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gnu: python-hicexplorer: Update to 3.7.4.

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* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.4.
[source]: Remove obsolete snippet.
[arguments]: Remove obsolete phase 'scipy-compatibility.
[propagated-inputs]: Replace python-cleanlab-1 with python-cleanlab.

Change-Id: Iac9a24cc4551b7d7e1d41d1f07a6db6d620b119e
This commit is contained in:
Ricardo Wurmus 2024-05-02 22:18:37 +02:00
parent 9692e2bb7c
commit 31f57ae7df
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GPG key ID: 197A5888235FACAC
1 changed files with 4 additions and 24 deletions
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gnu/packages/bioinformatics.scm
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@ -17981,7 +17981,7 @@ the HiCExplorer and pyGenomeTracks packages.")
(define-public python-hicexplorer
(package
(name "python-hicexplorer")
(version "3.7.2")
(version "3.7.4")
(source
(origin
;; The latest version is not available on Pypi.
@ -17992,16 +17992,7 @@ the HiCExplorer and pyGenomeTracks packages.")
(file-name (git-file-name name version))
(sha256
(base32
"1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))
(modules '((guix build utils)))
;; setup.py is malformed. The requirements are defined using a catchall
;; pattern for the patch version number. This has been fixed in version
;; 3.7.3, but we cannot upgrade to this version yet, since some Guix
;; packages are not new enough. (See upstream commit
;; 4845c715ec7b105e938d0c2426e27d0181690bfe for the fix).
(snippet '(substitute* "setup.py"
(("\\.\\*")
"")))))
"1cjr9l0vcngd0f4dmar388ri1ah1bqybnn53jc85xwh07wfacq7l"))))
(build-system pyproject-build-system)
(arguments
(list
@ -18079,21 +18070,10 @@ the HiCExplorer and pyGenomeTracks packages.")
"general/test_hicHyperoptDetectLoopsHiCCUPS.py"
"general/test_hicAggregateContacts.py"
"general/test_hicInterIntraTAD.py")
(("^memory =.*") "memory = 1\n")))))
;; This is fixed in version 3.7.3, but we cannot upgrade yet as we
;; don't have Pandas 2.
(add-after 'unpack 'scipy-compatibility
(lambda _
(substitute* "hicexplorer/hicAverageRegions.py"
(("from scipy.sparse import csr_matrix, save_npz, lil_matrix")
"from scipy.sparse import csr_matrix, save_npz, lil_matrix, coo_matrix")
(("summed_matrix = np.array\\(summed_matrix\\)")
"summed_matrix = coo_matrix(summed_matrix)")
(("data = summed_matrix\\[np.nonzero\\(summed_matrix\\)\\]")
"data = summed_matrix.toarray()[np.nonzero(summed_matrix)]")))))))
(("^memory =.*") "memory = 1\n"))))))))
(propagated-inputs
(list python-biopython
python-cleanlab-1
python-cleanlab
python-cooler
python-fit-nbinom
python-future