From 036f2e66c33d9dc3cae37f106d18bfe63c1c1ddb Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Thu, 24 Jul 2025 16:16:39 +0100
Subject: [PATCH] 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 ff4ff7e2440eaa1365a3a406744957294dec4e36..c92a5c5298fd3a3ff46ab39e6ca7b99f577ef98a 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