schematic editor and PCB layout tool from
+ * CadSoft) work from a read-only installation directory.
+ *
+ * When Eagle starts, it looks for the license file in <eagle>/bin/eagle.key
+ * (where <eagle> is the install path). If eagle.key is not found, Eagle checks
+ * for write access to <eagle>/bin/, shows a license dialog to the user and
+ * then attempts to write a license file to <eagle>/bin/.
+ *
+ * This will of course fail when Eagle is installed in the read-only Nix store.
+ * Hence this library that redirects accesses to the those paths in the
+ * following way:
+ *
+ *   <eagle>/bin              => $HOME
+ *   <eagle>/bin/eagle.key    => $HOME/.eagle.key
+ *
+ * Also, if copying an example project to ~/eagle/ (in the Eagle GUI), Eagle
+ * chmod's the destination with read-only permission bits (presumably because
+ * the source is read-only) and fails to complete the copy operation.
+ * Therefore, the mode argument in calls to chmod() is OR'ed with the S_IWUSR
+ * bit (write by owner).
+ *
+ * Usage:
+ *   gcc -shared -fPIC -DEAGLE_PATH="$out/eagle-${version}" eagle_fixer.c -o eagle_fixer.so -ldl
+ *   LD_PRELOAD=$PWD/eagle_fixer.so ./result/bin/eagle
+ *
+ * To see the paths that are modified at runtime, set the environment variable
+ * EAGLE_FIXER_DEBUG to 1.
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <fcntl.h>
+#include <dlfcn.h>
+#include <limits.h>
+#include <sys/stat.h>
+
+#ifndef EAGLE_PATH
+#error Missing EAGLE_PATH, path to the eagle-${version} installation directory.
+#endif
+
+typedef FILE *(*fopen_func_t)(const char *path, const char *mode);
+typedef int (*access_func_t)(const char *pathname, int mode);
+typedef int (*chmod_func_t)(const char *path, mode_t mode);
+
+/*
+ * Map <eagle>/bin to $HOME and <eagle>/bin/eagle.key to $HOME/.eagle.key
+ *
+ * Path is truncated if bigger than PATH_MAX. It's not threadsafe, but that's
+ * OK.
+ */
+static const char *redirect(const char *pathname)
+{
+	static char buffer[PATH_MAX];
+	const char *homepath;
+	const char *new_path;
+	static int have_warned;
+
+	homepath = getenv("HOME");
+	if (!homepath) {
+		homepath = "/";
+		if (!have_warned && getenv("EAGLE_FIXER_DEBUG")) {
+			fprintf(stderr, "eagle_fixer: HOME is unset, using \"/\" (root) instead.\n");
+			have_warned = 1;
+		}
+	}
+
+	new_path = pathname;
+	if (strcmp(EAGLE_PATH "/bin", pathname) == 0) {
+		/* redirect to $HOME */
+		new_path = homepath;
+	} else if (strcmp(EAGLE_PATH "/bin/eagle.key", pathname) == 0) {
+		/* redirect to $HOME/.eagle.key */
+		snprintf(buffer, PATH_MAX, "%s/.eagle.key", homepath);
+		buffer[PATH_MAX-1] = '\0';
+		new_path = buffer;
+	}
+
+	return new_path;
+}
+
+FILE *fopen(const char *pathname, const char *mode)
+{
+	FILE *fp;
+	const char *path;
+	fopen_func_t orig_fopen;
+
+	orig_fopen = (fopen_func_t)dlsym(RTLD_NEXT, "fopen");
+	path = redirect(pathname);
+	fp = orig_fopen(path, mode);
+
+	if (path != pathname && getenv("EAGLE_FIXER_DEBUG")) {
+		fprintf(stderr, "eagle_fixer: fopen(\"%s\", \"%s\") => \"%s\": fp=%p\n", pathname, mode, path, fp);
+	}
+
+	return fp;
+}
+
+int access(const char *pathname, int mode)
+{
+	int ret;
+	const char *path;
+	access_func_t orig_access;
+
+	orig_access = (access_func_t)dlsym(RTLD_NEXT, "access");
+	path = redirect(pathname);
+	ret = orig_access(path, mode);
+
+	if (path != pathname && getenv("EAGLE_FIXER_DEBUG")) {
+		fprintf(stderr, "eagle_fixer: access(\"%s\", %d) => \"%s\": ret=%d\n", pathname, mode, path, ret);
+	}
+
+	return ret;
+}
+
+int chmod(const char *pathname, mode_t mode)
+{
+	int ret;
+	mode_t new_mode;
+	chmod_func_t orig_chmod;
+
+	orig_chmod = (chmod_func_t)dlsym(RTLD_NEXT, "chmod");
+	new_mode = mode | S_IWUSR;
+	ret = orig_chmod(pathname, new_mode);
+
+	if (getenv("EAGLE_FIXER_DEBUG")) {
+		fprintf(stderr, "eagle_fixer: chmod(\"%s\", %o) => %o: ret=%d\n", pathname, mode, new_mode, ret);
+	}
+
+	return ret;
+}

pkgs/applications/science/electronics/fritzing/default.nix

@@ -0,0 +1,143 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  wrapQtAppsHook,
+  qmake,
+  pkg-config,
+  qtbase,
+  qtsvg,
+  qttools,
+  qtserialport,
+  qtwayland,
+  qt5compat,
+  boost,
+  libngspice,
+  libgit2,
+  quazip,
+  clipper,
+}:
+
+let
+  # SHA256 of the fritzing-parts HEAD on the master branch,
+  # which contains the latest stable parts definitions
+  partsSha = "76235099ed556e52003de63522fdd74e61d53a36";
+
+  parts = fetchFromGitHub {
+    owner = "fritzing";
+    repo = "fritzing-parts";
+    rev = partsSha;
+    hash = "sha256-1QVcPbRBOSYnNFsp7B2OyPXYuPaINRv9yEqGZFd662Y=";
+  };
+
+  # Header-only library
+  svgpp = fetchFromGitHub {
+    owner = "svgpp";
+    repo = "svgpp";
+    tag = "v1.3.1";
+    hash = "sha256-nW0ns06XWfUi22nOKZzFKgAOHVIlQqChW8HxUDOFMh4=";
+  };
+in
+
+stdenv.mkDerivation {
+  pname = "fritzing";
+  version = "1.0.4";
+
+  src = fetchFromGitHub {
+    owner = "fritzing";
+    repo = "fritzing-app";
+    rev = "a8c6ef7cf66f7a42b9b233d6137f1b70a9573a25";
+    hash = "sha256-a/bWAUeDPj3g8BECOlXuqyCi4JgGLLs1605m380Drt0=";
+  };
+
+  patches = [
+    # Fix build with Qt >= 6.9
+    ./fix-stricter-types.patch
+  ];
+
+  nativeBuildInputs = [
+    qmake
+    pkg-config
+    qttools
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    qtbase
+    qtsvg
+    qtserialport
+    qt5compat
+    boost
+    libgit2
+    quazip
+    libngspice
+    clipper
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isLinux [
+    qtwayland
+  ];
+
+  postPatch = ''
+    # Use packaged quazip, libgit and ngspice
+    sed -i "/pri\/quazipdetect.pri/d" phoenix.pro
+    sed -i "/pri\/spicedetect.pri/d" phoenix.pro
+    substituteInPlace pri/libgit2detect.pri \
+      --replace-fail 'LIBGIT_STATIC = true' 'LIBGIT_STATIC = false'
+
+    #TODO: Do not hardcode SHA.
+    substituteInPlace src/fapplication.cpp \
+      --replace-fail 'PartsChecker::getSha(dir.absolutePath());' '"${partsSha}";'
+
+    substituteInPlace phoenix.pro \
+      --replace-fail "6.5.10" "${qtbase.version}"
+
+    substituteInPlace src/simulation/ngspice_simulator.cpp \
+      --replace-fail 'path + "/" + libName' '"${libngspice}/lib/libngspice.so"'
+
+    mkdir parts
+    cp -a ${parts}/* parts/
+  '';
+
+  env = {
+    NIX_CFLAGS_COMPILE = lib.concatStringsSep " " [
+      "-I${lib.getDev quazip}/include/QuaZip-Qt${lib.versions.major qtbase.version}-${quazip.version}"
+      "-I${svgpp}/include"
+      "-I${clipper}/include/polyclipping"
+    ];
+    NIX_LDFLAGS = "-lquazip1-qt${lib.versions.major qtbase.version}";
+  };
+
+  qmakeFlags = [
+    "phoenix.pro"
+  ];
+
+  postInstall = lib.optionalString stdenv.hostPlatform.isDarwin ''
+    mkdir $out/Applications
+    mv $out/bin/Fritzing.app $out/Applications/Fritzing.app
+    cp FritzingInfo.plist $out/Applications/Fritzing.app/Contents/Info.plist
+    makeWrapper $out/Applications/Fritzing.app/Contents/MacOS/Fritzing $out/bin/Fritzing
+  '';
+
+  postFixup = ''
+    # generate the parts.db file
+    QT_QPA_PLATFORM=offscreen "$out/bin/Fritzing" \
+      -db "$out/share/fritzing/parts/parts.db" \
+      -pp "$out/share/fritzing/parts" \
+      -folder "$out/share/fritzing"
+  '';
+
+  meta = {
+    description = "Open source prototyping tool for Arduino-based projects";
+    homepage = "https://fritzing.org";
+    license = with lib.licenses; [
+      gpl3
+      cc-by-sa-30
+    ];
+    maintainers = with lib.maintainers; [
+      robberer
+      muscaln
+    ];
+    platforms = lib.platforms.unix;
+    mainProgram = "Fritzing";
+  };
+}

pkgs/applications/science/electronics/fritzing/fix-stricter-types.patch

@@ -0,0 +1,57 @@
+diff --git a/src/items/paletteitembase.cpp b/src/items/paletteitembase.cpp
+index 49db343e..8760ba55 100644
+--- a/src/items/paletteitembase.cpp
++++ b/src/items/paletteitembase.cpp
+@@ -626,7 +626,7 @@ QString PaletteItemBase::retrieveSvg(ViewLayer::ViewLayerID viewLayerID, QHash<Q
+ 
+ 	//DebugDialog::debug(QString("path: %1").arg(path));
+ 
+-	QString svg = svgHash.value(path + xmlName + QString(QChar(m_viewLayerPlacement)), "");
++	QString svg = svgHash.value(path + xmlName + QString(QChar(static_cast<ushort>(m_viewLayerPlacement))), "");
+ 	if (!svg.isEmpty()) return svg;
+ 
+ 	SvgFileSplitter splitter;
+@@ -657,7 +657,7 @@ QString PaletteItemBase::retrieveSvg(ViewLayer::ViewLayerID viewLayerID, QHash<Q
+ 		return "";
+ 	}
+ 	svg = splitter.elementString(xmlName);
+-	svgHash.insert(path + xmlName + QString(QChar(m_viewLayerPlacement)), svg);
++	svgHash.insert(path + xmlName + QString(QChar(static_cast<ushort>(m_viewLayerPlacement))), svg);
+ 	return svg;
+ }
+ 
+diff --git a/src/items/resistor.cpp b/src/items/resistor.cpp
+index e2a23fd8..3fb4c669 100644
+--- a/src/items/resistor.cpp
++++ b/src/items/resistor.cpp
+@@ -260,7 +260,7 @@ bool Resistor::collectExtraInfo(QWidget * parent, const QString & family, const
+ 		validator->setSymbol(OhmSymbol);
+ 		validator->setConverter(TextUtils::convertFromPowerPrefix);
+ 		validator->setBounds(MIN_RESISTANCE, MAX_RESISTANCE);
+-		validator->setRegularExpression(QRegularExpression(QString("((\\d{1,10})|(\\d{1,10}\\.)|(\\d{1,10}\\.\\d{1,5}))[\\x%1umkMG]{0,1}[\\x03A9]{0,1}").arg(TextUtils::MicroSymbolCode, 4, 16, QChar('0'))));
++		validator->setRegularExpression(QRegularExpression(QString("((\\d{1,10})|(\\d{1,10}\\.)|(\\d{1,10}\\.\\d{1,5}))[\\x%1umkMG]{0,1}[\\x03A9]{0,1}").arg(static_cast<int>(TextUtils::MicroSymbolCode), 4, 16, QChar('0'))));
+ 		focusOutComboBox->setValidator(validator);
+ 		connect(focusOutComboBox->validator(), SIGNAL(sendState(QValidator::State)), this, SLOT(textModified(QValidator::State)));
+ 		connect(focusOutComboBox, SIGNAL(currentIndexChanged(int)), this, SLOT(resistanceEntry(int)));
+diff --git a/src/utils/textutils.cpp b/src/utils/textutils.cpp
+index a1a28d51..3d3aa8e0 100644
+--- a/src/utils/textutils.cpp
++++ b/src/utils/textutils.cpp
+@@ -79,7 +79,7 @@ const QString TextUtils::AdobeIllustratorIdentifier = "Generator: Adobe Illustra
+ 
+ QList<QString> PowerPrefixes;
+ QList<double> PowerPrefixValues;
+-const QString TextUtils::PowerPrefixesString = QString("pnmkMGTu\\x%1").arg(MicroSymbolCode, 4, 16, QChar('0'));
++const QString TextUtils::PowerPrefixesString = QString("pnmkMGTu\\x%1").arg(static_cast<int>(MicroSymbolCode), 4, 16, QChar('0'));
+ 
+ typedef QHash<QString /*brokenFont*/, QString /*replacementFont*/> FixedFontsHash;
+ 
+@@ -763,7 +763,7 @@ QString TextUtils::convertExtendedChars(const QString & str)
+ 			result.append(c);
+ 		}
+ 		else {
+-			result.append(QString("&#x%1;").arg(c.unicode(), 0, 16));
++			result.append("&#x" + QString::number(c.unicode(), 16) + ";");
+ 		}
+ 	}
+ 

pkgs/applications/science/electronics/geda/default.nix

@@ -0,0 +1,58 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  fetchpatch,
+  autoreconfHook,
+  groff,
+  pkg-config,
+  guile,
+  gtk2,
+  flex,
+  gawk,
+  perl,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "geda";
+  version = "1.10.2";
+
+  src = fetchurl {
+    url = "http://ftp.geda-project.org/geda-gaf/stable/v${lib.versions.majorMinor version}/${version}/geda-gaf-${version}.tar.gz";
+    hash = "sha256-6GKrJBUoU4+jvuJzkmH1aAERArYMXjmi8DWGY8BCyKQ=";
+  };
+
+  patches = [
+    (fetchpatch {
+      name = "geda-1.10.2-drop-xorn.patch";
+      url = "https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-electronics/geda/files/geda-1.10.2-drop-xorn.patch?id=5589cc7bc6c4f18f75c40725a550b8d76e7f5ca1";
+      hash = "sha256-jPQaHjEDwCEfZqDGku+xyIMl5WlWlVcpPv1W6Xf8Grs=";
+    })
+  ];
+
+  configureFlags = [
+    "--disable-update-xdg-database"
+    "--without-libfam"
+  ];
+
+  nativeBuildInputs = [
+    autoreconfHook
+    groff
+    pkg-config
+  ];
+  buildInputs = [
+    guile
+    gtk2
+    flex
+    gawk
+    perl
+  ];
+
+  meta = with lib; {
+    description = "Full GPL'd suite of Electronic Design Automation tools";
+    homepage = "https://geda.sourceforge.net/";
+    maintainers = with maintainers; [ pjones ];
+    platforms = platforms.linux;
+    license = licenses.gpl2;
+  };
+}

pkgs/applications/science/electronics/gerbv/default.nix

@@ -0,0 +1,57 @@
+{
+  lib,
+  stdenv,
+  autoconf,
+  automake,
+  autoreconfHook,
+  cairo,
+  fetchFromGitHub,
+  gettext,
+  gtk2-x11,
+  libtool,
+  pkg-config,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "gerbv";
+  version = "2.10.0";
+
+  src = fetchFromGitHub {
+    owner = "gerbv";
+    repo = "gerbv";
+    tag = "v${version}";
+    hash = "sha256-sr48RGLYcMKuyH9p+5BhnR6QpKBvNOqqtRryw3+pbBk=";
+  };
+
+  postPatch = ''
+    sed -i '/AC_INIT/s/m4_esyscmd.*/${version}])/' configure.ac
+  '';
+
+  nativeBuildInputs = [
+    autoconf
+    automake
+    autoreconfHook
+    pkg-config
+  ];
+
+  buildInputs = [
+    cairo
+    gettext
+    gtk2-x11
+    libtool
+  ];
+
+  configureFlags = [
+    "--disable-update-desktop-database"
+  ];
+
+  meta = {
+    description = "Gerber (RS-274X) viewer";
+    mainProgram = "gerbv";
+    homepage = "https://gerbv.github.io/";
+    changelog = "https://github.com/gerbv/gerbv/releases/tag/v${version}";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ mog ];
+    platforms = lib.platforms.unix;
+  };
+}

pkgs/applications/science/electronics/kicad/addons/default.nix

@@ -0,0 +1,5 @@
+{ kicad }:
+{
+  kikit = kicad.callPackage ./kikit.nix { addonName = "kikit"; };
+  kikit-library = kicad.callPackage ./kikit.nix { addonName = "kikit-library"; };
+}

pkgs/applications/science/electronics/kicad/addons/kikit.nix

@@ -0,0 +1,57 @@
+# For building the multiple addons that are in the kikit repo.
+{
+  stdenv,
+  bc,
+  kikit,
+  zip,
+  python3,
+  addonName,
+  addonPath,
+}:
+let
+  # This python is only used when building the package, it's not the python
+  # environment that will ultimately run the code packaged here. The python env defined
+  # in KiCad will import the python code packaged here when KiCad starts up.
+  python = python3.withPackages (ps: with ps; [ click ]);
+  kikit-module = python3.pkgs.toPythonModule (kikit.override { inherit python3; });
+
+  # The following different addons can be built from the same source.
+  targetSpecs = {
+    "kikit" = {
+      makeTarget = "pcm-kikit";
+      resultZip = "pcm-kikit.zip";
+      description = "KiCad plugin and a CLI tool to automate several tasks in a standard KiCad workflow";
+    };
+    "kikit-library" = {
+      makeTarget = "pcm-lib";
+      resultZip = "pcm-kikit-lib.zip";
+      description = "KiKit uses these symbols and footprints to annotate your boards (e.g., to place a tab in a panel)";
+    };
+  };
+  targetSpec = targetSpecs.${addonName};
+in
+stdenv.mkDerivation {
+  pname = "kicadaddon-${addonName}";
+  inherit (kikit-module) src version;
+
+  nativeBuildInputs = [
+    python
+    bc
+    zip
+  ];
+  propagatedBuildInputs = [ kikit-module ];
+
+  buildPhase = ''
+    patchShebangs scripts/setJson.py
+    make ${targetSpec.makeTarget}
+  '';
+
+  installPhase = ''
+    mkdir $out
+    mv build/${targetSpec.resultZip} $out/${addonPath}
+  '';
+
+  meta = kikit-module.meta // {
+    description = targetSpec.description;
+  };
+}

pkgs/applications/science/electronics/kicad/base.nix

@@ -0,0 +1,214 @@
+{
+  lib,
+  stdenv,
+  cmake,
+  libGLU,
+  libGL,
+  zlib,
+  wxGTK,
+  gtk3,
+  libX11,
+  gettext,
+  glew,
+  glm,
+  cairo,
+  curl,
+  openssl,
+  boost,
+  pkg-config,
+  doxygen,
+  graphviz,
+  libpthreadstubs,
+  libXdmcp,
+  unixODBC,
+  libgit2,
+  libsecret,
+  libgcrypt,
+  libgpg-error,
+  ninja,
+  writableTmpDirAsHomeHook,
+
+  util-linuxMinimal,
+  libselinux,
+  libsepol,
+  libthai,
+  libdatrie,
+  libxkbcommon,
+  libepoxy,
+  dbus,
+  at-spi2-core,
+  libXtst,
+  pcre2,
+  libdeflate,
+
+  swig,
+  python,
+  wxPython,
+  opencascade-occt_7_6,
+  libngspice,
+  valgrind,
+  protobuf_29,
+  nng,
+
+  stable,
+  testing,
+  kicadSrc,
+  kicadVersion,
+  withNgspice,
+  withScripting,
+  withI18n,
+  debug,
+  sanitizeAddress,
+  sanitizeThreads,
+}:
+
+assert lib.assertMsg (
+  !(sanitizeAddress && sanitizeThreads)
+) "'sanitizeAddress' and 'sanitizeThreads' are mutually exclusive, use one.";
+assert testing -> !stable -> throw "testing implies stable and cannot be used with stable = false";
+
+let
+  opencascade-occt = opencascade-occt_7_6;
+  inherit (lib)
+    cmakeBool
+    cmakeFeature
+    optionals
+    optionalString
+    ;
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "kicad-base";
+  version = if stable then kicadVersion else builtins.substring 0 10 finalAttrs.src.rev;
+
+  src = kicadSrc;
+
+  patches = [
+    # upstream issue 12941 (attempted to upstream, but appreciably unacceptable)
+    ./writable.patch
+    # https://gitlab.com/kicad/code/kicad/-/issues/15687
+    ./runtime_stock_data_path.patch
+  ];
+
+  # tagged releases don't have "unknown"
+  # kicad testing and nightlies use git describe --dirty
+  # nix removes .git, so its approximated here
+  postPatch = lib.optionalString (!stable || testing) ''
+    substituteInPlace cmake/KiCadVersion.cmake \
+      --replace-fail "unknown" "${builtins.substring 0 10 finalAttrs.src.rev}"
+
+    substituteInPlace cmake/CreateGitVersionHeader.cmake \
+      --replace-fail "0000000000000000000000000000000000000000" "${finalAttrs.src.rev}"
+  '';
+
+  preConfigure = optionalString debug ''
+    export CFLAGS="''${CFLAGS:-} -Og -ggdb"
+    export CXXFLAGS="''${CXXFLAGS:-} -Og -ggdb"
+  '';
+
+  cmakeFlags = [
+    (cmakeBool "KICAD_USE_EGL" true)
+    (cmakeFeature "OCC_INCLUDE_DIR" "${opencascade-occt}/include/opencascade")
+    # https://gitlab.com/kicad/code/kicad/-/issues/17133
+    (cmakeFeature "CMAKE_CTEST_ARGUMENTS" "--exclude-regex;qa_spice")
+    (cmakeBool "KICAD_USE_CMAKE_FINDPROTOBUF" false)
+    (cmakeBool "KICAD_SCRIPTING_WXPYTHON" withScripting)
+    (cmakeBool "KICAD_BUILD_I18N" withI18n)
+    (cmakeBool "KICAD_BUILD_QA_TESTS" (!finalAttrs.doInstallCheck))
+    (cmakeBool "KICAD_STDLIB_DEBUG" debug)
+    (cmakeBool "KICAD_USE_VALGRIND" debug)
+    (cmakeBool "KICAD_SANITIZE_ADDRESS" sanitizeAddress)
+    (cmakeBool "KICAD_SANITIZE_THREADS" sanitizeThreads)
+    (cmakeBool "KICAD_SPICE" (!(stable && !withNgspice)))
+  ]
+  ++ optionals (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) [
+    (cmakeFeature "CMAKE_CTEST_ARGUMENTS" "--exclude-regex;'qa_spice|qa_cli'")
+  ];
+
+  cmakeBuildType = if debug then "Debug" else "Release";
+
+  nativeBuildInputs = [
+    cmake
+    ninja
+    doxygen
+    graphviz
+    pkg-config
+    libgit2
+    libsecret
+    libgcrypt
+    libgpg-error
+  ]
+  # wanted by configuration on linux, doesn't seem to affect performance
+  # no effect on closure size
+  ++ optionals (stdenv.hostPlatform.isLinux) [
+    util-linuxMinimal
+    libselinux
+    libsepol
+    libthai
+    libdatrie
+    libxkbcommon
+    libepoxy
+    dbus
+    at-spi2-core
+    libXtst
+    pcre2
+  ];
+
+  buildInputs = [
+    libGLU
+    libGL
+    zlib
+    libX11
+    wxGTK
+    gtk3
+    libXdmcp
+    gettext
+    glew
+    glm
+    libpthreadstubs
+    cairo
+    curl
+    openssl
+    boost
+    swig
+    python
+    unixODBC
+    libdeflate
+    opencascade-occt
+    protobuf_29
+
+    # This would otherwise cause a linking requirement for mbedtls.
+    (nng.override { mbedtlsSupport = false; })
+  ]
+  ++ optionals withScripting [ wxPython ]
+  ++ optionals withNgspice [ libngspice ]
+  ++ optionals debug [ valgrind ];
+
+  # debug builds fail all but the python test
+  doInstallCheck = !debug;
+  installCheckTarget = "test";
+
+  nativeInstallCheckInputs = [
+    (python.withPackages (
+      ps: with ps; [
+        numpy
+        pytest
+        cairosvg
+        pytest-image-diff
+      ]
+    ))
+    writableTmpDirAsHomeHook
+  ];
+
+  dontStrip = debug;
+
+  meta = {
+    description = "Just the built source without the libraries";
+    longDescription = ''
+      Just the build products, the libraries are passed via an env var in the wrapper, default.nix
+    '';
+    homepage = "https://www.kicad.org/";
+    license = lib.licenses.gpl3Plus;
+    platforms = lib.platforms.all;
+    broken = stdenv.hostPlatform.isDarwin;
+  };
+})

pkgs/applications/science/electronics/kicad/default.nix

@@ -0,0 +1,334 @@
+{
+  lib,
+  stdenv,
+  runCommand,
+  newScope,
+  fetchFromGitLab,
+  makeWrapper,
+  symlinkJoin,
+  callPackage,
+  callPackages,
+
+  adwaita-icon-theme,
+  dconf,
+  gtk3,
+  wxGTK32,
+  librsvg,
+  cups,
+  gsettings-desktop-schemas,
+  hicolor-icon-theme,
+
+  unzip,
+  jq,
+
+  pname ? "kicad",
+  stable ? true,
+  testing ? false,
+  withNgspice ? !stdenv.hostPlatform.isDarwin,
+  libngspice,
+  withScripting ? true,
+  python3,
+  addons ? [ ],
+  debug ? false,
+  sanitizeAddress ? false,
+  sanitizeThreads ? false,
+  with3d ? true,
+  withI18n ? true,
+  srcs ? { },
+}:
+
+# `addons`: https://dev-docs.kicad.org/en/addons/
+#
+# ```nix
+# kicad = pkgs.kicad.override {
+#   addons = with pkgs.kicadAddons; [ kikit kikit-library ];
+# };
+# ```
+
+# The `srcs` parameter can be used to override the kicad source code
+# and all libraries, which are otherwise inaccessible
+# to overlays since most of the kicad build expression has been
+# refactored into base.nix, most of the library build expressions have
+# been refactored into libraries.nix. Overrides are only applied when
+# building `kicad-unstable`. The `srcs` parameter has
+# no effect for stable `kicad`. `srcs` takes an attribute set in which
+# any of the following attributes are meaningful (though none are
+# mandatory): "kicad", "kicadVersion", "symbols", "templates",
+# "footprints", "packages3d", and "libVersion". "kicadVersion" and
+# "libVersion" should be set to a string with the desired value for
+# the version attribute in kicad's `mkDerivation` and the version
+# attribute in any of the library's `mkDerivation`, respectively.
+# "kicad", "symbols", "templates", "footprints", and "packages3d"
+# should be set to an appropriate fetcher (e.g. `fetchFromGitLab`).
+# So, for example, a possible overlay for kicad is:
+#
+# final: prev:
+
+# {
+#   kicad-unstable = (prev.kicad-unstable.override {
+#     srcs = {
+#       kicadVersion = "2020-10-08";
+#       kicad = prev.fetchFromGitLab {
+#         group = "kicad";
+#         owner = "code";
+#         repo = "kicad";
+#         rev = "fd22fe8e374ce71d57e9f683ba996651aa69fa4e";
+#         sha256 = "sha256-F8qugru/jU3DgZSpQXQhRGNFSk0ybFRkpyWb7HAGBdc=";
+#       };
+#     };
+#   });
+# }
+
+let
+  baseName =
+    if testing then
+      "kicad-testing"
+    else if stable then
+      "kicad"
+    else
+      "kicad-unstable";
+  versionsImport = import ./versions.nix;
+
+  # versions.nix does not provide us with version, src and rev. We
+  # need to turn this into appropriate fetcher calls.
+  kicadSrcFetch = fetchFromGitLab {
+    group = "kicad";
+    owner = "code";
+    repo = "kicad";
+    rev = versionsImport.${baseName}.kicadVersion.src.rev;
+    sha256 = versionsImport.${baseName}.kicadVersion.src.sha256;
+  };
+
+  libSrcFetch =
+    name:
+    fetchFromGitLab {
+      group = "kicad";
+      owner = "libraries";
+      repo = "kicad-${name}";
+      rev = versionsImport.${baseName}.libVersion.libSources.${name}.rev;
+      sha256 = versionsImport.${baseName}.libVersion.libSources.${name}.sha256;
+    };
+
+  # only override `src` or `version` if building `kicad-unstable` with
+  # the appropriate attribute defined in `srcs`.
+  srcOverridep = attr: (!stable && builtins.hasAttr attr srcs);
+
+  # use default source and version (as defined in versions.nix) by
+  # default, or use the appropriate attribute from `srcs` if building
+  # unstable with `srcs` properly defined.
+  kicadSrc = if srcOverridep "kicad" then srcs.kicad else kicadSrcFetch;
+  kicadVersion =
+    if srcOverridep "kicadVersion" then
+      srcs.kicadVersion
+    else
+      versionsImport.${baseName}.kicadVersion.version;
+
+  libSrc = name: if srcOverridep name then srcs.${name} else libSrcFetch name;
+  # TODO does it make sense to only have one version for all libs?
+  libVersion =
+    if srcOverridep "libVersion" then
+      srcs.libVersion
+    else
+      versionsImport.${baseName}.libVersion.version;
+
+  wxGTK = wxGTK32;
+  python = python3;
+  wxPython = python.pkgs.wxpython;
+  addonPath = "addon.zip";
+  addonsDrvs = map (pkg: pkg.override { inherit addonPath python3; }) addons;
+
+  addonsJoined =
+    runCommand "addonsJoined"
+      {
+        inherit addonsDrvs;
+        nativeBuildInputs = [
+          unzip
+          jq
+        ];
+      }
+      ''
+        mkdir $out
+
+        for pkg in $addonsDrvs; do
+          unzip $pkg/addon.zip -d unpacked
+
+          folder_name=$(jq .identifier unpacked/metadata.json --raw-output | tr . _)
+          for d in unpacked/*; do
+            if [ -d "$d" ]; then
+              dest=$out/share/kicad/scripting/$(basename $d)/$folder_name
+              mkdir -p $(dirname $dest)
+
+              mv $d $dest
+            fi
+          done
+          rm -r unpacked
+        done
+      '';
+
+  inherit (lib)
+    concatStringsSep
+    flatten
+    optionalString
+    optionals
+    ;
+in
+stdenv.mkDerivation rec {
+
+  # Common libraries, referenced during runtime, via the wrapper.
+  passthru.libraries = callPackages ./libraries.nix { inherit libSrc; };
+  passthru.callPackage = newScope { inherit addonPath python3; };
+  base = callPackage ./base.nix {
+    inherit stable testing;
+    inherit kicadSrc kicadVersion;
+    inherit wxGTK python wxPython;
+    inherit withNgspice withScripting withI18n;
+    inherit debug sanitizeAddress sanitizeThreads;
+  };
+
+  inherit pname;
+  version = if stable then kicadVersion else builtins.substring 0 10 src.src.rev;
+
+  src = base;
+  dontUnpack = true;
+  dontConfigure = true;
+  dontBuild = true;
+  dontFixup = true;
+
+  pythonPath =
+    optionals withScripting [
+      wxPython
+      python.pkgs.six
+      python.pkgs.requests
+    ]
+    ++ addonsDrvs;
+
+  nativeBuildInputs = [ makeWrapper ] ++ optionals withScripting [ python.pkgs.wrapPython ];
+
+  # KICAD7_TEMPLATE_DIR only works with a single path (it does not handle : separated paths)
+  # but it's used to find both the templates and the symbol/footprint library tables
+  # https://gitlab.com/kicad/code/kicad/-/issues/14792
+  template_dir = symlinkJoin {
+    name = "KiCad_template_dir";
+    paths = with passthru.libraries; [
+      "${templates}/share/kicad/template"
+      "${footprints}/share/kicad/template"
+      "${symbols}/share/kicad/template"
+    ];
+  };
+  # We are emulating wrapGAppsHook3, along with other variables to the wrapper
+  makeWrapperArgs =
+    with passthru.libraries;
+    [
+      "--prefix XDG_DATA_DIRS : ${base}/share"
+      "--prefix XDG_DATA_DIRS : ${hicolor-icon-theme}/share"
+      "--prefix XDG_DATA_DIRS : ${adwaita-icon-theme}/share"
+      "--prefix XDG_DATA_DIRS : ${gtk3}/share/gsettings-schemas/${gtk3.name}"
+      "--prefix XDG_DATA_DIRS : ${gsettings-desktop-schemas}/share/gsettings-schemas/${gsettings-desktop-schemas.name}"
+      # wrapGAppsHook3 did these two as well, no idea if it matters...
+      "--prefix XDG_DATA_DIRS : ${cups}/share"
+      "--prefix GIO_EXTRA_MODULES : ${dconf}/lib/gio/modules"
+      # required to open a bug report link in firefox-wayland
+      "--set-default MOZ_DBUS_REMOTE 1"
+      "--set-default KICAD9_FOOTPRINT_DIR ${footprints}/share/kicad/footprints"
+      "--set-default KICAD9_SYMBOL_DIR ${symbols}/share/kicad/symbols"
+      "--set-default KICAD9_TEMPLATE_DIR ${template_dir}"
+    ]
+    ++ optionals (addons != [ ]) (
+      let
+        stockDataPath = symlinkJoin {
+          name = "kicad_stock_data_path";
+          paths = [
+            "${base}/share/kicad"
+            "${addonsJoined}/share/kicad"
+          ];
+        };
+      in
+      [ "--set-default NIX_KICAD9_STOCK_DATA_PATH ${stockDataPath}" ]
+    )
+    ++ optionals with3d [
+      "--set-default KICAD9_3DMODEL_DIR ${packages3d}/share/kicad/3dmodels"
+    ]
+    ++ optionals withNgspice [ "--prefix LD_LIBRARY_PATH : ${libngspice}/lib" ]
+
+    # infinisil's workaround for #39493
+    ++ [ "--set GDK_PIXBUF_MODULE_FILE ${librsvg}/lib/gdk-pixbuf-2.0/2.10.0/loaders.cache" ];
+
+  # why does $makeWrapperArgs have to be added explicitly?
+  # $out and $program_PYTHONPATH don't exist when makeWrapperArgs gets set?
+  installPhase =
+    let
+      bin = if stdenv.hostPlatform.isDarwin then "*.app/Contents/MacOS" else "bin";
+      tools = [
+        "kicad"
+        "pcbnew"
+        "eeschema"
+        "gerbview"
+        "pcb_calculator"
+        "pl_editor"
+        "bitmap2component"
+        "kicad-cli"
+      ];
+      utils = [
+        "dxf2idf"
+        "idf2vrml"
+        "idfcyl"
+        "idfrect"
+      ];
+    in
+    (concatStringsSep "\n" (flatten [
+      "runHook preInstall"
+
+      (optionalString withScripting "buildPythonPath \"${base} $pythonPath\" \n")
+
+      # wrap each of the directly usable tools
+      (map (
+        tool:
+        "makeWrapper ${base}/${bin}/${tool} $out/bin/${tool} $makeWrapperArgs"
+        + optionalString withScripting " --set PYTHONPATH \"$program_PYTHONPATH\""
+      ) tools)
+
+      # link in the CLI utils
+      (map (util: "ln -s ${base}/${bin}/${util} $out/bin/${util}") utils)
+
+      "runHook postInstall"
+    ]));
+
+  postInstall = ''
+    mkdir -p $out/share
+    ln -s ${base}/share/applications $out/share/applications
+    ln -s ${base}/share/icons $out/share/icons
+    ln -s ${base}/share/mime $out/share/mime
+    ln -s ${base}/share/metainfo $out/share/metainfo
+  '';
+
+  passthru.updateScript = {
+    command = [
+      ./update.sh
+      "${pname}"
+    ];
+    supportedFeatures = [ "commit" ];
+  };
+
+  meta = {
+    description =
+      (
+        if stable then
+          "Open Source Electronics Design Automation suite"
+        else if testing then
+          "Open Source EDA suite, latest on stable branch"
+        else
+          "Open Source EDA suite, latest on master branch"
+      )
+      + (lib.optionalString (!with3d) ", without 3D models");
+    homepage = "https://www.kicad.org/";
+    longDescription = ''
+      KiCad is an open source software suite for Electronic Design Automation.
+      The Programs handle Schematic Capture, and PCB Layout with Gerber output.
+    '';
+    license = lib.licenses.gpl3Plus;
+    maintainers = [ ];
+    platforms = lib.platforms.all;
+    broken = stdenv.hostPlatform.isDarwin;
+    mainProgram = "kicad";
+  };
+}

pkgs/applications/science/electronics/kicad/libraries.nix

@@ -0,0 +1,47 @@
+{
+  lib,
+  stdenv,
+  cmake,
+  libSrc,
+  stepreduce,
+  parallel,
+  zip,
+}:
+let
+  mkLib =
+    name:
+    stdenv.mkDerivation {
+      pname = "kicad-${name}";
+      version = builtins.substring 0 10 (libSrc name).rev;
+
+      src = libSrc name;
+
+      nativeBuildInputs = [
+        cmake
+      ]
+      ++ lib.optionals (name == "packages3d") [
+        stepreduce
+        parallel
+        zip
+      ];
+
+      postInstall =
+        lib.optionalString (name == "packages3d") ''
+          find $out -type f -name '*.step' | parallel 'stepreduce {} {} && zip -9 {.}.stpZ {} && rm {}'
+        ''
+        + lib.optionalString (name == "footprints") ''
+          grep -rl '\.step' $out | xargs sed -i 's/\.step/.stpZ/g'
+        '';
+
+      meta = {
+        license = lib.licenses.cc-by-sa-40;
+        platforms = lib.platforms.all;
+      };
+    };
+in
+{
+  symbols = mkLib "symbols";
+  templates = mkLib "templates";
+  footprints = mkLib "footprints";
+  packages3d = mkLib "packages3d";
+}

pkgs/applications/science/electronics/kicad/runtime_stock_data_path.patch

@@ -0,0 +1,15 @@
+diff --git a/common/paths.cpp b/common/paths.cpp
+index a74cdd9..790cc58 100644
+--- a/common/paths.cpp
++++ b/common/paths.cpp
+@@ -151,6 +151,10 @@ wxString PATHS::GetStockDataPath( bool aRespectRunFromBuildDir )
+ {
+     wxString path;
+
++    if( wxGetEnv( wxT( "NIX_KICAD9_STOCK_DATA_PATH" ), &path ) ) {
++        return path;
++    }
++
+     if( aRespectRunFromBuildDir && wxGetEnv( wxT( "KICAD_RUN_FROM_BUILD_DIR" ), nullptr ) )
+     {
+         // Allow debugging from build dir by placing relevant files/folders in the build root

pkgs/applications/science/electronics/kicad/update.sh

@@ -0,0 +1,261 @@
+#!/usr/bin/env nix-shell
+#!nix-shell -i bash -p coreutils git nix curl jq nixfmt-tree
+# shellcheck shell=bash enable=all
+
+set -e
+shopt -s inherit_errexit
+
+# this script will generate versions.nix in the right location
+# this should contain the versions' revs and hashes
+# the stable revs are stored only for ease of skipping
+
+# by default nix-prefetch-url uses XDG_RUNTIME_DIR as tmp
+# which is /run/user/1000, which defaults to 10% of your RAM
+# unless you have over 64GB of ram that'll be insufficient
+# resulting in "tar: no space left on device" for packages3d
+# hence:
+export TMPDIR=/tmp
+
+# if something goes unrepairably wrong, run 'update.sh all clean'
+
+# TODO
+# support parallel instances for each pname
+#   currently risks reusing old data
+# no getting around manually checking if the build product works...
+# if there is, default to commiting?
+#   won't work when running in parallel?
+# remove items left in /nix/store?
+# reuse hashes of already checked revs (to avoid redownloading testing's packages3d)
+
+# nixpkgs' update.nix passes in UPDATE_NIX_PNAME to indicate which package is being updated
+# assigning a default value to that as shellcheck doesn't like the use of unassigned variables
+: "${UPDATE_NIX_PNAME:=""}"
+# update.nix can also parse JSON output of this script to formulate a commit
+# this requires we collect the version string in the old versions.nix for the updated package
+old_version=""
+new_version=""
+
+
+# get the latest tag that isn't an RC or *.99
+latest_tags="$(git ls-remote --tags --sort -version:refname https://gitlab.com/kicad/code/kicad.git)"
+# using a scratch variable to ensure command failures get caught (SC2312)
+scratch="$(grep -o 'refs/tags/[0-9]*\.[0-9]*\.[0-9]*$' <<< "${latest_tags}")"
+scratch="$(grep -ve '\.99' -e '\.9\.9' <<< "${scratch}")"
+scratch="$(sed -n '1p' <<< "${scratch}")"
+latest_tag="$(cut -d '/' -f 3 <<< "${scratch}")"
+
+# get the latest branch name for testing
+branches="$(git ls-remote --heads --sort -version:refname https://gitlab.com/kicad/code/kicad.git)"
+scratch="$(grep -o 'refs/heads/[0-9]*\.[0-9]*$' <<< "${branches}")"
+scratch="$(sed -n '1p' <<< "${scratch}")"
+testing_branch="$(cut -d '/' -f 3 <<< "${scratch}")"
+
+# "latest_tag" and "master" directly refer to what we want
+# "testing" uses "testing_branch" found above
+all_versions=( "${latest_tag}" testing master )
+
+prefetch="nix-prefetch-url --unpack --quiet"
+
+clean=""
+check_stable=""
+check_testing=1
+check_unstable=1
+commit=""
+
+for arg in "$@" "${UPDATE_NIX_PNAME}"; do
+  case "${arg}" in
+    help|-h|--help) echo "Read me!" >&2; exit 1; ;;
+    kicad|kicad-small|release|tag|stable|5*|6*|7*|8*) check_stable=1; check_testing=""; check_unstable="" ;;
+    *testing|kicad-testing-small) check_testing=1; check_unstable="" ;;
+    *unstable|*unstable-small|master|main) check_unstable=1; check_testing="" ;;
+    latest|now|today) check_unstable=1; check_testing=1 ;;
+    all|both|full) check_stable=1; check_testing=1; check_unstable=1 ;;
+    clean|fix|*fuck) check_stable=1; check_testing=1; check_unstable=1; clean=1 ;;
+    commit) commit=1 ;;
+    *) ;;
+  esac
+done
+
+here="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+commit_date() {
+  gitlab_json="$(curl -s https://gitlab.com/api/v4/projects/kicad%2Fcode%2Fkicad/repository/commits/"$1")"
+  commit_created="$(jq .created_at --raw-output <<< "${gitlab_json}")"
+  date --date="${commit_created}" --iso-8601 --utc
+}
+
+file="${here}/versions.nix"
+# just in case this runs in parallel
+tmp="${here}/,versions.nix.${RANDOM}"
+
+libs=( symbols templates footprints packages3d )
+
+get_rev() {
+    git ls-remote "$@"
+}
+
+gitlab="https://gitlab.com/kicad"
+# append commit hash or tag
+src_pre="https://gitlab.com/api/v4/projects/kicad%2Fcode%2Fkicad/repository/archive.tar.gz?sha="
+lib_pre="https://gitlab.com/api/v4/projects/kicad%2Flibraries%2Fkicad-"
+lib_mid="/repository/archive.tar.gz?sha="
+
+# number of items updated
+count=0
+
+printf "Latest tag is %s\n" "${latest_tag}" >&2
+
+if [[ ! -f ${file} ]]; then
+  echo "No existing file, generating from scratch" >&2
+  check_stable=1; check_testing=1; check_unstable=1; clean=1
+fi
+
+printf "Writing %s\n" "${tmp}" >&2
+
+# not a dangling brace, grouping the output to redirect to file
+{
+
+printf "# This file was generated by update.sh\n\n"
+printf "{\n"
+
+for version in "${all_versions[@]}"; do
+
+  src_version=${version};
+  lib_version=${version};
+  # testing is the stable branch on the main repo
+  # but the libraries don't have such a branch
+  # only the latest release tag and a master branch
+  if [[ ${version} == "testing" ]]; then
+      src_version=${testing_branch};
+      lib_version=${latest_tag};
+  fi
+
+  if [[ ${version} == "master" ]]; then
+    pname="kicad-unstable"
+  elif [[ ${version} == "testing" ]]; then
+    pname="kicad-testing"
+  else
+    pname="kicad"
+  fi
+
+  # skip a version if we don't want to check it
+  if [[ (-n ${check_stable} && ${version} != "master" && ${version} != "testing") \
+     || (-n ${check_testing} && ${version} == "testing") \
+     || (-n ${check_unstable} && ${version} == "master" ) ]]; then
+
+    now=$(commit_date "${src_version}")
+
+    if [[ ${version} == "master" ]]; then
+      pname="kicad-unstable"
+      new_version="${now}"
+    elif [[ ${version} == "testing" ]]; then
+      pname="kicad-testing"
+      new_version="${testing_branch}-${now}"
+    else
+      pname="kicad"
+      new_version="${version}"
+    fi
+
+    printf "\nChecking %s\n" "${pname}" >&2
+
+    printf "%2s\"%s\" = {\n" "" "${pname}"
+      printf "%4skicadVersion = {\n" ""
+        printf "%6sversion =\t\t\t\"%s\";\n" "" "${new_version}"
+        printf "%6ssrc = {\n" ""
+
+    echo "Checking src" >&2
+    scratch="$(get_rev "${gitlab}"/code/kicad.git "${src_version}")"
+    src_rev="$(cut -f1 <<< "${scratch}")"
+    has_rev="$(grep -sm 1 "\"${pname}\"" -A 4 "${file}" | grep -sm 1 "${src_rev}" || true)"
+    has_hash="$(grep -sm 1 "\"${pname}\"" -A 5 "${file}" | grep -sm 1 "sha256" || true)"
+    old_version="$(grep -sm 1 "\"${pname}\"" -A 3 "${file}" | grep -sm 1 "version" | awk -F "\"" '{print $2}' || true)"
+
+    if [[ -n ${has_rev} && -n ${has_hash} && -z ${clean} ]]; then
+      echo "Reusing old ${pname}.src.sha256, already latest .rev at ${old_version}" >&2
+      scratch=$(grep -sm 1 "\"${pname}\"" -A 5 "${file}")
+      grep -sm 1 "rev" -A 1 <<< "${scratch}"
+    else
+          prefetched="$(${prefetch} "${src_pre}${src_rev}")"
+          printf "%8srev =\t\t\t\"%s\";\n" "" "${src_rev}"
+          printf "%8ssha256 =\t\t\"%s\";\n" "" "${prefetched}"
+          count=$((count+1))
+    fi
+        printf "%6s};\n" ""
+      printf "%4s};\n" ""
+
+      printf "%4slibVersion = {\n" ""
+        printf "%6sversion =\t\t\t\"%s\";\n" "" "${new_version}"
+        printf "%6slibSources = {\n" ""
+
+          for lib in "${libs[@]}"; do
+            echo "Checking ${lib}" >&2
+            url="${gitlab}/libraries/kicad-${lib}.git"
+            scratch="$(get_rev "${url}" "${lib_version}")"
+            scratch="$(cut -f1 <<< "${scratch}")"
+            lib_rev="$(tail -n1 <<< "${scratch}")"
+            has_rev="$(grep -sm 1 "\"${pname}\"" -A 19 "${file}" | grep -sm 1 "${lib_rev}" || true)"
+            has_hash="$(grep -sm 1 "\"${pname}\"" -A 20 "${file}" | grep -sm 1 "${lib}.sha256" || true)"
+            if [[ -n ${has_rev} && -n ${has_hash} && -z ${clean} ]]; then
+              echo "Reusing old kicad-${lib}-${new_version}.src.sha256, already latest .rev" >&2
+              scratch="$(grep -sm 1 "\"${pname}\"" -A 20 "${file}")"
+              grep -sm 1 "${lib}" -A 1 <<< "${scratch}"
+            else
+              prefetched="$(${prefetch} "${lib_pre}${lib}${lib_mid}${lib_rev}")"
+              printf "%8s%s.rev =\t" "" "${lib}"
+              case "${lib}" in
+                symbols|templates) printf "\t" ;; *) ;;
+              esac
+              printf "\"%s\";\n" "${lib_rev}"
+              printf "%8s%s.sha256 =\t\"%s\";\n" "" "${lib}" "${prefetched}"
+              count=$((count+1))
+            fi
+          done
+        printf "%6s};\n" ""
+      printf "%4s};\n" ""
+    printf "%2s};\n" ""
+  else
+    printf "\nReusing old %s\n" "${pname}" >&2
+    grep -sm 1 "\"${pname}\"" -A 21 "${file}"
+  fi
+done
+printf "}\n"
+} > "${tmp}"
+
+if grep '""' "${tmp}"; then
+  echo "empty value detected, out of space?" >&2
+  exit "1"
+fi
+
+mv "${tmp}" "${file}"
+treefmt "${file}"
+
+printf "\nFinished\nMoved output to %s\n\n" "${file}" >&2
+
+if [[ ${count} -gt 0 ]]; then
+  if [[ ${count} -gt 1 ]]; then s="s"; else s=""; fi
+  echo "${count} revision${s} changed" >&2
+  if [[ -n ${commit} ]]; then
+    git commit -am "$(printf "kicad: automatic update of %s item%s\n" "${count}" "${s}")"
+  fi
+  echo "Please confirm the new versions.nix works before making a PR." >&2
+else
+  echo "No changes, those checked are up to date" >&2
+fi
+
+# using UPDATE_NIX_ATTR_PATH to detect if this is being called from update.nix
+# and output JSON to describe the changes
+if [[ -n ${UPDATE_NIX_ATTR_PATH} ]]; then
+
+  if [[ ${count} -eq 0 ]]; then echo "[{}]"; exit 0; fi
+
+  jq -n \
+    --arg attrpath "${UPDATE_NIX_PNAME}" \
+    --arg oldversion "${old_version}" \
+    --arg newversion "${new_version}" \
+    --arg file "${file}" \
+'[{
+  "attrPath": $attrpath,
+  "oldVersion": $oldversion,
+  "newVersion": $newversion,
+  "files": [ $file ]
+}]'
+fi

pkgs/applications/science/electronics/kicad/versions.nix

@@ -0,0 +1,70 @@
+# This file was generated by update.sh
+
+{
+  "kicad" = {
+    kicadVersion = {
+      version = "9.0.5";
+      src = {
+        rev = "3e59813c21b4d0a00c08978e86b5f2189ec27864";
+        sha256 = "0wmnkiyqv32c5nz4nvz94dld3rk5ir49nh71cycig6clvjvy11r5";
+      };
+    };
+    libVersion = {
+      version = "9.0.5";
+      libSources = {
+        symbols.rev = "884133df0afba238567e2be6c31e7d3b4a9d90be";
+        symbols.sha256 = "0msgq8p3zlfc3glqr1h8n0a1agk4hjdqxqdiny5b4d0hgiy6hhmx";
+        templates.rev = "204b42307fc78cf0b3ebec4e19eba9d710e392f4";
+        templates.sha256 = "0zs29zn8qjgxv0w1vyr8yxmj02m8752zagn4vcraqgik46dwg2id";
+        footprints.rev = "873e3e9dbad8371d664e57261efa516d42328161";
+        footprints.sha256 = "179y7xmz7mwsfsv4dcw2dx689xfzqk8y38d21s69yiaalyxflhh1";
+        packages3d.rev = "c25dce5aadce68076ac035edb0c792608f5f597c";
+        packages3d.sha256 = "1y7yhynrr87q80gcb8qlkyrdccz1sllsxqymrnghhxbfk4wbwwn8";
+      };
+    };
+  };
+  "kicad-testing" = {
+    kicadVersion = {
+      version = "9.0-2025-02-21";
+      src = {
+        rev = "c4c32aa7bbadd3862fb720457b71e7a19420604c";
+        sha256 = "01zbvg6n8kajilj3q1sp0zpaqz94bq28wrxjax1968wvwv05g0dp";
+      };
+    };
+    libVersion = {
+      version = "9.0-2025-02-21";
+      libSources = {
+        symbols.rev = "e1c3371228f97b36c6fd61b66d056184930f078e";
+        symbols.sha256 = "0l8da2ix917jlsj6v5zclc1cb5pvjaxwmys0gjdv55ic31hhfyyw";
+        templates.rev = "3ed4538b0f965d821df63a5fffc4441e723cfe7f";
+        templates.sha256 = "0zs29zn8qjgxv0w1vyr8yxmj02m8752zagn4vcraqgik46dwg2id";
+        footprints.rev = "ef91963f57028aa095f2d0c4239ba994ea822f73";
+        footprints.sha256 = "16zslgvjg4swgkkvnd9fmiks3wzg63364d03hixiyzcpjlgk2bbk";
+        packages3d.rev = "b40831fd7ea2ca8f9c7282143dbb7d2f5015cd69";
+        packages3d.sha256 = "0bg54lg1iw01gw06ajg34y7x4y36wm6ls3jnpjy13i18d4ik77g4";
+      };
+    };
+  };
+  "kicad-unstable" = {
+    kicadVersion = {
+      version = "2025-02-21";
+      src = {
+        rev = "878cf768d6552131494aa792dc20e6ccf67baf75";
+        sha256 = "0ky0a7y6gf409y8bwpngiirqin4ivbcjnk8gjdj1a6w79x559sr8";
+      };
+    };
+    libVersion = {
+      version = "2025-02-21";
+      libSources = {
+        symbols.rev = "da86acd48809fd61876223c8bf0e4e7793c52e9a";
+        symbols.sha256 = "1sdpg58wbyyrghjd0jqw5iw2094mjy2v9jmwn5zrj4jm6f51g1kd";
+        templates.rev = "3ed4538b0f965d821df63a5fffc4441e723cfe7f";
+        templates.sha256 = "0zs29zn8qjgxv0w1vyr8yxmj02m8752zagn4vcraqgik46dwg2id";
+        footprints.rev = "e515f1c3213317d436e492c8c06620ef4caca84e";
+        footprints.sha256 = "16zslgvjg4swgkkvnd9fmiks3wzg63364d03hixiyzcpjlgk2bbk";
+        packages3d.rev = "d5db5cea003fe2b4b1c9b145f5fcbd5fdb48f8ca";
+        packages3d.sha256 = "0bg54lg1iw01gw06ajg34y7x4y36wm6ls3jnpjy13i18d4ik77g4";
+      };
+    };
+  };
+}

pkgs/applications/science/electronics/kicad/writable.patch

@@ -0,0 +1,49 @@
+commit 6a72fd032405515e468797be91b5a6ebcbbb5fd8
+Author: Evils <evils.devils@protonmail.com>
+Date:   Wed Nov 23 19:49:13 2022 +0100
+
+    ensure new projects are writable
+
+diff --git a/kicad/kicad_manager_frame.cpp b/kicad/kicad_manager_frame.cpp
+index 7ee8090858..391514519c 100644
+--- a/kicad/kicad_manager_frame.cpp
++++ b/kicad/kicad_manager_frame.cpp
+@@ -638,6 +638,12 @@ void KICAD_MANAGER_FRAME::CreateNewProject( const wxFileName& aProjectFileName,
+ 
+                 // wxFFile dtor will close the file
+             }
++
++            if( destFileName.IsOk() && !destFileName.IsFileWritable() )
++            {
++                destFileName.SetPermissions(0644);
++            }
++
+         }
+     }
+ 
+diff --git a/kicad/project_template.cpp b/kicad/project_template.cpp
+index bf951fcddb..2bef94326b 100644
+--- a/kicad/project_template.cpp
++++ b/kicad/project_template.cpp
+@@ -282,6 +282,21 @@ bool PROJECT_TEMPLATE::CreateProject( wxFileName& aNewProjectPath, wxString* aEr
+ 
+             result = false;
+         }
++	else if( !destFile.IsFileWritable() && !destFile.SetPermissions(0644) )
++        {
++            if( aErrorMsg )
++            {
++                if( !aErrorMsg->empty() )
++                    *aErrorMsg += "\n";
++
++                wxString msg;
++
++                msg.Printf( _( "Cannot make file writable: '%s'." ), destFile.GetFullPath() );
++                *aErrorMsg += msg;
++            }
++
++            result = false;
++	}
+     }
+ 
+     return result;

pkgs/applications/science/electronics/librepcb/default.nix

@@ -0,0 +1,61 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  qtbase,
+  qttools,
+  qtsvg,
+  qt5compat,
+  opencascade-occt,
+  libGLU,
+  cmake,
+  wrapQtAppsHook,
+  rustPlatform,
+  cargo,
+  rustc,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "librepcb";
+  version = "1.3.0";
+
+  src = fetchFromGitHub {
+    owner = "librepcb";
+    repo = "librepcb";
+    rev = version;
+    hash = "sha256-J4y0ikZNuOguN9msmEQzgcY0/REnOEOoDkY/ga+Cfd8=";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [
+    cmake
+    qttools
+    qtsvg
+    qt5compat
+    wrapQtAppsHook
+    opencascade-occt
+    libGLU
+    rustPlatform.cargoSetupHook
+    cargo
+    rustc
+  ];
+  buildInputs = [ qtbase ];
+
+  cargoDeps = rustPlatform.fetchCargoVendor {
+    inherit src cargoRoot;
+    hash = "sha256-1td3WjxbDq2lX7c0trpYRhO82ChNAG/ZABBRsekYtq4=";
+  };
+
+  cargoRoot = "libs/librepcb/rust-core";
+
+  meta = with lib; {
+    description = "Free EDA software to develop printed circuit boards";
+    homepage = "https://librepcb.org/";
+    maintainers = with maintainers; [
+      luz
+      thoughtpolice
+    ];
+    license = licenses.gpl3Plus;
+    platforms = platforms.linux;
+  };
+}

pkgs/applications/science/electronics/linux-gpib/common.nix

@@ -0,0 +1,29 @@
+{
+  pname,
+  fetchurl,
+  lib,
+}:
+rec {
+  version = "4.3.6";
+  inherit pname;
+
+  src = fetchurl {
+    url = "mirror://sourceforge/project/linux-gpib/linux-gpib%20for%203.x.x%20and%202.6.x%20kernels/${version}/linux-gpib-${version}.tar.gz";
+    hash = "sha256-Gze4xrvkhEgn+J5Jhrycezjp2uhlD1v6aX0WGv4J2Jg=";
+  };
+
+  unpackPhase = ''
+    tar xf $src
+    tar xf linux-gpib-${version}/${pname}-${version}.tar.gz
+  '';
+
+  sourceRoot = "${pname}-${version}";
+
+  meta = with lib; {
+    description = "Support package for GPIB (IEEE 488) hardware";
+    homepage = "https://linux-gpib.sourceforge.io/";
+    license = licenses.gpl2Only;
+    maintainers = with maintainers; [ fsagbuya ];
+    platforms = platforms.linux;
+  };
+}

pkgs/applications/science/electronics/linux-gpib/kernel.nix

@@ -0,0 +1,30 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  kernel,
+  pahole,
+}:
+
+stdenv.mkDerivation (
+  import ./common.nix {
+    inherit fetchurl lib;
+    pname = "linux-gpib-kernel";
+  }
+  // {
+
+    postPatch = ''
+      sed -i 's@/sbin/depmod -A@@g' Makefile
+    '';
+
+    buildInputs = [ pahole ] ++ kernel.moduleBuildDependencies;
+
+    makeFlags = [
+      "LINUX_SRCDIR=${kernel.dev}/lib/modules/${kernel.modDirVersion}/build"
+    ];
+
+    installFlags = [
+      "INSTALL_MOD_PATH=$(out)"
+    ];
+  }
+)

pkgs/applications/science/electronics/linux-gpib/user.nix

@@ -0,0 +1,36 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  autoconf,
+  libtool,
+  bison,
+  flex,
+  automake,
+  udevCheckHook,
+}:
+
+stdenv.mkDerivation (
+  import ./common.nix {
+    inherit fetchurl lib;
+    pname = "linux-gpib-user";
+  }
+  // {
+
+    nativeBuildInputs = [
+      autoconf
+      libtool
+      bison
+      flex
+      automake
+      udevCheckHook
+    ];
+
+    configureFlags = [
+      "--sysconfdir=$(out)/etc"
+      "--prefix=$(out)"
+    ];
+
+    doInstallCheck = true;
+  }
+)

pkgs/applications/science/electronics/nanovna-saver/default.nix

@@ -0,0 +1,82 @@
+{
+  lib,
+  stdenv,
+  python3,
+  fetchFromGitHub,
+  qt6,
+  writeShellScriptBin,
+}:
+let
+  # Matches the pyside6-uic and pyside6-rcc implementations
+  # https://code.qt.io/cgit/pyside/pyside-setup.git/tree/sources/pyside-tools/pyside_tool.py?id=9b310d4c0654a244147766e382834b5e8bdeb762#n90
+  pyside-tools-uic = writeShellScriptBin "pyside6-uic" ''
+    exec ${qt6.qtbase}/libexec/uic -g python "$@"
+  '';
+  pyside-tools-rcc = writeShellScriptBin "pyside6-rcc" ''
+    exec ${qt6.qtbase}/libexec/rcc -g python "$@"
+  '';
+in
+python3.pkgs.buildPythonApplication rec {
+  pname = "nanovna-saver";
+  version = "0.7.3";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "NanoVNA-Saver";
+    repo = "nanovna-saver";
+    tag = "v${version}";
+    sha256 = "sha256-Asx4drb9W2NobdgOlbgdm1aAzB69hnIWvOM915F7sgA=";
+  };
+
+  nativeBuildInputs = [
+    qt6.wrapQtAppsHook
+    qt6.qtbase
+  ];
+
+  buildInputs = lib.optional stdenv.hostPlatform.isLinux qt6.qtwayland;
+
+  propagatedBuildInputs = with python3.pkgs; [
+    cython
+    scipy
+    pyqt6
+    pyserial
+    pyside6
+    numpy
+    setuptools
+    setuptools-scm
+  ];
+
+  doCheck = false;
+
+  dontWrapGApps = true;
+  dontWrapQtApps = true;
+
+  postPatch = ''
+    substituteInPlace src/tools/ui_compile.py \
+      --replace-fail "pyside6-uic" "${pyside-tools-uic}/bin/pyside6-uic" \
+      --replace-fail "pyside6-rcc" "${pyside-tools-rcc}/bin/pyside6-rcc"
+  '';
+
+  preFixup = ''
+    makeWrapperArgs+=(
+      "''${gappsWrapperArgs[@]}"
+      "''${qtWrapperArgs[@]}"
+    )
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/NanoVNA-Saver/nanovna-saver";
+    description = "Tool for reading, displaying and saving data from the NanoVNA";
+    mainProgram = "NanoVNASaver";
+    longDescription = ''
+      A multiplatform tool to save Touchstone files from the NanoVNA, sweep
+      frequency spans in segments to gain more than 101 data points, and
+      generally display and analyze the resulting data.
+    '';
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [
+      zaninime
+      tmarkus
+    ];
+  };
+}

pkgs/applications/science/electronics/openhantek6022/default.nix

@@ -0,0 +1,54 @@
+{
+  mkDerivation,
+  lib,
+  fetchFromGitHub,
+  makeWrapper,
+  cmake,
+  qtbase,
+  qttools,
+  fftw,
+  libusb1,
+  libglvnd,
+}:
+
+mkDerivation rec {
+  pname = "openhantek6022";
+  version = "3.4.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenHantek";
+    repo = "OpenHantek6022";
+    rev = version;
+    sha256 = "sha256-FT+DyfD5WHBblRXWXFnyB2xwoIgoh84oB+QN32wx78c=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    makeWrapper
+  ];
+  buildInputs = [
+    fftw
+    libusb1
+    libglvnd
+    qtbase
+    qttools
+  ];
+
+  postPatch = ''
+    # Fix up install paths & checks
+    sed -i 's#if(EXISTS ".*")#if(1)#g' CMakeLists.txt
+    sed -i 's#/lib/udev#lib/udev#g' CMakeLists.txt
+    sed -i 's#/usr/share#share#g' CMakeLists.txt
+  '';
+
+  doInstallCheck = true;
+
+  meta = with lib; {
+    description = "Free software for Hantek and compatible (Voltcraft/Darkwire/Protek/Acetech) USB digital signal oscilloscopes";
+    mainProgram = "OpenHantek";
+    homepage = "https://github.com/OpenHantek/OpenHantek6022";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ baracoder ];
+    platforms = qtbase.meta.platforms;
+  };
+}

pkgs/applications/science/electronics/pulseview/default.nix

@@ -0,0 +1,71 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  pkg-config,
+  cmake,
+  glib,
+  boost,
+  libsigrok,
+  libsigrokdecode,
+  libserialport,
+  libzip,
+  libftdi1,
+  hidapi,
+  glibmm,
+  pcre,
+  python3,
+  qtsvg,
+  qttools,
+  bluez,
+  wrapQtAppsHook,
+  desktopToDarwinBundle,
+}:
+
+stdenv.mkDerivation {
+  pname = "pulseview";
+  version = "0.4.2-unstable-2025-05-15";
+
+  src = fetchFromGitHub {
+    owner = "sigrokproject";
+    repo = "pulseview";
+    rev = "e2fe9dfb91c7de85c410922ee9268c3f526bcc54";
+    hash = "sha256-b9pqtsF5J9MA7XMIgFZltrVqi64ZPObBTiaws3zSDRg=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+    qttools
+    wrapQtAppsHook
+  ]
+  ++ lib.optional stdenv.hostPlatform.isDarwin desktopToDarwinBundle;
+
+  buildInputs = [
+    glib
+    boost
+    libsigrok
+    libsigrokdecode
+    libserialport
+    libzip
+    libftdi1
+    hidapi
+    glibmm
+    pcre
+    python3
+    qtsvg
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isLinux [ bluez ];
+
+  meta = with lib; {
+    description = "Qt-based LA/scope/MSO GUI for sigrok (a signal analysis software suite)";
+    mainProgram = "pulseview";
+    homepage = "https://sigrok.org/";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [
+      bjornfor
+      vifino
+    ];
+    platforms = platforms.unix;
+  };
+}

pkgs/applications/science/logic/abella/default.nix

@@ -0,0 +1,62 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  rsync,
+  ocamlPackages,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "abella";
+  version = "2.0.8";
+
+  src = fetchurl {
+    url = "http://abella-prover.org/distributions/abella-${finalAttrs.version}.tar.gz";
+    sha256 = "sha256-80b/RUpE3KRY0Qu8eeTxAbk6mwGG6jVTPOP0qFjyj2M=";
+  };
+
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    rsync
+  ]
+  ++ (with ocamlPackages; [
+    ocaml
+    dune_3
+    menhir
+    findlib
+  ]);
+  buildInputs = with ocamlPackages; [
+    cmdliner
+    yojson
+  ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    rsync -av _build/default/src/abella.exe    $out/bin/abella
+
+    mkdir -p $out/share/emacs/site-lisp/abella/
+    rsync -av emacs/    $out/share/emacs/site-lisp/abella/
+
+    mkdir -p $out/share/abella/examples
+    rsync -av examples/ $out/share/abella/examples/
+  '';
+
+  meta = {
+    description = "Interactive theorem prover";
+    mainProgram = "abella";
+    longDescription = ''
+      Abella is an interactive theorem prover based on lambda-tree syntax.
+      This means that Abella is well-suited for reasoning about the meta-theory
+      of programming languages and other logical systems which manipulate
+      objects with binding.
+    '';
+    homepage = "https://abella-prover.org";
+    license = lib.licenses.gpl3;
+    maintainers = with lib.maintainers; [
+      bcdarwin
+      ciil
+    ];
+    platforms = lib.platforms.unix;
+  };
+})

pkgs/applications/science/logic/cedille/Fix-to-string.agda-to-compile-with-Agda-2.6.1.patch

@@ -0,0 +1,31 @@
+From 563f023aba1034f4f433f412302b825b059ef5a5 Mon Sep 17 00:00:00 2001
+From: Mark Barbone <mark.l.barbone@gmail.com>
+Date: Sun, 19 Jul 2020 17:24:30 -0400
+Subject: [PATCH] Fix to-string.agda to compile with Agda 2.6.1
+
+---
+Adapted from https://github.com/cedille/cedille/pull/156.
+
+ src/to-string.agda | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/src/to-string.agda b/src/to-string.agda
+index 2505942..051a2da 100644
+--- a/src/to-string.agda
++++ b/src/to-string.agda
+@@ -100,9 +100,9 @@ no-parens {TK} _ _ _ = tt
+ no-parens {QUALIF} _ _ _ = tt
+ no-parens {ARG} _ _ _ = tt
+ 
+-pattern ced-ops-drop-spine = cedille-options.options.mk-options _ _ _ _ ff _ _ _ ff _
+-pattern ced-ops-conv-arr = cedille-options.options.mk-options _ _ _ _ _ _ _ _ ff _
+-pattern ced-ops-conv-abs = cedille-options.options.mk-options _ _ _ _ _ _ _ _ tt _
++pattern ced-ops-drop-spine = cedille-options.mk-options _ _ _ _ ff _ _ _ ff _
++pattern ced-ops-conv-arr = cedille-options.mk-options _ _ _ _ _ _ _ _ ff _
++pattern ced-ops-conv-abs = cedille-options.mk-options _ _ _ _ _ _ _ _ tt _
+ 
+ drop-spine : cedille-options.options → {ed : exprd} → ctxt → ⟦ ed ⟧ → ⟦ ed ⟧
+ drop-spine ops @ ced-ops-drop-spine = h
+-- 
+2.27.0
+

pkgs/applications/science/logic/cedille/default.nix

@@ -0,0 +1,67 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  alex,
+  happy,
+  Agda,
+  buildPackages,
+  ghcWithPackages,
+}:
+
+stdenv.mkDerivation rec {
+  version = "1.1.2";
+  pname = "cedille";
+
+  src = fetchFromGitHub {
+    owner = "cedille";
+    repo = "cedille";
+    rev = "v${version}";
+    sha256 = "1j745q9sd32fhcb96wjq6xvyqq1k6imppjnya6x0n99fyfnqzvg9";
+    fetchSubmodules = true;
+  };
+
+  patches = [
+    ./Fix-to-string.agda-to-compile-with-Agda-2.6.1.patch
+  ];
+
+  nativeBuildInputs = [
+    alex
+    happy
+  ];
+  buildInputs = [
+    Agda
+    (ghcWithPackages (ps: [ ps.ieee ]))
+  ];
+
+  LANG = "en_US.UTF-8";
+  LOCALE_ARCHIVE = lib.optionalString (
+    stdenv.buildPlatform.libc == "glibc"
+  ) "${buildPackages.glibcLocales}/lib/locale/locale-archive";
+
+  postPatch = ''
+    patchShebangs create-libraries.sh
+  '';
+
+  installPhase = ''
+    install -Dm755 -t $out/bin/ cedille
+    install -Dm755 -t $out/bin/ core/cedille-core
+    install -Dm644 -t $out/share/info docs/info/cedille-info-main.info
+
+    mkdir -p $out/lib/
+    cp -r lib/ $out/lib/cedille/
+  '';
+
+  meta = with lib; {
+    description = "Interactive theorem-prover and dependently typed programming language, based on extrinsic (aka Curry-style) type theory";
+    homepage = "https://cedille.github.io/";
+    license = licenses.mit;
+    maintainers = with maintainers; [ mpickering ];
+    platforms = platforms.unix;
+
+    # Broken due to Agda update.  See
+    # https://github.com/NixOS/nixpkgs/pull/129606#issuecomment-881107449.
+    broken = true;
+    hydraPlatforms = platforms.none;
+  };
+}

pkgs/applications/science/logic/coq/default.nix

@@ -0,0 +1,363 @@
+# - coqide compilation can be disabled by setting buildIde to false
+# - The csdp program used for the Micromega tactic is statically referenced.
+#   However, coq can build without csdp by setting it to null.
+#   In this case some Micromega tactics will search the user's path for the csdp program and will fail if it is not found.
+# - The exact version can be specified through the `version` argument to
+#   the derivation; it defaults to the latest stable version.
+
+{
+  lib,
+  stdenv,
+  fetchzip,
+  fetchurl,
+  writeText,
+  pkg-config,
+  gnumake42,
+  customOCamlPackages ? null,
+  ocamlPackages_4_09,
+  ocamlPackages_4_10,
+  ocamlPackages_4_12,
+  ocamlPackages_4_14,
+  rocqPackages, # for versions >= 9.0 that are transition shims on top of Rocq
+  ncurses,
+  buildIde ? null, # default is true for Coq < 8.14 and false for Coq >= 8.14
+  glib,
+  adwaita-icon-theme,
+  wrapGAppsHook3,
+  makeDesktopItem,
+  copyDesktopItems,
+  csdp ? null,
+  version,
+  coq-version ? null,
+}@args:
+let
+  lib = import ../../../../build-support/coq/extra-lib.nix { inherit (args) lib; };
+
+  release = {
+    "8.7.0".sha256 = "1h18b7xpnx3ix9vsi5fx4zdcbxy7bhra7gd5c5yzxmk53cgf1p9m";
+    "8.7.1".sha256 = "0gjn59jkbxwrihk8fx9d823wjyjh5m9gvj9l31nv6z6bcqhgdqi8";
+    "8.7.2".sha256 = "0a0657xby8wdq4aqb2xsxp3n7pmc2w4yxjmrb2l4kccs1aqvaj4w";
+    "8.8.0".sha256 = "13a4fka22hdxsjk11mgjb9ffzplfxyxp1sg5v1c8nk1grxlscgw8";
+    "8.8.1".sha256 = "1hlf58gwazywbmfa48219amid38vqdl94yz21i11b4map6jfwhbk";
+    "8.8.2".sha256 = "1lip3xja924dm6qblisk1bk0x8ai24s5xxqxphbdxj6djglj68fd";
+    "8.9.0".sha256 = "1dkgdjc4n1m15m1p724hhi5cyxpqbjw6rxc5na6fl3v4qjjfnizh";
+    "8.9.1".sha256 = "1xrq6mkhpq994bncmnijf8jwmwn961kkpl4mwwlv7j3dgnysrcv2";
+    "8.10.0".sha256 = "138jw94wp4mg5dgjc2asn8ng09ayz1mxdznq342n0m469j803gzg";
+    "8.10.1".sha256 = "072v2zkjzf7gj48137wpr3c9j0hg9pdhlr5l8jrgrwynld8fp7i4";
+    "8.10.2".sha256 = "0znxmpy71bfw0p6x47i82jf5k7v41zbz9bdpn901ysn3ir8l3wrz";
+    "8.11.0".sha256 = "1rfdic6mp7acx2zfwz7ziqk12g95bl9nyj68z4n20a5bcjv2pxpn";
+    "8.11.1".sha256 = "0qriy9dy36dajsv5qmli8gd6v55mah02ya334nw49ky19v7518m0";
+    "8.11.2".sha256 = "0f77ccyxdgbf1nrj5fa8qvrk1cyfy06fv8gj9kzfvlcgn0cf48sa";
+    "8.12.0".sha256 = "18dc7k0piv6v064zgdadpw6mkkxk7j663hb3svgj5236fihjr0cz";
+    "8.12.1".sha256 = "1rkcyjjrzcqw9xk93hsq0vvji4f8r5iq0f739mghk60bghkpnb7q";
+    "8.12.2".sha256 = "18gscfm039pqhq4msq01nraig5dm9ab98bjca94zldf8jvdv0x2n";
+    "8.13.0".sha256 = "1l2c63vskp8kiyxiyi5rpgbmnv67ysn3y4lybd6nj0li5llibifi";
+    "8.13.1".sha256 = "15drjcqhsgwqnv02bbidyhk316ypyhz1pxfz2gwsalci9svhkz0v";
+    "8.13.2".sha256 = "14d4alp35hngvga9m7cfp5d1nl62xdj0nm4811f2jjblk86gxxk4";
+    "8.14.0".sha256 = "0yxjx9kq9bfpk31dc1c6a0pz0827fz7jmrcwwd4n7dc07yi0arq8";
+    "8.14.1".sha256 = "0xdqiabgm4lrm6d7lw544zd8xwb1cdcavsxvwwlqq6yid2rl2yli";
+    "8.15.0".sha256 = "sha256:0q7jl3bn0d1v9cwdkxykw4frccww6wbh1p8hdrfqw489mkxmh5jh";
+    "8.15.1".sha256 = "sha256:1janvmnk3czimp0j5qmnfwx6509vhpjc2q7lcza1bc6dm6kn8n42";
+    "8.15.2".sha256 = "sha256:0qibbvzrhsvs6w3zpkhyclndp29jnr6bs9i5skjlpp431jdjjfqd";
+    "8.16.0".sha256 = "sha256-3V6kL9j2rn5FHBxq1mtmWWTZS9X5cAyvtUsS6DaM+is=";
+    "8.16.1".sha256 = "sha256-n7830+zfZeyYHEOGdUo57bH6bb2/SZs8zv8xJhV+iAc=";
+    "8.17.0".sha256 = "sha256-TGwm7S6+vkeZ8cidvp8pkiAd9tk008jvvPvYgfEOXhM=";
+    "8.17.1".sha256 = "sha256-x+RwkbxMg9aR0L3WSCtpIz8jwA5cJA4tXAtHMZb20y4=";
+    "8.18.0".sha256 = "sha256-WhiBs4nzPHQ0R24xAdM49kmxSCPOxiOVMA1iiMYunz4=";
+    "8.19.0".sha256 = "sha256-ixsYCvCXpBHqJ71hLQklphlwoOO3i/6w2PJjllKqf9k=";
+    "8.19.1".sha256 = "sha256-kmZ8Uk8jpzjOd67aAPp3C+vU2oNaBw9pr7+Uixcgg94=";
+    "8.19.2".sha256 = "sha256-q+i07JsMZp83Gqav6v1jxsgPLN7sPvp5/oszVnavmz0=";
+    "8.20.0".sha256 = "sha256-WFpZlA6CzFVAruPhWcHQI7VOBVhrGLdFzWrHW0DTSl0=";
+    "8.20.1".sha256 = "sha256-nRaLODPG4E3gUDzGrCK40vhl4+VhPyd+/fXFK/HC3Ig=";
+    "9.0.0".sha256 = "sha256-GRwYSvrJGiPD+I82gLOgotb+8Ra5xHZUJGcNwxWqZkU=";
+    "9.1.0".sha256 = "sha256-+QL7I1/0BfT87n7lSaOmpHj2jJuDB4idWhAxwzvVQOE=";
+  };
+  releaseRev = v: "V${v}";
+  fetched =
+    import ../../../../build-support/coq/meta-fetch/default.nix
+      {
+        inherit
+          lib
+          stdenv
+          fetchzip
+          fetchurl
+          ;
+      }
+      {
+        inherit release releaseRev;
+        location = {
+          owner = "coq";
+          repo = "coq";
+        };
+      }
+      args.version;
+  version = fetched.version;
+  coq-version =
+    args.coq-version or (if version != "dev" then lib.versions.majorMinor version else "dev");
+  coqAtLeast = v: coq-version == "dev" || lib.versionAtLeast coq-version v;
+  buildIde = args.buildIde or (!coqAtLeast "8.14");
+  ideFlags = lib.optionalString (
+    buildIde && !coqAtLeast "8.10"
+  ) "-lablgtkdir ${ocamlPackages.lablgtk}/lib/ocaml/*/site-lib/lablgtk2 -coqide opt";
+  csdpPatch = lib.optionalString (csdp != null) ''
+    substituteInPlace plugins/micromega/sos.ml --replace "; csdp" "; ${csdp}/bin/csdp"
+    substituteInPlace plugins/micromega/coq_micromega.ml --replace "System.is_in_system_path \"csdp\"" "true"
+  '';
+  ocamlPackages =
+    if customOCamlPackages != null then
+      customOCamlPackages
+    else
+      lib.switch coq-version [
+        {
+          case = lib.versions.range "8.16" "8.18";
+          out = ocamlPackages_4_14;
+        }
+        {
+          case = lib.versions.range "8.14" "8.15";
+          out = ocamlPackages_4_12;
+        }
+        {
+          case = lib.versions.range "8.11" "8.13";
+          out = ocamlPackages_4_10;
+        }
+        {
+          case = lib.versions.range "8.7" "8.10";
+          out = ocamlPackages_4_09;
+        }
+      ] ocamlPackages_4_14;
+  ocamlNativeBuildInputs = [
+    ocamlPackages.ocaml
+    ocamlPackages.findlib
+  ]
+  ++ lib.optional (coqAtLeast "8.14") ocamlPackages.dune_3;
+  ocamlPropagatedBuildInputs =
+    [ ]
+    ++ lib.optional (!coqAtLeast "8.10") ocamlPackages.camlp5
+    ++ lib.optional (!coqAtLeast "8.13") ocamlPackages.num
+    ++ lib.optional (coqAtLeast "8.13") ocamlPackages.zarith;
+  self = stdenv.mkDerivation {
+    pname = "coq";
+    inherit (fetched) version src;
+
+    passthru = {
+      inherit coq-version;
+      inherit ocamlPackages ocamlNativeBuildInputs;
+      inherit ocamlPropagatedBuildInputs;
+      # For compatibility
+      inherit (ocamlPackages)
+        ocaml
+        camlp5
+        findlib
+        num
+        ;
+      rocqPackages = lib.optionalAttrs (coqAtLeast "8.21") rocqPackages;
+      emacsBufferSetup = pkgs: ''
+        ; Propagate coq paths to children
+        (inherit-local-permanent coq-prog-name "${self}/bin/coqtop")
+        (inherit-local-permanent coq-dependency-analyzer "${self}/bin/coqdep")
+        (inherit-local-permanent coq-compiler "${self}/bin/coqc")
+        ; If the coq-library path was already set, re-set it based on our current coq
+        (when (fboundp 'get-coq-library-directory)
+          (inherit-local-permanent coq-library-directory (get-coq-library-directory))
+          (coq-prog-args))
+        (mapc (lambda (arg)
+          (when (file-directory-p (concat arg "/lib/coq/${coq-version}/user-contrib"))
+            (setenv "COQPATH" (concat (getenv "COQPATH") ":" arg "/lib/coq/${coq-version}/user-contrib")))) '(${
+              lib.concatStringsSep " " (map (pkg: "\"${pkg}\"") pkgs)
+            }))
+        ; TODO Abstract this pattern from here and nixBufferBuilders.withPackages!
+        (defvar nixpkgs--coq-buffer-count 0)
+        (when (eq nixpkgs--coq-buffer-count 0)
+          (make-variable-buffer-local 'nixpkgs--is-nixpkgs-coq-buffer)
+          (defun nixpkgs--coq-inherit (buf)
+            (inherit-local-inherit-child buf)
+            (with-current-buffer buf
+              (setq nixpkgs--coq-buffer-count (1+ nixpkgs--coq-buffer-count))
+              (add-hook 'kill-buffer-hook 'nixpkgs--decrement-coq-buffer-count nil t))
+            buf)
+          ; When generating a scomint buffer, do inherit-local inheritance and make it a nixpkgs-coq buffer
+          (defun nixpkgs--around-scomint-make (orig &rest r)
+            (if nixpkgs--is-nixpkgs-coq-buffer
+                (progn
+                  (advice-add 'get-buffer-create :filter-return #'nixpkgs--coq-inherit)
+                  (apply orig r)
+                  (advice-remove 'get-buffer-create #'nixpkgs--coq-inherit))
+              (apply orig r)))
+          (advice-add 'scomint-make :around #'nixpkgs--around-scomint-make)
+          ; When we have no more coq buffers, tear down the buffer handling
+          (defun nixpkgs--decrement-coq-buffer-count ()
+            (setq nixpkgs--coq-buffer-count (1- nixpkgs--coq-buffer-count))
+            (when (eq nixpkgs--coq-buffer-count 0)
+              (advice-remove 'scomint-make #'nixpkgs--around-scomint-make)
+              (fmakunbound 'nixpkgs--around-scomint-make)
+              (fmakunbound 'nixpkgs--coq-inherit)
+              (fmakunbound 'nixpkgs--decrement-coq-buffer-count))))
+        (setq nixpkgs--coq-buffer-count (1+ nixpkgs--coq-buffer-count))
+        (add-hook 'kill-buffer-hook 'nixpkgs--decrement-coq-buffer-count nil t)
+        (setq nixpkgs--is-nixpkgs-coq-buffer t)
+        (inherit-local 'nixpkgs--is-nixpkgs-coq-buffer)
+      '';
+    };
+
+    nativeBuildInputs = [
+      pkg-config
+    ]
+    ++ ocamlNativeBuildInputs
+    ++ lib.optional buildIde copyDesktopItems
+    ++ lib.optional (buildIde && coqAtLeast "8.10") wrapGAppsHook3
+    ++ lib.optional (!coqAtLeast "8.6") gnumake42;
+    buildInputs = [
+      ncurses
+    ]
+    ++ lib.optionals buildIde (
+      if coqAtLeast "8.10" then
+        [
+          ocamlPackages.lablgtk3-sourceview3
+          glib
+          adwaita-icon-theme
+        ]
+      else
+        [ ocamlPackages.lablgtk ]
+    );
+
+    propagatedBuildInputs = ocamlPropagatedBuildInputs;
+
+    postPatch = ''
+      UNAME=$(type -tp uname)
+      RM=$(type -tp rm)
+      substituteInPlace tools/beautify-archive --replace "/bin/rm" "$RM"
+      ${lib.optionalString (
+        !coqAtLeast "8.7"
+      ) "substituteInPlace configure.ml --replace \"md5 -q\" \"md5sum\""}
+      ${csdpPatch}
+    '';
+
+    setupHook = writeText "setupHook.sh" ''
+      addCoqPath () {
+        if test -d "''$1/lib/coq/${coq-version}/user-contrib"; then
+          export COQPATH="''${COQPATH-}''${COQPATH:+:}''$1/lib/coq/${coq-version}/user-contrib/"
+        fi
+      }
+
+      addEnvHooks "$targetOffset" addCoqPath
+    '';
+
+    preConfigure =
+      if coqAtLeast "8.10" then
+        ''
+          patchShebangs dev/tools/
+        ''
+      else
+        ''
+          configureFlagsArray=(
+            ${ideFlags}
+          )
+        '';
+
+    prefixKey = "-prefix ";
+
+    buildFlags = [
+      "revision"
+      "coq"
+    ]
+    ++ lib.optional buildIde "coqide"
+    ++ lib.optional (!coqAtLeast "8.14") "bin/votour";
+    enableParallelBuilding = true;
+
+    createFindlibDestdir = true;
+
+    desktopItems = lib.optional buildIde (makeDesktopItem {
+      name = "coqide";
+      exec = "coqide";
+      icon = "coq";
+      desktopName = "CoqIDE";
+      comment = "Graphical interface for the Coq proof assistant";
+      categories = [
+        "Development"
+        "Science"
+        "Math"
+        "IDE"
+        "GTK"
+      ];
+    });
+
+    postInstall =
+      let
+        suffix = lib.optionalString (coqAtLeast "8.14") "-core";
+      in
+      lib.optionalString (!coqAtLeast "8.17") ''
+        cp bin/votour $out/bin/
+      ''
+      + ''
+        ln -s $out/lib/coq${suffix} $OCAMLFIND_DESTDIR/coq${suffix}
+      ''
+      + lib.optionalString (coqAtLeast "8.14") ''
+        ln -s $out/lib/coqide-server $OCAMLFIND_DESTDIR/coqide-server
+      ''
+      + lib.optionalString buildIde ''
+        mkdir -p "$out/share/pixmaps"
+        ln -s "$out/share/coq/coq.png" "$out/share/pixmaps/"
+      '';
+
+    meta = with lib; {
+      description = "Coq proof assistant";
+      longDescription = ''
+        Coq is a formal proof management system.  It provides a formal language
+        to write mathematical definitions, executable algorithms and theorems
+        together with an environment for semi-interactive development of
+        machine-checked proofs.
+      '';
+      homepage = "https://coq.inria.fr";
+      license = licenses.lgpl21;
+      branch = coq-version;
+      maintainers = with maintainers; [
+        roconnor
+        thoughtpolice
+        vbgl
+        Zimmi48
+      ];
+      platforms = platforms.unix;
+      mainProgram = "coqide";
+    };
+  };
+in
+if coqAtLeast "8.21" then
+  self.overrideAttrs (o: {
+    # coq-core is now a shim for rocq
+    propagatedBuildInputs = o.propagatedBuildInputs ++ [
+      rocqPackages.rocq-core
+    ];
+    buildPhase = ''
+      runHook preBuild
+      dune build -p coq-core,coqide-server${lib.optionalString buildIde ",rocqide"} -j $NIX_BUILD_CORES
+      runHook postBuild
+    '';
+    installPhase = ''
+      runHook preInstall
+      dune install --prefix $out coq-core coqide-server${lib.optionalString buildIde " rocqide"}
+      # coq and rocq are now in different directories, which sometimes confuses coq_makefile
+      # which expects both in the same /nix/store/.../bin/ directory
+      # adding symlinks to content it
+      ROCQBIN=$(dirname ''$(command -v rocq))
+      for b in csdpcert ocamllibdep rocq rocq.byte rocqchk votour ; do
+        ln -s ''${ROCQBIN}/''${b} $out/bin/
+      done
+      runHook postInstall
+    '';
+  })
+else if coqAtLeast "8.17" then
+  self.overrideAttrs (_: {
+    buildPhase = ''
+      runHook preBuild
+      make dunestrap
+      dune build -p coq-core,coq-stdlib,coqide-server${lib.optionalString buildIde ",coqide"} -j $NIX_BUILD_CORES
+      runHook postBuild
+    '';
+    installPhase = ''
+      runHook preInstall
+      dune install --prefix $out coq-core coq-stdlib coqide-server${lib.optionalString buildIde " coqide"}
+      runHook postInstall
+    '';
+  })
+else
+  self

pkgs/applications/science/logic/cubicle/default.nix

@@ -0,0 +1,48 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  autoreconfHook,
+  which,
+  ocamlPackages,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "cubicle";
+  version = "1.2.0";
+  src = fetchurl {
+    url = "https://github.com/cubicle-model-checker/cubicle/archive/refs/tags/${version}.tar.gz";
+    hash = "sha256-/EtbXpyXqRm0jGcMfGLAEwdr92061edjFys1V7/w6/Y=";
+  };
+
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    autoreconfHook
+    which
+  ]
+  ++ (with ocamlPackages; [
+    findlib
+    ocaml
+  ]);
+
+  buildInputs = with ocamlPackages; [
+    functory
+    num
+  ];
+
+  # https://github.com/cubicle-model-checker/cubicle/issues/1
+  env = {
+    OCAMLC = "ocamlfind ocamlc -package num";
+    OCAMLOPT = "ocamlfind ocamlopt -package num";
+  };
+
+  meta = with lib; {
+    description = "Open source model checker for verifying safety properties of array-based systems";
+    mainProgram = "cubicle";
+    homepage = "https://cubicle.lri.fr/";
+    license = licenses.asl20;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ dwarfmaster ];
+  };
+}

pkgs/applications/science/logic/cvc3/cvc3-2.4.1-gccv6-fix.patch

@@ -0,0 +1,76 @@
+commit 4eb28b907e89be05d92eb704115f821b9b848e60
+Author: Matthew Dawson <matthew@mjdsystems.ca>
+Date:   Sun Oct 16 22:06:03 2016 -0400
+
+    Fix gcc v6 compile failures.
+    
+     * Use std::hash<const char*> over std::hash<char *>, as throwing away the const is not allowed.
+     * Use Hash::hash by default in CDMap over std::hash, to get Hash::hash<CVC3::expr>
+
+diff --git a/src/expr/expr_value.cpp b/src/expr/expr_value.cpp
+index 0c85ff6..e4dd251 100644
+--- a/src/expr/expr_value.cpp
++++ b/src/expr/expr_value.cpp
+@@ -29,7 +29,7 @@ namespace CVC3 {
+ // Class ExprValue static members
+ ////////////////////////////////////////////////////////////////////////
+ 
+-std::hash<char*> ExprValue::s_charHash;
++std::hash<const char*> ExprValue::s_charHash;
+ std::hash<long int> ExprValue::s_intHash;
+ 
+ ////////////////////////////////////////////////////////////////////////
+diff --git a/src/include/cdmap.h b/src/include/cdmap.h
+index faf682a..c3b094c 100644
+--- a/src/include/cdmap.h
++++ b/src/include/cdmap.h
+@@ -43,9 +43,9 @@ namespace CVC3 {
+ // Auxiliary class: almost the same as CDO (see cdo.h), but on
+ // setNull() call it erases itself from the map.
+ 
+-template <class Key, class Data, class HashFcn = std::hash<Key> > class CDMap;
++template <class Key, class Data, class HashFcn = Hash::hash<Key> > class CDMap;
+ 
+-template <class Key, class Data, class HashFcn = std::hash<Key> >
++template <class Key, class Data, class HashFcn = Hash::hash<Key> >
+ class CDOmap :public ContextObj {
+   Key d_key;
+   Data d_data;
+diff --git a/src/include/expr_hash.h b/src/include/expr_hash.h
+index b2107d7..baa2eab 100644
+--- a/src/include/expr_hash.h
++++ b/src/include/expr_hash.h
+@@ -20,7 +20,6 @@
+  * hash_set over Expr class.
+  */
+ /*****************************************************************************/
+-
+ #ifndef _cvc3__expr_h_
+ #include "expr.h"
+ #endif
+diff --git a/src/include/expr_value.h b/src/include/expr_value.h
+index 95102b2..f53aa4d 100644
+--- a/src/include/expr_value.h
++++ b/src/include/expr_value.h
+@@ -179,7 +179,7 @@ protected:
+   // Static hash functions.  They don't depend on the context
+   // (ExprManager and such), so it is still thread-safe to have them
+   // static.
+-  static std::hash<char*> s_charHash;
++  static std::hash<const char*> s_charHash;
+   static std::hash<long int> s_intHash;
+ 
+   static size_t pointerHash(void* p) { return s_intHash((long int)p); }
+diff --git a/src/theory_core/theory_core.cpp b/src/theory_core/theory_core.cpp
+index df5289f..37ccab9 100644
+--- a/src/theory_core/theory_core.cpp
++++ b/src/theory_core/theory_core.cpp
+@@ -710,7 +710,7 @@ TheoryCore::TheoryCore(ContextManager* cm,
+     //    d_termTheorems(cm->getCurrentContext()),
+     d_predicates(cm->getCurrentContext()),
+     d_solver(NULL),
+-    d_simplifyInPlace(false),
++    d_simplifyInPlace(NULL),
+     d_currentRecursiveSimplifier(NULL),
+     d_resourceLimit(0),
+     d_timeBase(0),

pkgs/applications/science/logic/cvc3/default.nix

@@ -0,0 +1,58 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  flex,
+  bison,
+  gmp,
+  perl,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "cvc3";
+  version = "2.4.1";
+
+  src = fetchurl {
+    url = "https://cs.nyu.edu/acsys/cvc3/releases/${version}/${pname}-${version}.tar.gz";
+    sha256 = "1xxcwhz3y6djrycw8sm6xz83wb4hb12rd1n0skvc7fng0rh1snym";
+  };
+
+  buildInputs = [
+    gmp
+    flex
+    bison
+    perl
+  ];
+
+  patches = [ ./cvc3-2.4.1-gccv6-fix.patch ];
+
+  # fails to configure on darwin due to gmp not found
+  configureFlags = [
+    "LIBS=-L${gmp}/lib"
+    "CXXFLAGS=-I${gmp.dev}/include"
+  ];
+
+  postPatch = ''
+    sed -e "s@ /bin/bash@bash@g" -i Makefile.std
+    find . -exec sed -e "s@/usr/bin/perl@${perl}/bin/perl@g" -i '{}' ';'
+
+    # bison 3.7 workaround
+    for f in parsePL parseLisp parsesmtlib parsesmtlib2 ; do
+      ln -s ../parser/''${f}_defs.h src/include/''${f}.hpp
+    done
+  '';
+
+  meta = with lib; {
+    description = "Prover for satisfiability modulo theory (SMT)";
+    mainProgram = "cvc3";
+    maintainers = with maintainers; [ raskin ];
+    platforms = platforms.unix;
+    license = licenses.free;
+    homepage = "https://cs.nyu.edu/acsys/cvc3/index.html";
+  };
+  passthru = {
+    updateInfo = {
+      downloadPage = "https://cs.nyu.edu/acsys/cvc3/download.html";
+    };
+  };
+}

pkgs/applications/science/logic/easycrypt/default.nix

@@ -0,0 +1,69 @@
+{
+  lib,
+  stdenv,
+  darwin,
+  fetchFromGitHub,
+  ocamlPackages,
+  why3,
+  python3,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "easycrypt";
+  version = "2025.08";
+
+  src = fetchFromGitHub {
+    owner = "easycrypt";
+    repo = "easycrypt";
+    tag = "r${version}";
+    hash = "sha256-WUms6hh7T5/gxRLFvbJQiT1ErLr8KFilFNOMTT/fIyY=";
+  };
+
+  nativeBuildInputs =
+    with ocamlPackages;
+    [
+      dune_3
+      findlib
+      menhir
+      ocaml
+      python3.pkgs.wrapPython
+    ]
+    ++ lib.optional stdenv.hostPlatform.isDarwin darwin.sigtool;
+
+  buildInputs = with ocamlPackages; [
+    batteries
+    dune-build-info
+    dune-site
+    inifiles
+    why3
+    yojson
+    zarith
+  ];
+
+  propagatedBuildInputs = [ why3.out ];
+
+  strictDeps = true;
+
+  postPatch = ''
+    substituteInPlace dune-project --replace-fail '(name easycrypt)' '(name easycrypt)(version ${version})'
+  '';
+
+  pythonPath = with python3.pkgs; [ pyyaml ];
+
+  installPhase = ''
+    runHook preInstall
+    dune install --prefix $out easycrypt
+    rm $out/bin/ec-runtest
+    wrapPythonProgramsIn "$out/lib/easycrypt/commands" "$pythonPath"
+    runHook postInstall
+  '';
+
+  meta = {
+    license = lib.licenses.mit;
+    maintainers = [ lib.maintainers.vbgl ];
+    platforms = lib.platforms.all;
+    homepage = "https://easycrypt.info/";
+    description = "Computer-Aided Cryptographic Proofs";
+    mainProgram = "easycrypt";
+  };
+}

pkgs/applications/science/logic/easycrypt/runtest.nix

@@ -0,0 +1,26 @@
+{ python3Packages, easycrypt }:
+
+python3Packages.buildPythonApplication {
+  inherit (easycrypt) src version;
+  format = "other";
+
+  pname = "easycrypt-runtest";
+
+  dontConfigure = true;
+  dontBuild = true;
+  doCheck = false;
+
+  pythonPath = with python3Packages; [ pyyaml ];
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out/bin
+    cp scripts/testing/runtest $out/bin/ec-runtest
+    runHook postInstall
+  '';
+
+  meta = easycrypt.meta // {
+    description = "Testing program for EasyCrypt formalizations";
+    mainProgram = "ec-runtest";
+  };
+}

pkgs/applications/science/logic/ekrhyper/default.nix

@@ -0,0 +1,33 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  ocaml,
+  perl,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "ekrhyper";
+  version = "1_4_21022014";
+
+  src = fetchurl {
+    url = "http://userpages.uni-koblenz.de/~bpelzer/ekrhyper/ekrh_${version}.tar.gz";
+    sha256 = "sha256-fEe0DIMGj7wO+79/BZf45kykgyTXpbZJsyFSt31XqpM=";
+  };
+
+  strictDeps = true;
+  nativeBuildInputs = [
+    ocaml
+    perl
+  ];
+  setSourceRoot = "export sourceRoot=$(echo */ekrh/src)";
+  preInstall = "export INSTALLDIR=$out";
+  postInstall = ''for i in "$out/casc"/*; do ln -s "$i" "$out/bin/ekrh-casc-$(basename $i)"; done '';
+
+  meta = with lib; {
+    description = "Automated first-order theorem prover";
+    license = licenses.gpl2;
+    maintainers = with maintainers; [ raskin ];
+    platforms = platforms.linux;
+  };
+}

pkgs/applications/science/logic/hol_light/0004-Fix-compilation-with-camlp5-7.11.patch

@@ -0,0 +1,66 @@
+From: Stephane Glondu <steph@glondu.net>
+Date: Wed, 12 Feb 2020 05:42:32 +0100
+Subject: Fix compilation with camlp5 7.11
+
+---
+ pa_j_4.xx_7.xx.ml | 17 +++++++++++------
+ 1 file changed, 11 insertions(+), 6 deletions(-)
+
+diff --git a/pa_j_4.xx_7.xx.ml b/pa_j_4.xx_7.xx.ml
+index 4f7ed60..e834058 100755
+--- a/pa_j/pa_j_4.xx_7.xx.ml
++++ b/pa_j/pa_j_4.xx_7.xx.ml
+@@ -410,9 +410,10 @@ and reloc_module_type floc sh =
+     | MtApp loc x1 x2 →
+         let loc = floc loc in
+         MtApp loc (self x1) (self x2)
+-    | MtFun loc x1 x2 x3 →
++    | MtFun loc x x3 →
+         let loc = floc loc in
+-        MtFun loc x1 (self x2) (self x3)
++        let x = vala_map (option_map (fun (x1, x2) -> (x1, self x2))) x in
++        MtFun loc x (self x3)
+     | MtLid loc x1 →
+         let loc = floc loc in
+         MtLid loc x1
+@@ -507,9 +508,10 @@ and reloc_module_expr floc sh =
+     | MeApp loc x1 x2 →
+         let loc = floc loc in
+         MeApp loc (self x1) (self x2)
+-    | MeFun loc x1 x2 x3 →
++    | MeFun loc x x3 →
+         let loc = floc loc in
+-        MeFun loc x1 (reloc_module_type floc sh x2) (self x3)
++        let x = vala_map (option_map (fun (x1, x2) -> (x1, reloc_module_type floc sh x2))) x in
++        MeFun loc x (self x3)
+     | MeStr loc x1 →
+         let loc = floc loc in
+         MeStr loc (vala_map (List.map (reloc_str_item floc sh)) x1)
+@@ -2007,7 +2009,7 @@ EXTEND
+       | -> <:vala< [] >> ] ]
+   ;
+   mod_binding:
+-    [ [ i = V UIDENT; me = mod_fun_binding -> (i, me) ] ]
++    [ [ i = V uidopt "uidopt"; me = mod_fun_binding -> (i, me) ] ]
+   ;
+   mod_fun_binding:
+     [ RIGHTA
+@@ -2070,7 +2072,7 @@ EXTEND
+           <:sig_item< value $lid:i$ : $t$ >> ] ]
+   ;
+   mod_decl_binding:
+-    [ [ i = V UIDENT; mt = module_declaration -> (i, mt) ] ]
++    [ [ i = V uidopt "uidopt"; mt = module_declaration -> (i, mt) ] ]
+   ;
+   module_declaration:
+     [ RIGHTA
+@@ -2092,6 +2094,9 @@ EXTEND
+       | "module"; i = V mod_ident ""; ":="; me = module_expr ->
+           <:with_constr< module $_:i$ := $me$ >> ] ]
+   ;
++  uidopt:
++    [ [ m = V UIDENT -> Some m ] ]
++  ;
+   (* Core expressions *)
+   expr:
+     [ "top" RIGHTA

pkgs/applications/science/logic/hol_light/default.nix

@@ -0,0 +1,85 @@
+{
+  lib,
+  stdenv,
+  runtimeShell,
+  fetchFromGitHub,
+  ocaml,
+  findlib,
+  num,
+  zarith,
+  camlp5,
+  camlp-streams,
+}:
+
+let
+  use_zarith = lib.versionAtLeast ocaml.version "4.14";
+  load_num =
+    if use_zarith then
+      ''
+        -I ${zarith}/lib/ocaml/${ocaml.version}/site-lib/zarith \
+        -I ${zarith}/lib/ocaml/${ocaml.version}/site-lib/stublibs \
+      ''
+    else
+      lib.optionalString (num != null) ''
+        -I ${num}/lib/ocaml/${ocaml.version}/site-lib/num \
+        -I ${num}/lib/ocaml/${ocaml.version}/site-lib/top-num \
+        -I ${num}/lib/ocaml/${ocaml.version}/site-lib/stublibs \
+      '';
+
+  start_script = ''
+    #!${runtimeShell}
+    cd $out/lib/hol_light
+    export OCAMLPATH="''${OCAMLPATH-}''${OCAMLPATH:+:}${camlp5}/lib/ocaml/${ocaml.version}/site-lib/"
+    exec ${ocaml}/bin/ocaml \
+      -I \`${camlp5}/bin/camlp5 -where\` \
+      ${load_num} \
+      -I ${findlib}/lib/ocaml/${ocaml.version}/site-lib/ \
+      -I ${camlp-streams}/lib/ocaml/${ocaml.version}/site-lib/camlp-streams camlp_streams.cma \
+      -init make.ml
+  '';
+in
+
+stdenv.mkDerivation {
+  pname = "hol_light";
+  version = "unstable-2024-07-07";
+
+  src = fetchFromGitHub {
+    owner = "jrh13";
+    repo = "hol-light";
+    rev = "16b184e30e7e3fe9add7d1ee93242323ed2e1726";
+    hash = "sha256-V0OtsmX5pa+CH3ZXmNG3juXwXZ5+A0k13eMCAfaRziQ=";
+  };
+
+  patches = [ ./0004-Fix-compilation-with-camlp5-7.11.patch ];
+
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    ocaml
+    findlib
+    camlp5
+  ];
+  propagatedBuildInputs = [
+    camlp-streams
+    (if use_zarith then zarith else num)
+  ];
+
+  installPhase = ''
+    mkdir -p "$out/lib/hol_light" "$out/bin"
+    cp -a  . $out/lib/hol_light
+    echo "${start_script}" > "$out/bin/hol_light"
+    chmod a+x "$out/bin/hol_light"
+  '';
+
+  meta = with lib; {
+    description = "Interactive theorem prover based on Higher-Order Logic";
+    homepage = "http://www.cl.cam.ac.uk/~jrh13/hol-light/";
+    license = licenses.bsd2;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [
+      thoughtpolice
+      maggesi
+      vbgl
+    ];
+  };
+}

pkgs/applications/science/logic/klee/default.nix

@@ -0,0 +1,281 @@
+{
+  lib,
+  llvmPackages,
+  callPackage,
+  fetchFromGitHub,
+  cmake,
+  python3,
+  z3,
+  stp,
+  cryptominisat,
+  gperftools,
+  sqlite,
+  gtest,
+  lit,
+  nix-update-script,
+
+  # Build KLEE in debug mode. Defaults to false.
+  debug ? false,
+
+  # Include debug info in the build. Defaults to true.
+  includeDebugInfo ? true,
+
+  # Enable KLEE asserts. Defaults to true, since LLVM is built with them.
+  asserts ? false,
+
+  # Build the KLEE runtime in debug mode. Defaults to true, as this improves
+  # stack traces of the software under test.
+  debugRuntime ? true,
+
+  # Enable runtime asserts. Default false.
+  runtimeAsserts ? false,
+
+  # Klee uclibc. Defaults to the bundled version.
+  kleeuClibc ? null,
+
+  # Extra klee-uclibc config for the default klee-uclibc.
+  extraKleeuClibcConfig ? { },
+}:
+
+let
+  # The chosen version of klee-uclibc.
+  chosenKleeuClibc =
+    if kleeuClibc == null then
+      callPackage ./klee-uclibc.nix {
+        llvmPackages = llvmPackages;
+        inherit extraKleeuClibcConfig debugRuntime runtimeAsserts;
+      }
+    else
+      kleeuClibc;
+
+  # Python used for KLEE tests.
+  kleePython = python3.withPackages (ps: with ps; [ tabulate ]);
+in
+llvmPackages.stdenv.mkDerivation {
+  pname = "klee";
+  version = "3.1-unstable-2025-07-11";
+
+  src = fetchFromGitHub {
+    owner = "klee";
+    repo = "klee";
+    rev = "1c9fbc1013a6000b39615cc9a5aba83e43a4bf75";
+    hash = "sha256-D93T0mBBrIhQTS42ScUHPrMoqCI55Y6Yp7snLmlriQM=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [
+    llvmPackages.llvm
+    cryptominisat
+    gperftools
+    sqlite
+    stp
+    z3
+  ];
+
+  nativeCheckInputs = [
+    gtest
+
+    # Should appear BEFORE lit, since lit passes through python rather
+    # than the python environment we make.
+    kleePython
+    (lit.override { python = kleePython; })
+  ];
+
+  cmakeBuildType =
+    if debug then
+      "Debug"
+    else if !debug && includeDebugInfo then
+      "RelWithDebInfo"
+    else
+      "MinSizeRel";
+
+  cmakeFlags =
+    let
+      onOff = val: if val then "ON" else "OFF";
+    in
+    [
+      "-DKLEE_RUNTIME_BUILD_TYPE=${if debugRuntime then "Debug" else "Release"}"
+      "-DLLVMCC=${llvmPackages.clang}/bin/clang"
+      "-DLLVMCXX=${llvmPackages.clang}/bin/clang++"
+      "-DKLEE_ENABLE_TIMESTAMP=${onOff false}"
+      "-DKLEE_UCLIBC_PATH=${chosenKleeuClibc}"
+      "-DENABLE_KLEE_ASSERTS=${onOff asserts}"
+      "-DENABLE_POSIX_RUNTIME=${onOff true}"
+      "-DENABLE_UNIT_TESTS=${onOff true}"
+      "-DENABLE_SYSTEM_TESTS=${onOff true}"
+      "-DLIT_ARGS=--verbose"
+      "-DGTEST_SRC_DIR=${gtest.src}"
+      "-DGTEST_INCLUDE_DIR=${gtest.src}/googletest/include"
+      "-Wno-dev"
+    ];
+
+  # Silence various warnings during the compilation of fortified bitcode.
+  env.NIX_CFLAGS_COMPILE = toString [ "-Wno-macro-redefined" ];
+
+  env.FILECHECK_OPTS = "--dump-input-filter=all";
+
+  env.LIT_XFAIL = lib.concatStringsSep ";" [
+    "KLEE :: ArrayOpt/test_expr_arbitrary.c"
+    "KLEE :: CXX/SimpleVirtual.cpp"
+    "KLEE :: CXX/StaticConstructor.cpp"
+    "KLEE :: CXX/StaticDestructor.cpp"
+    "KLEE :: Concrete/ConstantExpr.ll"
+    "KLEE :: Concrete/OverlappingPhiNodes.ll"
+    "KLEE :: Concrete/UnorderedPhiNodes.ll"
+    "KLEE :: DeterministicAllocation/nullpage-read.c"
+    "KLEE :: DeterministicAllocation/nullpage-write.c"
+    "KLEE :: DeterministicAllocation/use-after-free-loh.c"
+    "KLEE :: DeterministicAllocation/use-after-free.c"
+    "KLEE :: Dogfood/ImmutableSet.cpp"
+    "KLEE :: Feature/Atomic.c"
+    "KLEE :: Feature/DivCheck.c"
+    "KLEE :: Feature/ExtCall.c"
+    "KLEE :: Feature/ExtCallWarnings.c"
+    "KLEE :: Feature/FunctionAlias.c"
+    "KLEE :: Feature/FunctionAliasExit.c"
+    "KLEE :: Feature/LargeArrayBecomesSym.c"
+    "KLEE :: Feature/LowerSwitch.c"
+    "KLEE :: Feature/MakeSymbolicName.c"
+    "KLEE :: Feature/NoExternalCallsAllowed.c"
+    "KLEE :: Feature/Optimize.c"
+    "KLEE :: Feature/OvershiftCheck.c"
+    "KLEE :: Feature/ReadStringAtAddress.c"
+    "KLEE :: Feature/SeedConcretizeExternalCall.c"
+    "KLEE :: Feature/ShiftCheck.c"
+    "KLEE :: Feature/consecutive_divide_by_zero.c"
+    "KLEE :: Feature/srem.c"
+    "KLEE :: InlineAsm/RaiseAsm.c"
+    "KLEE :: InlineAsm/asm_lifting.ll"
+    "KLEE :: Intrinsics/IntrinsicTrap.ll"
+    "KLEE :: Intrinsics/IsConstant.ll"
+    "KLEE :: Intrinsics/Missing.ll"
+    "KLEE :: Intrinsics/Overflow.ll"
+    "KLEE :: Intrinsics/OverflowMul.ll"
+    "KLEE :: Intrinsics/Saturating.ll"
+    "KLEE :: Intrinsics/noalias-scope-decl.ll"
+    "KLEE :: Intrinsics/objectsize.ll"
+    "KLEE :: Replay/klee-replay/KleeZesti.c"
+    "KLEE :: Replay/libkleeruntest/replay_posix_runtime.c"
+    "KLEE :: Runtime/FreeStanding/memcpy_chk_err.c"
+    "KLEE :: Runtime/POSIX/CanonicalizeFileName.c"
+    "KLEE :: Runtime/POSIX/DirConsistency.c"
+    "KLEE :: Runtime/POSIX/DirSeek.c"
+    "KLEE :: Runtime/POSIX/Envp.c"
+    "KLEE :: Runtime/POSIX/FDNumbers.c"
+    "KLEE :: Runtime/POSIX/FD_Fail.c"
+    "KLEE :: Runtime/POSIX/FD_Fail2.c"
+    "KLEE :: Runtime/POSIX/Fcntl.c"
+    "KLEE :: Runtime/POSIX/FilePerm.c"
+    "KLEE :: Runtime/POSIX/FreeArgv.c"
+    "KLEE :: Runtime/POSIX/Futimesat.c"
+    "KLEE :: Runtime/POSIX/Getenv.c"
+    "KLEE :: Runtime/POSIX/Ioctl.c"
+    "KLEE :: Runtime/POSIX/Isatty.c"
+    "KLEE :: Runtime/POSIX/MixedConcreteSymbolic.c"
+    "KLEE :: Runtime/POSIX/Openat.c"
+    "KLEE :: Runtime/POSIX/PrgName.c"
+    "KLEE :: Runtime/POSIX/Read1.c"
+    "KLEE :: Runtime/POSIX/Replay.c"
+    "KLEE :: Runtime/POSIX/SeedAndFail.c"
+    "KLEE :: Runtime/POSIX/Stdin.c"
+    "KLEE :: Runtime/POSIX/SymFileConsistency.c"
+    "KLEE :: Runtime/POSIX/TestMain.c"
+    "KLEE :: Runtime/POSIX/Usage.c"
+    "KLEE :: Runtime/POSIX/Write1.c"
+    "KLEE :: Runtime/POSIX/Write2.c"
+    "KLEE :: Runtime/POSIX/_exit.c"
+    "KLEE :: Runtime/Uclibc/2007-10-08-optimization-calls-wrong-libc-functions.c"
+    "KLEE :: Runtime/klee-libc/mempcpy.c"
+    "KLEE :: Solver/Z3ConstantArray.c"
+    "KLEE :: UBSan/ubsan_alignment-type-mismatch.c"
+    "KLEE :: UBSan/ubsan_array_bounds.c"
+    "KLEE :: UBSan/ubsan_pointer_overflow-pointer_arithmetic.c"
+    "KLEE :: UBSan/ubsan_signed_integer_overflow.c"
+    "KLEE :: UBSan/ubsan_unsigned_integer_overflow.c"
+    "KLEE :: UBSan/ubsan_unsigned_shift_base.c"
+    "KLEE :: UBSan/ubsan_vla_bound.c"
+    "KLEE :: VarArgs/FunctionAliasVarArg.c"
+    "KLEE :: VarArgs/VarArg.c"
+    "KLEE :: VarArgs/VarArgAlignment.c"
+    "KLEE :: VarArgs/VarArgByVal.c"
+    "KLEE :: VarArgs/VarArgByValReported.c"
+    "KLEE :: VarArgs/VarArgLongDouble.c"
+    "KLEE :: VectorInstructions/floating_point_ops_constant.c"
+    "KLEE :: VectorInstructions/integer_ops_constant.c"
+    "KLEE :: VectorInstructions/integer_ops_signed_symbolic.c"
+    "KLEE :: VectorInstructions/integer_ops_unsigned_symbolic.c"
+    "KLEE :: VectorInstructions/memset.c"
+    "KLEE :: VectorInstructions/oob-write.c"
+    "KLEE :: VectorInstructions/shuffle_element.c"
+    "KLEE :: klee-stats/KleeStatsTermClasses.c"
+    "KLEE :: regression/2008-03-11-free-of-malloc-zero.c"
+    "KLEE :: regression/2014-07-04-unflushed-error-report.c"
+    "KLEE :: regression/2016-11-24-bitcast-weak-alias.c"
+  ];
+
+  prePatch = ''
+    patchShebangs --build .
+  '';
+
+  # https://github.com/klee/klee/issues/1690
+  hardeningDisable = [ "fortify" ];
+
+  enableParallelBuilding = true;
+  doCheck = true;
+
+  passthru = {
+    updateScript = nix-update-script {
+      extraArgs = [
+        "--version-regex"
+        "v(\\d\\.\\d)"
+      ];
+    };
+    # Let the user access the chosen uClibc outside the derivation.
+    uclibc = chosenKleeuClibc;
+  };
+
+  __structuredAttrs = true;
+
+  meta = with lib; {
+    mainProgram = "klee";
+    description = "Symbolic virtual machine built on top of LLVM";
+    longDescription = ''
+      KLEE is a symbolic virtual machine built on top of the LLVM compiler
+      infrastructure. Currently, there are two primary components:
+
+      1. The core symbolic virtual machine engine; this is responsible for
+         executing LLVM bitcode modules with support for symbolic values. This
+         is comprised of the code in lib/.
+
+      2. A POSIX/Linux emulation layer oriented towards supporting uClibc, with
+         additional support for making parts of the operating system environment
+         symbolic.
+
+      Additionally, there is a simple library for replaying computed inputs on
+      native code (for closed programs). There is also a more complicated
+      infrastructure for replaying the inputs generated for the POSIX/Linux
+      emulation layer, which handles running native programs in an environment
+      that matches a computed test input, including setting up files, pipes,
+      environment variables, and passing command line arguments.
+    '';
+    homepage = "https://klee.github.io";
+    license = licenses.ncsa;
+    platforms = [ "x86_64-linux" ];
+    maintainers = with maintainers; [ numinit ];
+    # Upstream is still working on support for LLVM ≥ 16; see:
+    #
+    # * <https://github.com/klee/klee/pull/1664>
+    # * <https://github.com/klee/klee/pull/1745>
+    # * <https://github.com/klee/klee/pull/1751>
+    # * <https://github.com/klee/klee/issues/1754>
+    #
+    # The package builds with LLVM 18 but 23% of the tests unexpectedly
+    # fail due to missing functionality for newer LLVM versions. We
+    # mark them as expected failures above to allow the package to
+    # build for those who want to experiment with KLEE, but mark it
+    # broken to avoid giving the impression that this is the expected
+    # user experience and level of support.
+    broken = true;
+  };
+}

pkgs/applications/science/logic/klee/klee-uclibc.nix

@@ -0,0 +1,116 @@
+{
+  lib,
+  llvmPackages,
+  fetchurl,
+  fetchFromGitHub,
+  linuxHeaders,
+  python3,
+  curl,
+  which,
+  nix-update-script,
+  debugRuntime ? true,
+  runtimeAsserts ? false,
+  extraKleeuClibcConfig ? { },
+}:
+
+let
+  localeSrcBase = "uClibc-locale-030818.tgz";
+  localeSrc = fetchurl {
+    url = "http://www.uclibc.org/downloads/${localeSrcBase}";
+    sha256 = "xDYr4xijjxjZjcz0YtItlbq5LwVUi7k/ZSmP6a+uvVc=";
+  };
+  resolvedExtraKleeuClibcConfig = lib.mapAttrsToList (name: value: "${name}=${value}") (
+    extraKleeuClibcConfig
+    // {
+      "UCLIBC_DOWNLOAD_PREGENERATED_LOCALE_DATA" = "n";
+      "RUNTIME_PREFIX" = "/";
+      "DEVEL_PREFIX" = "/";
+    }
+  );
+in
+llvmPackages.stdenv.mkDerivation rec {
+  pname = "klee-uclibc";
+  version = "1.4";
+  src = fetchFromGitHub {
+    owner = "klee";
+    repo = "klee-uclibc";
+    rev = "klee_uclibc_v${version}";
+    hash = "sha256-sogQK5Ed0k5tf4rrYwCKT4YRKyEovgT25p0BhGvJ1ok=";
+  };
+
+  nativeBuildInputs = [
+    llvmPackages.clang
+    llvmPackages.llvm
+    python3
+    curl
+    which
+  ];
+
+  # Some uClibc sources depend on Linux headers.
+  UCLIBC_KERNEL_HEADERS = "${linuxHeaders}/include";
+
+  # HACK: needed for cross-compile.
+  # See https://www.mail-archive.com/klee-dev@imperial.ac.uk/msg03141.html
+  KLEE_CFLAGS = "-idirafter ${llvmPackages.clang}/resource-root/include";
+
+  prePatch = ''
+    patchShebangs --build ./configure
+    patchShebangs --build ./extra
+  '';
+
+  # klee-uclibc configure does not support --prefix, so we override configurePhase entirely
+  configurePhase = ''
+    ./configure ${
+      lib.escapeShellArgs (
+        [ "--make-llvm-lib" ]
+        ++ lib.optional (!debugRuntime) "--enable-release"
+        ++ lib.optional runtimeAsserts "--enable-assertions"
+      )
+    }
+
+    # Set all the configs we care about.
+    configs=(
+      PREFIX=$out
+    )
+    for value in ${lib.escapeShellArgs resolvedExtraKleeuClibcConfig}; do
+      configs+=("$value")
+    done
+
+    for configFile in .config .config.cmd; do
+      for config in "''${configs[@]}"; do
+        prefix="''${config%%=*}="
+        if grep -q "$prefix" "$configFile"; then
+          sed -i "s"'\001'"''${prefix}"'\001'"#''${prefix}"'\001'"g" "$configFile"
+        fi
+        echo "$config" >> "$configFile"
+      done
+    done
+  '';
+
+  # Link the locale source into the correct place
+  preBuild = ''
+    ln -sf ${localeSrc} extra/locale/${localeSrcBase}
+  '';
+
+  makeFlags = [ "HAVE_DOT_CONFIG=y" ];
+
+  enableParallelBuilding = true;
+
+  passthru.updateScript = nix-update-script {
+    extraArgs = [
+      "--version-regex"
+      "v(\\d\\.\\d)"
+    ];
+  };
+
+  meta = with lib; {
+    description = "Modified version of uClibc for KLEE";
+    longDescription = ''
+      klee-uclibc is a bitcode build of uClibc meant for compatibility with the
+      KLEE symbolic virtual machine.
+    '';
+    homepage = "https://github.com/klee/klee-uclibc";
+    license = licenses.lgpl3;
+    maintainers = with maintainers; [ numinit ];
+  };
+}

pkgs/applications/science/logic/leo2/default.nix

@@ -0,0 +1,72 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  fetchpatch,
+  makeWrapper,
+  eprover,
+  ocaml,
+  camlp4,
+  perl,
+  zlib,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "leo2";
+  version = "1.7.0";
+
+  src = fetchurl {
+    url = "https://page.mi.fu-berlin.de/cbenzmueller/leo/leo2_v${version}.tgz";
+    sha256 = "sha256:1b2q7vsz6s9ighypsigqjm1mzjiq3xgnz5id5ssb4rh9zm190r82";
+  };
+
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    makeWrapper
+    eprover
+    ocaml
+    camlp4
+    perl
+  ];
+  buildInputs = [ zlib ];
+
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/niklasso/minisat/commit/7eb6015313561a2586032574788fcb133eeaa19f.patch";
+      stripLen = 1;
+      extraPrefix = "lib/";
+      sha256 = "sha256:01ln7hi6nvvkqkhn9hciqizizz5qspvqffgksvgmzn9x7kdd9pnh";
+    })
+  ];
+
+  preConfigure = ''
+    cd src
+    patchShebangs configure
+    substituteInPlace Makefile.pre \
+      --replace '+camlp4' "${camlp4}/lib/ocaml/${ocaml.version}/site-lib/camlp4"
+  '';
+
+  buildFlags = [ "opt" ];
+
+  env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-reserved-user-defined-literal";
+
+  preInstall = "mkdir -p $out/bin";
+
+  postInstall = ''
+    mkdir -p "$out/etc"
+    echo -e "e = ${eprover}/bin/eprover\\nepclextract = ${eprover}/bin/epclextract" > "$out/etc/leoatprc"
+
+    wrapProgram $out/bin/leo \
+      --add-flags "--atprc $out/etc/leoatprc"
+  '';
+
+  meta = with lib; {
+    description = "High-performance typed higher order prover";
+    mainProgram = "leo";
+    maintainers = [ maintainers.raskin ];
+    platforms = platforms.unix;
+    license = licenses.bsd3;
+    homepage = "http://www.leoprover.org/";
+  };
+}

pkgs/applications/science/logic/prooftree/default.nix

@@ -0,0 +1,58 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  pkg-config,
+  ncurses,
+  ocamlPackages,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "prooftree";
+  version = "0.14";
+
+  src = fetchurl {
+    url = "https://askra.de/software/prooftree/releases/prooftree-${version}.tar.gz";
+    sha256 = "sha256-nekV2UnjibOk4h0jZ1jV7W5pE/hXWb3fUoLTJb3Jzc0=";
+  };
+
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    pkg-config
+  ]
+  ++ (with ocamlPackages; [
+    ocaml
+    findlib
+    camlp5
+  ]);
+  buildInputs = [ ncurses ] ++ (with ocamlPackages; [ lablgtk ]);
+
+  prefixKey = "--prefix ";
+
+  meta = with lib; {
+    description = "Program for proof-tree visualization";
+    mainProgram = "prooftree";
+    longDescription = ''
+      Prooftree is a program for proof-tree visualization during interactive
+      proof development in a theorem prover. It is currently being developed
+      for Coq and Proof General. Prooftree helps against getting lost between
+      different subgoals in interactive proof development. It clearly shows
+      where the current subgoal comes from and thus helps in developing the
+      right plan for solving it.
+
+      Prooftree uses different colors for the already proven subgoals, the
+      current branch in the proof and the still open subgoals. Sequent texts
+      are not displayed in the proof tree itself, but they are shown as a
+      tool-tip when the mouse rests over a sequent symbol. Long proof commands
+      are abbreviated in the tree display, but show up in full length as
+      tool-tip. Both, sequents and proof commands, can be shown in the display
+      below the tree (on single click) or in a separate window (on double or
+      shift-click).
+    '';
+    homepage = "http://askra.de/software/prooftree";
+    platforms = platforms.unix;
+    maintainers = [ maintainers.jwiegley ];
+    license = licenses.gpl3;
+  };
+}

pkgs/applications/science/logic/rocq-core/default.nix

@@ -0,0 +1,186 @@
+# - The csdp program used for the Micromega tactic is statically referenced.
+#   However, rocq can build without csdp by setting it to null.
+#   In this case some Micromega tactics will search the user's path for the csdp program and will fail if it is not found.
+# - The exact version can be specified through the `version` argument to
+#   the derivation; it defaults to the latest stable version.
+
+{
+  lib,
+  stdenv,
+  fetchzip,
+  fetchurl,
+  writeText,
+  pkg-config,
+  customOCamlPackages ? null,
+  ocamlPackages_4_14,
+  ncurses,
+  csdp ? null,
+  version,
+  rocq-version ? null,
+}@args:
+let
+  lib = import ../../../../build-support/rocq/extra-lib.nix { inherit (args) lib; };
+
+  release = {
+    "9.0.0".sha256 = "sha256-GRwYSvrJGiPD+I82gLOgotb+8Ra5xHZUJGcNwxWqZkU=";
+    "9.1.0".sha256 = "sha256-+QL7I1/0BfT87n7lSaOmpHj2jJuDB4idWhAxwzvVQOE=";
+  };
+  releaseRev = v: "V${v}";
+  fetched =
+    import ../../../../build-support/coq/meta-fetch/default.nix
+      {
+        inherit
+          lib
+          stdenv
+          fetchzip
+          fetchurl
+          ;
+      }
+      {
+        inherit release releaseRev;
+        location = {
+          owner = "coq";
+          repo = "coq";
+        };
+      }
+      args.version;
+  version = fetched.version;
+  rocq-version =
+    args.rocq-version or (if version != "dev" then lib.versions.majorMinor version else "dev");
+  csdpPatch = lib.optionalString (csdp != null) ''
+    substituteInPlace plugins/micromega/sos.ml --replace-warn "; csdp" "; ${csdp}/bin/csdp"
+    substituteInPlace plugins/micromega/coq_micromega.ml --replace-warn "System.is_in_system_path \"csdp\"" "true"
+  '';
+  ocamlPackages = if customOCamlPackages != null then customOCamlPackages else ocamlPackages_4_14;
+  ocamlNativeBuildInputs = [
+    ocamlPackages.ocaml
+    ocamlPackages.findlib
+    ocamlPackages.dune_3
+  ];
+  ocamlPropagatedBuildInputs = [ ocamlPackages.zarith ];
+  self = stdenv.mkDerivation {
+    pname = "rocq";
+    inherit (fetched) version src;
+
+    passthru = {
+      inherit rocq-version;
+      inherit ocamlPackages ocamlNativeBuildInputs;
+      inherit ocamlPropagatedBuildInputs;
+      emacsBufferSetup = pkgs: ''
+        ; Propagate rocq paths to children
+        (inherit-local-permanent coq-prog-name "${self}/bin/rocq repl")
+        (inherit-local-permanent coq-dependency-analyzer "${self}/bin/rocq dep")
+        (inherit-local-permanent coq-compiler "${self}/bin/rocq c")
+        ; If the coq-library path was already set, re-set it based on our current rocq
+        (when (fboundp 'get-coq-library-directory)
+          (inherit-local-permanent coq-library-directory (get-coq-library-directory))
+          (coq-prog-args))
+        (mapc (lambda (arg)
+          (when (file-directory-p (concat arg "/lib/coq/${rocq-version}/user-contrib"))
+            (setenv "ROCQPATH" (concat (getenv "ROCQPATH") ":" arg "/lib/coq/${rocq-version}/user-contrib")))) '(${
+              lib.concatStringsSep " " (map (pkg: "\"${pkg}\"") pkgs)
+            }))
+        ; TODO Abstract this pattern from here and nixBufferBuilders.withPackages!
+        (defvar nixpkgs--rocq-buffer-count 0)
+        (when (eq nixpkgs--rocq-buffer-count 0)
+          (make-variable-buffer-local 'nixpkgs--is-nixpkgs-rocq-buffer)
+          (defun nixpkgs--rocq-inherit (buf)
+            (inherit-local-inherit-child buf)
+            (with-current-buffer buf
+              (setq nixpkgs--rocq-buffer-count (1+ nixpkgs--rocq-buffer-count))
+              (add-hook 'kill-buffer-hook 'nixpkgs--decrement-rocq-buffer-count nil t))
+            buf)
+          ; When generating a scomint buffer, do inherit-local inheritance and make it a nixpkgs-rocq buffer
+          (defun nixpkgs--around-scomint-make (orig &rest r)
+            (if nixpkgs--is-nixpkgs-rocq-buffer
+                (progn
+                  (advice-add 'get-buffer-create :filter-return #'nixpkgs--rocq-inherit)
+                  (apply orig r)
+                  (advice-remove 'get-buffer-create #'nixpkgs--rocq-inherit))
+              (apply orig r)))
+          (advice-add 'scomint-make :around #'nixpkgs--around-scomint-make)
+          ; When we have no more rocq buffers, tear down the buffer handling
+          (defun nixpkgs--decrement-rocq-buffer-count ()
+            (setq nixpkgs--rocq-buffer-count (1- nixpkgs--rocq-buffer-count))
+            (when (eq nixpkgs--rocq-buffer-count 0)
+              (advice-remove 'scomint-make #'nixpkgs--around-scomint-make)
+              (fmakunbound 'nixpkgs--around-scomint-make)
+              (fmakunbound 'nixpkgs--rocq-inherit)
+              (fmakunbound 'nixpkgs--decrement-rocq-buffer-count))))
+        (setq nixpkgs--rocq-buffer-count (1+ nixpkgs--rocq-buffer-count))
+        (add-hook 'kill-buffer-hook 'nixpkgs--decrement-rocq-buffer-count nil t)
+        (setq nixpkgs--is-nixpkgs-rocq-buffer t)
+        (inherit-local 'nixpkgs--is-nixpkgs-rocq-buffer)
+      '';
+    };
+
+    nativeBuildInputs = [ pkg-config ] ++ ocamlNativeBuildInputs;
+    buildInputs = [ ncurses ];
+
+    propagatedBuildInputs = ocamlPropagatedBuildInputs;
+
+    postPatch = ''
+      UNAME=$(type -tp uname)
+      RM=$(type -tp rm)
+      substituteInPlace tools/beautify-archive --replace-warn "/bin/rm" "$RM"
+      ${csdpPatch}
+    '';
+
+    setupHook = writeText "setupHook.sh" ''
+      addRocqPath () {
+        if test -d "''$1/lib/coq/${rocq-version}/user-contrib"; then
+          export ROCQPATH="''${ROCQPATH-}''${ROCQPATH:+:}''$1/lib/coq/${rocq-version}/user-contrib/"
+        fi
+      }
+
+      addEnvHooks "$targetOffset" addRocqPath
+    '';
+
+    preConfigure = ''
+      patchShebangs dev/tools/
+    '';
+
+    prefixKey = "-prefix ";
+
+    enableParallelBuilding = true;
+
+    createFindlibDestdir = true;
+
+    buildPhase = ''
+      runHook preBuild
+      make dunestrap
+      dune build -p rocq-runtime,rocq-core -j $NIX_BUILD_CORES
+      runHook postBuild
+    '';
+
+    installPhase = ''
+      runHook preInstall
+      dune install --prefix $out rocq-runtime rocq-core
+      ln -s $out/lib/rocq-runtime $OCAMLFIND_DESTDIR/rocq-runtime
+      ln -s $out/lib/rocq-core $OCAMLFIND_DESTDIR/rocq-core
+      runHook postInstall
+    '';
+
+    meta = with lib; {
+      description = "Rocq Prover";
+      longDescription = ''
+        The Rocq Prover is an interactive theorem prover, or proof assistant. It provides
+        a formal language to write mathematical definitions, executable
+        algorithms and theorems together with an environment for
+        semi-interactive development of machine-checked proofs.
+      '';
+      homepage = "https://rocq-prover.org";
+      license = licenses.lgpl21;
+      branch = rocq-version;
+      maintainers = with maintainers; [
+        proux01
+        roconnor
+        vbgl
+        Zimmi48
+      ];
+      platforms = platforms.unix;
+      mainProgram = "rocq";
+    };
+  };
+in
+self

pkgs/applications/science/logic/satallax/default.nix

@@ -0,0 +1,111 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  ocaml,
+  zlib,
+  which,
+  eprover,
+  makeWrapper,
+  coq,
+}:
+stdenv.mkDerivation rec {
+  pname = "satallax";
+  version = "2.7";
+
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    makeWrapper
+    ocaml
+    which
+    eprover
+    coq
+  ];
+  buildInputs = [ zlib ];
+
+  src = fetchurl {
+    url = "https://www.ps.uni-saarland.de/~cebrown/satallax/downloads/${pname}-${version}.tar.gz";
+    sha256 = "1kvxn8mc35igk4vigi5cp7w3wpxk2z3bgwllfm4n3h2jfs0vkpib";
+  };
+
+  patches = [
+    # GCC9 doesn't allow default value in friend declaration.
+    ./fix-declaration-gcc9.patch
+  ];
+
+  prePatch = ''
+    patch -p1 -i ${./minisat-fenv.patch} -d minisat
+  '';
+
+  preConfigure = ''
+    mkdir fake-tools
+    echo "echo 'Nix-build-host.localdomain'" > fake-tools/hostname
+    chmod a+x fake-tools/hostname
+    export PATH="$PATH:$PWD/fake-tools"
+
+    (
+      cd picosat-*
+      ./configure
+      make
+    )
+    export PATH="$PATH:$PWD/libexec/satallax"
+
+    mkdir -p "$out/libexec/satallax"
+    cp picosat-*/picosat picosat-*/picomus "$out/libexec/satallax"
+
+    (
+      cd minisat
+      export MROOT=$PWD
+      cd core
+      make
+      cd ../simp
+      make
+    )
+  '';
+
+  # error: invalid suffix on literal; C++11 requires a space between literal and identifier
+  env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.hostPlatform.isDarwin "-Wno-reserved-user-defined-literal";
+
+  installPhase = ''
+    mkdir -p "$out/share/doc/satallax" "$out/bin" "$out/lib" "$out/lib/satallax"
+    cp bin/satallax.opt "$out/bin/satallax"
+    wrapProgram "$out/bin/satallax" \
+      --suffix PATH : "${
+        lib.makeBinPath [
+          coq
+          eprover
+        ]
+      }:$out/libexec/satallax" \
+      --add-flags "-M" --add-flags "$out/lib/satallax/modes"
+
+    cp LICENSE README "$out/share/doc/satallax"
+
+    cp bin/*.so "$out/lib"
+
+    cp -r modes "$out/lib/satallax/"
+    cp -r problems "$out/lib/satallax/"
+    cp -r coq* "$out/lib/satallax/"
+  '';
+
+  doCheck = stdenv.hostPlatform.isLinux;
+
+  checkPhase = ''
+    runHook preCheck
+    if bash ./test | grep ERROR; then
+      echo "Tests failed"
+      exit 1
+    fi
+    runHook postCheck
+  '';
+
+  meta = {
+    description = "Automated theorem prover for higher-order logic";
+    mainProgram = "satallax";
+    license = lib.licenses.mit;
+    maintainers = [ lib.maintainers.raskin ];
+    platforms = lib.platforms.unix;
+    downloadPage = "http://www.ps.uni-saarland.de/~cebrown/satallax/downloads.php";
+    homepage = "http://www.ps.uni-saarland.de/~cebrown/satallax/index.php";
+  };
+}

pkgs/applications/science/logic/satallax/fix-declaration-gcc9.patch

@@ -0,0 +1,21 @@
+diff --git i/minisat/core/SolverTypes.h w/minisat/core/SolverTypes.h
+--- i/minisat/core/SolverTypes.h
++++ w/minisat/core/SolverTypes.h
+@@ -47,7 +47,7 @@ struct Lit {
+     int     x;
+ 
+     // Use this as a constructor:
+-    friend Lit mkLit(Var var, bool sign = false);
++    friend Lit mkLit(Var var, bool sign);
+ 
+     bool operator == (Lit p) const { return x == p.x; }
+     bool operator != (Lit p) const { return x != p.x; }
+@@ -55,7 +55,7 @@ struct Lit {
+ };
+ 
+ 
+-inline  Lit  mkLit     (Var var, bool sign) { Lit p; p.x = var + var + (int)sign; return p; }
++inline  Lit  mkLit     (Var var, bool sign = false) { Lit p; p.x = var + var + (int)sign; return p; }
+ inline  Lit  operator ~(Lit p)              { Lit q; q.x = p.x ^ 1; return q; }
+ inline  Lit  operator ^(Lit p, bool b)      { Lit q; q.x = p.x ^ (unsigned int)b; return q; }
+ inline  bool sign      (Lit p)              { return p.x & 1; }

pkgs/applications/science/logic/satallax/minisat-fenv.patch

@@ -0,0 +1,57 @@
+diff --git a/core/Main.cc b/core/Main.cc
+index 2b0d97b..9ba985d 100644
+--- a/core/Main.cc
++++ b/core/Main.cc
+@@ -77,9 +77,13 @@ int main(int argc, char** argv)
+         setUsageHelp("USAGE: %s [options] <input-file> <result-output-file>\n\n  where input may be either in plain or gzipped DIMACS.\n");
+         // printf("This is MiniSat 2.0 beta\n");
+         
+-#if defined(__linux__)
+-        fpu_control_t oldcw, newcw;
+-        _FPU_GETCW(oldcw); newcw = (oldcw & ~_FPU_EXTENDED) | _FPU_DOUBLE; _FPU_SETCW(newcw);
++#if defined(__linux__) && defined(__x86_64__)
++        fenv_t fenv;
++
++        fegetenv(&fenv);
++        fenv.__control_word &= ~0x300; /* _FPU_EXTENDED */
++        fenv.__control_word |= 0x200; /* _FPU_DOUBLE */
++        fesetenv(&fenv);
+         printf("WARNING: for repeatability, setting FPU to use double precision\n");
+ #endif
+         // Extra options:
+diff --git a/simp/Main.cc b/simp/Main.cc
+index 2804d7f..7fbdb33 100644
+--- a/simp/Main.cc
++++ b/simp/Main.cc
+@@ -78,9 +78,13 @@ int main(int argc, char** argv)
+         setUsageHelp("USAGE: %s [options] <input-file> <result-output-file>\n\n  where input may be either in plain or gzipped DIMACS.\n");
+         // printf("This is MiniSat 2.0 beta\n");
+         
+-#if defined(__linux__)
+-        fpu_control_t oldcw, newcw;
+-        _FPU_GETCW(oldcw); newcw = (oldcw & ~_FPU_EXTENDED) | _FPU_DOUBLE; _FPU_SETCW(newcw);
++#if defined(__linux__) && defined(__x86_64__)
++        fenv_t fenv;
++
++        fegetenv(&fenv);
++        fenv.__control_word &= ~0x300; /* _FPU_EXTENDED */
++        fenv.__control_word |= 0x200; /* _FPU_DOUBLE */
++        fesetenv(&fenv);
+         printf("WARNING: for repeatability, setting FPU to use double precision\n");
+ #endif
+         // Extra options:
+diff --git a/utils/System.h b/utils/System.h
+index 1758192..840bee5 100644
+--- a/utils/System.h
++++ b/utils/System.h
+@@ -21,8 +21,8 @@ OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWA
+ #ifndef Minisat_System_h
+ #define Minisat_System_h
+ 
+-#if defined(__linux__)
+-#include <fpu_control.h>
++#if defined(__linux__) && defined(__x86_64__)
++#include <fenv.h>
+ #endif
+ 
+ #include "mtl/IntTypes.h"

pkgs/applications/science/logic/statverif/default.nix

@@ -0,0 +1,41 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  ocaml,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "statverif";
+  version = "1.86pl4";
+
+  src = fetchurl {
+    url = "http://prosecco.gforge.inria.fr/personal/bblanche/proverif/proverif${version}.tar.gz";
+    sha256 = "163vdcixs764jj8xa08w80qm4kcijf7xj911yp8jvz6pi1q5g13i";
+  };
+
+  pf-patch = fetchurl {
+    url = "http://markryan.eu/research/statverif/files/proverif-${version}-statverif-2657ab4.patch";
+    sha256 = "113jjhi1qkcggbsmbw8fa9ln8vs7vy2r288szks7rn0jjn0wxmbw";
+  };
+
+  strictDeps = true;
+
+  nativeBuildInputs = [ ocaml ];
+
+  patchPhase = "patch -p1 < ${pf-patch}";
+  buildPhase = "./build";
+  installPhase = ''
+    mkdir -p $out/bin
+    cp ./proverif      $out/bin/statverif
+    cp ./proveriftotex $out/bin/statveriftotex
+  '';
+
+  meta = {
+    description = "Verification of stateful processes (via Proverif)";
+    homepage = "https://markryan.eu/research/statverif/";
+    license = lib.licenses.gpl2;
+    platforms = lib.platforms.unix;
+    maintainers = [ lib.maintainers.thoughtpolice ];
+  };
+}

pkgs/applications/science/logic/tamarin-prover/default.nix

@@ -0,0 +1,213 @@
+{
+  haskellPackages,
+  fetchFromGitHub,
+  lib,
+  stdenv,
+  # the following are non-haskell dependencies
+  makeWrapper,
+  which,
+  maude,
+  graphviz,
+  glibcLocales,
+}:
+
+let
+  inherit (haskellPackages) mkDerivation;
+
+  version = "1.10.0";
+  src = fetchFromGitHub {
+    owner = "tamarin-prover";
+    repo = "tamarin-prover";
+    rev = version;
+    hash = "sha256-v1BruU2p/Sg/g7b9a+QRza46bD7PkMtsGq82qFaNhpI=";
+  };
+
+  # tamarin has its own dependencies, but they're kept inside the repo,
+  # no submodules. this factors out the common metadata among all derivations
+  common = pname: src: {
+    inherit pname version src;
+
+    license = lib.licenses.gpl3;
+    homepage = "https://tamarin-prover.github.io";
+    description = "Security protocol verification in the symbolic model";
+    maintainers = [ lib.maintainers.thoughtpolice ];
+    hydraPlatforms = lib.platforms.linux; # maude is broken on darwin
+  };
+
+  # tamarin use symlinks to the LICENSE and Setup.hs files, so for these sublibraries
+  # we set the patchPhase to fix that. otherwise, cabal cries a lot.
+  replaceSymlinks = ''
+    cp --remove-destination ${src}/LICENSE .;
+    cp --remove-destination ${src}/Setup.hs .;
+  '';
+
+  tamarin-prover-utils = mkDerivation (
+    common "tamarin-prover-utils" (src + "/lib/utils")
+    // {
+      postPatch = replaceSymlinks;
+      libraryHaskellDepends = with haskellPackages; [
+        base64-bytestring
+        blaze-builder
+        list-t
+        dlist
+        exceptions
+        fclabels
+        haskellPackages.graphviz
+        safe
+        SHA
+        split
+        syb
+      ];
+    }
+  );
+
+  tamarin-prover-term = mkDerivation (
+    common "tamarin-prover-term" (src + "/lib/term")
+    // {
+      postPatch = replaceSymlinks;
+      libraryHaskellDepends =
+        (with haskellPackages; [
+          attoparsec
+          HUnit
+        ])
+        ++ [ tamarin-prover-utils ];
+    }
+  );
+
+  tamarin-prover-theory = mkDerivation (
+    common "tamarin-prover-theory" (src + "/lib/theory")
+    // {
+      postPatch = replaceSymlinks;
+      doHaddock = false; # broken
+      libraryHaskellDepends =
+        (with haskellPackages; [
+          aeson
+          aeson-pretty
+          parallel
+          uniplate
+          regex-pcre-builtin
+          regex-posix
+          split
+        ])
+        ++ [
+          tamarin-prover-utils
+          tamarin-prover-term
+        ];
+    }
+  );
+
+  tamarin-prover-sapic = mkDerivation (
+    common "tamarin-prover-sapic" (src + "/lib/sapic")
+    // {
+      postPatch = "cp --remove-destination ${src}/LICENSE .";
+      doHaddock = false; # broken
+      libraryHaskellDepends =
+        (with haskellPackages; [
+          raw-strings-qq
+        ])
+        ++ [ 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 = [
+        tamarin-prover-utils
+        tamarin-prover-term
+        tamarin-prover-theory
+        tamarin-prover-sapic
+      ];
+    }
+  );
+
+in
+mkDerivation (
+  common "tamarin-prover" src
+  // {
+    isLibrary = false;
+    isExecutable = true;
+
+    # strip out unneeded deps manually
+    doHaddock = false;
+    enableSharedExecutables = false;
+    postFixup = "rm -rf $out/lib $out/nix-support $out/share/doc";
+
+    # wrap the prover to be sure it can find maude, sapic, etc
+    executableToolDepends = [
+      makeWrapper
+      which
+      maude
+      graphviz
+    ];
+    postInstall = ''
+      wrapProgram $out/bin/tamarin-prover \
+    ''
+    + lib.optionalString stdenv.hostPlatform.isLinux ''
+      --set LOCALE_ARCHIVE "${glibcLocales}/lib/locale/locale-archive" \
+    ''
+    + ''
+        --prefix PATH : ${
+          lib.makeBinPath [
+            which
+            maude
+            graphviz
+          ]
+        }
+      # so that the package can be used as a vim plugin to install syntax coloration
+      install -Dt $out/share/vim-plugins/tamarin-prover/syntax/ etc/syntax/spthy.vim
+      install etc/filetype.vim -D $out/share/vim-plugins/tamarin-prover/ftdetect/tamarin.vim
+      mkdir -p $out/share/nvim
+      ln -s $out/share/vim-plugins/tamarin-prover $out/share/nvim/site
+      # Emacs SPTHY major mode
+      install -Dt $out/share/emacs/site-lisp etc/spthy-mode.el
+    '';
+
+    checkPhase = "./dist/build/tamarin-prover/tamarin-prover test";
+
+    executableHaskellDepends =
+      (with haskellPackages; [
+        binary-instances
+        binary-orphans
+        blaze-html
+        conduit
+        file-embed
+        gitrev
+        http-types
+        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
+      ];
+  }
+)

pkgs/applications/science/logic/tlaplus/tlaps.nix

@@ -0,0 +1,68 @@
+{
+  fetchurl,
+  lib,
+  stdenv,
+  ocaml,
+  isabelle,
+  cvc3,
+  perl,
+  wget,
+  which,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "tlaps";
+  version = "1.4.5";
+  src = fetchurl {
+    url = "https://tla.msr-inria.inria.fr/tlaps/dist/${version}/tlaps-${version}.tar.gz";
+    sha256 = "c296998acd14d5b93a8d5be7ee178007ef179957465966576bda26944b1b7fca";
+  };
+
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    ocaml
+    isabelle
+    cvc3
+    perl
+    wget
+    which
+  ];
+
+  installPhase = ''
+    mkdir -pv "$out"
+    export HOME="$out"
+    export PATH=$out/bin:$PATH
+
+    pushd zenon
+    ./configure --prefix $out
+    make
+    make install
+    popd
+
+    pushd isabelle
+    isabelle build -b Pure
+    popd
+
+    pushd tlapm
+    ./configure --prefix $out
+    make all
+    make install
+  '';
+
+  meta = {
+    description = "Mechanically check TLA+ proofs";
+    longDescription = ''
+      TLA+ is a general-purpose formal specification language that is
+      particularly useful for describing concurrent and distributed
+      systems. The TLA+ proof language is declarative, hierarchical,
+      and scalable to large system specifications. It provides a
+      consistent abstraction over the various “backend” verifiers.
+    '';
+    homepage = "https://tla.msr-inria.inria.fr/tlaps/content/Home.html";
+    license = lib.licenses.bsd2;
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [ florentc ];
+  };
+
+}

pkgs/applications/science/logic/why3/default.nix

@@ -0,0 +1,117 @@
+{
+  callPackage,
+  fetchurl,
+  lib,
+  stdenv,
+  ocamlPackages,
+  coqPackages,
+  rubber,
+  hevea,
+  emacs,
+  version ? "1.8.2",
+  ideSupport ? true,
+  wrapGAppsHook3,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "why3";
+  inherit version;
+
+  src = fetchurl {
+    url = "https://why3.gitlabpages.inria.fr/releases/${pname}-${version}.tar.gz";
+    hash =
+      {
+        "1.8.2" = "sha256-t9ES7dW8zmvM4AI9K8g06yrhocQteupE/6Ek1km1C+o=";
+        "1.7.2" = "sha256-VaSG/FiO2MDdSSFXGJJrIylQx0LPwtT8AF7TpPVZhCQ=";
+        "1.6.0" = "sha256-hFvM6kHScaCtcHCc6Vezl9CR7BFbiKPoTEh7kj0ZJxw=";
+      }
+      ."${version}";
+  };
+
+  strictDeps = true;
+
+  nativeBuildInputs =
+    lib.optional ideSupport wrapGAppsHook3
+    ++ (with ocamlPackages; [
+      ocaml
+      findlib
+      menhir
+    ])
+    ++ [
+      # Coq Support
+      coqPackages.coq
+    ];
+
+  buildInputs =
+    with ocamlPackages;
+    [
+      ocamlgraph
+      zarith
+      # Emacs compilation of why3.el
+      emacs
+      # Documentation
+      rubber
+      hevea
+    ]
+    ++
+      lib.optional ideSupport
+        # GUI
+        lablgtk3-sourceview3
+    ++ [
+      # WebIDE
+      js_of_ocaml
+      js_of_ocaml-ppx
+      # S-expression output for why3pp
+      ppx_deriving
+      ppx_sexp_conv
+    ]
+    ++
+      # Coq Support
+      (with coqPackages; [
+        coq
+        flocq
+      ]);
+
+  propagatedBuildInputs = with ocamlPackages; [
+    camlzip
+    menhirLib
+    (if lib.versionAtLeast version "1.8.0" then zarith else num)
+    re
+    sexplib
+  ];
+
+  enableParallelBuilding = true;
+
+  configureFlags = [
+    "--enable-verbose-make"
+    (lib.enableFeature ideSupport "ide")
+  ];
+
+  outputs = [
+    "out"
+    "dev"
+  ];
+
+  installTargets = [
+    "install"
+    "install-lib"
+  ];
+
+  postInstall = ''
+    mkdir -p $dev/lib
+    mv $out/lib/ocaml $dev/lib/
+  '';
+
+  passthru.withProvers = callPackage ./with-provers.nix { };
+
+  meta = with lib; {
+    description = "Platform for deductive program verification";
+    homepage = "https://why3.lri.fr/";
+    license = licenses.lgpl21;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [
+      thoughtpolice
+      vbgl
+    ];
+  };
+}

pkgs/applications/science/logic/why3/with-provers.nix

@@ -0,0 +1,38 @@
+{
+  stdenv,
+  makeWrapper,
+  runCommand,
+  why3,
+}:
+provers:
+let
+  configAwkScript = runCommand "why3-conf.awk" { inherit provers; } ''
+    for p in $provers; do
+      for b in $p/bin/*; do
+        BASENAME=$(basename $b)
+        echo "/^command =/{ gsub(\"$BASENAME\", \"$b\") }" >> $out
+      done
+    done
+    echo '{ print }' >> $out
+  '';
+in
+stdenv.mkDerivation {
+  pname = "${why3.pname}-with-provers";
+  version = why3.version;
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ why3 ] ++ provers;
+
+  dontUnpack = true;
+
+  buildPhase = ''
+    mkdir -p $out/share/why3/
+    why3 config detect -C $out/share/why3/why3.conf
+    awk -i inplace -f ${configAwkScript} $out/share/why3/why3.conf
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    makeWrapper ${why3}/bin/why3 $out/bin/why3 --add-flags "--config $out/share/why3/why3.conf"
+  '';
+}

pkgs/applications/science/machine-learning/openbugs/default.nix

@@ -0,0 +1,31 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+}:
+
+stdenv.mkDerivation {
+  pname = "OpenBUGS";
+  version = "3.2.3";
+
+  outputs = [ "out" ];
+
+  src = fetchFromGitHub {
+    owner = "jsta";
+    repo = "openbugs";
+    rev = "cd921342ba13ee89ee60f9aebd2e96c42bd59ae3";
+    sha256 = "sha256-11LrScN1kvtq0Fo7RWGjbQO0U5b5brCbipl5pdZnrFs=";
+  };
+
+  meta = with lib; {
+    description = "Software package for performing Bayesian analysis and simulation using Markov Chain Monte Carlo";
+    homepage = "https://github.com/jsta/openbugs/";
+    changelog = "https://github.com/jsta/openbugs/blob/master/ChangeLog";
+    platforms = [
+      "i686-linux"
+      "x86_64-linux"
+    ];
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ andresnav ];
+  };
+}

pkgs/applications/science/machine-learning/shogun/default.nix

@@ -0,0 +1,243 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  fetchurl,
+  # build
+  cmake,
+  ctags,
+  python3Packages,
+  swig,
+  # math
+  eigen,
+  blas,
+  lapack,
+  glpk,
+  # data
+  protobuf,
+  json_c,
+  libxml2,
+  hdf5,
+  curl,
+  # compression
+  libarchive,
+  bzip2,
+  xz,
+  snappy,
+  lzo,
+  # more math
+  nlopt,
+  lp_solve,
+  colpack,
+  # extra support
+  pythonSupport ? false,
+  opencvSupport ? false,
+  opencv ? null,
+  withSvmLight ? false,
+}:
+
+assert pythonSupport -> python3Packages != null;
+assert opencvSupport -> opencv != null;
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+let
+  pname = "shogun";
+  version = "6.1.4";
+
+  rxcppVersion = "4.0.0";
+  gtestVersion = "1.8.0";
+
+  srcs = {
+    toolbox = fetchFromGitHub {
+      owner = "shogun-toolbox";
+      repo = "shogun";
+      rev = "shogun_${version}";
+      hash = "sha256-38aULxK50wQ2+/ERosSpRyBmssmYSGv5aaWfWSlrSRc=";
+      fetchSubmodules = true;
+    };
+
+    # The CMake external projects expect the packed archives
+    rxcpp = fetchurl {
+      url = "https://github.com/Reactive-Extensions/RxCpp/archive/v${rxcppVersion}.tar.gz";
+      sha256 = "sha256-UOc5WrG8KgAA3xJsaSCjbdPE7gSnFJay9MEK31DWUXg=";
+    };
+
+    gtest = fetchurl {
+      url = "https://github.com/google/googletest/archive/release-${gtestVersion}.tar.gz";
+      sha256 = "sha256-WKb0J3yivIVlIis7vVihd2CenEiOinJkk1m6UUUNt9g=";
+    };
+  };
+in
+
+stdenv.mkDerivation (finalAttrs: {
+  inherit pname version;
+
+  outputs = [
+    "out"
+    "dev"
+    "doc"
+  ];
+
+  src = srcs.toolbox;
+
+  patches = [
+    # Fix compile errors with GCC 9+
+    # https://github.com/shogun-toolbox/shogun/pull/4811
+    (fetchpatch {
+      url = "https://github.com/shogun-toolbox/shogun/commit/c8b670be4790e0f06804b048a6f3d77c17c3ee95.patch";
+      sha256 = "sha256-MxsR3Y2noFQevfqWK3nmX5iK4OVWeKBl5tfeDNgjcXk=";
+    })
+    (fetchpatch {
+      url = "https://github.com/shogun-toolbox/shogun/commit/5aceefd9fb0e2132c354b9a0c0ceb9160cc9b2f7.patch";
+      sha256 = "sha256-AgJJKQA8vc5oKaTQDqMdwBR4hT4sn9+uW0jLe7GteJw=";
+    })
+
+    # Fix virtual destruction
+    (fetchpatch {
+      url = "https://github.com/shogun-toolbox/shogun/commit/ef0e4dc1cc4a33c9e6b17a108fa38a436de2d7ee.patch";
+      sha256 = "sha256-a9Rm0ytqkSAgC3dguv8m3SwOSipb+VByBHHdmV0d63w=";
+    })
+    ./fix-virtual-destruction.patch
+
+    # Fix compile errors with json-c
+    # https://github.com/shogun-toolbox/shogun/pull/4104
+    (fetchpatch {
+      url = "https://github.com/shogun-toolbox/shogun/commit/365ce4c4c700736d2eec8ba6c975327a5ac2cd9b.patch";
+      sha256 = "sha256-OhEWwrHtD/sOcjHmPY/C9zJ8ruww8yXrRcTw38nGEJU=";
+    })
+
+    # Fix compile errors with Eigen 3.4
+    ./eigen-3.4.patch
+
+  ]
+  ++ lib.optional (!withSvmLight) ./svmlight-scrubber.patch;
+
+  nativeBuildInputs = [
+    cmake
+    swig
+    ctags
+  ]
+  ++ (with python3Packages; [
+    python
+    jinja2
+    ply
+  ]);
+
+  buildInputs = [
+    eigen
+    blas
+    lapack
+    glpk
+    protobuf
+    json_c
+    libxml2
+    hdf5
+    curl
+    libarchive
+    bzip2
+    xz
+    snappy
+    lzo
+    nlopt
+    lp_solve
+    colpack
+  ]
+  ++ lib.optionals pythonSupport (
+    with python3Packages;
+    [
+      python
+      numpy
+    ]
+  )
+  ++ lib.optional opencvSupport opencv;
+
+  cmakeFlags =
+    let
+      excludeTestsRegex = lib.concatStringsSep "|" [
+        # segfault
+        "SerializationXML"
+        "TrainedModelSerialization"
+        # broken by openblas 0.3.21
+        "mathematics_lapack"
+        # fails on aarch64
+        "LinearTimeMMD"
+        "QuadraticTimeMMD"
+        "SGVectorTest"
+        "Statistics"
+        # hangs on aarch64
+        "PRange"
+        # these take too long on CI
+        "evaluation_cross_validation"
+        "modelselection_combined_kernel"
+        "modelselection_grid_search"
+      ];
+    in
+    [
+      (lib.cmakeBool "BUILD_META_EXAMPLES" true)
+      (lib.cmakeBool "CMAKE_DISABLE_FIND_PACKAGE_ARPACK" true)
+      (lib.cmakeBool "CMAKE_DISABLE_FIND_PACKAGE_ARPREC" true)
+      (lib.cmakeBool "CMAKE_DISABLE_FIND_PACKAGE_CPLEX" true)
+      (lib.cmakeBool "CMAKE_DISABLE_FIND_PACKAGE_Mosek" true)
+      (lib.cmakeBool "CMAKE_DISABLE_FIND_PACKAGE_TFLogger" true)
+      (lib.cmakeBool "CMAKE_DISABLE_FIND_PACKAGE_ViennaCL" true)
+      (lib.cmakeFeature "CMAKE_CTEST_ARGUMENTS" "--exclude-regex;'${excludeTestsRegex}'")
+      (lib.cmakeBool "ENABLE_TESTING" finalAttrs.finalPackage.doCheck)
+      (lib.cmakeBool "DISABLE_META_INTEGRATION_TESTS" true)
+      (lib.cmakeBool "TRAVIS_DISABLE_META_CPP" true)
+      (lib.cmakeBool "INTERFACE_PYTHON" pythonSupport)
+      (lib.cmakeBool "OpenCV" opencvSupport)
+      (lib.cmakeBool "USE_SVMLIGHT" withSvmLight)
+    ];
+
+  CXXFLAGS = "-faligned-new";
+
+  doCheck = true;
+
+  postUnpack = ''
+    mkdir -p $sourceRoot/third_party/{rxcpp,GoogleMock}
+    ln -s ${srcs.rxcpp} $sourceRoot/third_party/rxcpp/v${rxcppVersion}.tar.gz
+    ln -s ${srcs.gtest} $sourceRoot/third_party/GoogleMock/release-${gtestVersion}.tar.gz
+  '';
+
+  postPatch = ''
+    # Fix preprocessing SVMlight code
+    sed -i \
+        -e 's@#ifdef SVMLIGHT@#ifdef USE_SVMLIGHT@' \
+        -e '/^#ifdef USE_SVMLIGHT/,/^#endif/ s@#endif@#endif //USE_SVMLIGHT@' \
+        src/shogun/kernel/string/CommUlongStringKernel.cpp
+    sed -i -e 's/#if USE_SVMLIGHT/#ifdef USE_SVMLIGHT/' src/interfaces/swig/Machine.i
+    sed -i -e 's@// USE_SVMLIGHT@//USE_SVMLIGHT@' src/interfaces/swig/Transfer.i
+    sed -i -e 's@/\* USE_SVMLIGHT \*/@//USE_SVMLIGHT@' src/interfaces/swig/Transfer_includes.i
+  ''
+  + lib.optionalString (!withSvmLight) ''
+    # Run SVMlight scrubber
+    patchShebangs scripts/light-scrubber.sh
+    echo "removing SVMlight code"
+    ./scripts/light-scrubber.sh
+  '';
+
+  postInstall = ''
+    mkdir -p $doc/share/doc/shogun/examples
+    mv $out/share/shogun/examples/cpp $doc/share/doc/shogun/examples
+    cp ../examples/undocumented/libshogun/*.cpp $doc/share/doc/shogun/examples/cpp
+    rm -r $out/share
+  '';
+
+  postFixup = ''
+    # CMake incorrectly calculates library path from dev prefix
+    substituteInPlace $dev/lib/cmake/shogun/ShogunTargets-release.cmake \
+      --replace-fail "\''${_IMPORT_PREFIX}/lib/" "$out/lib/"
+  '';
+
+  meta = with lib; {
+    description = "Toolbox which offers a wide range of efficient and unified machine learning methods";
+    homepage = "http://shogun-toolbox.org/";
+    license = if withSvmLight then licenses.unfree else licenses.gpl3Plus;
+    maintainers = with maintainers; [
+      edwtjo
+      smancill
+    ];
+  };
+})

pkgs/applications/science/machine-learning/shogun/eigen-3.4.patch

@@ -0,0 +1,74 @@
+From: Sebastián Mancilla <smancill@smancill.dev>
+Subject: [PATCH] Fix compile errors when using Eigen 3.4
+
+---
+ .../machine/gp/MultiLaplaceInferenceMethod.cpp | 18 +++++++++---------
+ 1 file changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp b/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp
+index 2e27678d2..60050afea 100644
+--- a/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp
++++ b/src/shogun/machine/gp/MultiLaplaceInferenceMethod.cpp
+@@ -84,9 +84,9 @@ class CMultiPsiLine : public func_base
+ 		float64_t result=0;
+ 		for(index_t bl=0; bl<C; bl++)
+ 		{
+-			eigen_f.block(bl*n,0,n,1)=K*alpha->block(bl*n,0,n,1)*CMath::exp(log_scale*2.0);
+-			result+=alpha->block(bl*n,0,n,1).dot(eigen_f.block(bl*n,0,n,1))/2.0;
+-			eigen_f.block(bl*n,0,n,1)+=eigen_m;
++			eigen_f.segment(bl*n,n)=K*alpha->segment(bl*n,n)*CMath::exp(log_scale*2.0);
++			result+=alpha->segment(bl*n,n).dot(eigen_f.segment(bl*n,n))/2.0;
++			eigen_f.segment(bl*n,n)+=eigen_m;
+ 		}
+ 
+ 		// get first and second derivatives of log likelihood
+@@ -272,7 +272,7 @@ void CMultiLaplaceInferenceMethod::update_alpha()
+ 	{
+ 		Map<VectorXd> alpha(m_alpha.vector, m_alpha.vlen);
+ 		for(index_t bl=0; bl<C; bl++)
+-			eigen_mu.block(bl*n,0,n,1)=eigen_ktrtr*CMath::exp(m_log_scale*2.0)*alpha.block(bl*n,0,n,1);
++			eigen_mu.segment(bl*n,n)=eigen_ktrtr*CMath::exp(m_log_scale*2.0)*alpha.segment(bl*n,n);
+ 
+ 		//alpha'*(f-m)/2.0
+ 		Psi_New=alpha.dot(eigen_mu)/2.0;
+@@ -316,7 +316,7 @@ void CMultiLaplaceInferenceMethod::update_alpha()
+ 
+ 		for(index_t bl=0; bl<C; bl++)
+ 		{
+-			VectorXd eigen_sD=eigen_dpi.block(bl*n,0,n,1).cwiseSqrt();
++			VectorXd eigen_sD=eigen_dpi.segment(bl*n,n).cwiseSqrt();
+ 			LLT<MatrixXd> chol_tmp((eigen_sD*eigen_sD.transpose()).cwiseProduct(eigen_ktrtr*CMath::exp(m_log_scale*2.0))+
+ 				MatrixXd::Identity(m_ktrtr.num_rows, m_ktrtr.num_cols));
+ 			MatrixXd eigen_L_tmp=chol_tmp.matrixU();
+@@ -341,11 +341,11 @@ void CMultiLaplaceInferenceMethod::update_alpha()
+ 		VectorXd tmp2=m_tmp.array().rowwise().sum();
+ 
+ 		for(index_t bl=0; bl<C; bl++)
+-			eigen_b.block(bl*n,0,n,1)+=eigen_dpi.block(bl*n,0,n,1).cwiseProduct(eigen_mu.block(bl*n,0,n,1)-eigen_mean_bl-tmp2);
++			eigen_b.segment(bl*n,n)+=eigen_dpi.segment(bl*n,n).cwiseProduct(eigen_mu.segment(bl*n,n)-eigen_mean_bl-tmp2);
+ 
+ 		Map<VectorXd> &eigen_c=eigen_W;
+ 		for(index_t bl=0; bl<C; bl++)
+-			eigen_c.block(bl*n,0,n,1)=eigen_E.block(0,bl*n,n,n)*(eigen_ktrtr*CMath::exp(m_log_scale*2.0)*eigen_b.block(bl*n,0,n,1));
++			eigen_c.segment(bl*n,n)=eigen_E.block(0,bl*n,n,n)*(eigen_ktrtr*CMath::exp(m_log_scale*2.0)*eigen_b.segment(bl*n,n));
+ 
+ 		Map<MatrixXd> c_tmp(eigen_c.data(),n,C);
+ 
+@@ -409,7 +409,7 @@ float64_t CMultiLaplaceInferenceMethod::get_derivative_helper(SGMatrix<float64_t
+ 	{
+ 		result+=((eigen_E.block(0,bl*n,n,n)-eigen_U.block(0,bl*n,n,n).transpose()*eigen_U.block(0,bl*n,n,n)).array()
+ 			*eigen_dK.array()).sum();
+-		result-=(eigen_dK*eigen_alpha.block(bl*n,0,n,1)).dot(eigen_alpha.block(bl*n,0,n,1));
++		result-=(eigen_dK*eigen_alpha.segment(bl*n,n)).dot(eigen_alpha.segment(bl*n,n));
+ 	}
+ 
+ 	return result/2.0;
+@@ -489,7 +489,7 @@ SGVector<float64_t> CMultiLaplaceInferenceMethod::get_derivative_wrt_mean(
+ 		result[i]=0;
+ 		//currently only compute the explicit term
+ 		for(index_t bl=0; bl<C; bl++)
+-			result[i]-=eigen_alpha.block(bl*n,0,n,1).dot(eigen_dmu);
++			result[i]-=eigen_alpha.segment(bl*n,n).dot(eigen_dmu);
+ 	}
+ 
+ 	return result;

pkgs/applications/science/machine-learning/shogun/fix-virtual-destruction.patch

@@ -0,0 +1,20 @@
+From: Sebastián Mancilla <smancill@smancill.dev>
+Subject: Fix virtual destruction
+
+---
+ src/shogun/solver/LDASolver.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/shogun/solver/LDASolver.h b/src/shogun/solver/LDASolver.h
+index 9300a85c5..d500eca5d 100644
+--- a/src/shogun/solver/LDASolver.h
++++ b/src/shogun/solver/LDASolver.h
+@@ -87,7 +87,7 @@ namespace shogun
+ 			compute_within_cov();
+ 		}
+ 
+-		~LDASolver()
++		virtual ~LDASolver()
+ 		{
+ 			SG_UNREF(m_features)
+ 			SG_UNREF(m_labels)

pkgs/applications/science/machine-learning/shogun/svmlight-scrubber.patch

@@ -0,0 +1,76 @@
+From: Sebastián Mancilla <smancill@smancill.dev>
+Subject: Update SVMlight scrubber script
+
+This requires previously fixing a few wrong preprocessor directives that
+are supposed to fence code using SVMlight.
+
+- The script was too eager and removing *.light files in SVMlight format
+  that are used by other tests. The code reading those files doesn't use
+  any SVMlight code so it should be fine to keep it and run the tests.
+
+- The Python test *domainadaptationsvm.py was not removed because of
+  wrong globbing.
+
+- Remove a couple of examples using SVMlight that were missed.
+
+- The script is actually modifying (and breaking) itself because the
+  grep for the USE_SVMLIGHT macro is too eager again and matches itself
+  (and the version stored in upstream's Debian package control tarball
+  is broken because of it). Just fix it by grepping for preprocessor
+  directives only.
+
+- No need to fix the Transfer_includes.i file in the script with a final
+  %} when its preprocessor directives have been fixed.
+
+- The Swig files were moved to a new directory at some point but the
+  script was not updated accordingly.
+---
+ scripts/light-scrubber.sh | 16 ++++++----------
+ 1 file changed, 6 insertions(+), 10 deletions(-)
+
+diff a/scripts/light-scrubber.sh b/scripts/light-scrubber.sh
+--- a/scripts/light-scrubber.sh
++++ b/scripts/light-scrubber.sh
+@@ -26,14 +26,16 @@
+ # You should have received a copy of the GNU General Public License
+ # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ #
+-rm -rf	examples/*/*/{*light*,*_domainadaptationsvm_*}				\
++rm -rf	examples/*/*/{*light*.*,*domainadaptationsvm*}				\
+ 	examples/undocumented/matlab_and_octave/tests/*light*			\
++	examples/undocumented/python/serialization_string_kernels.py		\
++	examples/undocumented/python/mkl_binclass.py				\
+ 	src/shogun/classifier/svm/SVMLight.*					\
+ 	src/shogun/classifier/svm/SVMLightOneClass.*				\
+ 	src/shogun/regression/svr/SVRLight.*					\
+ 	doc/md/LICENSE_SVMlight*
+ 
+-for _file in `grep -rl USE_SVMLIGHT .`
++grep -rl '^#ifdef USE_SVMLIGHT' . | while read -r _file
+ do
+   sed -i.orig -e								\
+ 	'/\#ifdef USE_SVMLIGHT/,/\#endif \/\/USE_SVMLIGHT/c \\' ${_file} &&	\
+@@ -41,7 +43,7 @@ do
+   rm -rf ${_file}.orig
+ done
+ 
+-for _file in `find . -depth -name 'CMakeLists.txt'`
++find . -depth -name 'CMakeLists.txt' | while read -r _file
+ do
+   sed -i.orig -e 's!.*_sv[mr]light_.*!!g' ${_file} &&				\
+   touch -r ${_file}.orig ${_file} &&						\
+@@ -56,13 +58,7 @@ do
+   rm -rf ${_file}.orig
+ done
+ 
+-_file="src/interfaces/modular/Transfer_includes.i" &&				\
+-cp -a ${_file} ${_file}.orig &&							\
+-echo '%}' >> ${_file} &&							\
+-touch -r ${_file}.orig ${_file} &&						\
+-rm -rf ${_file}.orig
+-
+-_file="src/interfaces/modular/Machine.i" &&					\
++_file="src/interfaces/swig/Machine.i" &&					\
+ sed -i.orig -e '/.*CSVRLight.*/d' ${_file} &&					\
+ touch -r ${_file}.orig ${_file} &&						\
+ rm -rf ${_file}.orig

pkgs/applications/science/math/R/default.nix

@@ -0,0 +1,248 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  bzip2,
+  gfortran,
+  libX11,
+  libXmu,
+  libXt,
+  libjpeg,
+  libpng,
+  libtiff,
+  ncurses,
+  pango,
+  pcre2,
+  perl,
+  readline,
+  tcl,
+  texlive,
+  texliveSmall,
+  tk,
+  xz,
+  zlib,
+  less,
+  texinfo,
+  graphviz,
+  icu,
+  pkg-config,
+  bison,
+  which,
+  jdk,
+  blas,
+  lapack,
+  curl,
+  tzdata,
+  withRecommendedPackages ? true,
+  enableStrictBarrier ? false,
+  enableMemoryProfiling ? false,
+  # R as of writing does not support outputting both .so and .a files; it outputs:
+  #     --enable-R-static-lib conflicts with --enable-R-shlib and will be ignored
+  static ? false,
+  testers,
+}:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "R";
+  version = "4.5.1";
+
+  src =
+    let
+      inherit (finalAttrs) pname version;
+    in
+    fetchurl {
+      url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
+      hash = "sha256-tCp5IUADhmRbEBBbkcaHKHh9tcTIPJ9sMKzc5jLhu3A=";
+    };
+
+  outputs = [
+    "out"
+    "tex"
+  ];
+
+  nativeBuildInputs = [
+    bison
+    perl
+    pkg-config
+    tzdata
+    which
+  ];
+  buildInputs = [
+    bzip2
+    gfortran
+    libX11
+    libXmu
+    libXt
+    libXt
+    libjpeg
+    libpng
+    libtiff
+    ncurses
+    pango
+    pcre2
+    readline
+    (texliveSmall.withPackages (
+      ps: with ps; [
+        inconsolata
+        helvetic
+        ps.texinfo
+        fancyvrb
+        cm-super
+        rsfs
+      ]
+    ))
+    xz
+    zlib
+    less
+    texinfo
+    graphviz
+    icu
+    which
+    blas
+    lapack
+    curl
+    tcl
+    tk
+    jdk
+  ];
+  strictDeps = true;
+
+  patches = [
+    ./no-usr-local-search-paths.patch
+  ];
+
+  # Test of the examples for package 'tcltk' fails in Darwin sandbox. See:
+  # https://github.com/NixOS/nixpkgs/issues/146131
+  postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
+    substituteInPlace configure \
+      --replace "-install_name libRblas.dylib" "-install_name $out/lib/R/lib/libRblas.dylib" \
+      --replace "-install_name libRlapack.dylib" "-install_name $out/lib/R/lib/libRlapack.dylib" \
+      --replace "-install_name libR.dylib" "-install_name $out/lib/R/lib/libR.dylib"
+    substituteInPlace tests/Examples/Makefile.in \
+      --replace "test-Examples: test-Examples-Base" "test-Examples:" # do not test the examples
+  '';
+
+  dontDisableStatic = static;
+
+  preConfigure = ''
+    configureFlagsArray=(
+      --disable-lto
+      --with${lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages
+      --with-blas="-L${blas}/lib -lblas"
+      --with-lapack="-L${lapack}/lib -llapack"
+      --with-readline
+      --with-tcltk --with-tcl-config="${tcl}/lib/tclConfig.sh" --with-tk-config="${tk}/lib/tkConfig.sh"
+      --with-cairo
+      --with-libpng
+      --with-jpeglib
+      --with-libtiff
+      --with-ICU
+      ${lib.optionalString enableStrictBarrier "--enable-strict-barrier"}
+      ${lib.optionalString enableMemoryProfiling "--enable-memory-profiling"}
+      ${if static then "--enable-R-static-lib" else "--enable-R-shlib"}
+      AR=$(type -p ar)
+      AWK=$(type -p gawk)
+      CC=$(type -p cc)
+      CXX=$(type -p c++)
+      FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
+      JAVA_HOME="${jdk}"
+      RANLIB=$(type -p ranlib)
+      CURL_CONFIG="${lib.getExe' (lib.getDev curl) "curl-config"}"
+      r_cv_have_curl728=yes
+      R_SHELL="${stdenv.shell}"
+  ''
+  + lib.optionalString stdenv.hostPlatform.isDarwin ''
+    --disable-R-framework
+    --without-x
+    OBJC="clang"
+    CPPFLAGS="-isystem ${lib.getInclude stdenv.cc.libcxx}/include/c++/v1"
+    LDFLAGS="-L${lib.getLib stdenv.cc.libcxx}/lib"
+  ''
+  + ''
+    )
+    echo >>etc/Renviron.in "TCLLIBPATH=${tk}/lib"
+    echo >>etc/Renviron.in "TZDIR=${tzdata}/share/zoneinfo"
+  '';
+
+  installTargets = [
+    "install"
+    "install-info"
+    "install-pdf"
+  ];
+
+  # move tex files to $tex for use with texlive.combine
+  # add link in $out since ${R_SHARE_DIR}/texmf is hardcoded in several places
+  postInstall = ''
+    mv -T "$out/lib/R/share/texmf" "$tex"
+    ln -s "$tex" "$out/lib/R/share/texmf"
+  '';
+
+  # The store path to "which" is baked into src/library/base/R/unix/system.unix.R,
+  # but Nix cannot detect it as a run-time dependency because the installed file
+  # is compiled and compressed, which hides the store path.
+  postFixup = ''
+    echo ${which} > $out/nix-support/undetected-runtime-dependencies
+    ${lib.optionalString stdenv.hostPlatform.isLinux ''find $out -name "*.so" -exec patchelf {} --add-rpath $out/lib/R/lib \;''}
+  '';
+
+  doCheck = true;
+  preCheck = "export HOME=$TMPDIR; export TZ=CET; bin/Rscript -e 'sessionInfo()'";
+
+  enableParallelBuilding = true;
+
+  setupHook = ./setup-hook.sh;
+
+  passthru.tests.pkg-config = testers.testMetaPkgConfig finalAttrs.finalPackage;
+
+  # make tex output available to texlive.combine
+  passthru.pkgs = [ finalAttrs.finalPackage.tex ];
+  passthru.tlType = "run";
+  # dependencies (based on \RequirePackage in jss.cls, Rd.sty, Sweave.sty)
+  passthru.tlDeps = with texlive; [
+    amsfonts
+    amsmath
+    fancyvrb
+    graphics
+    hyperref
+    iftex
+    jknapltx
+    latex
+    lm
+    tools
+    upquote
+    url
+  ];
+
+  meta = with lib; {
+    homepage = "http://www.r-project.org/";
+    description = "Free software environment for statistical computing and graphics";
+    license = licenses.gpl2Plus;
+
+    longDescription = ''
+      GNU R is a language and environment for statistical computing and
+      graphics that provides a wide variety of statistical (linear and
+      nonlinear modelling, classical statistical tests, time-series
+      analysis, classification, clustering, ...) and graphical
+      techniques, and is highly extensible. One of R's strengths is the
+      ease with which well-designed publication-quality plots can be
+      produced, including mathematical symbols and formulae where
+      needed. R is an integrated suite of software facilities for data
+      manipulation, calculation and graphical display. It includes an
+      effective data handling and storage facility, a suite of operators
+      for calculations on arrays, in particular matrices, a large,
+      coherent, integrated collection of intermediate tools for data
+      analysis, graphical facilities for data analysis and display
+      either on-screen or on hardcopy, and a well-developed, simple and
+      effective programming language which includes conditionals, loops,
+      user-defined recursive functions and input and output facilities.
+    '';
+
+    pkgConfigModules = [ "libR" ];
+    platforms = platforms.all;
+
+    maintainers = with maintainers; [ jbedo ];
+    teams = [ teams.sage ];
+  };
+})

pkgs/applications/science/math/R/no-usr-local-search-paths.patch

@@ -0,0 +1,24 @@
+diff -ubr R-3.0.1-orig/configure R-3.0.1/configure
+--- R-3.0.1-orig/configure	2013-07-04 10:46:42.336133947 +0200
++++ R-3.0.1/configure	2013-07-04 10:46:17.181919960 +0200
+@@ -3800,13 +3800,13 @@
+ : ${LIBnn=$libnn}
+ ## We provide these defaults so that headers and libraries in
+ ## '/usr/local' are found (by the native tools, mostly).
+-if test -f "/sw/etc/fink.conf"; then
+-  : ${CPPFLAGS="-I/sw/include -I/usr/local/include"}
+-  : ${LDFLAGS="-L/sw/lib -L/usr/local/lib"}
+-else
+-  : ${CPPFLAGS="-I/usr/local/include"}
+-  : ${LDFLAGS="-L/usr/local/${LIBnn}"}
+-fi
++# if test -f "/sw/etc/fink.conf"; then
++#   : ${CPPFLAGS="-I/sw/include -I/usr/local/include"}
++#   : ${LDFLAGS="-L/sw/lib -L/usr/local/lib"}
++# else
++#   : ${CPPFLAGS="-I/usr/local/include"}
++#   : ${LDFLAGS="-L/usr/local/${LIBnn}"}
++# fi
+ 
+ ## take care not to  override the command-line setting
+ if test "${libdir}" = '${exec_prefix}/lib'; then

pkgs/applications/science/math/R/setup-hook.sh

@@ -0,0 +1,7 @@
+addRLibPath () {
+    if [[ -d "$1/library" ]]; then
+        addToSearchPath R_LIBS_SITE "$1/library"
+    fi
+}
+
+addEnvHooks "$targetOffset" addRLibPath

pkgs/applications/science/math/caffe/darwin.patch

@@ -0,0 +1,47 @@
+diff --git a/Makefile b/Makefile
+index c823f66e..65b90c5e 100644
+--- a/Makefile
++++ b/Makefile
+@@ -32,9 +32,9 @@ SRC_DIRS := $(shell find * -type d -exec bash -c "find {} -maxdepth 1 \
+ LIBRARY_NAME := $(PROJECT)
+ LIB_BUILD_DIR := $(BUILD_DIR)/lib
+ STATIC_NAME := $(LIB_BUILD_DIR)/lib$(LIBRARY_NAME).a
+-DYNAMIC_VERSION_MAJOR 		:= 1
+-DYNAMIC_VERSION_MINOR 		:= 0
+-DYNAMIC_VERSION_REVISION 	:= 0
++DYNAMIC_VERSION_MAJOR		:= 1
++DYNAMIC_VERSION_MINOR		:= 0
++DYNAMIC_VERSION_REVISION	:= 0
+ DYNAMIC_NAME_SHORT := lib$(LIBRARY_NAME).so
+ #DYNAMIC_SONAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR)
+ DYNAMIC_VERSIONED_NAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR).$(DYNAMIC_VERSION_MINOR).$(DYNAMIC_VERSION_REVISION)
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index c48255c8..cf4c580e 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -105,7 +105,6 @@ if(USE_OPENCV)
+ endif()
+ 
+ # ---[ BLAS
+-if(NOT APPLE)
+   set(BLAS "Atlas" CACHE STRING "Selected BLAS library")
+   set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL")
+ 
+@@ -123,17 +122,6 @@ if(NOT APPLE)
+     list(APPEND Caffe_LINKER_LIBS PUBLIC ${MKL_LIBRARIES})
+     list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_MKL)
+   endif()
+-elseif(APPLE)
+-  find_package(vecLib REQUIRED)
+-  list(APPEND Caffe_INCLUDE_DIRS PUBLIC ${vecLib_INCLUDE_DIR})
+-  list(APPEND Caffe_LINKER_LIBS PUBLIC ${vecLib_LINKER_LIBS})
+-
+-  if(VECLIB_FOUND)
+-    if(NOT vecLib_INCLUDE_DIR MATCHES "^/System/Library/Frameworks/vecLib.framework.*")
+-      list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_ACCELERATE)
+-    endif()
+-  endif()
+-endif()
+ 
+ # ---[ Python
+ if(BUILD_python)

pkgs/applications/science/math/caffe/default.nix

@@ -0,0 +1,182 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  fetchurl,
+  fetchpatch,
+  cmake,
+  boost,
+  gflags,
+  glog,
+  hdf5-cpp,
+  opencv4,
+  protobuf,
+  doxygen,
+  blas,
+  lmdbSupport ? true,
+  lmdb,
+  leveldbSupport ? true,
+  leveldb,
+  snappy,
+  pythonSupport ? false,
+  python ? null,
+  numpy ? null,
+  replaceVars,
+}:
+
+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 {
+  pname = "caffe";
+  version = "1.0";
+
+  src = fetchFromGitHub {
+    owner = "BVLC";
+    repo = "caffe";
+    rev = version;
+    sha256 = "104jp3cm823i3cdph7hgsnj6l77ygbwsy35mdmzhmsi4jxprd9j3";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    doxygen
+  ];
+
+  cmakeFlags =
+    # It's important that caffe is passed the major and minor version only because that's what
+    # boost_python expects
+    [
+      (if pythonSupport then "-Dpython_version=${python.pythonVersion}" else "-DBUILD_python=OFF")
+      "-DBLAS=open"
+      "-DCPU_ONLY=ON"
+    ]
+    ++ [ "-DUSE_LEVELDB=${toggle leveldbSupport}" ]
+    ++ [ "-DUSE_LMDB=${toggle lmdbSupport}" ];
+
+  buildInputs = [
+    boost
+    gflags
+    glog
+    protobuf
+    hdf5-cpp
+    opencv4
+    blas
+  ]
+  ++ lib.optional lmdbSupport lmdb
+  ++ lib.optionals leveldbSupport [
+    leveldb
+    snappy
+  ]
+  ++ lib.optionals pythonSupport [
+    python
+    numpy
+  ];
+
+  propagatedBuildInputs = lib.optionals pythonSupport (
+    # requirements.txt
+    let
+      pp = python.pkgs;
+    in
+    (
+      [
+        pp.numpy
+        pp.scipy
+        pp.scikit-image
+        pp.h5py
+        pp.matplotlib
+        pp.ipython
+        pp.networkx
+        pp.pandas
+        pp.python-dateutil
+        pp.protobuf
+        pp.gflags
+        pp.pyyaml
+        pp.pillow
+        pp.six
+      ]
+      ++ lib.optional leveldbSupport pp.leveldb
+    )
+  );
+
+  outputs = [
+    "bin"
+    "out"
+  ];
+  propagatedBuildOutputs = [ ]; # otherwise propagates out -> bin cycle
+
+  patches = [
+    ./darwin.patch
+    ./glog-cmake.patch
+    ./random-shuffle.patch
+    (fetchpatch {
+      name = "support-opencv4";
+      url = "https://github.com/BVLC/caffe/pull/6638/commits/0a04cc2ccd37ba36843c18fea2d5cbae6e7dd2b5.patch";
+      hash = "sha256-ZegTvp0tTHlopQv+UzHDigs6XLkP2VfqLCWXl6aKJSI=";
+    })
+  ]
+  ++ lib.optional pythonSupport (
+    replaceVars ./python.patch {
+      inherit (python.sourceVersion) major minor; # Should be changed in case of PyPy
+    }
+  );
+
+  postPatch = ''
+    substituteInPlace src/caffe/util/io.cpp --replace \
+      'SetTotalBytesLimit(kProtoReadBytesLimit, 536870912)' \
+      'SetTotalBytesLimit(kProtoReadBytesLimit)'
+  '';
+
+  preConfigure = lib.optionalString pythonSupport ''
+    # We need this when building with Python bindings
+    export BOOST_LIBRARYDIR="${boost.out}/lib";
+  '';
+
+  postInstall = ''
+    # Internal static library.
+    rm $out/lib/libproto.a
+
+    # Install models
+    cp -a ../models $out/share/Caffe/models
+
+    moveToOutput "bin" "$bin"
+  ''
+  + lib.optionalString pythonSupport ''
+    mkdir -p $out/${python.sitePackages}
+    mv $out/python/caffe $out/${python.sitePackages}
+    rm -rf $out/python
+  '';
+
+  doInstallCheck = false; # build takes more than 30 min otherwise
+  installCheckPhase = ''
+    model=bvlc_reference_caffenet
+    m_path="$out/share/Caffe/models/$model"
+    $bin/bin/caffe test \
+      -model "$m_path/deploy.prototxt" \
+      -solver "$m_path/solver.prototxt" \
+      -weights "${test_model_weights}"
+  '';
+
+  meta = with lib; {
+    description = "Deep learning framework";
+    longDescription = ''
+      Caffe is a deep learning framework made with expression, speed, and
+      modularity in mind. It is developed by the Berkeley Vision and Learning
+      Center (BVLC) and by community contributors.
+    '';
+    homepage = "http://caffe.berkeleyvision.org/";
+    maintainers = [ ];
+    broken =
+      (pythonSupport && (python.isPy310))
+      || !(leveldbSupport -> (leveldb != null && snappy != null))
+      || !(pythonSupport -> (python != null && numpy != null));
+    license = licenses.bsd2;
+    platforms = platforms.linux ++ platforms.darwin;
+  };
+}

pkgs/applications/science/math/caffe/glog-cmake.patch

@@ -0,0 +1,97 @@
+From 38b81bb53304d7a3f6aed36f7b4e77b6efa78338 Mon Sep 17 00:00:00 2001
+From: uku <hi@uku.moe>
+Date: Wed, 14 May 2025 16:55:15 +0200
+Subject: [PATCH] fix linking against glog 0.7.x
+
+---
+ cmake/Dependencies.cmake     |  2 +-
+ cmake/External/glog.cmake    |  4 +--
+ cmake/Modules/FindGlog.cmake | 48 ------------------------------------
+ 3 files changed, 3 insertions(+), 51 deletions(-)
+ delete mode 100644 cmake/Modules/FindGlog.cmake
+
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 4a5bac47..88aa123f 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -32,7 +32,7 @@ endif()
+ # ---[ Google-glog
+ include("cmake/External/glog.cmake")
+ list(APPEND Caffe_INCLUDE_DIRS PUBLIC ${GLOG_INCLUDE_DIRS})
+-list(APPEND Caffe_LINKER_LIBS PUBLIC ${GLOG_LIBRARIES})
++list(APPEND Caffe_LINKER_LIBS PUBLIC glog::glog)
+ 
+ # ---[ Google-gflags
+ include("cmake/External/gflags.cmake")
+diff --git a/cmake/External/glog.cmake b/cmake/External/glog.cmake
+index f9d0549c..43414544 100644
+--- a/cmake/External/glog.cmake
++++ b/cmake/External/glog.cmake
+@@ -5,8 +5,8 @@ if (NOT __GLOG_INCLUDED)
+   set(__GLOG_INCLUDED TRUE)
+ 
+   # try the system-wide glog first
+-  find_package(Glog)
+-  if (GLOG_FOUND)
++  find_package(glog REQUIRED)
++  if (glog_FOUND)
+       set(GLOG_EXTERNAL FALSE)
+   else()
+     # fetch and build glog from github
+diff --git a/cmake/Modules/FindGlog.cmake b/cmake/Modules/FindGlog.cmake
+deleted file mode 100644
+index 99abbe47..00000000
+--- a/cmake/Modules/FindGlog.cmake
++++ /dev/null
+@@ -1,48 +0,0 @@
+-# - Try to find Glog
+-#
+-# The following variables are optionally searched for defaults
+-#  GLOG_ROOT_DIR:            Base directory where all GLOG components are found
+-#
+-# The following are set after configuration is done:
+-#  GLOG_FOUND
+-#  GLOG_INCLUDE_DIRS
+-#  GLOG_LIBRARIES
+-#  GLOG_LIBRARYRARY_DIRS
+-
+-include(FindPackageHandleStandardArgs)
+-
+-set(GLOG_ROOT_DIR "" CACHE PATH "Folder contains Google glog")
+-
+-if(WIN32)
+-    find_path(GLOG_INCLUDE_DIR glog/logging.h
+-        PATHS ${GLOG_ROOT_DIR}/src/windows)
+-else()
+-    find_path(GLOG_INCLUDE_DIR glog/logging.h
+-        PATHS ${GLOG_ROOT_DIR})
+-endif()
+-
+-if(MSVC)
+-    find_library(GLOG_LIBRARY_RELEASE libglog_static
+-        PATHS ${GLOG_ROOT_DIR}
+-        PATH_SUFFIXES Release)
+-
+-    find_library(GLOG_LIBRARY_DEBUG libglog_static
+-        PATHS ${GLOG_ROOT_DIR}
+-        PATH_SUFFIXES Debug)
+-
+-    set(GLOG_LIBRARY optimized ${GLOG_LIBRARY_RELEASE} debug ${GLOG_LIBRARY_DEBUG})
+-else()
+-    find_library(GLOG_LIBRARY glog
+-        PATHS ${GLOG_ROOT_DIR}
+-        PATH_SUFFIXES lib lib64)
+-endif()
+-
+-find_package_handle_standard_args(Glog DEFAULT_MSG GLOG_INCLUDE_DIR GLOG_LIBRARY)
+-
+-if(GLOG_FOUND)
+-  set(GLOG_INCLUDE_DIRS ${GLOG_INCLUDE_DIR})
+-  set(GLOG_LIBRARIES ${GLOG_LIBRARY})
+-  message(STATUS "Found glog    (include: ${GLOG_INCLUDE_DIR}, library: ${GLOG_LIBRARY})")
+-  mark_as_advanced(GLOG_ROOT_DIR GLOG_LIBRARY_RELEASE GLOG_LIBRARY_DEBUG
+-                                 GLOG_LIBRARY GLOG_INCLUDE_DIR)
+-endif()
+-- 
+2.49.0
+

pkgs/applications/science/math/caffe/python.patch

@@ -0,0 +1,70 @@
+commit b14ca23651d390fcae4a929dedc7c33a83453a66
+Author: Frederik Rietdijk <fridh@fridh.nl>
+Date:   Sun Feb 17 08:41:27 2019 +0100
+
+    Find boost_pythonXX
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 08f56a33..0a04592a 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -99,10 +99,10 @@ add_subdirectory(docs)
+ add_custom_target(lint COMMAND ${CMAKE_COMMAND} -P ${PROJECT_SOURCE_DIR}/cmake/lint.cmake)
+ 
+ # ---[ pytest target
+-if(BUILD_python)
+-  add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python )
+-  add_dependencies(pytest pycaffe)
+-endif()
++# if(BUILD_python)
++#   add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python )
++#   add_dependencies(pytest pycaffe)
++# endif()
+ 
+ # ---[ uninstall target
+ configure_file(
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 4a5bac47..be026d43 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -141,37 +141,14 @@ if(BUILD_python)
+     # use python3
+     find_package(PythonInterp 3.0)
+     find_package(PythonLibs 3.0)
+-    find_package(NumPy 1.7.1)
+-    # Find the matching boost python implementation
+-    set(version ${PYTHONLIBS_VERSION_STRING})
+-
+-    STRING( REGEX REPLACE "[^0-9]" "" boost_py_version ${version} )
+-    find_package(Boost 1.46 COMPONENTS "python-py${boost_py_version}")
+-    set(Boost_PYTHON_FOUND ${Boost_PYTHON-PY${boost_py_version}_FOUND})
+-
+-    while(NOT "${version}" STREQUAL "" AND NOT Boost_PYTHON_FOUND)
+-      STRING( REGEX REPLACE "([0-9.]+).[0-9]+" "\\1" version ${version} )
+-
+-      STRING( REGEX REPLACE "[^0-9]" "" boost_py_version ${version} )
+-      find_package(Boost 1.46 COMPONENTS "python-py${boost_py_version}")
+-      set(Boost_PYTHON_FOUND ${Boost_PYTHON-PY${boost_py_version}_FOUND})
+-
+-      STRING( REGEX MATCHALL "([0-9.]+).[0-9]+" has_more_version ${version} )
+-      if("${has_more_version}" STREQUAL "")
+-        break()
+-      endif()
+-    endwhile()
+-    if(NOT Boost_PYTHON_FOUND)
+-      find_package(Boost 1.46 COMPONENTS python)
+-    endif()
+   else()
+     # disable Python 3 search
+     find_package(PythonInterp 2.7)
+     find_package(PythonLibs 2.7)
+-    find_package(NumPy 1.7.1)
+-    find_package(Boost 1.46 COMPONENTS python)
+   endif()
+-  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON_FOUND)
++  find_package(NumPy 1.7.1)
++  find_package(Boost 1.46 REQUIRED COMPONENTS python@major@@minor@)
++  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON@major@@minor@_FOUND)
+     set(HAVE_PYTHON TRUE)
+     if(BUILD_python_layer)
+       list(APPEND Caffe_DEFINITIONS PRIVATE -DWITH_PYTHON_LAYER)

pkgs/applications/science/math/caffe/random-shuffle.patch

@@ -0,0 +1,67 @@
+From 11e585e52ab92bb9d7a995c5002cb55fbff687b2 Mon Sep 17 00:00:00 2001
+From: uku <hi@uku.moe>
+Date: Thu, 15 May 2025 11:10:50 +0200
+Subject: [PATCH] fix: remove usages of random_shuffle
+
+---
+ src/caffe/layers/hdf5_data_layer.cpp | 17 ++++++++++++-----
+ 1 file changed, 12 insertions(+), 5 deletions(-)
+
+diff --git a/src/caffe/layers/hdf5_data_layer.cpp b/src/caffe/layers/hdf5_data_layer.cpp
+index 00716a92..01213691 100644
+--- a/src/caffe/layers/hdf5_data_layer.cpp
++++ b/src/caffe/layers/hdf5_data_layer.cpp
+@@ -61,7 +61,9 @@ void HDF5DataLayer<Dtype>::LoadHDF5FileData(const char* filename) {
+ 
+   // Shuffle if needed.
+   if (this->layer_param_.hdf5_data_param().shuffle()) {
+-    std::random_shuffle(data_permutation_.begin(), data_permutation_.end());
++    std::random_device rand_device;
++    std::default_random_engine rand_engine(rand_device());
++    std::shuffle(data_permutation_.begin(), data_permutation_.end(), rand_engine);
+     DLOG(INFO) << "Successfully loaded " << hdf_blobs_[0]->shape(0)
+                << " rows (shuffled)";
+   } else {
+@@ -104,7 +106,9 @@ void HDF5DataLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
+ 
+   // Shuffle if needed.
+   if (this->layer_param_.hdf5_data_param().shuffle()) {
+-    std::random_shuffle(file_permutation_.begin(), file_permutation_.end());
++    std::random_device rand_device;
++    std::default_random_engine rand_engine(rand_device());
++    std::shuffle(file_permutation_.begin(), file_permutation_.end(), rand_engine);
+   }
+ 
+   // Load the first HDF5 file and initialize the line counter.
+@@ -137,14 +141,17 @@ bool HDF5DataLayer<Dtype>::Skip() {
+ 
+ template<typename Dtype>
+ void HDF5DataLayer<Dtype>::Next() {
++  std::random_device rand_device;
++  std::default_random_engine rand_engine(rand_device());
+   if (++current_row_ == hdf_blobs_[0]->shape(0)) {
+     if (num_files_ > 1) {
+       ++current_file_;
+       if (current_file_ == num_files_) {
+         current_file_ = 0;
+         if (this->layer_param_.hdf5_data_param().shuffle()) {
+-          std::random_shuffle(file_permutation_.begin(),
+-                              file_permutation_.end());
++          std::shuffle(file_permutation_.begin(),
++                              file_permutation_.end(),
++                              rand_engine);
+         }
+         DLOG(INFO) << "Looping around to first file.";
+       }
+@@ -153,7 +160,7 @@ void HDF5DataLayer<Dtype>::Next() {
+     }
+     current_row_ = 0;
+     if (this->layer_param_.hdf5_data_param().shuffle())
+-      std::random_shuffle(data_permutation_.begin(), data_permutation_.end());
++      std::shuffle(data_permutation_.begin(), data_permutation_.end(), rand_engine);
+   }
+   offset_++;
+ }
+-- 
+2.49.0
+

pkgs/applications/science/math/cemu-ti/default.nix

@@ -0,0 +1,51 @@
+{
+  stdenv,
+  lib,
+  fetchFromGitHub,
+  cmake,
+  pkg-config,
+  qt6,
+  libarchive,
+  libpng,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "CEmu";
+  version = "2.0";
+  src = fetchFromGitHub {
+    owner = "CE-Programming";
+    repo = "CEmu";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-fohsIJrvPDMmYHoPbmYQlKLMnj/B3XEBaerZYuqxvd8=";
+    fetchSubmodules = true;
+  };
+
+  sourceRoot = "${finalAttrs.src.name}/gui/qt/";
+
+  patches = [
+    # This is resolved upstream, but I can't apply the patch because the
+    # sourceRoot isn't set to the base of the Git repo.
+    ./resolve-ambiguous-constexpr.patch
+  ];
+
+  nativeBuildInputs = [
+    cmake
+    qt6.wrapQtAppsHook
+    pkg-config
+  ];
+
+  buildInputs = [
+    qt6.qtbase
+    libarchive
+    libpng
+  ];
+
+  meta = with lib; {
+    description = "Third-party TI-84 Plus CE / TI-83 Premium CE emulator, focused on developer features";
+    mainProgram = "CEmu";
+    homepage = "https://ce-programming.github.io/CEmu";
+    license = licenses.gpl3Plus;
+    maintainers = [ ];
+    platforms = lib.platforms.unix;
+  };
+})

pkgs/applications/science/math/cemu-ti/resolve-ambiguous-constexpr.patch

@@ -0,0 +1,13 @@
+diff --git a/mainwindow.cpp b/mainwindow.cpp
+index f03a743e..70c29a45 100644
+--- a/mainwindow.cpp
++++ b/mainwindow.cpp
+@@ -970,7 +970,7 @@ void MainWindow::showEvent(QShowEvent *e) {
+ DockWidget *MainWindow::redistributeFindDock(const QPoint &pos) {
+     QWidget *child = childAt(pos);
+     if (QTabBar *tabBar = findSelfOrParent<QTabBar *>(child)) {
+-        child = childAt({pos.x(), tabBar->mapTo(this, QPoint{}).y() - 1});
++        child = childAt(QPoint({pos.x(), tabBar->mapTo(this, QPoint{}).y() - 1}));
+     }
+     return findSelfOrParent<DockWidget *>(child);
+ }

pkgs/applications/science/math/cplex/default.nix

@@ -0,0 +1,183 @@
+{
+  lib,
+  stdenv,
+  autoPatchelfHook,
+  makeDesktopItem,
+  copyDesktopItems,
+  makeWrapper,
+  alsa-lib,
+  glib,
+  glib-networking,
+  gsettings-desktop-schemas,
+  gtk3,
+  libsecret,
+  openjdk,
+  sqlite,
+  unixODBC,
+  gtk2,
+  xorg,
+  glibcLocales,
+  releasePath ? null,
+}:
+
+# To use this package, you need to download your own cplex installer from IBM
+# and override the releasePath attribute to point to the location of the file.
+#
+# Note: cplex creates an individual build for each license which screws
+# somewhat with the use of functions like requireFile as the hash will be
+# different for every user.
+
+stdenv.mkDerivation rec {
+  pname = "cplex";
+  version = "22.11";
+
+  src =
+    if releasePath == null then
+      throw ''
+        This nix expression requires that the cplex installer is already
+        downloaded to your machine. Get it from IBM:
+        https://www.ibm.com/support/pages/downloading-ibm-ilog-cplex-optimization-studio-2211
+
+        Set `cplex.releasePath = /path/to/download;` in your
+        ~/.config/nixpkgs/config.nix for `nix-*` commands, or
+        `config.cplex.releasePath = /path/to/download;` in your
+        `configuration.nix` for NixOS.
+      ''
+    else
+      releasePath;
+
+  nativeBuildInputs = [
+    autoPatchelfHook
+    copyDesktopItems
+    makeWrapper
+    openjdk
+  ];
+  buildInputs = [
+    alsa-lib
+    gsettings-desktop-schemas
+    gtk2
+    sqlite
+    unixODBC
+    xorg.libXtst
+    glibcLocales
+  ];
+
+  unpackPhase = "cp $src $name";
+
+  postPatch = ''
+    sed -i -e 's|/usr/bin/tr"|tr"         |' $name
+  '';
+
+  buildPhase = ''
+    runHook preBuild
+
+     export JAVA_TOOL_OPTIONS=-Djdk.util.zip.disableZip64ExtraFieldValidation=true
+    sh $name LAX_VM "$(command -v java)" -i silent -DLICENSE_ACCEPTED=TRUE -DUSER_INSTALL_DIR=$out
+
+    runHook postBuild
+  '';
+
+  installPhase =
+    let
+      libraryPath = lib.makeLibraryPath [
+        stdenv.cc.cc
+        glib
+        gtk2
+        gtk3
+        libsecret
+        xorg.libXtst
+      ];
+    in
+    ''
+      runHook preInstall
+
+      mkdir -p $out/bin
+
+      for pgm in \
+        $out/opl/bin/x86-64_linux/oplrun \
+        $out/opl/bin/x86-64_linux/oplrunjava \
+        $out/opl/oplide/oplide \
+        $out/cplex/bin/x86-64_linux/cplex \
+        $out/cpoptimizer/bin/x86-64_linux/cpoptimizer
+      do
+        makeWrapperArgs=(
+          --set-default LOCALE_ARCHIVE ${glibcLocales}/lib/locale/locale-archive
+        )
+
+        if [[ "$pgm" = "$out/opl/oplide/oplide" ]]; then
+          makeWrapperArgs+=(
+            --prefix LD_LIBRARY_PATH : ${libraryPath}
+            --prefix GIO_EXTRA_MODULES : "${glib-networking}/lib/gio/modules"
+            --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH"
+          )
+        fi
+
+        makeWrapper "$pgm" "$out/bin/$(basename "$pgm")" "''${makeWrapperArgs[@]}"
+      done
+
+      mkdir -p $out/share/pixmaps
+      ln -s $out/opl/oplide/icon.xpm $out/share/pixmaps/oplide.xpm
+
+      mkdir -p $out/share/doc
+      mv $out/doc $out/share/doc/$name
+
+      mkdir -p $out/share/licenses
+      mv $out/license $out/share/licenses/$name
+
+      runHook postInstall
+    '';
+
+  desktopItems = [
+    (makeDesktopItem {
+      name = "oplide";
+      desktopName = "IBM ILOG CPLEX Optimization Studio";
+      genericName = "Optimization Software";
+      icon = "oplide";
+      exec = "oplide";
+      categories = [
+        "Development"
+        "IDE"
+        "Math"
+        "Science"
+      ];
+    })
+  ];
+
+  fixupPhase = ''
+    runHook preFixup
+
+    rm -r $out/Uninstall
+
+    bins=(
+      $out/bin/*
+      $out/cplex/bin/x86-64_linux/cplex
+      $out/cplex/bin/x86-64_linux/cplexamp
+      $out/cpoptimizer/bin/x86-64_linux/cpoptimizer
+      $out/opl/bin/x86-64_linux/oplrun
+      $out/opl/bin/x86-64_linux/oplrunjava
+      $out/opl/oplide/jre/bin/*
+      $out/opl/oplide/oplide
+    )
+
+    find $out -type d -exec chmod 755 {} \;
+    find $out -type f -exec chmod 644 {} \;
+    chmod +111 "''${bins[@]}"
+
+    runHook postFixup
+  '';
+
+  passthru = {
+    libArch = "x86-64_linux";
+    libSuffix = "${version}0";
+  };
+
+  meta = with lib; {
+    description = "Optimization solver for mathematical programming";
+    homepage = "https://www.ibm.com/be-en/marketplace/ibm-ilog-cplex";
+    mainProgram = "cplex";
+    sourceProvenance = with sourceTypes; [ binaryNativeCode ];
+    license = licenses.unfree;
+    platforms = [ "x86_64-linux" ];
+    maintainers = with maintainers; [ bfortz ];
+  };
+}

pkgs/applications/science/math/engauge-digitizer/default.nix

@@ -0,0 +1,76 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fftw,
+  libjpeg,
+  log4cpp,
+  openjpeg,
+  libpng12,
+  poppler,
+  qtbase,
+  qt5,
+  qmake,
+  wrapQtAppsHook,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "engauge-digitizer";
+  version = "12.2.2";
+
+  src = fetchFromGitHub {
+    owner = "markummitchell";
+    repo = "engauge-digitizer";
+    rev = "v${version}";
+    sha256 = "sha256-Wj9o3wWbtHsEi6LFH4xDpwVR9BwcWc472jJ/QFDQZvY=";
+  };
+
+  nativeBuildInputs = [
+    qmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    qtbase
+    qt5.qttools
+    poppler
+    libpng12
+    openjpeg
+    openjpeg.dev
+    log4cpp
+    libjpeg
+    fftw
+  ];
+
+  qmakeFlags = [
+    "CONFIG+=jpeg2000"
+    "CONFIG+=pdf"
+    "CONFIG+=log4cpp_null"
+  ];
+
+  POPPLER_INCLUDE = "${poppler.dev}/include/poppler/qt5";
+
+  POPPLER_LIB = "${poppler}/lib";
+
+  OPENJPEG_INCLUDE = "${openjpeg.dev}/include/${openjpeg.pname}-${lib.versions.majorMinor openjpeg.version}";
+
+  OPENJPEG_LIB = "${openjpeg}/lib";
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin
+    cp bin/engauge $out/bin/
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Engauge Digitizer is a tool for recovering graph data from an image file";
+    mainProgram = "engauge";
+    homepage = "https://markummitchell.github.io/engauge-digitizer";
+    license = with licenses; [ gpl2Only ];
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/applications/science/math/glsurf/default.nix

@@ -0,0 +1,79 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  ocamlPackages,
+  makeWrapper,
+  libGLU,
+  libGL,
+  libglut,
+  mpfr,
+  gmp,
+  pkgsHostTarget,
+}:
+
+let
+  inherit (pkgsHostTarget.targetPackages.stdenv) cc;
+in
+
+stdenv.mkDerivation rec {
+  pname = "glsurf";
+  version = "3.3.1";
+
+  src = fetchurl {
+    url = "https://raffalli.eu/~christophe/glsurf/glsurf-${version}.tar.gz";
+    sha256 = "0w8xxfnw2snflz8wdr2ca9f5g91w5vbyp1hwlx1v7vg83d4bwqs7";
+  };
+
+  nativeBuildInputs = [
+    makeWrapper
+  ]
+  ++ (with ocamlPackages; [
+    ocaml
+    findlib
+  ]);
+
+  buildInputs = [
+    libglut
+    libGL
+    libGLU
+    mpfr
+    gmp
+  ]
+  ++ (with ocamlPackages; [
+    camlp4
+    lablgl
+    camlimages
+    num
+  ]);
+
+  postPatch = ''
+    for f in callbacks*/Makefile; do
+      substituteInPlace "$f" --replace-warn "+camlp4" \
+        "${ocamlPackages.camlp4}/lib/ocaml/${ocamlPackages.ocaml.version}/site-lib/camlp4"
+    done
+
+    # Fatal error: exception Sys_error("Mutex.unlock: Operation not permitted")
+    sed -i "/gl_started/d" src/draw.ml* src/main.ml
+
+    # Compatibility with camlimages ≥ 5.0.5
+    substituteInPlace src/Makefile --replace-warn camlimages.all_formats camlimages.core
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin $out/share/doc/glsurf
+    cp ./src/glsurf.opt $out/bin/glsurf
+    cp ./doc/doc.pdf $out/share/doc/glsurf
+    cp -r ./examples $out/share/doc/glsurf
+
+    wrapProgram "$out/bin/glsurf" --set CC "${cc}/bin/${cc.targetPrefix}cc"
+  '';
+
+  meta = {
+    homepage = "https://raffalli.eu/~christophe/glsurf/";
+    description = "Program to draw implicit surfaces and curves";
+    mainProgram = "glsurf";
+    license = lib.licenses.gpl2Plus;
+    platforms = lib.platforms.all;
+  };
+}

pkgs/applications/science/math/labplot/default.nix

@@ -0,0 +1,128 @@
+{
+  lib,
+  stdenv,
+  fetchpatch,
+  fetchurl,
+  cmake,
+  extra-cmake-modules,
+  shared-mime-info,
+  wrapQtAppsHook,
+
+  qtbase,
+
+  karchive,
+  kcompletion,
+  kconfig,
+  kcoreaddons,
+  kcrash,
+  kdoctools,
+  ki18n,
+  kiconthemes,
+  kio,
+  knewstuff,
+  kparts,
+  ktextwidgets,
+  kxmlgui,
+  syntax-highlighting,
+
+  gsl,
+
+  poppler,
+  fftw,
+  hdf5,
+  netcdf,
+  cfitsio,
+  libcerf,
+  # cantor,
+  zlib,
+  lz4,
+  readstat,
+  matio,
+  qtserialport,
+  discount,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "labplot";
+  version = "2.10.1";
+
+  src = fetchurl {
+    url = "mirror://kde/stable/labplot/labplot-${version}.tar.xz";
+    sha256 = "sha256-K24YFRfPtuDf/3uJXz6yDHzjWeZzLThUXgdXya6i2u8=";
+  };
+
+  cmakeFlags = [
+    # Disable Vector BLF since it depends on DBC parser which fails to be detected
+    "-DENABLE_VECTOR_BLF=OFF"
+  ];
+
+  patches = [
+    (fetchpatch {
+      name = "matio-fix-compilation-for-latest-version-1.5.27.patch";
+      url = "https://github.com/KDE/labplot/commit/d6142308ffa492d9f7cea00fad3b4cd1babfd00c.patch";
+      hash = "sha256-qD5jj6GxBKbQezKJb1Z8HnwFO84WJBGQDawS/6o/wHE=";
+    })
+  ];
+
+  nativeBuildInputs = [
+    cmake
+    extra-cmake-modules
+    shared-mime-info
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    qtbase
+
+    karchive
+    kcompletion
+    kconfig
+    kcoreaddons
+    kcrash
+    kdoctools
+    ki18n
+    kiconthemes
+    kio
+    knewstuff
+    kparts
+    ktextwidgets
+    kxmlgui
+
+    syntax-highlighting
+    gsl
+
+    poppler
+    fftw
+    hdf5
+    netcdf
+    cfitsio
+    libcerf
+    # cantor
+    zlib
+    lz4
+    readstat
+    matio
+    qtserialport
+    discount
+  ];
+
+  meta = with lib; {
+    description = "Free, open source and cross-platform data visualization and analysis software accessible to everyone";
+    homepage = "https://labplot.kde.org";
+    license = with licenses; [
+      asl20
+      bsd3
+      cc-by-30
+      cc0
+      gpl2Only
+      gpl2Plus
+      gpl3Only
+      gpl3Plus
+      lgpl3Plus
+      mit
+    ];
+    maintainers = with maintainers; [ hqurve ];
+    mainProgram = "labplot2";
+    platforms = platforms.unix;
+  };
+}

pkgs/applications/science/math/lp_solve/0001-fix-cross-compilation.patch

@@ -0,0 +1,53 @@
+diff --git a/lp_solve/ccc b/lp_solve/ccc
+index bd5a938..7fe0427 100644
+--- a/lp_solve/ccc
++++ b/lp_solve/ccc
+@@ -1,6 +1,6 @@
+ :
+ src='../lp_MDO.c ../shared/commonlib.c ../colamd/colamd.c ../shared/mmio.c ../shared/myblas.c ../ini.c ../fortify.c ../lp_rlp.c ../lp_crash.c ../bfp/bfp_LUSOL/lp_LUSOL.c ../bfp/bfp_LUSOL/LUSOL/lusol.c ../lp_Hash.c ../lp_lib.c ../lp_wlp.c ../lp_matrix.c ../lp_mipbb.c ../lp_MPS.c ../lp_params.c ../lp_presolve.c ../lp_price.c ../lp_pricePSE.c ../lp_report.c ../lp_scale.c ../lp_simplex.c lp_solve.c ../lp_SOS.c ../lp_utils.c ../yacc_read.c'
+-c=cc
++c=$CC
+ 
+ MYTMP=`mktemp -d "${TMPDIR:-/tmp}"/lp_solve_XXXXXX`
+ 
+@@ -10,7 +10,7 @@ echo '#include <stdlib.h>'>>"$MYTMP"/platform.c
+ echo '#include <stdio.h>'>>"$MYTMP"/platform.c
+ echo 'main(){printf("ux%d", (int) (sizeof(void *)*8));}'>>"$MYTMP"/platform.c
+ $c "$MYTMP"/platform.c -o "$MYTMP"/platform
+-PLATFORM=`"$MYTMP"/platform`
++PLATFORM=`@emulator@ "$MYTMP"/platform`
+ rm "$MYTMP"/platform "$MYTMP"/platform.c >/dev/null 2>&1
+ 
+ mkdir bin bin/$PLATFORM >/dev/null 2>&1
+diff --git a/lpsolve55/ccc b/lpsolve55/ccc
+index 999f5f6..ff69b17 100644
+--- a/lpsolve55/ccc
++++ b/lpsolve55/ccc
+@@ -1,6 +1,6 @@
+ :
+ src='../lp_MDO.c ../shared/commonlib.c ../shared/mmio.c ../shared/myblas.c ../ini.c ../fortify.c ../colamd/colamd.c ../lp_rlp.c ../lp_crash.c ../bfp/bfp_LUSOL/lp_LUSOL.c ../bfp/bfp_LUSOL/LUSOL/lusol.c ../lp_Hash.c ../lp_lib.c ../lp_wlp.c ../lp_matrix.c ../lp_mipbb.c ../lp_MPS.c ../lp_params.c ../lp_presolve.c ../lp_price.c ../lp_pricePSE.c ../lp_report.c ../lp_scale.c ../lp_simplex.c ../lp_SOS.c ../lp_utils.c ../yacc_read.c'
+-c=cc
++c=$CC
+ 
+ MYTMP=`mktemp -d "${TMPDIR:-/tmp}"/lp_solve_XXXXXX`
+ 
+@@ -10,7 +10,7 @@ echo '#include <stdlib.h>'>>"$MYTMP"/platform.c
+ echo '#include <stdio.h>'>>"$MYTMP"/platform.c
+ echo 'main(){printf("ux%d", (int) (sizeof(void *)*8));}'>>"$MYTMP"/platform.c
+ $c "$MYTMP"/platform.c -o "$MYTMP"/platform
+-PLATFORM=`"$MYTMP"/platform`
++PLATFORM=`@emulator@ "$MYTMP"/platform`
+ rm "$MYTMP"/platform "$MYTMP"/platform.c >/dev/null 2>&1
+ 
+ mkdir bin bin/$PLATFORM >/dev/null 2>&1
+@@ -42,8 +42,8 @@ fi
+ opts='-O3'
+ 
+ $c -s -c -I.. -I../shared -I../bfp -I../bfp/bfp_LUSOL -I../bfp/bfp_LUSOL/LUSOL -I../colamd $opts $def $NOISNAN -DYY_NEVER_INTERACTIVE -DPARSER_LP -DINVERSE_ACTIVE=INVERSE_LUSOL -DRoleIsExternalInvEngine $src
+-ar rv bin/$PLATFORM/liblpsolve55.a `echo $src|sed s/[.]c/.o/g|sed 's/[^ ]*\///g'`
+-ranlib bin/$PLATFORM/liblpsolve55.a
++$AR rv bin/$PLATFORM/liblpsolve55.a `echo $src|sed s/[.]c/.o/g|sed 's/[^ ]*\///g'`
++$RANLIB bin/$PLATFORM/liblpsolve55.a
+ 
+ if [ "$so" != "" ]
+ then

pkgs/applications/science/math/lp_solve/default.nix

@@ -0,0 +1,83 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  cctools,
+  fixDarwinDylibNames,
+  autoSignDarwinBinariesHook,
+  replaceVars,
+  buildPackages,
+  binutils,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "lp_solve";
+  version = "5.5.2.11";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/project/lpsolve/lpsolve/${version}/lp_solve_${version}_source.tar.gz";
+    sha256 = "sha256-bUq/9cxqqpM66ObBeiJt8PwLZxxDj2lxXUHQn+gfkC8=";
+  };
+
+  nativeBuildInputs = [
+    binutils
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isDarwin [
+    cctools
+    fixDarwinDylibNames
+  ]
+  ++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
+    autoSignDarwinBinariesHook
+  ];
+
+  env = {
+    NIX_CFLAGS_COMPILE = "-Wno-error=implicit-int";
+  }
+  // lib.optionalAttrs (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isx86_64) {
+    NIX_LDFLAGS = "-headerpad_max_install_names";
+  };
+
+  dontConfigure = true;
+
+  patches = [
+    (replaceVars ./0001-fix-cross-compilation.patch {
+      emulator = "${stdenv.hostPlatform.emulator buildPackages}";
+    })
+  ];
+
+  buildPhase =
+    let
+      ccc = if stdenv.hostPlatform.isDarwin then "ccc.osx" else "ccc";
+    in
+    ''
+      runHook preBuild
+
+      (cd lpsolve55 && bash -x -e ${ccc})
+      (cd lp_solve  && bash -x -e ${ccc})
+
+      runHook postBuild
+    '';
+
+  installPhase = ''
+    runHook preInstall
+
+    install -d -m755 $out/bin $out/lib $out/include/lpsolve
+    install -m755 lp_solve/bin/*/lp_solve -t $out/bin
+    install -m644 lpsolve55/bin/*/liblpsolve* -t $out/lib
+    install -m644 lp_*.h -t $out/include/lpsolve
+
+    rm $out/lib/liblpsolve*.a
+    rm $out/include/lpsolve/lp_solveDLL.h  # A Windows header
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Mixed Integer Linear Programming (MILP) solver";
+    mainProgram = "lp_solve";
+    homepage = "https://lpsolve.sourceforge.net";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ smironov ];
+    platforms = platforms.unix;
+  };
+}

pkgs/applications/science/math/maxima/5.47.0-CVE-2024-34490.patch

@@ -0,0 +1,86 @@
+Based on upstream https://sourceforge.net/p/maxima/code/ci/51704ccb090f6f971b641e4e0b7c1c22c4828bf7/
+adjusted to apply to 5.47.0
+
+diff --git a/src/gnuplot_def.lisp b/src/gnuplot_def.lisp
+index 80c174bd5..6fdc8da6d 100644
+--- a/src/gnuplot_def.lisp
++++ b/src/gnuplot_def.lisp
+@@ -286,7 +286,7 @@
+                (format nil "set term postscript eps color solid lw 2 size 16.4 cm, 12.3 cm font \",24\" ~a" gstrings)))
+      (if (getf plot-options :gnuplot_out_file)
+          (setq out-file (getf plot-options :gnuplot_out_file))
+-         (setq out-file "maxplot.ps")))
++         (setq out-file (format nil "~a.ps" (random-name 16)))))
+     ((eq (getf plot-options :gnuplot_term) '$dumb)
+      (if (getf plot-options :gnuplot_dumb_term_command)
+          (setq terminal-command
+@@ -294,7 +294,7 @@
+          (setq terminal-command "set term dumb 79 22"))
+      (if (getf plot-options :gnuplot_out_file)
+          (setq out-file (getf plot-options :gnuplot_out_file))
+-         (setq out-file "maxplot.txt")))
++         (setq out-file (format nil "~a.txt" (random-name 16)))))
+     ((eq (getf plot-options :gnuplot_term) '$default)
+      (if (getf plot-options :gnuplot_default_term_command)
+          (setq terminal-command
+diff --git a/src/plot.lisp b/src/plot.lisp
+index fb2b3136b..8877f7025 100644
+--- a/src/plot.lisp
++++ b/src/plot.lisp
+@@ -1755,16 +1755,24 @@ plot3d([cos(y)*(10.0+6*cos(x)), sin(y)*(10.0+6*cos(x)),-6*sin(x)],
+ 
+ (defvar $xmaxima_plot_command "xmaxima")
+ 
++;; random-file-name
++;; Creates a random word of 'count' alphanumeric characters
++(defun random-name (count)
++  (let ((chars "0123456789abcdefghijklmnopqrstuvwxyz") (name ""))
++    (setf *random-state* (make-random-state t))
++    (dotimes (i count)
++      (setq name (format nil "~a~a" name (aref chars (random 36)))))
++    name))
++
+ (defun plot-set-gnuplot-script-file-name (options)
+   (let ((gnuplot-term (getf options :gnuplot_term))
+ 	(gnuplot-out-file (getf options :gnuplot_out_file)))
+     (if (and (find (getf options :plot_format) '($gnuplot_pipes $gnuplot))
+              (eq gnuplot-term '$default) gnuplot-out-file)
+ 	(plot-file-path gnuplot-out-file t options)
+-      (plot-file-path
+-       (format nil "maxout~d.~(~a~)"
+-	       (getpid)
+-               (ensure-string (getf options :plot_format))) nil options))))
++      (plot-file-path (format nil "~a.~a" (random-name 16)
++                              (ensure-string (getf options :plot_format)))
++                      nil options))))
+ 
+ (defun plot-temp-file0 (file &optional (preserve-file nil))
+   (let ((filename 
+@@ -2577,9 +2585,13 @@ plot2d ( x^2+y^2 = 1, [x, -2, 2], [y, -2 ,2]);
+        (format dest "}~%"))
+   (format dest "}~%"))
+ 
++; TODO: Check whether this function is still being used (villate 20240325)
+ (defun show-open-plot (ans file)
+   (cond ($show_openplot
+-         (with-open-file (st1 (plot-temp-file (format nil "maxout~d.xmaxima" (getpid))) :direction :output :if-exists :supersede)
++         (with-open-file
++          (st1 (plot-temp-file
++                (format nil "~a.xmaxima" (random-name 16)))
++               :direction :output :if-exists :supersede)
+            (princ  ans st1))
+          ($system (concatenate 'string *maxima-prefix* 
+                                (if (string= *autoconf-windows* "true") "\\bin\\" "/bin/") 
+diff --git a/src/xmaxima_def.lisp b/src/xmaxima_def.lisp
+index b6513b564..5a13b6141 100644
+--- a/src/xmaxima_def.lisp
++++ b/src/xmaxima_def.lisp
+@@ -431,7 +431,7 @@
+         (format $pstream "}~%"))))))
+ 
+ (defmethod plot-shipout ((plot xmaxima-plot) options &optional output-file)
+-  (let ((file (plot-file-path (format nil "maxout~d.xmaxima" (getpid)))))
++  (let ((file (plot-file-path (format nil "~a.xmaxima" (random-name 16)))))
+     (cond ($show_openplot
+            (with-open-file (fl
+                             #+sbcl (sb-ext:native-namestring file)

pkgs/applications/science/math/maxima/default.nix

@@ -0,0 +1,125 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  fetchpatch,
+  texinfo,
+  perl,
+  python3,
+  makeWrapper,
+  autoreconfHook,
+  rlwrap ? null,
+  tk ? null,
+  gnuplot ? null,
+  lisp-compiler,
+}:
+
+let
+  # Allow to remove some executables from the $PATH of the wrapped binary
+  searchPath = lib.makeBinPath (
+    lib.filter (x: x != null) [
+      lisp-compiler
+      rlwrap
+      tk
+      gnuplot
+    ]
+  );
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "maxima";
+  version = "5.47.0";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/maxima/maxima-${finalAttrs.version}.tar.gz";
+    sha256 = "sha256-kQQCGyT9U+jAOpg1CctC6TepJejAyFwzXXcJoU/UD3o=";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+    lisp-compiler
+    makeWrapper
+    python3
+    texinfo
+  ];
+
+  strictDeps = true;
+
+  nativeCheckInputs = [
+    gnuplot
+  ];
+
+  postPatch = ''
+    substituteInPlace doc/info/Makefile.am --replace "/usr/bin/env perl" "${perl}/bin/perl"
+  '';
+
+  postInstall = ''
+    # Make sure that maxima can find its runtime dependencies.
+    for prog in "$out/bin/"*; do
+      wrapProgram "$prog" --prefix PATH ":" "$out/bin:${searchPath}"
+    done
+    # Move documentation into the right place.
+    mkdir -p $out/share/doc
+    ln -s ../maxima/${finalAttrs.version}/doc $out/share/doc/maxima
+  ''
+  + (lib.optionalString (lisp-compiler.pname == "ecl") ''
+    cp src/binary-ecl/maxima.fas* "$out/lib/maxima/${finalAttrs.version}/binary-ecl/"
+  '');
+
+  patches = [
+    # fix path to info dir (see https://trac.sagemath.org/ticket/11348)
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/maxima/patches/infodir.patch";
+      sha256 = "09v64n60f7i6frzryrj0zd056lvdpms3ajky4f9p6kankhbiv21x";
+    })
+
+    # fix https://sourceforge.net/p/maxima/bugs/2596/
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/maxima/patches/matrixexp.patch";
+      sha256 = "06961hn66rhjijfvyym21h39wk98sfxhp051da6gz0n9byhwc6zg";
+    })
+
+    # undo https://sourceforge.net/p/maxima/code/ci/f5e9b0f7eb122c4e48ea9df144dd57221e5ea0ca
+    # see https://trac.sagemath.org/ticket/13364#comment:93
+    (fetchpatch {
+      url = "https://raw.githubusercontent.com/sagemath/sage/07d6c37d18811e2b377a9689790a7c5e24da16ba/build/pkgs/maxima/patches/undoing_true_false_printing_patch.patch";
+      sha256 = "0fvi3rcjv6743sqsbgdzazy9jb6r1p1yq63zyj9fx42wd1hgf7yx";
+    })
+
+    ./5.47.0-CVE-2024-34490.patch
+  ];
+
+  # The test suite is disabled since 5.42.2 because of the following issues:
+  #
+  #   Error(s) found:
+  #   /build/maxima-5.44.0/share/linearalgebra/rtest_matrixexp.mac problems:
+  #   (20 21 22)
+  #   Tests that were expected to fail but passed:
+  #   /build/maxima-5.44.0/share/vector/rtest_vect.mac problem:
+  #   (19)
+  #   3 tests failed out of 16,184 total tests.
+  #
+  # These failures don't look serious. It would be nice to fix them, but I
+  # don't know how and probably won't have the time to find out.
+  doCheck = false; # try to re-enable after next version update
+
+  enableParallelBuilding = true;
+
+  passthru = {
+    inherit lisp-compiler;
+  };
+
+  meta = with lib; {
+    description = "Computer algebra system";
+    homepage = "http://maxima.sourceforge.net";
+    license = licenses.gpl2Plus;
+
+    longDescription = ''
+      Maxima is a fairly complete computer algebra system written in
+      lisp with an emphasis on symbolic computation. It is based on
+      DOE-MACSYMA and licensed under the GPL. Its abilities include
+      symbolic integration, 3D plotting, and an ODE solver.
+    '';
+    maintainers = with maintainers; [ doronbehar ];
+    platforms = platforms.unix;
+  };
+})

pkgs/applications/science/math/mpsolve/default.nix

@@ -0,0 +1,51 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  autoreconfHook,
+  bison,
+  flex,
+  gitUpdater,
+  gmp,
+  gtk3,
+  pkg-config,
+  qtbase,
+  wrapQtAppsHook,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "mpsolve";
+  version = "3.2.2";
+
+  src = fetchFromGitHub {
+    owner = "robol";
+    repo = "MPSolve";
+    rev = "de7ebfc7afc4834a0c9f92a04be7abdf5943d446";
+    hash = "sha256-BGXvNxWUbto0yMIpEIxZ9wOYv9w0ev4OgVcniNYIKoU=";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+    bison
+    flex
+    pkg-config
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    gmp
+    gtk3
+    qtbase
+  ];
+
+  passthru.updateScript = gitUpdater { };
+
+  meta = {
+    homepage = "https://numpi.dm.unipi.it/scientific-computing-libraries/mpsolve/";
+    description = "Multiprecision Polynomial Solver";
+    license = lib.licenses.gpl3Plus;
+    maintainers = with lib.maintainers; [ kilianar ];
+    mainProgram = "mpsolve";
+    platforms = lib.platforms.linux;
+  };
+})

pkgs/applications/science/math/wolfram-engine/default.nix

@@ -0,0 +1,157 @@
+{
+  lib,
+  stdenv,
+  autoPatchelfHook,
+  requireFile,
+  alsa-lib,
+  dbus,
+  fontconfig,
+  freetype,
+  gcc,
+  glib,
+  installShellFiles,
+  libssh2,
+  ncurses,
+  opencv4,
+  openssl,
+  unixODBC,
+  xkeyboard_config,
+  xorg,
+  zlib,
+  libxml2,
+  libuuid,
+  lang ? "en",
+  libGL,
+  libGLU,
+  wrapQtAppsHook,
+}:
+
+let
+  l10n = import ./l10ns.nix {
+    lib = lib;
+    inherit requireFile lang;
+  };
+  dirName = "WolframEngine";
+in
+stdenv.mkDerivation rec {
+  inherit (l10n) version name src;
+
+  nativeBuildInputs = [
+    autoPatchelfHook
+    installShellFiles
+    wrapQtAppsHook
+  ];
+  dontWrapQtApps = true;
+
+  buildInputs = [
+    alsa-lib
+    dbus
+    fontconfig
+    freetype
+    gcc.cc
+    gcc.libc
+    glib
+    libssh2
+    ncurses
+    opencv4
+    openssl
+    (lib.getLib stdenv.cc.cc)
+    unixODBC
+    xkeyboard_config
+    libxml2
+    libuuid
+    zlib
+    libGL
+    libGLU
+  ]
+  ++ (with xorg; [
+    libX11
+    libXext
+    libXtst
+    libXi
+    libXmu
+    libXrender
+    libxcb
+    libXcursor
+    libXfixes
+    libXrandr
+    libICE
+    libSM
+  ]);
+
+  # some bundled libs are found through LD_LIBRARY_PATH
+  autoPatchelfIgnoreMissingDeps = true;
+
+  ldpath =
+    lib.makeLibraryPath buildInputs
+    + lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") (
+      ":" + lib.makeSearchPathOutput "lib" "lib64" buildInputs
+    );
+
+  unpackPhase = ''
+    # find offset from file
+    offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src)
+    dd if="$src" ibs=$offset skip=1 | tar -xf -
+    cd Unix
+  '';
+
+  installPhase = ''
+    cd Installer
+    sed -i -e 's/^PATH=/# PATH=/' -e 's/=`id -[ug]`/=0/' MathInstaller
+
+    # Installer wants to write default config in HOME
+    export HOME=$(mktemp -d)
+
+    # Fix the installation script
+    patchShebangs MathInstaller
+    substituteInPlace MathInstaller \
+      --replace-fail '`hostname`' "" \
+      --replace-fail "chgrp" "# chgrp" \
+      --replace-fail "chown" ": # chown"
+
+    # Install the desktop items
+    export XDG_DATA_HOME="$out/share"
+
+    ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/${dirName} -silent
+
+    # Fix library paths
+    cd $out/libexec/${dirName}/Executables
+    for path in MathKernel math mcc wolfram; do
+      makeWrapper $out/libexec/${dirName}/Executables/$path $out/bin/$path --set LD_LIBRARY_PATH "${zlib}/lib:${lib.getLib stdenv.cc.cc}/lib:${libssh2}/lib:\''${LD_LIBRARY_PATH}"
+    done
+
+    for path in WolframKernel wolframscript; do
+      makeWrapper $out/libexec/${dirName}/SystemFiles/Kernel/Binaries/Linux-x86-64/$path $out/bin/$path --set LD_LIBRARY_PATH "${zlib}/lib:${lib.getLib stdenv.cc.cc}/lib:${libssh2}/lib:\''${LD_LIBRARY_PATH}"
+    done
+
+    wrapQtApp "$out/libexec/${dirName}/SystemFiles/FrontEnd/Binaries/Linux-x86-64/WolframPlayer" \
+      --set LD_LIBRARY_PATH "${zlib}/lib:${lib.getLib stdenv.cc.cc}/lib:${libssh2}/lib:\''${LD_LIBRARY_PATH}" \
+      --set QT_XKB_CONFIG_ROOT "${xkeyboard_config}/share/X11/xkb"
+    if ! isELF "$out/libexec/${dirName}/SystemFiles/FrontEnd/Binaries/Linux-x86-64/WolframPlayer"; then
+      substituteInPlace $out/libexec/${dirName}/SystemFiles/FrontEnd/Binaries/Linux-x86-64/WolframPlayer \
+        --replace-fail "TopDirectory=" "TopDirectory=$out/libexec/${dirName} #";
+    fi
+
+    for path in WolframPlayer wolframplayer; do
+      makeWrapper $out/libexec/${dirName}/Executables/$path $out/bin/$path
+    done
+
+    # Install man pages
+    installManPage $out/libexec/${dirName}/SystemFiles/SystemDocumentation/Unix/*
+  '';
+
+  # This is primarily an IO bound build; there's little benefit to building remotely.
+  preferLocalBuild = true;
+
+  # Stripping causes the program to core dump.
+  dontStrip = true;
+
+  meta = with lib; {
+    description = "Wolfram Engine computational software system";
+    homepage = "https://www.wolfram.com/engine/";
+    sourceProvenance = with sourceTypes; [ binaryNativeCode ];
+    license = licenses.unfree;
+    maintainers = with maintainers; [ fbeffa ];
+    platforms = [ "x86_64-linux" ];
+  };
+}

pkgs/applications/science/math/wolfram-engine/l10ns.nix

@@ -0,0 +1,88 @@
+{
+  lib,
+  requireFile,
+  lang,
+  majorVersion ? null,
+}:
+
+let
+  allVersions =
+    lib.flip map
+      # N.B. Versions in this list should be ordered from newest to oldest.
+      [
+        {
+          version = "14.1.0";
+          lang = "en";
+          language = "English";
+          sha256 = "1kxdvm3i7nn3ws784y972h2br1n0y82kkkjvz7c5llssv6d3pgj8";
+          installer = "WolframEngine_14.1.0_LIN.sh";
+        }
+        {
+          version = "13.3.0";
+          lang = "en";
+          language = "English";
+          sha256 = "96106ac8ed6d0e221a68d846117615c14025320f927e5e0ed95b1965eda68e31";
+          installer = "WolframEngine_13.3.0_LINUX.sh";
+        }
+        {
+          version = "13.2.0";
+          lang = "en";
+          language = "English";
+          sha256 = "1xvg1n64iq52jxnk9y551m5iwkkz6cxzwyw28h8d0kq36aaiky24";
+          installer = "WolframEngine_13.2.0_LINUX.sh";
+        }
+        {
+          version = "13.1.0";
+          lang = "en";
+          language = "English";
+          sha256 = "1659kyp38a8xknic95pynx9fsgn96i8jn9lnk89pc8n6vydw1460";
+          installer = "WolframEngine_13.1.0_LINUX.sh";
+        }
+        {
+          version = "13.0.1";
+          lang = "en";
+          language = "English";
+          sha256 = "1rrxi7d51m02407k719fq829jzanh550wr810i22n3irhk8axqga";
+          installer = "WolframEngine_13.0.1_LINUX.sh";
+        }
+        {
+          version = "13.0.0";
+          lang = "en";
+          language = "English";
+          sha256 = "10cpwllz9plxz22iqdh6xgkxqphl9s9nq8ax16pafjll6j9kqy1q";
+          installer = "WolframEngine_13.0.0_LINUX.sh";
+        }
+      ]
+      (
+        {
+          version,
+          lang,
+          language,
+          sha256,
+          installer,
+        }:
+        {
+          inherit version lang;
+          name = "wolfram-engine-${version}" + lib.optionalString (lang != "en") "-${lang}";
+          src = requireFile {
+            name = installer;
+            message = ''
+              This nix expression requires that ${installer} is
+              already part of the store. Download the file from
+              https://www.wolfram.com/engine/ and add it to the nix store
+              with nix-store --add-fixed sha256 <FILE>.
+            '';
+            inherit sha256;
+          };
+        }
+      );
+  minVersion =
+    if majorVersion == null then
+      lib.elemAt (builtins.splitVersion (lib.elemAt allVersions 0).version) 0
+    else
+      majorVersion;
+  maxVersion = toString (1 + builtins.fromJSON minVersion);
+in
+lib.findFirst (
+  l: (l.lang == lang && l.version >= minVersion && l.version < maxVersion)
+) (throw "Version ${minVersion} in language ${lang} not supported") allVersions

pkgs/applications/science/math/wxmaxima/default.nix

@@ -0,0 +1,56 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  wrapGAppsHook3,
+  cmake,
+  gettext,
+  maxima,
+  wxGTK,
+  adwaita-icon-theme,
+  glib,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "wxmaxima";
+  version = "25.04.0";
+
+  src = fetchFromGitHub {
+    owner = "wxMaxima-developers";
+    repo = "wxmaxima";
+    rev = "Version-${finalAttrs.version}";
+    hash = "sha256-AEy2a8BahV1yH67RIjcsVipuo5eUZcQZxR3HygSYGlU=";
+  };
+
+  buildInputs = [
+    wxGTK
+    maxima
+    # So it won't embed svg files into headers.
+    adwaita-icon-theme
+    # So it won't crash under Sway.
+    glib
+  ];
+
+  nativeBuildInputs = [
+    wrapGAppsHook3
+    cmake
+    gettext
+  ];
+
+  cmakeFlags = [
+    "-DwxWidgets_LIBRARIES=${wxGTK}/lib"
+  ];
+
+  preConfigure = ''
+    gappsWrapperArgs+=(--prefix PATH ":" ${maxima}/bin)
+  '';
+
+  meta = with lib; {
+    description = "Cross platform GUI for the computer algebra system Maxima";
+    mainProgram = "wxmaxima";
+    license = licenses.gpl2;
+    homepage = "https://wxmaxima-developers.github.io/wxmaxima/";
+    maintainers = with maintainers; [ doronbehar ];
+    platforms = platforms.linux;
+  };
+})

pkgs/applications/science/math/yacas/default.nix

@@ -0,0 +1,90 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  cmake,
+  perl,
+  enableGui ? false,
+  qtbase,
+  wrapQtAppsHook,
+  qtwebengine,
+  enableJupyter ? true,
+  boost,
+  jsoncpp,
+  openssl,
+  zmqpp,
+  enableJava ? false,
+  openjdk,
+  gtest,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "yacas";
+  version = "1.9.1";
+
+  src = fetchFromGitHub {
+    owner = "grzegorzmazur";
+    repo = "yacas";
+    rev = "v${version}";
+    sha256 = "0dqgqvsb6ggr8jb3ngf0jwfkn6xwj2knhmvqyzx3amc74yd3ckqx";
+  };
+
+  hardeningDisable = [ "format" ];
+
+  cmakeFlags = [
+    "-DENABLE_CYACAS_GUI=${if enableGui then "ON" else "OFF"}"
+    "-DENABLE_CYACAS_KERNEL=${if enableJupyter then "ON" else "OFF"}"
+    "-DENABLE_JYACAS=${if enableJava then "ON" else "OFF"}"
+    "-DENABLE_CYACAS_UNIT_TESTS=ON"
+  ];
+  patches = [
+    # upstream issue: https://github.com/grzegorzmazur/yacas/issues/340
+    # Upstream patch which doesn't apply on 1.9.1 is:
+    # https://github.com/grzegorzmazur/yacas/pull/342
+    ./jsoncpp-fix-include.patch
+    # Fixes testing - https://github.com/grzegorzmazur/yacas/issues/339
+    # PR: https://github.com/grzegorzmazur/yacas/pull/343
+    (fetchpatch {
+      url = "https://github.com/grzegorzmazur/yacas/commit/8bc22d517ecfdde3ac94800dc8506f5405564d48.patch";
+      sha256 = "sha256-aPO5T8iYNkGtF8j12YxNJyUPJJPKrXje1DmfCPt317A=";
+    })
+  ];
+  preCheck = ''
+    patchShebangs ../tests/test-yacas
+  '';
+  nativeCheckInputs = [
+    gtest
+  ];
+  doCheck = true;
+
+  nativeBuildInputs = [
+    cmake
+    # Perl is only for the documentation
+    perl
+  ]
+  ++ lib.optionals enableJava [
+    openjdk
+  ];
+  buildInputs = [
+  ]
+  ++ lib.optionals enableGui [
+    qtbase
+    wrapQtAppsHook
+    qtwebengine
+  ]
+  ++ lib.optionals enableJupyter [
+    boost
+    jsoncpp
+    openssl
+    zmqpp
+  ];
+
+  meta = {
+    description = "Easy to use, general purpose Computer Algebra System, optionally with GUI";
+    homepage = "http://www.yacas.org/";
+    license = lib.licenses.gpl2Plus;
+    maintainers = [ ];
+    platforms = with lib.platforms; linux;
+  };
+}

pkgs/applications/science/math/yacas/jsoncpp-fix-include.patch

@@ -0,0 +1,63 @@
+diff --git i/cyacas/yacas-kernel/CMakeLists.txt w/cyacas/yacas-kernel/CMakeLists.txt
+index fe1600aa..dcc329f8 100644
+--- i/cyacas/yacas-kernel/CMakeLists.txt
++++ w/cyacas/yacas-kernel/CMakeLists.txt
+@@ -22,8 +22,9 @@ find_library (ZEROMQ_LIBRARY NAMES zmq)
+ find_path (ZMQPP_INCLUDE_DIR zmqpp.hpp)
+ find_library (ZMQPP_LIBRARY NAMES zmqpp)
+ 
+-find_path (JSONCPP_INCLUDE_DIR json.h)
+-find_library (JSONCPP_LIBRARY NAMES jsoncpp)
++# https://github.com/open-source-parsers/jsoncpp/wiki/Building#another-approach-for-cmake
++find_package(jsoncpp REQUIRED)
++get_target_property(JSON_INC_PATH jsoncpp_lib INTERFACE_INCLUDE_DIRECTORIES)
+ 
+ find_package (OpenSSL)
+ find_package (Boost REQUIRED date_time filesystem)
+@@ -31,6 +32,6 @@ find_package (Boost REQUIRED date_time filesystem)
+ include_directories (include)
+ 
+ add_executable (yacas-kernel src/main.cpp src/yacas_kernel.cpp src/yacas_engine.cpp src/hmac_sha256.cpp src/base64.cpp)
+-target_link_libraries (yacas-kernel libyacas ${ZMQPP_LIBRARY} ${ZEROMQ_LIBRARY} ${JSONCPP_LIBRARY} ${OPENSSL_CRYPTO_LIBRARY} ${Boost_LIBRARIES} pthread ${CMAKE_DL_LIBS})
++target_link_libraries (yacas-kernel libyacas ${ZMQPP_LIBRARY} ${ZEROMQ_LIBRARY} jsoncpp_lib ${OPENSSL_CRYPTO_LIBRARY} ${Boost_LIBRARIES} pthread ${CMAKE_DL_LIBS})
+ 
+ install (TARGETS yacas-kernel DESTINATION ${CMAKE_INSTALL_BINDIR})
+diff --git i/cyacas/yacas-kernel/include/yacas_kernel.hpp w/cyacas/yacas-kernel/include/yacas_kernel.hpp
+index 91d36ac0..d12f905c 100644
+--- i/cyacas/yacas-kernel/include/yacas_kernel.hpp
++++ w/cyacas/yacas-kernel/include/yacas_kernel.hpp
+@@ -29,7 +29,7 @@
+ #include "yacas_engine.hpp"
+ 
+ #include <boost/uuid/random_generator.hpp>
+-#include <jsoncpp/json/json.h>
++#include <json/json.h>
+ #include <zmqpp/zmqpp.hpp>
+ 
+ #include <map>
+diff --git i/cyacas/yacas-kernel/src/main.cpp w/cyacas/yacas-kernel/src/main.cpp
+index c31f17f2..832e9128 100644
+--- i/cyacas/yacas-kernel/src/main.cpp
++++ w/cyacas/yacas-kernel/src/main.cpp
+@@ -24,7 +24,7 @@
+ 
+ #include "yacas_kernel.hpp"
+ 
+-#include <jsoncpp/json/json.h>
++#include <json/json.h>
+ 
+ #include <boost/dll/runtime_symbol_info.hpp>
+ 
+diff --git i/cyacas/yacas-kernel/src/yacas_engine.cpp w/cyacas/yacas-kernel/src/yacas_engine.cpp
+index 6ed60ca3..18e9b3fd 100644
+--- i/cyacas/yacas-kernel/src/yacas_engine.cpp
++++ w/cyacas/yacas-kernel/src/yacas_engine.cpp
+@@ -22,7 +22,7 @@
+  * Created on November 7, 2015, 12:52 PM
+  */
+ 
+-#include <jsoncpp/json/writer.h>
++#include <json/writer.h>
+ 
+ #include "yacas_engine.hpp"
+ 

pkgs/applications/science/misc/convertall/default.nix

@@ -0,0 +1,28 @@
+{
+  lib,
+  flutter329,
+  fetchFromGitHub,
+}:
+
+flutter329.buildFlutterApplication rec {
+  pname = "convertall";
+  version = "1.0.2";
+
+  src = fetchFromGitHub {
+    owner = "doug-101";
+    repo = "ConvertAll";
+    tag = "v${version}";
+    hash = "sha256-esc2xhL0Jx5SaqM0GnnVzdtnSN9bX8zln66We/2RqoA=";
+  };
+
+  pubspecLock = lib.importJSON ./pubspec.lock.json;
+
+  meta = {
+    homepage = "https://convertall.bellz.org";
+    description = "Graphical unit converter";
+    mainProgram = "convertall";
+    license = lib.licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ orivej ];
+    platforms = lib.platforms.linux;
+  };
+}

pkgs/applications/science/misc/convertall/pubspec.lock.json

@@ -0,0 +1,792 @@
+{
+  "packages": {
+    "archive": {
+      "dependency": "transitive",
+      "description": {
+        "name": "archive",
+        "sha256": "a7f37ff061d7abc2fcf213554b9dcaca713c5853afa5c065c44888bc9ccaf813",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "4.0.6"
+    },
+    "args": {
+      "dependency": "transitive",
+      "description": {
+        "name": "args",
+        "sha256": "d0481093c50b1da8910eb0bb301626d4d8eb7284aa739614d2b394ee09e3ea04",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.7.0"
+    },
+    "async": {
+      "dependency": "direct main",
+      "description": {
+        "name": "async",
+        "sha256": "d2872f9c19731c2e5f10444b14686eb7cc85c76274bd6c16e1816bff9a3bab63",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.12.0"
+    },
+    "boolean_selector": {
+      "dependency": "transitive",
+      "description": {
+        "name": "boolean_selector",
+        "sha256": "8aab1771e1243a5063b8b0ff68042d67334e3feab9e95b9490f9a6ebf73b42ea",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.1.2"
+    },
+    "characters": {
+      "dependency": "transitive",
+      "description": {
+        "name": "characters",
+        "sha256": "f71061c654a3380576a52b451dd5532377954cf9dbd272a78fc8479606670803",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.4.0"
+    },
+    "checked_yaml": {
+      "dependency": "transitive",
+      "description": {
+        "name": "checked_yaml",
+        "sha256": "feb6bed21949061731a7a75fc5d2aa727cf160b91af9a3e464c5e3a32e28b5ff",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.0.3"
+    },
+    "cli_util": {
+      "dependency": "transitive",
+      "description": {
+        "name": "cli_util",
+        "sha256": "ff6785f7e9e3c38ac98b2fb035701789de90154024a75b6cb926445e83197d1c",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.4.2"
+    },
+    "clock": {
+      "dependency": "transitive",
+      "description": {
+        "name": "clock",
+        "sha256": "fddb70d9b5277016c77a80201021d40a2247104d9f4aa7bab7157b7e3f05b84b",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.1.2"
+    },
+    "collection": {
+      "dependency": "transitive",
+      "description": {
+        "name": "collection",
+        "sha256": "2f5709ae4d3d59dd8f7cd309b4e023046b57d8a6c82130785d2b0e5868084e76",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.19.1"
+    },
+    "crypto": {
+      "dependency": "transitive",
+      "description": {
+        "name": "crypto",
+        "sha256": "1e445881f28f22d6140f181e07737b22f1e099a5e1ff94b0af2f9e4a463f4855",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.0.6"
+    },
+    "cupertino_icons": {
+      "dependency": "transitive",
+      "description": {
+        "name": "cupertino_icons",
+        "sha256": "ba631d1c7f7bef6b729a622b7b752645a2d076dba9976925b8f25725a30e1ee6",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.0.8"
+    },
+    "decimal": {
+      "dependency": "direct main",
+      "description": {
+        "name": "decimal",
+        "sha256": "24a261d5d5c87e86c7651c417a5dbdf8bcd7080dd592533910e8d0505a279f21",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.3.3"
+    },
+    "eval_ex": {
+      "dependency": "direct main",
+      "description": {
+        "name": "eval_ex",
+        "sha256": "3f8853d996ee41955f2232ad3730e95698fb1040d03f6ebc6ab01f1c2bc3be53",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.1.8"
+    },
+    "fake_async": {
+      "dependency": "transitive",
+      "description": {
+        "name": "fake_async",
+        "sha256": "6a95e56b2449df2273fd8c45a662d6947ce1ebb7aafe80e550a3f68297f3cacc",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.3.2"
+    },
+    "ffi": {
+      "dependency": "transitive",
+      "description": {
+        "name": "ffi",
+        "sha256": "289279317b4b16eb2bb7e271abccd4bf84ec9bdcbe999e278a94b804f5630418",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.1.4"
+    },
+    "file": {
+      "dependency": "transitive",
+      "description": {
+        "name": "file",
+        "sha256": "a3b4f84adafef897088c160faf7dfffb7696046cb13ae90b508c2cbc95d3b8d4",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "7.0.1"
+    },
+    "flutter": {
+      "dependency": "direct main",
+      "description": "flutter",
+      "source": "sdk",
+      "version": "0.0.0"
+    },
+    "flutter_launcher_icons": {
+      "dependency": "direct dev",
+      "description": {
+        "name": "flutter_launcher_icons",
+        "sha256": "bfa04787c85d80ecb3f8777bde5fc10c3de809240c48fa061a2c2bf15ea5211c",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.14.3"
+    },
+    "flutter_lints": {
+      "dependency": "direct dev",
+      "description": {
+        "name": "flutter_lints",
+        "sha256": "9e8c3858111da373efc5aa341de011d9bd23e2c5c5e0c62bccf32438e192d7b1",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.0.2"
+    },
+    "flutter_markdown_selectionarea": {
+      "dependency": "direct main",
+      "description": {
+        "name": "flutter_markdown_selectionarea",
+        "sha256": "d4bc27e70a5c40ebdab23a4b81f75d53696a214d4d1f13c12045b38a0ddc58a2",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.6.17+1"
+    },
+    "flutter_spinbox": {
+      "dependency": "direct main",
+      "description": {
+        "name": "flutter_spinbox",
+        "sha256": "38d8c1a3a39f0fa72823d4470785f5e165f2deb53531ca7803b54ba45e4dbd46",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.13.1"
+    },
+    "flutter_test": {
+      "dependency": "direct dev",
+      "description": "flutter",
+      "source": "sdk",
+      "version": "0.0.0"
+    },
+    "flutter_web_plugins": {
+      "dependency": "transitive",
+      "description": "flutter",
+      "source": "sdk",
+      "version": "0.0.0"
+    },
+    "http": {
+      "dependency": "transitive",
+      "description": {
+        "name": "http",
+        "sha256": "fe7ab022b76f3034adc518fb6ea04a82387620e19977665ea18d30a1cf43442f",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.3.0"
+    },
+    "http_parser": {
+      "dependency": "transitive",
+      "description": {
+        "name": "http_parser",
+        "sha256": "178d74305e7866013777bab2c3d8726205dc5a4dd935297175b19a23a2e66571",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "4.1.2"
+    },
+    "image": {
+      "dependency": "transitive",
+      "description": {
+        "name": "image",
+        "sha256": "4e973fcf4caae1a4be2fa0a13157aa38a8f9cb049db6529aa00b4d71abc4d928",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "4.5.4"
+    },
+    "json_annotation": {
+      "dependency": "transitive",
+      "description": {
+        "name": "json_annotation",
+        "sha256": "1ce844379ca14835a50d2f019a3099f419082cfdd231cd86a142af94dd5c6bb1",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "4.9.0"
+    },
+    "leak_tracker": {
+      "dependency": "transitive",
+      "description": {
+        "name": "leak_tracker",
+        "sha256": "c35baad643ba394b40aac41080300150a4f08fd0fd6a10378f8f7c6bc161acec",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "10.0.8"
+    },
+    "leak_tracker_flutter_testing": {
+      "dependency": "transitive",
+      "description": {
+        "name": "leak_tracker_flutter_testing",
+        "sha256": "f8b613e7e6a13ec79cfdc0e97638fddb3ab848452eff057653abd3edba760573",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.0.9"
+    },
+    "leak_tracker_testing": {
+      "dependency": "transitive",
+      "description": {
+        "name": "leak_tracker_testing",
+        "sha256": "6ba465d5d76e67ddf503e1161d1f4a6bc42306f9d66ca1e8f079a47290fb06d3",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.0.1"
+    },
+    "lints": {
+      "dependency": "transitive",
+      "description": {
+        "name": "lints",
+        "sha256": "cbf8d4b858bb0134ef3ef87841abdf8d63bfc255c266b7bf6b39daa1085c4290",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.0.0"
+    },
+    "markdown": {
+      "dependency": "transitive",
+      "description": {
+        "name": "markdown",
+        "sha256": "935e23e1ff3bc02d390bad4d4be001208ee92cc217cb5b5a6c19bc14aaa318c1",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "7.3.0"
+    },
+    "matcher": {
+      "dependency": "transitive",
+      "description": {
+        "name": "matcher",
+        "sha256": "dc58c723c3c24bf8d3e2d3ad3f2f9d7bd9cf43ec6feaa64181775e60190153f2",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.12.17"
+    },
+    "material_color_utilities": {
+      "dependency": "transitive",
+      "description": {
+        "name": "material_color_utilities",
+        "sha256": "f7142bb1154231d7ea5f96bc7bde4bda2a0945d2806bb11670e30b850d56bdec",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.11.1"
+    },
+    "meta": {
+      "dependency": "transitive",
+      "description": {
+        "name": "meta",
+        "sha256": "e3641ec5d63ebf0d9b41bd43201a66e3fc79a65db5f61fc181f04cd27aab950c",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.16.0"
+    },
+    "nested": {
+      "dependency": "transitive",
+      "description": {
+        "name": "nested",
+        "sha256": "03bac4c528c64c95c722ec99280375a6f2fc708eec17c7b3f07253b626cd2a20",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.0.0"
+    },
+    "package_info_plus": {
+      "dependency": "direct main",
+      "description": {
+        "name": "package_info_plus",
+        "sha256": "cb44f49b6e690fa766f023d5b22cac6b9affe741dd792b6ac7ad4fabe0d7b097",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "6.0.0"
+    },
+    "package_info_plus_platform_interface": {
+      "dependency": "transitive",
+      "description": {
+        "name": "package_info_plus_platform_interface",
+        "sha256": "9bc8ba46813a4cc42c66ab781470711781940780fd8beddd0c3da62506d3a6c6",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.0.1"
+    },
+    "path": {
+      "dependency": "transitive",
+      "description": {
+        "name": "path",
+        "sha256": "75cca69d1490965be98c73ceaea117e8a04dd21217b37b292c9ddbec0d955bc5",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.9.1"
+    },
+    "path_provider_linux": {
+      "dependency": "transitive",
+      "description": {
+        "name": "path_provider_linux",
+        "sha256": "f7a1fe3a634fe7734c8d3f2766ad746ae2a2884abe22e241a8b301bf5cac3279",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.2.1"
+    },
+    "path_provider_platform_interface": {
+      "dependency": "transitive",
+      "description": {
+        "name": "path_provider_platform_interface",
+        "sha256": "88f5779f72ba699763fa3a3b06aa4bf6de76c8e5de842cf6f29e2e06476c2334",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.1.2"
+    },
+    "path_provider_windows": {
+      "dependency": "transitive",
+      "description": {
+        "name": "path_provider_windows",
+        "sha256": "bd6f00dbd873bfb70d0761682da2b3a2c2fccc2b9e84c495821639601d81afe7",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.3.0"
+    },
+    "petitparser": {
+      "dependency": "transitive",
+      "description": {
+        "name": "petitparser",
+        "sha256": "07c8f0b1913bcde1ff0d26e57ace2f3012ccbf2b204e070290dad3bb22797646",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "6.1.0"
+    },
+    "platform": {
+      "dependency": "transitive",
+      "description": {
+        "name": "platform",
+        "sha256": "5d6b1b0036a5f331ebc77c850ebc8506cbc1e9416c27e59b439f917a902a4984",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.1.6"
+    },
+    "plugin_platform_interface": {
+      "dependency": "transitive",
+      "description": {
+        "name": "plugin_platform_interface",
+        "sha256": "4820fbfdb9478b1ebae27888254d445073732dae3d6ea81f0b7e06d5dedc3f02",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.1.8"
+    },
+    "posix": {
+      "dependency": "transitive",
+      "description": {
+        "name": "posix",
+        "sha256": "f0d7856b6ca1887cfa6d1d394056a296ae33489db914e365e2044fdada449e62",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "6.0.2"
+    },
+    "provider": {
+      "dependency": "direct main",
+      "description": {
+        "name": "provider",
+        "sha256": "489024f942069c2920c844ee18bb3d467c69e48955a4f32d1677f71be103e310",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "6.1.4"
+    },
+    "rational": {
+      "dependency": "transitive",
+      "description": {
+        "name": "rational",
+        "sha256": "cb808fb6f1a839e6fc5f7d8cb3b0a10e1db48b3be102de73938c627f0b636336",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.2.3"
+    },
+    "screen_retriever": {
+      "dependency": "transitive",
+      "description": {
+        "name": "screen_retriever",
+        "sha256": "6ee02c8a1158e6dae7ca430da79436e3b1c9563c8cf02f524af997c201ac2b90",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.1.9"
+    },
+    "shared_preferences": {
+      "dependency": "direct main",
+      "description": {
+        "name": "shared_preferences",
+        "sha256": "6e8bf70b7fef813df4e9a36f658ac46d107db4b4cfe1048b477d4e453a8159f5",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.5.3"
+    },
+    "shared_preferences_android": {
+      "dependency": "transitive",
+      "description": {
+        "name": "shared_preferences_android",
+        "sha256": "20cbd561f743a342c76c151d6ddb93a9ce6005751e7aa458baad3858bfbfb6ac",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.4.10"
+    },
+    "shared_preferences_foundation": {
+      "dependency": "transitive",
+      "description": {
+        "name": "shared_preferences_foundation",
+        "sha256": "6a52cfcdaeac77cad8c97b539ff688ccfc458c007b4db12be584fbe5c0e49e03",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.5.4"
+    },
+    "shared_preferences_linux": {
+      "dependency": "transitive",
+      "description": {
+        "name": "shared_preferences_linux",
+        "sha256": "580abfd40f415611503cae30adf626e6656dfb2f0cee8f465ece7b6defb40f2f",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.4.1"
+    },
+    "shared_preferences_platform_interface": {
+      "dependency": "transitive",
+      "description": {
+        "name": "shared_preferences_platform_interface",
+        "sha256": "57cbf196c486bc2cf1f02b85784932c6094376284b3ad5779d1b1c6c6a816b80",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.4.1"
+    },
+    "shared_preferences_web": {
+      "dependency": "transitive",
+      "description": {
+        "name": "shared_preferences_web",
+        "sha256": "c49bd060261c9a3f0ff445892695d6212ff603ef3115edbb448509d407600019",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.4.3"
+    },
+    "shared_preferences_windows": {
+      "dependency": "transitive",
+      "description": {
+        "name": "shared_preferences_windows",
+        "sha256": "94ef0f72b2d71bc3e700e025db3710911bd51a71cefb65cc609dd0d9a982e3c1",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.4.1"
+    },
+    "sky_engine": {
+      "dependency": "transitive",
+      "description": "flutter",
+      "source": "sdk",
+      "version": "0.0.0"
+    },
+    "source_span": {
+      "dependency": "transitive",
+      "description": {
+        "name": "source_span",
+        "sha256": "254ee5351d6cb365c859e20ee823c3bb479bf4a293c22d17a9f1bf144ce86f7c",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.10.1"
+    },
+    "stack_trace": {
+      "dependency": "transitive",
+      "description": {
+        "name": "stack_trace",
+        "sha256": "8b27215b45d22309b5cddda1aa2b19bdfec9df0e765f2de506401c071d38d1b1",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.12.1"
+    },
+    "stream_channel": {
+      "dependency": "transitive",
+      "description": {
+        "name": "stream_channel",
+        "sha256": "969e04c80b8bcdf826f8f16579c7b14d780458bd97f56d107d3950fdbeef059d",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.1.4"
+    },
+    "string_scanner": {
+      "dependency": "transitive",
+      "description": {
+        "name": "string_scanner",
+        "sha256": "921cd31725b72fe181906c6a94d987c78e3b98c2e205b397ea399d4054872b43",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.4.1"
+    },
+    "term_glyph": {
+      "dependency": "transitive",
+      "description": {
+        "name": "term_glyph",
+        "sha256": "7f554798625ea768a7518313e58f83891c7f5024f88e46e7182a4558850a4b8e",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.2.2"
+    },
+    "test_api": {
+      "dependency": "transitive",
+      "description": {
+        "name": "test_api",
+        "sha256": "fb31f383e2ee25fbbfe06b40fe21e1e458d14080e3c67e7ba0acfde4df4e0bbd",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.7.4"
+    },
+    "typed_data": {
+      "dependency": "transitive",
+      "description": {
+        "name": "typed_data",
+        "sha256": "f9049c039ebfeb4cf7a7104a675823cd72dba8297f264b6637062516699fa006",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.4.0"
+    },
+    "url_launcher": {
+      "dependency": "direct main",
+      "description": {
+        "name": "url_launcher",
+        "sha256": "9d06212b1362abc2f0f0d78e6f09f726608c74e3b9462e8368bb03314aa8d603",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "6.3.1"
+    },
+    "url_launcher_android": {
+      "dependency": "transitive",
+      "description": {
+        "name": "url_launcher_android",
+        "sha256": "8582d7f6fe14d2652b4c45c9b6c14c0b678c2af2d083a11b604caeba51930d79",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "6.3.16"
+    },
+    "url_launcher_ios": {
+      "dependency": "transitive",
+      "description": {
+        "name": "url_launcher_ios",
+        "sha256": "7f2022359d4c099eea7df3fdf739f7d3d3b9faf3166fb1dd390775176e0b76cb",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "6.3.3"
+    },
+    "url_launcher_linux": {
+      "dependency": "transitive",
+      "description": {
+        "name": "url_launcher_linux",
+        "sha256": "4e9ba368772369e3e08f231d2301b4ef72b9ff87c31192ef471b380ef29a4935",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.2.1"
+    },
+    "url_launcher_macos": {
+      "dependency": "transitive",
+      "description": {
+        "name": "url_launcher_macos",
+        "sha256": "17ba2000b847f334f16626a574c702b196723af2a289e7a93ffcb79acff855c2",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.2.2"
+    },
+    "url_launcher_platform_interface": {
+      "dependency": "transitive",
+      "description": {
+        "name": "url_launcher_platform_interface",
+        "sha256": "552f8a1e663569be95a8190206a38187b531910283c3e982193e4f2733f01029",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.3.2"
+    },
+    "url_launcher_web": {
+      "dependency": "transitive",
+      "description": {
+        "name": "url_launcher_web",
+        "sha256": "3ba963161bd0fe395917ba881d320b9c4f6dd3c4a233da62ab18a5025c85f1e9",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.4.0"
+    },
+    "url_launcher_windows": {
+      "dependency": "transitive",
+      "description": {
+        "name": "url_launcher_windows",
+        "sha256": "3284b6d2ac454cf34f114e1d3319866fdd1e19cdc329999057e44ffe936cfa77",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.1.4"
+    },
+    "vector_math": {
+      "dependency": "transitive",
+      "description": {
+        "name": "vector_math",
+        "sha256": "80b3257d1492ce4d091729e3a67a60407d227c27241d6927be0130c98e741803",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "2.1.4"
+    },
+    "vm_service": {
+      "dependency": "transitive",
+      "description": {
+        "name": "vm_service",
+        "sha256": "0968250880a6c5fe7edc067ed0a13d4bae1577fe2771dcf3010d52c4a9d3ca14",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "14.3.1"
+    },
+    "web": {
+      "dependency": "transitive",
+      "description": {
+        "name": "web",
+        "sha256": "97da13628db363c635202ad97068d47c5b8aa555808e7a9411963c533b449b27",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.5.1"
+    },
+    "win32": {
+      "dependency": "transitive",
+      "description": {
+        "name": "win32",
+        "sha256": "dc6ecaa00a7c708e5b4d10ee7bec8c270e9276dfcab1783f57e9962d7884305f",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "5.12.0"
+    },
+    "window_manager": {
+      "dependency": "direct main",
+      "description": {
+        "name": "window_manager",
+        "sha256": "8699323b30da4cdbe2aa2e7c9de567a6abd8a97d9a5c850a3c86dcd0b34bbfbf",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "0.3.9"
+    },
+    "xdg_directories": {
+      "dependency": "transitive",
+      "description": {
+        "name": "xdg_directories",
+        "sha256": "7a3f37b05d989967cdddcbb571f1ea834867ae2faa29725fd085180e0883aa15",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "1.1.0"
+    },
+    "xml": {
+      "dependency": "transitive",
+      "description": {
+        "name": "xml",
+        "sha256": "b015a8ad1c488f66851d762d3090a21c600e479dc75e68328c52774040cf9226",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "6.5.0"
+    },
+    "yaml": {
+      "dependency": "transitive",
+      "description": {
+        "name": "yaml",
+        "sha256": "b9da305ac7c39faa3f030eccd175340f968459dae4af175130b3fc47e40d76ce",
+        "url": "https://pub.dev"
+      },
+      "source": "hosted",
+      "version": "3.1.3"
+    }
+  },
+  "sdks": {
+    "dart": ">=3.7.0 <4.0.0",
+    "flutter": ">=3.27.0"
+  }
+}

pkgs/applications/science/misc/gplates/default.nix

@@ -0,0 +1,89 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  cmake,
+  doxygen,
+  graphviz,
+  boost,
+  cgal,
+  gdal,
+  glew,
+  gmp,
+  libGL,
+  libGLU,
+  libSM,
+  mpfr,
+  proj,
+  python3,
+  qtxmlpatterns,
+  qwt,
+  wrapQtAppsHook,
+}:
+
+let
+  python = python3.withPackages (
+    ps: with ps; [
+      numpy
+    ]
+  );
+  boost' = boost.override {
+    enablePython = true;
+    inherit python;
+  };
+  cgal' = cgal.override {
+    boost = boost';
+  };
+in
+stdenv.mkDerivation (finalAttrs: {
+  pname = "gplates";
+  version = "2.5";
+
+  src = fetchFromGitHub {
+    owner = "GPlates";
+    repo = "GPlates";
+    rev = "GPlates-${finalAttrs.version}";
+    hash = "sha256-3fEwm5EKK9RcRbnyUejgwfjdsXaujjZjoMbq/BbVMeM=";
+  };
+
+  patches = [
+    (fetchpatch {
+      name = "qwt-6.3-compile-error-fix.patch";
+      url = "https://github.com/GPlates/GPlates/commit/c4680ebe54f4535909085feacecd66410a91ff98.patch";
+      hash = "sha256-mw5+GLayMrmcSDd1ai+0JTuY3iedHT9u2kx5Dd2wMjg=";
+    })
+  ];
+
+  nativeBuildInputs = [
+    cmake
+    doxygen
+    graphviz
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    boost'
+    cgal'
+    gdal
+    glew
+    gmp
+    libGL
+    libGLU
+    libSM
+    mpfr
+    proj
+    python
+    qtxmlpatterns
+    qwt
+  ];
+
+  meta = with lib; {
+    description = "Desktop software for the interactive visualisation of plate-tectonics";
+    mainProgram = "gplates";
+    homepage = "https://www.gplates.org";
+    license = licenses.gpl2Only;
+    platforms = platforms.all;
+    broken = stdenv.hostPlatform.isDarwin; # FIX: this check: https://github.com/GPlates/GPlates/blob/gplates/cmake/modules/Config_h.cmake#L72
+  };
+})

pkgs/applications/science/misc/graphia/default.nix

@@ -0,0 +1,49 @@
+{
+  stdenv,
+  lib,
+  cmake,
+  git,
+  fetchFromGitHub,
+  wrapQtAppsHook,
+  qtbase,
+  qtdeclarative,
+  qtsvg,
+  qtwebengine,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "graphia";
+  version = "5.2";
+
+  src = fetchFromGitHub {
+    owner = "graphia-app";
+    repo = "graphia";
+    rev = version;
+    sha256 = "sha256-tS5oqpwpqvWGu67s8OuA4uQR3Zb5VzHTY/GnfVQki6k=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    git # needs to define some hash as a version
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    qtbase
+    qtdeclarative
+    qtsvg
+    qtwebengine
+  ];
+
+  meta = with lib; {
+    # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/graphia.x86_64-darwin
+    broken =
+      (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) || stdenv.hostPlatform.isDarwin;
+    description = "Visualisation tool for the creation and analysis of graphs";
+    homepage = "https://graphia.app";
+    license = licenses.gpl3Only;
+    mainProgram = "Graphia";
+    maintainers = [ maintainers.bgamari ];
+    platforms = platforms.all;
+  };
+}