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41/48: gnu: python-hicexplorer: Make compatible with latest scipy.
From: |
guix-commits |
Subject: |
41/48: gnu: python-hicexplorer: Make compatible with latest scipy. |
Date: |
Thu, 11 Jan 2024 07:39:07 -0500 (EST) |
rekado pushed a commit to branch wip-python-science
in repository guix.
commit dea60ee44d64dbb0f4c3c819e7c93d2bf34fdd54
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Jan 10 14:39:12 2024 +0100
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 7aed014a52..1df76d4d55 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17088,7 +17088,18 @@ 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
- branch wip-python-science created (now 39497b115c), guix-commits, 2024/01/11
- 01/48: gnu: Add python-cython-0.29.35., guix-commits, 2024/01/11
- 04/48: gnu: Add python-pyproject-metadata-0.7., guix-commits, 2024/01/11
- 06/48: gnu: meson-python: Update to 0.15.0., guix-commits, 2024/01/11
- 14/48: gnu: python-scikit-learn: Update to 1.3.2., guix-commits, 2024/01/11
- 12/48: gnu: python-pypng: Update to 0.20220715.0., guix-commits, 2024/01/11
- 13/48: gnu: python-matplotx: Disable test_png test., guix-commits, 2024/01/11
- 21/48: gnu: python-seaborn: Update to 0.13.1., guix-commits, 2024/01/11
- 31/48: gnu: cnvkit: Update to 0.9.10., guix-commits, 2024/01/11
- 40/48: gnu: python-hicmatrix: Update to 17.1., guix-commits, 2024/01/11
- 41/48: gnu: python-hicexplorer: Make compatible with latest scipy.,
guix-commits <=
- 42/48: gnu: python-pint: Add missing input., guix-commits, 2024/01/11
- 09/48: gnu: python-lazy-loader: Update to 0.3., guix-commits, 2024/01/11
- 32/48: gnu: python-plastid: Update to 0.6.1., guix-commits, 2024/01/11
- 02/48: gnu: Add pybind11-2.10., guix-commits, 2024/01/11
- 11/48: gnu: python-scikit-image: Update to 0.22.0., guix-commits, 2024/01/11
- 10/48: gnu: python-imageio: Update to 2.33.1., guix-commits, 2024/01/11
- 08/48: gnu: python-tifffile: Update to 2023.12.9., guix-commits, 2024/01/11
- 15/48: gnu: python-pynndescent: Update to 0.5.11., guix-commits, 2024/01/11
- 17/48: gnu: Add python-cppy., guix-commits, 2024/01/11
- 22/48: gnu: Add python-pytest-nunit., guix-commits, 2024/01/11