Add GitHub Copilot instructions for repository

Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>

Author: Copilot

.github/copilot-instructions.md

@@ -0,0 +1,224 @@
+# GitHub Copilot Instructions for openms-python
+
+## Repository Overview
+
+`openms-python` is a Pythonic wrapper around pyOpenMS for mass spectrometry data analysis. The goal is to provide an intuitive, Python-friendly interface that makes working with mass spectrometry data feel natural for Python developers and data scientists.
+
+**Key Principle**: Make pyOpenMS more Pythonic by wrapping verbose C++ bindings with intuitive Python APIs.
+
+## Code Style and Conventions
+
+### Python Style
+- Follow PEP 8 conventions
+- Use Black formatter with 100 character line length (configured in `pyproject.toml`)
+- Target Python 3.8+ compatibility
+- Use type hints for better IDE support and code clarity
+- Prefer clear, descriptive names over abbreviations
+
+### Wrapper Design Patterns
+
+1. **Properties over getters/setters**: Use `@property` decorators instead of verbose get/set methods
+   ```python
+   # Good
+   spec.retention_time
+   # Avoid
+   spec.getRT()
+   ```
+
+2. **Pythonic iteration**: Support Python's iteration protocols (`__iter__`, `__len__`, `__getitem__`)
+   ```python
+   for spec in experiment.ms1_spectra():
+       print(spec.retention_time)
+   ```
+
+3. **Method chaining**: Return `self` from mutation methods to enable fluent interfaces
+   ```python
+   exp.filter_by_ms_level(1).filter_by_rt(100, 500)
+   ```
+
+4. **DataFrame integration**: Provide `to_dataframe()` and `from_dataframe()` methods for pandas interoperability
+
+5. **Context managers**: Support `with` statements for file I/O operations
+
+6. **Mapping interface for metadata**: Classes wrapping `MetaInfoInterface` should support dict-like access
+   ```python
+   feature["label"] = "sample_a"
+   ```
+
+### Class Naming Convention
+- Wrapper classes use the `Py_` prefix (e.g., `Py_MSExperiment`, `Py_FeatureMap`)
+- This distinguishes them from pyOpenMS classes while maintaining recognizability
+
+### File Organization
+- Core wrapper classes: `py_*.py` files (e.g., `py_msexperiment.py`, `py_featuremap.py`)
+- I/O utilities: `io.py` and `_io_utils.py`
+- Helper utilities: `_meta_mapping.py` for metadata handling
+- Workflow helpers: `workflows.py` for high-level pipelines
+- Example data: `examples/` directory contains sample files like `small.mzML`
+
+## Testing Requirements
+
+### Test Structure
+- All tests in `tests/` directory
+- Test files follow `test_*.py` naming convention
+- Use pytest as the testing framework
+- Aim for good coverage of wrapper functionality
+
+### Running Tests
+```bash
+# Install development dependencies
+pip install -e ".[dev]"
+
+# Run all tests
+pytest -v
+
+# Run with coverage
+pytest -v --cov=openms_python --cov-report=term-missing
+```
+
+### Test Patterns
+- Test basic wrapper functionality (properties, methods)
+- Test DataFrame conversions (to/from)
+- Test file I/O (load/store operations)
+- Test iteration and filtering
+- Test method chaining
+- Use `conftest.py` for shared fixtures
+
+## Development Setup
+
+### Installation
+```bash
+git clone https://github.com/openms/openms-python.git
+cd openms-python
+pip install -e ".[dev]"
+```
+
+### Dependencies
+- **Core**: pyopenms (>=3.0.0), pandas (>=1.3.0), numpy (>=1.20.0)
+- **Dev**: pytest, pytest-cov, black, flake8, mypy
+
+### Code Formatting
+```bash
+# Format code with Black
+black openms_python tests
+
+# Check style with flake8
+flake8 openms_python tests
+```
+
+## Key Architecture Patterns
+
+### 1. Wrapper Pattern
+Most classes wrap a corresponding pyOpenMS class and delegate to it while providing Pythonic interfaces:
+```python
+class Py_MSExperiment:
+    def __init__(self, exp=None):
+        self._exp = exp if exp is not None else oms.MSExperiment()
+    
+    @property
+    def retention_time(self):
+        return self._exp.getRT()
+```
+
+### 2. Factory Methods
+Use class methods for alternative constructors:
+```python
+@classmethod
+def from_file(cls, filepath):
+    # Load from file and return new instance
+    
+@classmethod
+def from_dataframe(cls, df):
+    # Create from pandas DataFrame
+```
+
+### 3. Smart Filtering
+Provide multiple ways to filter data:
+- Method-based: `filter_by_rt(min_rt, max_rt)`
+- Property-based: `rt_filter[min:max]`
+- Iterator-based: `ms1_spectra()`, `ms2_spectra()`
+
+### 4. Metadata Handling
+Classes that wrap `MetaInfoInterface` should implement mapping protocol:
+- `__getitem__`, `__setitem__`, `__delitem__`
+- `__contains__`, `__iter__`, `__len__`
+- `get()`, `pop()`, `update()` methods
+
+## Common Tasks
+
+### Adding a New Wrapper Class
+1. Create a new `py_<classname>.py` file
+2. Wrap the corresponding pyOpenMS class
+3. Add Pythonic properties for common getters/setters
+4. Implement `__len__`, `__iter__`, `__getitem__` if applicable
+5. Add `to_dataframe()` and `from_dataframe()` if appropriate
+6. Add `load()` and `store()` methods for file I/O
+7. Write comprehensive tests in `tests/test_py_<classname>.py`
+8. Update `__init__.py` to export the new class
+9. Add examples to README.md
+
+### Adding Helper Functions
+- High-level workflow functions go in `workflows.py`
+- I/O utilities go in `io.py` or `_io_utils.py`
+- Metadata utilities go in `_meta_mapping.py`
+
+### Documentation
+- Add docstrings to all public classes and methods
+- Include usage examples in docstrings
+- Update README.md with new features
+- Keep API reference section in README current
+
+## Special Considerations
+
+### Memory Management
+- Be mindful of memory when working with large datasets
+- Provide streaming alternatives for large files (see `stream_mzml`)
+- Consider using generators for iteration over large collections
+
+### pyOpenMS Compatibility
+- The package depends on pyOpenMS >= 3.0.0
+- When wrapping pyOpenMS classes, preserve all functionality
+- Add convenience methods but don't remove or break existing capabilities
+
+### Error Handling
+- Provide clear, helpful error messages
+- Validate inputs before passing to pyOpenMS
+- Handle common edge cases (empty containers, missing files, etc.)
+
+### Performance
+- Wrapper overhead should be minimal
+- Avoid unnecessary data copies
+- Use NumPy arrays for peak data when possible
+- Consider performance implications of DataFrame conversions
+
+## Examples and Documentation
+
+The README.md contains extensive examples. When adding new features:
+1. Add code examples showing the improvement over pyOpenMS
+2. Use "Before (pyOpenMS)" vs "After (openms-python)" format
+3. Include practical use cases
+4. Show integration with pandas/numpy when relevant
+
+## CI/CD
+
+The repository uses GitHub Actions for continuous integration:
+- Workflow: `.github/workflows/integration-tests.yml`
+- Runs on: Python 3.10 (configurable via matrix)
+- Tests run automatically on push to main and on pull requests
+
+## Contributing Guidelines
+
+When contributing:
+1. Make minimal, focused changes
+2. Maintain backward compatibility unless explicitly breaking
+3. Add tests for new functionality
+4. Format code with Black
+5. Ensure all tests pass
+6. Update documentation as needed
+
+## Questions or Issues?
+
+- Check existing documentation in README.md
+- Review existing wrapper implementations for patterns
+- Look at test files for usage examples
+- Open a discussion on GitHub for design questions