From 31f57ae7dfc239aba2cbbed3bfa87cbcd837bae0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 2 May 2024 22:18:37 +0200
Subject: 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(-)

(limited to 'gnu/packages/bioinformatics.scm')

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
-- 
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