diff options
Diffstat (limited to 'pkgs/applications/science')
6 files changed, 32 insertions, 17 deletions
diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index f7be7119b85d..be663628a426 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchzip, jdk11, wrapGAppsHook }: +{ lib, stdenv, fetchzip, jdk17, testers, wrapGAppsHook, igv }: stdenv.mkDerivation rec { pname = "igv"; @@ -13,10 +13,10 @@ stdenv.mkDerivation rec { cp -Rv * $out/share/ sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igv.sh - sed -i 's#java#${jdk11}/bin/java#g' $out/share/igv.sh + sed -i 's#java#${jdk17}/bin/java#g' $out/share/igv.sh sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igvtools - sed -i 's#java#${jdk11}/bin/java#g' $out/share/igvtools + sed -i 's#java#${jdk17}/bin/java#g' $out/share/igvtools ln -s $out/share/igv.sh $out/bin/igv ln -s $out/share/igvtools $out/bin/igvtools @@ -26,6 +26,11 @@ stdenv.mkDerivation rec { ''; nativeBuildInputs = [ wrapGAppsHook ]; + passthru.tests.version = testers.testVersion { + package = igv; + }; + + meta = with lib; { homepage = "https://www.broadinstitute.org/igv/"; description = "A visualization tool for interactive exploration of genomic datasets"; diff --git a/pkgs/applications/science/logic/lean4/default.nix b/pkgs/applications/science/logic/lean4/default.nix index 092489f84456..97336c06b806 100644 --- a/pkgs/applications/science/logic/lean4/default.nix +++ b/pkgs/applications/science/logic/lean4/default.nix @@ -5,22 +5,23 @@ , git , gmp , perl +, testers }: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "lean4"; - version = "4.4.0"; + version = "4.5.0"; src = fetchFromGitHub { owner = "leanprover"; repo = "lean4"; - rev = "v${version}"; - hash = "sha256-lU67wjl6yJP2r97lHYxrJqn+JhqMcBIbz/+qlCgY3/o="; + rev = "v${finalAttrs.version}"; + hash = "sha256-KTCTk4Fpbmm7FsUo03tAvenC6HuB3zJGax6iGTwLaXM="; }; postPatch = '' substituteInPlace src/CMakeLists.txt \ - --replace 'set(GIT_SHA1 "")' 'set(GIT_SHA1 "${src.rev}")' + --replace 'set(GIT_SHA1 "")' 'set(GIT_SHA1 "${finalAttrs.src.rev}")' # Remove tests that fails in sandbox. # It expects `sourceRoot` to be a git repository. @@ -54,13 +55,19 @@ stdenv.mkDerivation rec { NIX_LDFLAGS = "-l${stdenv.cc.libcxx.cxxabi.libName}"; }; + passthru.tests = { + version = testers.testVersion { + package = finalAttrs.finalPackage; + }; + }; + meta = with lib; { description = "Automatic and interactive theorem prover"; homepage = "https://leanprover.github.io/"; - changelog = "https://github.com/leanprover/lean4/blob/${src.rev}/RELEASES.md"; + changelog = "https://github.com/leanprover/lean4/blob/${finalAttrs.src.rev}/RELEASES.md"; license = licenses.asl20; platforms = platforms.all; maintainers = with maintainers; [ marsam ]; mainProgram = "lean"; }; -} +}) diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 9ede6a922da6..b247599a0813 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -89,8 +89,8 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: in { z3_4_12 = common { - version = "4.12.4"; - sha256 = "sha256-cxl7D47dRn+uMVOHbF0avj5+ZFWjaJ7lXj/8l6r9q2I="; + version = "4.12.5"; + sha256 = "sha256-Qj9w5s02OSMQ2qA7HG7xNqQGaUacA1d4zbOHynq5k+A="; }; z3_4_11 = common { version = "4.11.2"; diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix index 45209881f7a9..b2a76f5fb252 100644 --- a/pkgs/applications/science/misc/boinc/default.nix +++ b/pkgs/applications/science/misc/boinc/default.nix @@ -27,14 +27,14 @@ stdenv.mkDerivation rec { pname = "boinc"; - version = "7.24.2"; + version = "7.24.3"; src = fetchFromGitHub { name = "${pname}-${version}-src"; owner = "BOINC"; repo = "boinc"; rev = "client_release/${lib.versions.majorMinor version}/${version}"; - hash = "sha256-Aaoqf53wagCkzkZUs7mVbE2Z2P6GvxiQYxPrL6ahGqA="; + hash = "sha256-0gyCO5t8t0SbOCBClVVu+C2VpBlxsnoRHBRYgI8nNO4="; }; nativeBuildInputs = [ libtool automake autoconf m4 pkg-config ]; diff --git a/pkgs/applications/science/misc/gplates/default.nix b/pkgs/applications/science/misc/gplates/default.nix index e6cebbc53b73..283a14e99650 100644 --- a/pkgs/applications/science/misc/gplates/default.nix +++ b/pkgs/applications/science/misc/gplates/default.nix @@ -12,6 +12,7 @@ , gmp , libGL , libGLU +, libSM , mpfr , proj , python3 @@ -58,6 +59,7 @@ in mkDerivation rec { gmp libGL libGLU + libSM mpfr proj python diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index 1daeeb81410a..b3a95034ca54 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -7,6 +7,7 @@ , perl , blas , lapack +, llvmPackages , mpi , cudaPackages , plumed @@ -40,8 +41,8 @@ let } else { - version = "2023.3"; - hash = "sha256-Tsj40MevdrE/j9FtuOLBIOdJ3kOa6VVNn2U/gS140cs="; + version = "2024"; + hash = "sha256-BNIm1SBmqLw6QuANYhPec3tOwpLiZwMGWST/AZVoAeI="; }; in stdenv.mkDerivation rec { @@ -77,7 +78,7 @@ in stdenv.mkDerivation rec { cudaPackages.cuda_cudart cudaPackages.libcufft cudaPackages.cuda_profiler_api - ]; + ] ++ lib.optional stdenv.isDarwin llvmPackages.openmp; propagatedBuildInputs = lib.optional enableMpi mpi; propagatedUserEnvPkgs = lib.optional enableMpi mpi; |