feat: Remove outdated testing documentation and add comprehensive development and feature guides

- Deleted `TESTING_SETUP.md` and `TEST_UPDATES_SUMMARY.md` as they were outdated. - Introduced `CHANGELOG.md` to document notable changes and version history. - Added `DEVELOPMENT.md` for detailed development setup, testing framework, and debugging guidance. - Created `FEATURES.md` to outline core features and functionalities of TheChart. - Established `README.md` as a centralized documentation index for users and developers.
2025-07-31 11:39:12 -07:00
parent e5e654a0b3
commit 33d7ae8d9f
15 changed files with 975 additions and 1485 deletions
--- a/README.md
+++ b/README.md
@@ -1,15 +1,34 @@
-# Thechart
-App to manage medication and see the evolution of its effects.
+# TheChart
+Advanced medication tracking application for monitoring treatment progress and symptom evolution.
+
+## Quick Start
+```bash
+# Install dependencies
+make install
+
+# Run the application
+make run
+
+# Run tests
+make test
+```
+
+## 📚 Documentation
+- **[Features Guide](docs/FEATURES.md)** - Complete feature documentation
+- **[Development Guide](docs/DEVELOPMENT.md)** - Testing, development, and architecture
+- **[Changelog](docs/CHANGELOG.md)** - Version history and feature evolution
+- **[Quick Reference](#quick-reference)** - Common commands and shortcuts

 ## Table of Contents
 - [Prerequisites](#prerequisites)
 - [Installation](#installation)
 - [Running the Application](#running-the-application)
+- [Key Features](#key-features)
 - [Development](#development)
 - [Deployment](#deployment)
 - [Docker Usage](#docker-usage)
 - [Troubleshooting](#troubleshooting)
- [Make Commands Reference](#make-commands-reference)
+- [Quick Reference](#quick-reference)

 ## Prerequisites

@@ -179,75 +198,85 @@ python src/main.py
 On first run, the application will:
 - Create a default CSV data file (`thechart_data.csv`) if it doesn't exist
 - Set up logging in the `logs/` directory
- Create necessary configuration files
+- Initialize medicine and pathology configuration files (`medicines.json`, `pathologies.json`)
+- Create necessary directory structure
+## Key Features
+
+### 🏥 Modular Medicine System
+- **Dynamic Medicine Management**: Add, edit, and remove medicines through the UI
+- **Configurable Properties**: Customize names, dosages, colors, and quick-dose options
+- **JSON Configuration**: Easy management through `medicines.json`
+- **Automatic UI Updates**: All components update when medicines change
+
+### 💊 Advanced Dose Tracking
+- **Precise Timestamps**: Record exact time and dose amounts
+- **Multiple Daily Doses**: Track multiple doses of the same medicine
+- **Comprehensive Interface**: Dedicated dose management in edit windows
+- **Historical Data**: Complete dose history with CSV persistence
+
+### 📊 Enhanced Visualizations
+- **Interactive Graphs**: Toggle visibility of symptoms and medicines
+- **Dose Bar Charts**: Visual representation of daily medication intake
+- **Enhanced Legends**: Multi-column layout with average dosage information
+- **Professional Styling**: Clean, informative chart design
+
+### 📈 Data Management
+- **Robust CSV Storage**: Human-readable and portable data format
+- **Automatic Backups**: Data protection during updates
+- **Backward Compatibility**: Seamless upgrades without data loss
+- **Dynamic Columns**: Adapts to new medicines and pathologies
+
+For complete feature documentation, see **[docs/FEATURES.md](docs/FEATURES.md)**.

 ## Development

-### Code Quality Tools
-The project includes several code quality tools that are automatically set up:
+### Testing Framework
+TheChart includes a comprehensive testing suite with **93% code coverage**:

-#### Formatting and Linting
-```shell
-make format  # Format code with ruff
-make lint    # Run linter checks
+```bash
+# Run all tests
+make test
+
+# Run tests with coverage report
+uv run pytest --cov=src --cov-report=html
+
+# Run specific test file
+uv run pytest tests/test_graph_manager.py -v
 ```

-**With uv directly:**
-```shell
-uv run ruff format .  # Format code
-uv run ruff check .   # Check for issues
-```
+**Testing Statistics:**
+- **112 total tests** across 6 test modules
+- **93% overall coverage** (482 statements, 33 missed)
+- **Pre-commit testing** prevents broken commits

-#### Running Tests
-```shell
-make test    # Run unit tests
-```
+### Code Quality
+```bash
+# Format code
+make format

-**With uv directly:**
-```shell
-uv run pytest  # Run tests with pytest
+# Check code quality
+make lint
+
+# Run pre-commit checks
+pre-commit run --all-files
 ```

 ### Package Management with uv
-
-#### Adding Dependencies
-```shell
-# Add a runtime dependency
+```bash
+# Add dependencies
 uv add package-name

-# Add a development dependency
+# Add development dependencies
 uv add --dev package-name

-# Add specific version
-uv add "package-name>=1.0.0"
-```
+# Update dependencies
+uv sync --upgrade

-#### Removing Dependencies
-```shell
+# Remove dependencies
 uv remove package-name
 ```

-#### Updating Dependencies
-```shell
-# Update all dependencies
-uv sync --upgrade
-
-# Update specific package
-uv add "package-name>=new-version"
-```
-
-#### Pre-commit Hooks
-Pre-commit hooks are automatically installed and will run on every commit to ensure code quality. They include:
- Code formatting with ruff
- Linting checks
- Import sorting
- Basic file checks
-
-### Development Dependencies
-The following development tools are included:
- **ruff** - Fast Python linter and formatter
- **pre-commit** - Git hook management
- **pyinstaller** - For creating standalone executables
+For detailed development information, see **[docs/DEVELOPMENT.md](docs/DEVELOPMENT.md)**.

 ## Deployment

@@ -312,43 +341,33 @@ python src/main.py

 ## Docker Usage

-## Docker Usage
-
-### Building the Container Image
-Build a multi-platform Docker image:
-```shell
+### Quick Start with Docker
+```bash
+# Build and start the application
 make build
-```
-
-### Running with Docker Compose
-The project includes Docker Compose configuration for easy container management:
-
-1. **Start the application:**
-```shell
 make start
-```

-2. **Stop the application:**
-```shell
+# Stop the application
 make stop
-```

-3. **Access container shell:**
-```shell
+# Access container shell
 make attach
 ```

 ### Manual Docker Commands
-If you prefer using Docker directly:
-
-```shell
+```bash
 # Build image
 docker build -t thechart .

-# Run container
-docker run -it --rm thechart
+# Run container with X11 forwarding (Linux)
+docker run -it --rm \
+  -e DISPLAY=$DISPLAY \
+  -v /tmp/.X11-unix:/tmp/.X11-unix:rw \
+  thechart
 ```

+**Note:** Docker support is primarily for development. For production use, consider the standalone executable deployment.
+
 ## Troubleshooting

 ### Common Issues
@@ -407,34 +426,10 @@ If you encounter issues not covered here:
 3. Try rebuilding the virtual environment
 4. Verify file permissions for deployment directories

-## Make Commands Reference
+## Quick Reference

-The project uses a Makefile to simplify common development and deployment tasks.
-
-### Show Help Menu
-```shell
-make help
-```
-
-### Available Commands
-| Command | Description |
-|---------|-------------|
-| `install` | Set up the development environment |
-| `run` | Run the application |
-| `shell` | Open a shell in the local environment |
-| `format` | Format the code with ruff |
-| `lint` | Run the linter |
-| `test` | Run the tests |
-| `requirements` | Export the requirements to a file |
-| `build` | Build the Docker image |
-| `start` | Start the app (Docker) |
-| `stop` | Stop the app (Docker) |
-| `attach` | Open a shell in the container |
-| `deploy` | Deploy standalone app executable |
-| `help` | Show this help |
-
-### Quick Reference
-```shell
+### Essential Commands
+```bash
 # Development workflow
 make install    # One-time setup
 make run        # Run application
@@ -451,6 +446,35 @@ make start      # Start containerized app
 make stop       # Stop containerized app
 ```

+### Project Structure
+```
+src/                 # Main application source code
+├── main.py         # Application entry point
+├── ui_manager.py   # User interface management
+├── data_manager.py # CSV data operations
+├── graph_manager.py # Visualization and plotting
+├── medicine_manager.py # Medicine system
+└── pathology_manager.py # Symptom tracking
+
+docs/               # Documentation
+├── FEATURES.md     # Complete feature guide
+└── DEVELOPMENT.md  # Development guide
+
+logs/               # Application logs
+deploy/             # Deployment configuration
+tests/              # Test suite
+medicines.json      # Medicine configuration
+pathologies.json    # Pathology configuration
+thechart_data.csv   # User data (created on first run)
+```
+
+### Key Files
+- **`medicines.json`**: Configure available medicines
+- **`pathologies.json`**: Configure tracked symptoms
+- **`thechart_data.csv`**: Your medication and symptom data
+- **`pyproject.toml`**: Project configuration and dependencies
+- **`uv.lock`**: Dependency lock file
+
 ---

 ## Why uv?
@@ -471,13 +495,3 @@ make stop       # Stop containerized app
 | Add package | `uv add package` | `poetry add package` |
 | Run command | `uv run command` | `poetry run command` |
 | Activate environment | `source .venv/bin/activate` | `poetry shell` |
-
-**Project Structure:**
- `src/` - Main application source code
- `logs/` - Application log files
- `deploy/` - Deployment configuration files
- `build/` - Build artifacts (created during deployment)
- `.venv/` - Virtual environment (created by uv)
- `uv.lock` - Lock file with exact dependency versions
- `pyproject.toml` - Project configuration and dependencies
- `thechart_data.csv` - Application data file