diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
1 files changed, 21 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6cfe82fc90..c1cfabc27f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -122,6 +122,7 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-science) @@ -11328,14 +11329,14 @@ implementation differs in these ways: (define-public python-scanpy (package (name "python-scanpy") - (version "1.4.6") + (version "1.7.2") (source (origin (method url-fetch) (uri (pypi-uri "scanpy" version)) (sha256 (base32 - "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l")))) + "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd")))) (build-system python-build-system) (arguments `(#:phases @@ -11346,12 +11347,25 @@ implementation differs in these ways: (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") (delete-file "scanpy/tests/test_datasets.py") + (delete-file "scanpy/tests/test_highly_variable_genes.py") ;; TODO: I can't get the plotting tests to work, even with Xvfb. (delete-file "scanpy/tests/test_plotting.py") (delete-file "scanpy/tests/test_preprocessing.py") (delete-file "scanpy/tests/test_read_10x.py") + ;; The following tests need anndata.tests, which aren't included + ;; in the final python-anndata package. + (delete-file "scanpy/tests/test_combat.py") + (delete-file "scanpy/tests/test_embedding_plots.py") + (delete-file "scanpy/tests/test_normalization.py") + (delete-file "scanpy/tests/test_pca.py") + (delete-file "scanpy/tests/external/test_scrublet.py") + + ;; The following tests requires 'scanorama', which isn't + ;; packaged yet. + (delete-file "scanpy/tests/external/test_scanorama_integrate.py") + (setenv "PYTHONPATH" (string-append (getcwd) ":" (getenv "PYTHONPATH"))) @@ -11376,11 +11390,14 @@ implementation differs in these ways: ("python-seaborn" ,python-seaborn) ("python-statsmodels" ,python-statsmodels) ("python-tables" ,python-tables) + ("python-pytoml" ,python-pytoml) ("python-tqdm" ,python-tqdm) ("python-umap-learn" ,python-umap-learn))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-setuptools-scm" ,python-setuptools-scm))) + `(("python-leidenalg" ,python-leidenalg) + ("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm) + ("python-sinfo" ,python-sinfo))) (home-page "https://github.com/theislab/scanpy") (synopsis "Single-Cell Analysis in Python.") (description "Scanpy is a scalable toolkit for analyzing single-cell gene |