diff options
Diffstat (limited to 'pkgs/applications/science')
23 files changed, 384 insertions, 301 deletions
diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix index a199e41d50aa..a7a1f77dfe90 100644 --- a/pkgs/applications/science/biology/deeptools/default.nix +++ b/pkgs/applications/science/biology/deeptools/default.nix @@ -1,19 +1,25 @@ -{ lib, python, fetchFromGitHub }: -with python.pkgs; -buildPythonApplication rec { - pname = "deepTools"; +{ lib +, python3 +, fetchFromGitHub +}: + +python3.pkgs.buildPythonApplication rec { + pname = "deeptools"; version = "3.5.4"; + pyproject = true; src = fetchFromGitHub { owner = "deeptools"; repo = "deepTools"; rev = version; - sha256 = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI="; + hash = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI="; }; - format = "pyproject"; + nativeBuildInputs = with python3.pkgs; [ + setuptools + ]; - propagatedBuildInputs = [ + propagatedBuildInputs = with python3.pkgs; [ numpy numpydoc scipy @@ -26,7 +32,21 @@ buildPythonApplication rec { importlib-metadata ]; - nativeCheckInputs = [ pytest ]; + nativeCheckInputs = with python3.pkgs; [ + pytestCheckHook + ]; + + preCheck = '' + export PATH="$out/bin:$PATH" + ''; + + disabledTestPaths = [ + # tests trip on `len(sys.argv) == 1` + "deeptools/test/test_bigwigAverage.py" + "deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py" + "deeptools/test/test_heatmapper.py" + "deeptools/test/test_multiBamSummary.py" + ]; meta = with lib; { homepage = "https://deeptools.readthedocs.io/en/develop"; diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index f7be7119b85d..be663628a426 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchzip, jdk11, wrapGAppsHook }: +{ lib, stdenv, fetchzip, jdk17, testers, wrapGAppsHook, igv }: stdenv.mkDerivation rec { pname = "igv"; @@ -13,10 +13,10 @@ stdenv.mkDerivation rec { cp -Rv * $out/share/ sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igv.sh - sed -i 's#java#${jdk11}/bin/java#g' $out/share/igv.sh + sed -i 's#java#${jdk17}/bin/java#g' $out/share/igv.sh sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igvtools - sed -i 's#java#${jdk11}/bin/java#g' $out/share/igvtools + sed -i 's#java#${jdk17}/bin/java#g' $out/share/igvtools ln -s $out/share/igv.sh $out/bin/igv ln -s $out/share/igvtools $out/bin/igvtools @@ -26,6 +26,11 @@ stdenv.mkDerivation rec { ''; nativeBuildInputs = [ wrapGAppsHook ]; + passthru.tests.version = testers.testVersion { + package = igv; + }; + + meta = with lib; { homepage = "https://www.broadinstitute.org/igv/"; description = "A visualization tool for interactive exploration of genomic datasets"; diff --git a/pkgs/applications/science/biology/obitools/obitools3.nix b/pkgs/applications/science/biology/obitools/obitools3.nix index b38af2f64b54..9bf579a80c3b 100644 --- a/pkgs/applications/science/biology/obitools/obitools3.nix +++ b/pkgs/applications/science/biology/obitools/obitools3.nix @@ -17,8 +17,8 @@ python3Packages.buildPythonApplication rec { ''; preBuild = '' - substituteInPlace src/CMakeLists.txt --replace \$'{PYTHONLIB}' "$out/lib/${python3.libPrefix}/site-packages"; - export NIX_CFLAGS_COMPILE="-L $out/lib/${python3.libPrefix}/site-packages $NIX_CFLAGS_COMPILE" + substituteInPlace src/CMakeLists.txt --replace \$'{PYTHONLIB}' "$out/${python3.sitePackages}"; + export NIX_CFLAGS_COMPILE="-L $out/${python3.sitePackages} $NIX_CFLAGS_COMPILE" ''; dontConfigure = true; diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index 7db1edcbe9e9..70f436a088e1 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "samtools"; - version = "1.19"; + version = "1.19.2"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-+ms7GOIIUbbzy1WvrzIF0C/LedrjuEn89S6PwQ/wi4M="; + hash = "sha256-cfYEmWaOTAjn10X7/yTBXMigl3q6sazV0rtBm9sGXpY="; }; # tests require `bgzip` from the htslib package diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index 2d41342ff585..73ee9a3996da 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.49"; + version = "16.1.51"; pname = "jmol"; src = let baseVersion = "${lib.versions.major version}.${lib.versions.minor version}"; in fetchurl { url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; - hash = "sha256-rzW0dB6LkKnbqHMLII6u3a6iJ1nz6gys/TN0fZFcrBk="; + hash = "sha256-7YOBpUeGutFPbMlQ1NnJ6BNyLbw54Meezwfs6mL71BQ="; }; patchPhase = '' diff --git a/pkgs/applications/science/chemistry/mopac/default.nix b/pkgs/applications/science/chemistry/mopac/default.nix index c0cdc4eff410..4e8e29c993e1 100644 --- a/pkgs/applications/science/chemistry/mopac/default.nix +++ b/pkgs/applications/science/chemistry/mopac/default.nix @@ -12,13 +12,13 @@ assert blas.isILP64 == lapack.isILP64; stdenv.mkDerivation rec { pname = "mopac"; - version = "22.1.0"; + version = "22.1.1"; src = fetchFromGitHub { owner = "openmopac"; repo = pname; rev = "v${version}"; - hash = "sha256-4jQ0WCHK07CXWUPj5Z1zSXObKxnitMj+FJQbLDiS2Dc="; + hash = "sha256-tdVb/u89EBggfG3Ofz1ICBE2ug4fbMsUWAILwJP9Ito="; }; nativeBuildInputs = [ gfortran cmake ]; diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix index db08de018804..93fec7149604 100644 --- a/pkgs/applications/science/chemistry/octopus/default.nix +++ b/pkgs/applications/science/chemistry/octopus/default.nix @@ -1,5 +1,23 @@ -{ lib, stdenv, fetchFromGitLab, gfortran, which, perl, procps -, libyaml, libxc, fftw, blas, lapack, gsl, netcdf, arpack, autoreconfHook +{ lib +, stdenv +, fetchFromGitLab +, gfortran +, which +, perl +, procps +, libvdwxc +, libyaml +, libxc +, fftw +, blas +, lapack +, gsl +, netcdf +, arpack +, autoreconfHook +, scalapack +, mpi +, enableMpi ? true , python3 , enableFma ? stdenv.hostPlatform.fmaSupport , enableFma4 ? stdenv.hostPlatform.fma4Support @@ -38,8 +56,12 @@ stdenv.mkDerivation rec { fftw netcdf arpack + libvdwxc (python3.withPackages (ps: [ ps.pyyaml ])) - ]; + ] ++ lib.optional enableMpi scalapack; + + propagatedBuildInputs = lib.optional enableMpi mpi; + propagatedUserEnvPkgs = lib.optional enableMpi mpi; configureFlags = with lib; [ "--with-yaml-prefix=${lib.getDev libyaml}" @@ -48,12 +70,22 @@ stdenv.mkDerivation rec { "--with-fftw-prefix=${lib.getDev fftw}" "--with-gsl-prefix=${lib.getDev gsl}" "--with-libxc-prefix=${lib.getDev libxc}" + "--with-libvdwxc" "--enable-openmp" - ] ++ optional enableFma "--enable-fma3" - ++ optional enableFma4 "--enable-fma4" - ++ optional enableAvx "--enable-avx" - ++ optional enableAvx512 "--enable-avx512"; + ] + ++ optional enableFma "--enable-fma3" + ++ optional enableFma4 "--enable-fma4" + ++ optional enableAvx "--enable-avx" + ++ optional enableAvx512 "--enable-avx512" + ++ optionals enableMpi [ + "--enable-mpi" + "--with-scalapack=-lscalapack" + "CC=mpicc" + "FC=mpif90" + ]; + + nativeCheckInputs = lib.optional.enableMpi mpi; doCheck = false; checkTarget = "check-short"; @@ -67,6 +99,8 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; + passthru = lib.attrsets.optionalAttrs enableMpi { inherit mpi; }; + meta = with lib; { description = "Real-space time dependent density-functional theory code"; homepage = "https://octopus-code.org"; diff --git a/pkgs/applications/science/electronics/dsview/default.nix b/pkgs/applications/science/electronics/dsview/default.nix index 98c35c37e8d5..ec53e976aec5 100644 --- a/pkgs/applications/science/electronics/dsview/default.nix +++ b/pkgs/applications/science/electronics/dsview/default.nix @@ -1,6 +1,6 @@ { stdenv, lib, fetchFromGitHub, pkg-config, cmake, wrapQtAppsHook , libzip, boost, fftw, qtbase, qtwayland, qtsvg, libusb1 -, python3, fetchpatch +, python3, fetchpatch, desktopToDarwinBundle }: stdenv.mkDerivation rec { @@ -20,18 +20,19 @@ stdenv.mkDerivation rec { ./install.patch ]; - nativeBuildInputs = [ cmake pkg-config wrapQtAppsHook ]; + nativeBuildInputs = [ cmake pkg-config wrapQtAppsHook ] + ++ lib.optional stdenv.isDarwin desktopToDarwinBundle; buildInputs = [ - boost fftw qtbase qtwayland qtsvg libusb1 libzip + boost fftw qtbase qtsvg libusb1 libzip python3 - ]; + ] ++ lib.optional stdenv.isLinux qtwayland; meta = with lib; { description = "A GUI program for supporting various instruments from DreamSourceLab, including logic analyzer, oscilloscope, etc"; homepage = "https://www.dreamsourcelab.com/"; license = licenses.gpl3Plus; - platforms = platforms.linux; - maintainers = with maintainers; [ bachp ]; + platforms = platforms.unix; + maintainers = with maintainers; [ bachp carlossless ]; }; } diff --git a/pkgs/applications/science/electronics/dsview/install.patch b/pkgs/applications/science/electronics/dsview/install.patch index 9fd9133e2795..9fc660bf8148 100644 --- a/pkgs/applications/science/electronics/dsview/install.patch +++ b/pkgs/applications/science/electronics/dsview/install.patch @@ -16,8 +16,8 @@ index eb9be42..220817c 100644 - 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 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) diff --git a/pkgs/applications/science/electronics/fritzing/default.nix b/pkgs/applications/science/electronics/fritzing/default.nix index 46307a133de3..efe70f125d04 100644 --- a/pkgs/applications/science/electronics/fritzing/default.nix +++ b/pkgs/applications/science/electronics/fritzing/default.nix @@ -1,7 +1,6 @@ { stdenv , lib , fetchFromGitHub -, fetchpatch , wrapQtAppsHook , qmake , pkg-config @@ -15,6 +14,7 @@ , libngspice , libgit2 , quazip +, clipper }: let @@ -38,25 +38,17 @@ let }; in -stdenv.mkDerivation rec { +stdenv.mkDerivation { pname = "fritzing"; - version = "1.0.1"; + version = "1.0.2"; src = fetchFromGitHub { - owner = pname; + owner = "fritzing"; repo = "fritzing-app"; - rev = "8f5f1373835050ce014299c78d91c24beea9b633"; - hash = "sha256-jLVNzSh2KwXpi3begtp/53sdBmQQbCnKMCm2p770etg="; + rev = "dbdbe34c843677df721c7b3fc3e32c0f737e7e95"; + hash = "sha256-Xi5sPU2RGkqh7T+EOvwxJJKKYDhJfccyEZ8LBBTb2s4="; }; - patches = [ - # Fix error caused by implicit call - (fetchpatch { - url = "https://aur.archlinux.org/cgit/aur.git/plain/0003-ParseResult-operator-bool-in-explicit.patch?h=fritzing&id=b2c79b55f0a2811e80bb1136b1e021fbc56937c9"; - hash = "sha256-9HdcNqLHEB0HQbF7AaTdUIJUbafwsRKPA+wfF4g8veU="; - }) - ]; - nativeBuildInputs = [ qmake pkg-config qttools wrapQtAppsHook ]; buildInputs = [ qtbase @@ -68,6 +60,7 @@ stdenv.mkDerivation rec { libgit2 quazip libngspice + clipper ]; postPatch = '' @@ -81,13 +74,17 @@ stdenv.mkDerivation rec { substituteInPlace src/fapplication.cpp \ --replace 'PartsChecker::getSha(dir.absolutePath());' '"${partsSha}";' + substituteInPlace phoenix.pro \ + --replace "6.5.10" "${qtbase.version}" + 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}/quazip" + "-I${lib.getDev quazip}/include/QuaZip-Qt${lib.versions.major qtbase.version}-${quazip.version}" "-I${svgpp}/include" + "-I${clipper}/include/polyclipping" ]; env.NIX_LDFLAGS = "-lquazip1-qt${lib.versions.major qtbase.version}"; diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix index ffab1ba75121..11837638e1ab 100644 --- a/pkgs/applications/science/electronics/kicad/versions.nix +++ b/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,36 +3,36 @@ { "kicad" = { kicadVersion = { - version = "7.0.9"; + version = "7.0.10"; src = { - rev = "1c81053cc40579ecd5febef1aeb1164008039deb"; - sha256 = "1hq9rba1gcks14zwbr8nbicpsil4imslgfch6ll33fhizbks3fq4"; + rev = "7daac78752749fc919e932be6156914aa83c926f"; + sha256 = "0z459yi0s02mwdgbr3xxw43gn9yjhvfkjnsxmns5mksgzsr5nmhh"; }; }; libVersion = { - version = "7.0.9"; + version = "7.0.10"; libSources = { - symbols.rev = "1ed4ed6c0696e50165b8e3d7978136a05db2d7c3"; - symbols.sha256 = "0ynsnjq3z126cjkgm1fjbjvdvpc0walnr42ya9dv46l27kxy2j77"; - templates.rev = "856bacc6782ea8c9bcb5a49a2d438a4689e0579b"; - templates.sha256 = "11582ldnv7hkljmhaym83962kixq1hjbfmdrn5laq7l4jk3l19vh"; - footprints.rev = "fe7b9aec7635caabbaa85fa8a15b85038394099b"; - footprints.sha256 = "16a4c2xs4i8wbm01a901yxabxk0qdsjkzlccfawddv82bkh4b87h"; - packages3d.rev = "5bc66f3c0f6dabf09df6c5188b8d955968500eab"; - packages3d.sha256 = "1cly28vc07i54v487zbb8d1h70nrd3naxvq146b0xnbrjwnd2q28"; + symbols.rev = "eedf6c9ddac2816023e817d4dc91032f9d7390b9"; + symbols.sha256 = "0nlgmxf9z1vf4g350dfkxql1dawgmw275wqxkgszsfxmhdfpmi9v"; + templates.rev = "9ce98cc45f3778e05c404edebf0f98de5c247ffe"; + templates.sha256 = "0mykfwwik7472i4r0isc5szj3dnmvd0538p0vlmzh4rcgj3pj3vm"; + footprints.rev = "7061fc9847ecc1b838e60dc6826db534028494f6"; + footprints.sha256 = "1az6fzh1lma71mj12bc4bblnmzjayrxhkb8w9rjvlhvvgv33cdmy"; + packages3d.rev = "d7345b34daaa23acf0d4506ed937fb424b5b18cd"; + packages3d.sha256 = "0xzyi4mgyifwc6dppdzh6jq294mkj0a71cwkqw2ymz1kfbksw626"; }; }; }; "kicad-testing" = { kicadVersion = { - version = "7.0-2024-01-07"; + version = "7.0-2024-01-27"; src = { - rev = "ace6439758f8d211001235f36f02a60488337e41"; - sha256 = "0z4p2srz9rld7mq6k2y5fipz8mgsdhh2506wam4388nklzzkrccr"; + rev = "13fcb571f7e5bf4bf142d151651fc577aca32053"; + sha256 = "0wvk3wx5lm2jvyip6b96ja464hdzp9klb7b7ng5i3mdldabh0jba"; }; }; libVersion = { - version = "7.0-2024-01-07"; + version = "7.0-2024-01-27"; libSources = { symbols.rev = "eedf6c9ddac2816023e817d4dc91032f9d7390b9"; symbols.sha256 = "0nlgmxf9z1vf4g350dfkxql1dawgmw275wqxkgszsfxmhdfpmi9v"; diff --git a/pkgs/applications/science/logic/btor2tools/default.nix b/pkgs/applications/science/logic/btor2tools/default.nix index 0cb9c8037cb2..ce73ea636f29 100644 --- a/pkgs/applications/science/logic/btor2tools/default.nix +++ b/pkgs/applications/science/logic/btor2tools/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, cmake, fetchFromGitHub, fixDarwinDylibNames }: +{ lib, stdenv, cmake, fetchFromGitHub, fetchpatch, fixDarwinDylibNames }: stdenv.mkDerivation rec { pname = "btor2tools"; @@ -11,6 +11,14 @@ stdenv.mkDerivation rec { sha256 = "0mfqmkgvyw8fa2c09kww107dmk180ch1hp98r5kv41vnc04iqb0s"; }; + patches = [ + (fetchpatch { + name = "gcc-13.patch"; + url = "https://github.com/Boolector/btor2tools/commit/037f1fa88fb439dca6f648ad48a3463256d69d8b.patch"; + hash = "sha256-FX1yy9XdUs1tAReOxhEzNHu48DrISzNNMSYoIrhHoFY="; + }) + ]; + nativeBuildInputs = [ cmake ] ++ lib.optional stdenv.isDarwin fixDarwinDylibNames; installPhase = '' diff --git a/pkgs/applications/science/logic/cvc5/default.nix b/pkgs/applications/science/logic/cvc5/default.nix index 142668f382c3..4da837ca46f6 100644 --- a/pkgs/applications/science/logic/cvc5/default.nix +++ b/pkgs/applications/science/logic/cvc5/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cvc5"; - version = "1.1.0"; + version = "1.1.1"; src = fetchFromGitHub { owner = "cvc5"; repo = "cvc5"; rev = "cvc5-${version}"; - hash = "sha256-BWmIxQz+if402f7zsFROWG1TXbcsg50FJbnffJFYun4="; + hash = "sha256-TU2ZG6/9bXRPozvEVUiSWixImY38iavD3huhSU8DbCw="; }; nativeBuildInputs = [ pkg-config cmake flex ]; diff --git a/pkgs/applications/science/logic/easycrypt/default.nix b/pkgs/applications/science/logic/easycrypt/default.nix index 36ff9f2046f8..2869bcd6e1e3 100644 --- a/pkgs/applications/science/logic/easycrypt/default.nix +++ b/pkgs/applications/science/logic/easycrypt/default.nix @@ -22,11 +22,12 @@ stdenv.mkDerivation rec { batteries dune-build-info inifiles + why3 yojson zarith ]; - propagatedBuildInputs = [ why3 ]; + propagatedBuildInputs = [ why3.out ]; strictDeps = true; diff --git a/pkgs/applications/science/logic/egglog/Cargo.lock b/pkgs/applications/science/logic/egglog/Cargo.lock index cb023f2e05c1..0d2fbadc10bc 100644 --- a/pkgs/applications/science/logic/egglog/Cargo.lock +++ b/pkgs/applications/science/logic/egglog/Cargo.lock @@ -4,9 +4,9 @@ version = 3 [[package]] name = "ahash" -version = "0.7.6" +version = "0.7.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47" +checksum = "5a824f2aa7e75a0c98c5a504fceb80649e9c35265d44525b5f94de4771a395cd" dependencies = [ "getrandom", "once_cell", @@ -15,56 +15,56 @@ dependencies = [ [[package]] name = "ahash" -version = "0.8.3" +version = "0.8.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f" +checksum = "91429305e9f0a25f6205c5b8e0d2db09e0708a7a6df0f42212bb56c32c8ac97a" dependencies = [ "cfg-if 1.0.0", "once_cell", "version_check", + "zerocopy", ] [[package]] name = "aho-corasick" -version = "1.0.2" +version = "1.1.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "43f6cb1bf222025340178f382c426f13757b2960e89779dfcb319c32542a5a41" +checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0" dependencies = [ "memchr", ] [[package]] name = "allocator-api2" -version = "0.2.15" +version = "0.2.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "56fc6cf8dc8c4158eed8649f9b8b0ea1518eb62b544fe9490d66fa0b349eafe9" +checksum = "0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5" [[package]] name = "anstream" -version = "0.3.2" +version = "0.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163" +checksum = "2ab91ebe16eb252986481c5b62f6098f3b698a45e34b5b98200cf20dd2484a44" dependencies = [ "anstyle", "anstyle-parse", "anstyle-query", "anstyle-wincon", "colorchoice", - "is-terminal", "utf8parse", ] [[package]] name = "anstyle" -version = "1.0.1" +version = "1.0.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3a30da5c5f2d5e72842e00bcb57657162cdabef0931f40e2deb9b4140440cecd" +checksum = "7079075b41f533b8c61d2a4d073c4676e1f8b249ff94a393b0595db304e0dd87" [[package]] name = "anstyle-parse" -version = "0.2.1" +version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "938874ff5980b03a87c5524b3ae5b59cf99b1d6bc836848df7bc5ada9643c333" +checksum = "317b9a89c1868f5ea6ff1d9539a69f45dffc21ce321ac1fd1160dfa48c8e2140" dependencies = [ "utf8parse", ] @@ -80,9 +80,9 @@ dependencies = [ [[package]] name = "anstyle-wincon" -version = "1.0.1" +version = "3.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "180abfa45703aebe0093f79badacc01b8fd4ea2e35118747e5811127f926e188" +checksum = "f0699d10d2f4d628a98ee7b57b289abbc98ff3bad977cb3152709d4bf2330628" dependencies = [ "anstyle", "windows-sys", @@ -126,9 +126,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" [[package]] name = "bitflags" -version = "2.3.3" +version = "2.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "630be753d4e58660abd17930c71b647fe46c27ea6b63cc59e1e3851406972e42" +checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07" [[package]] name = "block-buffer" @@ -141,15 +141,9 @@ dependencies = [ [[package]] name = "bumpalo" -version = "3.13.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a3e2c3daef883ecc1b5d58c15adae93470a91d425f3532ba1695849656af3fc1" - -[[package]] -name = "cc" -version = "1.0.79" +version = "3.14.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f" +checksum = "7f30e7476521f6f8af1a1c4c0b8cc94f0bee37d91763d0ca2665f299b6cd8aec" [[package]] name = "cfg-if" @@ -165,20 +159,19 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" [[package]] name = "clap" -version = "4.3.11" +version = "4.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1640e5cc7fb47dbb8338fd471b105e7ed6c3cb2aeb00c2e067127ffd3764a05d" +checksum = "ac495e00dcec98c83465d5ad66c5c4fabd652fd6686e7c6269b117e729a6f17b" dependencies = [ "clap_builder", "clap_derive", - "once_cell", ] [[package]] name = "clap_builder" -version = "4.3.11" +version = "4.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "98c59138d527eeaf9b53f35a77fcc1fad9d883116070c63d5de1c7dc7b00c72b" +checksum = "c77ed9a32a62e6ca27175d00d29d05ca32e396ea1eb5fb01d8256b669cec7663" dependencies = [ "anstream", "anstyle", @@ -188,21 +181,21 @@ dependencies = [ [[package]] name = "clap_derive" -version = "4.3.2" +version = "4.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b8cd2b2a819ad6eec39e8f1d6b53001af1e5469f8c177579cdaeb313115b825f" +checksum = "cf9804afaaf59a91e75b022a30fb7229a7901f60c755489cc61c9b423b836442" dependencies = [ "heck", "proc-macro2", "quote", - "syn 2.0.25", + "syn 2.0.38", ] [[package]] name = "clap_lex" -version = "0.5.0" +version = "0.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2da6da31387c7e4ef160ffab6d5e7f00c42626fe39aea70a7b0f1773f7dd6c1b" +checksum = "702fc72eb24e5a1e48ce58027a675bc24edd52096d5397d4aea7c6dd9eca0bd1" [[package]] name = "colorchoice" @@ -222,9 +215,9 @@ dependencies = [ [[package]] name = "cpufeatures" -version = "0.2.9" +version = "0.2.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a17b76ff3a4162b0b27f354a0c87015ddad39d35f9c0c36607a3bdd175dde1f1" +checksum = "ce420fe07aecd3e67c5f910618fe65e94158f6dcc0adf44e00d69ce2bdfe0fd0" dependencies = [ "libc", ] @@ -304,10 +297,11 @@ dependencies = [ "clap", "egraph-serialize", "env_logger", + "generic_symbolic_expressions", "getrandom", "glob", - "hashbrown 0.14.0", - "indexmap 2.0.0", + "hashbrown 0.14.2", + "indexmap", "instant", "lalrpop", "lalrpop-util", @@ -323,17 +317,17 @@ dependencies = [ "serde_json", "smallvec", "symbol_table", - "symbolic_expressions", "thiserror", ] [[package]] name = "egraph-serialize" version = "0.1.0" -source = "git+https://github.com/egraphs-good/egraph-serialize?rev=e406ffcec8c6e841089fd3e4f9b76c35ce448950#e406ffcec8c6e841089fd3e4f9b76c35ce448950" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a41150f383849cfc16ae6230f592112b3c0a2c0e3ec43eb0b09db037bfcce703" dependencies = [ "graphviz-rust", - "indexmap 2.0.0", + "indexmap", "once_cell", "ordered-float", "serde", @@ -342,9 +336,9 @@ dependencies = [ [[package]] name = "either" -version = "1.8.1" +version = "1.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7fcaabb2fef8c910e7f4c7ce9f67a1283a1715879a7c230ca9d6d1ae31f16d91" +checksum = "a26ae43d7bcc3b814de94796a5e736d4029efb0ee900c12e2d54c993ad1a1e07" [[package]] name = "ena" @@ -376,30 +370,19 @@ checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5" [[package]] name = "errno" -version = "0.3.1" +version = "0.3.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4bcfec3a70f97c962c307b2d2c56e358cf1d00b558d74262b5f929ee8cc7e73a" +checksum = "ac3e13f66a2f95e32a39eaa81f6b95d42878ca0e1db0c7543723dfe12557e860" dependencies = [ - "errno-dragonfly", "libc", "windows-sys", ] [[package]] -name = "errno-dragonfly" -version = "0.1.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf" -dependencies = [ - "cc", - "libc", -] - -[[package]] name = "fastrand" -version = "2.0.0" +version = "2.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6999dc1837253364c2ebb0704ba97994bd874e8f195d665c50b7548f6ea92764" +checksum = "25cbce373ec4653f1a01a31e8a5e5ec0c622dc27ff9c4e6606eefef5cbbed4a5" [[package]] name = "fixedbitset" @@ -418,6 +401,11 @@ dependencies = [ ] [[package]] +name = "generic_symbolic_expressions" +version = "5.0.3" +source = "git+https://github.com/oflatt/symbolic-expressions?rev=655b6a4c06b4b3d3b2300e17779860b4abe440f0#655b6a4c06b4b3d3b2300e17779860b4abe440f0" + +[[package]] name = "getrandom" version = "0.2.10" source = "registry+https://github.com/rust-lang/crates.io-index" @@ -458,16 +446,16 @@ version = "0.12.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888" dependencies = [ - "ahash 0.7.6", + "ahash 0.7.7", ] [[package]] name = "hashbrown" -version = "0.14.0" +version = "0.14.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c6201b9ff9fd90a5a3bac2e56a830d0caa509576f0e503818ee82c181b3437a" +checksum = "f93e7192158dbcda357bdec5fb5788eebf8bbac027f3f33e719d29135ae84156" dependencies = [ - "ahash 0.8.3", + "ahash 0.8.6", "allocator-api2", ] @@ -479,9 +467,9 @@ checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8" [[package]] name = "hermit-abi" -version = "0.3.2" +version = "0.3.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "443144c8cdadd93ebf52ddb4056d257f5b52c04d3c804e657d19eb73fc33668b" +checksum = "d77f7ec81a6d05a3abb01ab6eb7590f6083d08449fe5a1c8b1e620283546ccb7" [[package]] name = "humantime" @@ -491,22 +479,12 @@ checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" [[package]] name = "indexmap" -version = "1.9.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99" -dependencies = [ - "autocfg", - "hashbrown 0.12.3", -] - -[[package]] -name = "indexmap" -version = "2.0.0" +version = "2.0.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d5477fe2230a79769d8dc68e0eabf5437907c0457a5614a9e8dddb67f65eb65d" +checksum = "8adf3ddd720272c6ea8bf59463c04e0f93d0bbf7c5439b691bca2987e0270897" dependencies = [ "equivalent", - "hashbrown 0.14.0", + "hashbrown 0.14.2", "serde", ] @@ -595,7 +573,7 @@ dependencies = [ "petgraph", "pico-args", "regex", - "regex-syntax", + "regex-syntax 0.7.5", "string_cache", "term", "tiny-keccak", @@ -619,9 +597,9 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" [[package]] name = "libc" -version = "0.2.147" +version = "0.2.149" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b4668fb0ea861c1df094127ac5f1da3409a82116a4ba74fca2e58ef927159bb3" +checksum = "a08173bc88b7955d1b3145aa561539096c421ac8debde8cbc3612ec635fee29b" [[package]] name = "libtest-mimic" @@ -636,15 +614,15 @@ dependencies = [ [[package]] name = "linux-raw-sys" -version = "0.4.3" +version = "0.4.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "09fc20d2ca12cb9f044c93e3bd6d32d523e6e2ec3db4f7b2939cd99026ecd3f0" +checksum = "da2479e8c062e40bf0066ffa0bc823de0a9368974af99c9f6df941d2c231e03f" [[package]] name = "lock_api" -version = "0.4.10" +version = "0.4.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c1cc9717a20b1bb222f333e6a92fd32f7d8a18ddc5a3191a11af45dcbf4dcd16" +checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45" dependencies = [ "autocfg", "scopeguard", @@ -652,15 +630,15 @@ dependencies = [ [[package]] name = "log" -version = "0.4.19" +version = "0.4.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b06a4cde4c0f271a446782e3eff8de789548ce57dbc8eca9292c27f4a42004b4" +checksum = "b5e6163cb8c49088c2c36f57875e58ccd8c87c7427f7fbd50ea6710b2f3f2e8f" [[package]] name = "memchr" -version = "2.5.0" +version = "2.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d" +checksum = "f665ee40bc4a3c5590afb1e9677db74a508659dfd71e126420da8274909a0167" [[package]] name = "memory_units" @@ -676,9 +654,9 @@ checksum = "e4a24736216ec316047a1fc4252e27dabb04218aa4a3f37c6e7ddbf1f9782b54" [[package]] name = "num-bigint" -version = "0.4.3" +version = "0.4.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f93ab6289c7b344a8a9f60f88d80aa20032336fe78da341afc91c8a2341fc75f" +checksum = "608e7659b5c3d7cba262d894801b9ec9d00de989e8a82bd4bef91d08da45cdc0" dependencies = [ "autocfg", "num-integer", @@ -709,9 +687,9 @@ dependencies = [ [[package]] name = "num-traits" -version = "0.2.15" +version = "0.2.17" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd" +checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c" dependencies = [ "autocfg", ] @@ -734,9 +712,9 @@ checksum = "dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d" [[package]] name = "ordered-float" -version = "3.7.0" +version = "3.9.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2fc2dbde8f8a79f2102cc474ceb0ad68e3b80b85289ea62389b60e66777e4213" +checksum = "f1e1c390732d15f1d48471625cd92d154e66db2c56645e29a9cd26f4699f72dc" dependencies = [ "num-traits", "rand", @@ -755,32 +733,33 @@ dependencies = [ [[package]] name = "parking_lot_core" -version = "0.9.8" +version = "0.9.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "93f00c865fe7cabf650081affecd3871070f26767e7b2070a3ffae14c654b447" +checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e" dependencies = [ "cfg-if 1.0.0", "libc", - "redox_syscall 0.3.5", + "redox_syscall 0.4.1", "smallvec", "windows-targets", ] [[package]] name = "pest" -version = "2.7.2" +version = "2.7.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1acb4a4365a13f749a93f1a094a7805e5cfa0955373a9de860d962eaa3a5fe5a" +checksum = "ae9cee2a55a544be8b89dc6848072af97a20f2422603c10865be2a42b580fff5" dependencies = [ + "memchr", "thiserror", "ucd-trie", ] [[package]] name = "pest_derive" -version = "2.7.2" +version = "2.7.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "666d00490d4ac815001da55838c500eafb0320019bbaa44444137c48b443a853" +checksum = "81d78524685f5ef2a3b3bd1cafbc9fcabb036253d9b1463e726a91cd16e2dfc2" dependencies = [ "pest", "pest_generator", @@ -788,22 +767,22 @@ dependencies = [ [[package]] name = "pest_generator" -version = "2.7.2" +version = "2.7.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "68ca01446f50dbda87c1786af8770d535423fa8a53aec03b8f4e3d7eb10e0929" +checksum = "68bd1206e71118b5356dae5ddc61c8b11e28b09ef6a31acbd15ea48a28e0c227" dependencies = [ "pest", "pest_meta", "proc-macro2", "quote", - "syn 2.0.25", + "syn 2.0.38", ] [[package]] name = "pest_meta" -version = "2.7.2" +version = "2.7.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "56af0a30af74d0445c0bf6d9d051c979b516a1a5af790d251daee76005420a48" +checksum = "7c747191d4ad9e4a4ab9c8798f1e82a39affe7ef9648390b7e5548d18e099de6" dependencies = [ "once_cell", "pest", @@ -812,12 +791,12 @@ dependencies = [ [[package]] name = "petgraph" -version = "0.6.3" +version = "0.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4dd7d28ee937e54fe3080c91faa1c3a46c06de6252988a7f4592ba2310ef22a4" +checksum = "e1d3afd2628e69da2be385eb6f2fd57c8ac7977ceeff6dc166ff1657b0e386a9" dependencies = [ "fixedbitset", - "indexmap 1.9.3", + "indexmap", ] [[package]] @@ -849,18 +828,18 @@ checksum = "925383efa346730478fb4838dbe9137d2a47675ad789c546d150a6e1dd4ab31c" [[package]] name = "proc-macro2" -version = "1.0.64" +version = "1.0.69" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "78803b62cbf1f46fde80d7c0e803111524b9877184cfe7c3033659490ac7a7da" +checksum = "134c189feb4956b20f6f547d2cf727d4c0fe06722b20a0eec87ed445a97f92da" dependencies = [ "unicode-ident", ] [[package]] name = "quote" -version = "1.0.29" +version = "1.0.33" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "573015e8ab27661678357f27dc26460738fd2b6c86e46f386fde94cb5d913105" +checksum = "5267fca4496028628a95160fc423a33e8b2e6af8a5302579e322e4b520293cae" dependencies = [ "proc-macro2", ] @@ -908,9 +887,9 @@ dependencies = [ [[package]] name = "redox_syscall" -version = "0.3.5" +version = "0.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "567664f262709473930a4bf9e51bf2ebf3348f2e748ccc50dea20646858f8f29" +checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa" dependencies = [ "bitflags 1.3.2", ] @@ -928,32 +907,38 @@ dependencies = [ [[package]] name = "regex" -version = "1.9.1" +version = "1.10.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b2eae68fc220f7cf2532e4494aded17545fce192d59cd996e0fe7887f4ceb575" +checksum = "380b951a9c5e80ddfd6136919eef32310721aa4aacd4889a8d39124b026ab343" dependencies = [ "aho-corasick", "memchr", "regex-automata", - "regex-syntax", + "regex-syntax 0.8.2", ] [[package]] name = "regex-automata" -version = "0.3.2" +version = "0.4.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "83d3daa6976cffb758ec878f108ba0e062a45b2d6ca3a2cca965338855476caf" +checksum = "5f804c7828047e88b2d32e2d7fe5a105da8ee3264f01902f796c8e067dc2483f" dependencies = [ "aho-corasick", "memchr", - "regex-syntax", + "regex-syntax 0.8.2", ] [[package]] name = "regex-syntax" -version = "0.7.4" +version = "0.7.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e5ea92a5b6195c6ef2a0295ea818b312502c6fc94dde986c5553242e18fd4ce2" +checksum = "dbb5fb1acd8a1a18b3dd5be62d25485eb770e05afb408a9627d14d451bae12da" + +[[package]] +name = "regex-syntax" +version = "0.8.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f" [[package]] name = "rustc-hash" @@ -963,11 +948,11 @@ checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2" [[package]] name = "rustix" -version = "0.38.4" +version = "0.38.21" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0a962918ea88d644592894bc6dc55acc6c0956488adcebbfb6e273506b7fd6e5" +checksum = "2b426b0506e5d50a7d8dafcf2e81471400deb602392c7dd110815afb4eaf02a3" dependencies = [ - "bitflags 2.3.3", + "bitflags 2.4.1", "errno", "libc", "linux-raw-sys", @@ -976,9 +961,9 @@ dependencies = [ [[package]] name = "rustversion" -version = "1.0.13" +version = "1.0.14" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dc31bd9b61a32c31f9650d18add92aa83a49ba979c143eefd27fe7177b05bd5f" +checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4" [[package]] name = "ryu" @@ -988,37 +973,37 @@ checksum = "1ad4cc8da4ef723ed60bced201181d83791ad433213d8c24efffda1eec85d741" [[package]] name = "scopeguard" -version = "1.1.0" +version = "1.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd" +checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49" [[package]] name = "serde" -version = "1.0.171" +version = "1.0.190" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "30e27d1e4fd7659406c492fd6cfaf2066ba8773de45ca75e855590f856dc34a9" +checksum = "91d3c334ca1ee894a2c6f6ad698fe8c435b76d504b13d436f0685d648d6d96f7" dependencies = [ "serde_derive", ] [[package]] name = "serde_derive" -version = "1.0.171" +version = "1.0.190" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "389894603bd18c46fa56231694f8d827779c0951a667087194cf9de94ed24682" +checksum = "67c5609f394e5c2bd7fc51efda478004ea80ef42fee983d5c67a65e34f32c0e3" dependencies = [ "proc-macro2", "quote", - "syn 2.0.25", + "syn 2.0.38", ] [[package]] name = "serde_json" -version = "1.0.103" +version = "1.0.108" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d03b412469450d4404fe8499a268edd7f8b79fecb074b0d812ad64ca21f4031b" +checksum = "3d1c7e3eac408d115102c4c24ad393e0821bb3a5df4d506a80f85f7a742a526b" dependencies = [ - "indexmap 2.0.0", + "indexmap", "itoa", "ryu", "serde", @@ -1026,9 +1011,9 @@ dependencies = [ [[package]] name = "sha2" -version = "0.10.7" +version = "0.10.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "479fb9d862239e610720565ca91403019f2f00410f1864c5aa7479b950a76ed8" +checksum = "793db75ad2bcafc3ffa7c68b215fee268f537982cd901d132f89c6343f3a3dc8" dependencies = [ "cfg-if 1.0.0", "cpufeatures", @@ -1037,15 +1022,15 @@ dependencies = [ [[package]] name = "siphasher" -version = "0.3.10" +version = "0.3.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7bd3e3206899af3f8b12af284fafc038cc1dc2b41d1b89dd17297221c5d225de" +checksum = "38b58827f4464d87d377d175e90bf58eb00fd8716ff0a62f80356b5e61555d0d" [[package]] name = "smallvec" -version = "1.11.0" +version = "1.11.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "62bb4feee49fdd9f707ef802e22365a35de4b7b299de4763d44bfea899442ff9" +checksum = "942b4a808e05215192e39f4ab80813e599068285906cc91aa64f923db842bd5a" [[package]] name = "string_cache" @@ -1068,19 +1053,15 @@ checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623" [[package]] name = "symbol_table" -version = "0.2.0" -source = "git+https://github.com/mwillsey/symbol_table?rev=acddcf8938d1b4ed2fce048c9d83c30203d404b9#acddcf8938d1b4ed2fce048c9d83c30203d404b9" +version = "0.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "828f672b631c220bf6ea8a1d3b82c7d0fc998e5ba8373383d8604bc1e2a6245a" dependencies = [ - "ahash 0.7.6", + "ahash 0.7.7", "hashbrown 0.12.3", ] [[package]] -name = "symbolic_expressions" -version = "5.0.3" -source = "git+https://github.com/oflatt/symbolic-expressions?rev=4c0ea5ca008f972450b2af72387e64d2c1c6a791#4c0ea5ca008f972450b2af72387e64d2c1c6a791" - -[[package]] name = "syn" version = "1.0.109" source = "registry+https://github.com/rust-lang/crates.io-index" @@ -1093,9 +1074,9 @@ dependencies = [ [[package]] name = "syn" -version = "2.0.25" +version = "2.0.38" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "15e3fc8c0c74267e2df136e5e5fb656a464158aa57624053375eb9c8c6e25ae2" +checksum = "e96b79aaa137db8f61e26363a0c9b47d8b4ec75da28b7d1d614c2303e232408b" dependencies = [ "proc-macro2", "quote", @@ -1104,13 +1085,13 @@ dependencies = [ [[package]] name = "tempfile" -version = "3.7.1" +version = "3.8.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dc02fddf48964c42031a0b3fe0428320ecf3a73c401040fc0096f97794310651" +checksum = "7ef1adac450ad7f4b3c28589471ade84f25f731a7a0fe30d71dfa9f60fd808e5" dependencies = [ "cfg-if 1.0.0", "fastrand", - "redox_syscall 0.3.5", + "redox_syscall 0.4.1", "rustix", "windows-sys", ] @@ -1128,31 +1109,31 @@ dependencies = [ [[package]] name = "termcolor" -version = "1.2.0" +version = "1.3.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "be55cf8942feac5c765c2c993422806843c9a9a45d4d5c407ad6dd2ea95eb9b6" +checksum = "6093bad37da69aab9d123a8091e4be0aa4a03e4d601ec641c327398315f62b64" dependencies = [ "winapi-util", ] [[package]] name = "thiserror" -version = "1.0.43" +version = "1.0.50" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a35fc5b8971143ca348fa6df4f024d4d55264f3468c71ad1c2f365b0a4d58c42" +checksum = "f9a7210f5c9a7156bb50aa36aed4c95afb51df0df00713949448cf9e97d382d2" dependencies = [ "thiserror-impl", ] [[package]] name = "thiserror-impl" -version = "1.0.43" +version = "1.0.50" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "463fe12d7993d3b327787537ce8dd4dfa058de32fc2b195ef3cde03dc4771e8f" +checksum = "266b2e40bc00e5a6c09c3584011e08b06f123c00362c92b975ba9843aaaa14b8" dependencies = [ "proc-macro2", "quote", - "syn 2.0.25", + "syn 2.0.38", ] [[package]] @@ -1175,9 +1156,9 @@ dependencies = [ [[package]] name = "typenum" -version = "1.16.0" +version = "1.17.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "497961ef93d974e23eb6f433eb5fe1b7930b659f06d12dec6fc44a8f554c0bba" +checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825" [[package]] name = "ucd-trie" @@ -1187,9 +1168,9 @@ checksum = "ed646292ffc8188ef8ea4d1e0e0150fb15a5c2e12ad9b8fc191ae7a8a7f3c4b9" [[package]] name = "unicode-ident" -version = "1.0.10" +version = "1.0.12" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "22049a19f4a68748a168c0fc439f9516686aa045927ff767eca0a85101fb6e73" +checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b" [[package]] name = "unicode-xid" @@ -1236,7 +1217,7 @@ dependencies = [ "once_cell", "proc-macro2", "quote", - "syn 2.0.25", + "syn 2.0.38", "wasm-bindgen-shared", ] @@ -1258,7 +1239,7 @@ checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b" dependencies = [ "proc-macro2", "quote", - "syn 2.0.25", + "syn 2.0.38", "wasm-bindgen-backend", "wasm-bindgen-shared", ] @@ -1334,9 +1315,9 @@ checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6" [[package]] name = "winapi-util" -version = "0.1.5" +version = "0.1.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178" +checksum = "f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596" dependencies = [ "winapi", ] @@ -1358,9 +1339,9 @@ dependencies = [ [[package]] name = "windows-targets" -version = "0.48.1" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "05d4b17490f70499f20b9e791dcf6a299785ce8af4d709018206dc5b4953e95f" +checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c" dependencies = [ "windows_aarch64_gnullvm", "windows_aarch64_msvc", @@ -1373,42 +1354,62 @@ dependencies = [ [[package]] name = "windows_aarch64_gnullvm" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "91ae572e1b79dba883e0d315474df7305d12f569b400fcf90581b06062f7e1bc" +checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8" [[package]] name = "windows_aarch64_msvc" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b2ef27e0d7bdfcfc7b868b317c1d32c641a6fe4629c171b8928c7b08d98d7cf3" +checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc" [[package]] name = "windows_i686_gnu" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "622a1962a7db830d6fd0a69683c80a18fda201879f0f447f065a3b7467daa241" +checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e" [[package]] name = "windows_i686_msvc" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4542c6e364ce21bf45d69fdd2a8e455fa38d316158cfd43b3ac1c5b1b19f8e00" +checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406" [[package]] name = "windows_x86_64_gnu" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ca2b8a661f7628cbd23440e50b05d705db3686f894fc9580820623656af974b1" +checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e" [[package]] name = "windows_x86_64_gnullvm" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7896dbc1f41e08872e9d5e8f8baa8fdd2677f29468c4e156210174edc7f7b953" +checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc" [[package]] name = "windows_x86_64_msvc" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a" +checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538" + +[[package]] +name = "zerocopy" +version = "0.7.20" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dd66a62464e3ffd4e37bd09950c2b9dd6c4f8767380fabba0d523f9a775bc85a" +dependencies = [ + "zerocopy-derive", +] + +[[package]] +name = "zerocopy-derive" +version = "0.7.20" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "255c4596d41e6916ced49cfafea18727b24d67878fa180ddfd69b9df34fd1726" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.38", +] diff --git a/pkgs/applications/science/logic/egglog/default.nix b/pkgs/applications/science/logic/egglog/default.nix index eedd90315db8..ab5653b50912 100644 --- a/pkgs/applications/science/logic/egglog/default.nix +++ b/pkgs/applications/science/logic/egglog/default.nix @@ -5,21 +5,21 @@ rustPlatform.buildRustPackage { pname = "egglog"; - version = "unstable-2023-09-12"; + version = "0-unstable-2024-01-26"; src = fetchFromGitHub { owner = "egraphs-good"; repo = "egglog"; - rev = "4d67f262a6f27aa5cfb62a2cfc7df968959105df"; - hash = "sha256-1mc7dW2pgaK4D7ZmlSHohb+6lcr7M9SRLUV/Dod8Rv0="; + rev = "b78f69ca1f7187c363bb31271c8e8958f477f15d"; + hash = "sha256-/1ktyz8wU1yLTdAFPnupK6jUFjiK6nQfotGRNOWiOsA="; }; + useNextest = true; + cargoLock = { lockFile = ./Cargo.lock; outputHashes = { - "egraph-serialize-0.1.0" = "sha256-sdkn7lmtmbLwAopabLWkrD6GjM3LIHseysuvwPz26G4="; - "symbol_table-0.2.0" = "sha256-f9UclMOUig+N5L3ibBXou0pJ4S/CQqtaji7tnebVbis="; - "symbolic_expressions-5.0.3" = "sha256-mSxnhveAItlTktQC4hM8o6TYjgtCUgkdZj7i6MR4Oeo="; + "generic_symbolic_expressions-5.0.3" = "sha256-UX6fS470YJMdNnn0GR3earMGQK3p/YvaFia7IEvGGKg="; }; }; diff --git a/pkgs/applications/science/logic/lean4/default.nix b/pkgs/applications/science/logic/lean4/default.nix index 092489f84456..97336c06b806 100644 --- a/pkgs/applications/science/logic/lean4/default.nix +++ b/pkgs/applications/science/logic/lean4/default.nix @@ -5,22 +5,23 @@ , git , gmp , perl +, testers }: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "lean4"; - version = "4.4.0"; + version = "4.5.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "lean4"; - rev = "v${version}"; - hash = "sha256-lU67wjl6yJP2r97lHYxrJqn+JhqMcBIbz/+qlCgY3/o="; + rev = "v${finalAttrs.version}"; + hash = "sha256-KTCTk4Fpbmm7FsUo03tAvenC6HuB3zJGax6iGTwLaXM="; }; postPatch = '' substituteInPlace src/CMakeLists.txt \ - --replace 'set(GIT_SHA1 "")' 'set(GIT_SHA1 "${src.rev}")' + --replace 'set(GIT_SHA1 "")' 'set(GIT_SHA1 "${finalAttrs.src.rev}")' # Remove tests that fails in sandbox. # It expects `sourceRoot` to be a git repository. @@ -54,13 +55,19 @@ stdenv.mkDerivation rec { NIX_LDFLAGS = "-l${stdenv.cc.libcxx.cxxabi.libName}"; }; + passthru.tests = { + version = testers.testVersion { + package = finalAttrs.finalPackage; + }; + }; + meta = with lib; { description = "Automatic and interactive theorem prover"; homepage = "https://leanprover.github.io/"; - changelog = "https://github.com/leanprover/lean4/blob/${src.rev}/RELEASES.md"; + changelog = "https://github.com/leanprover/lean4/blob/${finalAttrs.src.rev}/RELEASES.md"; license = licenses.asl20; platforms = platforms.all; maintainers = with maintainers; [ marsam ]; mainProgram = "lean"; }; -} +}) diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix index f0567fdda3b6..1676ca4c2a4f 100644 --- a/pkgs/applications/science/logic/why3/default.nix +++ b/pkgs/applications/science/logic/why3/default.nix @@ -1,6 +1,8 @@ { callPackage, fetchurl, lib, stdenv , ocamlPackages, coqPackages, rubber, hevea, emacs -, version ? "1.7.0" +, version ? "1.7.1" +, ideSupport ? true +, wrapGAppsHook }: stdenv.mkDerivation rec { @@ -10,15 +12,18 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://why3.gitlabpages.inria.fr/releases/${pname}-${version}.tar.gz"; hash = { - "1.7.0" = "sha256-rygrjzuJVukOvpuXTG/yeoEP98ZFkLQHObgc3My1PVY="; + "1.7.1" = "sha256-rG1hcxFhQ2PlE9RTz9ELliDjCuSzLnJ1togRY637cU4="; "1.6.0" = "sha256-hFvM6kHScaCtcHCc6Vezl9CR7BFbiKPoTEh7kj0ZJxw="; }."${version}"; }; strictDeps = true; - nativeBuildInputs = with ocamlPackages; [ + nativeBuildInputs = lib.optional ideSupport + wrapGAppsHook + ++ (with ocamlPackages; [ ocaml findlib menhir + ]) ++ [ # Coq Support coqPackages.coq ]; @@ -29,8 +34,10 @@ stdenv.mkDerivation rec { emacs # Documentation rubber hevea + ] ++ lib.optional ideSupport # GUI lablgtk3-sourceview3 + ++ [ # WebIDE js_of_ocaml js_of_ocaml-ppx # S-expression output for why3pp @@ -44,10 +51,19 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - configureFlags = [ "--enable-verbose-make" ]; + configureFlags = [ "--enable-verbose-make" + (lib.enableFeature ideSupport "ide") + ]; + + outputs = [ "out" "dev" ]; installTargets = [ "install" "install-lib" ]; + postInstall = '' + mkdir -p $dev/lib + mv $out/lib/ocaml $dev/lib/ + ''; + passthru.withProvers = callPackage ./with-provers.nix {}; meta = with lib; { diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 9ede6a922da6..b247599a0813 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -89,8 +89,8 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: in { z3_4_12 = common { - version = "4.12.4"; - sha256 = "sha256-cxl7D47dRn+uMVOHbF0avj5+ZFWjaJ7lXj/8l6r9q2I="; + version = "4.12.5"; + sha256 = "sha256-Qj9w5s02OSMQ2qA7HG7xNqQGaUacA1d4zbOHynq5k+A="; }; z3_4_11 = common { version = "4.11.2"; diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index 3cd9384ecf1f..e23d252e3f27 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2024-01-22"; + version = "unstable-2024-01-23"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "db4b22cd536cefbdf0b6c928f11c793a5580da0b"; - hash = "sha256-T1GXh1go08XVTToEg5Dq4BuwTCxxqYwQsx+c8g1RPxg="; + rev = "1d55696b742fee0b4ef8e39b7a420c00c2f1e329"; + hash = "sha256-AQdCFKDUWfNKxZoWp82DdxUA2GiMGWyuyh7Fkofm9kc="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/pkgs/applications/science/misc/foldingathome/client.nix b/pkgs/applications/science/misc/foldingathome/client.nix index f61fe5b01857..108dcc284ea9 100644 --- a/pkgs/applications/science/misc/foldingathome/client.nix +++ b/pkgs/applications/science/misc/foldingathome/client.nix @@ -8,13 +8,13 @@ , extraPkgs ? [ ] }: let - version = "8.1.18"; + version = "8.3.1"; cbangSrc = fetchFromGitHub { owner = "cauldrondevelopmentllc"; repo = "cbang"; rev = "bastet-v${version}"; - hash = "sha256-G0rknVmZiyC4sRTOowFjf7EQ5peGf+HLPPcLWXXFlX4="; + hash = "sha256-cuyfJG5aDJ6e2SllxwKTViG0j8FWHvjcTaaBBtkgEdU="; }; fah-client = stdenv.mkDerivation { @@ -25,7 +25,7 @@ let owner = "FoldingAtHome"; repo = "fah-client-bastet"; rev = "v${version}"; - hash = "sha256-IgT/5NqCwN8N8OObjtASuT4IRb2EN4bdixxUdjiyddI="; + hash = "sha256-Ztc2im4Xmk8f6GotGRgA5zDkcyQFnodUvroJVl+ApT4="; }; nativeBuildInputs = [ scons ]; @@ -45,14 +45,15 @@ let installPhase = '' runHook preInstall - mkdir -p $out/{bin,share/applications,share/feh-client} + mkdir -p $out/{bin,share/applications} cp fah-client $out/bin/fah-client - cp install/lin/fah-client.desktop $out/share/applications/ - cp -r images $out/share/feh-client/ - - sed -e "s|Icon=.*|Icon=$out/share/feh-client/images/fahlogo.png|g" -i $out/share/applications/fah-client.desktop + cp install/lin/fah-client.desktop.in $out/share/applications/fah-client.desktop + sed \ + -e "s|Icon=.*|Icon=$out/share/feh-client/images/fahlogo.png|g" \ + -e "s|%(PACKAGE_URL)s|https://github.com/FoldingAtHome/fah-client-bastet|g" \ + -i $out/share/applications/fah-client.desktop runHook postInstall ''; diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index ee3610c5f6f6..c5534c18d7bb 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -2,7 +2,6 @@ , lib , callPackage , fetchurl -, fetchpatch , makeWrapper , cmake , coreutils @@ -58,7 +57,7 @@ stdenv.mkDerivation rec { pname = "root"; - version = "6.30.02"; + version = "6.30.04"; passthru = { tests = import ./tests { inherit callPackage; }; @@ -66,7 +65,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://root.cern.ch/download/root_v${version}.source.tar.gz"; - hash = "sha256-eWWkVtGtHuDV/kdpv1qP7Cka9oTtk9sPMICpw2JDUYM="; + hash = "sha256-K0GAtpjznMZdkQhNgzqIRRWzJbxfZzyOOavoGLAl2Mw="; }; nativeBuildInputs = [ makeWrapper cmake pkg-config git ]; @@ -110,13 +109,6 @@ stdenv.mkDerivation rec { patches = [ ./sw_vers.patch - - # Fix for builtin_llvm=OFF - # https://github.com/root-project/root/pull/14238 - (fetchpatch { - url = "https://github.com/root-project/root/commit/1477d3adebf27a19f3a8b85f21c27a0a5649c7ff.diff"; - hash = "sha256-g+FqXBTWXA7t7F/rMarnmOK2014oCNnNJbHhjH+Tvjw="; - }) ]; preConfigure = '' diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index 1daeeb81410a..80eee27eb2d9 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -40,8 +40,8 @@ let } else { - version = "2023.3"; - hash = "sha256-Tsj40MevdrE/j9FtuOLBIOdJ3kOa6VVNn2U/gS140cs="; + version = "2024"; + hash = "sha256-BNIm1SBmqLw6QuANYhPec3tOwpLiZwMGWST/AZVoAeI="; }; in stdenv.mkDerivation rec { |