diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 66 |
1 files changed, 19 insertions, 47 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5d0c53d45e..9f33caa8e0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16917,55 +16917,26 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.8.11") + (version "0.9.1") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn")))) - (build-system python-build-system) + "0capn4jj3mkxfwcc65cg644zvrv4sqr2wxr0ylx5w767jx3yb7p2")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - ;; cooler requests cytoolz<0.11. It only uses cytoolz for "compose", - ;; which composes two functions. - (add-after 'unpack 'use-recent-cytoolz - (lambda _ - (substitute* '("requirements.txt" - "cooler.egg-info/requires.txt") - (("cytoolz.*<.*0.11") "cytoolz")))) - ;; This version of flake8 just won't work with this version of - ;; pytest, because of dependency pinning. - (add-after 'unpack 'do-not-use-flake8 - (lambda _ - (substitute* "setup.cfg" - (("addopts = --flake8") "addopts = ")))) - (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")) - ;; See https://github.com/open2c/cooler/issues/287 - (("skipif\\(six.PY2, reason=\"Scipy on Py2 is too old\"") - "skip(reason=\"Scipy is too new\"")) - ;; 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"))))))) + (list + #:test-flags + '(list "-k" + (string-append + ;; These tests download files from the internet. + "not test_fetch_chromsizes" + " and not test_roundtrip" + ;; This test depends on ipytree, which contains a lot of + ;; minified JavaScript. + " and not test_print_trees")))) (propagated-inputs (list python-asciitree python-biopython @@ -16981,12 +16952,13 @@ fasta subsequences.") python-pysam python-pyyaml python-scipy - python-simplejson - python-six - python-sparse)) + python-simplejson)) (native-inputs - (list python-codecov python-mock python-pytest python-pytest-cov - python-pytest-flake8)) + (list python-coverage + python-hatchling + python-isort + python-pytest + python-pytest-cov)) ;; 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") |