diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 31 |
1 files changed, 16 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5b625337b3..fe9e74bdc5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1024,7 +1024,7 @@ Python.") (define-public python-biom-format (package (name "python-biom-format") - (version "2.1.7") + (version "2.1.10") (source (origin (method git-fetch) @@ -1036,18 +1036,21 @@ Python.") (file-name (git-file-name name version)) (sha256 (base32 - "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v")) + "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8")) (modules '((guix build utils))) - (snippet '(begin - ;; Delete generated C files. - (for-each delete-file (find-files "." "\\.c")) - #t)))) + ;; Delete generated C files. + (snippet + '(for-each delete-file (find-files "." "\\.c"))))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-cython - (lambda _ (setenv "USE_CYTHON" "1") #t)) + (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" @@ -1059,24 +1062,22 @@ Python.") (("^(.+)def test_from_hdf5_issue_731" m indent) (string-append indent "@npt.dec.skipif(True, msg='Guix')\n" - m))) - #t)) + m))))) + (add-before 'reset-gzip-timestamps 'make-files-writable (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (for-each (lambda (file) (chmod file #o644)) - (find-files out "\\.gz")) - #t)))))) + (find-files out "\\.gz")))))))) (propagated-inputs - `(("python-numpy" ,python-numpy) + `(("python-anndata" ,python-anndata) + ("python-numpy" ,python-numpy) ("python-scipy" ,python-scipy) ("python-flake8" ,python-flake8) ("python-future" ,python-future) ("python-click" ,python-click) ("python-h5py" ,python-h5py) - ;; FIXME: Upgrade to pandas 1.0 when - ;; https://github.com/biocore/biom-format/issues/837 is resolved. - ("python-pandas" ,python-pandas-0.25))) + ("python-pandas" ,python-pandas))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) |