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python3Packages.cnvkit: fix build error and failing tests (#431215)
authored by
Gaétan Lepage
and committed by
GitHub
b14a5f5b
8998e096
+85
-55
+68
-18
pkgs/development/python-modules/cnvkit/default.nix
+68
-18
pkgs/development/python-modules/cnvkit/default.nix
···
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buildPythonPackage,
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fetchFromGitHub,
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fetchpatch,
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-
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python,
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makeWrapper,
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# dependencies
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R,
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biopython,
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matplotlib,
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numpy,
···
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pomegranate,
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pyfaidx,
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pysam,
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rPackages,
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reportlab,
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rPackages,
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scikit-learn,
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scipy,
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R,
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# tests
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pytestCheckHook,
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}:
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}:
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buildPythonPackage rec {
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pname = "cnvkit";
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version = "0.9.12";
···
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"pomegranate"
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];
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# Numpy 2 compatibility
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postPatch = ''
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substituteInPlace skgenome/intersect.py \
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--replace-fail "np.string_" "np.bytes_"
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'';
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nativeBuildInputs = [
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makeWrapper
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];
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buildInputs = [
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R
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];
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postPatch =
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let
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rscript = lib.getExe' R "Rscript";
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in
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# Numpy 2 compatibility
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''
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substituteInPlace skgenome/intersect.py \
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--replace-fail "np.string_" "np.bytes_"
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''
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# Patch shebang lines in R scripts
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+ ''
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substituteInPlace cnvlib/segmentation/flasso.py \
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--replace-fail "#!/usr/bin/env Rscript" "#!${rscript}"
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substituteInPlace cnvlib/segmentation/cbs.py \
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--replace-fail "#!/usr/bin/env Rscript" "#!${rscript}"
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substituteInPlace cnvlib/segmentation/__init__.py \
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--replace-fail 'rscript_path="Rscript"' 'rscript_path="${rscript}"'
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substituteInPlace cnvlib/commands.py \
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--replace-fail 'default="Rscript"' 'default="${rscript}"'
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'';
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dependencies = [
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biopython
···
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pomegranate
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pyfaidx
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pysam
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rPackages.DNAcopy
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reportlab
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rPackages.DNAcopy
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scikit-learn
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scipy
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];
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# Make sure R can find the DNAcopy package
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postInstall = ''
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wrapProgram $out/bin/cnvkit.py \
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--set R_LIBS_SITE "${rPackages.DNAcopy}/library" \
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--set MPLCONFIGDIR "/tmp/matplotlib-config"
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'';
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installCheckPhase = ''
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runHook preInstallCheck
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${python.executable} -m pytest --deselect=test/test_commands.py::CommandTests::test_batch \
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--deselect=test/test_commands.py::CommandTests::test_segment_hmm
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cd test
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# Set matplotlib config directory for the tests
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export MPLCONFIGDIR="/tmp/matplotlib-config"
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export HOME="/tmp"
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mkdir -p "$MPLCONFIGDIR"
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# Use the installed binary - it's already wrapped with R_LIBS_SITE
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make cnvkit="$out/bin/cnvkit.py" || {
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echo "Make tests failed"
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exit 1
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}
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runHook postInstallCheck
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'';
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doInstallCheck = true;
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pythonImportsCheck = [ "cnvlib" ];
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nativeCheckInputs = [
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pytestCheckHook
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R
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];
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disabledTests = [
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# AttributeError: module 'pomegranate' has no attribute 'NormalDistribution'
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# https://github.com/etal/cnvkit/issues/815
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"test_batch"
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"test_segment_hmm"
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];
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meta = {
+17
-37
pkgs/development/python-modules/pomegranate/default.nix
+17
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pkgs/development/python-modules/pomegranate/default.nix
···
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stdenv,
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buildPythonPackage,
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fetchFromGitHub,
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# build-system
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fetchpatch,
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pytestCheckHook,
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setuptools,
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# dependencies
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apricot-select,
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networkx,
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numpy,
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scikit-learn,
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scipy,
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torch,
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# tests
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pytestCheckHook,
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}:
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buildPythonPackage rec {
···
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src = fetchFromGitHub {
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repo = "pomegranate";
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owner = "jmschrei";
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# tag = "v${version}";
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# No tag for 1.1.2
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rev = "e9162731f4f109b7b17ecffde768734cacdb839b";
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hash = "sha256-vVoAoZ+mph11ZfINT+yxRyk9rXv6FBDgxBz56P2K95Y=";
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tag = "v${version}";
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hash = "sha256-p2Gn0FXnsAHvRUeAqx4M1KH0+XvDl3fmUZZ7MiMvPSs=";
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};
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# _pickle.UnpicklingError: Weights only load failed.
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# https://pytorch.org/docs/stable/generated/torch.load.html
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postPatch = ''
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substituteInPlace \
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tests/distributions/test_bernoulli.py \
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tests/distributions/test_categorical.py \
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tests/distributions/test_exponential.py \
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tests/distributions/test_gamma.py \
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tests/distributions/test_independent_component.py \
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tests/distributions/test_normal_diagonal.py \
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tests/distributions/test_normal_full.py \
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tests/distributions/test_poisson.py \
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tests/distributions/test_student_t.py \
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tests/distributions/test_uniform.py \
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tests/test_bayes_classifier.py \
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tests/test_gmm.py \
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tests/test_kmeans.py \
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--replace-fail \
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'torch.load(".pytest.torch")' \
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'torch.load(".pytest.torch", weights_only=False)'
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'';
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build-system = [ setuptools ];
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···
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pytestCheckHook
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];
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disabledTestPaths = lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isx86_64) [
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patches = [
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# Fix tests for pytorch 2.6
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(fetchpatch {
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name = "python-2.6.patch";
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url = "https://github.com/jmschrei/pomegranate/pull/1142/commits/9ff5d5e2c959b44e569937e777b26184d1752a7b.patch";
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hash = "sha256-BXsVhkuL27QqK/n6Fa9oJCzrzNcL3EF6FblBeKXXSts=";
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})
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];
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pytestFlagsArray = lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isx86_64) [
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# AssertionError: Arrays are not almost equal to 6 decimals
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"=tests/distributions/test_normal_full.py::test_fit"
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"=tests/distributions/test_normal_full.py::test_from_summaries"
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"=tests/distributions/test_normal_full.py::test_serialization"
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"--deselect=tests/distributions/test_normal_full.py::test_fit"
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"--deselect=tests/distributions/test_normal_full.py::test_from_summaries"
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"--deselect=tests/distributions/test_normal_full.py::test_serialization"
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];
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disabledTests = [