diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 34 |
1 files changed, 24 insertions, 10 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 97d2404bf3..da0edcdf40 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11945,21 +11945,35 @@ variational inference.") (define-public python-loompy (package (name "python-loompy") - (version "2.0.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "loompy" version)) - (sha256 - (base32 - "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51")))) + (version "2.0.17") + ;; The tarball on Pypi does not include the tests. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linnarsson-lab/loompy.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07")))) (build-system python-build-system) - ;; There are no tests - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" + (getenv "PYTHONPATH"))) + (invoke "pytest" "tests") + #t))))) (propagated-inputs `(("python-h5py" ,python-h5py) ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/linnarsson-lab/loompy") (synopsis "Work with .loom files for single-cell RNA-seq data") (description "The loom file format is an efficient format for very large |