Merge branch 'spikesorting-populator-v1' of https://github.com/LorenFrankLab/spyglass into spikesorting-populator-v1

Author: edeno

.github/codecov.yml

@@ -0,0 +1,8 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 68%
+    patch:
+      default:
+        enabled: false

.github/pull_request_template.md

@@ -14,13 +14,12 @@ This PR.
 # Checklist:
 
 <!--
-For items below with choices, select one (e.g., yes, no) 
-and check the box to indicate that a choice was selected.
-If not applicable, check the box and add `N/A` after the box.
+For items below with `if`, please mark those that do not apply with N/A
+
 For example:
-- [X] This has a choice: no
-- [X] N/A. If choice, other item.
-This comment may be deleted on submission.
+- [X] N/A. If this PR X, related item.
+- [X] If this PR Y, other item.
+- [X] I have updated the `CHANGELOG.md` ...
 
 Alter notes example:
 ```python
@@ -29,10 +28,8 @@ Table.alter() # Comment regarding the change
 ```
 -->
 
-- [ ] This PR should be accompanied by a release: (yes/no/unsure)
-- [ ] If release, I have updated the `CITATION.cff`
-- [ ] This PR makes edits to table definitions: (yes/no)
-- [ ] If table edits, I have included an `alter` snippet for release notes.
+- [ ] If this PR should be accompanied by a release, I have updated the `CITATION.cff`
+- [ ] If this PR edits table definitions, I have included an `alter` snippet for release notes.
 - [ ] If this PR makes changes to position, I ran the relevant tests locally.
+- [ ] If this PR makes user-facing changes, I have added/edited docs/notebooks to reflect the changes
 - [ ] I have updated the `CHANGELOG.md` with PR number and description.
-- [ ] I have added/edited docs/notebooks to reflect the changes

.github/workflows/lint.yml

@@ -1,8 +1,10 @@
 name: Lint
+permissions:
+  contents: read
 
 on:
   push:
-    branches: 
+    branches:
       - '!documentation'
   pull_request:
 

CHANGELOG.md

@@ -1,7 +1,6 @@
 # Change Log
 
-<!--
-## [0.5.6] (Unreleased) - WHEN UNCOMMENTING, ADD LINK AT BOTTOM
+## [0.5.6] (Unreleased)
 
 ### Release Notes
 
@@ -12,15 +11,32 @@ When altering tables, import all foreign key references.
 #
 ```
 
+### Documentation
+
+- Delete extra pyscripts that were renamed # 1363
+- Add note on fetching changes to setup notebook #1371
+
 ### Infrastructure
 
-- Thing
+- Set default codecov threshold for test fail, disable patch check #1370, #1372
+- Simplify PR template #1370
 
-### Pipelines
+### Behavior
 
-- Common
-    - Thing
--->
+- Add methods for calling moseq visualization functions #1374
+
+### Decoding
+
+- Ensure results directory is created if it doesn't exist #1362
+
+### Position
+
+- Ensure video files are properly added to `DLCProject` #1367
+- DLC parameter handling improvements and default value corrections #1379
+
+### Spikesorting
+
+- Implement short-transaction `SpikeSortingRecording.make` for v0 #1338
 
 ## [0.5.5] (Aug 6, 2025)
 

notebooks/00_Setup.ipynb

@@ -245,7 +245,23 @@
     "`pip install spyglass-neuro`, but downloading from GitHub will also download\n",
     "other files, like this tutorial.\n",
     "2. Developers who wish to work on the code base may want to do an editable\n",
-    "install from within their conda environment: `pip install -e /path/to/spyglass/`\n"
+    "install from within their conda environment: `pip install -e /path/to/spyglass/`\n",
+    "\n",
+    "### Staying up to date \n",
+    "\n",
+    "To get the latest updates and bugfixes between releases, you should occasionally\n",
+    "navigate to your spyglass directory and run ...\n",
+    "\n",
+    "```bash\n",
+    "cd /your/project/directory/spyglass/\n",
+    "git pull # update files from GitHub\n",
+    "pip install . -U # update install from this directory\n",
+    "```\n",
+    "\n",
+    "Adding `--no-deps` to this last install command will skip over dependency checks,\n",
+    "for a faster first pass.\n",
+    "\n",
+    "If you encounter issues, please try updating first."
    ]
   },
   {

notebooks/60_MoSeq.ipynb

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.16.7
+#       jupytext_version: 1.14.5
 #   kernelspec:
 #     display_name: spyglass
 #     language: python
@@ -223,6 +223,21 @@
 # 2. Developers who wish to work on the code base may want to do an editable
 # install from within their conda environment: `pip install -e /path/to/spyglass/`
 #
+# ### Staying up to date
+#
+# To get the latest updates and bugfixes between releases, you should occasionally
+# navigate to your spyglass directory and run ...
+#
+# ```bash
+# # cd /your/project/directory/spyglass/
+# git pull # update files from GitHub
+# pip install . -U # update install from this directory
+# ```
+#
+# Adding `--no-deps` to this last install command will skip over dependency checks,
+# for a faster first pass.
+#
+# If you encounter issues, please try updating first.
 
 # ### Optional Dependencies
 #