~ruther/guix-local: gnu: python-hicexplorer: Make compatible with latest scipy.

cda0f029d6542b81e0a019299ff0c59d01eb2af1 — Ricardo Wurmus 2 years ago 3ce25c2

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

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

Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad

patch browse .tar.gz

1 files changed, 12 insertions(+), 1 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +12 -1

@@ 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