Reuse `skip_unless_executable` test decorator for conda and singularity

lib/galaxy/util/unittest_utils/__init__.py

@@ -5,8 +5,11 @@ from typing import (
 )
 from unittest import SkipTest
 
+import pytest
 import requests
 
+from galaxy.util.commands import which
+
 
 def is_site_up(url: str) -> bool:
     try:
@@ -30,3 +33,13 @@ def skip_if_site_down(url: str) -> Callable:
 
 
 skip_if_github_down = skip_if_site_down("https://github.com/")
+
+
+def _identity(func: Callable) -> Callable:
+    return func
+
+
+def skip_unless_executable(executable):
+    if which(executable):
+        return _identity
+    return pytest.mark.skip(f"PATH doesn't contain executable {executable}")

lib/galaxy_test/driver/integration_util.py

@@ -24,8 +24,11 @@ import pytest
 from galaxy.app import UniverseApplication
 from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.util import safe_makedirs
-from galaxy.util.commands import which
 from galaxy.util.unittest import TestCase
+from galaxy.util.unittest_utils import (
+    _identity,
+    skip_unless_executable,
+)
 from galaxy_test.base.api import (
     UsesApiTestCaseMixin,
     UsesCeleryTasks,
@@ -43,10 +46,6 @@ SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 VAULT_CONF = os.path.join(SCRIPT_DIRECTORY, "vault_conf.yml")
 
 
-def _identity(func):
-    return func
-
-
 def skip_if_jenkins(cls):
     if os.environ.get("BUILD_NUMBER", ""):
         return skip
@@ -66,12 +65,6 @@ def skip_unless_postgres():
     return pytest.mark.skip("GALAXY_TEST_DBURI does not point to postgres database, required for this test.")
 
 
-def skip_unless_executable(executable):
-    if which(executable):
-        return _identity
-    return pytest.mark.skip(f"PATH doesn't contain executable {executable}")
-
-
 def skip_unless_docker():
     return skip_unless_executable("docker")
 

test/unit/tool_util/mulled/test_mulled_search.py

@@ -1,13 +1,13 @@
 import pytest
 
 from galaxy.tool_util.deps.mulled.mulled_search import (
-    conda_path,
     CondaSearch,
     get_package_hash,
     GitHubSearch,
     QuaySearch,
     singularity_search,
 )
+from galaxy.util.unittest_utils import skip_unless_executable
 from ..util import external_dependency_management
 
 
@@ -22,7 +22,7 @@ def test_quay_search():
 
 
 @external_dependency_management
-@pytest.mark.skipif(not conda_path, reason="requires conda on path")
+@skip_unless_executable("conda")
 def test_conda_search():
     t = CondaSearch("bioconda")
     search1 = t.get_json("asdfasdf")

test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py

@@ -1,14 +1,12 @@
 import os
 
-import pytest
-
 from galaxy.tool_util.deps.mulled.get_tests import main_test_search
 from galaxy.tool_util.deps.mulled.mulled_update_singularity_containers import (
     docker_to_singularity,
     get_list_from_file,
     singularity_container_test,
 )
-from galaxy.util import which
+from galaxy.util.unittest_utils import skip_unless_executable
 from ..util import external_dependency_management
 
 
@@ -26,14 +24,14 @@ def test_get_list_from_file(tmp_path) -> None:
 
 
 @external_dependency_management
-@pytest.mark.skipif(not which("singularity"), reason="requires singularity but singularity not on PATH")
+@skip_unless_executable("singularity")
 def test_docker_to_singularity(tmp_path) -> None:
     docker_to_singularity("abundancebin:1.0.1--0", "singularity", tmp_path, no_sudo=True)
     assert tmp_path.joinpath("abundancebin:1.0.1--0").exists()
 
 
 @external_dependency_management
-@pytest.mark.skipif(not which("singularity"), reason="requires singularity but singularity not on PATH")
+@skip_unless_executable("singularity")
 def test_singularity_container_test(tmp_path) -> None:
     containers = [
         "pybigwig:0.3.22--py36h54a71a5_0",  # test Python imports