Fix missing package dependencies

lib/galaxy/tool_util/cwl/cwltool_deps.py

@@ -12,6 +12,14 @@ warnings.filterwarnings("ignore", message=r"[\n.]DEPRECATION: Python 2", module=
 
 from galaxy.util import requests
 
+try:
+    from cwl_utils.types import CWLObjectType
+except ImportError:
+    try:
+        from cwltool.utils import CWLObjectType  # type: ignore[attr-defined, unused-ignore]
+    except ImportError:
+        CWLObjectType = object  # type: ignore[assignment, misc]
+
 try:
     from cwltool import (
         main,
@@ -67,13 +75,11 @@ except ImportError:
 
 try:
     from cwltool.utils import (
-        CWLObjectType,
         JobsType,
         normalizeFilesDirs,
         visit_class,
     )
 except ImportError:
-    CWLObjectType = object  # type: ignore[assignment, misc]
     JobsType = object  # type: ignore[misc, unused-ignore]
     visit_class = None  # type: ignore[assignment]
     normalizeFilesDirs = None  # type: ignore[assignment]

packages/app/setup.cfg

@@ -41,7 +41,7 @@ install_requires =
     galaxy-tool-util[cwl,edam]
     galaxy-tool-shed-schema
     galaxy-tours
-    galaxy-util[image-util]
+    galaxy-util[image-util,jstree]
     galaxy-web-framework
     galaxy-web-stack
     Beaker
@@ -91,6 +91,8 @@ test =
     pykwalify
     pytest
     pytest-asyncio
+    pytest-mock
+    responses
     testfixtures
 
 [options.entry_points]

packages/data/setup.cfg

@@ -69,6 +69,7 @@ python_requires = >=3.10
 
 [options.extras_require]
 test = 
+    galaxy-config
     pytest
     roc-validator
 

packages/files/setup.cfg

@@ -45,6 +45,7 @@ test =
     galaxy-test-base
     pytest
     gcsfs
+    responses
     s3fs>=2023.1.0
 
 [options.entry_points]

packages/schema/setup.cfg

@@ -31,6 +31,7 @@ version = 26.0.1.dev1
 [options]
 include_package_data = True
 install_requires =
+    galaxy-tool-util-models
     galaxy-util
     pydantic[email]>=2.7.4
 packages = find:

packages/tool_shed/setup.cfg

@@ -59,7 +59,8 @@ packages = find:
 python_requires = >=3.10
 
 [options.extras_require]
-test = 
+test =
+    galaxy-test-base
     pytest
 
 [options.packages.find]

packages/tool_util/setup.cfg

@@ -34,7 +34,7 @@ version = 26.0.1.dev1
 include_package_data = True
 install_requires =
     galaxy-tool-util-models
-    galaxy-util[image-util]>=22.1
+    galaxy-util[template,image-util]>=22.1
     conda-package-streaming
     lxml!=4.2.2
     MarkupSafe
@@ -64,6 +64,7 @@ console_scripts =
 
 [options.extras_require]
 cwl =
+    cwl-utils
     cwltool>=3.1.20230624081518
 mulled =
     jinja2

packages/tours/setup.cfg

@@ -32,6 +32,8 @@ version = 26.0.1.dev1
 include_package_data = True
 install_requires =
     galaxy-navigation
+    galaxy-schema
+    galaxy-util
     pydantic>=2.7.4
     PyYAML
 packages = find:
@@ -41,6 +43,10 @@ python_requires = >=3.10
 console_scripts =
         gx-validate-tours = galaxy.tours.validate:main
 
+[options.extras_require]
+test =
+    pytest
+
 [options.packages.find]
 exclude =
     tests*

packages/util/setup.cfg

@@ -56,6 +56,7 @@ template =
     fissix;python_version>='3.13'
     future>=1.0.0
 config-template =
+    galaxy-tool-util-models
     Jinja2
     pydantic>=2.7.4
 test =

test/unit/data/security/test_validate_user_input.py

@@ -80,7 +80,7 @@ class TestIsEmailBanned:
         assert is_email_banned("ab+bar@gmail.com", "_", rules)
         assert not is_email_banned("ab-bar@gmail.com", "_", rules)  # different sub-addressing delimiter
 
-    def test_no_canonical_rules(self, monkeypatch, appconfig):
+    def test_no_canonical_rules(self, monkeypatch):
         """No rules loaded."""
         monkeypatch.setattr(validate_user_input, "_read_email_ban_list", lambda a: self.mock_ban_list)
 
@@ -97,7 +97,7 @@ class TestIsEmailBanned:
         assert not is_email_banned("a.b@gmail.com", "_", rules)
         assert not is_email_banned("ab+bar@gmail.com", "_", rules)
 
-    def test_custom_canonical_rules(self, monkeypatch, appconfig):
+    def test_custom_canonical_rules(self, monkeypatch):
         """No rules loaded."""
         monkeypatch.setattr(validate_user_input, "_read_email_ban_list", lambda a: self.mock_ban_list)
 

test/unit/selenium/test_has_driver.py

@@ -888,7 +888,7 @@ class TestUtilityMethods:
     def test_prepend_timeout_message(self, has_driver_instance, request):
         """Test prepending message to timeout exception."""
         backend = request.node.callspec.params.get("has_driver_instance")
-        if backend == "selenium":
+        if backend in ("selenium", "proxy-selenium"):
             original_selenium_exc = SeleniumTimeoutException(msg="original message")
             new_selenium_exception = has_driver_instance.prepend_timeout_message(original_selenium_exc, "New prefix:")
             assert "New prefix:" in new_selenium_exception.msg