From 3228266ed53285ef22b9898c96a01f4e62955c2e Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Mon, 29 Dec 2025 17:54:27 +0000
Subject: [PATCH] gnu: python-biopython: Update to 1.86.

* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.86,
use G-Expressions.
[arguments] <phases>: Remove 'numpy-compatibility.
[native-inputs]: Remove python-wheel.

Change-Id: I060455d474934b6b09c5adbbdec213b89496d9a5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
---
 gnu/packages/bioinformatics.scm | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e9bae52a279a9c1c8e2be10266c10373938af5cc..d38b78605be434b7f78e3b22d1692e5868b5bfc4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4409,33 +4409,32 @@ sequencing.")
 (define-public python-biopython
   (package
     (name "python-biopython")
-    (version "1.85")
+    (version "1.86")
     (source (origin
               (method url-fetch)
               ;; use PyPi rather than biopython.org to ease updating
               (uri (pypi-uri "biopython" version))
               (sha256
                (base32
-                "19m03s5rwcyiq5cs1kq9dzj7qvmfvm76idgn967ygr4x0msapbsx"))))
+                "1zwj1lfpinl1iv5kamdsiwfpdic3ylzd169gmdlfqb2dd9c0p9ck"))))
     (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'set-home
-           ;; Some tests require a home directory to be set.
-           (lambda _ (setenv "HOME" "/tmp")))
-         (add-after 'unpack 'numpy-compatibility
-           (lambda _
-             (substitute* "Bio/Cluster/__init__.py"
-               (("np.True_") "True"))))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (with-directory-excursion "Tests"
-                 (invoke "python3" "run_tests.py" "--offline"))))))))
+     (list
+      ;; tests: 500 passed
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'set-home
+            ;; Some tests require a home directory to be set.
+            (lambda _ (setenv "HOME" "/tmp")))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (with-directory-excursion "Tests"
+                  (invoke "python" "run_tests.py" "--offline"))))))))
+    (native-inputs
+     (list python-setuptools))
     (propagated-inputs
      (list python-numpy))
-    (native-inputs (list python-setuptools python-wheel))
     (home-page "https://biopython.org/")
     (synopsis "Tools for biological computation in Python")
     (description