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gnu: python-pyrodigal: Update to 3.6.3.

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* 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
This commit is contained in:
Sharlatan Hellseher 2025-07-24 16:16:39 +01:00
parent f01390b916
commit 036f2e66c3
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1 changed files with 16 additions and 20 deletions
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@ -20202,41 +20202,37 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
(define-public python-pyrodigal (define-public python-pyrodigal
(package (package
(name "python-pyrodigal") (name "python-pyrodigal")
(version "3.3.0") (version "3.6.3")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/althonos/pyrodigal") (url "https://github.com/althonos/pyrodigal")
(commit (string-append "v" version)) (commit (string-append "v" version))
(recursive? #t))) ;; XXX: vendor -> <https://github.com/hyattpd/Prodigal>
(recursive? #t)))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 "10vxbm9i33wari0ifsr78xnfn7d0yqwzqpc5pchirjflf1mmnr6w")))) (base32 "1gcvdrx0q730i0r3lndl7l7h0h8xvzsi09ymf14b498mj03yjdq9"))))
(build-system pyproject-build-system) (build-system pyproject-build-system)
(arguments (arguments
(list (list
#:modules '((ice-9 ftw)
(srfi srfi-1)
(srfi srfi-26)
(guix build utils)
(guix build pyproject-build-system))
#:phases #:phases
#~(modify-phases %standard-phases #~(modify-phases %standard-phases
(add-after 'unpack 'patch-pyproject
(lambda _
(substitute* "pyproject.toml"
;; Extra keys present in "project": 'platform'
(("platform =.*") ""))))
(replace 'check (replace 'check
(lambda* (#:key tests? #:allow-other-keys) (lambda* (#:key tests? #:allow-other-keys)
(when tests? (when tests?
(let ((cwd (getcwd)) (invoke "python" "-m" "unittest" "pyrodigal.tests" "-vv")))))))
(libdir (find (cut string-prefix? "lib." <>) (propagated-inputs (list python-archspec))
(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))
(native-inputs (native-inputs
(list python-cython-3 (list cmake-minimal
python-mock python-cython-3
python-unittest2 python-scikit-build-core))
python-wheel))
(home-page "https://github.com/althonos/pyrodigal") (home-page "https://github.com/althonos/pyrodigal")
(synopsis "Cython bindings and Python interface for Prodigal") (synopsis "Cython bindings and Python interface for Prodigal")
(description (description