diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2022-12-02 21:45:40 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-12-02 21:46:36 +0100 |
| commit | fd44d489b541a3c8798c6702898693ccadfdb19c (patch) | |
| tree | fa0a7a62eaf5684edb6bab0600a0bd7d8154709b | |
| parent | b93e21a213827afaf635e6c7f6749bd2f5e329dc (diff) | |
gnu: python-biom-format: Update to 2.1.12.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12.
[arguments]: Remove "relax" phase; update "disable-broken-tests" phase.
[propagated-inputs]: Add python-scikit-bio.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 26 |
1 files changed, 12 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0fed480b32..3a7dc1a1b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1033,7 +1033,7 @@ use-case, we encourage users to compose functions to achieve their goals.") (define-public python-biom-format (package (name "python-biom-format") - (version "2.1.10") + (version "2.1.12") (source (origin (method git-fetch) @@ -1045,25 +1045,22 @@ use-case, we encourage users to compose functions to achieve their goals.") (file-name (git-file-name name version)) (sha256 (base32 - "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8")) + "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f")) (modules '((guix build utils))) ;; Delete generated C files. (snippet '(for-each delete-file (find-files "." "\\.c"))))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'use-cython (lambda _ (setenv "USE_CYTHON" "1"))) - (add-after 'unpack 'relax - (lambda _ - (substitute* "setup.py" - (("pytest < 5.3.4") "pytest")))) (add-after 'unpack 'disable-broken-tests (lambda _ - (substitute* "biom/tests/test_cli/test_validate_table.py" - (("^(.+)def test_invalid_hdf5" m indent) + (substitute* "biom/tests/test_util.py" + (("^(.+)def test_biom_open_hdf5_no_h5py" m indent) (string-append indent "@npt.dec.skipif(True, msg='Guix')\n" m))) @@ -1074,13 +1071,14 @@ use-case, we encourage users to compose functions to achieve their goals.") m)))))))) (propagated-inputs (list python-anndata - python-numpy - python-scipy + python-click python-flake8 python-future - python-click python-h5py - python-pandas)) + python-numpy + python-pandas + python-scikit-bio + python-scipy)) (native-inputs (list python-cython python-pytest python-pytest-cov python-nose)) (home-page "http://www.biom-format.org") |