guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 92097d2f6bd544281d791188d8c62e1e95531c07
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Mon Dec 29 17:54:27 2025 +0000
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
---
gnu/packages/bioinformatics.scm | 33 ++++++++++++++++-----------------
1 file changed, 16 insertions(+), 17 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8989082bad..051966e44a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4408,33 +4408,32 @@ 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
