ci(pre-commit): migrate linting to Ruff and update hooks:

- Replace black, flake8, and isort with Ruff for linting and formatting.
- Update pre-commit configuration and dependencies, add Ruff config to
pyproject.toml, and apply automatic fixes across the codebase.

Author: harryswift01

.github/CONTRIBUTING.md

@@ -10,7 +10,7 @@ This guide explains how to set up your environment, make changes, and submit the
 
 ## Getting Started
 
-Before contributing, please review the [Developer Guide](https://codeentropy.readthedocs.io/en/latest/developer_guide.html).  
+Before contributing, please review the [Developer Guide](https://codeentropy.readthedocs.io/en/latest/developer_guide.html).
 It covers CodeEntropy’s architecture, setup instructions, and contribution workflow.
 
 If you’re new to the project, we also recommend:
@@ -23,19 +23,19 @@ If you’re new to the project, we also recommend:
 
 When you’re ready to submit your work:
 
-1. **Push your branch** to GitHub.  
-2. **Open a [pull request](https://help.github.com/articles/using-pull-requests/)** against the `main` branch.  
+1. **Push your branch** to GitHub.
+2. **Open a [pull request](https://help.github.com/articles/using-pull-requests/)** against the `main` branch.
 3. **Fill out the PR template**, including:
-   - A concise summary of what your PR does  
-   - A list of all changes introduced  
-   - Details on how these changes affect the repository (features, tests, documentation, etc.)  
+   - A concise summary of what your PR does
+   - A list of all changes introduced
+   - Details on how these changes affect the repository (features, tests, documentation, etc.)
 4. **Verify before submission**:
-   - All tests pass  
-   - Pre-commit checks succeed  
-   - Documentation is updated where applicable  
+   - All tests pass
+   - Pre-commit checks succeed
+   - Documentation is updated where applicable
 5. **Review process**:
-   - Your PR will be reviewed by the core development team.  
-   - At least **one approval** is required before merging.  
+   - Your PR will be reviewed by the core development team.
+   - At least **one approval** is required before merging.
 
 We aim to provide constructive feedback quickly and appreciate your patience during the review process.
 
@@ -45,12 +45,12 @@ We aim to provide constructive feedback quickly and appreciate your patience dur
 
 Found a bug or have a feature request?
 
-1. **Open a new issue** on GitHub.  
-2. Provide a **clear and descriptive title**.  
+1. **Open a new issue** on GitHub.
+2. Provide a **clear and descriptive title**.
 3. Include:
-   - Steps to reproduce the issue (if applicable)  
-   - Expected vs. actual behavior  
-   - Relevant logs, screenshots, or input files  
+   - Steps to reproduce the issue (if applicable)
+   - Expected vs. actual behavior
+   - Relevant logs, screenshots, or input files
 
 Well-documented issues help us address problems faster and keep CodeEntropy stable and robust.
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -12,11 +12,11 @@ assignees: ''
 
 ---
 
-## To Reproduce  
+## To Reproduce
 <!-- Provide the YAML configuration and the exact CLI command that reproduces the issue. -->
 
 ### YAML configuration
-<!-- Paste the YAML file or the smallest excerpt that reproduces the issue.  
+<!-- Paste the YAML file or the smallest excerpt that reproduces the issue.
 Remove unrelated fields to make it minimal. -->
 ```yaml
 # Paste the YAML snippet here
@@ -46,7 +46,7 @@ Remove unrelated fields to make it minimal. -->
 - Python Version:
 - Package list:
   - If using conda, run: `conda list > packages.txt` and paste the contents here.
-    
+
     ``` bash
     # Paste packages.txt here
     ```

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,16 +5,16 @@
 <!-- List all the changes introduced in this PR. -->
 ### Change 1 <!-- Rename Change 1 to reflect change title -->:
 - <!-- Bullet point the changes in update 1. -->
--  
+-
 
 ### Change 2 <!-- Rename Change 2 to reflect change title -->:
 - <!-- Bullet point the changes in update 2. -->
--  
+-
 
 ### Change 3 <!-- Rename Change 3 to reflect change title -->:
 - <!-- Bullet point the changes in update 3. -->
--  
+-
 
 ## Impact
 - <!-- Bullet point the expected impact this PR will have on the codebase. -->
--  
+-

.github/renovate.json

@@ -18,4 +18,4 @@
       "automerge": false
     }
   ]
-}
+}

.github/workflows/daily.yaml

@@ -63,4 +63,4 @@ jobs:
         uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
-          file: coverage.xml
+          file: coverage.xml

.github/workflows/pr.yaml

@@ -135,4 +135,4 @@ jobs:
             git status --short
             git diff
             exit 1
-          }
+          }

.github/workflows/release.yaml

@@ -146,4 +146,3 @@ jobs:
       env:
         FLIT_USERNAME: __token__
         FLIT_PASSWORD:  ${{ secrets.PYPI_API_TOKEN }}
- 

.github/workflows/weekly-docs.yaml

@@ -2,7 +2,7 @@ name: CodeEntropy Weekly Docs
 
 on:
   schedule:
-    - cron: '0 8 * * 1' 
+    - cron: '0 8 * * 1'
   workflow_dispatch:
 
 concurrency:
@@ -43,4 +43,4 @@ jobs:
         with:
           name: docs-${{ matrix.os }}-py${{ matrix.python-version }}-failure
           path: |
-            docs/_build/**
+            docs/_build/**

.github/workflows/weekly-regression.yaml

@@ -49,4 +49,4 @@ jobs:
             /tmp/pytest-of-*/pytest-*/**/config.yaml
             /tmp/pytest-of-*/pytest-*/**/codeentropy_stdout.txt
             /tmp/pytest-of-*/pytest-*/**/codeentropy_stderr.txt
-            /tmp/pytest-of-*/pytest-*/**/codeentropy_output.json
+            /tmp/pytest-of-*/pytest-*/**/codeentropy_output.json

.gitignore

@@ -126,4 +126,4 @@ job*
 *.com
 *.txt
 
-.testdata/
+.testdata/