diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
42 files changed, 183 insertions, 143 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/celestia/default.nix b/nixpkgs/pkgs/applications/science/astronomy/celestia/default.nix index 7f979596148f..d9130223e836 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/celestia/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/celestia/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { pname = "celestia"; - version = "1.6.3"; + version = "1.6.4"; src = fetchFromGitHub { owner = "CelestiaProject"; repo = "Celestia"; rev = version; - sha256 = "sha256-iBlrP9Yr/l3tzR1PpRf8C87WfrL6mZDwDtWyd2yJ7Dc="; + sha256 = "sha256-MkElGo1ZR0ImW/526QlDE1ePd+VOQxwkX7l+0WyZ6Vs="; }; nativeBuildInputs = [ pkg-config autoreconfHook ]; diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix index 3b61c8dac2b8..cad727c75fd6 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix @@ -18,17 +18,19 @@ , indilib , libnova , qttools +, exiv2 +, nlopt }: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "stellarium"; - version = "23.3"; + version = "23.4"; src = fetchFromGitHub { owner = "Stellarium"; repo = "stellarium"; - rev = "v${version}"; - hash = "sha256-bYvGmYu9jMHk2IUICz2kCVh56Ymz8JHqurdWV+xEdJY="; + rev = "v${finalAttrs.version}"; + hash = "sha256-rDqDs6sFaZQbqJcCRhY5w8sFM2mYHHvw0Ud2Niimg4Y="; }; patches = [ @@ -66,12 +68,14 @@ stdenv.mkDerivation rec { qxlsx indilib libnova + exiv2 + nlopt ] ++ lib.optionals stdenv.isLinux [ qtwayland ]; preConfigure = '' - export SOURCE_DATE_EPOCH=$(date -d 20${lib.versions.major version}0101 +%s) + export SOURCE_DATE_EPOCH=$(date -d 20${lib.versions.major finalAttrs.version}0101 +%s) '' + lib.optionalString stdenv.isDarwin '' export LC_ALL=en_US.UTF-8 ''; @@ -89,11 +93,11 @@ stdenv.mkDerivation rec { qtWrapperArgs+=("''${gappsWrapperArgs[@]}") ''; - meta = with lib; { + meta = { description = "Free open-source planetarium"; homepage = "https://stellarium.org/"; - license = licenses.gpl2Plus; - platforms = platforms.unix; - maintainers = with maintainers; [ kilianar ]; + license = lib.licenses.gpl2Plus; + platforms = lib.platforms.unix; + maintainers = with lib.maintainers; [ kilianar ]; }; -} +}) diff --git a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix index fa96f32e8c93..19e5f99fe2f6 100644 --- a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "bcftools"; - version = "1.18"; + version = "1.19"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-2bnTYpPkzGKrdHOqJTk4nU4d55sakn1IP26R88POrH4="; + sha256 = "sha256-eCtfG8aQQVGSIx6CITs0k7BH9F5jDcjvbxVNYSarPmg="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/delly/default.nix b/nixpkgs/pkgs/applications/science/biology/delly/default.nix index 52e2980980af..b483b3d57bef 100644 --- a/nixpkgs/pkgs/applications/science/biology/delly/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/delly/default.nix @@ -13,13 +13,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "delly"; - version = "1.1.8"; + version = "1.2.6"; src = fetchFromGitHub { owner = "dellytools"; repo = "delly"; rev = "v${finalAttrs.version}"; - hash = "sha256-IxZPbcM52E1bzy6msGmka6Ykgc+OLWTMhWBCn0E4mFI="; + hash = "sha256-OO5nnaIcfNAV8pc03Z8YS5kE96bFOrJXA9QTiLi7vPc="; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/gatk/default.nix b/nixpkgs/pkgs/applications/science/biology/gatk/default.nix index 43e5382b5d50..9884e3a77111 100644 --- a/nixpkgs/pkgs/applications/science/biology/gatk/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/gatk/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "gatk"; - version = "4.4.0.0"; + version = "4.5.0.0"; src = fetchzip { url = "https://github.com/broadinstitute/gatk/releases/download/${version}/gatk-${version}.zip"; - sha256 = "sha256-svOtIS6gz9nwVgVmVQbk9z6Ufyobpn6bFbZY4zurvUI="; + sha256 = "sha256-c3YZsSCjZY75jooiqtc8x/xsWTvYm9labUcOydDlSRQ="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix index 607b1ee51cc5..ed8690cd9c85 100644 --- a/nixpkgs/pkgs/applications/science/biology/last/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1518"; + version = "1519"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-a6i5BfJhVHkXTLd7SVFxISEB+Kwl7BhjUUkF8ItMOak="; + hash = "sha256-659YiC7NA6ottOR41jo3ayh4lwReWj46NKMhMPuebF4="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix index 456e8f42dbac..d4ce4071a274 100644 --- a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix @@ -1,14 +1,14 @@ { lib, stdenv, fetchFromGitHub, cmake, gcc, gcc-unwrapped }: stdenv.mkDerivation rec { - version = "4.0.1"; + version = "4.1"; pname = "messer-slim"; src = fetchFromGitHub { owner = "MesserLab"; repo = "SLiM"; rev = "v${version}"; - sha256 = "sha256-KC9MbIJi//ZYreoRS+DED8eQW7e4IPvGT+rLI+f7Zrk="; + sha256 = "sha256-mb6xcu28QYAFm2906lRNY0zciQBKSGcz3q/cvOEh/VE="; }; nativeBuildInputs = [ cmake gcc gcc-unwrapped ]; diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix index b5743df9a7ca..7db1edcbe9e9 100644 --- a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "samtools"; - version = "1.18"; + version = "1.19"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-1ob/piECO6YYIqKlC3DoXQsY55Nx3lrbB4KFGdP8BuE="; + sha256 = "sha256-+ms7GOIIUbbzy1WvrzIF0C/LedrjuEn89S6PwQ/wi4M="; }; # tests require `bgzip` from the htslib package diff --git a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix index 3c6ac4545442..7d1778867921 100644 --- a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix @@ -5,16 +5,16 @@ buildGoModule rec { pname = "seqkit"; - version = "2.6.0"; + version = "2.6.1"; src = fetchFromGitHub { owner = "shenwei356"; repo = "seqkit"; rev = "v${version}"; - sha256 = "sha256-ahCLPYRRH6xIRFhgpjvnw7G1AIOfrkzLKPA8t9+k9gg="; + sha256 = "sha256-zdn5jyb8mQ8CXHu3bHpZ7+c6K6lwoSLnmhMspMeDzy0="; }; - vendorHash = "sha256-OpLLJdwEW7UnMKr6r8+EDUlpiahfa5k9AkBqcd+SE5k="; + vendorHash = "sha256-iVsLJ7UcUVTg14yEdThb6HBx6XutG0m+S9OW4iiFPUE="; meta = with lib; { description = "cross-platform and ultrafast toolkit for FASTA/Q file manipulation"; diff --git a/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix b/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix index 2ff0cab1847a..dad31b738a84 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/avogadro2/default.nix +++ b/nixpkgs/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/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix index 59ff285c1537..5794d7077af9 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -68,6 +68,7 @@ stdenv.mkDerivation rec { license = lib.licenses.gpl2; platforms = with lib.platforms; linux ++ darwin; maintainers = [ lib.maintainers.cge ]; - broken = true; # Build error: h5py-3.9.0 not supported for interpreter python2.7 + # never built on aarch64-darwin since first introduction in nixpkgs + broken = stdenv.isDarwin && stdenv.isAarch64; }; } diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index f006df2ae5c0..ce3b279deab1 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.45"; + 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/nixpkgs/pkgs/applications/science/chemistry/wxmacmolplt/default.nix b/nixpkgs/pkgs/applications/science/chemistry/wxmacmolplt/default.nix index 13bcf2d1dc66..e2a4fdf0cb18 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/wxmacmolplt/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/wxmacmolplt/default.nix @@ -11,13 +11,13 @@ stdenv.mkDerivation rec { pname = "wxmacmolplt"; - version = "7.7.2"; + version = "7.7.3"; src = fetchFromGitHub { owner = "brettbode"; repo = pname; rev = "v${version}"; - hash = "sha256-sNxCjIEJUrDWtcUqBQqvanNfgNQ7T4cabYy+x9D1U+Q="; + hash = "sha256-gFGstyq9bMmBaIS4QE6N3EIC9GxRvyJYUr8DUvwRQBc="; }; nativeBuildInputs = [ pkg-config autoreconfHook ]; diff --git a/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix b/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix index 9b15ef8939c3..73c3c9a11f17 100644 --- a/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix +++ b/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "QtRVSim"; - version = "0.9.5"; + version = "0.9.6"; src = fetchFromGitHub { owner = "cvut"; repo = "qtrvsim"; rev = "refs/tags/v${version}"; - sha256 = "sha256-TKF7nkhnp+JXTD2J/FyVxQoVZgOSKX1IQ/RPqRBOI/4="; + sha256 = "sha256-cC3DvQj2VBnGad6ZDn3x4gHQfsPpySzjTi17PQoaxPU="; }; nativeBuildInputs = [ cmake wrapQtAppsHook ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/csxcad/default.nix b/nixpkgs/pkgs/applications/science/electronics/csxcad/default.nix index abdb0716f370..83ee992f4b28 100644 --- a/nixpkgs/pkgs/applications/science/electronics/csxcad/default.nix +++ b/nixpkgs/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/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix index 8d28e4da0f14..2e4ef8003d15 100644 --- a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -13,11 +13,11 @@ stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.449"; + version = "8.3.454"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-y0+HS1LkIFwcgDbHEvs5SXJY2b340RDT7KVupp+ZX9Y="; + sha256 = "sha256-nHZJ2L54J2x+H7S29TeGPInTgjEhRFv3h2ki0ccGYB0="; }; nativeBuildInputs = [ python3 ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix index 284a0b15830b..a6f2c9d44731 100644 --- a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation rec { pname = "nvc"; - version = "1.11.0"; + version = "1.11.1"; src = fetchFromGitHub { owner = "nickg"; repo = "nvc"; rev = "r${version}"; - hash = "sha256-95vIyBQ38SGpI+gnDqK1MRRzOT6uiYjDr1c//folqZ8="; + hash = "sha256-aBH3TtPFuJXtVvGTJcGJev5DYVwqjUAM9cf5PatJq9Y="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/electronics/picoscope/default.nix b/nixpkgs/pkgs/applications/science/electronics/picoscope/default.nix index 596f220242bb..c7242117b68c 100644 --- a/nixpkgs/pkgs/applications/science/electronics/picoscope/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/picoscope/default.nix @@ -1,5 +1,5 @@ { stdenv, lib, fetchurl, dpkg, makeWrapper , mono, gtk-sharp-3_0 -, glib, libusb1 , zlib, gtk3-x11, callPackage +, glib, libusb1 , zlib, gtk3-x11, callPackage, writeTextDir , scopes ? [ "picocv" "ps2000" @@ -114,7 +114,7 @@ in stdenv.mkDerivation rec { # services.udev.packages = [ pkgs.picoscope.rules ]; # users.groups.pico = {}; # users.users.you.extraGroups = [ "pico" ]; - passthru.rules = lib.writeTextDir "lib/udev/rules.d/95-pico.rules" '' + passthru.rules = writeTextDir "lib/udev/rules.d/95-pico.rules" '' SUBSYSTEMS=="usb", ATTRS{idVendor}=="0ce9", MODE="664",GROUP="pico" ''; diff --git a/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix b/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix index 663d6e025c5c..93c155038a22 100644 --- a/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/xyce/default.nix @@ -32,21 +32,21 @@ assert withMPI -> trilinos.withMPI; let - version = "7.6.0"; + version = "7.8.0"; # 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-${version}"; - sha256 = "sha256-HYIzmODMWXBuVRZhcC7LntTysuyXN5A9lb2DeCQQtVw="; + sha256 = "sha256-+aNy2bGuFQ517FZUvU0YqN0gmChRpVuFEmFGTCx9AgY="; }; regression_src = fetchFromGitHub { owner = "Xyce"; repo = "Xyce_Regression"; rev = "Release-${version}"; - sha256 = "sha256-uEoiKpYyHmdK7LZ1UNm2d3Jk8+sCwBwB0TCoHilIh74="; + sha256 = "sha256-Fxi/NpXXIw/bseWaLi2iQ4sg4S9Z+othGgSvQoxyJ9c="; }; in @@ -82,11 +82,13 @@ stdenv.mkDerivation rec { libtool_2 ] ++ lib.optionals enableDocs [ (texliveMedium.withPackages (ps: with ps; [ + enumitem koma-script optional framed enumitem multirow + newtx preprint ])) ]; @@ -154,8 +156,11 @@ 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/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix index bc8c6ae48587..d84aa5b6918a 100644 --- a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/nixpkgs/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/nixpkgs/pkgs/applications/science/logic/cadical/default.nix b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix index 85406dbaf38a..b7524e47b315 100644 --- a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cadical"; - version = "1.9.1"; + version = "1.9.3"; src = fetchFromGitHub { owner = "arminbiere"; repo = "cadical"; rev = "rel-${version}"; - sha256 = "sha256-WQNaRkjJyWc3PDkK5uwLHEymlnpytVkbJqIVbc7HgZY="; + sha256 = "sha256-kjvbWFcoEe7Df2HDKKc2txrxpS8/StwiCLbS2RqnkyE="; }; outputs = [ "out" "dev" "lib" ]; diff --git a/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/nixpkgs/pkgs/applications/science/logic/coq/default.nix index 9717e69e9c26..039a5334969e 100644 --- a/nixpkgs/pkgs/applications/science/logic/coq/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/coq/default.nix @@ -56,6 +56,7 @@ let "8.17.0".sha256 = "sha256-TGwm7S6+vkeZ8cidvp8pkiAd9tk008jvvPvYgfEOXhM="; "8.17.1".sha256 = "sha256-x+RwkbxMg9aR0L3WSCtpIz8jwA5cJA4tXAtHMZb20y4="; "8.18.0".sha256 = "sha256-WhiBs4nzPHQ0R24xAdM49kmxSCPOxiOVMA1iiMYunz4="; + "8.19+rc1".sha256 = "sha256-hQ57tLj8lXTbMrW+F0skPtzpHJnXbqPIc/EzocRV5qo="; }; releaseRev = v: "V${v}"; fetched = import ../../../../build-support/coq/meta-fetch/default.nix diff --git a/nixpkgs/pkgs/applications/science/logic/cvc5/default.nix b/nixpkgs/pkgs/applications/science/logic/cvc5/default.nix index 7c483ec185c7..142668f382c3 100644 --- a/nixpkgs/pkgs/applications/science/logic/cvc5/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cvc5/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cvc5"; - version = "1.0.8"; + version = "1.1.0"; src = fetchFromGitHub { owner = "cvc5"; repo = "cvc5"; rev = "cvc5-${version}"; - hash = "sha256-2sJKHD7Wzznut4hKOyxgc4LR4H+4u3m8Gq02+v+m5lM="; + hash = "sha256-BWmIxQz+if402f7zsFROWG1TXbcsg50FJbnffJFYun4="; }; nativeBuildInputs = [ pkg-config cmake flex ]; diff --git a/nixpkgs/pkgs/applications/science/logic/dafny/default.nix b/nixpkgs/pkgs/applications/science/logic/dafny/default.nix index 7da1958af386..5f56d612ab24 100644 --- a/nixpkgs/pkgs/applications/science/logic/dafny/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/dafny/default.nix @@ -8,36 +8,32 @@ buildDotnetModule rec { pname = "Dafny"; - version = "4.3.0"; + version = "4.4.0"; src = fetchFromGitHub { owner = "dafny-lang"; repo = "dafny"; rev = "v${version}"; - hash = "sha256-bnKaaqh1/921SRwnwqgYb31SJ8vguEBtzywPTz79S6I="; + hash = "sha256-rnPZms60vRtefEV+3IeVXoZJU9WMjVxPVioRaEcyw/o="; }; - postPatch = - # This version number seems to be hardcoded and didn't get updated with the - # version bump from 4.2.0 to 4.3.0. - let dafnyRuntimeJarVersion = "4.2.0"; - in '' - cp ${ - writeScript "fake-gradlew-for-dafny" '' - mkdir -p build/libs/ - javac $(find -name "*.java" | grep "^./src/main") -d classes - jar cf build/libs/DafnyRuntime-${dafnyRuntimeJarVersion}.jar -C classes dafny - ''} Source/DafnyRuntime/DafnyRuntimeJava/gradlew + postPatch = '' + cp ${ + writeScript "fake-gradlew-for-dafny" '' + mkdir -p build/libs/ + javac $(find -name "*.java" | grep "^./src/main") -d classes + jar cf build/libs/DafnyRuntime-${version}.jar -C classes dafny + ''} Source/DafnyRuntime/DafnyRuntimeJava/gradlew - # Needed to fix - # "error NETSDK1129: The 'Publish' target is not supported without - # specifying a target framework. The current project targets multiple - # frameworks, you must specify the framework for the published - # application." - substituteInPlace Source/DafnyRuntime/DafnyRuntime.csproj \ - --replace TargetFrameworks TargetFramework \ - --replace "netstandard2.0;net452" net6.0 - ''; + # Needed to fix + # "error NETSDK1129: The 'Publish' target is not supported without + # specifying a target framework. The current project targets multiple + # frameworks, you must specify the framework for the published + # application." + substituteInPlace Source/DafnyRuntime/DafnyRuntime.csproj \ + --replace TargetFrameworks TargetFramework \ + --replace "netstandard2.0;net452" net6.0 + ''; buildInputs = [ jdk11 ]; nugetDeps = ./deps.nix; diff --git a/nixpkgs/pkgs/applications/science/logic/dafny/deps.nix b/nixpkgs/pkgs/applications/science/logic/dafny/deps.nix index 895c359ce335..a786d8b3d6fd 100644 --- a/nixpkgs/pkgs/applications/science/logic/dafny/deps.nix +++ b/nixpkgs/pkgs/applications/science/logic/dafny/deps.nix @@ -2,21 +2,20 @@ # Please dont edit it manually, your changes might get overwritten! { fetchNuGet }: [ - (fetchNuGet { pname = "Boogie"; version = "2.16.0"; sha256 = "1zcbbqhn7brxnywp3m5pfd7rcapg5w1xjr5pkfsqmmv8fk36nfja"; }) - (fetchNuGet { pname = "Boogie.AbstractInterpretation"; version = "2.16.8"; sha256 = "1a4pfzc7r6yxzwixsij2xijiyk50ii84zlwl151naw0y05yj4zxn"; }) - (fetchNuGet { pname = "Boogie.BaseTypes"; version = "2.16.8"; sha256 = "17zii7d31bqlhn2ygfjh5a37nb98wkn377z8rm6fg44f83788ll9"; }) - (fetchNuGet { pname = "Boogie.CodeContractsExtender"; version = "2.16.8"; sha256 = "18aixxw5xrivzpwrwj91dyhdnj3xd1apmjrgbdgg5f0z6p9863nq"; }) - (fetchNuGet { pname = "Boogie.Concurrency"; version = "2.16.8"; sha256 = "1qsp24ckvjz01mjq1fxssdvpsx6kvrdx8l7hd2rll86rrh1bc6w4"; }) - (fetchNuGet { pname = "Boogie.Core"; version = "2.16.8"; sha256 = "1qp6yaa0h16ihqrr2vgbgnakmvshd76skdhqrp1v7jcp7mw8af7n"; }) - (fetchNuGet { pname = "Boogie.ExecutionEngine"; version = "2.16.8"; sha256 = "1q3x8im85i68vz8ls51ywd4ayjsy53ygra01byscbnhc1qflpzia"; }) - (fetchNuGet { pname = "Boogie.Graph"; version = "2.16.8"; sha256 = "1pyd35rfv0bn0b1xxvqzixnprwjbps54zs0yaily9xxsyg33y1jr"; }) - (fetchNuGet { pname = "Boogie.Houdini"; version = "2.16.8"; sha256 = "1n6dlr84y9kni1sskgd6zx4cfflw28yavwwaz6hmmm01l8zg8y6w"; }) - (fetchNuGet { pname = "Boogie.Model"; version = "2.16.8"; sha256 = "0cbq5lyprz0m1kv6a8yyjnhyx42k1jbl00ljrj1bldlj7dz4ahw3"; }) - (fetchNuGet { pname = "Boogie.Provers.SMTLib"; version = "2.16.8"; sha256 = "1q48xzmzch4mc8z0wg2ap8f9glmxcj59i9a645ybysf1jah6yphy"; }) - (fetchNuGet { pname = "Boogie.VCExpr"; version = "2.16.8"; sha256 = "130jmlvvjd2ls95ry7ds0y2h7pxa109dikx1p3a3psb9dph7zxkr"; }) - (fetchNuGet { pname = "Boogie.VCGeneration"; version = "2.16.8"; sha256 = "0fim2d7p1y6ms1m8f1d5yl4pq3167pi4i7nwink5ydv3fvsckh08"; }) + (fetchNuGet { pname = "Boogie"; version = "3.0.9"; sha256 = "12700rvm3zj73pkkjaypfa72fvqz8bp78hi3jkh89dqavhg3l7p5"; }) + (fetchNuGet { pname = "Boogie.AbstractInterpretation"; version = "3.0.9"; sha256 = "1612d1x7smhcczmk21z9kswjjvq3h0r5mlf1zb8mznyx0154pckg"; }) + (fetchNuGet { pname = "Boogie.BaseTypes"; version = "3.0.9"; sha256 = "0v6x8k61rl6bvp1zbvbhnlpkakbw11c2mf8glafmf4znrakwil23"; }) + (fetchNuGet { pname = "Boogie.CodeContractsExtender"; version = "3.0.9"; sha256 = "045z0j7bhsb8fypzkz8spixfqdchcpsq3bb9bfwb95if2mna4zx2"; }) + (fetchNuGet { pname = "Boogie.Concurrency"; version = "3.0.9"; sha256 = "00k08qh614vciadzk7lr1dcwsvrcfpslvs342amq12c25rxh3125"; }) + (fetchNuGet { pname = "Boogie.Core"; version = "3.0.9"; sha256 = "03fip919iw7y3vwk5nj53jj73ry43z9fpn752j5fbgygkl2zbx4q"; }) + (fetchNuGet { pname = "Boogie.ExecutionEngine"; version = "3.0.9"; sha256 = "098l1qmya021raqgdapxvwq3pra4v7wpv7j3dmmhsnpg8zs30jgi"; }) + (fetchNuGet { pname = "Boogie.Graph"; version = "3.0.9"; sha256 = "1y8aai7wmsyh2pn9bl1rp2nifs3k9b8kb2lqx5rgs1fdiyk2q24j"; }) + (fetchNuGet { pname = "Boogie.Houdini"; version = "3.0.9"; sha256 = "1ssr82swqmjsap6v344v2kwkfsv70gx082dk54x7vpapr56f1fgp"; }) + (fetchNuGet { pname = "Boogie.Model"; version = "3.0.9"; sha256 = "1cy04a7dr1z7dxfkx6l9kfm30rx5wsn7g50b0wyzp4ns6sbkh47f"; }) + (fetchNuGet { pname = "Boogie.Provers.SMTLib"; version = "3.0.9"; sha256 = "1ijzn67wl82ycr1k7gbh8dhq99zxqqjdc48glf4ld832l7sp3vam"; }) + (fetchNuGet { pname = "Boogie.VCExpr"; version = "3.0.9"; sha256 = "0hivg31c8v9ix5b8mici6mxz1yzydwiyvgb510bnghxciwbnd4gp"; }) + (fetchNuGet { pname = "Boogie.VCGeneration"; version = "3.0.9"; sha256 = "1j9853vixzpgdfd60c3hr5padfdj3sbrbhmr6jg9a0cr3afk72sm"; }) (fetchNuGet { pname = "CocoR"; version = "2014.12.24"; sha256 = "0ps8h7aawkcc1910qnh13llzb01pvgsjmg862pxp0p4wca2dn7a2"; }) - (fetchNuGet { pname = "dotnet-format"; version = "5.1.250801"; sha256 = "1i0icx2yyp9141rjb2a221a71fvsy0knrfyvv631vb56r8fnsywh"; }) (fetchNuGet { pname = "JetBrains.Annotations"; version = "2021.1.0"; sha256 = "07pnhxxlgx8spmwmakz37nmbvgyb6yjrbrhad5rrn6y767z5r1gb"; }) (fetchNuGet { pname = "MediatR"; version = "8.1.0"; sha256 = "0cqx7yfh998xhsfk5pr6229lcjcs1jxxyqz7dwskc9jddl6a2akp"; }) (fetchNuGet { pname = "Microsoft.Bcl.AsyncInterfaces"; version = "1.1.1"; sha256 = "0a1ahssqds2ympr7s4xcxv5y8jgxs7ahd6ah6fbgglj4rki1f1vw"; }) diff --git a/nixpkgs/pkgs/applications/science/logic/lean4/default.nix b/nixpkgs/pkgs/applications/science/logic/lean4/default.nix index 0f3d9c99ba88..092489f84456 100644 --- a/nixpkgs/pkgs/applications/science/logic/lean4/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/lean4/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "lean4"; - version = "4.3.0"; + version = "4.4.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "lean4"; rev = "v${version}"; - hash = "sha256-2F6sibGMG1U5By/aKGluLgkXIlMpZ7m06gVEG2Uz4RQ="; + hash = "sha256-lU67wjl6yJP2r97lHYxrJqn+JhqMcBIbz/+qlCgY3/o="; }; postPatch = '' @@ -46,6 +46,7 @@ stdenv.mkDerivation rec { cmakeFlags = [ "-DUSE_GITHASH=OFF" + "-DINSTALL_LICENSE=OFF" ]; # Work around https://github.com/NixOS/nixpkgs/issues/166205. diff --git a/nixpkgs/pkgs/applications/science/logic/z3/default.nix b/nixpkgs/pkgs/applications/science/logic/z3/default.nix index 26848e1397aa..9ede6a922da6 100644 --- a/nixpkgs/pkgs/applications/science/logic/z3/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/z3/default.nix @@ -89,8 +89,8 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: in { z3_4_12 = common { - version = "4.12.2"; - sha256 = "sha256-DTgpKEG/LtCGZDnicYvbxG//JMLv25VHn/NaF307JYA="; + version = "4.12.4"; + sha256 = "sha256-cxl7D47dRn+uMVOHbF0avj5+ZFWjaJ7lXj/8l6r9q2I="; }; z3_4_11 = common { version = "4.11.2"; diff --git a/nixpkgs/pkgs/applications/science/machine-learning/uarmsolver/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/uarmsolver/default.nix index a4de341166fd..811f1bd23c80 100644 --- a/nixpkgs/pkgs/applications/science/machine-learning/uarmsolver/default.nix +++ b/nixpkgs/pkgs/applications/science/machine-learning/uarmsolver/default.nix @@ -6,13 +6,13 @@ stdenv.mkDerivation rec { pname = "uarmsolver"; - version = "0.2.5"; + version = "0.2.6"; src = fetchFromGitHub { owner = "firefly-cpp"; repo = "uARMSolver"; rev = version; - sha256 = "sha256-t5Nep99dH/TvJzI9woLSuBrAWSqXZvLncXl7/43Z7sA="; + sha256 = "sha256-E8hc7qoIDaNERMUhVlh+iBvQX1odzd/szeMSh8TCNFo="; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix index a2743b163247..561c9c66a50e 100644 --- a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix +++ b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2023-12-12"; + version = "unstable-2023-12-31"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "bec2c9bd0750ec7970f6c701e619565c9d348e84"; - hash = "sha256-+VohU8mkFjZ0zhjmri0KY1kTzPLn2q5Au4nEBdXcR+8="; + rev = "cc92936e226b0a4c77cdc5d00b7a02c472746f6f"; + hash = "sha256-wY06pZzqcgYdBS7ecB3ZnvmK74ve651n6aHHAN5DWdw="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/nixpkgs/pkgs/applications/science/math/gretl/default.nix b/nixpkgs/pkgs/applications/science/math/gretl/default.nix index f7ccbf8905c0..2c3963cecec9 100644 --- a/nixpkgs/pkgs/applications/science/math/gretl/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gretl/default.nix @@ -19,11 +19,11 @@ stdenv.mkDerivation (finalAttrs: { pname = "gretl"; - version = "2023b"; + version = "2023c"; src = fetchurl { url = "mirror://sourceforge/gretl/gretl-${finalAttrs.version}.tar.xz"; - hash = "sha256-Hf025JjFxde43TN/1m9PeA1uHqxKTZMI8+1qf3XJLGs="; + hash = "sha256-vTxCmHrTpYTo9CIPousUCnpcalS6cN1u8bRaOJyu6MI="; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/math/pspp/default.nix b/nixpkgs/pkgs/applications/science/math/pspp/default.nix index 56f3fdcb1e40..032ae257c564 100644 --- a/nixpkgs/pkgs/applications/science/math/pspp/default.nix +++ b/nixpkgs/pkgs/applications/science/math/pspp/default.nix @@ -6,11 +6,11 @@ stdenv.mkDerivation rec { pname = "pspp"; - version = "1.6.2"; + version = "2.0.0"; src = fetchurl { url = "mirror://gnu/pspp/${pname}-${version}.tar.gz"; - sha256 = "sha256-cylMovWy9/xBu/i3jFiIyAdfQ8YJf9SCq7BPhasIR7Y="; + sha256 = "sha256-qPbLiGr1sIOENXm81vsZHAVKzOKMxotY58XwmZai2N8="; }; nativeBuildInputs = [ pkg-config texinfo python3 makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix index 97754c04d95c..96b1adb562f4 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix @@ -131,6 +131,20 @@ stdenv.mkDerivation rec { url = "https://github.com/sagemath/sage/commit/461727b453712550a2c5dc0ae11933523255aaed.diff"; sha256 = "sha256-mC8084VQoUBk4hocALF+Y9Cwb38Zt360eldi/SSjna8="; }) + + # https://github.com/sagemath/sage/pull/36218, landed in 10.2.beta3 + (fetchpatch { + name = "sageenv-disable-file-validation.patch"; + url = "https://github.com/sagemath/sage/commit/31a764f4a9ec54d3ea970aa9514a088c4e603ebd.diff"; + sha256 = "sha256-NhYUTTmYlyjss3eS8HZXP8U11TElQY0cv6KW4wBOaJY="; + }) + + # https://github.com/sagemath/sage/pull/36235, landed in 10.2.beta3 + (fetchpatch { + name = "ecl-23.9.9.patch"; + url = "https://github.com/sagemath/sage/commit/b6b50a80e9660c002d069019f5b8f04e9324a423.diff"; + sha256 = "sha256-nF+5oKad1VYms6Dxr1t9/V0XBkoMfhy0KCY/ZPddrm0="; + }) ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; diff --git a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix index 23e4ffc8b5a5..eff8969cbbe3 100644 --- a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix +++ b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix @@ -12,13 +12,13 @@ stdenv.mkDerivation (finalAttrs:{ pname = "wxmaxima"; - version = "23.11.0"; + version = "23.12.0"; src = fetchFromGitHub { owner = "wxMaxima-developers"; repo = "wxmaxima"; rev = "Version-${finalAttrs.version}"; - sha256 = "sha256-QOXRtWFY76aIvRPSN+i8jkvMZvuPO3Yr3yqFOh0PSXY="; + sha256 = "sha256-5MOj4loZsD1Fhy+D7V6ZL4QFyVkWyIaxTcHe7R2xypo="; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix index 9fe06f6d7969..ee3610c5f6f6 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix @@ -58,7 +58,7 @@ stdenv.mkDerivation rec { pname = "root"; - version = "6.28.10"; + version = "6.30.02"; passthru = { tests = import ./tests { inherit callPackage; }; @@ -66,7 +66,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://root.cern.ch/download/root_v${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(''${link} clang)' "" # Don't require textutil on macOS @@ -136,8 +143,8 @@ stdenv.mkDerivation rec { substituteInPlace rootx/src/rootx.cxx --replace "gNoLogo = false" "gNoLogo = true" '' + lib.optionalString stdenv.isDarwin '' # Eliminate impure reference to /System/Library/PrivateFrameworks - substituteInPlace core/CMakeLists.txt \ - --replace "-F/System/Library/PrivateFrameworks" "" + substituteInPlace core/macosx/CMakeLists.txt \ + --replace "-F/System/Library/PrivateFrameworks " "" '' + lib.optionalString (stdenv.isDarwin && lib.versionAtLeast stdenv.hostPlatform.darwinMinVersion "11") '' MACOSX_DEPLOYMENT_TARGET=10.16 ''; @@ -184,6 +191,7 @@ stdenv.mkDerivation rec { "-Dsqlite=OFF" "-Dssl=ON" "-Dtmva=ON" + "-Dtmva-pymva=OFF" "-Dvdt=OFF" "-Dwebgui=ON" "-Dxml=ON" diff --git a/nixpkgs/pkgs/applications/science/misc/root/sw_vers.patch b/nixpkgs/pkgs/applications/science/misc/root/sw_vers.patch index 836bbb5b17a4..54ad1091392e 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/sw_vers.patch +++ b/nixpkgs/pkgs/applications/science/misc/root/sw_vers.patch @@ -1,8 +1,8 @@ diff a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake --- a/cmake/modules/SetUpMacOS.cmake +++ b/cmake/modules/SetUpMacOS.cmake -@@ -28,17 +28,10 @@ if(CMAKE_VERSION VERSION_LESS 3.14.4) - endif() +@@ -8,17 +8,10 @@ + set(ROOT_PLATFORM macosx) if (CMAKE_SYSTEM_NAME MATCHES Darwin) - EXECUTE_PROCESS(COMMAND sw_vers "-productVersion" @@ -19,7 +19,7 @@ diff a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake #TODO: check haveconfig and rpath -> set rpath true #TODO: check Thread, define link command #TODO: more stuff check configure script -@@ -57,22 +50,7 @@ if (CMAKE_SYSTEM_NAME MATCHES Darwin) +@@ -37,22 +30,7 @@ SET(CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS "${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 $features ; do diff --git a/nixpkgs/pkgs/applications/science/misc/tulip/default.nix b/nixpkgs/pkgs/applications/science/misc/tulip/default.nix index 947cc2c7c3bb..02b5ad0c0458 100644 --- a/nixpkgs/pkgs/applications/science/misc/tulip/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/tulip/default.nix @@ -4,11 +4,11 @@ stdenv.mkDerivation rec { pname = "tulip"; - version = "5.7.2"; + version = "5.7.3"; src = fetchurl { url = "mirror://sourceforge/auber/tulip-${version}_src.tar.gz"; - hash = "sha256-b+XFCS6Ks+EpwxgYFzWdRomfCpHXmZHXnrQM+ZSLN/0="; + hash = "sha256-arpC+FsDYGMf47phtSzyjjvDg/UYZS+akOe5CYfajdU="; }; nativeBuildInputs = [ cmake wrapQtAppsHook ] @@ -20,8 +20,12 @@ stdenv.mkDerivation rec { qtWrapperArgs = [ ''--prefix PATH : ${lib.makeBinPath [ python3 ]}'' ]; - # error: format string is not a string literal (potentially insecure) - env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-Wno-format-security"; + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin (toString [ + # fatal error: 'Python.h' file not found + "-I${python3}/include/${python3.libPrefix}" + # error: format string is not a string literal (potentially insecure) + "-Wno-format-security" + ]); # FIXME: "make check" needs Docbook's DTD 4.4, among other things. doCheck = false; diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix index cf4584979ba2..a13a071584fd 100644 --- a/nixpkgs/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix +++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix @@ -20,6 +20,9 @@ stdenv.mkDerivation { cp -v ../build/MakePAR Makefile ''; + # https://gitlab.com/DL_POLY_Classic/dl_poly/-/blob/master/README + env.NIX_CFLAGS_COMPILE = "-fallow-argument-mismatch"; + buildPhase = '' make dlpoly ''; @@ -33,7 +36,7 @@ stdenv.mkDerivation { homepage = "https://www.ccp5.ac.uk/DL_POLY_C"; description = "DL_POLY Classic is a general purpose molecular dynamics simulation package"; license = licenses.bsdOriginal; - platforms = [ "x86_64-linux" ]; + platforms = platforms.unix; maintainers = [ maintainers.costrouc ]; }; } diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/lammps/default.nix index 7924d044c2ab..a6dc8592ae3c 100644 --- a/nixpkgs/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -46,14 +46,14 @@ stdenv.mkDerivation (finalAttrs: { # LAMMPS has weird versioning convention. Updates should go smoothly with: # nix-update --commit lammps --version-regex 'stable_(.*)' - version = "2Aug2023_update1"; + version = "2Aug2023_update2"; pname = "lammps"; src = fetchFromGitHub { owner = "lammps"; repo = "lammps"; rev = "stable_${finalAttrs.version}"; - hash = "sha256-Zmn87a726qdidBfyvJlYleYv9jqyFAakxjGrg3lipc0="; + hash = "sha256-E918Jv6RAfXmHxyHZos2F7S8HFWzU6KjxDwXYNAYFMY="; }; preConfigure = '' cd cmake @@ -108,8 +108,8 @@ stdenv.mkDerivation (finalAttrs: { funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). ''; - homepage = "https://lammps.sandia.gov"; - license = licenses.gpl2Plus; + homepage = "https://www.lammps.org"; + license = licenses.gpl2Only; platforms = platforms.linux; # compiling lammps with 64 bit support blas and lapack might cause runtime # segfaults. In anycase both blas and lapack should have the same #bits diff --git a/nixpkgs/pkgs/applications/science/physics/nnpdf/default.nix b/nixpkgs/pkgs/applications/science/physics/nnpdf/default.nix index ec29c02054df..f6d3e94c1a05 100644 --- a/nixpkgs/pkgs/applications/science/physics/nnpdf/default.nix +++ b/nixpkgs/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/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix b/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix index 3d9615cf5329..eb60c12e9f0c 100644 --- a/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix @@ -1,11 +1,14 @@ -{ mkDerivation, lib, fetchzip, qmake }: +{ mkDerivation, lib, qmake, fetchsvn }: mkDerivation rec { pname = "xflr5"; version = "6.61"; - src = fetchzip { - url = "https://sourceforge.net/code-snapshots/svn/x/xf/xflr5/code/xflr5-code-r1481-tags-v6.61-xflr5.zip"; - sha256 = "sha256-voWnXiBo7+kBPiZLVpSiXyBsYJv/Phd3noA81SQ5Vtw="; + + sourceRoot = "${src.name}/xflr5"; + src = fetchsvn { + url = "https://svn.code.sf.net/p/xflr5/code/trunk"; + rev = "1480"; + sha256 = "sha256-Uj6R15OT5i5tAJEYWqyFyN5Z51Wz5RjO26mWC3Y6QAI="; }; nativeBuildInputs = [ qmake ]; diff --git a/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix b/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix index 139e1140e7c9..95d3e1269350 100644 --- a/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix +++ b/nixpkgs/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 ]; diff --git a/nixpkgs/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/nixpkgs/pkgs/applications/science/robotics/qgroundcontrol/default.nix index 0ff923375669..25b1f4e5d5ce 100644 --- a/nixpkgs/pkgs/applications/science/robotics/qgroundcontrol/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/qgroundcontrol/default.nix @@ -4,7 +4,7 @@ stdenv.mkDerivation rec { pname = "qgroundcontrol"; - version = "4.2.9"; + version = "4.3.0"; propagatedBuildInputs = [ qtbase qtcharts qtlocation qtserialport qtsvg qtquickcontrols2 @@ -67,7 +67,7 @@ stdenv.mkDerivation rec { owner = "mavlink"; repo = pname; rev = "v${version}"; - sha256 = "sha256-nzBap5ldlLLLBB1ILkOktt9FnBqbo8MALLOETiqoAzk="; + sha256 = "sha256-a0+cpT413qi88PvaWQPxKABHfK7vbPE7B42n84n/SAk="; fetchSubmodules = true; }; |