np-workflows 1.6.89__py3-none-any.whl → 1.6.91__py3-none-any.whl

np_workflows/shared/npxc.py

@@ -1,21 +1,22 @@
 import contextlib
 import datetime
-import inspect
 import pathlib
 import shutil
 import sys
 import time
-from typing import Any, Generator, Sequence, Type
 import zlib
+from collections.abc import Generator, Sequence
 
 import fabric
 import np_config
 import np_logging
+import np_services
 import np_session
-from np_services import Initializable, Testable, TestError, Finalizable, Service
-from np_services import Sync, VideoMVR, ImageMVR, Cam3d, ScriptCamstim, OpenEphys  
-import np_services 
-from np_config import Rig
+from np_services import (
+    Finalizable,
+    Initializable,
+    Service,
+)
 
 logger = np_logging.getLogger(__name__)
 
@@ -36,24 +37,25 @@ CONFIG = RIG.config
 
 lims_user_ids: tuple[str, ...] = tuple(
     sorted(
-        CONFIG.get('lims_user_ids',
+        CONFIG.get(
+            "lims_user_ids",
             [
-            "hannah.belski",
-            "hannah.cabasco",
-            "ryan.gillis",
-            "henry.loeffler",
-            "corbettb",
-            "ben.hardcastle",
-            "samg",
-            "ethan.mcbride",
-            "jackie.kuyat",
-            "andrew.shelton",
-            ]
+                "hannah.belski",
+                "hannah.cabasco",
+                "ryan.gillis",
+                "henry.loeffler",
+                "corbettb",
+                "ben.hardcastle",
+                "samg",
+                "ethan.mcbride",
+                "jackie.kuyat",
+                "andrew.shelton",
+            ],
         )
     )
 )
 
-default_mouse_id: int = int(CONFIG.get('default_mouse_id', 366122))
+default_mouse_id: int = int(CONFIG.get("default_mouse_id", 366122))
 
 
 def get_operators() -> list[str]:
@@ -74,9 +76,10 @@ def print_countdown_timer(seconds: int | float | datetime.timedelta = 0, **kwarg
         print(f"Waiting {wait} \t{time_remaining()}", end="\r", flush=True)
         time.sleep(0.1)
 
+
 def photodoc(img_name: str) -> pathlib.Path:
     """Capture image with `label` appended to filename, and return the filepath.
-            
+
     If multiple images are captured, only the last will remain in the Imager.data_files list.
     """
     if RIG.idx == 0:
@@ -84,104 +87,133 @@ def photodoc(img_name: str) -> pathlib.Path:
     else:
         from np_services import ImageMVR as ImageCamera
     from np_services import NewScaleCoordinateRecorder
-    
+
     ImageCamera.label = img_name
-    if isinstance(ImageCamera, Initializable) and not getattr(ImageCamera, 'initialization', None):
+    if isinstance(ImageCamera, Initializable) and not getattr(
+        ImageCamera, "initialization", None
+    ):
         ImageCamera.initialize()
-        
+
     ImageCamera.start()
-    
+
     if isinstance(ImageCamera, Finalizable):
         ImageCamera.finalize()
-        
-    if isinstance(NewScaleCoordinateRecorder, Initializable) and not getattr(NewScaleCoordinateRecorder, 'initialization', None):
+
+    if isinstance(NewScaleCoordinateRecorder, Initializable) and not getattr(
+        NewScaleCoordinateRecorder, "initialization", None
+    ):
         NewScaleCoordinateRecorder.initialize()
     NewScaleCoordinateRecorder.label = img_name
     NewScaleCoordinateRecorder.start()
-    
+
     # remove all but latest file with the current label
     if img_name and ImageCamera.data_files:
-        views = 2 if ImageCamera.__name__ == 'Cam3d' else 1
+        views = 2 if ImageCamera.__name__ == "Cam3d" else 1
+
         def files_with_label():
             return sorted([_ for _ in ImageCamera.data_files if img_name in _.name])
+
         while len(files_with_label()) > views:
             ImageCamera.data_files.remove(files_with_label()[0])
-            
+
     return ImageCamera.data_files[-1]
 
+
 def copy_files(services: Sequence[Service], session_folder: pathlib.Path):
     """Copy files from raw data storage to session folder for all services."""
-    password = input(f'Enter password for svc_neuropix:')
+    password = input("Enter password for svc_neuropix:")
     for service in services:
         match service.__class__.__name__:
             case "OpenEphys" | "open_ephys":
-                continue # copy ephys after other files
+                continue  # copy ephys after other files
             case _:
                 with contextlib.suppress(AttributeError):
-                    files = service.data_files or service.get_latest_data('*')
+                    files = service.data_files or service.get_latest_data("*")
                     if not files:
                         continue
                     files = set(files)
                     print(files)
                     for file in files:
                         shutil.copy2(file, session_folder)
-    
-    password = np_config.fetch('/logins')['svc_neuropix']['password']
-    ssh = fabric.Connection(host=np_services.OpenEphys.host, user='svc_neuropix', connect_kwargs=dict(password=password))
+
+    password = np_config.fetch("/logins")["svc_neuropix"]["password"]
+    ssh = fabric.Connection(
+        host=np_services.OpenEphys.host,
+        user="svc_neuropix",
+        connect_kwargs=dict(password=password),
+    )
     for ephys_folder in np_services.OpenEphys.data_files:
 
         with contextlib.suppress(Exception):
             with ssh:
                 ssh.run(
-                f'robocopy "{ephys_folder}" "{session_folder / ephys_folder.name}" /j /s /xo' 
-                # /j unbuffered, /s incl non-empty subdirs, /xo exclude src files older than dest
+                    f'robocopy "{ephys_folder}" "{session_folder / ephys_folder.name}" /j /s /xo'
+                    # /j unbuffered, /s incl non-empty subdirs, /xo exclude src files older than dest
                 )
-            
-            
+
+
 import warnings
 
-def hide_warning_lines(msg:str,category:str,*args,**kwargs):
-    print("\n{}: {}\n".format(category.__name__, msg))
+
+def hide_warning_lines(msg: str, category: str, *args, **kwargs):
+    print(f"\n{category.__name__}: {msg}\n")
+
+
 warnings.showwarning = hide_warning_lines
 
 import IPython
+
+
 def toggle_tracebacks() -> Generator[None, None, None]:
     if ipython := IPython.get_ipython():
         show_traceback = ipython.showtraceback
-        
-        def hide_traceback(exc_tuple=None, filename=None, tb_offset=None,
-                        exception_only=False, running_compiled_code=False):
+
+        def hide_traceback(
+            exc_tuple=None,
+            filename=None,
+            tb_offset=None,
+            exception_only=False,
+            running_compiled_code=False,
+        ):
             etype, value, tb = sys.exc_info()
-            return ipython._showtraceback(etype, value, ipython.InteractiveTB.get_exception_only(etype, value))
-        
+            return ipython._showtraceback(
+                etype, value, ipython.InteractiveTB.get_exception_only(etype, value)
+            )
+
         hidden = True
         while True:
             ipython.showtraceback = hide_traceback if hidden else show_traceback
             hidden = yield
     else:
         raise RuntimeError("Not in IPython")
-    
+
+
 with contextlib.suppress(RuntimeError):
     toggle_tb = toggle_tracebacks()
 
     toggle_tb.send(None)
+
     def show_tracebacks():
         toggle_tb.send(False)
+
     def hide_tracebacks():
         toggle_tb.send(True)
-        
+
+
 def now() -> str:
     return np_services.utils.normalize_time(time.time())
 
+
 def validate_or_overwrite(validate: str | pathlib.Path, src: str | pathlib.Path):
     "Checksum validate against `src`, (over)write `validate` as `src` if different."
     validate, src = pathlib.Path(validate), pathlib.Path(src)
+
     def copy():
         logger.debug("Copying %s to %s", src, validate)
         shutil.copy2(src, validate)
-    while (
-        validate.exists() == False
-        or (v := zlib.crc32(validate.read_bytes())) != (c := zlib.crc32(pathlib.Path(src).read_bytes()))
-        ):
+
+    while validate.exists() == False or (v := zlib.crc32(validate.read_bytes())) != (
+        c := zlib.crc32(pathlib.Path(src).read_bytes())
+    ):
         copy()
-    logger.debug("Validated %s CRC32: %08X", validate, (v & 0xFFFFFFFF) )
+    logger.debug("Validated %s CRC32: %08X", validate, (v & 0xFFFFFFFF))