Bring main and prettier in

.copier-answers.yml

@@ -2,7 +2,7 @@
 _commit: v0.4.1
 _src_path: https://github.com/linkml/linkml-project-copier
 add_example: false
-copyright_year: '2025'
+copyright_year: "2025"
 email: robert.carroll@vumc.org
 full_name: Robert Carroll
 gh_action_docs_preview: true

.pre-commit-config.yaml

@@ -1,45 +1,47 @@
----
 # https://pre-commit.com/
+
+#exclude: "^(project/|generated/|target/|docs/|src/linkml/schema/submodules/|src/common_access_model/datamodel/|tests/)"
+exclude: "^(project|src/common_access_model/datamodel/|tests/)"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
       - id: check-toml
       - id: check-yaml
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-        args: [--markdown-linebreak-ext=md]
 
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.37.0
     hooks:
       - id: yamllint
         args: [-c=.yamllint.yaml]
 
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
     hooks:
-      - id: codespell
-        additional_dependencies:
-          - tomli
+      - id: prettier
+        types_or: [yaml]
+        language_version: "20.11.0"
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
 
   - repo: https://github.com/crate-ci/typos
     rev: v1.31.1
     hooks:
       - id: typos
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.11.3
+    rev: v0.16.3 # Upgraded version
     hooks:
-      # Run the linter.
-      - id: ruff
+      - id: ruff-check # Works perfectly here
         args: [--fix, --exit-non-zero-on-fix]
-      # Run the formatter.
       - id: ruff-format
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    # uv version.
     rev: 0.6.12
     hooks:
       - id: uv-lock

.yamllint.yaml

@@ -3,10 +3,10 @@
 extends: default
 
 rules:
-  document-start: disable  # Don't check if document has a start marker (---).
+  document-start: disable # Don't check if document has a start marker (---).
   line-length:
     max: 80
     level: warning
     allow-non-breakable-words: true
     allow-non-breakable-inline-mappings: true
-  new-lines: disable  # Don't check for type of new line characters.
+  new-lines: disable # Don't check for type of new line characters.

COLLABORATORS.md

@@ -0,0 +1,155 @@
+## Welcome to the Common Access Model 🚀
+
+This repository represents the core model, Common Access Model (CAM). In order
+to allow downstream models to extend a common set of classes and their
+properties, those models should adhere to use this model as a Git submodule.
+
+## Key Integration Guidelines
+
+All changes to this model should be made with the understanding that those
+changes are completely valid for all or many of the downstream models. Those
+changes should be made directly within this repository and not as changes to the
+versions from the submodules themselves.
+
+Please see the following notes when integrating this model as a submodule within
+one of the downtream modules:
+
+- Do Not Modify the Submodule from within this repository: All foundational
+  classes, slots, and enums live in the core submodule. Any program-specific
+  customizations must happen strictly in your downstream files.
+- Leverage Imports: At this time, the current model imports the
+  common_access_model.yaml directly within the main model definition.
+- Extend via Inheritance: Use the is_a or mixins keys to create program-specific
+  subclasses that inherit core slots while allowing you to add local attributes.
+- Refine via Slot Usage: If you need to restrict or change the behavior of an
+  inherited core slot just for your program's classes, use the slot_usage
+  feature.
+
+## Getting Started
+
+If you aren't already familiar with working with submodules, there are just a
+couple of key takeaways to keep in mind:
+
+- The submodule has been pinned to a specific git commit hash to avoid
+  unexpected changes the CAM creeping into downstream model interfering with
+  local builds, CI/CD scripts, etc.
+- The submodule itself should only be updated by deliberate action with the
+  expectation that downstream model changes may be required to reflect incoming
+  updates.
+
+### Initializing the submodule
+
+Before you can actually compile the model on a new machine, you'll need to pull
+the submodule's content down. A convenient just recipe has been created for
+exactly that:
+
+```bash
+just init-submodule
+```
+
+or, if you prefer to do it directly yourself:
+
+```bash
+git submodule update --init --recursive
+# make sure nothing is broken
+just lint && just test
+```
+
+Subsequent calls can drop the init if you know for a fact that no other
+submodules have been added. The just recipe does call the linter and runs the
+linkml test as a subsequent dependency, in case there are upstream changes that
+invalidate the downstream model.
+
+### Updating the pinned hash
+
+Once it has been decided that it is time to update the CAM to use the latest
+version, the maintainer should run the following commands to fetch, test and
+lock the new version into the downstream model's main.
+
+```bash
+# Navigate into the submodule directory
+cd src/kf_access_model/schema/common_access_model
+
+# Fetch and check out the desired remote target (e.g., main branch)
+git fetch origin
+git checkout origin/main
+
+# Move back to the repository root
+cd -
+
+# Run linter and tests
+just lint && just test
+
+
+# Commit the new submodule hash pointer to this repository
+git add src/kf_access_model/schema/common_access_model
+git commit -m "chore: update common_access_model submodule to latest hash"
+```
+
+## Release Artifacts
+
+There are a number of artifacts which are used by various scripts including the
+dbt utilities which are built via github actions during release. To trigger the
+build, create releases linked to a semantic version preceded with a v (i.e.
+v1.0.1).
+
+These artifacts include:
+
+- SQL Alchemy model
+- dbt model yml file
+- SQL Schema
+- data dictionary conformant to the current FTD spec
+- enumerations csv file extracted from all of the permissible values
+
+The last two are used by this group's dbt utilities tooling. The SQL Alchemy
+model is used by a handful of other scripts.
+
+## Beautification
+
+### Code Quality & Formatting with pre-commit
+
+We use `pre-commit` to catch minor issues automatically before your changes
+reach code review. This saves you time by automating formatting and linting
+tasks, allowing code reviews to focus strictly on functionality and logic rather
+than style choices.
+
+The hooks automatically run the following optimizations when you execute a
+`git commit`:
+
+- **Formatting:** Standardizes Python code via **Ruff** and YAML configurations
+  via **Prettier** (matching the default styling behavior of editors like Zed).
+- **Linting:** Analyzes code patterns and auto-fixes formatting anomalies on the
+  fly.
+- **Checks:** Verifies structural syntax sanity for TOML/YAML layouts, removes
+  trailing whitespace, and forces trailing newlines.
+
+#### Getting Started (First-Time Setup)
+
+If you are setting up the repository for the first time, you don't even need to
+install `pre-commit` globally on your system. You can handle everything through
+**`uv`**:
+
+1. **Register the Git hook scripts** inside the local `.git/` directory using
+   `uv run`:
+   ```bash
+   uv run pre-commit install
+   ```
+
+---
+
+#### Subsequent Uses & Everyday Workflow
+
+Once registered, the tool seamlessly hooks into your normal Git workflow without
+any manual intervention:
+
+- **Automatic Execution:** Every time you run `git commit`, the hooks
+  automatically run against your _staged changes_. `uv` will transparently
+  manage the tool environments in the background.
+- **If a hook modifies a file (or fails):** The commit is safely aborted so you
+  can inspect the adjustments. Simply stage the updated files (`git add .`) and
+  run your `git commit` command again.
+- **Manual Repository Check:** If you ever want to force formatting across the
+  entire repository manually without creating a commit, run:
+  ```bash
+  uv run pre-commit run --all-files
+  ```

config.yaml

@@ -60,5 +60,4 @@ generator_args:
   typescript:
     mergeimports: true
     metadata: true
-
 ...

mkdocs.yml

@@ -25,7 +25,7 @@ watch:
   - src/common_access_model/schema
 
 nav:
-#  - Home: index.md
+  #  - Home: index.md
   - Schema: elements/index.md
   - ER Diagram: elements/erdiagram.md
   - dbt: dbt_artifacts.md

src/common_access_model/_version.py

@@ -1,4 +1,4 @@
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import PackageNotFoundError, version
 
 try:
     __version__ = version(__name__)

src/common_access_model/datamodel/__init__.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+
 from .common_access_model import *
 
 THIS_PATH = Path(__file__).parent