gnu: python-decoupler-py: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0.
[arguments]: Do not disable test_plot_volcano test.

Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def

1 files changed, 55 insertions, 64 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78c71447d5..dff8ba4d87 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2026,71 +2026,62 @@ parsing of Variant Call Format (VCF) files.")
     (license license:expat)))
 
 (define-public python-decoupler-py
-  ;; This latest commit fixes a bug in test_omnip.py.
-  (let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace")
-        (revision "1"))
-    (package
-      (name "python-decoupler-py")
-      (version (git-version "1.5.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/saezlab/decoupler-py")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "1c0xk006iilyffdaqar2d05qdhik22fbkny387zx0bndkgqifxhl"))))
-      (build-system pyproject-build-system)
-      (arguments
-       (list
-        #:test-flags
-        '(list "-k"
-               ;; These tests require internet access
-               (string-append "not test_get_resource"
-                              " and not test_show_resources"
-                              " and not test_get_dorothea"
-                              " and not test_get_progeny"
-                              " and not test_get_ksn_omnipath"
-                              ;; XXX module 'omnipath.interactions' has no
-                              ;; attribute 'CollecTRI'
-                              " and not test_get_collectri"
-                              ;; XXX This one fails because the "texts" list
-                              ;; is empty, so there are no texts to adjust.
-                              ;; It is not clear whether this a compatibility
-                              ;; problem with our adjusttext package.
-                              " and not test_plot_volcano"))
-        #:phases
-        '(modify-phases %standard-phases
-           (add-before 'check 'set-home
-             ;; Some tests require a home directory to be set.
-             (lambda _ (setenv "HOME" "/tmp")))
-           ;; Numba needs a writable dir to cache functions.
-           (add-before 'build 'set-numba-cache-dir
-             (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
-      (propagated-inputs (list python-adjusttext
-                               python-anndata
-                               python-ipython
-                               python-matplotlib
-                               python-nbsphinx
-                               python-numba
-                               python-numpy
-                               python-numpydoc
-                               python-omnipath
-                               python-scanpy
-                               python-scikit-learn
-                               python-scipy
-                               python-skranger
-                               python-tqdm
-                               python-typing-extensions))
-      (native-inputs (list python-pytest))
-      (home-page "https://github.com/saezlab/decoupler-py")
-      (synopsis
-       "Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
-      (description
-       "This package provides different statistical methods to extract
+  (package
+    (name "python-decoupler-py")
+    (version "1.6.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/saezlab/decoupler-py")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1mqkp0i8k5hzhfnka4nc2f0phmrs0k404ynbl1lqfjzywx25y75h"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             ;; These tests require internet access
+             (string-append "not test_get_resource"
+                            " and not test_show_resources"
+                            " and not test_get_dorothea"
+                            " and not test_get_progeny"
+                            " and not test_get_ksn_omnipath"
+                            ;; This attempts to download things for Omnipath
+                            " and not test_get_collectri"))
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'check 'set-home
+           ;; Some tests require a home directory to be set.
+           (lambda _ (setenv "HOME" "/tmp")))
+         ;; Numba needs a writable dir to cache functions.
+         (add-before 'build 'set-numba-cache-dir
+           (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+    (propagated-inputs (list python-adjusttext
+                             python-anndata
+                             python-ipython
+                             python-matplotlib
+                             python-nbsphinx
+                             python-numba
+                             python-numpy
+                             python-numpydoc
+                             python-omnipath
+                             python-scanpy
+                             python-scikit-learn
+                             python-scipy
+                             python-skranger
+                             python-tqdm
+                             python-typing-extensions))
+    (native-inputs (list python-pytest))
+    (home-page "https://github.com/saezlab/decoupler-py")
+    (synopsis
+     "Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
+    (description
+     "This package provides different statistical methods to extract
 biological activities from omics data within a unified framework.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public python-demuxem
   (package