Merge pull request #13 from CompOmics/update-docs-model

Update-docs-model

Author: rodvrees

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+# Pre-commit configuration for IM2Deep
+# Install with: pip install pre-commit && pre-commit install
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: debug-statements
+
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        language_version: python3
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: [--max-line-length=99]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.3.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-requests]

CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+- This CHANGELOG file
+- Comprehensive documentation with API reference, development guide, and tutorial
+- Enhanced error handling with custom exceptions
+- Input validation throughout the codebase
+- Type hints for better code clarity
+- Detailed logging with different verbosity levels
+
+### Changed
+- Improved function signatures with better parameter validation
+- Enhanced docstrings with NumPy style documentation
+- Better error messages with more context
+- Improved CLI with better help text and validation
+- More robust file handling with proper encoding
+- Enhanced calibration functions with edge case handling
+
+### Fixed
+- Import error handling for optional dependencies
+- File path validation in CLI
+- Memory management improvements
+- Edge cases in CCS/ion mobility conversions
+- Calibration edge cases with insufficient data

CONTRIBUTING.md

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+# Contributing to IM2Deep
+
+We welcome contributions to IM2Deep! This document provides guidelines for contributing to the project.
+
+## Getting Started
+
+1. Fork the repository on GitHub
+2. Clone your fork locally
+3. Set up the development environment
+4. Create a feature branch
+5. Make your changes
+6. Run tests
+7. Submit a pull request
+
+## Development Setup
+
+```bash
+# Clone your fork
+git clone https://github.com/yourusername/IM2Deep.git
+cd IM2Deep
+
+# Create virtual environment
+python -m venv venv
+source venv/bin/activate  # On Windows: venv\Scripts\activate
+
+# Install in development mode
+pip install -e .[dev,test]
+```
+
+## Code Standards
+
+### Style Guide
+- Follow PEP 8
+- Use Black for code formatting: `black im2deep/`
+- Use isort for imports: `isort im2deep/`
+- Maximum line length: 99 characters
+
+### Documentation
+- Use NumPy-style docstrings
+- Include type hints
+- Provide examples in docstrings
+- Update documentation for new features
+
+## Pull Request Process
+
+1. Create a feature branch from `main`
+2. Make your changes
+3. Add tests for new functionality
+4. Update documentation
+5. Ensure all tests pass
+6. Update CHANGELOG.md
+7. Submit pull request
+
+## Code of Conduct
+
+- Be respectful and inclusive
+- Provide constructive feedback
+- Focus on the code, not the person
+- Help others learn and grow
+
+## Questions?
+
+Feel free to open an issue for questions or discussion!

im2deep/__init__.py

@@ -1,3 +1,54 @@
-"""IM2Deep: Deep learning framework for peptide collisional cross section prediction."""
+"""
+IM2Deep: Deep learning framework for peptide collisional cross section prediction.
 
-__version__ = "1.0.3"
+IM2Deep is a Python package that provides accurate CCS (Collisional Cross Section)
+prediction for peptides and modified peptides using deep learning models trained
+specifically for TIMS (Trapped Ion Mobility Spectrometry) data.
+
+Key Features:
+    - Single-conformer CCS prediction using ensemble of neural networks
+    - Multi-conformer CCS prediction for peptides with multiple conformations
+    - Linear calibration using reference datasets
+    - Support for modified peptides
+    - Ion mobility conversion utilities
+    - Command-line interface for easy usage
+
+Example:
+    Basic usage for CCS prediction:
+
+    >>> from im2deep.im2deep import predict_ccs
+    >>> from psm_utils.psm_list import PSMList
+    >>> predictions = predict_ccs(psm_list, calibration_data)
+
+Dependencies:
+    - deeplc: For deep learning model infrastructure
+    - psm_utils: For peptide and PSM handling
+    - pandas: For data manipulation
+    - numpy: For numerical computations
+    - click: For command-line interface
+
+Authors:
+    - Robbe Devreese
+    - Robbin Bouwmeester
+    - Ralf Gabriels
+
+License:
+    Apache License 2.0
+"""
+
+__version__ = "1.1.0"
+
+# Import main functionality for easier access
+from im2deep.im2deep import predict_ccs
+from im2deep.calibrate import linear_calibration
+from im2deep.utils import ccs2im, im2ccs
+from im2deep._exceptions import IM2DeepError, CalibrationError
+
+__all__ = [
+    "predict_ccs",
+    "linear_calibration",
+    "ccs2im",
+    "im2ccs",
+    "IM2DeepError",
+    "CalibrationError",
+]