guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 63e1e0d63e407086485aa668ef9dccf0e739318c
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Mon Dec 8 20:32:47 2025 +0000
gnu: checkm: Update to 1.2.4.
* gnu/packages/bioinformatics.scm (checkm): Update to 1.2.4.
[source] <pypi-uri>: Fix PyPI archive name.
[arguments] <tests?, test-flags>: Enable them.
[native-inputs]: Remove python-wheel.
Change-Id: I6486d073cbc50f005bf781b0a59a28b4f234c69d
---
gnu/packages/bioinformatics.scm | 40 +++++++++++++++++++++++++++++-----------
1 file changed, 29 insertions(+), 11 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e24f029c9a..25e65c7947 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21399,23 +21399,41 @@ sequence for paired-ended data, for which this
information is not available.")
(define-public checkm
(package
(name "checkm")
- (version "1.1.3")
+ (version "1.2.4")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "checkm-genome" version))
+ (uri (pypi-uri "checkm_genome" version))
(sha256
- (base32 "0i2nnki639hgjag17wlva2x0ymn37b4krqsf6akxddykhfbkdnkz"))))
+ (base32 "0wdjrz9v5cb6fa6rcd56v3x09yyffx18jjd9g8iw0i6i0lmw9abx"))))
(build-system pyproject-build-system)
(arguments
- `(#:tests? #f ;Some tests fail for unknown reasons.
- #:phases (modify-phases %standard-phases
- (add-before 'check 'set-HOME
- (lambda _
- (setenv "HOME" "/tmp"))))))
- (inputs (list python-dendropy python-matplotlib python-numpy python-pysam
- python-scipy))
- (native-inputs (list python-setuptools python-wheel))
+ (list
+ #:test-flags
+ #~(list "-k" (string-append
+ ;; AttributeError: 'BinStatistics' object has no attribute
+ ;; '_BinStatistics__calculateCodingBases'
+ "not testCodingBases"
+ ;; KeyError: 'GC'
+ " and not testGC"
+ ;; AttributeError: 'BinStatistics' object
+ ;; has no attribute
+ ;; 'calculateScaffoldLengthStats'
+ " and not testScaffoldLengthStats"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'set-HOME
+ (lambda _
+ (setenv "HOME" "/tmp"))))))
+ (native-inputs
+ (list python-pytest
+ python-setuptools))
+ (inputs
+ (list python-dendropy
+ python-matplotlib
+ python-numpy
+ python-pysam
+ python-scipy))
(home-page "https://ecogenomics.github.io/CheckM/";)
(synopsis "Assess the quality of putative genome bins")
(description
