diff options
| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-12-29 17:54:27 +0000 |
|---|---|---|
| committer | Rutherther <rutherther@ditigal.xyz> | 2026-01-25 21:19:51 +0100 |
| commit | 3228266ed53285ef22b9898c96a01f4e62955c2e (patch) | |
| tree | b4ce4d442039c8f33011ecfdb26aa45c76da935f /gnu | |
| parent | 09407e20138e48c808c0338980ac0c4f43ab955d (diff) | |
gnu: python-biopython: Update to 1.86.
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.86,
use G-Expressions.
[arguments] <phases>: Remove 'numpy-compatibility.
[native-inputs]: Remove python-wheel.
Change-Id: I060455d474934b6b09c5adbbdec213b89496d9a5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 33 |
1 files changed, 16 insertions, 17 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e9bae52a27..d38b78605b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4409,33 +4409,32 @@ sequencing.") (define-public python-biopython (package (name "python-biopython") - (version "1.85") + (version "1.86") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "19m03s5rwcyiq5cs1kq9dzj7qvmfvm76idgn967ygr4x0msapbsx")))) + "1zwj1lfpinl1iv5kamdsiwfpdic3ylzd169gmdlfqb2dd9c0p9ck")))) (build-system pyproject-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - (add-before 'check 'set-home - ;; Some tests require a home directory to be set. - (lambda _ (setenv "HOME" "/tmp"))) - (add-after 'unpack 'numpy-compatibility - (lambda _ - (substitute* "Bio/Cluster/__init__.py" - (("np.True_") "True")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (with-directory-excursion "Tests" - (invoke "python3" "run_tests.py" "--offline")))))))) + (list + ;; tests: 500 passed + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'set-home + ;; Some tests require a home directory to be set. + (lambda _ (setenv "HOME" "/tmp"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "Tests" + (invoke "python" "run_tests.py" "--offline")))))))) + (native-inputs + (list python-setuptools)) (propagated-inputs (list python-numpy)) - (native-inputs (list python-setuptools python-wheel)) (home-page "https://biopython.org/") (synopsis "Tools for biological computation in Python") (description |