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41/59: gnu: python-hicexplorer: Make compatible with latest scipy.
From: |
guix-commits |
Subject: |
41/59: gnu: python-hicexplorer: Make compatible with latest scipy. |
Date: |
Tue, 16 Jan 2024 05:24:32 -0500 (EST) |
rekado pushed a commit to branch wip-python-science
in repository guix.
commit 87f408eeb8004df38e3363ced321b3f94f30d707
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 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
- 54/59: gnu: python-geopandas: Update to 0.14.2., (continued)
- 54/59: gnu: python-geopandas: Update to 0.14.2., guix-commits, 2024/01/16
- 37/59: gnu: scvelo: Make compatible with latest matplotlib., guix-commits, 2024/01/16
- 20/59: gnu: python-matplotlib: Update to 3.8.2., guix-commits, 2024/01/16
- 42/59: gnu: python-pint: Add missing input., guix-commits, 2024/01/16
- 52/59: gnu: python-xarray: Update to 2023.12.0., guix-commits, 2024/01/16
- 53/59: gnu: python-dask: Propagate click., guix-commits, 2024/01/16
- 50/59: gnu: python-mysql-connector-python: Defuse time bomb., guix-commits, 2024/01/16
- 32/59: gnu: python-plastid: Update to 0.6.1., guix-commits, 2024/01/16
- 35/59: gnu: python-demuxem: Disable tests., guix-commits, 2024/01/16
- 29/59: gnu: python-pegasusio: Disable tests., guix-commits, 2024/01/16
- 41/59: gnu: python-hicexplorer: Make compatible with latest scipy.,
guix-commits <=
- 28/59: gnu: python-pyani: Disable tests., guix-commits, 2024/01/16
- 59/59: gnu: gourmet: Add missing input., guix-commits, 2024/01/16
- 58/59: gnu: python-pyrdfa3: Update to 3.6.2., guix-commits, 2024/01/16
- 33/59: gnu: python-cooler: Update to 0.9.1., guix-commits, 2024/01/16
- 39/59: gnu: python-scikit-optimize: Make compatible with latest sklearn., guix-commits, 2024/01/16
- 23/59: gnu: python-scanpy: Update to 1.9.6., guix-commits, 2024/01/16
- 30/59: gnu: python-reportlab: Update to 4.0.8., guix-commits, 2024/01/16
- 08/59: gnu: python-tifffile: Update to 2023.12.9., guix-commits, 2024/01/16
- 22/59: gnu: Add python-pytest-nunit., guix-commits, 2024/01/16
- 43/59: gnu: python-metpy: Update to 1.6.0., guix-commits, 2024/01/16