diff options
Diffstat (limited to 'pkgs/applications/science')
23 files changed, 95 insertions, 65 deletions
diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index d656c39d0bc0..3b61c8dac2b8 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -70,7 +70,9 @@ stdenv.mkDerivation rec { qtwayland ]; - preConfigure = lib.optionalString stdenv.isDarwin '' + preConfigure = '' + export SOURCE_DATE_EPOCH=$(date -d 20${lib.versions.major version}0101 +%s) + '' + lib.optionalString stdenv.isDarwin '' export LC_ALL=en_US.UTF-8 ''; diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix index 92cb420139df..76780298120e 100644 --- a/pkgs/applications/science/biology/bedtools/default.nix +++ b/pkgs/applications/science/biology/bedtools/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "bedtools"; - version = "2.31.0"; + version = "2.31.1"; src = fetchFromGitHub { owner = "arq5x"; repo = "bedtools2"; rev = "v${version}"; - sha256 = "sha256-LBD3z0+zGbQJ67oyPRFPgbiMY9EP17vSk1EKz3DrkEc="; + sha256 = "sha256-rrk+FSv1bGL0D1lrIOsQu2AT7cw2T4lkDiCnzil5fpg="; }; strictDeps = true; diff --git a/pkgs/applications/science/biology/kssd/default.nix b/pkgs/applications/science/biology/kssd/default.nix index 34d997252f5b..8f60b8b991ed 100644 --- a/pkgs/applications/science/biology/kssd/default.nix +++ b/pkgs/applications/science/biology/kssd/default.nix @@ -1,38 +1,57 @@ -{ lib, stdenv, fetchFromGitHub, fetchpatch, zlib, automake, autoconf, libtool }: +{ lib +, stdenv +, fetchFromGitHub +, fetchpatch +, zlib +, kssd +, runCommand +}: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "kssd"; - version = "1.1"; + version = "2.21"; src = fetchFromGitHub { owner = "yhg926"; repo = "public_kssd"; - rev = "v${version}"; - sha256 = "sha256-8jzYqo9LXF66pQ1EIusm+gba2VbTYpJz2K3NVlA3QxY="; + rev = "v${finalAttrs.version}"; + hash = "sha256-D/s1jL2oKE0rSdRMVljskYFsw5UPOv1L95Of+K+e17w="; }; patches = [ - # Pull upstream patch for -fno-common toolchain support: - # https://github.com/yhg926/public_kssd/pull/9 + # https://github.com/yhg926/public_kssd/pull/11 (fetchpatch { - name = "fno-common.patch"; - url = "https://github.com/yhg926/public_kssd/commit/cdd1e8aae256146f5913a3b4c723b638d53bdf27.patch"; - sha256 = "sha256-HhaTRqPfKR+ouh0PwEH6u22pbuqbX2OypRzw8BXm0W4="; + name = "allocate-enough-memory.patch"; + url = "https://github.com/yhg926/public_kssd/commit/b1e66bbcc04687bc3201301cd742a0b26a87cb5d.patch"; + hash = "sha256-yFyJetpsGKeu+H6Oxrmn5ea4ESVtblb3YJDja4JEAEM="; }) ]; - nativeBuildInputs = [ autoconf automake ]; - buildInputs = [ zlib libtool ]; + buildInputs = [ zlib ]; installPhase = '' - install -vD kssd $out/bin/kssd + runHook preInstall + + install -vD kssd $out/bin/kssd + + runHook postInstall ''; + passthru.tests = { + simple = runCommand "${finalAttrs.pname}-test" { } '' + mkdir $out + ${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -r ${kssd.src}/test_fna/seqs1 -o $out/reference + ${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -o $out/query ${kssd.src}/test_fna/seqs2 + ${lib.getExe kssd} dist -r $out/reference -o $out/distout $out/query + ''; + }; + meta = with lib; { description = "K-mer substring space decomposition"; license = licenses.asl20; homepage = "https://github.com/yhg926/public_kssd"; maintainers = with maintainers; [ unode ]; - platforms = [ "x86_64-linux" ]; + platforms = platforms.linux; + mainProgram = "kssd"; }; -} +}) diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 8ec08f22b7d1..7cf1560d2492 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1471"; + version = "1499"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-HQ2C7SFfJS6TOJZUm6szhu+hMm41BnH8A7DZE5yh9fM="; + hash = "sha256-uofXtGGDloM1FxW0PYKKwfDOPlAJiapGVKwd1clFzp8="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/mmseqs2/default.nix b/pkgs/applications/science/biology/mmseqs2/default.nix index 253f4a43a81c..3e39fcb2918b 100644 --- a/pkgs/applications/science/biology/mmseqs2/default.nix +++ b/pkgs/applications/science/biology/mmseqs2/default.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation rec { pname = "mmseqs2"; - version = "14-7e284"; + version = "15-6f452"; src = fetchFromGitHub { owner = "soedinglab"; repo = pname; rev = version; - sha256 = "sha256-pVryZGblgMEqJl5M20CHxav269yGY6Y4ci+Gxt6SHOU="; + sha256 = "sha256-L+zOWrGkCLz/wqpBuji8H4/93sDFpcfnDOE8FHq1j84="; }; nativeBuildInputs = [ cmake xxd perl installShellFiles ]; diff --git a/pkgs/applications/science/biology/quast/default.nix b/pkgs/applications/science/biology/quast/default.nix index e5ee4b53089f..f280f81fae84 100644 --- a/pkgs/applications/science/biology/quast/default.nix +++ b/pkgs/applications/science/biology/quast/default.nix @@ -27,7 +27,7 @@ pythonPackages.buildPythonApplication rec { --replace "/bin/bash" "${bash}/bin/bash" mkdir -p "$out/${python.sitePackages}" export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH" - ${python.pythonForBuild.interpreter} setup.py install \ + ${python.pythonOnBuildForHost.interpreter} setup.py install \ --install-lib=$out/${python.sitePackages} \ --prefix="$out" ''; diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index d6d371bf5054..89fb3534c607 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -21,10 +21,10 @@ in stdenv.mkDerivation rec { pname = "gwyddion"; - version = "2.63"; + version = "2.64"; src = fetchurl { url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz"; - sha256 = "sha256-FSs/Dbnr1shEw/W51DhUFPb61tM+0atc6wxY81EiTdM="; + sha256 = "sha256-FDL4XDHH6WYF47OsnhxpM7s7YadutiCDjcJKCF8ZlCw="; }; nativeBuildInputs = [ pkg-config file ]; diff --git a/pkgs/applications/science/chemistry/nwchem/default.nix b/pkgs/applications/science/chemistry/nwchem/default.nix index 062c61fa5c9e..a7d9462a7fbd 100644 --- a/pkgs/applications/science/chemistry/nwchem/default.nix +++ b/pkgs/applications/science/chemistry/nwchem/default.nix @@ -54,13 +54,13 @@ let in stdenv.mkDerivation rec { pname = "nwchem"; - version = "7.2.1"; + version = "7.2.2"; src = fetchFromGitHub { owner = "nwchemgit"; repo = "nwchem"; rev = "v${version}-release"; - hash = "sha256-nnNTZ+c7VVGAqwOBMkBlW3rImNjs08Ne35XRkI3ssGo="; + hash = "sha256-BcYRqPaPR24OTRY0MJgBxi46HvUG4uFaY0unZmu5b9k="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/chemistry/openmolcas/default.nix b/pkgs/applications/science/chemistry/openmolcas/default.nix index 42cf5ddc9511..33c77c063bf9 100644 --- a/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -8,7 +8,7 @@ , blas-ilp64 , hdf5-cpp , python3 -, texlive +, texliveMinimal , armadillo , libxc , makeWrapper @@ -78,7 +78,7 @@ stdenv.mkDerivation { perl gfortran cmake - texlive.combined.scheme-minimal + texliveMinimal makeWrapper autoPatchelfHook ]; diff --git a/pkgs/applications/science/electronics/xyce/default.nix b/pkgs/applications/science/electronics/xyce/default.nix index aee1d25a04cc..663d6e025c5c 100644 --- a/pkgs/applications/science/electronics/xyce/default.nix +++ b/pkgs/applications/science/electronics/xyce/default.nix @@ -16,7 +16,7 @@ , trilinos , withMPI ? false # for doc -, texlive +, texliveMedium , pandoc , enableDocs ? true # for tests @@ -81,16 +81,14 @@ stdenv.mkDerivation rec { gfortran libtool_2 ] ++ lib.optionals enableDocs [ - (texlive.combine { - inherit (texlive) - scheme-medium + (texliveMedium.withPackages (ps: with ps; [ koma-script optional framed enumitem multirow - preprint; - }) + preprint + ])) ]; buildInputs = [ diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index fe8180899c0a..9717e69e9c26 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -217,7 +217,7 @@ self = stdenv.mkDerivation { together with an environment for semi-interactive development of machine-checked proofs. ''; - homepage = "http://coq.inria.fr"; + homepage = "https://coq.inria.fr"; license = licenses.lgpl21; branch = coq-version; maintainers = with maintainers; [ roconnor thoughtpolice vbgl Zimmi48 ]; diff --git a/pkgs/applications/science/logic/uhdm/default.nix b/pkgs/applications/science/logic/uhdm/default.nix index 7312f989cb66..ec25d58efcbf 100644 --- a/pkgs/applications/science/logic/uhdm/default.nix +++ b/pkgs/applications/science/logic/uhdm/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "UHDM"; # When updating this package, also consider updating science/logic/surelog - version = "1.76"; + version = "1.77"; src = fetchFromGitHub { owner = "chipsalliance"; repo = finalAttrs.pname; rev = "v${finalAttrs.version}"; - hash = "sha256-Q/u5lvILYDT5iScES3CTPIm/B5apoOHXOQmCsZ73NlU="; + hash = "sha256-JKhpcPG4hWlcn2C+Wlx7yNIMXXurAMxLSK4xWN2akMQ="; fetchSubmodules = false; # we use all dependencies from nix }; diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 9fe39c8cef89..6165cfe8bd22 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -47,7 +47,7 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: configurePhase = concatStringsSep " " ( - [ "${python.pythonForBuild.interpreter} scripts/mk_make.py --prefix=$out" ] + [ "${python.pythonOnBuildForHost.interpreter} scripts/mk_make.py --prefix=$out" ] ++ optional javaBindings "--java" ++ optional ocamlBindings "--ml" ++ optional pythonBindings "--python --pypkgdir=$out/${python.sitePackages}" diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index ee0d35414255..f4cc1f1fbfea 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -1,5 +1,5 @@ { lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng -, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texLive, tk, xz, zlib +, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texliveSmall, tk, xz, zlib , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack , curl, Cocoa, Foundation, libobjc, libcxx, tzdata , withRecommendedPackages ? true @@ -31,7 +31,7 @@ stdenv.mkDerivation (finalAttrs: { nativeBuildInputs = [ pkg-config ]; buildInputs = [ bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses - pango pcre2 perl readline texLive xz zlib less texinfo graphviz icu + pango pcre2 perl readline (texliveSmall.withPackages (ps: with ps; [ inconsolata helvetic ps.texinfo fancyvrb cm-super rsfs ])) xz zlib less texinfo graphviz icu bison imake which blas lapack curl tcl tk jdk tzdata ] ++ lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ]; diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix index 752b05fe4feb..0dc12b6dcb05 100644 --- a/pkgs/applications/science/math/giac/default.nix +++ b/pkgs/applications/science/math/giac/default.nix @@ -1,4 +1,4 @@ -{ stdenv, lib, fetchurl, fetchpatch, texlive, bison, flex, lapack, blas +{ stdenv, lib, fetchurl, fetchpatch, texliveSmall, bison, flex, lapack, blas , autoreconfHook, gmp, mpfr, pari, ntl, gsl, mpfi, ecm, glpk, nauty , buildPackages, readline, gettext, libpng, libao, gfortran, perl , enableGUI ? false, libGL, libGLU, xorg, fltk @@ -60,7 +60,7 @@ stdenv.mkDerivation rec { ''; nativeBuildInputs = [ - autoreconfHook texlive.combined.scheme-small bison flex + autoreconfHook texliveSmall bison flex ]; # perl is only needed for patchShebangs fixup. diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix index 44647ce81398..2480ff3eba81 100644 --- a/pkgs/applications/science/math/pari/default.nix +++ b/pkgs/applications/science/math/pari/default.nix @@ -7,7 +7,7 @@ , libpthreadstubs , perl , readline -, tex +, texliveBasic , withThread ? true }: @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { libX11 perl readline - tex + texliveBasic ] ++ lib.optionals withThread [ libpthreadstubs ]; diff --git a/pkgs/applications/science/math/polymake/default.nix b/pkgs/applications/science/math/polymake/default.nix index 2e79ca03635a..fe9210641d2e 100644 --- a/pkgs/applications/science/math/polymake/default.nix +++ b/pkgs/applications/science/math/polymake/default.nix @@ -28,13 +28,13 @@ in stdenv.mkDerivation rec { pname = "polymake"; - version = "4.10"; + version = "4.11"; src = fetchurl { # "The minimal version is a packager friendly version which omits # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality." url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2"; - sha256 = "sha256-YDiyZtbUC76ZVe3oRtzPRBfkEU+qh+d1ZWFhzUyi+Pg="; + sha256 = "sha256-XfbwrNcAEZvQxLV2Z2KFL/vYV3ZbXcyIgC/10hCK3SM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index 1f06f0d1aef3..f77bd5a92243 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -17,7 +17,7 @@ # use letters instead of numbers for post-appendix chapters, and we # want it to match the upstream format because sage depends on it. , texinfo4 -, texlive +, texliveSmall , enableDocs ? !stdenv.isDarwin , enableGfanlib ? true }: @@ -86,7 +86,7 @@ stdenv.mkDerivation rec { graphviz latex2html texinfo4 - texlive.combined.scheme-small + texliveSmall ] ++ lib.optionals stdenv.isDarwin [ getconf ]; depsBuildBuild = [ buildPackages.stdenv.cc ]; diff --git a/pkgs/applications/science/misc/root/5.nix b/pkgs/applications/science/misc/root/5.nix index 4a8411cd34f9..2d830e3d1016 100644 --- a/pkgs/applications/science/misc/root/5.nix +++ b/pkgs/applications/science/misc/root/5.nix @@ -64,6 +64,9 @@ stdenv.mkDerivation rec { url = "https://github.com/root-project/root/commit/c75458024082de0cc35b45505c652b8460a9e71b.patch"; sha256 = "sha256-A5zEjQE9OGPFp/L1HUs4NIdxQMRiwbwCRNWOLN2ENrM="; }) + # Backport Python 3.11 fix to v5 from v6.26 + # https://github.com/root-project/root/commit/484deb056dacf768aba4954073b41105c431bffc + ./root5-python311-fix.patch ]; # https://github.com/root-project/root/issues/13216 diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index a03709c1437d..d2172f614f64 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -110,18 +110,6 @@ stdenv.mkDerivation rec { patches = [ ./sw_vers.patch - # glibc >=2.38 already has strlcat implemented. - # merged upstream, remove on next package bump. - (fetchpatch { - url = "https://github.com/root-project/root/commit/8fb0e35446ed67c9d56639b4708c8f05459b7f84.patch"; - hash = "sha256-7EabmYanqlQsYSQsi+S9eWs1v1pY6MncopL420Y3D4w="; - }) - ] ++ lib.optionals (python.pkgs.pythonAtLeast "3.11") [ - # Fix build against Python 3.11 - (fetchpatch { - url = "https://github.com/root-project/root/commit/484deb056dacf768aba4954073b41105c431bffc.patch"; - hash = "sha256-4qur2e3SxMIPgOg4IjlvuULR2BObuP7xdvs+LmNT2/s="; - }) ]; preConfigure = '' diff --git a/pkgs/applications/science/misc/root/root5-python311-fix.patch b/pkgs/applications/science/misc/root/root5-python311-fix.patch new file mode 100644 index 000000000000..3005b3a73f9b --- /dev/null +++ b/pkgs/applications/science/misc/root/root5-python311-fix.patch @@ -0,0 +1,17 @@ +diff --git a/bindings/pyroot/src/MethodProxy.cxx b/bindings/pyroot/src/MethodProxy.cxx +--- a/bindings/pyroot/src/MethodProxy.cxx ++++ b/bindings/pyroot/src/MethodProxy.cxx +@@ -4,10 +4,10 @@ + // Bindings + #include "PyROOT.h" + #include "structmember.h" // from Python +-#if PY_VERSION_HEX >= 0x02050000 +-#include "code.h" // from Python +-#else ++#if PY_VERSION_HEX < 0x02050000 + #include "compile.h" // from Python ++#elif PY_VERSION_HEX < 0x030b0000 ++#include "code.h" // from Python + #endif + #ifndef CO_NOFREE + // python2.2 does not have CO_NOFREE defined diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index 1eded1e419c4..3acd66f79084 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -5,14 +5,14 @@ python3.pkgs.buildPythonApplication rec { pname = "snakemake"; - version = "7.29.0"; + version = "7.32.4"; format = "setuptools"; src = fetchFromGitHub { owner = "snakemake"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-UfUzvDo5OE1LGCBBGoDpxG96RKOaShbqu5TOOILG3AY="; + hash = "sha256-9KuMPqvM8ZCTuomc0R9MBxsK3KIpukDTrlwU6MHysK0="; }; propagatedBuildInputs = with python3.pkgs; [ @@ -49,6 +49,7 @@ python3.pkgs.buildPythonApplication rec { pandas pytestCheckHook requests-mock + pillow ]; disabledTestPaths = [ @@ -56,6 +57,8 @@ python3.pkgs.buildPythonApplication rec { "tests/test_tes.py" "tests/test_tibanna.py" "tests/test_linting.py" + "tests/test_google_lifesciences.py" + "tests/test_conda_python_script/test_script.py" ]; disabledTests = [ diff --git a/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/pkgs/applications/science/robotics/qgroundcontrol/default.nix index 9f88fe58e3c4..0ff923375669 100644 --- a/pkgs/applications/science/robotics/qgroundcontrol/default.nix +++ b/pkgs/applications/science/robotics/qgroundcontrol/default.nix @@ -4,7 +4,7 @@ stdenv.mkDerivation rec { pname = "qgroundcontrol"; - version = "4.2.8"; + version = "4.2.9"; propagatedBuildInputs = [ qtbase qtcharts qtlocation qtserialport qtsvg qtquickcontrols2 @@ -67,7 +67,7 @@ stdenv.mkDerivation rec { owner = "mavlink"; repo = pname; rev = "v${version}"; - sha256 = "sha256-EmGtVy/cHiZ2SqOOKmt9vCUQbyT5Sl8XnkRlhn9BdvA="; + sha256 = "sha256-nzBap5ldlLLLBB1ILkOktt9FnBqbo8MALLOETiqoAzk="; fetchSubmodules = true; }; |