~ruther/guix-local

94754588855782ce8a121dc6d3a3635d5e04bb58 — Sharlatan Hellseher 7 months ago 11eec1e 
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
patch browse .tar.gz 
1 files changed, 12 insertions(+), 9 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +12 -9
@@ 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