From cda0f029d6542b81e0a019299ff0c59d01eb2af1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 10 Jan 2024 14:39:12 +0100 Subject: [PATCH] gnu: python-hicexplorer: Make compatible with latest scipy. * gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add 'scipy-compatibility phase. Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad --- gnu/packages/bioinformatics.scm | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 36dbad592ef6c0bc701719c77be15f9a65273a60..c05ca190224d8d42c38ffba8dc05ddd4157ed1f3 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