diff options
Diffstat (limited to 'pkgs/applications/science')
17 files changed, 64 insertions, 48 deletions
diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index fa96f32e8c93..19e5f99fe2f6 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "bcftools"; - version = "1.18"; + version = "1.19"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-2bnTYpPkzGKrdHOqJTk4nU4d55sakn1IP26R88POrH4="; + sha256 = "sha256-eCtfG8aQQVGSIx6CITs0k7BH9F5jDcjvbxVNYSarPmg="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/gatk/default.nix b/pkgs/applications/science/biology/gatk/default.nix index 43e5382b5d50..9884e3a77111 100644 --- a/pkgs/applications/science/biology/gatk/default.nix +++ b/pkgs/applications/science/biology/gatk/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "gatk"; - version = "4.4.0.0"; + version = "4.5.0.0"; src = fetchzip { url = "https://github.com/broadinstitute/gatk/releases/download/${version}/gatk-${version}.zip"; - sha256 = "sha256-svOtIS6gz9nwVgVmVQbk9z6Ufyobpn6bFbZY4zurvUI="; + sha256 = "sha256-c3YZsSCjZY75jooiqtc8x/xsWTvYm9labUcOydDlSRQ="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 607b1ee51cc5..ed8690cd9c85 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1518"; + version = "1519"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-a6i5BfJhVHkXTLd7SVFxISEB+Kwl7BhjUUkF8ItMOak="; + hash = "sha256-659YiC7NA6ottOR41jo3ayh4lwReWj46NKMhMPuebF4="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/chemistry/avogadro2/default.nix b/pkgs/applications/science/chemistry/avogadro2/default.nix index 2ff0cab1847a..dad31b738a84 100644 --- a/pkgs/applications/science/chemistry/avogadro2/default.nix +++ b/pkgs/applications/science/chemistry/avogadro2/default.nix @@ -6,19 +6,19 @@ let avogadroI18N = fetchFromGitHub { owner = "OpenChemistry"; repo = "avogadro-i18n"; - rev = "3b8a86cc37e988b043d1503d2f11068389b0aca3"; - sha256 = "9wLY7/EJyIZYnlUAMsViCwD5kGc1vCNbk8vUhb90LMQ="; + rev = "7eef0b83ded6221a3ddb85c0118cc26f9a35375c"; + hash = "sha256-AR/y70zeYR9xBzWDB5JXjJdDM+NLOX6yxCQte2lYN/U="; }; in stdenv.mkDerivation rec { pname = "avogadro2"; - version = "1.97.0"; + version = "1.98.1"; src = fetchFromGitHub { owner = "OpenChemistry"; repo = "avogadroapp"; rev = version; - hash = "sha256-gZpMgFSPz70QNfd8gH5Jb9RTxQfQalWx33LkgXLEqOQ="; + hash = "sha256-N35WGYZbgfjKnorzGKCnbBvlrlt9Vr04YIG2R3k+b8A="; }; postUnpack = '' diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index f006df2ae5c0..ce3b279deab1 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 = "16.1.45"; + version = "16.1.47"; 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-${version}-binary.tar.gz"; - hash = "sha256-rLq0QrY1M0OptmRZ/dKUVssREnH1im9Ti89AbpsiFtg="; + hash = "sha256-3hsH+RkPPoViKp1bc/88GDVSG8jf9hiPKPkUfe9PIkk="; }; patchPhase = '' diff --git a/pkgs/applications/science/electronics/csxcad/default.nix b/pkgs/applications/science/electronics/csxcad/default.nix index abdb0716f370..83ee992f4b28 100644 --- a/pkgs/applications/science/electronics/csxcad/default.nix +++ b/pkgs/applications/science/electronics/csxcad/default.nix @@ -4,7 +4,7 @@ , fparser , tinyxml , hdf5 -, cgal_5 +, cgal , vtk , boost , gmp @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { patches = [./searchPath.patch ]; buildInputs = [ - cgal_5 + cgal boost gmp mpfr diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix index 8d28e4da0f14..77ee3d97c9c8 100644 --- a/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -13,11 +13,11 @@ stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.449"; + version = "8.3.453"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-y0+HS1LkIFwcgDbHEvs5SXJY2b340RDT7KVupp+ZX9Y="; + sha256 = "sha256-1G8vm9AGboIElufXUIa9ZABaHVjx4UiBNA0ZTYeuVtU="; }; nativeBuildInputs = [ python3 ]; diff --git a/pkgs/applications/science/electronics/nvc/default.nix b/pkgs/applications/science/electronics/nvc/default.nix index 284a0b15830b..a6f2c9d44731 100644 --- a/pkgs/applications/science/electronics/nvc/default.nix +++ b/pkgs/applications/science/electronics/nvc/default.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation rec { pname = "nvc"; - version = "1.11.0"; + version = "1.11.1"; src = fetchFromGitHub { owner = "nickg"; repo = "nvc"; rev = "r${version}"; - hash = "sha256-95vIyBQ38SGpI+gnDqK1MRRzOT6uiYjDr1c//folqZ8="; + hash = "sha256-aBH3TtPFuJXtVvGTJcGJev5DYVwqjUAM9cf5PatJq9Y="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/electronics/xyce/default.nix b/pkgs/applications/science/electronics/xyce/default.nix index 663d6e025c5c..30d8e0b8186d 100644 --- a/pkgs/applications/science/electronics/xyce/default.nix +++ b/pkgs/applications/science/electronics/xyce/default.nix @@ -32,21 +32,21 @@ assert withMPI -> trilinos.withMPI; let - version = "7.6.0"; + version = "7.7.0"; # useing fetchurl or fetchFromGitHub doesn't include the manuals # due to .gitattributes files xyce_src = fetchgit { url = "https://github.com/Xyce/Xyce.git"; rev = "Release-${version}"; - sha256 = "sha256-HYIzmODMWXBuVRZhcC7LntTysuyXN5A9lb2DeCQQtVw="; + sha256 = "sha256-F0kO86eliD1AfUUjeVllxJ231ZElXkfBfGJ3jhT0s9w="; }; regression_src = fetchFromGitHub { owner = "Xyce"; repo = "Xyce_Regression"; rev = "Release-${version}"; - sha256 = "sha256-uEoiKpYyHmdK7LZ1UNm2d3Jk8+sCwBwB0TCoHilIh74="; + sha256 = "sha256-iDxm0Vcn3JuuREciCt3/b7q94E8GhXoIUD/BCx0mW6Q="; }; in @@ -154,8 +154,11 @@ stdenv.mkDerivation rec { "doc/Reference_Guide/Xyce_RG" "doc/Release_Notes/Release_Notes_${lib.versions.majorMinor version}/Release_Notes_${lib.versions.majorMinor version}") - # Release notes refer to an image not in the repo. - sed -i -E 's/\\includegraphics\[height=(0.5in)\]\{snllineblubrd\}/\\mbox\{\\rule\{0mm\}\{\1\}\}/' ''${docFiles[2]}.tex + # SANDIA LaTeX class and some organization logos are not publicly available see + # https://groups.google.com/g/xyce-users/c/MxeViRo8CT4/m/ppCY7ePLEAAJ + for img in "snllineblubrd" "snllineblk" "DOEbwlogo" "NNSA_logo"; do + sed -i -E "s/\\includegraphics\[height=(0.[1-9]in)\]\{$img\}/\\mbox\{\\rule\{0mm\}\{\1\}\}/" ''${docFiles[2]}.tex + done install -d $doc/share/doc/${pname}-${version}/ for d in ''${docFiles[@]}; do diff --git a/pkgs/applications/science/logic/alt-ergo/default.nix b/pkgs/applications/science/logic/alt-ergo/default.nix index bc8c6ae48587..d84aa5b6918a 100644 --- a/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/pkgs/applications/science/logic/alt-ergo/default.nix @@ -1,4 +1,4 @@ -{ fetchurl, fetchpatch, lib, ocamlPackages }: +{ darwin, fetchurl, lib, ocamlPackages, stdenv }: let pname = "alt-ergo"; @@ -28,7 +28,7 @@ ocamlPackages.buildDunePackage { inherit pname version src; - nativeBuildInputs = [ ocamlPackages.menhir ]; + nativeBuildInputs = [ ocamlPackages.menhir ] ++ lib.optionals stdenv.isDarwin [ darwin.sigtool ]; buildInputs = [ alt-ergo-parsers ] ++ (with ocamlPackages; [ cmdliner dune-site ]); meta = { diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 9717e69e9c26..039a5334969e 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -56,6 +56,7 @@ let "8.17.0".sha256 = "sha256-TGwm7S6+vkeZ8cidvp8pkiAd9tk008jvvPvYgfEOXhM="; "8.17.1".sha256 = "sha256-x+RwkbxMg9aR0L3WSCtpIz8jwA5cJA4tXAtHMZb20y4="; "8.18.0".sha256 = "sha256-WhiBs4nzPHQ0R24xAdM49kmxSCPOxiOVMA1iiMYunz4="; + "8.19+rc1".sha256 = "sha256-hQ57tLj8lXTbMrW+F0skPtzpHJnXbqPIc/EzocRV5qo="; }; releaseRev = v: "V${v}"; fetched = import ../../../../build-support/coq/meta-fetch/default.nix diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index 9fe06f6d7969..ee3610c5f6f6 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -58,7 +58,7 @@ stdenv.mkDerivation rec { pname = "root"; - version = "6.28.10"; + version = "6.30.02"; passthru = { tests = import ./tests { inherit callPackage; }; @@ -66,7 +66,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://root.cern.ch/download/root_v${version}.source.tar.gz"; - hash = "sha256-adb962B+ayC9AsdX+mIXAkwLYTLB6bHf9Nhdmiu35R4="; + hash = "sha256-eWWkVtGtHuDV/kdpv1qP7Cka9oTtk9sPMICpw2JDUYM="; }; nativeBuildInputs = [ makeWrapper cmake pkg-config git ]; @@ -110,6 +110,13 @@ 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 = '' @@ -121,7 +128,7 @@ stdenv.mkDerivation rec { substituteInPlace cmake/modules/SearchInstalledSoftware.cmake \ --replace 'set(lcgpackages ' '#set(lcgpackages ' - substituteInPlace interpreter/llvm/src/tools/clang/tools/driver/CMakeLists.txt \ + substituteInPlace interpreter/llvm-project/clang/tools/driver/CMakeLists.txt \ --replace 'add_clang_symlink(''${link} clang)' "" # Don't require textutil on macOS @@ -136,8 +143,8 @@ stdenv.mkDerivation rec { substituteInPlace rootx/src/rootx.cxx --replace "gNoLogo = false" "gNoLogo = true" '' + lib.optionalString stdenv.isDarwin '' # Eliminate impure reference to /System/Library/PrivateFrameworks - substituteInPlace core/CMakeLists.txt \ - --replace "-F/System/Library/PrivateFrameworks" "" + substituteInPlace core/macosx/CMakeLists.txt \ + --replace "-F/System/Library/PrivateFrameworks " "" '' + lib.optionalString (stdenv.isDarwin && lib.versionAtLeast stdenv.hostPlatform.darwinMinVersion "11") '' MACOSX_DEPLOYMENT_TARGET=10.16 ''; @@ -184,6 +191,7 @@ stdenv.mkDerivation rec { "-Dsqlite=OFF" "-Dssl=ON" "-Dtmva=ON" + "-Dtmva-pymva=OFF" "-Dvdt=OFF" "-Dwebgui=ON" "-Dxml=ON" diff --git a/pkgs/applications/science/misc/root/sw_vers.patch b/pkgs/applications/science/misc/root/sw_vers.patch index 836bbb5b17a4..54ad1091392e 100644 --- a/pkgs/applications/science/misc/root/sw_vers.patch +++ b/pkgs/applications/science/misc/root/sw_vers.patch @@ -1,8 +1,8 @@ diff a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake --- a/cmake/modules/SetUpMacOS.cmake +++ b/cmake/modules/SetUpMacOS.cmake -@@ -28,17 +28,10 @@ if(CMAKE_VERSION VERSION_LESS 3.14.4) - endif() +@@ -8,17 +8,10 @@ + set(ROOT_PLATFORM macosx) if (CMAKE_SYSTEM_NAME MATCHES Darwin) - EXECUTE_PROCESS(COMMAND sw_vers "-productVersion" @@ -19,7 +19,7 @@ diff a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake #TODO: check haveconfig and rpath -> set rpath true #TODO: check Thread, define link command #TODO: more stuff check configure script -@@ -57,22 +50,7 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin) +@@ -37,22 +30,7 @@ SET(CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS "${CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS} -m64") SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64") SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -m64") @@ -42,7 +42,7 @@ diff a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake if (CMAKE_COMPILER_IS_GNUCXX) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pipe -W -Wshadow -Wall -Woverloaded-virtual -fsigned-char -fno-common") -@@ -130,7 +108,6 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin) +@@ -96,7 +74,6 @@ endif() #---Set Linker flags---------------------------------------------------------------------- @@ -53,7 +53,7 @@ diff a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake diff a/config/root-config.in b/config/root-config.in --- a/config/root-config.in +++ b/config/root-config.in -@@ -312,12 +312,6 @@ macosxicc) +@@ -307,12 +307,6 @@ ;; macosx64|macosxarm64) # MacOS X with gcc (GNU cc v4.x) in 64 bit mode @@ -66,7 +66,7 @@ diff a/config/root-config.in b/config/root-config.in auxcflags="${cxxversionflag} -m64" auxldflags="-m64" auxlibs="-lm -ldl" -@@ -378,18 +372,11 @@ freebsd* | openbsd* | linux*) +@@ -387,17 +381,11 @@ done ;; macosx*) @@ -74,7 +74,6 @@ diff a/config/root-config.in b/config/root-config.in auxcflags="-pthread $auxcflags" auxlibs="-lpthread $auxlibs" - else -- auxcflags="-D_REENTRANT $auxcflags" - auxlibs="-lpthread $auxlibs" - fi for f in $features ; do diff --git a/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix b/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix index cf4584979ba2..a13a071584fd 100644 --- a/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix +++ b/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix @@ -20,6 +20,9 @@ stdenv.mkDerivation { cp -v ../build/MakePAR Makefile ''; + # https://gitlab.com/DL_POLY_Classic/dl_poly/-/blob/master/README + env.NIX_CFLAGS_COMPILE = "-fallow-argument-mismatch"; + buildPhase = '' make dlpoly ''; @@ -33,7 +36,7 @@ stdenv.mkDerivation { homepage = "https://www.ccp5.ac.uk/DL_POLY_C"; description = "DL_POLY Classic is a general purpose molecular dynamics simulation package"; license = licenses.bsdOriginal; - platforms = [ "x86_64-linux" ]; + platforms = platforms.unix; maintainers = [ maintainers.costrouc ]; }; } diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix index 7924d044c2ab..feb7a98bd59d 100644 --- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -46,14 +46,14 @@ stdenv.mkDerivation (finalAttrs: { # LAMMPS has weird versioning convention. Updates should go smoothly with: # nix-update --commit lammps --version-regex 'stable_(.*)' - version = "2Aug2023_update1"; + version = "2Aug2023_update2"; pname = "lammps"; src = fetchFromGitHub { owner = "lammps"; repo = "lammps"; rev = "stable_${finalAttrs.version}"; - hash = "sha256-Zmn87a726qdidBfyvJlYleYv9jqyFAakxjGrg3lipc0="; + hash = "sha256-E918Jv6RAfXmHxyHZos2F7S8HFWzU6KjxDwXYNAYFMY="; }; preConfigure = '' cd cmake diff --git a/pkgs/applications/science/physics/nnpdf/default.nix b/pkgs/applications/science/physics/nnpdf/default.nix index ec29c02054df..f6d3e94c1a05 100644 --- a/pkgs/applications/science/physics/nnpdf/default.nix +++ b/pkgs/applications/science/physics/nnpdf/default.nix @@ -15,13 +15,13 @@ stdenv.mkDerivation rec { pname = "nnpdf"; - version = "4.0.6"; + version = "4.0.7"; src = fetchFromGitHub { owner = "NNPDF"; repo = pname; rev = version; - hash = "sha256-mwOMNlYFhHZq/wakO1/HGwcxvKGKh5OyFa2D9d3Y3IA="; + hash = "sha256-J5l+ZO+5pfxKlpFuy4PEQynbqs1QIqMK6hhMFvmb/zs="; }; postPatch = '' diff --git a/pkgs/applications/science/robotics/mujoco/default.nix b/pkgs/applications/science/robotics/mujoco/default.nix index 139e1140e7c9..95d3e1269350 100644 --- a/pkgs/applications/science/robotics/mujoco/default.nix +++ b/pkgs/applications/science/robotics/mujoco/default.nix @@ -22,8 +22,8 @@ let benchmark = fetchFromGitHub { owner = "google"; repo = "benchmark"; - rev = "344117638c8ff7e239044fd0fa7085839fc03021"; - hash = "sha256-gztnxui9Fe/FTieMjdvfJjWHjkImtlsHn6fM1FruyME="; + rev = "e45585a4b8e75c28479fa4107182c28172799640"; + hash = "sha256-pgHvmRpPd99ePUVRsi7WXLVSZngZ5q6r1vWW4mdGvxY="; }; ccd = fetchFromGitHub { owner = "danfis"; @@ -34,8 +34,8 @@ let eigen3 = fetchFromGitLab { owner = "libeigen"; repo = "eigen"; - rev = "e8515f78ac098329ab9f8cab21c87caede090a3f"; - hash = "sha256-HXKtFJsKGpug+wNPjYynTuyaG0igo3oG4rFQktveh1g="; + rev = "454f89af9d6f3525b1df5f9ef9c86df58bf2d4d3"; + hash = "sha256-a9QAnv6vIM8a9Bn8ZmfeMT0+kbtb0QGxM0+m5xwIqm8="; }; googletest = fetchFromGitHub { owner = "google"; @@ -129,13 +129,15 @@ let in stdenv.mkDerivation rec { pname = "mujoco"; - version = "3.0.1"; + version = "3.1.0"; + # Bumping version? Make sure to look though the MuJoCo's commit + # history for bumped dependency pins! src = fetchFromGitHub { owner = "google-deepmind"; repo = pname; rev = version; - hash = "sha256-UXE+7KDti8RarpoJoo9Ei3TgW/Qdnj3ASRo8uTWhGrU="; + hash = "sha256-a8h30psoAlj9dI4j8IfY3WzWjY4MrRosGbvgt79s1BQ="; }; patches = [ ./mujoco-system-deps-dont-fetch.patch ]; |