rekado pushed a commit to branch wip-python-team
in repository guix.
commit 31f57ae7dfc239aba2cbbed3bfa87cbcd837bae0
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Thu May 2 22:18:37 2024 +0200
gnu: python-hicexplorer: Update to 3.7.4.
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.4.
[source]: Remove obsolete snippet.
[arguments]: Remove obsolete phase 'scipy-compatibility.
[propagated-inputs]: Replace python-cleanlab-1 with python-cleanlab.
Change-Id: Iac9a24cc4551b7d7e1d41d1f07a6db6d620b119e
---
gnu/packages/bioinformatics.scm | 28 ++++------------------------
1 file changed, 4 insertions(+), 24 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cbc37c836f..78c71447d5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17981,7 +17981,7 @@ the HiCExplorer and pyGenomeTracks packages.")
(define-public python-hicexplorer
(package
(name "python-hicexplorer")
- (version "3.7.2")
+ (version "3.7.4")
(source
(origin
;; The latest version is not available on Pypi.
@@ -17992,16 +17992,7 @@ the HiCExplorer and pyGenomeTracks packages.")
(file-name (git-file-name name version))
(sha256
(base32
- "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))
- (modules '((guix build utils)))
- ;; setup.py is malformed. The requirements are defined using a catchall
- ;; pattern for the patch version number. This has been fixed in version
- ;; 3.7.3, but we cannot upgrade to this version yet, since some Guix
- ;; packages are not new enough. (See upstream commit
- ;; 4845c715ec7b105e938d0c2426e27d0181690bfe for the fix).
- (snippet '(substitute* "setup.py"
- (("\\.\\*")
- "")))))
+ "1cjr9l0vcngd0f4dmar388ri1ah1bqybnn53jc85xwh07wfacq7l"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -18079,21 +18070,10 @@ the HiCExplorer and pyGenomeTracks packages.")
"general/test_hicHyperoptDetectLoopsHiCCUPS.py"
"general/test_hicAggregateContacts.py"
"general/test_hicInterIntraTAD.py")
- (("^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)]")))))))
+ (("^memory =.*") "memory = 1\n"))))))))
(propagated-inputs
(list python-biopython
- python-cleanlab-1
+ python-cleanlab
python-cooler
python-fit-nbinom
python-future
