diff options
| -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 |