sl-shared-assets 1.0.0rc28__py3-none-any.whl → 1.0.2__py3-none-any.whl

sl_shared_assets/cli.py

@@ -33,7 +33,7 @@ from .data_classes import (
     show_default=True,
     default=False,
     help=(
-        "Determines whether to created the processed data hierarchy. This flag should be disabled for most runtimes. "
+        "Determines whether to create the processed data hierarchy. This flag should be disabled for most runtimes. "
         "Primarily, it is used by lab acquisition system code to generate processed data directories on the remote "
         "compute servers as part of the data preprocessing pipeline."
     ),

sl_shared_assets/data_classes/configuration_data.py

@@ -207,7 +207,7 @@ class MesoscopeMicroControllers:
     PC, conserving communication bandwidth."""
     torque_averaging_pool_size: int = 10
     """The number of torque sensor readouts to average together to produce the final torque sensor readout value."""
-    wheel_encoder_ppr = 8192
+    wheel_encoder_ppr: int = 8192
     """The resolution of the managed quadrature encoder, in Pulses Per Revolution (PPR). This is the number of 
     quadrature pulses the encoder emits per full 360-degree rotation."""
     wheel_encoder_report_cw: bool = False
@@ -219,9 +219,9 @@ class MesoscopeMicroControllers:
     wheel_encoder_delta_threshold_pulse: int = 15
     """The minimum difference, in encoder pulse counts, between two encoder readouts for the change to be reported to 
     the PC. This is used to prevent reporting idle readouts and filter out sub-threshold noise."""
-    wheel_encoder_polling_delay_us = 500
+    wheel_encoder_polling_delay_us: int = 500
     """The delay, in microseconds, between any two successive encoder state readouts."""
-    cm_per_unity_unit = 10.0
+    cm_per_unity_unit: float = 10.0
     """The length of each Unity 'unit' in real-world centimeters recorded by the running wheel encoder."""
     screen_trigger_pulse_duration_ms: int = 500
     """The duration of the HIGH phase of the TTL pulse used to toggle the VR screens between ON and OFF states."""

sl_shared_assets/data_classes/configuration_data.pyi

@@ -97,12 +97,12 @@ class MesoscopeMicroControllers:
     torque_signal_threshold_adc: int = ...
     torque_delta_threshold_adc: int = ...
     torque_averaging_pool_size: int = ...
-    wheel_encoder_ppr = ...
+    wheel_encoder_ppr: int = ...
     wheel_encoder_report_cw: bool = ...
     wheel_encoder_report_ccw: bool = ...
     wheel_encoder_delta_threshold_pulse: int = ...
-    wheel_encoder_polling_delay_us = ...
-    cm_per_unity_unit = ...
+    wheel_encoder_polling_delay_us: int = ...
+    cm_per_unity_unit: float = ...
     screen_trigger_pulse_duration_ms: int = ...
     auditory_tone_duration_ms: int = ...
     valve_calibration_pulse_count: int = ...

sl_shared_assets/data_classes/session_data.py

@@ -587,7 +587,7 @@ class SessionData(YamlConfig):
 
         # Unless a different root is provided for processed data, it uses the same root as raw_data.
         if processed_data_root is None:
-            processed_data_root = new_root
+            processed_data_root = local_root
 
         # Regenerates the processed_data path depending on the root resolution above
         instance.processed_data.resolve_paths(

sl_shared_assets/server/server.py

@@ -75,7 +75,7 @@ class Server:
     """
 
     def __init__(self, credentials_path: Path) -> None:
-        # Tracker used to prevent __del__ from classing stop() for a partially initialized class.
+        # Tracker used to prevent __del__ from calling stop() for a partially initialized class.
         self._open: bool = False
 
         # Loads the credentials from the provided .yaml file
@@ -95,6 +95,7 @@ class Server:
                     self._credentials.host, username=self._credentials.username, password=self._credentials.password
                 )
                 console.echo(f"Connected to {self._credentials.host}", level=LogLevel.SUCCESS)
+                self._open = True
                 break
             except paramiko.AuthenticationException:
                 message = (

sl_shared_assets/tools/packaging_tools.py

@@ -21,6 +21,7 @@ _excluded_files = {
     "multi_day_suite2p.bin",
     "behavior.bin",
     "dlc.bin",
+    "verified.bin",
 }
 
 

sl_shared_assets/tools/project_management_tools.py

@@ -176,6 +176,11 @@ def verify_session_checksum(
         make_processed_data_directory=create_processed_data_directory,
     )
 
+    # Unlinks the verified.bin marker if it exists. The presence or absence of the marker is used as the
+    # primary heuristic for determining if the session data passed verification. Unlinking it early helps in the case
+    # the verification procedure aborts unexpectedly for any reason.
+    session_data.raw_data.verified_bin_path.unlink(missing_ok=True)
+
     # Re-calculates the checksum for the raw_data directory
     calculated_checksum = calculate_directory_checksum(
         directory=session_data.raw_data.raw_data_path, batch=False, save_checksum=False
@@ -191,10 +196,6 @@ def verify_session_checksum(
         # all other Sun lab runtimes.
         session_data.raw_data.telomere_path.unlink(missing_ok=True)
 
-        # Also unlinks the verified.bin marker if it exists. The presence or absence of the marker is used as the
-        # primary heuristic for determining if the session data passed verification.
-        session_data.raw_data.verified_bin_path.unlink(missing_ok=True)
-
     # Otherwise, ensures that the session is marked with the verified.bin marker file.
     else:
         session_data.raw_data.verified_bin_path.touch(exist_ok=True)

{sl_shared_assets-1.0.0rc28.dist-info → sl_shared_assets-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.0.0rc28
+Version: 1.0.2
 Summary: Stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/
@@ -768,16 +768,16 @@ ___
 
 ## Detailed Description
 
-Primarily, this library is designed to make the two main Sun lab libraries used in data acquisition 
+Primarily, this library is designed to make the two main Sun lab libraries used for data acquisition 
 ([sl-experiment](https://github.com/Sun-Lab-NBB/sl-experiment)) and processing 
 ([sl-forgery](https://github.com/Sun-Lab-NBB/sl-forgery)) independent of each other. This is beneficial, as both 
-libraries feature an extensive and potentially incompatible set of runtime dependencies. Moreover, having a shared
+libraries feature an extensive and largely incompatible set of runtime dependencies. Moreover, having a shared
 repository of classes and tools reused across Sun lab pipelines streamlines the maintenance of these tools.
 
 The library broadly stores two types of assets. First, it stores various dataclasses used to save the data acquired 
-during experiments in the lab. Moreover, it also stores the dataclasses used to configure data acquisition and 
-processing runtimes. Secondly, it stores the tools used to safely move the data between the computers used in the data 
-acquisition and processing and provides the API for accessing the lab’s main computation server.
+during experiments in the lab and the dataclasses used to configure data acquisition and processing runtimes. Secondly, 
+it stores the tools used to safely move the data between the machines (computers) used in the data acquisition and 
+processing, and provides the API for running various data processing jobs on remote compute servers.
 
 ---
 
@@ -819,7 +819,10 @@ Use the following command to install the library using pip: ```pip install sl-sh
 ## Usage
 
 All library components are intended to be used via other Sun lab libraries. Developers should study the API and CLI 
-documentation below to learn how to use library components in other Sun lab libraries.
+documentation below to learn how to use library components in other Sun lab libraries. For notes on using shared 
+assets for data acquisition, see the [sl-experiment](https://github.com/Sun-Lab-NBB/sl-experiment) library ReadMe.
+For notes on using shared assets for data processing, see the [sl-forgery](https://github.com/Sun-Lab-NBB/sl-forgery) 
+library ReadMe.
 
 ---
 

{sl_shared_assets-1.0.0rc28.dist-info → sl_shared_assets-1.0.2.dist-info}/RECORD

@@ -1,15 +1,15 @@
 sl_shared_assets/__init__.py,sha256=rscR353jiyUQ-wpguTLOM-A5Lqr1ftQtuTan1D0AtR0,2196
 sl_shared_assets/__init__.pyi,sha256=Ye6eY_y_l9CTqwbCf-OxXOphxXKfn9UJnuw09DdLEtc,2405
-sl_shared_assets/cli.py,sha256=9PXEfRgKb9-6xb1icmtr_ijdWur-AIsdMwvgA0aAeto,17434
+sl_shared_assets/cli.py,sha256=Rfc0W0yUgFi3ohL7Jmx6kh_V-h3qsqPYSpxjqNYtnEE,17433
 sl_shared_assets/cli.pyi,sha256=p1tUflODySXx1_2IrLZ_uqixopbQPTearuJvqJ4jKI4,6075
 sl_shared_assets/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sl_shared_assets/data_classes/__init__.py,sha256=b0BwTAJCD1zbwjd2UdpXheq61q1sgBuYhtAL-GHA2h4,1835
 sl_shared_assets/data_classes/__init__.pyi,sha256=e2082sm5pSw3bxNZGqwcRhuKLH8T7hcEo6kWtOZNDBU,1968
-sl_shared_assets/data_classes/configuration_data.py,sha256=wuPFz3zx1DN12KimPhH-fU1geU3pFzRuRB53JEJ2T6I,30343
-sl_shared_assets/data_classes/configuration_data.pyi,sha256=FWQG6LlF6gSDV5bU0KvMvIE6wf0Jfrz5wRbuHwyCKHw,9600
+sl_shared_assets/data_classes/configuration_data.py,sha256=ZVk1ynk25CfVuQfMofoH90BUaOPqk7zW8ukY6ls_Pp0,30360
+sl_shared_assets/data_classes/configuration_data.pyi,sha256=h7AV3z73SC2ITXWcnsShczuezC1Is7L4WSMnEWGSLPQ,9617
 sl_shared_assets/data_classes/runtime_data.py,sha256=Q7Ykf9hgrw1jYKXa53mn_LW8G2cPmLLuxgGkP6qQcc4,15483
 sl_shared_assets/data_classes/runtime_data.pyi,sha256=PxaCbeF9COR4ri91pdzh7zVrqaz2KEDYB1EoLhZQC_c,6618
-sl_shared_assets/data_classes/session_data.py,sha256=oAiTNqNlQi6NQHv5WsaQb3KglBrDGAmBv1EVPPuM6Y4,38329
+sl_shared_assets/data_classes/session_data.py,sha256=Rd3KFKWTHCUgMrMZ0HHfZq6Bc-9tZSzvIX6KFHrDJwk,38331
 sl_shared_assets/data_classes/session_data.pyi,sha256=eLemAagVD6TQ-9pzMIc0eXDgnh-quJwEidKHYitvsjQ,13243
 sl_shared_assets/data_classes/surgery_data.py,sha256=qsMj3NkjhylAT9b_wHBY-1XwTu2xsZcZatdECmkA7Bs,7437
 sl_shared_assets/data_classes/surgery_data.pyi,sha256=rf59lJ3tGSYKHQlEGXg75MnjajBwl0DYhL4TClAO4SM,2605
@@ -17,20 +17,20 @@ sl_shared_assets/server/__init__.py,sha256=nyX6-9ACcrQeRQOCNvBVrWSTHGjRPANIG_u0a
 sl_shared_assets/server/__init__.pyi,sha256=7o99f8uf6NuBjMZjNAM1FX69Qbu5uBluRSAyaUWbXOU,263
 sl_shared_assets/server/job.py,sha256=GB31yYPEqXR6MgwNmnQrSQuHRJqUHFXcd6p7hb38q_c,7928
 sl_shared_assets/server/job.pyi,sha256=cxgHMpuwHsJGf_ZcTSSa2tZNzeR_GxqlICOsYGV_oy0,5655
-sl_shared_assets/server/server.py,sha256=Rsc5rSmthFcKMsY3fH0la2GRCZsmB1j7fnz7T0RkSok,9381
+sl_shared_assets/server/server.py,sha256=SkFJA8eYlZrm2dag7sF_CyPiBphFgoq32zV10kqnedc,9414
 sl_shared_assets/server/server.pyi,sha256=SoTRqSPJ1GQ5i5gV3N57rDT9xzeT47RjMRH1FYKsOkg,4143
 sl_shared_assets/tools/__init__.py,sha256=N95ZPMz-_HdNPrbVieCFza-QSVS6BV2KRB4K1OLRttc,636
 sl_shared_assets/tools/__init__.pyi,sha256=xeDF8itMc0JRgLrO_IN_9gW7cp_Ld-Gf-rjtrgWvQ2I,551
 sl_shared_assets/tools/ascension_tools.py,sha256=kIqYGX9F8lRao_LaVOacIiT8J9SypTvarb9mgaI9ZPs,15387
 sl_shared_assets/tools/ascension_tools.pyi,sha256=tQCDdWZ20ZjUjpMs8aGIN0yBg5ff3j6spi62b3Han4o,3755
-sl_shared_assets/tools/packaging_tools.py,sha256=oY-EWuTiMfWobYllVZy0piGlVnTHCpPY1GF-WmqQdj4,7269
+sl_shared_assets/tools/packaging_tools.py,sha256=2yaIysL11g5m-j0i4I2MRVzHA6_37WdyLYqXMl2FPAc,7289
 sl_shared_assets/tools/packaging_tools.pyi,sha256=vgGbAQCExwg-0A5F72MzEhzHxu97Nqg1yuz-5P89ycU,3118
-sl_shared_assets/tools/project_management_tools.py,sha256=Z1wEo0ei6xuV-8_DZQPejHwJGPFvE3AGKwvASW6cevY,11126
+sl_shared_assets/tools/project_management_tools.py,sha256=aMOCq3nCR2xOTDMQpXbXEh90IuKOvSbIfeKh2VaZIXw,11215
 sl_shared_assets/tools/project_management_tools.pyi,sha256=HiU1qqumscmXtAXNX6eaSrkwanGHEvk-lromwZ2ijD8,3445
 sl_shared_assets/tools/transfer_tools.py,sha256=J26kwOp_NpPSY0-xu5FTw9udte-rm_mW1FJyaTNoqQI,6606
 sl_shared_assets/tools/transfer_tools.pyi,sha256=FoH7eYZe7guGHfPr0MK5ggO62uXKwD2aJ7h1Bu7PaEE,3294
-sl_shared_assets-1.0.0rc28.dist-info/METADATA,sha256=3XV5KTtWCVfvMZnFkPbVEgTC6WUqZcu7n2xqFPvhxMw,48613
-sl_shared_assets-1.0.0rc28.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-sl_shared_assets-1.0.0rc28.dist-info/entry_points.txt,sha256=76c00fRS4IuXBP2xOBdvycT15Zen-lHiDg2FaSt-HB4,547
-sl_shared_assets-1.0.0rc28.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-sl_shared_assets-1.0.0rc28.dist-info/RECORD,,
+sl_shared_assets-1.0.2.dist-info/METADATA,sha256=fMc6X-sMqNzyERNvE6DrkRKLgeubNLmk9KVh8KuFD8Y,48890
+sl_shared_assets-1.0.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+sl_shared_assets-1.0.2.dist-info/entry_points.txt,sha256=76c00fRS4IuXBP2xOBdvycT15Zen-lHiDg2FaSt-HB4,547
+sl_shared_assets-1.0.2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+sl_shared_assets-1.0.2.dist-info/RECORD,,