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gnu: python-loompy: Fix build.

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* gnu/packages/bioinformatics.scm (python-loompy)[build-system]: Use
pyproject-build-system.
[arguments]: Remove custom 'check phase; add phase 'numpy-compatibility.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I2a3121e042fb7f7980bae14cea3e256fd4c9b115
This commit is contained in:
Ricardo Wurmus 2024-12-15 20:16:29 +01:00
parent de4ab8c770
commit ba450f1879
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GPG key ID: 197A5888235FACAC
1 changed files with 10 additions and 9 deletions
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gnu/packages/bioinformatics.scm
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@ -16456,24 +16456,25 @@ (define-public python-loompy
(sha256
(base32
"0xmw2yv1y3y7vh5jcbrmlkn43nmfs0pf6z78k1yxqs3qy248m9b0"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(list
#:phases
'(modify-phases %standard-phases
;; 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')"))))
(add-after 'unpack 'numpy-compatibility
(lambda _
(substitute* "tests/test_connection.py"
(("np.int") "int"))))
;; 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")))))))
(setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs
(list python-click
python-h5py
@ -16483,7 +16484,7 @@ (define-public python-loompy
python-pandas
python-scipy))
(native-inputs
(list python-pytest))
(list python-pytest python-setuptools python-wheel))
(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