Merge branch 'master' into moseq

CHANGELOG.md

@@ -1,16 +1,23 @@
 # Change Log
 
-## [0.5.4] (Unreleased)
+
+## [0.5.5] (Unreleased)
 
 ### Infrastructure
 
+- Ensure merge tables are declared during file insertion #1205
+- Update URL for DANDI Docs #1210
 - Add common method `get_position_interval_epoch` #1056
 
 ### Pipelines
 
+- Position
+    - Allow population of missing `PositionIntervalMap` entries during population of `DLCPoseEstimation` #1208
+
 - Behavior
     - Implement pipeline for keypoint-moseq extraction of behavior syllables #1056
 
+
 ## [0.5.4] (December 20, 2024)
 
 ### Infrastructure

notebooks/05_Export.ipynb

@@ -928,9 +928,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The first step you will need to do is to [create a Dandi account](https://www.dandiarchive.org/handbook/16_account/). \n",
+    "The first step you will need to do is to [create a Dandi account](https://docs.dandiarchive.org/16_account/). \n",
     "With this account you can then [register a new dandiset](https://dandiarchive.org/dandiset/create) by providing a name and basic metadata. \n",
-    "Dandi's instructions for these steps are available [here](https://www.dandiarchive.org/handbook/13_upload/).\n",
+    "Dandi's instructions for these steps are available [here](https://docs.dandiarchive.org/13_upload/).\n",
     "\n",
     "The key information you will need from your registration is the `dandiset ID` and your account `api_key`, both of which are available from your registered account.\n",
     "\n",

notebooks/py_scripts/05_Export.py

@@ -252,9 +252,9 @@
 
 # ### Dandiset Upload
 
-# The first step you will need to do is to [create a Dandi account](https://www.dandiarchive.org/handbook/16_account/).
+# The first step you will need to do is to [create a Dandi account](https://docs.dandiarchive.org/16_account/).
 # With this account you can then [register a new dandiset](https://dandiarchive.org/dandiset/create) by providing a name and basic metadata.
-# Dandi's instructions for these steps are available [here](https://www.dandiarchive.org/handbook/13_upload/).
+# Dandi's instructions for these steps are available [here](https://docs.dandiarchive.org/13_upload/).
 #
 # The key information you will need from your registration is the `dandiset ID` and your account `api_key`, both of which are available from your registered account.
 #

src/spyglass/common/common_behav.py

@@ -536,6 +536,9 @@ def _no_transaction_make(self, key):
         EPSILON = 0.51  # tolerated time diff in bounds across epoch/pos
         no_pop_msg = "CANNOT POPULATE PositionIntervalMap"
 
+        # Strip extra info from key if not passed via populate call
+        key = {k: v for k, v in key.items() if k in self.primary_key}
+
         nwb_file_name = key["nwb_file_name"]
         pos_intervals = get_pos_interval_list_names(nwb_file_name)
         null_key = dict(key, position_interval_name="")

src/spyglass/common/populate_all_common.py

@@ -20,6 +20,7 @@
 from spyglass.common.common_task import TaskEpoch
 from spyglass.common.common_usage import InsertError
 from spyglass.utils import logger
+from spyglass.utils.dj_helper_fn import declare_all_merge_tables
 
 
 def log_insert_error(
@@ -117,6 +118,8 @@ def populate_all_common(
     """
     from spyglass.spikesorting.imported import ImportedSpikeSorting
 
+    declare_all_merge_tables()
+
     error_constants = dict(
         dj_user=dj.config["database.user"],
         connection_id=dj.conn().connection_id,

src/spyglass/position/v1/position_dlc_pose_estimation.py

@@ -254,7 +254,6 @@ def _logged_make(self, key):
                     "nwb_file_name": key["nwb_file_name"],
                     "epoch": key["epoch"],
                 },
-                populate_missing=False,
             )
         )
         if interval_list_name:

src/spyglass/utils/dj_helper_fn.py

@@ -68,6 +68,20 @@ def ensure_names(
     return getattr(table, "full_table_name", None)
 
 
+def declare_all_merge_tables():
+    """Ensures all merge tables in the spyglass core package are declared.
+    - Prevents circular imports
+    - Prevents errors from table declaration within a transaction
+    - Run during nwb insertion
+    """
+    from spyglass.decoding.decoding_merge import DecodingOutput  # noqa: F401
+    from spyglass.lfp.lfp_merge import LFPOutput  # noqa: F401
+    from spyglass.position.position_merge import PositionOutput  # noqa: F401
+    from spyglass.spikesorting.spikesorting_merge import (  # noqa: F401
+        SpikeSortingOutput,
+    )
+
+
 def fuzzy_get(index: Union[int, str], names: List[str], sources: List[str]):
     """Given lists of items/names, return item at index or by substring."""
     if isinstance(index, int):