~ruther/guix-local

02c6d0183fa49af454cf51625a42af9dd83cf971 — Sharlatan Hellseher 4 months ago 38b8260 
gnu: python-drep: Update to 3.6.2-0.7b4b8fb.

* gnu/packages/bioinformatics.scm (python-drep): Update to
7b4b8fbf9dfdfef61caf949f1aa1d4fc3be61d5a commit.
[source]: Switch to git-fetch providing tests.
[arguments] <test-flags>: Skip some tests requiring not available
optional packages.
[build-system]: Switch to pyproject-build-system.
[propagated-inputs]: Remove python-pytest; add python-networkx.
[native-inputs]: Add mash, python-pytest, and python-setuptools.

Change-Id: I5e22f7c142e267592b2ed74cf1c1d37a02472992
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
patch browse .tar.gz 
1 files changed, 70 insertions(+), 7 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +70 -7
@@ 19915,21 19915,84 @@ altering the counts or PCA space.")
(define-public python-drep
  (package
    (name "python-drep")
    (version "3.2.0")
    ;; PyPI has no tests, Git does not tag the latest version.
    (properties '((commit . "7b4b8fbf9dfdfef61caf949f1aa1d4fc3be61d5a")
                  (revision . "0")))
    (version (git-version "3.6.2"
                          (assoc-ref properties 'revision)
                          (assoc-ref properties 'commit)))
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "drep" version))
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/MrOlm/drep")
              (commit (assoc-ref properties 'commit))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "08vk0x6v5c5n7afgd5pcjhsvb424absypxy22hw1cm1n9kirbi77"))))
    (build-system python-build-system)
        (base32 "0rys4r9mmknzayvqcsdpgqi9sigl1x0a1nh0x8h2sjz13qqmklly"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      ;; tests: 27 passed, 12 skipped, 39 deselected, 1 warning
      #:test-flags
      ;; Tests depend on "near essential" and "optional" dependencies.
      #~(list #$@(map (lambda (test) (string-append "--deselect="
                                                    "tests/tests/"
                                                    test))
                      (list "test_analyze.py::test_plot_5_1"
                            "test_analyze.py::test_plot_5_2"
                            "test_analyze.py::test_plot_6_1"
                            "test_analyze.py::test_plotting_functional_1"
                            "test_bonus.py::test_drep_scaffold_level"
                            "test_bonus.py::test_drep_scaffold_level_2"
                            "test_bonus.py::test_drep_scaffold_level_3"
                            "test_bonus.py::test_drep_scaffold_level_4"
                            "test_bonus.py::test_drep_scaffold_level_5"
                            "test_bonus.py::test_parse_stb_2"
                            "test_choose.py::test_centrality_1"
                            "test_choose.py::test_centrality_2"
                            "test_choose.py::test_choose_2"
                            "test_choose.py::test_choose_3"
                            "test_cluster.py::test_cluster_functional_1"
                            "test_cluster.py::test_cluster_functional_3"
                            "test_cluster.py::test_cluster_functional_4"
                            "test_cluster.py::test_cluster_functional_5"
                            "test_cluster.py::test_compare_genomes"
                            "test_cluster.py::test_fastANI"
                            "test_cluster.py::test_goANI"
                            "test_cluster.py::test_goANI2"
                            "test_cluster.py::test_list_genome_load"
                            "test_cluster.py::test_low_ram_primary_clustering"
                            "test_cluster.py::test_skani"
                            "test_dereplicate.py::test_dereplicate_10"
                            "test_dereplicate.py::test_dereplicate_2"
                            "test_dereplicate.py::test_dereplicate_3"
                            "test_dereplicate.py::test_dereplicate_6"
                            "test_evaluate.py::test_tertiary_clustering_1"
                            "test_evaluate.py::test_tertiary_clustering_2"
                            "test_filter.py::test_filer_functional_3"
                            "test_greedy.py::test_greedy_secondary_clustering_1"
                            "test_greedy.py::test_greedy_secondary_clustering_2"
                            "test_greedy.py::test_multiround_primary_clustering_1"
                            "test_greedy.py::test_multiround_primary_clustering_2"
                            "test_rerun.py::test_unit_1"
                            "test_rerun.py::test_unit_3"
                            "test_rerun.py::test_unit_4")))))
    (native-inputs
     (list mash
           ;; nsimscan
           ;; mummer             ;https://github.com/mummer4/mummer, asl2.0
           ;; fastani            ;https://github.com/ParBLiSS/FastANI, asl2.0
           ;; checkm             ;https://ecogenomics.github.io/CheckM/, gpl3
           ;; skani
           python-pytest
           python-setuptools))
    (propagated-inputs
     (list python-biopython
           python-matplotlib
           python-networkx
           python-numpy
           python-pandas
           python-pytest
           python-scikit-learn
           python-seaborn
           python-tqdm))