guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 4582f183e5bb81c2c78f7ade98b6c8afdf011d6e
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Mon Dec 29 13:55:53 2025 +0000
gnu: python-biom-format: Update to 2.1.17.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.17.
[source] <snippet>: Remove redundant logic.
[arguments] <test-flags>: Only skip some doctest requiring Nose test
runner.
<phases>: Remove 'use-cython, 'build-extensions, and
'pandas-compatibility; add 'remove-local-source.
[propagated-inputs]: Remove python-flake8 and python-future.
[native-inputs]: Remove python-pytest-cov and python-wheel; add
python-setuptools.
Change-Id: Ib497f771e5de40b07df4964ebcddf6c40c15fc85
---
gnu/packages/bioinformatics.scm | 63 ++++++++++++++++-------------------------
1 file changed, 24 insertions(+), 39 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6071e17d6e..cd9b7d03ce 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4112,60 +4112,45 @@ use-case, we encourage users to compose functions to
achieve their goals.")
(define-public python-biom-format
(package
(name "python-biom-format")
- (version "2.1.16")
+ (version "2.1.17")
(source
(origin
(method git-fetch)
- ;; Use GitHub as source because PyPI distribution does not contain
- ;; test data: https://github.com/biocore/biom-format/issues/693
(uri (git-reference
- (url "https://github.com/biocore/biom-format";)
- (commit version)))
+ (url "https://github.com/biocore/biom-format";)
+ (commit version)))
(file-name (git-file-name name version))
(sha256
- (base32
- "1npxjsi7r0w8diq6s37q21cqgrqifl7f483lfn72bn7qrvkvbpyz"))
- (modules '((guix build utils)))
- ;; Delete generated C files.
- (snippet
- '(for-each delete-file (find-files "." "\\.c")))))
+ (base32 "0fmlrxcn8bgh8wccs2qzz5q08ivd3r3zva9h8zzr1jsbff7904fz"))))
(build-system pyproject-build-system)
(arguments
(list
+ ;; tests: 380 passed, 4 skipped, 16 warnings
#:test-flags
- '(list "-k"
- (string-append ;; Unclear why this one fails. There is no
backtrace.
- "not test_to_dataframe_is_sparse"
- ;; These need skbio, but that needs biom-format.
- " and not test_align_tree_intersect_obs"
- " and not test_align_tree_intersect_tips"
- " and not test_align_tree_sample"))
+ ;; Doctests depend on Nose.
+ #~(list "--ignore=doc/sphinxext/numpydoc/numpydoc/tests/")
#:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'use-cython
- (lambda _ (setenv "USE_CYTHON" "1")))
- (add-before 'check 'build-extensions
- (lambda _
- ;; Cython extensions have to be built before running the tests.
- (invoke "python" "setup.py" "build_ext" "--inplace")))
- (add-after 'unpack 'pandas-compatibility
- (lambda _
- (substitute* "biom/tests/test_table.py"
- (("import pandas.util.testing")
- "import pandas.testing")))))))
+ #~(modify-phases %standard-phases
+ (add-before 'check 'remove-local-source
+ (lambda _
+ (copy-recursively "biom/tests" "tests")
+ (delete-file-recursively "biom")
+ (substitute* "tests/test_cli/test_validate_table.py"
+ ;; Help finding "examples" directory.
+ (("cur_path.rsplit\\(os.path.sep, 3\\)\\[0\\]")
+ (format #f "~s" (getcwd)))))))))
+ (native-inputs
+ (list python-cython
+ python-pytest
+ python-setuptools))
(propagated-inputs
- (list python-anndata
- python-click
- python-flake8
- python-future
+ (list python-click
python-h5py
python-numpy
python-pandas
- ;;python-scikit-bio ;mutually recursive dependency
- python-scipy))
- (native-inputs
- (list python-cython python-pytest python-pytest-cov
- python-wheel))
+ python-scipy
+ ;; [optional]
+ python-anndata))
(home-page "https://www.biom-format.org";)
(synopsis "Biological Observation Matrix (BIOM) format utilities")
(description
