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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-03-13 22:43:43 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-03-13 22:48:52 +0100 |
| commit | 55a0a3c853dc9177afeb9d438f3e4bdc1a1379e7 (patch) | |
| tree | 818b411a6df58581fd8cace5e737b0664ffe9684 | |
| parent | 1f058eced3a4dad4fe0c7f46a1abcc621ffe4ce3 (diff) | |
| download | patches-55a0a3c853dc9177afeb9d438f3e4bdc1a1379e7.tar patches-55a0a3c853dc9177afeb9d438f3e4bdc1a1379e7.tar.gz | |
gnu: python-loompy: Update to 2.0.17.
* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17.
[source]: Fetch via git.
[arguments]: Enable tests, replace "check" phase.
[propagated-inputs]: Add python-pandas.
[native-inputs]: Add python-pytest.
| -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 |