From cf4296ecb1c451162144bf6b98e129f522d2056e Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Wed, 31 Dec 2025 17:33:09 +0000
Subject: [PATCH] gnu: cnvkit: Fix tests.

* gnu/packages/bioinformatics.scm (cnvkit):
[arguments] <phases>: Add 'fix-pytest-config.
[propagated-inputs]: Remove python-future.

Change-Id: I845709c8e91e8ed86dcc25a9d5dc0469e8005f0b
---
 gnu/packages/bioinformatics.scm | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71c4845416307f10ee32064f5380f9f3a4028c34..a702188bf4565ab68c2d650d383822456af1709c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21060,15 +21060,24 @@ polymorphisms) and indels with respect to a reference genome and more.")
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/etal/cnvkit")
-             (commit (string-append "v" version))))
+              (url "https://github.com/etal/cnvkit")
+              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32 "090yh17symcahddx399kcx0mcw4gdrcc2jil3p8lb92r8c8kglb5"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; tests: 70 passed, 1 warning
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              (substitute* "pyproject.toml"
+                (("filterwarnings =.*")
+                 "")))))))
     (propagated-inputs
      (list python-biopython
-           python-future
            python-matplotlib
            python-numpy
            python-pandas