diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
17 files changed, 151 insertions, 58 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix index 96182dc835d5..a3faca60c2a6 100644 --- a/nixpkgs/pkgs/applications/science/biology/last/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1540"; + version = "1541"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-oGGpPWWQ5EVK9n5BLQwt1Wch2Xn24B+NrKg6+VrsUMY="; + hash = "sha256-gEesPeGY2RozoViZpBWNTXFJriKVb/r0Efw9XEXwXmM="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/megahit/default.nix b/nixpkgs/pkgs/applications/science/biology/megahit/default.nix index 7f054a51d5e0..5fa9420bc87c 100644 --- a/nixpkgs/pkgs/applications/science/biology/megahit/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/megahit/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, cmake, zlib }: +{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, zlib }: stdenv.mkDerivation rec { pname = "megahit"; @@ -11,6 +11,16 @@ stdenv.mkDerivation rec { sha256 = "1r5d9nkdmgjsbrpj43q9hy3s8jwsabaz3ji561v18hy47v58923c"; }; + patches = [ + # Fix gcc-13 build failure: + # https://github.com/voutcn/megahit/pull/366 + (fetchpatch { + name = "gcc-13.patch"; + url = "https://github.com/voutcn/megahit/commit/4cb2f793503087163bda8592222f105f27e33e66.patch"; + hash = "sha256-b5mhzif+OPcMjmg+BnaUc5CB6Acn/KTBOJEw+WYEhbs="; + }) + ]; + nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; diff --git a/nixpkgs/pkgs/applications/science/biology/svaba/default.nix b/nixpkgs/pkgs/applications/science/biology/svaba/default.nix index 441c7ed6dcc3..d36c4b668ec3 100644 --- a/nixpkgs/pkgs/applications/science/biology/svaba/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/svaba/default.nix @@ -14,6 +14,13 @@ stdenv.mkDerivation rec { buildInputs = [ zlib bzip2 xz ]; + postPatch = '' + # Fix gcc-13 build failure due to missing includes + sed -e '1i #include <cstdint>' -i \ + SeqLib/src/non_api/Histogram.h \ + src/svaba/Histogram.h + ''; + # Workaround build failure on -fno-common toolchains like upstream # gcc-10. Otherwise build fails as: # ld: ./libfml.a(rle.o):/build/source/SeqLib/fermi-lite/rle.h:33: multiple definition of diff --git a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix index 0aeb01c2916b..cefe83446662 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -13,7 +13,7 @@ , libxc , makeWrapper , gsl -, boost175 +, boost180 , autoPatchelfHook # Note that the CASPT2 module is broken with MPI # See https://gitlab.com/Molcas/OpenMolcas/-/issues/169 @@ -93,7 +93,7 @@ stdenv.mkDerivation { armadillo libxc gsl.dev - boost175 + boost180 ] ++ lib.optionals enableMpi [ mpi globalarrays @@ -155,7 +155,7 @@ stdenv.mkDerivation { homepage = "https://gitlab.com/Molcas/OpenMolcas"; maintainers = [ maintainers.markuskowa ]; license = with licenses; [ lgpl21Only bsd3 ]; - platforms = [ "x86_64-linux" ]; + platforms = [ "aarch64-linux" "x86_64-linux" ]; mainProgram = "pymolcas"; }; } diff --git a/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix b/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix index 73c3c9a11f17..c60ee224aa2a 100644 --- a/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix +++ b/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "QtRVSim"; - version = "0.9.6"; + version = "0.9.7"; src = fetchFromGitHub { owner = "cvut"; repo = "qtrvsim"; rev = "refs/tags/v${version}"; - sha256 = "sha256-cC3DvQj2VBnGad6ZDn3x4gHQfsPpySzjTi17PQoaxPU="; + sha256 = "sha256-SelmqHauj5Yxg043NZqR4bhqW5clwg1h7UD8mW7j7vE="; }; nativeBuildInputs = [ cmake wrapQtAppsHook ]; diff --git a/nixpkgs/pkgs/applications/science/computer-architecture/timeloop/default.nix b/nixpkgs/pkgs/applications/science/computer-architecture/timeloop/default.nix index 4e794aaa29e2..ec8ec3ed8abc 100644 --- a/nixpkgs/pkgs/applications/science/computer-architecture/timeloop/default.nix +++ b/nixpkgs/pkgs/applications/science/computer-architecture/timeloop/default.nix @@ -15,13 +15,13 @@ stdenv.mkDerivation rec { pname = "timeloop"; - version = "unstable-2022-11-29"; + version = "3.0.3"; src = fetchFromGitHub { owner = "NVlabs"; repo = "timeloop"; - rev = "905ba953432c812772de935d57fd0a674a89d3c1"; - hash = "sha256-EXiWXf8hdX4vFRNk9wbFSOsix/zVkwrafGUtFrsoAN0="; + rev = "v${version}"; + hash = "sha256-CGPhrBNzFdERAA/Eym2v0+FvFUe+VkBLnwYEqEMHE9k="; }; nativeBuildInputs = [ scons ]; @@ -46,10 +46,14 @@ stdenv.mkDerivation rec { env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-fno-lto"; postPatch = '' + # Fix gcc-13 build failure due to missing includes: + sed -e '1i #include <cstdint>' -i \ + include/compound-config/compound-config.hpp + # use nix ar/ranlib substituteInPlace ./SConstruct \ - --replace "env.Replace(AR = \"gcc-ar\")" "" \ - --replace "env.Replace(RANLIB = \"gcc-ranlib\")" "" + --replace-fail "env.Replace(AR = \"gcc-ar\")" "pass" \ + --replace-fail "env.Replace(RANLIB = \"gcc-ranlib\")" "pass" '' + lib.optionalString stdenv.isDarwin '' # prevent clang from dying on errors that gcc is fine with substituteInPlace ./src/SConscript --replace "-Werror" "-Wno-inconsistent-missing-override" diff --git a/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix b/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix index 593e9d9187b7..4117638a1fda 100644 --- a/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/qucs-s/default.nix @@ -18,13 +18,13 @@ stdenv.mkDerivation rec { pname = "qucs-s"; - version = "2.1.0"; + version = "24.1.0"; src = fetchFromGitHub { owner = "ra3xdh"; repo = "qucs_s"; rev = version; - sha256 = "sha256-C7TLOuC0CHredDiWFIAFmOlV8ivX0j4bs3b8IB8FsqE="; + sha256 = "sha256-ei9CPlJg+Kfjh7vu5VnT6DNLmmnA8wZ2A1jXnm//Fgo="; }; nativeBuildInputs = [ flex bison wrapQtAppsHook cmake ]; diff --git a/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix index 66ba807c8dd8..5c15b8a17241 100644 --- a/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "cryptoverif"; - version = "2.07"; + version = "2.08pl1"; src = fetchurl { url = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${version}.tar.gz"; - hash = "sha256-GXXql4+JZ396BM6W2I3kN0u59xos7UCAtzR0IjMIETY="; + hash = "sha256-rmORSZuhds9W2WpNgYf4AJM2jgEUPoJit4G64qLqj5w="; }; /* Fix up the frontend to load the 'default' cryptoverif library diff --git a/nixpkgs/pkgs/applications/science/logic/elan/default.nix b/nixpkgs/pkgs/applications/science/logic/elan/default.nix index b0df275085e6..6a899eec4dc8 100644 --- a/nixpkgs/pkgs/applications/science/logic/elan/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/elan/default.nix @@ -3,16 +3,16 @@ rustPlatform.buildRustPackage rec { pname = "elan"; - version = "3.0.0"; + version = "3.1.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "elan"; rev = "v${version}"; - sha256 = "sha256-VrCEwAoWKhb1qfJUv3OreTzuKEVQADwZpEQIVEhjwHA="; + hash = "sha256-IC/xb4tZer2cbwIusdCwXxJS3K7kN/XFoU4mxKW4dVc="; }; - cargoHash = "sha256-SMKFSu5C5mc3U266hEa6RB3GH5te3jIrUZAzj3YNa2E="; + cargoHash = "sha256-F80iiXb0UpV+N9q7Msef6/Uzas1DGjMKPWuOKrk8tqU="; nativeBuildInputs = [ pkg-config makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/logic/potassco/clingo.nix b/nixpkgs/pkgs/applications/science/logic/potassco/clingo.nix index a3c324d0dbb8..ad3af12429a2 100644 --- a/nixpkgs/pkgs/applications/science/logic/potassco/clingo.nix +++ b/nixpkgs/pkgs/applications/science/logic/potassco/clingo.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "clingo"; - version = "5.6.2"; + version = "5.7.1"; src = fetchFromGitHub { owner = "potassco"; repo = "clingo"; rev = "v${version}"; - sha256 = "sha256-2vOscD5jengY3z9gHoY9y9y6RLfdzUj7BNKLyppNRac="; + sha256 = "sha256-S0JAfMwg49aryKABbC/2oLCEkndVpMVcFE6X0vkbtNc="; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/logic/stp/default.nix b/nixpkgs/pkgs/applications/science/logic/stp/default.nix index 42926a870816..fb41ea07f5a1 100644 --- a/nixpkgs/pkgs/applications/science/logic/stp/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/stp/default.nix @@ -11,6 +11,20 @@ stdenv.mkDerivation rec { rev = version; sha256 = "1yg2v4wmswh1sigk47drwsxyayr472mf4i47lqmlcgn9hhbx1q87"; }; + patches = [ + # Fix missing type declaration + # due to undeterminisitic compilation + # of circularly dependent headers + ./stdint.patch + ]; + + postPatch = '' + # Upstream fix for gcc-13 support: + # https://github.com/stp/stp/pull/462 + # Can't apply it as is as patch context changed in ither patches. + # TODO: remove me on 2.4 release + sed -e '1i #include <cstdint>' -i include/stp/AST/ASTNode.h + ''; buildInputs = [ boost zlib minisat cryptominisat python3 ]; nativeBuildInputs = [ cmake bison flex perl ]; @@ -26,7 +40,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Simple Theorem Prover"; - maintainers = with maintainers; [ ]; + maintainers = with maintainers; [ McSinyx ]; platforms = platforms.linux; license = licenses.mit; }; diff --git a/nixpkgs/pkgs/applications/science/logic/stp/stdint.patch b/nixpkgs/pkgs/applications/science/logic/stp/stdint.patch new file mode 100644 index 000000000000..6595d5561731 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/stp/stdint.patch @@ -0,0 +1,16 @@ +diff --git a/include/stp/AST/ASTNode.h b/include/stp/AST/ASTNode.h +index 91acd726182c..0a17db23ffbf 100644 +--- a/include/stp/AST/ASTNode.h ++++ b/include/stp/AST/ASTNode.h +@@ -24,9 +24,10 @@ THE SOFTWARE. + #ifndef ASTNODE_H + #define ASTNODE_H + ++#include "stp/AST/ASTInternal.h" + #include "stp/AST/NodeFactory/HashingNodeFactory.h" ++#include "stp/AST/UsefulDefs.h" + #include "stp/Util/Attributes.h" +-#include "ASTInternal.h" + #include "stp/Globals/Globals.h" + + namespace stp diff --git a/nixpkgs/pkgs/applications/science/misc/openmvg/default.nix b/nixpkgs/pkgs/applications/science/misc/openmvg/default.nix index c5434c869909..5cf4dc437752 100644 --- a/nixpkgs/pkgs/applications/science/misc/openmvg/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/openmvg/default.nix @@ -1,34 +1,63 @@ -{ lib, stdenv, fetchFromGitHub, pkg-config, cmake, cereal, openmp -, libjpeg ? null -, zlib ? null -, libpng ? null -, eigen ? null -, libtiff ? null +{ lib, stdenv, fetchFromGitHub, pkg-config, cmake +, cereal , ceres-solver +, clp +, coin-utils +, eigen +, lemon-graph +, libjpeg +, libpng +, libtiff +, nix-update-script +, openmp +, osi +, zlib , enableShared ? !stdenv.hostPlatform.isStatic , enableExamples ? false , enableDocs ? false }: stdenv.mkDerivation rec { - version = "unstable-2022-12-30"; + version = "2.1"; pname = "openmvg"; src = fetchFromGitHub { owner = "openmvg"; repo = "openmvg"; - rev = "e1bbfe801986cd7171f36443a1573b0f69f3702d"; - sha256 = "sha256-DngfmejNFw5pogTo7Ec5aUey2LUQIojvJybLmtCfvVY="; - fetchSubmodules = true; + rev = "v${version}"; + hash = "sha256-vG+tW9Gl/DAUL8DeY+rJVDJH/oMPH3XyZMUgzjtwFv0="; }; - buildInputs = [ libjpeg zlib libpng eigen libtiff cereal openmp ceres-solver ]; + # Pretend we checked out the dependency submodules + postPatch = '' + mkdir src/dependencies/cereal/include + ''; + + buildInputs = [ + cereal + ceres-solver + clp + coin-utils + eigen + lemon-graph + libjpeg + libpng + libtiff + openmp + osi + zlib + ]; nativeBuildInputs = [ cmake pkg-config ]; + # flann is missing because the lz4 dependency isn't propagated: https://github.com/openMVG/openMVG/issues/1265 cmakeFlags = [ "-DOpenMVG_BUILD_EXAMPLES=${if enableExamples then "ON" else "OFF"}" "-DOpenMVG_BUILD_DOC=${if enableDocs then "ON" else "OFF"}" "-DTARGET_ARCHITECTURE=generic" + "-DCLP_INCLUDE_DIR_HINTS=${lib.getDev clp}/include" + "-DCOINUTILS_INCLUDE_DIR_HINTS=${lib.getDev coin-utils}/include" + "-DLEMON_INCLUDE_DIR_HINTS=${lib.getDev lemon-graph}/include" + "-DOSI_INCLUDE_DIR_HINTS=${lib.getDev osi}/include" ] ++ lib.optional enableShared "-DOpenMVG_BUILD_SHARED=ON"; cmakeDir = "./src"; @@ -41,6 +70,8 @@ stdenv.mkDerivation rec { # Without hardeningDisable, certain flags are passed to the compile that break the build (primarily string format errors) hardeningDisable = [ "all" ]; + passthru.updateScript = nix-update-script { }; + meta = { broken = stdenv.isDarwin && stdenv.isx86_64; description = "A library for computer-vision scientists and targeted for the Multiple View Geometry community"; diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix index c5534c18d7bb..9548db1c7c47 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix @@ -2,6 +2,7 @@ , lib , callPackage , fetchurl +, fetchpatch , makeWrapper , cmake , coreutils @@ -109,6 +110,17 @@ stdenv.mkDerivation rec { patches = [ ./sw_vers.patch + + # compatibility with recent XRootD + # https://github.com/root-project/root/pull/13752 + (fetchpatch { + url = "https://github.com/root-project/root/commit/3d3cda6c520791282298782189cdb8ca07ace4b9.diff"; + hash = "sha256-O3aXzrOEQiPjZgbAj9TL6Wt/adN1kKFwjooeaFRyT4I="; + }) + (fetchpatch { + url = "https://github.com/root-project/root/commit/6e7798e62dbed1ffa8b91a180fa5a080b7c04ba3.diff"; + hash = "sha256-47/J631DBnVlvM1Pm9iicKXDKAqN8v9hjAstQuHmH8Q="; + }) ]; preConfigure = '' @@ -202,13 +214,10 @@ stdenv.mkDerivation rec { # suppress warnings from compilation of the vendored clang to avoid running into log limits on the Hydra NIX_CFLAGS_COMPILE = lib.optionals stdenv.cc.isGNU [ "-Wno-shadow" "-Wno-maybe-uninitialized" ]; - # Workaround the xrootd runpath bug #169677 by prefixing [DY]LD_LIBRARY_PATH with ${lib.makeLibraryPath xrootd}. - # TODO: Remove the [DY]LDLIBRARY_PATH prefix for xrootd when #200830 get merged. postInstall = '' for prog in rootbrowse rootcp rooteventselector rootls rootmkdir rootmv rootprint rootrm rootslimtree; do wrapProgram "$out/bin/$prog" \ - --set PYTHONPATH "$out/lib" \ - --set ${lib.optionalString stdenv.isDarwin "DY"}LD_LIBRARY_PATH "$out/lib:${lib.makeLibraryPath [ xrootd ]}" + --set PYTHONPATH "$out/lib" done # Make ldd and sed available to the ROOT executable by prefixing PATH. @@ -217,8 +226,7 @@ stdenv.mkDerivation rec { gnused # sed stdenv.cc # c++ ld etc. stdenv.cc.libc # ldd - ]}" \ - --prefix ${lib.optionalString stdenv.hostPlatform.isDarwin "DY"}LD_LIBRARY_PATH : "${lib.makeLibraryPath [ xrootd ]}" + ]}" # Patch thisroot.{sh,csh,fish} diff --git a/nixpkgs/pkgs/applications/science/misc/sasview/default.nix b/nixpkgs/pkgs/applications/science/misc/sasview/default.nix index ddc0cdfa4e5b..e896b19ede83 100644 --- a/nixpkgs/pkgs/applications/science/misc/sasview/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/sasview/default.nix @@ -1,30 +1,21 @@ { lib , python3 , fetchFromGitHub -, fetchpatch , wrapQtAppsHook }: python3.pkgs.buildPythonApplication rec { pname = "sasview"; - version = "5.0.4"; + version = "5.0.6"; + pyproject = true; src = fetchFromGitHub { owner = "SasView"; repo = "sasview"; - rev = "v${version}"; - hash = "sha256-TjcchqA6GCvkr59ZgDuGglan2RxLp+aMjJk28XhvoiY="; + rev = "refs/tags/v${version}"; + hash = "sha256-cwP9VuvO4GPlbAxCqw31xISTi9NoF5RoBQmjWusrnzc="; }; - patches = [ - # Fix `asscalar` numpy API removal. - # See https://github.com/SasView/sasview/pull/2178 - (fetchpatch { - url = "https://github.com/SasView/sasview/commit/b1ab08c2a4e8fdade7f3e4cfecf3dfec38b8f3c5.patch"; - hash = "sha256-IH8g4XPziVAnkmBdzLH1ii8vN6kyCmOgrQlH2HEbm5o="; - }) - ]; - # AttributeError: module 'numpy' has no attribute 'float'. postPatch = '' substituteInPlace src/sas/sascalc/pr/p_invertor.py \ @@ -33,6 +24,7 @@ python3.pkgs.buildPythonApplication rec { nativeBuildInputs = [ python3.pkgs.pyqt5 + python3.pkgs.setuptools wrapQtAppsHook ]; @@ -66,12 +58,21 @@ python3.pkgs.buildPythonApplication rec { unittest-xml-reporting ]; - pytestFlagsArray = [ "test" ]; + pytestFlagsArray = [ + "test" + ]; + + disabledTests = [ + # NoKnownLoaderException + "test_invalid_cansas" + "test_data_reader_exception" + ]; meta = with lib; { - homepage = "https://www.sasview.org"; description = "Fitting and data analysis for small angle scattering data"; - maintainers = with maintainers; [ rprospero ]; + homepage = "https://www.sasview.org"; + changelog = "https://github.com/SasView/sasview/releases/tag/v${version}"; license = licenses.bsd3; + maintainers = with maintainers; [ rprospero ]; }; } diff --git a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix index ba9cfb41f09c..465ae196b47d 100644 --- a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix @@ -6,14 +6,14 @@ python3.pkgs.buildPythonApplication rec { pname = "snakemake"; - version = "8.4.4"; + version = "8.4.8"; format = "setuptools"; src = fetchFromGitHub { owner = "snakemake"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-d3pUVhn9oi1ILDR4sfRh6HypbDn2JZMha27h0twixPc="; + hash = "sha256-iF5+slcPTRK/3SmqR+4KK5KAK5LhKAe+nt+U/B5C3/8="; # https://github.com/python-versioneer/python-versioneer/issues/217 postFetch = '' sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#' diff --git a/nixpkgs/pkgs/applications/science/physics/xfitter/default.nix b/nixpkgs/pkgs/applications/science/physics/xfitter/default.nix index 1852ef3ff1c8..77b57e08e2bb 100644 --- a/nixpkgs/pkgs/applications/science/physics/xfitter/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/xfitter/default.nix @@ -47,6 +47,8 @@ stdenv.mkDerivation rec { env.NIX_CFLAGS_COMPILE = lib.optionalString (stdenv.hostPlatform.libc == "glibc") "-I${libtirpc.dev}/include/tirpc"; NIX_LDFLAGS = lib.optional (stdenv.hostPlatform.libc == "glibc") "-ltirpc"; + hardeningDisable = [ "format" ]; + # workaround wrong library IDs postInstall = lib.optionalString stdenv.isDarwin '' ln -sv "$out/lib/xfitter/"* "$out/lib/" |