guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 036f2e66c33d9dc3cae37f106d18bfe63c1c1ddb
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Thu Jul 24 16:16:39 2025 +0100
gnu: python-pyrodigal: Update to 3.6.3.
* gnu/packages/bioinformatics.scm (python-pyrodigal): Update to 3.6.3.
Fix indentation.
[propagated-inputs]: Remove python-importlib-resources.
[arguments] <phases>: Add 'patch-pyproject; simplify custom 'check
phase.
[native-inputs]: Remove python-mock, python-unittest2, and
python-wheel; add cmake-minimal and python-scikit-build-core.
Change-Id: Id50fe9bd78c466d2dd5938c8a124d244c69da082
---
gnu/packages/bioinformatics.scm | 36 ++++++++++++++++--------------------
1 file changed, 16 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ff4ff7e244..c92a5c5298 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -20202,41 +20202,37 @@ bgzipped text file that contains a pair of genomic
coordinates per line.")
(define-public python-pyrodigal
(package
(name "python-pyrodigal")
- (version "3.3.0")
+ (version "3.6.3")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/althonos/pyrodigal";)
- (commit (string-append "v" version))
- (recursive? #t)))
+ (url "https://github.com/althonos/pyrodigal";)
+ (commit (string-append "v" version))
+ ;; XXX: vendor -> <https://github.com/hyattpd/Prodigal>
+ (recursive? #t)))
(file-name (git-file-name name version))
(sha256
- (base32 "10vxbm9i33wari0ifsr78xnfn7d0yqwzqpc5pchirjflf1mmnr6w"))))
+ (base32 "1gcvdrx0q730i0r3lndl7l7h0h8xvzsi09ymf14b498mj03yjdq9"))))
(build-system pyproject-build-system)
(arguments
(list
- #:modules '((ice-9 ftw)
- (srfi srfi-1)
- (srfi srfi-26)
- (guix build utils)
- (guix build pyproject-build-system))
#:phases
#~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-pyproject
+ (lambda _
+ (substitute* "pyproject.toml"
+ ;; Extra keys present in "project": 'platform'
+ (("platform =.*") ""))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
- (let ((cwd (getcwd))
- (libdir (find (cut string-prefix? "lib." <>)
- (scandir "build"))))
- (with-directory-excursion (string-append cwd "/build/"
libdir)
- (invoke "python3" "-m" "unittest" "pyrodigal.tests"
"-vv")))))))))
- (propagated-inputs (list python-archspec python-importlib-resources))
+ (invoke "python" "-m" "unittest" "pyrodigal.tests" "-vv")))))))
+ (propagated-inputs (list python-archspec))
(native-inputs
- (list python-cython-3
- python-mock
- python-unittest2
- python-wheel))
+ (list cmake-minimal
+ python-cython-3
+ python-scikit-build-core))
(home-page "https://github.com/althonos/pyrodigal";)
(synopsis "Cython bindings and Python interface for Prodigal")
(description
