diff options
| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2026-01-07 14:33:42 +0000 |
|---|---|---|
| committer | Rutherther <rutherther@ditigal.xyz> | 2026-01-25 21:22:11 +0100 |
| commit | f2b9ff86a87946f05a028785e2c0d5b41f5a3b77 (patch) | |
| tree | 0ab3717fa8d457b589ad9ec22fb66b772c221db7 /gnu/packages | |
| parent | 7161915f0391caefe186a5226a975b3df098cdce (diff) | |
gnu: python-phenograph: Fix tests.
* gnu/packages/bioinformatics.scm (python-phenograph):
[arguments] <test-flags>: Skip 3 more tests.
<phases>: Remove 'disable-leiden-test, and move logic to <#:test-flags>.
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.
Change-Id: Id7a7cb67adb13749bde59ad93d5c1125f2903065
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 22 |
1 files changed, 14 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 30a1a9c8d75..43a789a98af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3509,6 +3509,7 @@ genomics data.") (license license:bsd-3))) (define-public python-phenograph + ;; XXX: No updates since 2020, probably not compatible with current NumPy stack. (package (name "python-phenograph") (version "1.5.7") @@ -3525,14 +3526,19 @@ genomics data.") (build-system pyproject-build-system) (arguments (list + ;; tests: 3 passed, 4 deselected, 1 warning + #:test-flags + ;; ValueError: 'scipy.sparse.linalg.bicgstab' called with invalid + ;; `atol`=legacy; if set, `atol` must be a real, non-negative number. + #~(list "--deselect=tests/test_classify.py::test_classify_generated" + "--deselect=tests/test_classify.py::test_classify_fixed" + "--deselect=tests/test_classify.py::test_random_walk_probabilities_fixed" + ;; This test can never succeed because Q_leiden is never set to + ;; anything other than None. + ;; assert 0.6666666666666665 == None + "--deselect=tests/test_cluster.py::test_run_leiden") #:phases #~(modify-phases %standard-phases - ;; This test can never succeed because Q_leiden is never set to - ;; anything other than None. - (add-after 'unpack 'disable-leiden-test - (lambda _ - (substitute* "tests/test_cluster.py" - (("def test_run_leiden") "def _test_run_leiden")))) (add-after 'unpack 'patch-louvain (lambda* (#:key inputs #:allow-other-keys) (substitute* "phenograph/core.py" @@ -3554,12 +3560,12 @@ weight.astype(\"str\") + '\\n')"))))))) (list louvain)) (propagated-inputs (list python-leidenalg - python-numpy + python-numpy-1 python-psutil python-scikit-learn python-scipy)) (native-inputs - (list python-pytest python-setuptools python-wheel)) + (list python-pytest python-setuptools)) (home-page "https://github.com/dpeerlab/PhenoGraph.git") (synopsis "Graph-based clustering for high-dimensional single-cell data") (description |