diff options
Diffstat (limited to 'pkgs/applications/science')
20 files changed, 74 insertions, 50 deletions
diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index d656c39d0bc..3b61c8dac2b 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 92cb420139d..76780298120 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${version}"; - sha256 = "sha256-LBD3z0+zGbQJ67oyPRFPgbiMY9EP17vSk1EKz3DrkEc="; + sha256 = "sha256-rrk+FSv1bGL0D1lrIOsQu2AT7cw2T4lkDiCnzil5fpg="; }; strictDeps = true; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 8ec08f22b7d..7cf1560d249 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1471"; + version = "1499"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-HQ2C7SFfJS6TOJZUm6szhu+hMm41BnH8A7DZE5yh9fM="; + hash = "sha256-uofXtGGDloM1FxW0PYKKwfDOPlAJiapGVKwd1clFzp8="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/quast/default.nix b/pkgs/applications/science/biology/quast/default.nix index e5ee4b53089..f280f81fae8 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/electronics/magic-vlsi/0001-strip-bin-prefix.patch b/pkgs/applications/science/electronics/magic-vlsi/0001-strip-bin-prefix.patch deleted file mode 100644 index 1cef96ea140..00000000000 --- a/pkgs/applications/science/electronics/magic-vlsi/0001-strip-bin-prefix.patch +++ /dev/null @@ -1,10 +0,0 @@ -diff --git a/scripts/makedbh b/scripts/makedbh -index 01e4fa5..d6299c6 100755 ---- a/scripts/makedbh -+++ b/scripts/makedbh -@@ -1,4 +1,4 @@ --#!/bin/csh -f -+#!/usr/bin/env tcsh - # - # makes the "database.h" (1st argument, $1) file from "database.h.in" - # (2nd argument, $2), setting various mask operation definitions diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix index fc68969bd49..c816b356267 100644 --- a/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -13,11 +13,11 @@ stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.277"; + version = "8.3.447"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-cS3KaIVwGN/mMfRKjJxzdY6DeNV7tw2fATIHrFBV0fY="; + sha256 = "sha256-t/gJ43VIdBIiozLfqaTy7tJsXK674gWBbW1aPHKEj3U="; }; nativeBuildInputs = [ python3 ]; @@ -46,10 +46,6 @@ stdenv.mkDerivation rec { env.NIX_CFLAGS_COMPILE = "-Wno-implicit-function-declaration"; - patches = [ - ./0001-strip-bin-prefix.patch - ]; - meta = with lib; { description = "VLSI layout tool written in Tcl"; homepage = "http://opencircuitdesign.com/magic/"; diff --git a/pkgs/applications/science/logic/abc/default.nix b/pkgs/applications/science/logic/abc/default.nix index 1d4a11bfb3f..1685bb7aba3 100644 --- a/pkgs/applications/science/logic/abc/default.nix +++ b/pkgs/applications/science/logic/abc/default.nix @@ -1,32 +1,39 @@ -{ lib, stdenv, fetchFromGitHub -, readline, cmake +{ lib +, stdenv +, fetchFromGitHub +, readline +, cmake }: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "abc-verifier"; - version = "unstable-2023-09-13"; + version = "unstable-2023-10-13"; src = fetchFromGitHub { owner = "yosyshq"; repo = "abc"; - rev = "daad9ede0137dc58487a0abc126253e671a85b14"; - hash = "sha256-5XeFYvdqT08xduFUDC5yK1jEOV1fYzyQD7N9ZmG3mpQ="; + rev = "896e5e7dedf9b9b1459fa019f1fa8aa8101fdf43"; + hash = "sha256-ou+E2lvDEOxXRXNygE/TyVi7quqk+CJHRI+HDI0xljE="; }; nativeBuildInputs = [ cmake ]; buildInputs = [ readline ]; - installPhase = "mkdir -p $out/bin && mv abc $out/bin"; + installPhase = '' + runHook preInstall + install -Dm755 'abc' "$out/bin/abc" + runHook postInstall + ''; # needed by yosys - passthru.rev = src.rev; + passthru.rev = finalAttrs.src.rev; meta = with lib; { description = "A tool for squential logic synthesis and formal verification"; homepage = "https://people.eecs.berkeley.edu/~alanmi/abc"; license = licenses.mit; - maintainers = with maintainers; [ thoughtpolice ]; + maintainers = with maintainers; [ thoughtpolice Luflosi ]; mainProgram = "abc"; platforms = platforms.unix; }; -} +}) diff --git a/pkgs/applications/science/logic/aiger/default.nix b/pkgs/applications/science/logic/aiger/default.nix index 15c45466b13..4f3f585c220 100644 --- a/pkgs/applications/science/logic/aiger/default.nix +++ b/pkgs/applications/science/logic/aiger/default.nix @@ -5,7 +5,7 @@ stdenv.mkDerivation rec { version = "1.9.9"; src = fetchurl { - url = "http://fmv.jku.at/aiger/${pname}-${version}.tar.gz"; + url = "https://fmv.jku.at/aiger/${pname}-${version}.tar.gz"; sha256 = "1ish0dw0nf9gyghxsdhpy1jjiy5wp54c993swp85xp7m6vdx6l0y"; }; @@ -47,7 +47,7 @@ stdenv.mkDerivation rec { meta = { description = "And-Inverter Graph (AIG) utilities"; - homepage = "http://fmv.jku.at/aiger/"; + homepage = "https://fmv.jku.at/aiger/"; license = lib.licenses.mit; maintainers = with lib.maintainers; [ thoughtpolice ]; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/logic/cadical/default.nix b/pkgs/applications/science/logic/cadical/default.nix index 9bfadc41f60..a9b27877ab1 100644 --- a/pkgs/applications/science/logic/cadical/default.nix +++ b/pkgs/applications/science/logic/cadical/default.nix @@ -43,6 +43,6 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ shnarazk ]; platforms = platforms.unix; license = licenses.mit; - homepage = "http://fmv.jku.at/cadical"; + homepage = "https://fmv.jku.at/cadical/"; }; } diff --git a/pkgs/applications/science/logic/cvc3/default.nix b/pkgs/applications/science/logic/cvc3/default.nix index cfa8f62990c..0385909610e 100644 --- a/pkgs/applications/science/logic/cvc3/default.nix +++ b/pkgs/applications/science/logic/cvc3/default.nix @@ -5,7 +5,7 @@ stdenv.mkDerivation rec { version = "2.4.1"; src = fetchurl { - url = "http://www.cs.nyu.edu/acsys/cvc3/releases/${version}/${pname}-${version}.tar.gz"; + url = "https://cs.nyu.edu/acsys/cvc3/releases/${version}/${pname}-${version}.tar.gz"; sha256 = "1xxcwhz3y6djrycw8sm6xz83wb4hb12rd1n0skvc7fng0rh1snym"; }; @@ -32,11 +32,11 @@ stdenv.mkDerivation rec { [ raskin ]; platforms = platforms.unix; license = licenses.free; - homepage = "http://www.cs.nyu.edu/acsys/cvc3/index.html"; + homepage = "https://cs.nyu.edu/acsys/cvc3/index.html"; }; passthru = { updateInfo = { - downloadPage = "http://www.cs.nyu.edu/acsys/cvc3/download.html"; + downloadPage = "https://cs.nyu.edu/acsys/cvc3/download.html"; }; }; } diff --git a/pkgs/applications/science/logic/kissat/default.nix b/pkgs/applications/science/logic/kissat/default.nix index 2941952287b..d1703340527 100644 --- a/pkgs/applications/science/logic/kissat/default.nix +++ b/pkgs/applications/science/logic/kissat/default.nix @@ -48,6 +48,6 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ shnarazk ]; platforms = platforms.unix; license = licenses.mit; - homepage = "http://fmv.jku.at/kissat"; + homepage = "https://fmv.jku.at/kissat"; }; } diff --git a/pkgs/applications/science/logic/picosat/default.nix b/pkgs/applications/science/logic/picosat/default.nix index 48def5fc2e4..1fef05069a6 100644 --- a/pkgs/applications/science/logic/picosat/default.nix +++ b/pkgs/applications/science/logic/picosat/default.nix @@ -5,7 +5,7 @@ stdenv.mkDerivation rec { version = "965"; src = fetchurl { - url = "http://fmv.jku.at/picosat/${pname}-${version}.tar.gz"; + url = "https://fmv.jku.at/picosat/${pname}-${version}.tar.gz"; sha256 = "0m578rpa5rdn08d10kr4lbsdwp4402hpavrz6n7n53xs517rn5hm"; }; @@ -36,7 +36,7 @@ stdenv.mkDerivation rec { meta = { description = "SAT solver with proof and core support"; - homepage = "http://fmv.jku.at/picosat/"; + homepage = "https://fmv.jku.at/picosat/"; license = lib.licenses.mit; platforms = lib.platforms.unix; maintainers = with lib.maintainers; [ roconnor thoughtpolice ]; diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 9fe39c8cef8..6165cfe8bd2 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 814f54f3863..f4cc1f1fbfe 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation (finalAttrs: { pname = "R"; - version = "4.3.1"; + version = "4.3.2"; src = let inherit (finalAttrs) pname version; in fetchurl { url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-jdC/JPECPG9hjDsxc4PSkbSklPQNc7mDrCL/6pnkupk="; + sha256 = "sha256-s/V2CsLu6AJqPw7vyyW0dyPZeAOO7o6ER2IJTIYMRSo="; }; outputs = [ "out" "tex" ]; diff --git a/pkgs/applications/science/math/colpack/default.nix b/pkgs/applications/science/math/colpack/default.nix index 3cc9290a762..d5ab38ff751 100644 --- a/pkgs/applications/science/math/colpack/default.nix +++ b/pkgs/applications/science/math/colpack/default.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A package comprising of implementations of algorithms for vertex coloring and derivative computation"; - homepage = "http://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities"; + homepage = "https://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities"; license = licenses.lgpl3Plus; platforms = platforms.unix; maintainers = with maintainers; [ edwtjo ]; diff --git a/pkgs/applications/science/math/polymake/default.nix b/pkgs/applications/science/math/polymake/default.nix index 2e79ca03635..fe9210641d2 100644 --- a/pkgs/applications/science/math/polymake/default.nix +++ b/pkgs/applications/science/math/polymake/default.nix @@ -28,13 +28,13 @@ in stdenv.mkDerivation rec { pname = "polymake"; - version = "4.10"; + version = "4.11"; src = fetchurl { # "The minimal version is a packager friendly version which omits # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality." url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2"; - sha256 = "sha256-YDiyZtbUC76ZVe3oRtzPRBfkEU+qh+d1ZWFhzUyi+Pg="; + sha256 = "sha256-XfbwrNcAEZvQxLV2Z2KFL/vYV3ZbXcyIgC/10hCK3SM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/misc/root/5.nix b/pkgs/applications/science/misc/root/5.nix index 4a8411cd34f..2d830e3d101 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/root5-python311-fix.patch b/pkgs/applications/science/misc/root/root5-python311-fix.patch new file mode 100644 index 00000000000..3005b3a73f9 --- /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 1eded1e419c..3acd66f7908 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/physics/xnec2c/default.nix b/pkgs/applications/science/physics/xnec2c/default.nix index 47fb7cf61df..87daa8cac85 100644 --- a/pkgs/applications/science/physics/xnec2c/default.nix +++ b/pkgs/applications/science/physics/xnec2c/default.nix @@ -2,6 +2,7 @@ , stdenv , fetchurl , autoreconfHook +, wrapGAppsHook , pkg-config , which , gtk3 @@ -20,7 +21,12 @@ stdenv.mkDerivation rec { hash = "sha256-6Yrx6LkJjfnMA/kJUDWLhGzGopZeecARSrcR++UScsU="; }; - nativeBuildInputs = [ autoreconfHook pkg-config which ]; + nativeBuildInputs = [ + autoreconfHook + wrapGAppsHook + pkg-config + which + ]; buildInputs = [ gtk3 blas lapack ]; meta = with lib; { |