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Merge pull request #175357 from risicle/ris-cnvkit-0.9.9

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python3Packages.cnvkit: 0.9.7 -> 0.9.9, skip broken test
This commit is contained in:
Justin Bedő 2022-05-30 09:05:34 +10:00 committed by GitHub
commit fda1a42e93
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1 changed files with 15 additions and 9 deletions
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24
pkgs/development/python-modules/cnvkit/default.nix
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@ -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";