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author | github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> | 2024-05-01 00:14:08 +0000 |
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committer | GitHub <noreply@github.com> | 2024-05-01 00:14:08 +0000 |
commit | 4b95256443d294623e14de34fbdb305cd5f065c7 (patch) | |
tree | 55841aff50961e24e5c6600dc0907af60c4748e4 /pkgs/applications/science | |
parent | d80578ab520f20ecf0b5e77d821f38038398901f (diff) | |
parent | 097de5af21721e8e36a2e0d015dc3a5917de3fa0 (diff) |
Merge master into haskell-updates
Diffstat (limited to 'pkgs/applications/science')
4 files changed, 61 insertions, 20 deletions
diff --git a/pkgs/applications/science/biology/seqtk/default.nix b/pkgs/applications/science/biology/seqtk/default.nix index 417bec9c062fb..856248de917db 100644 --- a/pkgs/applications/science/biology/seqtk/default.nix +++ b/pkgs/applications/science/biology/seqtk/default.nix @@ -19,14 +19,13 @@ stdenv.mkDerivation rec { buildInputs = [ zlib libdeflate isa-l ]; - makeFlags = [ "CC=cc" ]; + makeFlags = [ + "CC:=$(CC)" + "BINDIR=$(out)/bin" + ]; - installPhase = '' - runHook preInstall - - install -Dm755 -t $out/bin seqtk - - runHook postInstall + preInstall = '' + mkdir -p "$out/bin" ''; meta = with lib; { diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 0e4728dd65d6f..1733ba2f236c9 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -38,33 +38,75 @@ let in python3Packages.buildPythonApplication rec { inherit pname; - version = "2.5.0"; + version = "3.0.0"; + pyproject = true; + src = fetchFromGitHub { owner = "schrodinger"; repo = "pymol-open-source"; rev = "v${version}"; - sha256 = "sha256-JdsgcVF1w1xFPZxVcyS+GcWg4a1Bd4SvxFOuSdlz9SM="; + hash = "sha256-GhTHxacjGN7XklZ6gileBMRZAGq4Pp4JknNL+qGqrVE="; }; + postPatch = '' + substituteInPlace setup.py \ + --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3.sitePackages}"' + ''; + + build-system = [ + python3Packages.setuptools + ]; + nativeBuildInputs = [ qt5.wrapQtAppsHook ]; buildInputs = [ python3Packages.numpy python3Packages.pyqt5 glew glm libpng libxml2 freetype msgpack netcdf ]; env.NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2"; - hardeningDisable = [ "format" ]; - - installPhase = '' - python setup.py install --home="$out" - runHook postInstall - ''; postInstall = with python3Packages; '' wrapProgram $out/bin/pymol \ --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]} mkdir -p "$out/share/icons/" - ln -s ../../lib/python/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg" + ln -s $out/${python3.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg" + '' + lib.optionalString stdenv.hostPlatform.isLinux '' cp -r "${desktopItem}/share/applications/" "$out/share/" ''; + pythonImportsCheck = [ + "pymol" + ]; + + nativeCheckInputs = with python3Packages; [ + python3Packages.msgpack + pillow + pytestCheckHook + ]; + + # some tests hang for some reason + doCheck = !(stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64); + + disabledTestPaths = [ + # require biopython which is broken as of 2024-04-20 + "tests/api/seqalign.py" + ]; + + disabledTests = [ + # the output image does not exactly match + "test_commands" + # touch the network + "testFetch" + # requires collada2gltf which is not included in nixpkgs + "testglTF" + # require mmtf-cpp which does not support darwin + "testMMTF" + "testSave_symmetry__mmtf" + ]; + + preCheck = '' + cd testing + ''; + + __darwinAllowLocalNetworking = true; + preFixup = '' wrapQtApp "$out/bin/pymol" ''; @@ -74,6 +116,6 @@ python3Packages.buildPythonApplication rec { mainProgram = "pymol"; homepage = "https://www.pymol.org/"; license = licenses.mit; - maintainers = with maintainers; [ samlich ]; + maintainers = with maintainers; [ natsukium samlich ]; }; } diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index 029138a852fad..feddf92821c63 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,7 +7,7 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2024-04-26"; + version = "0-unstable-2024-04-26"; src = fetchFromGitHub { owner = "georgeweigt"; diff --git a/pkgs/applications/science/physics/xnec2c/default.nix b/pkgs/applications/science/physics/xnec2c/default.nix index 26ec1518fed5f..60afa09ecc8cd 100644 --- a/pkgs/applications/science/physics/xnec2c/default.nix +++ b/pkgs/applications/science/physics/xnec2c/default.nix @@ -14,11 +14,11 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation rec { pname = "xnec2c"; - version = "4.4.12"; + version = "4.4.16"; src = fetchurl { url = "https://www.xnec2c.org/releases/${pname}-v${version}.tar.gz"; - hash = "sha256-6Yrx6LkJjfnMA/kJUDWLhGzGopZeecARSrcR++UScsU="; + hash = "sha256-XiZi8pfmfHjGpePkRy/pF1TA+5RdxX4AGuKzG5Wqrmk="; }; nativeBuildInputs = [ |