Update Python dependencies

lib/galaxy/app.py

@@ -541,8 +541,8 @@ def __init__(self, configure_logging=True, use_converters=True, use_display_appl
         self.job_manager = self._register_singleton(JobManager)
 
         self.task_manager = self._register_abstract_singleton(
-            AsyncTasksManager, CeleryAsyncTasksManager  # type: ignore[type-abstract]
-        )  # Ignored because of https://github.com/python/mypy/issues/4717
+            AsyncTasksManager, CeleryAsyncTasksManager  # type: ignore[type-abstract]  # https://github.com/python/mypy/issues/4717
+        )
 
         # ConfiguredFileSources
         self.file_sources = self._register_singleton(

lib/galaxy/datatypes/binary.py

@@ -170,7 +170,7 @@ class Cel(Binary):
     """
 
     # cel 3 is a text format
-    is_binary = "maybe"  # type: ignore[assignment]  # https://github.com/python/mypy/issues/8796
+    is_binary = "maybe"
     file_ext = "cel"
     edam_format = "format_1638"
     edam_data = "data_3110"
@@ -243,7 +243,7 @@ class MashSketch(Binary):
 
     file_ext = "msh"
     # example data is actually text, maybe text would be a better base
-    is_binary = "maybe"  # type: ignore[assignment]  # https://github.com/python/mypy/issues/8796
+    is_binary = "maybe"
 
 
 class CompressedArchive(Binary):
@@ -254,7 +254,7 @@ class CompressedArchive(Binary):
 
     file_ext = "compressed_archive"
     compressed = True
-    is_binary = "maybe"  # type: ignore[assignment]  # https://github.com/python/mypy/issues/8796
+    is_binary = "maybe"
 
     def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
         if not dataset.dataset.purged:

lib/galaxy/datatypes/constructive_solid_geometry.py

@@ -745,7 +745,7 @@ class GmshMsh(Binary):
     """Gmsh Mesh File"""
 
     file_ext = "gmsh.msh"
-    is_binary = "maybe"  # type: ignore[assignment]  # https://github.com/python/mypy/issues/8796
+    is_binary = "maybe"
     MetadataElement(name="version", default=None, desc="version", readonly=True, visible=True)
     MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True)
 

lib/galaxy/dependencies/dev-requirements.txt

@@ -23,7 +23,7 @@ click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.12"
 click==8.1.3 ; python_version >= "3.7" and python_version < "3.12"
 codespell==2.2.4 ; 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 python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
-coverage[toml]==7.2.2 ; python_version >= "3.7" and python_version < "3.12"
+coverage[toml]==7.2.3 ; python_version >= "3.7" and python_version < "3.12"
 cryptography==40.0.1 ; python_version >= "3.7" and python_version < "3.12"
 cwltest==2.3.20230108193615 ; python_version >= "3.7" and python_version < "3.12"
 cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -68,7 +68,7 @@ numpy==1.24.2 ; python_version >= "3.8" and python_version < "3.12"
 outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==21.3 ; python_version >= "3.7" and python_version < "3.12"
 pathspec==0.11.1 ; python_version >= "3.7" and python_version < "3.12"
-pillow==9.4.0 ; 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"
 platformdirs==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 pluggy==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -95,8 +95,8 @@ pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12"
 pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
 pytest==7.2.2 ; python_version >= "3.7" and python_version < "3.12"
 python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12"
-python-irodsclient==1.1.6 ; python_version >= "3.7" and python_version < "3.12"
-pytz==2023.2 ; python_version >= "3.7" and python_version < "3.12"
+python-irodsclient==1.1.7 ; 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"
 rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
 requests==2.28.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -108,8 +108,8 @@ schema-salad==8.4.20230213094415 ; python_version >= "3.7" and python_version <
 scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.12"
 selenium==4.8.3 ; python_version >= "3.7" and python_version < "3.12"
-seletools==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
-setuptools==67.6.0 ; python_version >= "3.7" and python_version < "3.12"
+seletools==1.4.0 ; python_version >= "3.7" and python_version < "3.12"
+setuptools==67.6.1 ; python_version >= "3.7" and python_version < "3.12"
 six==1.16.0 ; python_version >= "3.7" and python_version < "3.12"
 sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
 snowballstemmer==2.2.0 ; 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==0.0.259
+ruff==0.0.261
 typing_extensions==4.5.0
 zipp==3.15.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -8,7 +8,7 @@ aiohttp==3.8.4 ; 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-utils==0.8.1 ; python_version >= "3.7" and python_version < "3.12"
-alembic==1.10.2 ; python_version >= "3.7" and python_version < "3.12"
+alembic==1.10.3 ; python_version >= "3.7" and python_version < "3.12"
 amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12"
 anyio==3.6.2 ; python_version >= "3.7" and python_version < "3.12"
 apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -134,7 +134,7 @@ pyfaidx==0.7.2.1 ; python_version >= "3.7" and python_version < "3.12"
 pygments==2.14.0 ; python_version >= "3.7" and python_version < "3.12"
 pyjwt==2.6.0 ; python_version >= "3.7" and python_version < "3.12"
 pykwalify==1.8.0 ; python_version >= "3.7" and python_version < "3.12"
-pylibmagic==0.2.2 ; python_version >= "3.7" and python_version < "3.12"
+pylibmagic==0.3.0 ; 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"
 pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12"
@@ -146,7 +146,7 @@ python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12"
 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==2023.2 ; 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"
 pyzmq==25.0.2 ; python_version >= "3.7" and python_version < "3.12"
 rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -165,7 +165,7 @@ ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
 s3fs==2023.1.0 ; python_version >= "3.7" and python_version < "3.12"
 schema-salad==8.4.20230213094415 ; python_version >= "3.7" and python_version < "3.12"
 setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.12"
-setuptools==67.6.0 ; python_version >= "3.7" and python_version < "3.12"
+setuptools==67.6.1 ; python_version >= "3.7" and python_version < "3.12"
 shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.12"
 six==1.16.0 ; python_version >= "3.7" and python_version < "3.12"
 sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12"

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

@@ -1,6 +1,6 @@
 cffi==1.15.1
 cryptography==40.0.1
-mypy==1.1.1
+mypy==1.2.0
 mypy-extensions==1.0.0
 pycparser==2.21
 pydantic==1.10.7
@@ -11,12 +11,12 @@ types-boto==2.49.18.7
 types-contextvars==2.4.7.2
 types-dataclasses==0.6.6
 types-docutils==0.19.1.7
-types-Markdown==3.4.2.6
-types-paramiko==3.0.0.5
+types-Markdown==3.4.2.7
+types-paramiko==3.0.0.7
 types-pkg-resources==0.1.3
-types-python-dateutil==2.8.19.11
+types-python-dateutil==2.8.19.12
 types-PyYAML==6.0.12.9
-types-requests==2.28.11.16
-types-six==1.16.21.7
-types-urllib3==1.26.25.9
+types-requests==2.28.11.17
+types-six==1.16.21.8
+types-urllib3==1.26.25.10
 typing_extensions==4.5.0

lib/galaxy/jobs/__init__.py

@@ -1257,7 +1257,7 @@ def get_special():
             self.app.interactivetool_manager.create_interactivetool(job, self.tool, self.interactivetools)
 
         # Ensure galaxy_lib_dir is set in case there are any later chdirs
-        self.galaxy_lib_dir
+        self.galaxy_lib_dir  # noqa: B018
         if self.tool.requires_galaxy_python_environment or self.remote_command_line:
             # These tools (upload, metadata, data_source) may need access to the datatypes registry.
             self.app.datatypes_registry.to_xml_file(os.path.join(self.working_directory, "registry.xml"))
@@ -1387,7 +1387,7 @@ def fail(
         # self.get_destination_configuration() below accesses self.job_destination and will just cause
         # JobMappingException to be raised again.
         try:
-            self.job_destination
+            self.job_destination  # noqa: B018
         except JobMappingException as exc:
             log.debug(
                 "(%s) fail(): Job destination raised JobMappingException('%s'), caching fake '__fail__' "
@@ -2602,7 +2602,7 @@ def prepare(self, compute_environment=None):
             self.extra_filenames.extend(extra_filenames)
 
         # Ensure galaxy_lib_dir is set in case there are any later chdirs
-        self.galaxy_lib_dir
+        self.galaxy_lib_dir  # noqa: B018
 
         # We need command_line persisted to the db in order for Galaxy to re-queue the job
         # if the server was stopped and restarted before the job finished

lib/galaxy/jobs/runners/pbs.py

@@ -104,7 +104,7 @@ def __init__(self, app, nworkers):
 
         # Set the default server during startup
         self.__default_pbs_server = None
-        self.default_pbs_server  # this is a method with a property decorator, so this causes the default server to be set
+        self.default_pbs_server  # noqa: B018 this is a method with a property decorator, so this causes the default server to be set
 
         # Proceed with general initialization
         super().__init__(app, nworkers)

lib/galaxy/managers/tags.py

@@ -13,7 +13,7 @@
 )
 
 taggable_item_names = {item: item for item in ItemTagAssociation.associated_item_names}
-# This Enum is generated dynamically and mypy can not statically infer it's real type
+# This Enum is generated dynamically and mypy can not statically infer its real type,
 # so it should be ignored. See: https://github.com/python/mypy/issues/4865#issuecomment-592560696
 TaggableItemClass = Enum("TaggableItemClass", taggable_item_names)  # type: ignore[misc]
 

lib/galaxy/tools/__init__.py

@@ -1572,8 +1572,8 @@ def parse_input_elem(
                     group_c.test_param.refresh_on_change = True
                     for attr in value_from[1].split("."):
                         temp_value_from = getattr(temp_value_from, attr)
-                    group_c.value_from = temp_value_from  # type: ignore[assignment]
-                    # ^^ due to https://github.com/python/mypy/issues/2427
+                    assert callable(temp_value_from)
+                    group_c.value_from = temp_value_from
                     for case_value, case_inputs in group_c.value_from(context, group_c, self).items():
                         case = ConditionalWhen()
                         case.value = case_value

lib/galaxy/tools/cache.py

@@ -146,7 +146,7 @@ def __init__(self):
     def assert_hashes_initialized(self):
         if not self._hashes_initialized:
             for tool_hash in self._hash_by_tool_paths.values():
-                tool_hash.hash
+                tool_hash.hash  # noqa: B018
             self._hashes_initialized = True
 
     def cleanup(self):
@@ -261,7 +261,7 @@ def __init__(self, path, modtime=None, lazy_hash=False):
         self.modtime = modtime or os.path.getmtime(path)
         self._tool_hash = None
         if not lazy_hash:
-            self.hash
+            self.hash  # noqa: B018
 
     @property
     def hash(self):

lib/galaxy/tools/parameters/dynamic_options.py

@@ -570,7 +570,7 @@ def load_from_parameter(from_parameter, transform_lines=None):
         self._tool_data_table = None
         self.elem = elem
         self.column_elem = elem.find("column")
-        self.tool_data_table  # Need to touch tool data table once to populate self.columns
+        self.tool_data_table  # noqa: B018 Need to touch tool data table once to populate self.columns
 
         # Options are defined by parsing tabular text data from a data file
         # on disk, a dataset, or the value of another parameter

lib/galaxy/webapps/galaxy/api/short_term_storage.py

@@ -19,8 +19,7 @@
 
 @router.cbv
 class FastAPIShortTermStorage:
-    # typing here is not ideal, mypy is the issue xref https://github.com/python/mypy/issues/5374
-    short_term_storage_monitor: ShortTermStorageMonitor = depends(ShortTermStorageMonitor)  # type: ignore[type-abstract]
+    short_term_storage_monitor: ShortTermStorageMonitor = depends(ShortTermStorageMonitor)  # type: ignore[type-abstract]  # https://github.com/python/mypy/issues/4717
 
     @router.get(
         "/api/short_term_storage/{storage_request_id}/ready",

lib/galaxy/webapps/galaxy/api/tours.py

@@ -21,8 +21,7 @@
 
 @router.cbv
 class FastAPITours:
-    # ugh - mypy https://github.com/python/mypy/issues/5374
-    registry: ToursRegistry = depends(ToursRegistry)  # type: ignore[type-abstract]
+    registry: ToursRegistry = depends(ToursRegistry)  # type: ignore[type-abstract]  # https://github.com/python/mypy/issues/4717
 
     @router.get("/api/tours")
     def index(self) -> TourList:

lib/galaxy/webapps/galaxy/services/tools.py

@@ -67,7 +67,7 @@ def create_fetch(
                 with tempfile.NamedTemporaryFile(
                     dir=trans.app.config.new_file_path, prefix="upload_file_data_", delete=False
                 ) as dest:
-                    shutil.copyfileobj(upload_file.file, dest)
+                    shutil.copyfileobj(upload_file.file, dest)  # type: ignore[misc]  # https://github.com/python/mypy/issues/15031
                 upload_file.file.close()
                 files_payload[f"files_{i}|file_data"] = FilesPayload(
                     filename=upload_file.filename, local_filename=dest.name

lib/galaxy/workflow/run_request.py

@@ -502,9 +502,8 @@ def add_parameter(name: str, value: str, type: WorkflowRequestInputParameter.typ
         workflow_invocation.step_states.append(step_state)
 
         if step.type == "subworkflow":
-            step.workflow_outputs
-            assert step.subworkflow
-            subworkflow: Workflow = step.subworkflow
+            subworkflow = step.subworkflow
+            assert subworkflow
             effective_outputs: Optional[List[EffectiveOutput]] = None
             if run_config.preferred_intermediate_object_store_id or run_config.preferred_outputs_object_store_id:
                 step_outputs = step.workflow_outputs

lib/galaxy_test/base/decorators.py

@@ -50,9 +50,7 @@ def using_requirement(tag: KnownRequirementT):
 
 def _attach_requirements(method, tag: KnownRequirementT):
     requirement = f"requires_{tag}"
-    try:
-        method.__required_galaxy_features
-    except AttributeError:
+    if not hasattr(method, "__required_galaxy_features"):
         method.__required_galaxy_features = []
     method.__required_galaxy_features.append(tag)
     getattr(pytest.mark, requirement)(method)

lib/tool_shed/util/repository_content_util.py

@@ -30,7 +30,6 @@ def upload_tar(
         message = "{} Invalid paths were: {}".format(" ".join(check_results.errors), ", ".join(check_results.invalid))
         return False, message, [], "", undesirable_dirs_removed, undesirable_files_removed
     else:
-        repository.hg_repo
         repo_dir = repository.repo_path(trans.app)
         if upload_point is not None:
             full_path = os.path.abspath(os.path.join(repo_dir, upload_point))

scripts/microbes/harvest_bacteria.py

@@ -137,7 +137,7 @@ def scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url):
                     results = None
                     time.sleep(1)  # Throttle Connection
             if results is None:
-                "URL COMPLETELY FAILED TO LOAD:", url
+                print("URL COMPLETELY FAILED TO LOAD:", url)
                 return
 
             # do special processing for each file type:
@@ -246,7 +246,7 @@ def __main__():
         # get ftp contents
         ftp_contents = get_ftp_contents(ftp_url)
         if ftp_contents is None:
-            "FTP COMPLETELY FAILED TO LOAD", "org:", org_num, "ftp:", ftp_url
+            print("FTP COMPLETELY FAILED TO LOAD", "org:", org_num, "ftp:", ftp_url)
         else:
             for refseq in chroms:
                 scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url)

test/unit/app/tools/test_toolbox.py

@@ -384,14 +384,14 @@ def test_writes_integrate_tool_panel(self):
         self._add_config("""<toolbox><tool file="tool.xml" /></toolbox>""")
 
         self.assert_integerated_tool_panel(exists=False)
-        self.toolbox
+        self.toolbox  # noqa: B018
         self.assert_integerated_tool_panel(exists=True)
 
     def test_groups_tools_in_section(self):
         self._init_tool()
         self._setup_two_versions_in_config(section=True)
         self._setup_two_versions()
-        self.toolbox
+        self.toolbox  # noqa: B018
         self.__verify_two_test_tools()
 
         # Assert only newer version of the tool loaded into the panel.
@@ -602,7 +602,7 @@ def __verify_get_tool_for_default_lineage(self):
     def __setup_shed_tool_conf(self):
         self._add_config("""<toolbox tool_path="."></toolbox>""")
 
-        self.toolbox  # create toolbox
+        self.toolbox  # noqa: B018 create toolbox
         assert not self.reindexed
 
         os.remove(self.integrated_tool_panel_path)

test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py

@@ -131,7 +131,6 @@ def test_plugin_load(self):
         assert not vis2.serves_templates
 
         mock_app_dir.remove()
-        template_cache_dir
 
     def test_script_entry(self):
         """"""

test/unit/data/test_dataset_materialization.py

@@ -320,8 +320,8 @@ def _ensure_relations_attached_and_expunge(deferred_hda: HistoryDatasetAssociati
     # make sure everything needed is in session (sources, hashes, and metadata)...
     # point here is exercise deferred_hda.history throws a detached error.
     [s.hashes for s in deferred_hda.dataset.sources]
-    deferred_hda.dataset.hashes
-    deferred_hda._metadata
+    deferred_hda.dataset.hashes  # noqa: B018
+    deferred_hda._metadata  # noqa: B018
     sa_session = fixture_context.sa_session
     sa_session.expunge_all()
 

test/unit/data/test_galaxy_mapping.py

@@ -753,7 +753,7 @@ def test_flush_refreshes(self):
         assert "id" in inspect(galaxy_model_object_new).unloaded
 
         # Verify a targeted flush prevent expiring unrelated objects.
-        galaxy_model_object_new.id
+        galaxy_model_object_new.id  # noqa: B018
         assert "id" not in inspect(galaxy_model_object_new).unloaded
         session.flush(model.GalaxySession())
         assert "id" not in inspect(galaxy_model_object_new).unloaded

test/unit/util/test_unittest.py

@@ -19,8 +19,8 @@ def test_setUp(self):
 
     def test_assertRaises(self):
         with self.assertRaises(ZeroDivisionError):
-            1 / 0
+            1 / 0  # noqa: B018
 
     def test_assertRaisesRegex(self):
         with self.assertRaisesRegex(ZeroDivisionError, "^division .* zero"):
-            1 / 0
+            1 / 0  # noqa: B018

tools/data_source/upload.py

@@ -123,9 +123,7 @@ def add_file(dataset, registry, output_path: str) -> Dict[str, str]:
     # auto_decompress is a request flag that can be swapped off to prevent Galaxy from automatically
     # decompressing archive files before sniffing.
     auto_decompress = dataset.get("auto_decompress", True)
-    try:
-        dataset.file_type
-    except AttributeError:
+    if not hasattr(dataset, "file_type"):
         raise UploadProblemException("Unable to process uploaded file, missing file_type parameter.")
 
     if dataset.type == "url":