[technical debt]: updated black to 26.3.1 and reran pre-commit

.pre-commit-config.yaml

@@ -30,7 +30,7 @@ repos:
         name: isort (python)
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 26.3.1
     hooks:
       - id: black
         language_version: python3

docs/scripts/object_orientated_programming_poc/synapse_project.py

@@ -10,6 +10,7 @@
 
 All steps also include setting a number of annotations for the objects.
 """
+
 import os
 import uuid
 from datetime import datetime, timedelta, timezone

docs/tutorials/python/tutorial_scripts/upload_data_in_bulk.py

@@ -66,19 +66,19 @@
 
 # After finding the row we want to update let's go ahead and add a relationship to
 # another file in our manifest. This allows us to say "We used 'this' file in some way".
-df.loc[
-    row_index, "used"
-] = f"{DIRECTORY_FOR_MY_PROJECT}/single_cell_RNAseq_batch_1/SRR12345678_R1.fastq.gz"
+df.loc[row_index, "used"] = (
+    f"{DIRECTORY_FOR_MY_PROJECT}/single_cell_RNAseq_batch_1/SRR12345678_R1.fastq.gz"
+)
 
 # Let's also link to the pipeline that we ran in order to produce these results. In a
 # real scenario you may want to link to a specific run of the tool where the results
 # were produced.
 df.loc[row_index, "executed"] = "https://nf-co.re/rnaseq/3.14.0"
 
 # Let's also add a description for this Activity/Provenance
-df.loc[
-    row_index, "activityDescription"
-] = "Experiment results created as a result of the linked data while running the pipeline."
+df.loc[row_index, "activityDescription"] = (
+    "Experiment results created as a result of the linked data while running the pipeline."
+)
 
 # Write the DataFrame back to the manifest file
 df.to_csv(PATH_TO_MANIFEST_FILE, sep="\t", index=False)

docs/tutorials/python/tutorial_scripts/wiki.py

@@ -12,6 +12,7 @@
 7. Delete wiki pages
 
 """
+
 import os
 
 from synapseclient import Synapse

docs/tutorials/python/wiki.md

@@ -31,7 +31,7 @@ In this tutorial you will:
 ## 1. Create a Wiki page
 ### Initial setup
 ```python
-{!docs/tutorials/python/tutorial_scripts/wiki.py!lines=15-31}
+{!docs/tutorials/python/tutorial_scripts/wiki.py!lines=16-31}
 ```
 A Wiki page requires an owner object, a title, and markdown. Here is an example to create a new root Wiki page for your project with plain text markdown:
 ```python

synapseclient/activity.py

@@ -223,9 +223,9 @@ def used(
 
             resource = target
             if "concreteType" not in resource:
-                resource[
-                    "concreteType"
-                ] = "org.sagebionetworks.repo.model.provenance.UsedEntity"
+                resource["concreteType"] = (
+                    "org.sagebionetworks.repo.model.provenance.UsedEntity"
+                )
 
         # -- Used URL
         elif is_used_url(target):
@@ -234,9 +234,9 @@ def used(
 
             resource = target
             if "concreteType" not in resource:
-                resource[
-                    "concreteType"
-                ] = "org.sagebionetworks.repo.model.provenance.UsedURL"
+                resource["concreteType"] = (
+                    "org.sagebionetworks.repo.model.provenance.UsedURL"
+                )
 
         # -- Synapse Entity
         elif is_synapse_entity(target):

synapseclient/api/docker_commit_services.py

@@ -1,6 +1,7 @@
 """This module is responsible for exposing the services defined at:
 <https://rest-docs.synapse.org/rest/#org.sagebionetworks.repo.web.controller.DockerCommitController>
 """
+
 from typing import TYPE_CHECKING, Optional
 
 if TYPE_CHECKING:

synapseclient/api/file_services.py

@@ -269,7 +269,7 @@ async def post_external_filehandle(
         "contentSize": file_size,
     }
     if mimetype is None:
-        (mimetype, _) = mimetypes.guess_type(external_url, strict=False)
+        mimetype, _ = mimetypes.guess_type(external_url, strict=False)
     if mimetype is not None:
         file_handle["contentType"] = mimetype
     return await client.rest_post_async(

synapseclient/client.py

@@ -2,6 +2,7 @@
 The `Synapse` object encapsulates a connection to the Synapse service and is used for building projects, uploading and
 retrieving data, and recording provenance of data analysis.
 """
+
 import asyncio
 import collections
 import collections.abc
@@ -607,9 +608,7 @@ def _init_logger(self):
         logger_name = (
             SILENT_LOGGER_NAME
             if self.silent
-            else DEBUG_LOGGER_NAME
-            if self.debug
-            else DEFAULT_LOGGER_NAME
+            else DEBUG_LOGGER_NAME if self.debug else DEFAULT_LOGGER_NAME
         )
         self.logger = logging.getLogger(logger_name)
         logging.getLogger("py.warnings").handlers = self.logger.handlers
@@ -2672,9 +2671,11 @@ async def main():
                 fileHandle = await upload_file_handle_async(
                     self,
                     parent_id_for_upload,
-                    local_state["path"]
-                    if (synapseStore or local_state_fh.get("externalURL") is None)
-                    else local_state_fh.get("externalURL"),
+                    (
+                        local_state["path"]
+                        if (synapseStore or local_state_fh.get("externalURL") is None)
+                        else local_state_fh.get("externalURL")
+                    ),
                     synapse_store=synapseStore,
                     md5=local_file_md5_hex or local_state_fh.get("contentMd5"),
                     file_size=local_state_fh.get("contentSize"),
@@ -3243,9 +3244,10 @@ def get_download_list(self, downloadLocation: str = None) -> str:
         dl_list_path = self.get_download_list_manifest()
         downloaded_files = []
         new_manifest_path = f"manifest_{time.time_ns()}.csv"
-        with open(dl_list_path) as manifest_f, open(
-            new_manifest_path, "w"
-        ) as write_obj:
+        with (
+            open(dl_list_path) as manifest_f,
+            open(new_manifest_path, "w") as write_obj,
+        ):
             reader = csv.DictReader(manifest_f)
             columns = reader.fieldnames
             columns.extend(["path", "error"])
@@ -4925,9 +4927,11 @@ def _convertProvenanceList(self, usedList: list, limitSearch: str = None) -> lis
         if usedList is None:
             return None
         usedList = [
-            self.get(target, limitSearch=limitSearch)
-            if (os.path.isfile(target) if isinstance(target, str) else False)
-            else target
+            (
+                self.get(target, limitSearch=limitSearch)
+                if (os.path.isfile(target) if isinstance(target, str) else False)
+                else target
+            )
             for target in usedList
         ]
         return usedList
@@ -5468,7 +5472,7 @@ def _createExternalFileHandle(
             "contentSize": fileSize,
         }
         if mimetype is None:
-            (mimetype, enc) = mimetypes.guess_type(externalURL, strict=False)
+            mimetype, enc = mimetypes.guess_type(externalURL, strict=False)
         if mimetype is not None:
             fileHandle["contentType"] = mimetype
         return self.restPOST(
@@ -5893,16 +5897,16 @@ async def create_s3_storage_location_async(
         }
 
         if bucket_name:
-            storage_location_kwargs[
-                "concreteType"
-            ] = concrete_types.EXTERNAL_S3_STORAGE_LOCATION_SETTING
+            storage_location_kwargs["concreteType"] = (
+                concrete_types.EXTERNAL_S3_STORAGE_LOCATION_SETTING
+            )
             storage_location_kwargs["bucket"] = bucket_name
             if base_key:
                 storage_location_kwargs["baseKey"] = base_key
         else:
-            storage_location_kwargs[
-                "concreteType"
-            ] = concrete_types.SYNAPSE_S3_STORAGE_LOCATION_SETTING
+            storage_location_kwargs["concreteType"] = (
+                concrete_types.SYNAPSE_S3_STORAGE_LOCATION_SETTING
+            )
 
         storage_location_setting = self.restPOST(
             "/storageLocation", json.dumps(storage_location_kwargs)

synapseclient/core/download/download_functions.py

@@ -479,13 +479,13 @@ async def download_by_file_handle(
 
     while retries > 0:
         try:
-            file_handle_result: Dict[
-                str, str
-            ] = await get_file_handle_for_download_async(
-                file_handle_id=file_handle_id,
-                synapse_id=synapse_id,
-                entity_type=entity_type,
-                synapse_client=syn,
+            file_handle_result: Dict[str, str] = (
+                await get_file_handle_for_download_async(
+                    file_handle_id=file_handle_id,
+                    synapse_id=synapse_id,
+                    entity_type=entity_type,
+                    synapse_client=syn,
+                )
             )
             file_handle = file_handle_result["fileHandle"]
             concrete_type = file_handle["concreteType"]

synapseclient/core/dozer.py

@@ -5,6 +5,7 @@
 
 sleep while checking registered _listeners
 """
+
 import time
 
 from opentelemetry import trace

synapseclient/core/models/custom_json.py

@@ -1,6 +1,7 @@
 """
 When imported, monkey-patches the 'json' module's encoder with a custom json encoding function.
 """
+
 import datetime
 import json
 

synapseclient/core/otel_config.py

@@ -1,4 +1,5 @@
 """OpenTelemetry configuration for Synapse Python Client."""
+
 import os
 import sys
 from typing import Any, Dict, List, Optional

synapseclient/core/transfer_bar.py

@@ -1,4 +1,5 @@
 """Logic used to handle progress bars for file uploads and downloads."""
+
 try:
     import threading as _threading
 except ImportError:

synapseclient/core/utils.py

@@ -278,7 +278,7 @@ def id_of(obj: typing.Union[str, collections.abc.Mapping, numbers.Number]) -> st
 
 
 def validate_submission_id(
-    submission_id: typing.Union[str, int, collections.abc.Mapping]
+    submission_id: typing.Union[str, int, collections.abc.Mapping],
 ) -> str:
     """
     Ensures that a given submission ID is either an integer or a string that
@@ -462,7 +462,7 @@ def is_synapse_id_str(obj: str) -> typing.Union[str, None]:
 
 
 def get_synid_and_version(
-    obj: typing.Union[str, collections.abc.Mapping]
+    obj: typing.Union[str, collections.abc.Mapping],
 ) -> typing.Tuple[str, typing.Union[int, None]]:
     """Extract the Synapse ID and version number from input entity
 
@@ -698,7 +698,7 @@ def to_unix_epoch_time(dt: typing.Union[datetime.date, datetime.datetime, str])
 
 
 def to_unix_epoch_time_secs(
-    dt: typing.Union[datetime.date, datetime.datetime]
+    dt: typing.Union[datetime.date, datetime.datetime],
 ) -> float:
     """
     Convert either [datetime.date or datetime.datetime objects](http://docs.python.org/2/library/datetime.html) to UNIX time.

synapseclient/extensions/curator/record_based_metadata_task.py

@@ -5,6 +5,7 @@
 This module provides library functions for creating record-based metadata curation tasks
 in Synapse, including RecordSet creation, CurationTask setup, and Grid view initialization.
 """
+
 import tempfile
 from typing import Any, Dict, List, Optional, Tuple, Union
 

synapseclient/extensions/curator/schema_generation.py

@@ -343,18 +343,18 @@ def find_and_convert_ints(
     if (
         dataframe.size < large_manifest_cutoff_size
     ):  # If small manifest, iterate as normal for improved performance
-        ints = dataframe.map(  # type:ignore
+        ints = dataframe.map(  # type: ignore
             lambda cell: convert_ints(cell), na_action="ignore"
         ).fillna(False)
 
     else:  # parallelize iterations for large manifests
         pandarallel.initialize(verbose=1)
-        ints = dataframe.parallel_applymap(  # type:ignore
+        ints = dataframe.parallel_applymap(  # type: ignore
             lambda cell: convert_ints(cell), na_action="ignore"
         ).fillna(False)
 
     # Identify cells converted to integers
-    is_int = ints.map(is_integer)  # type:ignore
+    is_int = ints.map(is_integer)  # type: ignore
 
     assert isinstance(ints, DataFrame)
     assert isinstance(is_int, DataFrame)
@@ -2049,6 +2049,7 @@ class PropertyTemplate:
 @dataclass
 class ClassTemplate:
     "Class Template"
+
     magic_id: str = field(default="", metadata=config(field_name="@id"))
     magic_type: str = field(default="rdfs:Class", metadata=config(field_name="@type"))
     magic_comment: str = field(default="", metadata=config(field_name="rdfs:comment"))
@@ -3876,7 +3877,7 @@ def match_node_names_with_reserved_names(
 
 
 def create_reserve_name_error_messages(
-    reserved_names_found: list[Tuple[str, str]]
+    reserved_names_found: list[Tuple[str, str]],
 ) -> list[str]:
     """Creates the error messages when a reserved name is used
 
@@ -3943,7 +3944,7 @@ def get_missing_fields_from(
 
 
 def create_missing_fields_error_messages(
-    missing_fields: list[Tuple[str, str]]
+    missing_fields: list[Tuple[str, str]],
 ) -> list[str]:
     """Creates the error message for when a node is missing a required field
 
@@ -4119,7 +4120,7 @@ def export_schema(schema: dict, file_path: str, logger: Logger) -> None:
 
 
 def parsed_model_as_dataframe(
-    parsed_model: dict[str, dict[str, Any]]
+    parsed_model: dict[str, dict[str, Any]],
 ) -> DATA_FRAME_TYPE:
     """Convert parsed model dictionary to an unpacked pandas DataFrame.
     Args:
@@ -5168,7 +5169,7 @@ def add_conditional_dependency(
 
     @staticmethod
     def _convert_conditional_properties_to_all_of(
-        conditional_dependencies: dict[tuple[str, str], list[str]]
+        conditional_dependencies: dict[tuple[str, str], list[str]],
     ) -> list[AllOf]:
         """
         Converts the conditional dependencies dict to a list of JSON Schema allOf conditions

synapseclient/models/agent.py

@@ -199,9 +199,9 @@ class AgentSession(AgentSessionSynchronousProtocol):
     """The unique ID of the agent session.
     Can only be used by the user that created it."""
 
-    access_level: Optional[
-        AgentSessionAccessLevel
-    ] = AgentSessionAccessLevel.PUBLICLY_ACCESSIBLE
+    access_level: Optional[AgentSessionAccessLevel] = (
+        AgentSessionAccessLevel.PUBLICLY_ACCESSIBLE
+    )
     """The access level of the agent session.
         One of PUBLICLY_ACCESSIBLE, READ_YOUR_PRIVATE_DATA, or
         WRITE_YOUR_PRIVATE_DATA. Defaults to PUBLICLY_ACCESSIBLE.

synapseclient/models/annotations.py

@@ -93,9 +93,7 @@ async def store_async(
         return self
 
     @classmethod
-    def from_dict(
-        cls, synapse_annotations: dict
-    ) -> Union[
+    def from_dict(cls, synapse_annotations: dict) -> Union[
         Dict[
             str,
             Union[

synapseclient/models/curation.py

@@ -132,7 +132,7 @@ def to_synapse_request(self) -> Dict[str, Any]:
 
 
 def _create_task_properties_from_dict(
-    properties_dict: Dict[str, Any]
+    properties_dict: Dict[str, Any],
 ) -> Union[FileBasedMetadataTaskProperties, RecordBasedMetadataTaskProperties]:
     """
     Factory method to create the appropriate FileBasedMetadataTaskProperties/RecordBasedMetadataTaskProperties