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gnu: python-umap-learn: Update to 0.5.5.

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* gnu/packages/machine-learning.scm (python-umap-learn): Update to 0.5.5.
[build-system]: Use pyproject-build-system.
[arguments]: Remove 'numpy-compatibility and custom 'check phases.

Change-Id: I2123f66519730d43e454d9536e8cb7b6c4569d56
This commit is contained in:
Ricardo Wurmus 2024-01-08 16:22:52 +01:00
parent ca1749c243
commit fa5d8c839a
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1 changed files with 5 additions and 25 deletions
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gnu/packages/machine-learning.scm
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@ -3787,46 +3787,26 @@ (define-public python-tensorly
(define-public python-umap-learn (define-public python-umap-learn
(package (package
(name "python-umap-learn") (name "python-umap-learn")
(version "0.5.3") (version "0.5.5")
(source (source
(origin (origin
(method git-fetch) ;no tests in pypi release (method git-fetch) ;no tests in pypi release
(uri (git-reference (uri (git-reference
(url "https://github.com/lmcinnes/umap") (url "https://github.com/lmcinnes/umap")
(commit version))) (commit (string-append "release-" version))))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1315jkb0h1b579y9m59632f0nnpksilm01nxx46in0rq8zna8vsb")))) "0ijyiaqycynwj1383cxp519c765gjbg1f6fjwbvqj1gims710w3d"))))
(build-system python-build-system) (build-system pyproject-build-system)
(arguments (arguments
(list (list
#:phases #:phases
#~(modify-phases %standard-phases #~(modify-phases %standard-phases
(add-after 'unpack 'numpy-compatibility
(lambda _
(substitute* "umap/tests/test_umap_metrics.py"
;; See commit a714b59bd9e2ca2e63312bc3491b2b037a42f2f2
(("sparse_binary_data.todense\\(\\),")
"np.asarray(sparse_binary_data.todense()),")
;; See commit c7d05683325589ad432a55e109cacb9d631cfaa9
(("sparse_spatial_data.todense\\(\\),")
"np.asarray(sparse_spatial_data.todense()),"))
;; See commit 949abd082524fce8c45dfb147bcd8e8ef49eade3
(substitute* "umap/tests/test_umap_ops.py"
(("np.random,") "None,"))))
;; Numba needs a writable dir to cache functions. ;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir (add-before 'check 'set-numba-cache-dir
(lambda _ (lambda _
(setenv "NUMBA_CACHE_DIR" "/tmp"))) (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "HOME" "/tmp")
(invoke "pytest" "-vv" "umap"
;; This test can fail because trust may only be
;; 0.9679405204460967 >= 0.97
"-k" "not test_densmap_trustworthiness_on_iris_supervised")))))))
(native-inputs (list python-pytest)) (native-inputs (list python-pytest))
(propagated-inputs (propagated-inputs
(list python-numba (list python-numba