pysam: 0.15.3 -> 0.15.4 (and disabling tests) #80625
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@ofborg build python37Packages.pysam |
unode
changed the title
|
Tests have been disabled due to upstream test data incompatibilities with Tests are to be re-enabled once upstream issues are fixed. |
jonringer
reviewed
Feb 21, 2020
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I tried my hand at this as well, do you mind incorporating some of my adjustments (mostly the pythonImportsCheck and meta)
{ lib
, buildPythonPackage
, fetchFromGitHub
, bzip2
, bcftools
, curl
, cython
, htslib
, lzma
, pytest
, samtools
, zlib
}:
buildPythonPackage rec {
pname = "pysam";
version = "0.15.4";
# Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
# missing some files which cause test failures.
# Tracked at: https://github.com/pysam-developers/pysam/issues/616
src = fetchFromGitHub {
owner = "pysam-developers";
repo = "pysam";
rev = "v${version}";
sha256 = "04w6h6mv6lsr74hj9gy4r2laifcbhgl2bjcr4r1l9r73xdd45mdy";
};
nativeBuildInputs = [ samtools ];
buildInputs = [ bzip2 curl cython lzma zlib ];
checkInputs = [ pytest bcftools htslib ];
checkPhase = "py.test";
# tests require samtools<=1.9
doCheck = false;
preCheck = ''
export HOME=$(mktemp -d)
make -C tests/pysam_data
make -C tests/cbcf_data
'';
pythonImportsCheck = [
"pysam"
"pysam.bcftools"
"pysam.libcutils"
"pysam.libcvcf"
];
meta = with lib; {
description = "A python module for reading, manipulating and writing genome data sets";
homepage = "https://pysam.readthedocs.io/";
maintainers = with maintainers; [ unode ];
license = licenses.mit;
platforms = [ "i686-linux" "x86_64-linux" ];
};
}
Also disable tests until upstream test data issues are resolved. See link in comment in code for more information.
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@jonringer Thanks. Included your recipe. |
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Also backported to 20.03 in 07f20d0, which is fine since this is strictly a bugfix release: https://github.com/pysam-developers/pysam/releases/tag/v0.15.4 |
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This is a reopen of #80360