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tieneupintieneupin
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Applied Ruff formatting changes
1 parent c8c5056 commit 3f6f3db

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20 files changed

+65
-78
lines changed

20 files changed

+65
-78
lines changed

‎src/murfey/cli/generate_route_manifest.py‎

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -68,7 +68,6 @@ def is_implicitly_resolved(value: str) -> bool:
6868

6969

7070
def find_routers(name: str) -> dict[str, APIRouter]:
71-
7271
def _extract_routers_from_module(module: ModuleType):
7372
routers = {}
7473
for name, obj in inspect.getmembers(module):
@@ -115,7 +114,6 @@ def _extract_routers_from_module(module: ModuleType):
115114

116115

117116
def get_route_manifest(routers: dict[str, APIRouter]):
118-
119117
manifest = {}
120118

121119
for router_name, router in routers.items():

‎src/murfey/cli/inject_spa_processing.py‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -173,7 +173,6 @@ def run():
173173
/ str(ppath.stem + "_motion_corrected.mrc")
174174
)
175175
if proc_params:
176-
177176
detached_ids = [c.id for c in collected_ids]
178177

179178
if not mrc_out.parent.exists():

‎src/murfey/client/contexts/clem.py‎

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,6 @@ def _get_image_elements(root: ET.Element) -> List[ET.Element]:
6565
def _find_elements_recursively(
6666
node: ET.Element,
6767
) -> Generator[ET.Element, None, None]:
68-
6968
# Find items labelled "Element" under current node
7069
elem_list = node.findall("./Children/Element")
7170
if len(elem_list) < 1: # Try alternative path for top-level of XML tree
@@ -103,7 +102,6 @@ def post_transfer(
103102
environment: Optional[MurfeyInstanceEnvironment] = None,
104103
**kwargs,
105104
) -> bool:
106-
107105
super().post_transfer(transferred_file, environment=environment, **kwargs)
108106

109107
# Process files generated by "auto-save" acquisition mode
@@ -188,7 +186,6 @@ def post_transfer(
188186

189187
# Process XLIF files
190188
if transferred_file.suffix == ".xlif":
191-
192189
# Skip processing of "_histo" histogram XLIF files
193190
if transferred_file.stem.endswith("_histo"):
194191
logger.debug(

‎src/murfey/client/tui/progress.py‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -71,7 +71,6 @@ def _get_pulse_segments(
7171
def __rich_console__(
7272
self, console: Console, options: ConsoleOptions
7373
) -> RenderResult:
74-
7574
width = min(self.width or options.max_width, options.max_width)
7675
ascii = options.ascii_only
7776
if self.pulse:

‎src/murfey/client/tui/screens.py‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -193,7 +193,6 @@ def __init__(
193193
self._context = SPAModularContext
194194

195195
def compose(self):
196-
197196
machine_data = capture_get(
198197
base_url=str(self.app._environment.url.geturl()),
199198
router_name="session_control.router",

‎src/murfey/server/api/auth.py‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -147,7 +147,7 @@ def validate_session_against_visit(session_id: int, visit: str):
147147

148148

149149
async def validate_instrument_token(
150-
token: Annotated[str, Depends(instrument_oauth2_scheme)]
150+
token: Annotated[str, Depends(instrument_oauth2_scheme)],
151151
):
152152
"""
153153
Used by the backend routers to check the incoming instrument server token.
@@ -334,7 +334,6 @@ def validate_user(username: str, password: str) -> bool:
334334

335335

336336
def create_access_token(data: dict, token: str = "") -> str:
337-
338337
# If authenticating with password, auth URL needs a 'mint_session_token' endpoint
339338
if security_config.auth_type == "password":
340339
if auth_url and data.get("session"):
@@ -420,6 +419,6 @@ async def mint_session_token(session_id: MurfeySessionIDFrontend, db=murfey_db):
420419

421420
@router.get("/validate_token")
422421
async def simple_token_validation(
423-
token: Annotated[str, Depends(validate_instrument_token)]
422+
token: Annotated[str, Depends(validate_instrument_token)],
424423
):
425424
return {"valid": True}

‎src/murfey/server/api/clem.py‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -409,7 +409,6 @@ def register_clem_metadata(
409409
associated_stacks: list[Path] = [],
410410
db: Session = murfey_db,
411411
):
412-
413412
# Return database entry if it already exists
414413
try:
415414
clem_metadata: CLEMImageMetadata = get_db_entry(

‎src/murfey/server/api/workflow.py‎

Lines changed: 6 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -435,7 +435,6 @@ async def request_spa_preprocessing(
435435
)
436436
foil_hole_id = None
437437
if proc_params:
438-
439438
detached_ids = [c.id for c in collected_ids]
440439

441440
murfey_ids = _murfey_id(detached_ids[3], db, number=2, close=False)
@@ -494,9 +493,9 @@ async def request_spa_preprocessing(
494493
}
495494
# log.info(f"Sending Zocalo message {zocalo_message}")
496495
if _transport_object:
497-
zocalo_message["parameters"][
498-
"feedback_queue"
499-
] = _transport_object.feedback_queue
496+
zocalo_message["parameters"]["feedback_queue"] = (
497+
_transport_object.feedback_queue
498+
)
500499
_transport_object.send("processing_recipe", zocalo_message)
501500
else:
502501
logger.error(
@@ -723,9 +722,9 @@ async def request_tomography_preprocessing(
723722
},
724723
}
725724
if _transport_object:
726-
zocalo_message["parameters"][
727-
"feedback_queue"
728-
] = _transport_object.feedback_queue
725+
zocalo_message["parameters"]["feedback_queue"] = (
726+
_transport_object.feedback_queue
727+
)
729728
_transport_object.send("processing_recipe", zocalo_message)
730729
else:
731730
logger.error(

‎src/murfey/server/feedback.py‎

Lines changed: 36 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -390,9 +390,9 @@ def _release_2d_hold(message: dict, _db):
390390
_db.commit()
391391
_db.close()
392392
if murfey.server._transport_object:
393-
zocalo_message["parameters"][
394-
"feedback_queue"
395-
] = murfey.server._transport_object.feedback_queue
393+
zocalo_message["parameters"]["feedback_queue"] = (
394+
murfey.server._transport_object.feedback_queue
395+
)
396396
murfey.server._transport_object.send(
397397
"processing_recipe", zocalo_message, new_connection=True
398398
)
@@ -466,9 +466,9 @@ def _release_3d_hold(message: dict, _db):
466466
"recipes": ["em-spa-class3d"],
467467
}
468468
if murfey.server._transport_object:
469-
zocalo_message["parameters"][
470-
"feedback_queue"
471-
] = murfey.server._transport_object.feedback_queue
469+
zocalo_message["parameters"]["feedback_queue"] = (
470+
murfey.server._transport_object.feedback_queue
471+
)
472472
murfey.server._transport_object.send(
473473
"processing_recipe", zocalo_message, new_connection=True
474474
)
@@ -547,9 +547,9 @@ def _release_refine_hold(message: dict, _db):
547547
"recipes": ["em-spa-refine"],
548548
}
549549
if murfey.server._transport_object:
550-
zocalo_message["parameters"][
551-
"feedback_queue"
552-
] = murfey.server._transport_object.feedback_queue
550+
zocalo_message["parameters"]["feedback_queue"] = (
551+
murfey.server._transport_object.feedback_queue
552+
)
553553
murfey.server._transport_object.send(
554554
"processing_recipe", zocalo_message, new_connection=True
555555
)
@@ -662,9 +662,9 @@ def _register_incomplete_2d_batch(message: dict, _db, demo: bool = False):
662662
"recipes": ["em-spa-class2d"],
663663
}
664664
if murfey.server._transport_object:
665-
zocalo_message["parameters"][
666-
"feedback_queue"
667-
] = murfey.server._transport_object.feedback_queue
665+
zocalo_message["parameters"]["feedback_queue"] = (
666+
murfey.server._transport_object.feedback_queue
667+
)
668668
murfey.server._transport_object.send(
669669
"processing_recipe", zocalo_message, new_connection=True
670670
)
@@ -825,9 +825,9 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
825825
"recipes": ["em-spa-class2d"],
826826
}
827827
if murfey.server._transport_object:
828-
zocalo_message["parameters"][
829-
"feedback_queue"
830-
] = murfey.server._transport_object.feedback_queue
828+
zocalo_message["parameters"]["feedback_queue"] = (
829+
murfey.server._transport_object.feedback_queue
830+
)
831831
murfey.server._transport_object.send(
832832
"processing_recipe", zocalo_message, new_connection=True
833833
)
@@ -894,9 +894,9 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
894894
"recipes": ["em-spa-class2d"],
895895
}
896896
if murfey.server._transport_object:
897-
zocalo_message["parameters"][
898-
"feedback_queue"
899-
] = murfey.server._transport_object.feedback_queue
897+
zocalo_message["parameters"]["feedback_queue"] = (
898+
murfey.server._transport_object.feedback_queue
899+
)
900900
murfey.server._transport_object.send(
901901
"processing_recipe", zocalo_message, new_connection=True
902902
)
@@ -984,9 +984,9 @@ def _flush_class2d(
984984
"recipes": ["em-spa-class2d"],
985985
}
986986
if murfey.server._transport_object:
987-
zocalo_message["parameters"][
988-
"feedback_queue"
989-
] = murfey.server._transport_object.feedback_queue
987+
zocalo_message["parameters"]["feedback_queue"] = (
988+
murfey.server._transport_object.feedback_queue
989+
)
990990
murfey.server._transport_object.send(
991991
"processing_recipe", zocalo_message, new_connection=True
992992
)
@@ -1351,9 +1351,9 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
13511351
"recipes": ["em-spa-class3d"],
13521352
}
13531353
if murfey.server._transport_object:
1354-
zocalo_message["parameters"][
1355-
"feedback_queue"
1356-
] = murfey.server._transport_object.feedback_queue
1354+
zocalo_message["parameters"]["feedback_queue"] = (
1355+
murfey.server._transport_object.feedback_queue
1356+
)
13571357
murfey.server._transport_object.send(
13581358
"processing_recipe", zocalo_message, new_connection=True
13591359
)
@@ -1394,9 +1394,9 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
13941394
"recipes": ["em-spa-class3d"],
13951395
}
13961396
if murfey.server._transport_object:
1397-
zocalo_message["parameters"][
1398-
"feedback_queue"
1399-
] = murfey.server._transport_object.feedback_queue
1397+
zocalo_message["parameters"]["feedback_queue"] = (
1398+
murfey.server._transport_object.feedback_queue
1399+
)
14001400
murfey.server._transport_object.send(
14011401
"processing_recipe", zocalo_message, new_connection=True
14021402
)
@@ -1512,9 +1512,9 @@ def _flush_tomography_preprocessing(message: dict, _db):
15121512
f"Launching tomography preprocessing with Zocalo message: {zocalo_message}"
15131513
)
15141514
if murfey.server._transport_object:
1515-
zocalo_message["parameters"][
1516-
"feedback_queue"
1517-
] = murfey.server._transport_object.feedback_queue
1515+
zocalo_message["parameters"]["feedback_queue"] = (
1516+
murfey.server._transport_object.feedback_queue
1517+
)
15181518
murfey.server._transport_object.send(
15191519
"processing_recipe", zocalo_message, new_connection=True
15201520
)
@@ -1695,9 +1695,9 @@ def _register_refinement(message: dict, _db, demo: bool = False):
16951695
"recipes": ["em-spa-refine"],
16961696
}
16971697
if murfey.server._transport_object:
1698-
zocalo_message["parameters"][
1699-
"feedback_queue"
1700-
] = murfey.server._transport_object.feedback_queue
1698+
zocalo_message["parameters"]["feedback_queue"] = (
1699+
murfey.server._transport_object.feedback_queue
1700+
)
17011701
murfey.server._transport_object.send(
17021702
"processing_recipe", zocalo_message, new_connection=True
17031703
)
@@ -1818,9 +1818,9 @@ def _register_bfactors(message: dict, _db, demo: bool = False):
18181818
"recipes": ["em-spa-bfactor"],
18191819
}
18201820
if murfey.server._transport_object:
1821-
zocalo_message["parameters"][
1822-
"feedback_queue"
1823-
] = murfey.server._transport_object.feedback_queue
1821+
zocalo_message["parameters"]["feedback_queue"] = (
1822+
murfey.server._transport_object.feedback_queue
1823+
)
18241824
murfey.server._transport_object.send(
18251825
"processing_recipe", zocalo_message, new_connection=True
18261826
)

‎src/murfey/server/ispyb.py‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -706,7 +706,6 @@ def get_session_id(
706706
visit_number: str,
707707
db: Session | None,
708708
) -> int | None:
709-
710709
# Log received lookup parameters
711710
log.debug(
712711
"Looking up ISPyB BLSession ID using the following values:\n"

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