Ordered list increment; update pre-commit versions

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ exclude: (^.github/|^docs/site/|^images/)
 repos:
   - repo: https://github.com/executablebooks/mdformat
     # Do this before other tools "fixing" the line endings
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
       - id: mdformat
         name: Format Markdown
@@ -22,7 +22,7 @@ repos:
           - mdformat-gfm
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-toml
       - id: check-yaml
@@ -43,7 +43,7 @@ repos:
       - id: fix-byte-order-marker
 
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.29.0
+    rev: v1.33.0
     hooks:
       - id: yamllint
         args:
@@ -52,7 +52,7 @@ repos:
           - "{extends: relaxed, rules: {line-length: {max: 80}}}"
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.254
+    rev: v0.1.6
     hooks:
       - id: ruff
         args: [
@@ -64,12 +64,12 @@ repos:
         # E501: Line too long - Allow longer lines in table definitions
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.1
+    rev: v2.2.1
     hooks:
       - id: autoflake
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+    rev: v2.2.6
     hooks:
       - id: codespell
         args: [--toml, pyproject.toml]

docs/README.md

@@ -6,7 +6,7 @@
 section of this file. New pages should be either:
 
 1. A markdown file in the `docs/` directory.
-1. A Jupyter notebook in the `notebooks/` directory.
+2. A Jupyter notebook in the `notebooks/` directory.
 
 The remainder of `mkdocs.yml` specifies the site's
 [configuration](https://www.mkdocs.org/user-guide/configuration/)

docs/src/contribute.md

@@ -243,10 +243,10 @@ Spyglass follows [Semantic Versioning](https://semver.org/) with versioning of
 the form `X.Y.Z` (e.g., `0.4.2`).
 
 1. In `CITATION.cff`, update the `version` key.
-1. Make a pull request with changes.
-1. After the pull request is merged, pull this merge commit and tag it with
+2. Make a pull request with changes.
+3. After the pull request is merged, pull this merge commit and tag it with
     `git tag {version}`
-1. Publish the new release tag. Run `git push origin {version}`. This will
+4. Publish the new release tag. Run `git push origin {version}`. This will
     rebuild docs and push updates to PyPI.
-1. Make a new
+5. Make a new
     [release on GitHub](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository).

docs/src/misc/insert_data.md

@@ -34,7 +34,7 @@ particular probe is stored in the `ProbeType` and `Probe` tables of
     )
     ```
 
-1. define these entries in a special YAML file called `entries.yaml` that is
+2. define these entries in a special YAML file called `entries.yaml` that is
     processed when `spyglass` is imported. One can think of `entries.yaml` as a
     place to define information that the database should come pre-equipped
     prior to ingesting any NWB files. The `entries.yaml` file should be placed
@@ -43,9 +43,11 @@ particular probe is stored in the `ProbeType` and `Probe` tables of
 
     ```yaml
     TableName:
-    - TableEntry1Field1: Value
-    TableEntry1Field2: Value
-    - TableEntry2Field1: Value
+        - TableEntry1Field1: Value
+
+    TableEntry1Field2:
+        - TableEntry2Field1: Value
+
     TableEntry2Field2: Value
     ```
 

docs/src/misc/merge_tables.md

@@ -28,7 +28,7 @@ pipeline. By convention...
     one secondary attribute, `source`, which gives the part table name. Both
     are managed with the custom `insert` function of this class.
 
-1. Each part table has inherits the final table in its respective pipeline, and
+2. Each part table has inherits the final table in its respective pipeline, and
     shares the same name as this table.
 
 ```python

notebooks/README.md

@@ -18,7 +18,7 @@ For folks running ephys analysis, one could use the either one or both of the
 following...
 
 1. Spike Sorting, and optionally the Curation notebooks
-1. LFP, and optionally Theta notebooks
+2. LFP, and optionally Theta notebooks
 
 ## 2. Position