Fetch upstream, resolve conflicts

.github/workflows/publish-docs.yml

@@ -1,11 +1,8 @@
 name: Publish docs
 on:
-  pull_request:
-    branches:
-      - master
-    types:
-      - closed
   push:
+    tags: # See PEP 440 for valid version format
+      - "*.*.*" # For docs bump, use X.X.XaX
     branches:
       - test_branch
 

CHANGELOG.md

@@ -1,11 +1,11 @@
 # Change Log
 
-## 0.4.1 (Unreleased)
+## [0.4.1] (June 30, 2023)
 
 - Add mkdocs automated deployment. #527, #537, #549, #551
-- Add class for Merge Tables. #556, #564
+- Add class for Merge Tables. #556, #564, #565
 
-## 0.4.0 (May 22, 2023)
+## [0.4.0] (May 22, 2023)
 
 - Updated call to `spikeinterface.preprocessing.whiten` to use dtype np.float16.
   #446,
@@ -33,7 +33,7 @@
 - Updated `environment_position.yml`. #502
 - Renamed `FirFilter` class to `FirFilterParameters`. #512
 
-## 0.3.4 (March 30, 2023)
+## [0.3.4] (March 30, 2023)
 
 - Fixed error in spike sorting pipeline referencing the "probe_type" column
   which is no longer accessible from the `Electrode` table. #437
@@ -44,18 +44,28 @@
 - Fixed inconsistency between capitalized/uncapitalized versions of "Intan" for
   DataAcquisitionAmplifier and DataAcquisitionDevice.adc_circuit. #430, #438
 
-## 0.3.3 (March 29, 2023)
+## [0.3.3] (March 29, 2023)
 
 - Fixed errors from referencing the changed primary key for `Probe`. #429
 
-## 0.3.2 (March 28, 2023)
+## [0.3.2] (March 28, 2023)
 
 - Fixed import of `common_nwbfile`. #424
 
-## 0.3.1 (March 24, 2023)
+## [0.3.1] (March 24, 2023)
 
 - Fixed import error due to `sortingview.Workspace`. #421
 
-## 0.3.0 (March 24, 2023)
+## [0.3.0] (March 24, 2023)
 
-To be added.
+- Refactor common for non Frank Lab data, allow file-based mods #420
+- Allow creation and linkage of device metadata from YAML #400
+- Move helper functions to utils directory #386
+
+[0.4.1]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.4.1
+[0.4.0]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.4.0
+[0.3.4]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.3.4
+[0.3.3]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.3.3
+[0.3.2]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.3.2
+[0.3.1]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.3.1
+[0.3.0]: https://github.com/LorenFrankLab/spyglass/releases/tag/0.3.0

docs/src/misc/merge_tables.md

@@ -70,12 +70,19 @@ These functions are described in the
 
 ### Restricting
 
-One quirk of these utilities is that they take restrictions as arguments,
-rather than with operators. So `Table & "field='value'"` becomes
-`MergeTable.merge_view(restriction={'field':'value}`). This is because
-`merge_view` is a `Union` rather than a true Table. While `merge_view` can
-accept all valid restrictions, `merge_get_part` and `merge_get_parent` have
-additional restriction logic when supplied with `dicts`.
+In short: restrict Merge Tables with arguments, not the `&` operator.
+
+- Normally: `Table & "field='value'"`
+- Instead: `MergeTable.merge_view(restriction="field='value'"`).
+
+_Caution_. The `&` operator may look like it's working when using `dict`, but
+this is because invalid keys will be ignored. `Master & {'part_field':'value'}`
+is equivalent to `Master` alone
+([source](https://docs.datajoint.org/python/queries/06-Restriction.html#restriction-by-a-mapping)).
+
+When provided as arguments, methods like `merge_get_part` and `merge_get_parent`
+will override the permissive treatment of mappings described above to only
+return relevant tables.
 
 ### Building Downstream
 
@@ -171,8 +178,7 @@ There are also functions for retrieving part/parent table(s) and fetching data.
    the format specified by keyword arguments and one's DataJoint config.
 
 ```python
-result3 = (LFPOutput & common_keys_CH[0]).merge_get_part(join_master=True)
-result4 = LFPOutput().merge_get_part(restriction=common_keys_CH[0])
+result4 = LFPOutput.merge_get_part(restriction=common_keys_CH[0],join_master=True)
 result5 = LFPOutput.merge_get_parent(restriction='nwb_file_name LIKE "CH%"')
 result6 = result5.fetch('lfp_sampling_rate') # Sample rate for all CH* files
 result7 = LFPOutput.merge_fetch("filter_name", "nwb_file_name")

environment.yml

@@ -5,7 +5,7 @@ channels:
   - franklab
   - edeno
 dependencies:
-  - python>=3.8,<3.10
+  - python>=3.9,<3.10
   - jupyterlab>=3.*
   - pydotplus
   - dask

environment_position.yml

@@ -15,7 +15,7 @@ channels:
   - franklab
   - edeno
 dependencies:
-  - python>=3.8, <3.10
+  - python>=3.9, <3.10
   - jupyterlab>=3.*
   - pydotplus>=2.0.*
   - libgcc

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "spyglass-neuro"
 description = "Neuroscience data analysis framework for reproducible research"
 readme = "README.md"
-requires-python = ">=3.8,<3.10"
+requires-python = ">=3.9,<3.10"
 license = { file = "LICENSE" }
 authors = [
     { name = "Loren Frank", email = "[email protected]" },
@@ -78,7 +78,7 @@ test = [
     "kachery-cloud",
 ]
 docs = [
-    "hatch",                 # Get version from env 
+    "hatch",                 # Get version from env
     "mike",                  # Docs versioning
     "mkdocs",                # Docs core
     "mkdocs-exclude",        # Docs exclude files

src/spyglass/lfp/v1/lfp_artifact.py

@@ -96,7 +96,7 @@ def make(self, key):
         ).fetch1("artifact_params")
 
         artifact_detection_algorithm = artifact_params[
-            "ripple_detection_algorithm"
+            "artifact_detection_algorithm"
         ]
         artifact_detection_params = artifact_params[
             "artifact_detection_algorithm_params"
@@ -121,11 +121,13 @@ def make(self, key):
         # set up a name for no-artifact times using recording id
         # we need some name here for recording_name
         key["artifact_removed_interval_list_name"] = "_".join(
-            key["nwb_file_name"],
-            key["target_interval_list_name"],
-            "LFP",
-            key["artifact_params_name"],
-            "artifact_removed_valid_times",
+            [
+                key["nwb_file_name"],
+                key["target_interval_list_name"],
+                "LFP",
+                key["artifact_params_name"],
+                "artifact_removed_valid_times",
+            ]
         )
 
         LFPArtifactRemovedIntervalList.insert1(key, replace=True)