[SYNPY-1798]: updated black to 26.3.1 and reran pre-commit (#1341)

* update black to 26.3.1 and rerun pre-commit

* update the tutorial line

---------

Co-authored-by: Lingling Peng <lpeng@w290.local>
Co-authored-by: Lingling Peng <lpeng@Mac.SageCorpWiFi>

Author: 3 people

.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

Pipfile.lock

@@ -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/scripts/object_orientated_programming_poc/synapse_project.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/upload_data_in_bulk.py

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

docs/tutorials/python/tutorial_scripts/wiki.py

@@ -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

docs/tutorials/python/wiki.md

@@ -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/activity.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/docker_commit_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/api/file_services.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)