COG-3395: Chore: pre-commit, pre-commit action, contribution guide update (#1979)

## Description
Revisited the `CONTRIBUTING.md`:
* Added the `Required tools`
* Pre-commit requirement. It replaces `ruff` and other linting guides
* Fixed `test_library.py` paths. Made sure that the testing guide is
complete and works
* Added a `pre-commit` step to `Pre-Test` workflow. It will fail if
`pre-commit` has issues and no other tests will be triggered
* Added a sufficient LLM configuration example for tests. Moved
`cognee/.env.example` to the project root for convenience

>>> Requires: https://github.com/topoteretes/cognee/pull/1980 <<<

## Acceptance Criteria
`pre-commit` action works 
Tested pre-commit locally. If a commit violates the rules - it rejects
it and fixes the issues. Then we need to `git commit ...` again.

## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [x] Other (please specify): CI and DevExp improvement

## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->

## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **I have tested my changes thoroughly before submitting this PR**
- [ ] **This PR contains minimal changes necessary to address the
issue/feature**
- [ ] My code follows the project's coding standards and style
guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
- [ ] I have linked any relevant issues in the description
- [ ] My commits have clear and descriptive messages

## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **Documentation**
* Expanded contributor guide with setup, required tools, testing
instructions, examples, and updated PR submission guidance.
* Updated pull-request checklist to reference contributing instructions.

* **Chores**
* Added three new local environment variables for LLM configuration and
updated example env file.
  * Added a pre-commit validation step to CI.
  * Updated ignore list to exclude a local environment file.

<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

.env.example

@@ -3,3 +3,7 @@
 # CORS_ALLOWED_ORIGINS="https://yourdomain.com,https://another.com"
 # For local development, you might use:
 # CORS_ALLOWED_ORIGINS="http://localhost:3000"
+
+LLM_API_KEY="your-openai-api-key"
+LLM_MODEL="openai/gpt-4o-mini"
+LLM_PROVIDER="openai"

.github/pull_request_template.md

@@ -29,7 +29,7 @@ DO NOT use AI-generated descriptions. We want to understand your thought process
 
 ## Pre-submission Checklist
 <!-- Please check all boxes that apply before submitting your PR -->
-- [ ] **I have tested my changes thoroughly before submitting this PR**
+- [ ] **I have tested my changes thoroughly before submitting this PR** (See `CONTRIBUTING.md`)
 - [ ] **This PR contains minimal changes necessary to address the issue/feature**
 - [ ] My code follows the project's coding standards and style guidelines
 - [ ] I have added tests that prove my fix is effective or that my feature works

.github/workflows/pre_test.yml

@@ -5,7 +5,7 @@ permissions:
   contents: read
 jobs:
   check-uv-lock:
-    name: Validate uv lockfile and project metadata
+    name: Lockfile and Pre-commit Hooks
     runs-on: ubuntu-22.04
     steps:
       - name: Check out repository
@@ -20,3 +20,6 @@ jobs:
 
       - name: Validate uv lockfile and project metadata
         run: uv lock --check || { echo "'uv lock --check' failed."; echo "Run 'uv lock' and push your changes."; exit 1; }
+
+      - name: Run pre-commit hooks
+        uses: pre-commit/action@v3.0.1

.gitignore

@@ -147,6 +147,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+mise.toml
 
 # Spyder project settings
 .spyderproject

CONTRIBUTING.md

@@ -62,6 +62,11 @@ Looking for a place to start? Try filtering for [good first issues](https://gith
 
 ## 2. 🛠️ Development Setup
 
+### Required tools
+* [Python](https://www.python.org/downloads/)
+* [uv](https://docs.astral.sh/uv/getting-started/installation/)
+* pre-commit: `uv run pip install pre-commit && pre-commit install`
+
 ### Fork and Clone
 
 1. Fork the [**cognee**](https://github.com/topoteretes/cognee) repository
@@ -93,29 +98,31 @@ git checkout -b feature/your-feature-name
 4. **Commits**: Write clear commit messages
 
 ### Running Tests
+
+Rename `.env.example` into `.env` and provide your OPENAI_API_KEY as LLM_API_KEY
+
 ```shell
-python cognee/cognee/tests/test_library.py
+uv run python cognee/tests/test_library.py
 ```
 
 ### Running Simple Example
 
-Change .env.example into .env and provide your OPENAI_API_KEY as LLM_API_KEY
+Rename `.env.example` into `.env` and provide your OPENAI_API_KEY as LLM_API_KEY
 
 Make sure to run ```shell uv sync ``` in the root cloned folder or set up a virtual environment to run cognee
 
 ```shell
-python cognee/cognee/examples/python/simple_example.py
+python examples/python/simple_example.py
 ```
 or
 
 ```shell
-uv run python cognee/cognee/examples/python/simple_example.py
+uv run python examples/python/simple_example.py
 ```
 
 ## 4. 📤 Submitting Changes
 
-1. Install ruff on your system
-2. Run ```ruff format .``` and ``` ruff check ``` and fix the issues
+1. Make sure that `pre-commit` and hooks are installed. See `Required tools` section for more information. Try executing `pre-commit run` if you are not sure.
 3. Push your changes:
 ```shell
 git add .