merge master

Author: samuelbray32

CHANGELOG.md

@@ -10,19 +10,22 @@
 - Improve cron job documentation and script #1226, #1241
 - Update export process to include `~external` tables #1239
 - Only add merge parts to `source_class_dict` if present in codebase #1237
+- Remove cli module #1250
+- Fix column error in `check_threads` method #1256
 
 ### Pipelines
 
 - Common
     - Set `probe_id` as `probe_description` when inserting from nwb file #1220
     - Default `AnalysisNwbfile.create` permissions are now 777 #1226
+    - Make `Nwbfile.fetch_nwb` functional # 1256
 - Position
     - Allow population of missing `PositionIntervalMap` entries during population
         of `DLCPoseEstimation` #1208
     - Enable import of existing pose data to `ImportedPose` in position pipeline #1247
 - Spikesorting
     - Fix compatibility bug between v1 pipeline and `SortedSpikesGroup` unit
-        filtering #1238
+        filtering #1238, #1249
     - Speedup `get_sorting` on `CurationV1` #1246
 - Behavior
     - Implement pipeline for keypoint-moseq extraction of behavior syllables #1056

pyproject.toml

@@ -79,7 +79,6 @@ moseq-cpu = [
 ]
 
 test = [
-    "click",                  # for CLI subpackage only
     "docker",                 # for tests in a container
     "ghostipy",
     "kachery",                # database access
@@ -105,9 +104,6 @@ docs = [
     "mkdocstrings[python]",  # Docs API docstrings
 ]
 
-[project.scripts]
-spyglass_cli = "spyglass.cli:cli"
-
 [project.urls]
 "Homepage" = "https://github.com/LorenFrankLab/spyglass"
 "Bug Tracker" = "https://github.com/LorenFrankLab/spyglass/issues"
@@ -173,7 +169,6 @@ source = ["*/src/spyglass/*"]
 omit = [ # which submodules have no tests
     "*/__init__.py",
     "*/_version.py",
-    "*/cli/*",
     # "*/common/*",
     "*/data_import/*",
     "*/decoding/v0/*",