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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.
master
Ricardo Wurmus 2022-03-31 14:35:41 +02:00
parent 38b2026515
commit a69a44bf59
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1 changed files with 22 additions and 5 deletions
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@ -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 _
(invoke "pytest" "tests"))))))
(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 _
(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")