diff --git a/pkgs/development/python-modules/scikit-bio/default.nix b/pkgs/development/python-modules/scikit-bio/default.nix index ef4e4ed9719b..151ae1f21f42 100644 --- a/pkgs/development/python-modules/scikit-bio/default.nix +++ b/pkgs/development/python-modules/scikit-bio/default.nix @@ -1,26 +1,30 @@ { lib, + stdenv, buildPythonPackage, fetchFromGitHub, + # build-system setuptools, cython, oldest-supported-numpy, - requests, + # dependencies + array-api-compat, + biom-format, decorator, + h5py, natsort, numpy, pandas, - scipy, - h5py, - biom-format, - statsmodels, patsy, - array-api-compat, + requests, + scipy, + statsmodels, - python, + # tests pytestCheckHook, + python, }: buildPythonPackage rec { @@ -42,29 +46,37 @@ buildPythonPackage rec { ]; dependencies = [ - requests + array-api-compat + biom-format decorator + h5py natsort numpy pandas - scipy - h5py - biom-format - statsmodels patsy - array-api-compat + requests + scipy + statsmodels ]; - nativeCheckInputs = [ pytestCheckHook ]; + nativeCheckInputs = [ + pytestCheckHook + ]; # only the $out dir contains the built cython extensions, so we run the tests inside there enabledTestPaths = [ "${placeholder "out"}/${python.sitePackages}/skbio" ]; + # The trick above makes test collection fail on darwin: + # PermissionError: [Errno 1] Operation not permitted: '/nix/.Trashes' + doCheck = !stdenv.hostPlatform.isDarwin; + pythonImportsCheck = [ "skbio" ]; meta = { - homepage = "http://scikit-bio.org/"; description = "Data structures, algorithms and educational resources for bioinformatics"; + homepage = "http://scikit-bio.org/"; + downloadPage = "https://github.com/scikit-bio/scikit-bio"; + changelog = "https://github.com/scikit-bio/scikit-bio/blob/${version}/CHANGELOG.md"; license = lib.licenses.bsd3; maintainers = with lib.maintainers; [ tomasajt ]; };