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author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2021-06-06 02:06:51 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2021-06-06 08:33:21 +0200 |
commit | d1e7b50dbf58c59c100f1bf5a7ea735daa3a203f (patch) | |
tree | 8c4a3e487c42956837dbeae766c44242c4907f1f /gnu/packages/bioinformatics.scm | |
parent | 78469645fd26036c0742abf56d59768b49dc65c4 (diff) | |
download | guix-d1e7b50dbf58c59c100f1bf5a7ea735daa3a203f.tar.gz |
gnu: python-cooler: Update to 0.8.11.
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11. [arguments]: Add build phase "patch-tests"; replace "check" phase. [native-inputs]: Add python-codecov, python-pytest-cov, and python-pytest-flake8. [propagated-inputs]: Add python-six and python-sparse.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 42 |
1 files changed, 36 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dab097381a..2de8a59d3c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11717,15 +11717,39 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.8.7") + (version "0.8.11") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp")))) + "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "tests/test_create.py" + (("def test_roundtrip") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_roundtrip"))) + (substitute* "tests/test_util.py" + (("def test_fetch_chromsizes") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_fetch_chromsizes"))) + ;; This test depends on ipytree, which contains a lot of minified + ;; JavaScript. + (substitute* "tests/test_fileops.py" + (("def test_print_trees") + "def _test_print_trees")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs `(("python-asciitree" ,python-asciitree) ("python-biopython" ,python-biopython) @@ -11741,11 +11765,17 @@ fasta subsequences.") ("python-pysam" ,python-pysam) ("python-pyyaml" ,python-pyyaml) ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson))) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six) + ("python-sparse" ,python-sparse))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) - (home-page "https://github.com/mirnylab/cooler") + `(("python-codecov" ,python-codecov) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-flake8" ,python-pytest-flake8))) + ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella + (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") (description "Cooler is a support library for a sparse, compressed, binary persistent |