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| author | Robert Scott <code@humanleg.org.uk> | 2022-05-29 21:39:06 +0100 |
|---|---|---|
| committer | github-actions[bot] <github-actions[bot]@users.noreply.github.com> | 2022-05-29 23:11:56 +0000 |
| commit | d20913a939d6ee799b857abaaba5337c949b087e (patch) | |
| tree | a236bad62f022fbc7d9b4e18eea125eab417b2cd | |
| parent | genimage: 9 -> 15 (diff) | |
| download | nixpkgs-d20913a939d6ee799b857abaaba5337c949b087e.tar.gz | |
python3Packages.cnvkit: 0.9.7 -> 0.9.9, skip broken test
(cherry picked from commit 798d9f9f3bc5dcbcb75d2ebff35c2e0e580d61d1)
| -rw-r--r-- | pkgs/development/python-modules/cnvkit/default.nix | 24 |
1 files changed, 15 insertions, 9 deletions
diff --git a/pkgs/development/python-modules/cnvkit/default.nix b/pkgs/development/python-modules/cnvkit/default.nix index 6347c8552bf6..36e4bcf2760d 100644 --- a/pkgs/development/python-modules/cnvkit/default.nix +++ b/pkgs/development/python-modules/cnvkit/default.nix @@ -21,22 +21,23 @@ buildPythonPackage rec { pname = "CNVkit"; - version = "0.9.7"; + version = "0.9.9"; src = fetchFromGitHub { owner = "etal"; repo = "cnvkit"; rev = "v${version}"; - sha256 = "022zplgqil5l76vri647cyjx427vnbg5r2gw6lw712d2janvdjm7"; + sha256 = "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1"; }; - patches = [ - # Fix: AttributeError: module 'pandas.io.common' has no attribute 'EmptyDataError' - (fetchpatch { - url = "https://github.com/etal/cnvkit/commit/392adfffedfa0415e635b72c5027835b0a8d7ab5.patch"; - sha256 = "0s0gwyy0hybmhc3jij2v9l44b6lkcmclii8bkwsazzj2kc24m2rh"; - }) - ]; + postPatch = '' + # see https://github.com/etal/cnvkit/issues/589 + substituteInPlace setup.py \ + --replace 'joblib < 1.0' 'joblib' + # see https://github.com/etal/cnvkit/issues/680 + substituteInPlace test/test_io.py \ + --replace 'test_read_vcf' 'dont_test_read_vcf' + ''; propagatedBuildInputs = [ biopython @@ -63,8 +64,13 @@ buildPythonPackage rec { ${python.interpreter} test_cnvlib.py ${python.interpreter} test_commands.py ${python.interpreter} test_r.py + popd # test/ ''; + pythonImportsCheck = [ + "cnvlib" + ]; + meta = with lib; { homepage = "https://cnvkit.readthedocs.io"; description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data"; |