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| author | Ricardo Wurmus <rekado@elephly.net> | 2022-03-31 14:35:41 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-03-31 14:37:58 +0200 |
| commit | a69a44bf598301cee2b74c46a49301efc0b3be3f (patch) | |
| tree | 8cb692983f84bf77e51aaf89e17a9e1f95153f71 | |
| parent | 38b2026515a56761b7644d5463b5a3f0c76e175d (diff) | |
| download | guix-patches-a69a44bf598301cee2b74c46a49301efc0b3be3f.tar guix-patches-a69a44bf598301cee2b74c46a49301efc0b3be3f.tar.gz | |
gnu: python-loompy: Update to 3.0.7.
* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7.
[arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir;
respect TESTS? argument in 'check phase.
[propagated-inputs]: Add python-click, python-numba, and
python-numpy-groupies.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 27 |
1 files changed, 22 insertions, 5 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4e1028b3ce..693158798a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10266,7 +10266,7 @@ variational inference.") (define-public python-loompy (package (name "python-loompy") - (version "2.0.17") + (version "3.0.7") ;; The tarball on Pypi does not include the tests. (source (origin (method git-fetch) @@ -10276,16 +10276,33 @@ variational inference.") (file-name (git-file-name name version)) (sha256 (base32 - "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07")))) + "0xmw2yv1y3y7vh5jcbrmlkn43nmfs0pf6z78k1yxqs3qy248m9b0")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (replace 'check + ;; See https://github.com/linnarsson-lab/loompy/issues/169 + (add-after 'unpack 'fix-h5py-error + (lambda _ + (substitute* "tests/test_file_attribute_manager.py" + (("h5py.File\\(f.name\\)") + "h5py.File(f.name, 'a')")))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir (lambda _ - (invoke "pytest" "tests")))))) + (setenv "NUMBA_CACHE_DIR" "/tmp"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "tests"))))))) (propagated-inputs - (list python-h5py python-numpy python-pandas python-scipy)) + (list python-click + python-h5py + python-numba + python-numpy + python-numpy-groupies + python-pandas + python-scipy)) (native-inputs (list python-pytest)) (home-page "https://github.com/linnarsson-lab/loompy") |