Applied recommended changes

Author: tieneupin

src/murfey/cli/spa_ispyb_messages.py

@@ -14,8 +14,7 @@
     DataCollectionGroup,
     ProcessingJob,
 )
-from sqlmodel import Session as MurfeySession
-from sqlmodel import create_engine, select
+from sqlmodel import Session as MurfeySession, create_engine, select
 
 from murfey.client.contexts.spa import _get_xml_list_index
 from murfey.server.feedback import _murfey_id, _register

src/murfey/cli/transfer.py

@@ -9,8 +9,8 @@
 from rich.console import Console
 from rich.prompt import Confirm
 
-from murfey.util.client import read_config
 from murfey.util.api import url_path_for
+from murfey.util.client import read_config
 from murfey.util.config import MachineConfig
 
 

src/murfey/server/api/auth.py

@@ -23,8 +23,7 @@
 from murfey.server.murfey_db import murfey_db, url
 from murfey.util.api import url_path_for
 from murfey.util.config import get_security_config
-from murfey.util.db import MurfeyUser as User
-from murfey.util.db import Session as MurfeySession
+from murfey.util.db import MurfeyUser as User, Session as MurfeySession
 
 # Set up logger
 logger = getLogger("murfey.server.api.auth")

src/murfey/server/api/clem.py

@@ -24,8 +24,8 @@
     CLEMImageStack,
     CLEMLIFFile,
     CLEMTIFFFile,
+    Session as MurfeySession,
 )
-from murfey.util.db import Session as MurfeySession
 
 # Set up logger
 logger = getLogger("murfey.server.api.clem")

src/murfey/server/api/file_io_frontend.py

@@ -2,10 +2,14 @@
 
 from fastapi import APIRouter, Depends
 
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
-from murfey.server.api.auth import validate_token
-from murfey.server.api.file_io_shared import GainReference
-from murfey.server.api.file_io_shared import process_gain as _process_gain
+from murfey.server.api.auth import (
+    MurfeySessionIDFrontend as MurfeySessionID,
+    validate_token,
+)
+from murfey.server.api.file_io_shared import (
+    GainReference,
+    process_gain as _process_gain,
+)
 from murfey.server.murfey_db import murfey_db
 
 logger = getLogger("murfey.server.api.file_io_frontend")

src/murfey/server/api/file_io_instrument.py

@@ -8,10 +8,14 @@
 from sqlmodel import select
 from werkzeug.utils import secure_filename
 
-from murfey.server.api.auth import MurfeySessionIDInstrument as MurfeySessionID
-from murfey.server.api.auth import validate_instrument_token
-from murfey.server.api.file_io_shared import GainReference
-from murfey.server.api.file_io_shared import process_gain as _process_gain
+from murfey.server.api.auth import (
+    MurfeySessionIDInstrument as MurfeySessionID,
+    validate_instrument_token,
+)
+from murfey.server.api.file_io_shared import (
+    GainReference,
+    process_gain as _process_gain,
+)
 from murfey.server.murfey_db import murfey_db
 from murfey.util import sanitise, secure_path
 from murfey.util.config import get_machine_config

src/murfey/server/api/instrument.py

@@ -14,9 +14,9 @@
 from werkzeug.utils import secure_filename
 
 import murfey.server.prometheus as prom
-from murfey.server.api.auth import MurfeyInstrumentNameFrontend as MurfeyInstrumentName
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
 from murfey.server.api.auth import (
+    MurfeyInstrumentNameFrontend as MurfeyInstrumentName,
+    MurfeySessionIDFrontend as MurfeySessionID,
     create_access_token,
     instrument_server_tokens,
     oauth2_scheme,

src/murfey/server/api/processing_parameters.py

@@ -6,8 +6,10 @@
 from pydantic import BaseModel
 from sqlmodel import Session, select
 
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
-from murfey.server.api.auth import validate_token
+from murfey.server.api.auth import (
+    MurfeySessionIDFrontend as MurfeySessionID,
+    validate_token,
+)
 from murfey.server.murfey_db import murfey_db
 from murfey.util.db import SessionProcessingParameters
 

src/murfey/server/api/session_control.py

@@ -13,23 +13,20 @@
 
 import murfey.server.prometheus as prom
 from murfey.server import _transport_object
-from murfey.server.api.auth import MurfeySessionIDInstrument as MurfeySessionID
-from murfey.server.api.auth import validate_instrument_token
-from murfey.server.api.shared import get_foil_hole as _get_foil_hole
-from murfey.server.api.shared import (
-    get_foil_holes_from_grid_square as _get_foil_holes_from_grid_square,
+from murfey.server.api.auth import (
+    MurfeySessionIDInstrument as MurfeySessionID,
+    validate_instrument_token,
 )
-from murfey.server.api.shared import get_grid_squares as _get_grid_squares
 from murfey.server.api.shared import (
+    get_foil_hole as _get_foil_hole,
+    get_foil_holes_from_grid_square as _get_foil_holes_from_grid_square,
+    get_grid_squares as _get_grid_squares,
     get_grid_squares_from_dcg as _get_grid_squares_from_dcg,
-)
-from murfey.server.api.shared import (
     get_machine_config_for_instrument,
     get_upstream_tiff_dirs,
     remove_session_by_id,
 )
-from murfey.server.ispyb import DB as ispyb_db
-from murfey.server.ispyb import get_all_ongoing_visits
+from murfey.server.ispyb import DB as ispyb_db, get_all_ongoing_visits
 from murfey.server.murfey_db import murfey_db
 from murfey.util import sanitise
 from murfey.util.config import MachineConfig, get_machine_config
@@ -57,8 +54,6 @@
 from murfey.workflows.spa.atlas import atlas_jpg_from_mrc
 from murfey.workflows.spa.flush_spa_preprocess import (
     register_foil_hole as _register_foil_hole,
-)
-from murfey.workflows.spa.flush_spa_preprocess import (
     register_grid_square as _register_grid_square,
 )
 from murfey.workflows.tomo.tomo_metadata import (

src/murfey/server/api/session_info.py

@@ -12,24 +12,21 @@
 import murfey.server.api.websocket as ws
 from murfey.server import _transport_object
 from murfey.server.api import templates
-from murfey.server.api.auth import MurfeyInstrumentNameFrontend as MurfeyInstrumentName
-from murfey.server.api.auth import MurfeySessionIDFrontend as MurfeySessionID
-from murfey.server.api.auth import validate_token
-from murfey.server.api.shared import get_foil_hole as _get_foil_hole
-from murfey.server.api.shared import (
-    get_foil_holes_from_grid_square as _get_foil_holes_from_grid_square,
+from murfey.server.api.auth import (
+    MurfeyInstrumentNameFrontend as MurfeyInstrumentName,
+    MurfeySessionIDFrontend as MurfeySessionID,
+    validate_token,
 )
-from murfey.server.api.shared import get_grid_squares as _get_grid_squares
 from murfey.server.api.shared import (
+    get_foil_hole as _get_foil_hole,
+    get_foil_holes_from_grid_square as _get_foil_holes_from_grid_square,
+    get_grid_squares as _get_grid_squares,
     get_grid_squares_from_dcg as _get_grid_squares_from_dcg,
-)
-from murfey.server.api.shared import (
     get_machine_config_for_instrument,
     get_upstream_tiff_dirs,
     remove_session_by_id,
 )
-from murfey.server.ispyb import DB as ispyb_db
-from murfey.server.ispyb import get_all_ongoing_visits
+from murfey.server.ispyb import DB as ispyb_db, get_all_ongoing_visits
 from murfey.server.murfey_db import murfey_db
 from murfey.util import sanitise
 from murfey.util.config import MachineConfig, get_machine_config