Type annotation fix for mypy 1.16.0 during package testing

Fix the following traceback:

```
galaxy/selenium/context.py:25: error: Cannot override writeable attribute with
read-only property  [override]
        def driver(self):
        ^
```

This error didn't happen during the normal `tox -e mypy` because
the `selenium` package was not installed into the tox virtual environment.

To prevent this issue and improve the code type checking, this commit
defines a new `test` dependency group and corresponding
`lib/galaxy/dependencies/pinned-test-requirements.txt` requirements
file to be used by mypy and other tests that don't need packages
used purely for developing (like black, isort, Sphinx...).

Fix the 6 new mypy errors resulting from installing the test
dependencies into the tox virtual environment.

.github/workflows/check_test_class_names.yaml

@@ -25,6 +25,6 @@ jobs:
           cache: 'pip'
           cache-dependency-path: 'requirements.txt'
       - name: Install Python dependencies
-        run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt
+        run: pip install -r requirements.txt -r lib/galaxy/dependencies/pinned-test-requirements.txt
       - name: Run tests
         run: .ci/check_test_class_names.sh

lib/galaxy/datatypes/molecules.py

@@ -34,7 +34,7 @@ from galaxy.util import (
 try:
     from ase import io as ase_io
 except ImportError:
-    ase_io = None
+    ase_io = None  # type: ignore[assignment, unused-ignore]
 
 log = logging.getLogger(__name__)
 
@@ -245,10 +245,7 @@ class AtomicStructFile(GenericMolFile):
         Find Atom IDs for metadata.
         """
         self.meta_error = False
-        if ase_io is None:
-            # Don't have optional dependency, can't set advanced values
-            return
-        else:
+        if ase_io is not None:
             # enhanced metadata
             try:
                 ase_data = ase_io.read(dataset.get_file_name(), index=":", format=self.ase_format)

lib/galaxy/dependencies/pinned-test-requirements.txt

@@ -0,0 +1,156 @@
+# This file was autogenerated by uv via the following command:
+#    uv export --frozen --no-annotate --no-hashes --only-group=test
+aiohappyeyeballs==2.6.1
+aiohttp==3.11.18
+aiosignal==1.3.2
+anyio==4.9.0
+ase==3.25.0
+async-timeout==5.0.1 ; python_full_version < '3.11'
+attrs==25.3.0
+axe-selenium-python==2.1.6
+boto3==1.37.3
+botocore==1.37.3
+cachecontrol==0.14.3
+cattrs==24.1.3
+certifi==2025.4.26
+cffi==1.17.1 ; implementation_name != 'pypy' and os_name == 'nt'
+charset-normalizer==3.4.2
+click==8.1.8 ; python_full_version < '3.10'
+click==8.2.1 ; python_full_version >= '3.10'
+colorama==0.4.6 ; sys_platform == 'win32'
+colorlog==6.9.0
+contourpy==1.3.0 ; python_full_version < '3.10'
+contourpy==1.3.2 ; python_full_version >= '3.10'
+coverage==7.8.2
+cwltest==2.6.20250314152537
+cycler==0.12.1
+decorator==5.2.1
+defusedxml==0.7.1
+dogpile-cache==1.2.2
+enum-tools==0.12.0 ; python_full_version >= '3.10'
+exceptiongroup==1.3.0 ; python_full_version < '3.11'
+filelock==3.18.0
+fluent-logger==0.11.1
+fonttools==4.58.0
+frozenlist==1.6.0
+greenlet==3.2.2
+h11==0.16.0
+html5lib==1.1
+httpcore==1.0.9
+httpx==0.28.1
+idna==3.10
+importlib-metadata==8.7.0 ; python_full_version < '3.12'
+importlib-resources==6.5.2 ; python_full_version < '3.10'
+iniconfig==2.1.0
+inquirerpy==0.3.4
+isodate==0.7.2 ; python_full_version < '3.11'
+jinja2==3.1.6
+jmespath==1.0.1
+jsonschema==4.23.0
+jsonschema-specifications==2025.4.1
+junit-xml==1.9
+kiwisolver==1.4.7 ; python_full_version < '3.10'
+kiwisolver==1.4.8 ; python_full_version >= '3.10'
+lxml==5.4.0
+markdown-it-py==3.0.0
+markupsafe==3.0.2
+matplotlib==3.9.4 ; python_full_version < '3.10'
+matplotlib==3.10.3 ; python_full_version >= '3.10'
+mdurl==0.1.2
+mirakuru==2.6.0
+mistune==3.0.2
+msgpack==1.1.0
+multidict==6.4.4
+mypy-extensions==1.1.0
+numpy==2.0.2 ; python_full_version < '3.10'
+numpy==2.2.6 ; python_full_version >= '3.10'
+onedatafilerestclient==21.2.5.2
+outcome==1.3.0.post0
+owlrl==6.0.2
+packaging==24.2 ; python_full_version < '3.10'
+packaging==25.0 ; python_full_version >= '3.10'
+pbr==6.1.1
+pfzy==0.3.4
+pillow==11.2.1
+pkce==1.0.3
+platformdirs==4.3.8
+playwright==1.52.0
+pluggy==1.6.0
+port-for==0.7.4
+prettytable==3.16.0
+prompt-toolkit==3.0.51
+propcache==0.3.1
+psutil==7.0.0 ; sys_platform != 'cygwin'
+psycopg==3.2.9
+pycparser==2.22 ; implementation_name != 'pypy' and os_name == 'nt'
+pyee==13.0.0
+pygments==2.19.1
+pyparsing==3.2.3
+pyshacl==0.26.0
+pysocks==1.7.1
+pytest==7.4.4
+pytest-asyncio==0.23.8
+pytest-base-url==2.1.0
+pytest-cov==6.1.1
+pytest-html==4.1.1
+pytest-httpserver==1.1.3
+pytest-json-report==1.5.0
+pytest-metadata==3.1.1
+pytest-mock==3.14.0
+pytest-playwright==0.7.0
+pytest-postgresql==7.0.2
+pytest-shard==0.1.2
+python-dateutil==2.9.0.post0
+python-irodsclient==3.1.0
+python-slugify==8.0.4
+pyyaml==6.0.2
+rdflib==7.1.4
+referencing==0.36.2
+requests==2.32.4
+requests-cache==1.2.1
+responses==0.25.7
+rich==13.9.4
+rich-click==1.8.9
+roc-validator==0.4.2 ; python_full_version < '3.9.20'
+roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
+roc-validator==0.7.0 ; python_full_version >= '3.10'
+rpds-py==0.25.1
+ruamel-yaml==0.18.10
+ruamel-yaml-clib==0.2.12 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
+rucio-clients==37.3.0
+s3transfer==0.11.3
+schema-salad==8.9.20250408123006
+scipy==1.13.1 ; python_full_version < '3.10'
+scipy==1.15.3 ; python_full_version >= '3.10'
+selenium==4.32.0 ; python_full_version < '3.10'
+selenium==4.33.0 ; python_full_version >= '3.10'
+seletools==1.5.0
+setuptools==80.8.0
+six==1.17.0
+sniffio==1.3.1
+sortedcontainers==2.4.0
+statsd==4.0.1
+stevedore==5.4.1
+tabulate==0.9.0
+testfixtures==8.3.0
+text-unidecode==1.3
+tinydb==4.8.2
+toml==0.10.2
+tomli==2.2.1 ; python_full_version <= '3.11'
+trio==0.30.0
+trio-websocket==0.12.2
+tuspy==1.1.0
+twill==3.3
+typing-extensions==4.13.2
+tzdata==2025.2 ; sys_platform == 'win32'
+url-normalize==2.2.1
+urllib3==1.26.20 ; python_full_version < '3.10'
+urllib3==2.4.0 ; python_full_version >= '3.10'
+watchdog==6.0.0
+wcwidth==0.2.13
+webencodings==0.5.1
+websocket-client==1.8.0
+werkzeug==3.1.3
+wsproto==1.2.0
+yarl==1.20.0
+zipp==3.21.0 ; python_full_version < '3.12'

lib/galaxy/dependencies/update.sh

@@ -44,5 +44,6 @@ fi
 # Update pinned requirements files.
 UV_EXPORT_OPTIONS='--frozen --no-annotate --no-hashes'
 ${uv} export ${UV_EXPORT_OPTIONS} --no-dev > "$this_directory/pinned-requirements.txt"
+${uv} export ${UV_EXPORT_OPTIONS} --only-group=test > "$this_directory/pinned-test-requirements.txt"
 ${uv} export ${UV_EXPORT_OPTIONS} --only-group=dev > "$this_directory/dev-requirements.txt"
 ${uv} export ${UV_EXPORT_OPTIONS} --only-group=typecheck > "$this_directory/pinned-typecheck-requirements.txt"

lib/galaxy/objectstore/onedata.py

@@ -13,7 +13,7 @@ try:
         OnedataRESTError,
     )
 except ImportError:
-    OnedataFileRESTClient = None
+    OnedataFileRESTClient = None  # type: ignore[assignment, misc, unused-ignore]
 
 from galaxy.util import (
     mapped_chars,
@@ -303,6 +303,6 @@ def _is_not_found_onedata_rest_error(ex):
             return True
 
         if ex.http_code == 400 and ex.category == "posix":
-            return ex.details["errno"] == "enoent"
+            return isinstance(ex.details, dict) and ex.details["errno"] == "enoent"
 
     return False

lib/galaxy/selenium/context.py

@@ -1,6 +1,9 @@
 import os
 from abc import abstractmethod
-from typing import Optional
+from typing import (
+    Optional,
+    TYPE_CHECKING,
+)
 from urllib.parse import urljoin
 
 import yaml
@@ -8,6 +11,9 @@ import yaml
 from .driver_factory import ConfiguredDriver
 from .navigates_galaxy import NavigatesGalaxy
 
+if TYPE_CHECKING:
+    from selenium.webdriver.remote.webdriver import WebDriver
+
 
 class GalaxySeleniumContext(NavigatesGalaxy):
     url: str
@@ -22,7 +28,7 @@ class GalaxySeleniumContext(NavigatesGalaxy):
         return urljoin(base, url)
 
     @property
-    def driver(self):
+    def driver(self) -> "WebDriver":  # type: ignore[override]
         return self.configured_driver.driver
 
     def screenshot(self, label: str):

pyproject.toml

@@ -116,20 +116,13 @@ Repository = "https://github.com/galaxyproject/galaxy"
 "Bug Tracker" = "https://github.com/galaxyproject/galaxy/issues"
 
 [dependency-groups]
-dev = [
+test = [
     "ase>=3.18.1",
     "axe-selenium-python",
-    "black",
     "boto3",
-    "codespell",
     "cwltest>=2.5.20240906231108",  # Python 3.13 support
-    "darker",
     "fluent-logger",
-    "galaxy-release-util",
-    "isort",
     "lxml!=4.2.2",
-    "markdown-it-reporter",
-    "myst-parser",
     "onedatafilerestclient==21.2.5.2",
     "pkce",
     "playwright>=1.48.0",  # Python 3.13 support
@@ -149,8 +142,6 @@ dev = [
     "rucio-clients>=37.2.0",  # https://github.com/rucio/rucio/pull/7665
     "selenium",
     "seletools",
-    "Sphinx>=4.0",  # support docutils 0.17
-    "sphinx-rtd-theme",
     "statsd",
     "testfixtures",
     "tuspy",
@@ -158,6 +149,18 @@ dev = [
     "watchdog",
     "Werkzeug",
 ]
+dev = [
+    {include-group = "test"},
+    "black",
+    "codespell",
+    "darker",
+    "galaxy-release-util",
+    "isort",
+    "markdown-it-reporter",
+    "myst-parser",
+    "Sphinx>=4.0",  # support docutils 0.17
+    "sphinx-rtd-theme",
+]
 typecheck = [
     "boto3-stubs[s3]",
     "lxml-stubs",

tox.ini

@@ -55,6 +55,7 @@ deps =
     lint,lint_docstring,lint_docstring_include_list: -rlib/galaxy/dependencies/pinned-lint-requirements.txt
     mypy: -rlib/galaxy/dependencies/pinned-typecheck-requirements.txt
     mypy: -rlib/galaxy/dependencies/pinned-requirements.txt
+    mypy: -rlib/galaxy/dependencies/pinned-test-requirements.txt
     test_galaxy_packages,test_galaxy_packages_for_pulsar: pyyaml
     unit: mock-ssh-server