rearrange(all): major refactor of modules

Author: ttngu207

CHANGELOG.md

@@ -3,6 +3,15 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
  [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+
+## [1.0.0] - 2024-09-10
+
++ Update - No longer support multiple variation of ephys module, keep only `ephys_no_curation` module, renamed to `ephys`
++ Update - Remove other ephys modules (e.g. `ephys_acute`, `ephys_chronic`) (moved to different branches)
++ Update - Add support for `SpikeInterface`
++ Update - Remove support for `ecephys_spike_sorting` (moved to a different branch)
++ Update - Simplify the "activate" mechanism
+
 ## [0.4.0] - 2024-08-16
 
 + Add - support for SpikeInterface version >= 0.101.0 (updated API)

element_array_ephys/__init__.py

@@ -1 +1,3 @@
-from . import ephys_acute as ephys
+from . import ephys
+
+ephys_no_curation = ephys  # alias for backward compatibility

element_array_ephys/ephys_no_curation.py renamed to element_array_ephys/ephys.py

@@ -10,7 +10,7 @@
 import pandas as pd
 from element_interface.utils import dict_to_uuid, find_full_path, find_root_directory
 
-from . import ephys_report, probe
+from . import probe
 from .readers import kilosort, openephys, spikeglx
 
 logger = dj.logger
@@ -22,7 +22,6 @@
 
 def activate(
     ephys_schema_name: str,
-    probe_schema_name: str = None,
     *,
     create_schema: bool = True,
     create_tables: bool = True,
@@ -32,7 +31,6 @@ def activate(
 
     Args:
         ephys_schema_name (str): A string containing the name of the ephys schema.
-        probe_schema_name (str): A string containing the name of the probe schema.
         create_schema (bool): If True, schema will be created in the database.
         create_tables (bool): If True, tables related to the schema will be created in the database.
         linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.
@@ -46,7 +44,6 @@ def activate(
         get_ephys_root_data_dir(): Returns absolute path for root data director(y/ies) with all electrophysiological recording sessions, as a list of string(s).
         get_session_direction(session_key: dict): Returns path to electrophysiology data for the a particular session as a list of strings.
         get_processed_data_dir(): Optional. Returns absolute path for processed data. Defaults to root directory.
-
     """
 
     if isinstance(linking_module, str):
@@ -58,17 +55,15 @@ def activate(
     global _linking_module
     _linking_module = linking_module
 
-    # activate
-    probe.activate(
-        probe_schema_name, create_schema=create_schema, create_tables=create_tables
-    )
+    if not probe.schema.is_activated():
+        raise RuntimeError("Please activate the `probe` schema first.")
+
     schema.activate(
         ephys_schema_name,
         create_schema=create_schema,
         create_tables=create_tables,
         add_objects=_linking_module.__dict__,
     )
-    ephys_report.activate(f"{ephys_schema_name}_report", ephys_schema_name)
 
 
 # -------------- Functions required by the elements-ephys  ---------------