191/397: gnu: python-liana-py: Update to 1.4.0.

[guix-commits]

rekado pushed a commit to branch python-team
in repository guix.

commit e83f4e980efa1252557657544e61e21078c81b6e
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Jan 8 20:19:06 2025 +0100

    gnu: python-liana-py: Update to 1.4.0.
    
    * gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.4.0.
    [arguments]: Adjust disabled tests.
    
    Change-Id: I9245285e2d043b5e7cbce5fb95a30982cd981597
---
 gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8e79c259eb..57f37e2a65 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2679,7 +2679,7 @@ servers supporting the protocol.")
 (define-public python-liana-py
   (package
     (name "python-liana-py")
-    (version "1.1.0")
+    (version "1.4.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2688,7 +2688,7 @@ servers supporting the protocol.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0f5al0v55haja91q9gd409v7q78mmp1wv9znsplsbjp6lfspjfnw"))))
+                "1kwbhfmsjhfc6m4kcp4zc2xgzg1qf16ywfkdamn868anwwrvjxzb"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2696,20 +2696,36 @@ servers supporting the protocol.")
       '(list "-k"
              ;; These tests require internet access.
              (string-append "not test_generate_lr_resource"
+                            " and not test_get_hcop"
                             " and not test_get_metalinks"
                             " and not test_get_metalinks_values"
                             " and not test_describe_metalinks"
                             " and not test_generate_nondefault_lr_resource"
+                            " and not test_translate_resource"
                             ;; Minor accuracy difference
                             " and not test_bivar_morans_perms"
+                            ;; XXX "local_scores" array has wrong type.
+                            ;; See 
https://github.com/saezlab/liana-py/issues/147
+                            " and not test_morans_analytical"
+                            " and not test_cosine_permutation"
+                            " and not test_jaccard_pval_none_cats"
+                            " and not test_large_adata"
+                            ;; XXX ligand column differs: the left column
+                            ;; contains duplicates.
+                            " and not test_liana_pipe_not_defaults"
+                            " and not test_liana_pipe_defaults"
                             ;; XXX unclear failure: 'coo_matrix' object is not
                             ;; subscriptable
                             " and not test_bivar_product"
-                            )
+                            ;; XXX unclear failure: large difference in data
+                            ;; frames.
+                            " and not test_aggregate_res")
              ;; These need the optional squidpy, which we don't have yet.
              "--ignore=liana/tests/test_misty.py"
              ;; These need the optional corneto.
-             "--ignore=liana/tests/test_causalnet.py")
+             "--ignore=liana/tests/test_causalnet.py"
+             ;; Needs internet access.
+             "--ignore=liana/tests/test_orthology.py")
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements