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gnu: python-cooler: Update to 0.9.1.

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* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom build phases; disable tests via #:test-flags.
[propagated-inputs]: Remove python-six and python-sparse.
[native-inputs]: Remove python-codecov, python-mock, and python-pytest-flake8;
add python-coverage, python-hatchling, and python-isort.

Change-Id: I48b6a9c07a2bc1c213971585d7191573fd5d5aca
This commit is contained in:
Ricardo Wurmus 2024-01-09 14:33:23 +01:00
parent 3d3a55ec19
commit 1c01f7e5c6
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GPG key ID: 197A5888235FACAC
1 changed files with 19 additions and 47 deletions
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@ -16917,55 +16917,26 @@ (define-public python-pyfaidx
(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 @@ (define-public python-cooler
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")