From ae0efdd3ec0037fddf0a8039d287ab889165a60f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 27 Dec 2024 22:24:41 +0100
Subject: [PATCH] gnu: cwltool: Use test-flags.

* gnu/packages/bioinformatics.scm (cwltool)[arguments]: Use #:test-flags
instead of deleting and patching tests in 'modify-tests phase.

Change-Id: I0e4f16d48fba23e4197b69bf1c3923828f178cd0
---
 gnu/packages/bioinformatics.scm | 28 +++++++++++-----------------
 1 file changed, 11 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 49de4384a7..8a7c898e1c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6195,6 +6195,17 @@ (define-public cwltool
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      ;; These tests try to connect to the internet.
+      '(list "--ignore=tests/test_content_type.py"
+             "--ignore=tests/test_udocker.py"
+             "--ignore=tests/test_http_input.py"
+             "-k"
+             (string-append
+              "not test_env_filtering"
+              " and not test_load_graph_fragment_from_packed"
+              ;; Tries to use cwl-runners.
+              " and not test_v1_0_arg_empty_prefix_separate_false"))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'loosen-version-restrictions
@@ -6209,23 +6220,6 @@ (define-public cwltool
                  (string-append "version=\"" #$version "\"")))))
           (add-after 'unpack 'modify-tests
             (lambda _
-              ;; Tries to connect to the internet.
-              (delete-file "tests/test_content_type.py")
-              (delete-file "tests/test_udocker.py")
-              (delete-file "tests/test_http_input.py")
-              (substitute* "tests/test_load_tool.py"
-                (("def test_load_graph_fragment_from_packed")
-                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
-                                "def test_load_graph_fragment_from_packed")))
-              (substitute* "tests/test_examples.py"
-                (("def test_env_filtering")
-                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
-                                "def test_env_filtering")))
-              ;; Tries to use cwl-runners.
-              (substitute* "tests/test_examples.py"
-                (("def test_v1_0_arg_empty_prefix_separate_false")
-                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
-                                "def test_v1_0_arg_empty_prefix_separate_false")))
               (substitute* '("tests/subgraph/env-tool2.cwl"
                              "tests/subgraph/env-tool2_req.cwl"
                              "tests/subgraph/env-wf2_subwf-packed.cwl"