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| author | Ricardo Wurmus <rekado@elephly.net> | 2024-01-10 14:39:12 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-01-16 12:44:36 +0100 |
| commit | cda0f029d6542b81e0a019299ff0c59d01eb2af1 (patch) | |
| tree | 3f5efc5a6b1d4d0b2cddc06fb794b594abb1f3b2 | |
| parent | 3ce25c212f4bc86d0ceeebd2d668590dbc780249 (diff) | |
gnu: python-hicexplorer: Make compatible with latest scipy.
* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add
'scipy-compatibility phase.
Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 13 |
1 files changed, 12 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 36dbad592e..c05ca19022 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |