Merge pull request galaxyproject#16436 from galaxybot/dev_auto_update…

…_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,4 +1,4 @@
-aiohttp==3.8.4 ; python_version >= "3.7" and python_version < "3.12"
+aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12"
 aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 alabaster==0.7.13 ; python_version >= "3.7" and python_version < "3.12"
 amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -22,7 +22,7 @@ charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.5 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.6 ; python_version >= "3.7" and python_version < "3.12"
 codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12"
@@ -81,7 +81,7 @@ pathspec==0.11.1 ; python_version >= "3.7" and python_version < "3.12"
 pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12"
-platformdirs==3.8.1 ; python_version >= "3.7" and python_version < "3.12"
+platformdirs==3.9.1 ; python_version >= "3.7" and python_version < "3.12"
 pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 port-for==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -91,7 +91,7 @@ py==1.11.0 ; python_version >= "3.7" and python_version < "3.12"
 pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
 pygithub==1.59.0 ; python_version >= "3.7" and python_version < "3.12"
 pygments==2.15.1 ; python_version >= "3.7" and python_version < "3.12"
-pyjwt[crypto]==2.7.0 ; python_version >= "3.7" and python_version < "3.12"
+pyjwt[crypto]==2.8.0 ; python_version >= "3.7" and python_version < "3.12"
 pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12"
 pyproject-hooks==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -111,7 +111,7 @@ python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12"
 python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.12"
 pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12"
 pywin32-ctypes==0.2.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "win32"
-pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.12"
+pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
 rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
 readme-renderer==37.3 ; python_version >= "3.7" and python_version < "3.12"
 requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -153,7 +153,7 @@ tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12"
 twill==3.1 ; python_version >= "3.7" and python_version < "3.12"
 twine==4.0.2 ; python_version >= "3.7" and python_version < "3.12"
 typed-ast==1.5.5 ; python_version < "3.8" and implementation_name == "cpython" and python_version >= "3.7"
-types-pyyaml==6.0.12.10 ; python_version >= "3.7" and python_version < "3.12"
+types-pyyaml==6.0.12.11 ; python_version >= "3.7" and python_version < "3.12"
 typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12"
 urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12"
 urllib3[socks]==1.26.16 ; python_version >= "3.7" and python_version < "3.12"

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

@@ -5,6 +5,6 @@ importlib-metadata==4.2.0
 mccabe==0.7.0
 pycodestyle==2.9.1
 pyflakes==2.5.0
-ruff==0.0.278
+ruff==0.0.279
 typing_extensions==4.7.1
 zipp==3.15.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -4,7 +4,7 @@ a2wsgi==1.7.0 ; python_version >= "3.7" and python_version < "3.12"
 adal==1.2.7 ; python_version >= "3.7" and python_version < "3.12"
 aiobotocore==2.4.2 ; python_version >= "3.7" and python_version < "3.12"
 aiofiles==23.1.0 ; python_version >= "3.7" and python_version < "3.12"
-aiohttp==3.8.4 ; python_version >= "3.7" and python_version < "3.12"
+aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12"
 aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
 aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 alembic==1.11.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -42,7 +42,7 @@ circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.5 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.6 ; python_version >= "3.7" and python_version < "3.12"
 cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
 cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
@@ -52,7 +52,7 @@ cryptography==41.0.2 ; python_version >= "3.7" and python_version < "3.12"
 cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12"
 cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12"
 cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12"
-cython==0.29.36 ; python_version >= "3.7" and python_version < "3.12"
+cython==3.0.0 ; python_version >= "3.7" and python_version < "3.12"
 decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
 defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -75,7 +75,7 @@ galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.1
 galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
 gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "win32" or platform_machine == "WIN32" or platform_machine == "AMD64" or platform_machine == "amd64" or platform_machine == "x86_64" or platform_machine == "ppc64le" or platform_machine == "aarch64") and python_version < "3.12"
-gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.12"
+gunicorn==21.2.0 ; python_version >= "3.7" and python_version < "3.12"
 gxformat2==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
 h5grove==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -123,7 +123,7 @@ pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9
 prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12"
 prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12"
 psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12"
-pulsar-galaxy-lib==0.15.2 ; python_version >= "3.7" and python_version < "3.12"
+pulsar-galaxy-lib==0.15.3 ; python_version >= "3.7" and python_version < "3.12"
 pyasn1==0.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
 pycryptodome==3.18.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -134,8 +134,8 @@ pydot==1.4.2 ; python_version >= "3.7" and python_version < "3.12"
 pyeventsystem==0.1.0 ; python_version >= "3.7" and python_version < "3.12"
 pyfaidx==0.7.2.1 ; python_version >= "3.7" and python_version < "3.12"
 pygments==2.15.1 ; python_version >= "3.7" and python_version < "3.12"
-pyjwt==2.7.0 ; python_version >= "3.7" and python_version < "3.12"
-pyjwt[crypto]==2.7.0 ; python_version >= "3.7" and python_version < "3.12"
+pyjwt==2.8.0 ; python_version >= "3.7" and python_version < "3.12"
+pyjwt[crypto]==2.8.0 ; python_version >= "3.7" and python_version < "3.12"
 pykwalify==1.8.0 ; python_version >= "3.7" and python_version < "3.12"
 pylibmagic==0.4.0 ; python_version >= "3.7" and python_version < "3.12"
 pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -150,7 +150,7 @@ python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12"
 python-multipart==0.0.6 ; python_version >= "3.7" and python_version < "3.12"
 python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12"
-pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.12"
+pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"
 pyzmq==25.1.0 ; python_version >= "3.7" and python_version < "3.12"
 rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
 refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.12"

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

@@ -6,17 +6,17 @@ pycparser==2.21
 pydantic==1.10.11
 tomli==2.0.1
 typed-ast==1.5.5
-types-bleach==6.0.0.3
-types-boto==2.49.18.8
+types-bleach==6.0.0.4
+types-boto==2.49.18.9
 types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
 types-docutils==0.20.0.1
-types-Markdown==3.4.2.9
-types-paramiko==3.2.0.0
+types-Markdown==3.4.2.10
+types-paramiko==3.2.0.1
 types-pkg-resources==0.1.3
-types-python-dateutil==2.8.19.13
-types-PyYAML==6.0.12.10
-types-requests==2.31.0.1
-types-six==1.16.21.8
-types-urllib3==1.26.25.13
+types-python-dateutil==2.8.19.14
+types-PyYAML==6.0.12.11
+types-requests==2.31.0.2
+types-six==1.16.21.9
+types-urllib3==1.26.25.14
 typing_extensions==4.7.1

lib/galaxy/model/__init__.py

@@ -616,15 +616,13 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
                 label_usage=label_usage
             )
         else:
-            statement = """
+            statement = f"""
 INSERT INTO user_quota_source_usage(user_id, quota_source_label, disk_usage)
 VALUES(:id, :label, ({label_usage}))
 ON CONFLICT
 ON constraint uqsu_unique_label_per_user
 DO UPDATE SET disk_usage = excluded.disk_usage
-""".format(
-                label_usage=label_usage
-            )
+"""
         statements.append(
             (statement, {"id": user_id, "label": quota_source_label, "include_object_store_ids": object_store_ids})
         )
@@ -1399,12 +1397,12 @@ def finished(self):
         ]
 
     def io_dicts(self, exclude_implicit_outputs=False) -> IoDicts:
-        inp_data: Dict[str, Optional["DatasetInstance"]] = {da.name: da.dataset for da in self.input_datasets}
-        out_data: Dict[str, "DatasetInstance"] = {da.name: da.dataset for da in self.output_datasets}
+        inp_data: Dict[str, Optional[DatasetInstance]] = {da.name: da.dataset for da in self.input_datasets}
+        out_data: Dict[str, DatasetInstance] = {da.name: da.dataset for da in self.output_datasets}
         inp_data.update([(da.name, da.dataset) for da in self.input_library_datasets])
         out_data.update([(da.name, da.dataset) for da in self.output_library_datasets])
 
-        out_collections: Dict[str, Union["DatasetCollectionInstance", "DatasetCollection"]]
+        out_collections: Dict[str, Union[DatasetCollectionInstance, DatasetCollection]]
         if not exclude_implicit_outputs:
             out_collections = {
                 obj.name: obj.dataset_collection_instance for obj in self.output_dataset_collection_instances
@@ -8660,7 +8658,7 @@ def preferred_object_stores(self) -> WorkflowInvocationStepObjectStores:
         preferred_object_store_id = None
         preferred_outputs_object_store_id = None
         preferred_intermediate_object_store_id = None
-        step_effective_outputs: Optional[List["EffectiveOutput"]] = None
+        step_effective_outputs: Optional[List[EffectiveOutput]] = None
 
         workflow_invocation = self.workflow_invocation
         for input_parameter in workflow_invocation.input_parameters:

lib/galaxy/model/store/__init__.py

@@ -1337,7 +1337,7 @@ def __init__(self) -> None:
         self.hdca_copied_from_sinks = {}
         self.jobs_by_key = {}
         self.invocations_by_key: Dict[str, model.WorkflowInvocation] = {}
-        self.implicit_collection_jobs_by_key: Dict[str, "ImplicitCollectionJobs"] = {}
+        self.implicit_collection_jobs_by_key: Dict[str, ImplicitCollectionJobs] = {}
         self.workflows_by_key: Dict[str, model.Workflow] = {}
         self.requires_hid = []
 

lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py

@@ -74,7 +74,7 @@ def install_data_managers(
         repository,
         repository_tools_tups,
     ) -> List["DataManager"]:
-        rval: List["DataManager"] = []
+        rval: List[DataManager] = []
         if "data_manager" in metadata_dict:
             tpm = tool_panel_manager.ToolPanelManager(self.app)
             repository_tools_by_guid = {}

lib/galaxy/tool_util/deps/__init__.py

@@ -145,7 +145,7 @@ def __init__(
             plugin_source = self.__build_dependency_resolvers_plugin_source(conf_file)
         self.dependency_resolvers = self.__parse_resolver_conf_plugins(plugin_source)
         self._enabled_container_types: List[str] = []
-        self._destination_for_container_type: Dict[str, Dict[str, "JobDestination"]] = {}
+        self._destination_for_container_type: Dict[str, Dict[str, JobDestination]] = {}
 
     def set_enabled_container_types(self, container_types_to_destinations):
         """Set the union of all enabled container types."""

lib/galaxy/tool_util/deps/containers.py

@@ -66,7 +66,7 @@ def __init__(self, app_info: "AppInfo", mulled_resolution_cache: Optional["Cache
         self.app_info = app_info
         self.mulled_resolution_cache = mulled_resolution_cache
         self.default_container_registry = ContainerRegistry(app_info, mulled_resolution_cache=mulled_resolution_cache)
-        self.destination_container_registeries: Dict[str, "ContainerRegistry"] = {}
+        self.destination_container_registeries: Dict[str, ContainerRegistry] = {}
 
     def _enabled_container_types(self, destination_info: Dict[str, Any]) -> List[str]:
         return [t for t in ALL_CONTAINER_TYPES if self.__container_type_enabled(t, destination_info)]
@@ -317,7 +317,7 @@ def _parse_resolver_conf(self, plugin_source: "PluginConfigSource") -> List["Con
         return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds)
 
     def __default_container_resolvers(self) -> List["ContainerResolver"]:
-        default_resolvers: List["ContainerResolver"] = [
+        default_resolvers: List[ContainerResolver] = [
             ExplicitContainerResolver(self.app_info),
             ExplicitSingularityContainerResolver(self.app_info),
         ]

lib/galaxy/tools/actions/__init__.py

@@ -457,7 +457,7 @@ def execute(
         # wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed
         wrapped_params = self._wrapped_params(trans, tool, incoming, inp_data)
 
-        out_data: Dict[str, "DatasetInstance"] = {}
+        out_data: Dict[str, DatasetInstance] = {}
         input_collections = LegacyUnprefixedDict({k: v[0][0] for k, v in inp_dataset_collections.items()})
         input_collections._legacy_mapping = inp_dataset_collections._legacy_mapping
         output_collections = OutputCollections(

lib/galaxy/tools/parameters/grouping.py

@@ -723,7 +723,7 @@ class Conditional(Group):
 
     def __init__(self):
         Group.__init__(self)
-        self.test_param: Optional["ToolParameter"] = None
+        self.test_param: Optional[ToolParameter] = None
         self.cases = []
         self.value_ref = None
         self.value_ref_in_group = True  # When our test_param is not part of the conditional Group, this is False

lib/galaxy/tools/wrappers.py

@@ -301,7 +301,7 @@ def __init__(
             compute_environment: Optional["ComputeEnvironment"] = None,
         ) -> None:
             self.dataset = dataset
-            self.metadata: "MetadataCollection" = dataset.metadata
+            self.metadata: MetadataCollection = dataset.metadata
             self.compute_environment = compute_environment
 
         def __getattr__(self, name: str) -> Any:

lib/galaxy/webapps/galaxy/services/dataset_collections.py

@@ -190,7 +190,7 @@ def show(
         """
         Returns information about a particular dataset collection.
         """
-        dataset_collection_instance: Union["HistoryDatasetCollectionAssociation", "LibraryDatasetCollectionAssociation"]
+        dataset_collection_instance: Union[HistoryDatasetCollectionAssociation, LibraryDatasetCollectionAssociation]
         if instance_type == "history":
             dataset_collection_instance = self.collection_manager.get_dataset_collection_instance(trans, "history", id)
             parent = dataset_collection_instance.history
@@ -249,7 +249,7 @@ def contents(
             raise exceptions.RequestParameterInvalidException(
                 "Parameter instance_type not being 'history' is not yet implemented."
             )
-        hdca: "HistoryDatasetCollectionAssociation" = self.collection_manager.get_dataset_collection_instance(
+        hdca: HistoryDatasetCollectionAssociation = self.collection_manager.get_dataset_collection_instance(
             trans, "history", hdca_id, check_ownership=True
         )
 

test/integration/test_page_revision_json_encoding.py

@@ -76,10 +76,8 @@ def test_page_encoding_markdown(self, history_id: str):
             not in content
         ), content
         assert (
-            """```galaxy
-history_dataset_display(history_dataset_id={})
-```""".format(
-                dataset_id
-            )
+            f"""```galaxy
+history_dataset_display(history_dataset_id={dataset_id})
+```"""
             in content
         ), content

test/unit/app/tools/test_wrappers.py

@@ -42,13 +42,11 @@ def selectwrapper(tool, value, multiple=False, optional=False):
     optional = 'optional="true"' if optional else ""
     multiple = 'multiple="true"' if multiple else ""
     xml = XML(
-        """<param name="blah" type="select" {} {}>
+        f"""<param name="blah" type="select" {multiple} {optional}>
         <option value="x">I am X</option>
         <option value="y" selected="true">I am Y</option>
         <option value="z">I am Z</option>
-    </param>""".format(
-            multiple, optional
-        )
+    </param>"""
     )
     parameter = SelectToolParameter(tool, xml)
     return SelectToolParameterWrapper(parameter, value)