~ruther/guix-local

036f2e66c33d9dc3cae37f106d18bfe63c1c1ddb — Sharlatan Hellseher 10 months ago f01390b 
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
patch browse .tar.gz 
1 files changed, 16 insertions(+), 20 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +16 -20
@@ 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