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gnu: python-hic2cool: Update to 1.0.1, fix build.

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* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 1.0.1.
[build-system]: Switch to pyproject-build-system.
[arguments]: Drop all, tests passed successfully, replied on
<https://github.com/4dn-dcic/hic2cool/issues/58>.
[native-inputs]: Add python-poetry-core.

Change-Id: I69f5bdfa91f52bff7e84f30fb7a68a6f0526ecb0
This commit is contained in:
Sharlatan Hellseher 2025-09-26 00:19:17 +01:00
parent 56f909eefd
commit 8d731c4f6c
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1 changed files with 9 additions and 26 deletions
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@ -20729,7 +20729,7 @@ efficiently.")
(define-public python-hic2cool (define-public python-hic2cool
(package (package
(name "python-hic2cool") (name "python-hic2cool")
(version "0.8.3") (version "1.0.1")
;; pypi sources do not contain the test_data directory and no test can be ;; pypi sources do not contain the test_data directory and no test can be
;; run ;; run
(source (source
@ -20741,32 +20741,15 @@ efficiently.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl")))) "0k0i43z43rxbpna4hfci406ma906w893frfj3cha1n8drvhdql6c"))))
(build-system python-build-system) (build-system pyproject-build-system)
(arguments (native-inputs
`(#:phases (list python-poetry-core))
(modify-phases %standard-phases
;; Two of the test-data files need to be writable.
(add-after 'unpack 'make-test-data-writable
(lambda _
(for-each make-file-writable
(list "test_data/hic2cool_0.4.2_single_res.cool"
"test_data/hic2cool_0.7.0_multi_res.mcool"))))
;; See https://github.com/4dn-dcic/hic2cool/issues/58
(add-after 'unpack 'fix-incompatibility-with-h5py-3
(lambda _
(substitute* "test.py"
(("h5py.File\\(fname\\)") "h5py.File(fname, 'r')"))
(substitute* "hic2cool/hic2cool_updates.py"
(("h5py.File\\(writefile\\)")
"h5py.File(writefile, 'a')"))))
;; These two tests fail for unknown reasons.
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "test.py"
(("def test_convert") "def _test_convert")))))))
(propagated-inputs (propagated-inputs
(list python-cooler python-h5py python-numpy python-pandas (list python-cooler
python-h5py
python-numpy
python-pandas
python-scipy)) python-scipy))
(home-page "https://github.com/4dn-dcic/hic2cool") (home-page "https://github.com/4dn-dcic/hic2cool")
(synopsis "Converter for .hic and .cool files") (synopsis "Converter for .hic and .cool files")