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| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-09-23 15:26:56 +0100 |
|---|---|---|
| committer | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-09-25 09:36:59 +0100 |
| commit | 94754588855782ce8a121dc6d3a3635d5e04bb58 (patch) | |
| tree | 021887ecbdbc6eaf7053f1ae3c2da053bd847c6a /gnu/packages | |
| parent | 11eec1e912e0e4dba356d810197721f750e3122e (diff) | |
gnu: python-taggd: Switch to pyproject, fix tests.
* gnu/packages/bioinformatics.scm (python-taggd)[build-system]: Switch
to pyproject-build-system.
[arguments] <test-flags>: Move skipping tests options here.
<phases>: Remove 'disable-broken-tests; add 'remove-local-taggd.
[propagated-inputs]: Remove python-setuptools.
[native-inputs]: Add python-pytest and python-setuptools.
Change-Id: I8cd3a72b2469dbb0d53c21f2fda30c0b004a6c8d
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 21 |
1 files changed, 12 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ede8eb70b27..26847d6edcf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12167,20 +12167,23 @@ interpretation.") (snippet '(for-each delete-file (find-files "taggd" "\\.c$"))))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments (list + #:test-flags + ;; AssertionError: 0 is not true : Running Normal BAM test failed. + #~(list "-k" "not test_normal_bam_run") #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'disable-broken-tests - (lambda _ - (substitute* "tests/taggd_demultiplex_test.py" - (("def test_normal_bam_run") - "def _disabled_test_normal_bam_run"))))))) + #~(modify-phases %standard-phases + (add-before 'check 'remove-local-taggd + (lambda _ + ;; This would otherwise interfere with finding the installed + ;; taggd when running tests. + (delete-file-recursively "taggd")))))) (propagated-inputs - (list python-numpy python-pysam python-setuptools)) + (list python-numpy python-pysam)) (native-inputs - (list python-cython)) + (list python-cython python-pytest python-setuptools)) (home-page "https://github.com/SpatialTranscriptomicsResearch/taggd") (synopsis "Genetic barcode demultiplexing") (description "This package provides TagGD barcode demultiplexing utilities |