Linting fixes

examples/alcf_compute_endpoint_test.py

@@ -34,7 +34,7 @@
     token_response = auth_client.oauth2_client_credentials_tokens(requested_scopes=SCOPES)
     compute_tokens = token_response.by_resource_server['compute.api.globus.org']
     access_token = compute_tokens['access_token']
-    
+
     # Initialize the ComputeClient with the token
     compute_client = ComputeClient(authorizer=globus_sdk.AccessTokenAuthorizer(access_token))
 

examples/test_cc_auth.py

@@ -10,11 +10,8 @@
 # Set the client ID and fetch client secret from environment
 CLIENT_ID = os.getenv('GLOBUS_CLIENT_ID')
 CLIENT_SECRET = os.getenv('GLOBUS_CLIENT_SECRET')
-
-# SCOPES = ['urn:globus:auth:scope:transfer.api.globus.org:all[*https://auth.globus.org/scopes/55c3adf6-31f1-4647-9a38-52591642f7e7/data_access]']
 SCOPES = "urn:globus:auth:scope:transfer.api.globus.org:all"
-# ENDPOINT_ID = "d40248e6-d874-4f7b-badd-2c06c16f1a58" # NERSC DTN alsdev Collab
-ENDPOINT_ID = "55c3adf6-31f1-4647-9a38-52591642f7e7" #ALCF Iribeta CGS
+ENDPOINT_ID = "UUID"
 
 
 def initialize_transfer_client():
@@ -62,6 +59,7 @@ def list_directory(transfer_client, endpoint_id, path):
         elapsed_time = time.time() - start_time
         logger.info(f"list_directory task took {elapsed_time:.2f} seconds")
 
+
 @task
 def create_directory(transfer_client, endpoint_id, base_path, directory_name):
     logger = get_run_logger()
@@ -72,7 +70,7 @@ def create_directory(transfer_client, endpoint_id, base_path, directory_name):
             base_path += '/'
         if base_path.startswith('/'):
             base_path = base_path.lstrip('/')
-        
+
         full_path = base_path + directory_name
 
         # Validate the path
@@ -89,7 +87,7 @@ def create_directory(transfer_client, endpoint_id, base_path, directory_name):
         if err.info.consent_required:
             logger.error(f"Got a ConsentRequired error with scopes: {err.info.consent_required.required_scopes}")
         elif err.code == "PermissionDenied":
-            logger.error(f"Permission denied for creating directory {full_path}. Ensure proper permissions are set.")
+            logger.error(f"Permission denied for creating directory {full_path}. Ensure proper permissions.")
         elif err.http_status == 500:
             logger.error(f"Server error when creating directory {full_path} in endpoint {endpoint_id}.")
         else:
@@ -107,7 +105,8 @@ def remove_directory(transfer_client, endpoint_id, path):
         delete_data = globus_sdk.DeleteData(transfer_client, endpoint_id, recursive=True)
         delete_data.add_item(path)
         transfer_result = transfer_client.submit_delete(delete_data)
-        logger.info(f"Successfully submitted request to remove directory {path} in endpoint {endpoint_id}. Task ID: {transfer_result['task_id']}")
+        logger.info(f"Successfully submitted request to remove directory {path} in endpoint {endpoint_id}.")
+        logger.info(f"Task ID: {transfer_result['task_id']}")
     except globus_sdk.GlobusAPIError as err:
         logger.error(f"Error removing directory {path} in endpoint {endpoint_id}: {err.message}")
         if err.info.consent_required:
@@ -134,18 +133,19 @@ def main_flow():
 
     # List the contents of the root directory
     logger = get_run_logger()
-    # logger.info("Listing / directory:")
-    # list_directory(transfer_client, endpoint_id, base_path)
+    logger.info("Listing / directory:")
+    list_directory(transfer_client, endpoint_id, base_path)
 
     # Create a new directory in the root directory
-    # new_directory_name = "test/"
-    # create_directory(transfer_client, endpoint_id, base_path, new_directory_name)
+    new_directory_name = "test/"
+    create_directory(transfer_client, endpoint_id, base_path, new_directory_name)
 
     remove_directory(transfer_client, endpoint_id, "bl832_test/scratch/BLS-00564_dyparkinson/")
 
     # List the contents again to verify the new directory
-    # logger.info(f"\nListing / directory after creating {new_directory_name}:")
-    # list_directory(transfer_client, endpoint_id, base_path+new_directory_name)
+    logger.info(f"\nListing / directory after creating {new_directory_name}:")
+    list_directory(transfer_client, endpoint_id, base_path+new_directory_name)
+
 
 if __name__ == "__main__":
     main_flow()

examples/tiff_to_zarr.py

@@ -2,22 +2,25 @@
 
 import os
 import argparse
-import zarr
 from ngff_zarr import (
     detect_cli_io_backend,
     cli_input_to_ngff_image,
     to_multiscales,
     to_ngff_zarr,
-    Methods,
-    config
+    Methods
 )
 
+
 def parse_arguments():
     parser = argparse.ArgumentParser(description='Convert TIFF files to NGFF Zarr format.')
     parser.add_argument('tiff_directory', type=str, help='Directory containing the TIFF files.')
-    parser.add_argument('--zarr_directory', type=str, default=None, help='Directory to store the Zarr output. Defaults to a new folder in the input directory.')
+    parser.add_argument('--zarr_directory',
+                        type=str,
+                        default=None,
+                        help='Directory to store Zarr output. Default is new folder in input directory.')
     return parser.parse_args()
 
+
 def set_permissions_recursive(path, permissions=0o2775):
     for root, dirs, files in os.walk(path):
         for dir in dirs:
@@ -26,11 +29,12 @@ def set_permissions_recursive(path, permissions=0o2775):
             os.chmod(os.path.join(root, file), permissions)
     os.chmod(path, permissions)  # Also set permissions for the top-level directory
 
+
 def main():
     args = parse_arguments()
 
     tiff_dir = args.tiff_directory
-    zarr_dir = args.zarr_directory 
+    zarr_dir = args.zarr_directory
 
     if not os.path.isdir(tiff_dir):
         raise TypeError("The specified TIFF directory is not a valid directory")
@@ -51,7 +55,6 @@ def main():
     print('Output directory: ' + zarr_dir)
 
     # Build NGFF Zarr directory
-    # config.cache_store = zarr.storage.DirectoryStore("/alsuser/pscratch/zarr-ngff-cache", dimension_separator="/")
     backend = detect_cli_io_backend(file_paths)
     image = cli_input_to_ngff_image(backend, file_paths)
     # The scale and axis units are the same as the one printed in the reconstruction script
@@ -66,4 +69,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    main()

orchestration/_tests/test_globus_flow.py

@@ -1,33 +1,30 @@
-from pydantic import BaseModel, ConfigDict, PydanticDeprecatedSince20
-import warnings
-import pytest
-from unittest.mock import MagicMock, patch
-from typing import List, Optional, Dict, Any
-from uuid import UUID, uuid4
+from globus_sdk import ConfidentialAppAuthClient, TransferClient
+from globus_sdk.authorizers.client_credentials import ClientCredentialsAuthorizer
+from globus_compute_sdk.sdk.client import Client
 from orchestration.flows.bl832.alcf import (
     process_new_832_ALCF_flow
 )
 from orchestration.flows.bl832.config import Config832
-
 from prefect.testing.utilities import prefect_test_harness
 from prefect.blocks.system import JSON, Secret
-
-from orchestration._tests.test_globus import MockTransferClient
-
-from globus_sdk import ConfidentialAppAuthClient, TransferClient
-from globus_sdk.authorizers.client_credentials import ClientCredentialsAuthorizer
-from globus_compute_sdk.sdk.client import Client
+from pydantic import BaseModel, ConfigDict, PydanticDeprecatedSince20
+import pytest
+from typing import List, Optional, Dict, Any
+from unittest.mock import MagicMock, patch
+from uuid import UUID, uuid4
+import warnings
 
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 warnings.filterwarnings("ignore", category=PydanticDeprecatedSince20)
 
+
 @pytest.fixture(autouse=True, scope="session")
 def prefect_test_fixture():
     with prefect_test_harness():
-        globus_client_id = Secret(value =  "test-globus-client-id")
-        globus_client_id.save(name = "globus-client-id")
-        globus_client_secret = Secret(value = "your_globus_client_secret")
-        globus_client_secret.save(name = "globus-client-secret")
+        globus_client_id = Secret(value="test-globus-client-id")
+        globus_client_id.save(name="globus-client-id")
+        globus_client_secret = Secret(value="your_globus_client_secret")
+        globus_client_secret.save(name="globus-client-secret")
         pruning_config = JSON(value={"max_wait_seconds": 600})
         pruning_config.save(name="pruning-config")
         yield
@@ -103,8 +100,10 @@ def __init__(self) -> None:
             "nersc832": MockEndpoint(root_path="mock_nersc832_path", uuid_value=str(uuid4())),
             "nersc_test": MockEndpoint(root_path="mock_nersc_test_path", uuid_value=str(uuid4())),
             "nersc_alsdev": MockEndpoint(root_path="mock_nersc_alsdev_path", uuid_value=str(uuid4())),
-            "nersc832_alsdev_raw": MockEndpoint(root_path="mock_nersc832_alsdev_raw_path", uuid_value=str(uuid4())),
-            "nersc832_alsdev_scratch": MockEndpoint(root_path="mock_nersc832_alsdev_scratch_path", uuid_value=str(uuid4())),
+            "nersc832_alsdev_raw": MockEndpoint(root_path="mock_nersc832_alsdev_raw_path",
+                                                uuid_value=str(uuid4())),
+            "nersc832_alsdev_scratch": MockEndpoint(root_path="mock_nersc832_alsdev_scratch_path",
+                                                    uuid_value=str(uuid4())),
             "alcf832_raw": MockEndpoint(root_path="mock_alcf832_raw_path", uuid_value=str(uuid4())),
             "alcf832_scratch": MockEndpoint(root_path="mock_alcf832_scratch_path", uuid_value=str(uuid4())),
         }
@@ -156,7 +155,7 @@ def get_result(self, task_id):
         # Mock getting the result of a task
         return "mock_result"
 
-# Update your test to include this mocking
+
 @pytest.fixture(autouse=True)
 def mock_globus_compute_client(monkeypatch):
     monkeypatch.setattr(Client, "__init__", MockGlobusComputeClient.__init__)
@@ -172,14 +171,12 @@ class MockFlowsClient:
     def __init__(self):
         self.flows = {}
 
-
     def create_flow(self, request: CreateFlowRequest) -> Dict[str, Any]:
         """Mock method for initializing a new flow with Globus Flows"""
         flow_id = UUID("123e4567-e89b-12d3-a456-426614174000")
         self.flows[flow_id] = request.model_dump()
         return {"flow_id": str(flow_id)}
 
-
     def get_flow(self, flow_id: UUID) -> Dict[str, Any]:
         """Mock method for getting a flow"""
         return self.flows.get(flow_id, {})
@@ -191,14 +188,12 @@ def __init__(self, flow_id: UUID):
         self.flow_id = flow_id
         self.runs = {}
 
-
     def run_flow(self, request: RunFlowRequest) -> Dict[str, Any]:
         """Mock method for running a registered flow function"""
         run_id = UUID("123e4567-e89b-12d3-a456-426614174001")
         self.runs[run_id] = request.model_dump()
         return {"run_id": str(run_id), "status": "SUCCEEDED"}
 
-
     def get_run(self, run_id: UUID) -> Dict[str, Any]:
         """Mock method for getting a run"""
         return self.runs.get(run_id, {})
@@ -266,7 +261,9 @@ def mock_oauth2_client_credentials_tokens(self):
             "expires_in": 3600,
         }
 
-    monkeypatch.setattr(ConfidentialAppAuthClient, "oauth2_client_credentials_tokens", mock_oauth2_client_credentials_tokens)
+    monkeypatch.setattr(ConfidentialAppAuthClient,
+                        "oauth2_client_credentials_tokens",
+                        mock_oauth2_client_credentials_tokens)
 
     def mock_get_new_access_token(self):
         pass