diff options
Diffstat (limited to 'pkgs/applications/science/misc')
18 files changed, 267 insertions, 190 deletions
diff --git a/pkgs/applications/science/misc/bada-bib/default.nix b/pkgs/applications/science/misc/bada-bib/default.nix new file mode 100644 index 0000000000000..356630329bbe9 --- /dev/null +++ b/pkgs/applications/science/misc/bada-bib/default.nix @@ -0,0 +1,78 @@ +{ lib +, meson +, ninja +, fetchFromGitHub +, appstream-glib +, desktop-file-utils +, gdk-pixbuf +, gettext +, glib +, gnome +, gobject-introspection +, gtk3 +, libxml2 +, pkg-config +, python3Packages +, wrapGAppsHook }: + +python3Packages.buildPythonApplication rec { + pname = "bada-bib"; + version = "0.4.1"; + format = "other"; + strictDeps = false; # https://github.com/NixOS/nixpkgs/issues/56943 + + src = fetchFromGitHub { + owner = "RogerCrocker"; + repo = "BadaBib"; + rev = "v${version}"; + sha256 = "sha256-kub2lLauru2RrinzxMDyBVC0htPx0Niv/M6bbmTS7Hk="; + }; + + nativeBuildInputs = [ + gettext + gobject-introspection + libxml2 + meson + ninja + pkg-config + wrapGAppsHook + ]; + + buildInputs = [ + gdk-pixbuf + glib + gtk3 + ]; + + checkInputs = [ + appstream-glib + desktop-file-utils + ]; + + pythonPath = with python3Packages; [ + bibtexparser + pygobject3 + watchgod + ]; + + postPatch = '' + patchShebangs build-aux/meson/postinstall.py + ''; + + dontWrapGApps = true; # Needs python wrapper + + preFixup = '' + makeWrapperArgs+=("''${gappsWrapperArgs[@]}") + ''; + + postFixup = '' + wrapPythonProgramsIn "$out/libexec" "$out $pythonPath" + ''; + + meta = with lib; { + homepage = "https://github.com/RogerCrocker/BadaBib"; + description = "A simple BibTeX Viewer and Editor"; + maintainers = [ maintainers.Cogitri ]; + license = licenses.gpl3Plus; + }; +} diff --git a/pkgs/applications/science/misc/colmap/default.nix b/pkgs/applications/science/misc/colmap/default.nix index 60f9810dfb6a0..c41c8593a5c49 100644 --- a/pkgs/applications/science/misc/colmap/default.nix +++ b/pkgs/applications/science/misc/colmap/default.nix @@ -7,13 +7,13 @@ assert !cudaSupport || cudatoolkit != null; let boost_static = boost17x.override { enableStatic = true; }; in mkDerivation rec { - version = "3.6"; + version = "3.7"; pname = "colmap"; src = fetchFromGitHub { owner = "colmap"; repo = "colmap"; rev = version; - sha256 = "1kfivdmhpmdxjjf30rr57y2iy7xmdpg4h8aw3qgacv8ckfpgda3n"; + sha256 = "sha256-uVAw6qwhpgIpHkXgxttKupU9zU+vD0Za0maw2Iv4x+I="; }; buildInputs = [ @@ -30,7 +30,7 @@ mkDerivation rec { with a graphical and command-line interface. ''; homepage = "https://colmap.github.io/index.html"; - license = licenses.bsd2; + license = licenses.bsd3; platforms = platforms.linux; maintainers = with maintainers; [ lebastr ]; }; diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix index 7cbd9354a372e..5cfd7be8e64a7 100644 --- a/pkgs/applications/science/misc/cwltool/default.nix +++ b/pkgs/applications/science/misc/cwltool/default.nix @@ -7,21 +7,20 @@ python3.pkgs.buildPythonApplication rec { pname = "cwltool"; - version = "3.1.20211104071347"; + version = "3.1.20220217190813"; format = "setuptools"; - disabled = python3.pythonOlder "3.6"; - src = fetchFromGitHub { owner = "common-workflow-language"; repo = pname; rev = version; - sha256 = "sha256-tp4SdilW2PKav7b3/BchXYl33W9U0aQH6FPdOhHSvIQ="; + sha256 = "sha256-2Zd1Z/Tv8wAiqlaYkZRflsUVl8OAOXdufq9k4j4L7f0="; }; postPatch = '' substituteInPlace setup.py \ - --replace 'prov == 1.5.1' 'prov' \ + --replace "ruamel.yaml >= 0.15, < 0.17.18" "ruamel.yaml" \ + --replace "prov == 1.5.1" "prov" \ --replace "setup_requires=PYTEST_RUNNER," "" ''; diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix index 783381f9db03e..a907a5f8c169d 100644 --- a/pkgs/applications/science/misc/cytoscape/default.nix +++ b/pkgs/applications/science/misc/cytoscape/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "cytoscape"; - version = "3.9.0"; + version = "3.9.1"; src = fetchurl { url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-unix-${version}.tar.gz"; - sha256 = "sha256-7YDmojzQujHrsDuB7WC0C3Z2srTd9QUveh1baod3KvU="; + sha256 = "sha256-I4C2yGiIygnFUkRBC4LBSQFgjZlVKCoQGRphynVpscw="; }; patches = [ diff --git a/pkgs/applications/science/misc/foldingathome/control.nix b/pkgs/applications/science/misc/foldingathome/control.nix index 1430881a3f08c..e5cc02edcfbe6 100644 --- a/pkgs/applications/science/misc/foldingathome/control.nix +++ b/pkgs/applications/science/misc/foldingathome/control.nix @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { installPhase = "cp -ar usr $out"; postFixup = '' - sed -e 's|/usr/bin|$out/bin|g' -i $out/share/applications/FAHControl.desktop + sed -e "s|/usr/bin|$out/bin|g" -i $out/share/applications/FAHControl.desktop wrapProgram "$out/bin/FAHControl" \ --suffix PATH : "${fahviewer.outPath}/bin" \ --set PYTHONPATH "$out/lib/python2.7/dist-packages" diff --git a/pkgs/applications/science/misc/foldingathome/viewer.nix b/pkgs/applications/science/misc/foldingathome/viewer.nix index 52ca9c9e623ff..75e900a0a72c5 100644 --- a/pkgs/applications/science/misc/foldingathome/viewer.nix +++ b/pkgs/applications/science/misc/foldingathome/viewer.nix @@ -38,7 +38,7 @@ stdenv.mkDerivation rec { unpackPhase = '' dpkg-deb -x ${src} ./ - sed -e 's|/usr/bin|$out/bin|g' -i usr/share/applications/FAHViewer.desktop + sed -e "s|/usr/bin|$out/bin|g" -i usr/share/applications/FAHViewer.desktop ''; installPhase = '' diff --git a/pkgs/applications/science/misc/golly/default.upstream b/pkgs/applications/science/misc/golly/default.upstream deleted file mode 100644 index e8ce81586a8db..0000000000000 --- a/pkgs/applications/science/misc/golly/default.upstream +++ /dev/null @@ -1,5 +0,0 @@ -url https://sourceforge.net/projects/golly/files/golly/ -version_link '[-][0-9.]+/$' -SF_version_tarball 'src' -SF_redirect -minimize_overwrite diff --git a/pkgs/applications/science/misc/gplates/default.nix b/pkgs/applications/science/misc/gplates/default.nix index 67ab202160ca3..7cbf37fcaf8ae 100644 --- a/pkgs/applications/science/misc/gplates/default.nix +++ b/pkgs/applications/science/misc/gplates/default.nix @@ -1,4 +1,5 @@ { lib +, stdenv , mkDerivation , fetchurl , cmake @@ -65,5 +66,6 @@ in mkDerivation rec { homepage = "https://www.gplates.org"; license = licenses.gpl2Only; platforms = platforms.all; + broken = stdenv.isDarwin; # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/gplates.x86_64-darwin }; } diff --git a/pkgs/applications/science/misc/graphia/default.nix b/pkgs/applications/science/misc/graphia/default.nix index 4b45a3c06fe1d..4f452c96b8e73 100644 --- a/pkgs/applications/science/misc/graphia/default.nix +++ b/pkgs/applications/science/misc/graphia/default.nix @@ -29,5 +29,6 @@ stdenv.mkDerivation rec { license = licenses.gpl3Only; maintainers = [ maintainers.bgamari ]; platforms = platforms.all; + broken = stdenv.isDarwin; # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/graphia.x86_64-darwin }; } diff --git a/pkgs/applications/science/misc/nextinspace/default.nix b/pkgs/applications/science/misc/nextinspace/default.nix index 390b2c58ca682..fd7e581831448 100644 --- a/pkgs/applications/science/misc/nextinspace/default.nix +++ b/pkgs/applications/science/misc/nextinspace/default.nix @@ -1,24 +1,44 @@ -{ lib, fetchPypi, python3Packages }: +{ lib +, fetchFromGitHub +, python3 +}: -python3Packages.buildPythonPackage rec { +python3.pkgs.buildPythonApplication rec { pname = "nextinspace"; - version = "1.0.6"; + version = "2.0.3"; + format = "pyproject"; - src = fetchPypi { - inherit pname version; - sha256 = "1h3dksxyy5gq071fa7i2p73s50918y1bkk38hgfwr4226c3wipvg"; + src = fetchFromGitHub { + owner = "not-stirred"; + repo = pname; + rev = "v${version}"; + hash = "sha256-Macx2pQglB95Bhc939TFVCHd1qvqJsco91EXKCIQLgg="; }; - pythonPath = with python3Packages; [ + nativeBuildInputs = with python3.pkgs; [ + poetry-core + ]; + + pythonPath = with python3.pkgs; [ requests tzlocal colorama ]; + checkInputs = with python3.pkgs; [ + pytest-lazy-fixture + pytestCheckHook + requests-mock + ]; + + pythonImportsCheck = [ + "nextinspace" + ]; + meta = with lib; { description = "Print upcoming space-related events in your terminal"; homepage = "https://github.com/The-Kid-Gid/nextinspace"; - license = licenses.gpl3; + license = licenses.gpl3Only; maintainers = with maintainers; [ penguwin ]; }; } diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index 225a81f1f66a4..f8037c01e087b 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -9,6 +9,7 @@ , gl2ps , glew , gsl +, lapack , libX11 , libXpm , libXft @@ -19,6 +20,7 @@ , llvm_9 , lz4 , xz +, openblas , pcre , nlohmann_json , pkg-config @@ -55,11 +57,13 @@ stdenv.mkDerivation rec { pcre zlib zstd + lapack libxml2 llvm_9 lz4 xz gsl + openblas xxHash libAfterImage giflib @@ -116,7 +120,6 @@ stdenv.mkDerivation rec { cmakeFlags = [ "-Drpath=ON" - "-DCMAKE_CXX_STANDARD=17" "-DCMAKE_INSTALL_BINDIR=bin" "-DCMAKE_INSTALL_LIBDIR=lib" "-DCMAKE_INSTALL_INCLUDEDIR=include" @@ -153,6 +156,7 @@ stdenv.mkDerivation rec { "-Droot7=OFF" "-Dsqlite=OFF" "-Dssl=OFF" + "-Dtmva=ON" "-Dvdt=OFF" "-Dwebgui=OFF" "-Dxml=ON" @@ -171,7 +175,8 @@ stdenv.mkDerivation rec { postInstall = '' for prog in rootbrowse rootcp rooteventselector rootls rootmkdir rootmv rootprint rootrm rootslimtree; do wrapProgram "$out/bin/$prog" \ - --prefix PYTHONPATH : "$out/lib" + --set PYTHONPATH "$out/lib" \ + --set ${lib.optionalString stdenv.isDarwin "DY"}LD_LIBRARY_PATH "$out/lib" done ''; diff --git a/pkgs/applications/science/misc/sasview/default.nix b/pkgs/applications/science/misc/sasview/default.nix index bbbe80eb65686..51dea2755785e 100644 --- a/pkgs/applications/science/misc/sasview/default.nix +++ b/pkgs/applications/science/misc/sasview/default.nix @@ -1,70 +1,57 @@ -{ lib, fetchFromGitHub, gcc, python }: +{ lib +, python3 +, fetchFromGitHub +, which +, wrapQtAppsHook +}: + +python3.pkgs.buildPythonApplication rec { + pname = "sasview"; + version = "5.0.4"; -let - xhtml2pdf = import ./xhtml2pdf.nix { - inherit lib; - fetchPypi = python.pkgs.fetchPypi; - buildPythonPackage = python.pkgs.buildPythonPackage; - html5lib = python.pkgs.html5lib; - httplib2 = python.pkgs.httplib2; - nose = python.pkgs.nose; - pillow = python.pkgs.pillow; - pypdf2 = python.pkgs.pypdf2; - reportlab = python.pkgs.reportlab; + src = fetchFromGitHub { + owner = "SasView"; + repo = "sasview"; + rev = "v${version}"; + hash = "sha256-TjcchqA6GCvkr59ZgDuGglan2RxLp+aMjJk28XhvoiY="; }; -in - -python.pkgs.buildPythonApplication rec { - pname = "sasview"; - version = "4.2.0"; - - checkInputs = with python.pkgs; [ - pytest - unittest-xml-reporting + nativeBuildInputs = [ + python3.pkgs.pyqt5 + wrapQtAppsHook ]; - checkPhase = '' - # fix the following error: - # imported module 'sas.sascalc.data_util.uncertainty' has this __file__ attribute: - # /build/source/build/lib.linux-x86_64-2.7/sas/sascalc/data_util/uncertainty.py - # which is not the same as the test file we want to collect: - # /build/source/dist/tmpbuild/sasview/sas/sascalc/data_util/uncertainty.py - rm -r dist/tmpbuild - - HOME=$(mktemp -d) py.test - ''; - - propagatedBuildInputs = with python.pkgs; [ + propagatedBuildInputs = with python3.pkgs; [ bumps - gcc h5py - libxslt lxml - matplotlib - numpy - pyparsing periodictable pillow - pylint - pyopencl - reportlab + pyparsing + pyqt5 + qt5reactor sasmodels scipy - six - sphinx - wxPython + setuptools xhtml2pdf ]; - src = fetchFromGitHub { - owner = "SasView"; - repo = "sasview"; - rev = "v${version}"; - sha256 = "0k3486h46k6406h0vla8h68fd78wh3dcaq5w6f12jh6g4cjxv9qa"; - }; + postBuild = '' + ${python3.interpreter} src/sas/qtgui/convertUI.py + ''; + + dontWrapQtApps = true; + + makeWrapperArgs = [ + "\${qtWrapperArgs[@]}" + ]; + + checkInputs = with python3.pkgs; [ + pytestCheckHook + unittest-xml-reporting + ]; - patches = [ ./pyparsing-fix.patch ./local_config.patch ]; + pytestFlagsArray = [ "test" ]; meta = with lib; { homepage = "https://www.sasview.org"; diff --git a/pkgs/applications/science/misc/sasview/local_config.patch b/pkgs/applications/science/misc/sasview/local_config.patch deleted file mode 100644 index 5b6c3436494af..0000000000000 --- a/pkgs/applications/science/misc/sasview/local_config.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/src/sas/_config.py b/src/sas/_config.py -index ece08fd4c..926768593 100644 ---- a/src/sas/_config.py -+++ b/src/sas/_config.py -@@ -67,8 +67,8 @@ def load_local_config(app_dir): - logger.info("GuiManager loaded %s", path) - return module - except Exception as exc: -- logger.critical("Error loading %s: %s", path, exc) -- sys.exit() -+ import sas.sasview.local_config -+ return sas.sasview.local_config - - def make_custom_config_path(user_dir): - """ -@@ -116,4 +116,4 @@ def load_custom_config(path): - - from sas.sasview import custom_config - logger.info("GuiManager custom_config defaults to sas.sasview.custom_config") -- return custom_config -\ No newline at end of file -+ return custom_config diff --git a/pkgs/applications/science/misc/sasview/pyparsing-fix.patch b/pkgs/applications/science/misc/sasview/pyparsing-fix.patch deleted file mode 100644 index c3cd164a899a3..0000000000000 --- a/pkgs/applications/science/misc/sasview/pyparsing-fix.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/setup.py b/setup.py -index 866ab7e36..78727b276 100755 ---- a/setup.py -+++ b/setup.py -@@ -401,7 +401,7 @@ package_data['sas.sasview'] = ['images/*', - packages.append("sas.sasview") - - required = [ -- 'bumps>=0.7.5.9', 'periodictable>=1.5.0', 'pyparsing>=2.0.0', -+ 'bumps>=0.7.5.9', 'periodictable>=1.5.0', - - # 'lxml>=2.2.2', - 'lxml', 'h5py', diff --git a/pkgs/applications/science/misc/simgrid/default.nix b/pkgs/applications/science/misc/simgrid/default.nix index 23815442da7e6..888419fbc86fd 100644 --- a/pkgs/applications/science/misc/simgrid/default.nix +++ b/pkgs/applications/science/misc/simgrid/default.nix @@ -1,13 +1,14 @@ -{ lib, stdenv, fetchFromGitLab, fetchpatch, cmake, perl, python3, boost, valgrind -# Optional requirements -# Lua 5.3 needed and not available now -#, luaSupport ? false, lua5 +{ stdenv, lib, fetchFromGitLab, cmake, perl, python3, boost , fortranSupport ? false, gfortran -, buildDocumentation ? false, transfig, ghostscript, doxygen +, buildDocumentation ? false, fig2dev, ghostscript, doxygen , buildJavaBindings ? false, openjdk +, buildPythonBindings ? true, python3Packages , modelCheckingSupport ? false, libunwind, libevent, elfutils # Inside elfutils: libelf and libdw +, minimalBindings ? false , debug ? false +, optimize ? (!debug) , moreTests ? false +, withoutBin ? false }: with lib; @@ -18,54 +19,35 @@ in stdenv.mkDerivation rec { pname = "simgrid"; - version = "3.28"; + version = "3.30"; src = fetchFromGitLab { domain = "framagit.org"; owner = pname; repo = pname; rev = "v${version}"; - sha256 = "0vylwgd4i89bvhbgfay0wq953324dwfmmr8jp9b4vvlc9m0017r9"; + sha256 = "1dg8ywqif20g0fs8dnd6364n080nvwx7f444zcfwqwz6iax61qv1"; }; - patches = [ - (fetchpatch { - name = "fix-smpi-dirs-absolute.patch"; - url = "https://framagit.org/simgrid/simgrid/-/commit/71f01e667577be1076646eb841e0a57bd5388545.patch"; - sha256 = "0x3y324b6269687zfy43ilc48bwrs4nb7svh2mpg88lrz53rky15"; - }) - ]; - propagatedBuildInputs = [ boost ]; - nativeBuildInputs = [ cmake perl python3 valgrind ] - ++ optionals fortranSupport [ gfortran ] - ++ optionals buildJavaBindings [ openjdk ] - ++ optionals buildDocumentation [ transfig ghostscript doxygen ] - ++ optionals modelCheckingSupport [ libunwind libevent elfutils ]; + nativeBuildInputs = [ cmake perl python3 ] + ++ optionals fortranSupport [ gfortran ] + ++ optionals buildJavaBindings [ openjdk ] + ++ optionals buildPythonBindings [ python3Packages.pybind11 ] + ++ optionals buildDocumentation [ fig2dev ghostscript doxygen ] + ++ optionals modelCheckingSupport [ libunwind libevent elfutils ]; - #buildInputs = optional luaSupport lua5; - - # Make it so that libsimgrid.so will be found when running programs from - # the build dir. - preConfigure = '' - export LD_LIBRARY_PATH="$PWD/build/lib" - ''; + outputs = [ "out" ] + ++ optionals buildPythonBindings [ "python" ]; - # Release mode is not supported in SimGrid + # "Release" does not work. non-debug mode is Debug compiled with optimization cmakeBuildType = "Debug"; - - # Disable/Enable functionality - # Note: those packages are not packaged in Nixpkgs yet so some options - # are disabled: - # - papi: for enable_smpi_papi - # - ns3: for enable_ns3 - # - lua53: for enable_lua - # - # For more information see: - # https://simgrid.org/doc/3.22/Installing_SimGrid.html#simgrid-compilation-options) cmakeFlags = [ "-Denable_documentation=${optionOnOff buildDocumentation}" "-Denable_java=${optionOnOff buildJavaBindings}" + "-Denable_python=${optionOnOff buildPythonBindings}" + "-DSIMGRID_PYTHON_LIBDIR=./" # prevents CMake to install in ${python3} dir + "-Denable_msg=${optionOnOff buildJavaBindings}" "-Denable_fortran=${optionOnOff fortranSupport}" "-Denable_model-checking=${optionOnOff modelCheckingSupport}" "-Denable_ns3=off" @@ -75,27 +57,28 @@ stdenv.mkDerivation rec { "-Denable_mallocators=on" "-Denable_debug=on" "-Denable_smpi=on" + "-Dminimal-bindings=${optionOnOff minimalBindings}" "-Denable_smpi_ISP_testsuite=${optionOnOff moreTests}" "-Denable_smpi_MPICH3_testsuite=${optionOnOff moreTests}" - "-Denable_compile_warnings=${optionOnOff debug}" - "-Denable_compile_optimizations=${optionOnOff (!debug)}" - "-Denable_lto=${optionOnOff (!debug)}" - # "-Denable_lua=${optionOnOff luaSupport}" - # "-Denable_smpi_papi=${optionOnOff moreTests}" + "-Denable_compile_warnings=off" + "-Denable_compile_optimizations=${optionOnOff optimize}" + "-Denable_lto=${optionOnOff optimize}" ]; - makeFlags = optional debug "VERBOSE=1"; - # Some Perl scripts are called to generate test during build which - # is before the fixupPhase, so do this manualy here: + # needed to run tests and to ensure correct shabangs in output scripts preBuild = '' patchShebangs .. ''; - doCheck = true; + # needed by tests (so libsimgrid.so is found) + preConfigure = '' + export LD_LIBRARY_PATH="$PWD/build/lib" + ''; - # Prevent the execution of tests known to fail. + doCheck = true; preCheck = '' + # prevent the execution of tests known to fail cat <<EOW >CTestCustom.cmake SET(CTEST_CUSTOM_TESTS_IGNORE smpi-replay-multiple) EOW @@ -104,6 +87,20 @@ stdenv.mkDerivation rec { make tests -j $NIX_BUILD_CORES ''; + postInstall = lib.optionalString withoutBin '' + # remove bin from output if requested. + # having a specific bin output would be cleaner but it does not work currently (circular references) + rm -rf $out/bin + '' + lib.optionalString buildPythonBindings '' + # manually install the python binding if requested. + mkdir -p $python/lib/python${lib.versions.majorMinor python3.version}/site-packages/ + cp ./lib/simgrid.cpython*.so $python/lib/python${lib.versions.majorMinor python3.version}/site-packages/ + ''; + + # improve debuggability if requested + hardeningDisable = lib.optionals debug [ "fortify" ]; + dontStrip = debug; + meta = { description = "Framework for the simulation of distributed applications"; longDescription = '' @@ -118,5 +115,6 @@ stdenv.mkDerivation rec { license = licenses.lgpl2Plus; maintainers = with maintainers; [ mickours mpoquet ]; platforms = platforms.all; + broken = stdenv.isDarwin; }; } diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index 40c102fc68220..f4a3da9711dda 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -1,8 +1,8 @@ -{ lib, python3Packages }: +{ lib, python3Packages, fetchFromGitHub }: python3Packages.buildPythonApplication rec { pname = "snakemake"; - version = "6.10.0"; + version = "6.15.5"; propagatedBuildInputs = with python3Packages; [ appdirs @@ -29,12 +29,31 @@ python3Packages.buildPythonApplication rec { wrapt ]; - src = python3Packages.fetchPypi { - inherit pname version; - sha256 = "199a86c8d1fcfdb88c4271a1507b0ab371a15bc407f2dad9b0ab8c43438adff8"; + src = fetchFromGitHub { + owner = "snakemake"; + repo = pname; + rev = "v${version}"; + sha256 = "sha256-i8C7gPLzUzSxNH9xwpr+fUKI1SvpYFsFBlspS74LoWU="; }; - doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json + # See + # https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99 + # for the current basic test suite. Tibanna and Tes require extra + # setup. + + checkInputs = with python3Packages; [ + pandas + pytestCheckHook + requests-mock + ]; + + disabledTestPaths = [ + "tests/test_tes.py" + "tests/test_tibanna.py" + "tests/test_linting.py" + ]; + + pythonImportsCheck = [ "snakemake" ]; meta = with lib; { homepage = "https://snakemake.github.io"; diff --git a/pkgs/applications/science/misc/toil/default.nix b/pkgs/applications/science/misc/toil/default.nix index a25fbe7565ce5..b13ad0ad10ca3 100644 --- a/pkgs/applications/science/misc/toil/default.nix +++ b/pkgs/applications/science/misc/toil/default.nix @@ -1,39 +1,46 @@ -{ lib, fetchFromGitHub, python3Packages }: +{ lib +, fetchFromGitHub +, python3 +}: -python3Packages.buildPythonApplication rec { +python3.pkgs.buildPythonApplication rec { pname = "toil"; - version = "5.4.0"; + version = "5.6.0"; + format = "setuptools"; - src = python3Packages.fetchPypi { + src = python3.pkgs.fetchPypi { inherit pname version; - sha256 = "73c0648828bd3610c07b7648dd06d6ec27efefdb09473bf01d05d91eb899c9fd"; + sha256 = "sha256-m6tzrRCCLULO+wB8htUlt0KESLm/vdIeTzBrihnAo/I="; }; - postPatch = '' - substituteInPlace setup.py \ - --replace "docker = " "docker = 'docker' #" \ - --replace "addict = " "addict = 'addict' #" - ''; - - propagatedBuildInputs = with python3Packages; [ + propagatedBuildInputs = with python3.pkgs; [ addict docker pytz pyyaml enlighten psutil + py-tes python-dateutil dill ]; - checkInputs = with python3Packages; [ pytestCheckHook ]; - pytestFlagsArray = [ "src/toil/test" ]; - pythonImportsCheck = [ "toil" ]; + checkInputs = with python3.pkgs; [ + pytestCheckHook + ]; + + pytestFlagsArray = [ + "src/toil/test" + ]; + + pythonImportsCheck = [ + "toil" + ]; meta = with lib; { + description = "Workflow engine written in pure Python"; homepage = "https://toil.ucsc-cgl.org/"; license = with licenses; [ asl20 ]; - description = "Workflow engine written in pure Python"; maintainers = with maintainers; [ veprbl ]; }; } diff --git a/pkgs/applications/science/misc/tulip/default.nix b/pkgs/applications/science/misc/tulip/default.nix index 62d638717f807..87a05f146e9e6 100644 --- a/pkgs/applications/science/misc/tulip/default.nix +++ b/pkgs/applications/science/misc/tulip/default.nix @@ -1,19 +1,20 @@ -{ fetchurl, lib, stdenv, libxml2, freetype, libGLU, libGL, glew, qt4 -, cmake, makeWrapper, libjpeg, python }: +{ fetchurl, lib, stdenv, libxml2, freetype, libGLU, libGL, glew +, qtbase, wrapQtAppsHook, python3 +, cmake, libjpeg }: -let version = "5.2.1"; in stdenv.mkDerivation rec { pname = "tulip"; - inherit version; + version = "5.6.1"; src = fetchurl { url = "mirror://sourceforge/auber/${pname}-${version}_src.tar.gz"; - sha256 = "0bqmqy6sri87a8xv5xf7ffaq5zin4hiaa13g0l64b84i7yckfwky"; + sha256 = "1fy3nvgxv3igwc1d23zailcgigj1d0f2kkh7a5j24c0dyqz5zxmw"; }; - buildInputs = [ libxml2 freetype glew libGLU libGL qt4 libjpeg python ]; + buildInputs = [ libxml2 freetype glew libGLU libGL libjpeg qtbase python3 ]; + nativeBuildInputs = [ cmake wrapQtAppsHook ]; - nativeBuildInputs = [ cmake makeWrapper ]; + qtWrapperArgs = [ ''--prefix PATH : ${lib.makeBinPath [ python3 ]}'' ]; # FIXME: "make check" needs Docbook's DTD 4.4, among other things. doCheck = false; |