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41/53: gnu: python-hicexplorer: Make compatible with latest scipy.
From: |
guix-commits |
Subject: |
41/53: gnu: python-hicexplorer: Make compatible with latest scipy. |
Date: |
Thu, 11 Jan 2024 09:43:03 -0500 (EST) |
rekado pushed a commit to branch wip-python-science
in repository guix.
commit 8752fb3f3f5630601fec678c4d553debc47898c6
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
- 22/53: gnu: Add python-pytest-nunit., (continued)
- 22/53: gnu: Add python-pytest-nunit., guix-commits, 2024/01/11
- 20/53: gnu: python-matplotlib: Update to 3.8.2., guix-commits, 2024/01/11
- 09/53: gnu: python-lazy-loader: Update to 0.3., guix-commits, 2024/01/11
- 21/53: gnu: python-seaborn: Update to 0.13.1., guix-commits, 2024/01/11
- 26/53: gnu: python-captum: Update to 0.7.0., guix-commits, 2024/01/11
- 38/53: gnu: python-fit-nbinom: Disable tests., guix-commits, 2024/01/11
- 40/53: gnu: python-hicmatrix: Update to 17.1., guix-commits, 2024/01/11
- 47/53: gnu: python-pandas: Update to 1.5.3., guix-commits, 2024/01/11
- 11/53: gnu: python-scikit-image: Update to 0.22.0., guix-commits, 2024/01/11
- 19/53: gnu: Add python-contourpy., guix-commits, 2024/01/11
- 41/53: gnu: python-hicexplorer: Make compatible with latest scipy.,
guix-commits <=
- 10/53: gnu: python-imageio: Update to 2.33.1., guix-commits, 2024/01/11
- 13/53: gnu: python-matplotx: Disable test_png test., guix-commits, 2024/01/11
- 17/53: gnu: Add python-cppy., guix-commits, 2024/01/11
- 23/53: gnu: python-scanpy: Update to 1.9.6., guix-commits, 2024/01/11
- 04/53: gnu: Add python-pyproject-metadata-0.7., guix-commits, 2024/01/11
- 07/53: gnu: python-scipy: Update to 1.11.4., guix-commits, 2024/01/11
- 14/53: gnu: python-scikit-learn: Update to 1.3.2., guix-commits, 2024/01/11
- 37/53: gnu: scvelo: Make compatible with latest matplotlib., guix-commits, 2024/01/11
- 35/53: gnu: python-demuxem: Disable tests., guix-commits, 2024/01/11
- 27/53: gnu: tadbit: Add missing input., guix-commits, 2024/01/11