diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 35 |
1 files changed, 26 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5c001f917a..4953a4cdb4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19860,8 +19860,8 @@ set.") (name "instrain") ;; Git repository does not tag releases, use the latest commit from master ;; branch. - (properties '((commit . "6180be7b49a61b7e1ffe9f1489da5c6aa2ff9ac3") - (revision . "0"))) + (properties '((commit . "f172367e599851a6cb90048ae890d1bb6569063f") + (revision . "1"))) (version (git-version "1.10.0" (assoc-ref properties 'revision) (assoc-ref properties 'commit))) @@ -19873,18 +19873,32 @@ set.") (commit (assoc-ref properties 'commit)))) (file-name (git-file-name name version)) (sha256 - (base32 "1njsxjf3248121yw3q1ig6asf6b3wa5fgjfyc6dkgk6nd4ih8wni")))) + (base32 "12rrkcckna7k095clir9100cz6i5dn77anih6aq1blbsg4yhprnr")))) (build-system pyproject-build-system) (arguments (list - ;; Tests assume that test files exist (they don't) and are located in - ;; the developer's home directory, see: - ;; <https://github.com/MrOlm/inStrain/issues/218>. - #:tests? #false + ;; tests: 10 failed, 86 passed, 15 skipped, 220 warnings + #:test-flags + #~(list #$@(map (lambda (test) + (string-append "--deselect=test/tests/" test)) + ;; Mixture of "FileNotFoundError" and "AssertionError" + ;; errors. + (list "test_genes.py::test_genes_0" + "test_genes.py::test_genes_1" + "test_genes.py::test_genes_2" + "test_genes.py::test_genes_3" + "test_parse_gene_annotations.py::test_PA_2" + "test_polymorpher.py::test_polymorpher_unit_0" + "test_polymorpher.py::test_polymorpher_unit_3" + "test_quick_profile.py::test_quick_profile_0" + "test_quick_profile.py::test_quick_profile_1" + "test_quick_profile.py::test_quick_profile_2"))) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'patch-relative-imports (lambda _ + ;; See: <https://github.com/MrOlm/inStrain/issues/218>. + (mkdir "test/test_backend/") (substitute* (find-files "test/tests" "test_.*\\.py") (("from test_utils import BTO") "from .test_utils import BTO") @@ -19897,9 +19911,10 @@ set.") (add-after 'unpack 'relax-requirements (lambda _ (substitute* "setup.py" + (("biopython<=1.74") "biopython") ((".*pytest.*") ""))))))) (propagated-inputs - (list python-biopython-1.73 + (list python-biopython python-h5py python-lmfit python-matplotlib @@ -19911,7 +19926,9 @@ set.") python-seaborn python-tqdm)) (native-inputs - (list python-setuptools)) + (list python-boto3 + python-pytest + python-setuptools)) (home-page "https://github.com/MrOlm/inStrain") (synopsis "Calculation of strain-level metrics") (description |