diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2024-05-02 22:18:37 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-05-05 22:38:17 +0200 |
| commit | 31f57ae7dfc239aba2cbbed3bfa87cbcd837bae0 (patch) | |
| tree | a177d06256bffb1af0d89bdc8c41d3db8e26ec24 /gnu/packages/bioinformatics.scm | |
| parent | 9692e2bb7c49ba9526dd023dba3b5d24404f466b (diff) | |
| download | guix-31f57ae7dfc239aba2cbbed3bfa87cbcd837bae0.tar guix-31f57ae7dfc239aba2cbbed3bfa87cbcd837bae0.tar.gz | |
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
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 28 |
1 files 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 |