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| author | Ricardo Wurmus <rekado@elephly.net> | 2024-12-15 20:16:29 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-12-15 20:16:29 +0100 |
| commit | ba450f1879569ae44c326203b5350eedf84f8004 (patch) | |
| tree | 68e51392f2981622b38de6c7d20a643880065c13 /gnu/packages/bioinformatics.scm | |
| parent | de4ab8c7705a2ba7f84c3d0c8577ed9cc7ccf614 (diff) | |
gnu: python-loompy: Fix build.
* 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
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 19 |
1 files changed, 10 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6c2cb730fb..14ca46a1dc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16456,24 +16456,25 @@ traversal from leaf to root.") (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 @@ traversal from leaf to root.") 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 |