diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 32 |
1 files changed, 19 insertions, 13 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f75254ed9f..1f707a31c1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16449,7 +16449,7 @@ implementation differs in these ways: (define-public python-scanpy (package (name "python-scanpy") - (version "1.9.1") + (version "1.9.6") (source (origin (method git-fetch) @@ -16459,21 +16459,28 @@ implementation differs in these ways: (file-name (git-file-name name version)) (sha256 (base32 - "0k524xnx3dvpz5yx65p316wghvi01zs17is8w2m3w2qywiswk0sl")))) + "12rz0a9151fkry6ws1a8p5wnc4n5qbjl6xlynj7kxy223iz8isds")))) (build-system pyproject-build-system) (arguments (list #:test-flags '(list "-k" ;; Plot tests that fail. - (string-append "not test_dotplot_matrixplot_stacked_violin" - " and not test_violin_without_raw" - " and not test_correlation" - " and not test_scatterplots" - " and not test_scatter_embedding_add_outline_vmin_vmax_norm" - " and not test_paga" + (string-append "not test_clustermap" + " and not test_dotplot_matrixplot_stacked_violin" " and not test_paga_compare" - " and not test_clustermap" + " and not test_paga_path" + " and not test_paga_pie" + " and not test_paga_plots" + " and not test_violin" + " and not test_scatter_no_basis_per_obs" + + ;; Type mismatch + " and not test_obs_df" + " and not test_var_df" + + ;; Minor accuracy problem + " and not test_consistency[morans_i-allclose]" ;; These try to connect to the network " and not test_scrublet_plots" @@ -16505,10 +16512,6 @@ implementation differs in these ways: ;; These two fail with "ValueError: I/O operation on closed file." (delete-file "scanpy/tests/test_neighbors_key_added.py") - ;; TODO: these fail with TypingError and "Use of unsupported - ;; NumPy function 'numpy.split'". - (delete-file "scanpy/tests/test_metrics.py") - ;; The following tests requires 'scanorama', which isn't ;; packaged yet. (delete-file "scanpy/tests/external/test_scanorama_integrate.py") @@ -16549,8 +16552,11 @@ implementation differs in these ways: `(;; This package needs anndata.tests, which is not installed. ("python-anndata:source" ,(package-source python-anndata)) ("python-flit" ,python-flit) + ("python-hatchling" ,python-hatchling) + ("python-hatch-vcs" ,python-hatch-vcs) ("python-leidenalg" ,python-leidenalg) ("python-pytest" ,python-pytest) + ("python-pytest-nunit" ,python-pytest-nunit) ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/theislab/scanpy") (synopsis "Single-Cell Analysis in Python") |