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| author | Alyssa Ross <hi@alyssa.is> | 2021-01-15 10:30:44 +0000 |
|---|---|---|
| committer | Alyssa Ross <hi@alyssa.is> | 2021-01-15 10:30:44 +0000 |
| commit | e0794be8a0d11e90461e5a9c85012a36b93ec976 (patch) | |
| tree | efd9cbc55ea3322867bf601c4d536758a3dd5fcc /nixpkgs/pkgs/development/python-modules/cnvkit/default.nix | |
| parent | 3538874082ded7647b1ccec0343c7c1e882cfef3 (diff) | |
| parent | 1a57d96edd156958b12782e8c8b6a374142a7248 (diff) | |
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Merge commit '1a57d96edd156958b12782e8c8b6a374142a7248'
Diffstat (limited to 'nixpkgs/pkgs/development/python-modules/cnvkit/default.nix')
| -rw-r--r-- | nixpkgs/pkgs/development/python-modules/cnvkit/default.nix | 33 |
1 files changed, 28 insertions, 5 deletions
diff --git a/nixpkgs/pkgs/development/python-modules/cnvkit/default.nix b/nixpkgs/pkgs/development/python-modules/cnvkit/default.nix index 6677ab06334f..92af67fa183a 100644 --- a/nixpkgs/pkgs/development/python-modules/cnvkit/default.nix +++ b/nixpkgs/pkgs/development/python-modules/cnvkit/default.nix @@ -1,5 +1,6 @@ { lib -, fetchPypi +, fetchFromGitHub +, fetchpatch , rPackages , rWrapper , buildPythonPackage @@ -15,17 +16,29 @@ , pillow , pomegranate , pyfaidx +, python +, R }: buildPythonPackage rec { pname = "CNVkit"; version = "0.9.7"; - src = fetchPypi { - inherit pname version; - sha256 = "d68adc0121e17c61a3aa28c0a9ba6526510a5a0df0f0a6eb1818bab71b7e927a"; + src = fetchFromGitHub { + owner = "etal"; + repo = "cnvkit"; + rev = "v${version}"; + sha256 = "022zplgqil5l76vri647cyjx427vnbg5r2gw6lw712d2janvdjm7"; }; + patches = [ + # Fix: AttributeError: module 'pandas.io.common' has no attribute 'EmptyDataError' + (fetchpatch { + url = "https://github.com/etal/cnvkit/commit/392adfffedfa0415e635b72c5027835b0a8d7ab5.patch"; + sha256 = "0s0gwyy0hybmhc3jij2v9l44b6lkcmclii8bkwsazzj2kc24m2rh"; + }) + ]; + propagatedBuildInputs = [ biopython numpy @@ -39,6 +52,7 @@ buildPythonPackage rec { future pillow pomegranate + rPackages.DNAcopy ]; postPatch = '' @@ -46,7 +60,16 @@ buildPythonPackage rec { --replace "pandas >= 0.20.1, < 0.25.0" "pandas" ''; - pythonImportsCheck = [ "cnvlib" ]; + checkInputs = [ R ]; + + checkPhase = '' + pushd test/ + ${python.interpreter} test_io.py + ${python.interpreter} test_genome.py + ${python.interpreter} test_cnvlib.py + ${python.interpreter} test_commands.py + ${python.interpreter} test_r.py + ''; meta = with lib; { homepage = "https://cnvkit.readthedocs.io"; |