Add pre-commit hooks for Ruff and blacken-docs with global exclusions

.github/workflows/cd.yml

@@ -17,24 +17,24 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      
+
       - name: Set up Python 3.10.11
         uses: actions/setup-python@v3
         with:
           python-version: "3.10.11"
-          
+
       - name: Check Python Version
         run: python --version
 
       - name: Install dependencies
         run: |
           python -m pip install ".[docs]"
-     
+
       - name: Build API documentation
         run: |
           make -C docs clean
           make -C docs html
-       
+
       - name: Deploy API documentation
         uses: peaceiris/[email protected]
         with:

.github/workflows/cd_manual.yml

@@ -13,24 +13,24 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      
+
       - name: Set up Python 3.10.11
         uses: actions/setup-python@v3
         with:
           python-version: "3.10.11"
-          
+
       - name: Check Python Version
         run: python --version
 
       - name: Install dependencies
         run: |
           python -m pip install ".[docs]"
-     
+
       - name: Build API documentation
         run: |
           make -C docs clean
           make -C docs html
-       
+
       - name: Archive documentation as artifact
         uses: actions/upload-artifact@v4
         with:

.github/workflows/ci.yml

@@ -20,15 +20,15 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: python -m pip install ".[test]"
-      
+
       - name: Test with pytest
         run: python -m pytest
 

.github/workflows/ci_manual.yml

@@ -16,14 +16,14 @@ jobs:
     steps:
       - name:
         uses: actions/checkout@v3
-      
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: python -m pip install ".[test]"
-       
+
       - name: Test with pytest
         run: python -m pytest

.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+# .pre-commit-config.yaml
+# WaveDiff pre-commit configuration
+# Globally excludes notebooks and historical papers directories
+
+default_stages: [commit]
+
+# Apply globally to all hooks
+exclude: '(^papers/|\.ipynb$)'
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-toml
+      - id: check-yaml
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.10.0
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+
+      - id: ruff-format
+
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.19.1
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.10.0]
+        args: [-l, '120', -t, py312]
+
+  - repo: local
+    hooks:
+      - id: check-scriv-fragment
+        name: Ensure Scriv fragment exists for PR
+        entry: bash -c
+        args:
+          - |
+            CHANGED_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep -E "\.py$|\.md$|\.rst$|\.yaml$" | grep -v "^docs/")
+            FRAGMENTS=$(git diff --cached --name-only --diff-filter=ACM | grep "^changelog.d/")
+            if [ -n "$CHANGED_FILES" ] && [ -z "$FRAGMENTS" ]; then
+              echo "ERROR: Please add a Scriv changelog fragment in changelog.d/ for this PR."
+              exit 1
+            fi
+        language: system

DEV_WORKFLOW.md

@@ -1,20 +1,20 @@
 # **WaveDiff Development Plan**
 
 ## 1.  **Define a Milestone**
-    
+
 
   * **Purpose**: Milestones mark the completion of project cycles and achievement of predefined goals. A milestone is a timeline point marking the end of a project cycle, where a set of goals defined at the start of the cycle have been completed.  Goals could be tasks associated with feature development, testing phase completion, etc. List & Open issues. 
-    
+
   * **Types of Milestones:** Differentiate between major, minor and patch release releases to track progress effectively.
-    
+
 
 Make a milestone related to a release on possibly a minor release schedule (e.g. monthly schedule). Differentiate between the different types of releases (minor, major, patch).
 
 ## 2.  **Git Workflow Branching Model (Made with** [**mermaid**](https://mermaid.js.org)**)**
 ![](assets/Git-Branching-Model.png)
 
    *   **main**: Stores official release history with tagged version numbers (see top row in the diagram above).
-    
+
    *   **develop**: This branch is the integration branch for features.
 
    *   **feature**: Branch off of `develop` for new feature development.  Features get merged to `develop` (never to main).
@@ -30,7 +30,7 @@ Make a milestone related to a release on possibly a minor release schedule (e.g.
 
 
 ## 3.  **New Branch naming conventions**
-    
+
 
 Branches created for the purpose of a Pull Request should be directly related to an open issue within the project’s issue tracker.  This ensures that all code changes are tied to specific tasks or features, facilitating better organisation and tracking of contributions. Below are the branch naming conventions:
 
@@ -51,41 +51,41 @@ Branches created for the purpose of a Pull Request should be directly related to
 Replace with the corresponding issue number and provide a brief description of the changes in \`short\_description\`.
 
 ## 4.  **Feature branch creation** 
-    
+
 
 *   Pull the latest changes from the remote repository
 
 *   Checkout `develop`
 
 *   Create a new feature branch
-    
+
 *   Ensure the feature branch’s commits align with the defined scope
-    
+
 
 **Tip**: Keep feature branch development focused on the defined scope outlined in the corresponding issue. Avoid introducing unrelated changes. Instead, open a new issue for out-of-scope features or bugs, creating a separate branch for their development.
 
 ## 5.  **Completion of development** 
-    
+
 
 *   Run training and metrics validation tests locally to confirm no breaking behaviour or errors were introduced.  Include test reports as per the PR template.
 
 *   Open a Pull Request to start the review process, ensuring to map the branch correctly to the target branch (i.e. `feature` -> `develop` or `hotfix` -> `main`).
 
 *   In the description of the Pull Request, explicitly state whether the PR resolves or closes an open issue by using one of the following formats:
-    
+
     *   "Solves #"
-        
+
     *   "Closes #"
-        
+
 
 Example: "Solves #12345" or "Closes #8679".
 
 *   Ensure that the PR meets the defined requirements and passes Continuous Integration (CI) tests.
-    
+
 *   Assign a reviewer, assign yourself as assignee, select the correct project, choose the correct label that describes the nature of the issue (e.g. bug, enhancement, etc), choose Milestone if applicable if the issue is associated with a specific milestone or target release.
-    
+
 *   Address reviewer feedback in threads and iterate as needed, implementing the requested changes or explaining why the task is implemented in the manner it is.  Respect the rule: Whoever opens the thread/conversation in the Pull Request is responsible for closing it.
-    
+
 
 ## 6.  **Merging Pull Requests** 
 
@@ -138,28 +138,28 @@ This separation keeps release notes accurate and enables clean backports
 *   Ensure all checklist items for the release are completed.
 
 *   Merge the PR into main and tag the release.
-    
+
 
 ## 9.  **Continuous Improvement**
 
 
 *   Regularly review and refine the workflow based on team feedback and lessons learned.
-    
+
 *   Encourage collaboration and communication among team members to streamline processes and enhance productivity.
-    
+
 
 ## 10.  **Documentation and Training**
 
 
 *   Maintain up-to-date documentation outlining the development workflow and procedures.
-    
+
 *   Provide training to new team members and ensure existing members are familiar with the workflow and best practices.
 
 
 ## 11.  **Automation and Tooling**
 
 
 *   Explore automation tools to streamline repetitive tasks, such as testing, code formatting, and deployment.
-    
+
 *   Integrate with CI/CD pipelines for automated testing and deployment processes.
-    
+

README.md

@@ -1,5 +1,5 @@
-[![arXiv:2203.04908](https://img.shields.io/badge/astro--ph.IM-arXiv%3A2203.04908-B31B1B.svg)](http://arxiv.org/abs/2203.04908) 
-[![yapf](https://img.shields.io/badge/code%20style-yapf-blue.svg)](https://www.python.org/dev/peps/pep-0008/) 
+[![arXiv:2203.04908](https://img.shields.io/badge/astro--ph.IM-arXiv%3A2203.04908-B31B1B.svg)](http://arxiv.org/abs/2203.04908)
+[![yapf](https://img.shields.io/badge/code%20style-yapf-blue.svg)](https://www.python.org/dev/peps/pep-0008/)
 [![License](https://img.shields.io/badge/License-MIT-brigthgreen.svg)](https://github.com/tobias-liaudat/wf-psf/tree/master/LICENSE)
 [![Documentation](https://img.shields.io/badge/docs-online-blue)](https://cosmostat.github.io/wf-psf/)
 <h1 align='center'>WaveDiff</h1>

changelog.d/20260123_154449_jennifer.pollack_add_pre_commit_hooks.md

@@ -0,0 +1,38 @@
+<!--
+A new scriv changelog fragment.
+
+Uncomment the section that is right (remove the HTML comment wrapper).
+For top level release notes, leave all the headers commented out.
+-->
+
+<!--
+### Breaking changes
+
+- A bullet item for the Breaking changes category.
+
+-->
+<!--
+### New features
+
+- A bullet item for the New features category.
+
+-->
+<!--
+### Bug fixes
+
+- A bullet item for the Bug fixes category.
+
+-->
+<!--
+### Performance improvements
+
+- A bullet item for the Performance improvements category.
+
+-->
+
+### Internal changes
+
+- Added pre-commit hooks for code quality, formatting, and changelog enforcement
+
+
+

config/data_config.yaml

@@ -11,7 +11,7 @@ data:
     SEDS: null
     zernike_coef: null
     C_poly: null
-    params: # 
+    params: #
       d_max: 2
       max_order: 45
       x_lims: [0, 1000.0]