guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit b7b40e616d385da8124863c0ea3e663e5faf3855
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Fri Jan 2 23:02:15 2026 +0000
gnu: python-presto: Improve package, fix tests.
* gnu/packages/bioinformatics.scm (python-presto): Refresh package style.
[arguments] <test-flags>: Skip 3 tests.
[native-inputs]: Remove python-wheel.
Change-Id: I5992e127fd653aa04711647cf0a458586029b3d4
---
gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++--------------
1 file changed, 22 insertions(+), 14 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7dd62c99aa..163bd956be 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4778,18 +4778,35 @@ in a modular way.")
(package
(name "python-presto")
(version "0.7.6")
- (home-page "https://github.com/immcantation/presto";)
(source
(origin
(method git-fetch)
(uri (git-reference
- (url home-page)
+ (url "https://github.com/immcantation/presto";)
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32
- "1mcngwrxiw8r1j26r5crf7j0dscvhg3b8g1is3j3vq5jpnyn8jmz"))))
+ (base32 "1mcngwrxiw8r1j26r5crf7j0dscvhg3b8g1is3j3vq5jpnyn8jmz"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ #:build-backend "setuptools.build_meta"
+ ;; tests: 29 passed, 6 skipped, 3 deselected, 8 warnings
+ #:test-flags
+ ;; FileNotFoundError: [Errno 2] No such file or directory: 'cd-hit-est'
+ #~(list "--ignore=tests/test_ClusterSets.py"
+ ;; TypeError: seq argument should be a Seq or MutableSeq object
+ #$@(map (lambda (test) (string-append "--deselect="
+ "tests/"
+ "test_EstimateError.py::"
+ "TestEstimateError::"
+ test))
+ (list "test_calculateDistances"
+ "test_countMismatches"
+ "test_initializeMismatchDictionary")))))
+ (native-inputs
+ (list python-pytest
+ python-setuptools))
(propagated-inputs
(list muscle
python-biopython
@@ -4798,16 +4815,7 @@ in a modular way.")
python-pyyaml
python-scipy
vsearch))
- (native-inputs
- (list python-pytest
- python-setuptools
- python-wheel))
- (arguments
- (list
- #:build-backend "setuptools.build_meta"
- #:test-flags
- ;; FileNotFoundError: [Errno 2] No such file or directory: 'cd-hit-est'
- '(list "--ignore=tests/test_ClusterSets.py")))
+ (home-page "https://github.com/immcantation/presto";)
(synopsis "The REpertoire Sequencing TOolkit")
(description "Presto is a python toolkit for processing raw reads from
high-throughput sequencing of B cell and T cell repertoires.")
