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gnu: python-hicexplorer: Make compatible with latest scipy. 

* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add
'scipy-compatibility phase.

Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
master
Ricardo Wurmus 2024-01-10 14:39:12 +01:00
parent 3ce25c212f
commit cda0f029d6
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GPG Key ID: 197A5888235FACAC
1 changed files with 12 additions and 1 deletions
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gnu/packages/bioinformatics.scm
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@ -17147,7 +17147,18 @@ the HiCExplorer and pyGenomeTracks packages.")
"general/test_hicHyperoptDetectLoopsHiCCUPS.py"
"general/test_hicAggregateContacts.py"
"general/test_hicInterIntraTAD.py")
(("^memory =.*") "memory = 1\n"))))))))
(("^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)]")))))))
(propagated-inputs
(list python-biopython
python-cleanlab-1