feat: Center main window on screen during initialization

- Deleted `TESTING_SETUP.md` and `TEST_UPDATES_SUMMARY.md` as they were outdated.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.

.gitea/workflows/build.yaml

@@ -14,6 +14,8 @@ jobs:
     steps:
       - name: Check out repository code
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Fetch full history for release notes generation
 
       - name: Install Docker
         run: curl -fsSL https://get.docker.com | sh
@@ -55,3 +57,49 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           cache-from: type=registry,ref=gitea-http.taildb3494.ts.net/will/thechart:buildcache
           cache-to: type=registry,ref=gitea-http.taildb3494.ts.net/will/thechart:buildcache,mode=max
+
+      - name: Generate release notes
+        id: release_notes
+        if: startsWith(gitea.ref, 'refs/tags/')
+        run: |
+          # Get the current tag
+          CURRENT_TAG=${GITEA_REF#refs/tags/}
+
+          # Get the previous tag
+          PREVIOUS_TAG=$(git describe --tags --abbrev=0 HEAD^ 2>/dev/null || echo "")
+
+          # Generate release notes from commits
+          if [ -n "$PREVIOUS_TAG" ]; then
+            echo "## Changes from $PREVIOUS_TAG to $CURRENT_TAG" > release_notes.md
+            echo "" >> release_notes.md
+            git log --pretty=format:"- %s (%h)" $PREVIOUS_TAG..$CURRENT_TAG >> release_notes.md
+          else
+            echo "## Initial Release $CURRENT_TAG" > release_notes.md
+            echo "" >> release_notes.md
+            git log --pretty=format:"- %s (%h)" >> release_notes.md
+          fi
+
+          # Add Docker image information
+          echo "" >> release_notes.md
+          echo "## Docker Images" >> release_notes.md
+          echo "" >> release_notes.md
+          echo "This release includes multi-platform Docker images:" >> release_notes.md
+          echo "- \`gitea-http.taildb3494.ts.net/will/thechart:$CURRENT_TAG\`" >> release_notes.md
+          echo "- \`gitea-http.taildb3494.ts.net/will/thechart:latest\`" >> release_notes.md
+
+          # Output the release notes content for use in next step
+          echo "release_notes<<EOF" >> $GITEA_OUTPUT
+          cat release_notes.md >> $GITEA_OUTPUT
+          echo "EOF" >> $GITEA_OUTPUT
+
+      - name: Create Release
+        if: startsWith(gitea.ref, 'refs/tags/')
+        uses: actions/create-release@v1
+        env:
+          RELEASE_TOKEN: ${{ secrets.RELEASE_TOKEN }}
+        with:
+          tag_name: ${{ gitea.ref_name }}
+          release_name: Release ${{ gitea.ref_name }}
+          body: ${{ steps.release_notes.outputs.release_notes }}
+          draft: false
+          prerelease: false

.gitignore

@@ -1,13 +1,83 @@
-*.csv
+# Data files (except example data)
+thechart_data.csv
+### !thechart_data.csv
+
+# Environment files
 .env
+.env.local
+.env.*.local
+
+# Build and distribution
 build/
 dist/
+*.egg-info/
+
+# Python bytecode
 *.pyc
+*.pyo
+*.pyd
 __pycache__/
+
+# PyInstaller
 *.spec
+
+# Logs
 *.log
 logs/
+
+# Virtual environments
 .venv/
 .poetry/
+venv/
+env/
+ENV/
+
+# Testing
 .pytest_cache/
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+.tox/
+.nox/
+
+# Code quality tools
 .ruff_cache/
+.mypy_cache/
+.pylint.d/
+
+# IDEs and editors
+#.vscode/
+!.vscode/tasks.json
+!.vscode/launch.json
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+Thumbs.db
+
+# Databases
+*.db
+*.sqlite3
+*.sqlite
+
+# uv lock files (keep for reproducibility)
+# uv.lock
+
+# Docker
+.dockerignore.bak
+
+# Temporary files
+*.tmp
+*.temp
+.cache/
+
+# OS generated files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db

.pre-commit-config.yaml

@@ -65,3 +65,23 @@ repos:
       # - id: uv-export
       # - id: pip-compile
       #   args: [requirements.in, -o, requirements.txt]
+  ########################################################
+  # Run core tests before commit to ensure basic functionality
+  - repo: local
+    hooks:
+      - id: pytest-check
+        name: pytest-check (core tests)
+        entry: uv run pytest
+        language: system
+        pass_filenames: false
+        always_run: true
+        args:
+          [
+            --tb=short,
+            --quiet,
+            --no-cov,
+            "tests/test_data_manager.py::TestDataManager::test_init",
+            "tests/test_data_manager.py::TestDataManager::test_initialize_csv_creates_file_with_headers",
+            "tests/test_data_manager.py::TestDataManager::test_load_data_with_valid_data",
+          ]
+        stages: [pre-commit]

.vscode/settings.json

@@ -11,7 +11,7 @@
         },
         "editor.autoIndent": "advanced"
     },
-    "ansible.python.interpreterPath": "/home/will/Code/thechart/.venv/bin/python",
+    "ansible.python.interpreterPath": "${workspaceFolder}/.venv/bin/python",
     "makefile.configureOnOpen": true,
     "vs-kubernetes": {
         "vs-kubernetes.crd-code-completion": "enabled",
@@ -36,5 +36,6 @@
     "editor.formatOnSave": true,
     "diffEditor.codeLens": true,
     "github.copilot.nextEditSuggestions.enabled": true,
-    "github.copilot.selectedCompletionModel": ""
+    "github.copilot.selectedCompletionModel": "",
+    "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python"
 }

.vscode/tasks.json

@@ -4,10 +4,30 @@
 		{
 			"label": "Run TheChart App",
 			"type": "shell",
-			"command": "cd /home/will/Code/thechart && python -m src.main",
+			"command": "/home/will/Code/thechart/.venv/bin/python",
+			"args": [
+				"src/main.py"
+			],
+			"options": {
+				"cwd": "/home/will/Code/thechart"
+			},
 			"group": "build",
 			"isBackground": false,
 			"problemMatcher": []
+		},
+		{
+			"label": "Test Dose Tracking UI",
+			"type": "shell",
+			"command": "/home/will/Code/thechart/.venv/bin/python",
+			"args": [
+				"scripts/test_dose_tracking_ui.py"
+			],
+			"options": {
+				"cwd": "/home/will/Code/thechart"
+			},
+			"group": "test",
+			"isBackground": false,
+			"problemMatcher": []
 		}
 	]
 }

Dockerfile

@@ -53,6 +53,11 @@ RUN sh -c "pyinstaller --name ${TARGET} --optimize 2 --onefile --windowed --hidd
 RUN chown -R ${UID}:${GUID} /home/docker_user/
 RUN chmod -R 777 /home/docker_user/${TARGET}
 
+RUN mkdir -p /app/logs && \
+    touch /app/logs/app.log && \
+    chown -R ${UID}:${GUID} /app/logs && \
+    chmod 666 /app/logs/app.log
+
 # Set environment variables for X11 forwarding
 ENV DISPLAY=:0
 ENV XAUTHORITY=/tmp/.docker.xauth

Makefile

@@ -1,32 +1,105 @@
 TARGET=thechart
-VERSION=1.0.0
+VERSION=1.6.1
 ROOT=/home/will
 ICON=chart-671.png
-SHELL=/bin/fish
+SHELL=fish
+
+# Virtual environment variables
+VENV_DIR=.venv
+VENV_ACTIVATE=$(VENV_DIR)/bin/activate
+PYTHON=$(VENV_DIR)/bin/python
+
 help: ## Show this help
 	@grep -E -h '\s##\s' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'
+
+clean: ## Clean up build artifacts and virtual environment
+	@echo "Cleaning up build artifacts and virtual environment..."
+	@rm -rf $(VENV_DIR)
+	@rm -rf build/
+	@rm -rf dist/
+	@rm -rf htmlcov/
+	@rm -rf .pytest_cache/
+	@rm -rf .ruff_cache/
+	@rm -rf src/__pycache__/
+	@rm -rf tests/__pycache__/
+	@rm -f .coverage
+	@rm -f coverage.xml
+	@echo "✅ Cleanup complete!"
+
+reinstall: clean install ## Clean and reinstall the development environment
+
+check-env: ## Check if the development environment is properly set up
+	@echo "Checking development environment..."
+	@bash -c 'if [ ! -d "$(VENV_DIR)" ]; then \
+		echo "❌ Virtual environment not found at $(VENV_DIR)"; \
+		echo "   Run \"make install\" to set up the environment"; \
+		exit 1; \
+	fi'
+	@bash -c 'if [ ! -f "$(PYTHON)" ]; then \
+		echo "❌ Python executable not found at $(PYTHON)"; \
+		echo "   Run \"make install\" to set up the environment"; \
+		exit 1; \
+	fi'
+	@echo "✅ Virtual environment: $(VENV_DIR)"
+	@echo "✅ Python executable: $(PYTHON)"
+	@$(PYTHON) --version
+	@$(PYTHON) -c "import sys; print(f'✅ Python path: {sys.executable}')"
+	@bash -c 'if cd /home/will/Code/thechart && $(PYTHON) -c "import sys; sys.path.insert(0, \"src\"); import main" 2>/dev/null; then \
+		echo "✅ Main module imports successfully"; \
+	else \
+		echo "❌ Main module import failed"; \
+		exit 1; \
+	fi'
+	@bash -c 'if $(PYTHON) -c "import pre_commit" 2>/dev/null; then \
+		echo "✅ Pre-commit is installed"; \
+	else \
+		echo "⚠️  Pre-commit not found (run \"make install\" to fix)"; \
+	fi'
+	@echo "✅ Environment check completed successfully!"
 install: ## Set up the development environment
 	@echo "Setting up the development environment..."
-# 	poetry env use 3.13
-# 	eval $(poetry env use 3.13) # bash/zsh/csh
-	eval (poetry env activate)
-	poetry install --no-root
-	poetry run pre-commit install --install-hooks --overwrite
-	poetry run pre-commit autoupdate
-	poetry run pre-commit run --all-files
+	@echo "Creating virtual environment..."
+	@bash -c 'if [ -d "$(VENV_DIR)" ]; then \
+		echo "Virtual environment already exists. Recreating..."; \
+		rm -rf $(VENV_DIR); \
+	fi'
+	uv venv $(VENV_DIR) --python=python3.13
+	@echo "Installing dependencies..."
+	uv sync --dev --no-cache-dir
+	@echo "Installing pre-commit hooks..."
+	$(PYTHON) -m pre_commit install
+	@echo "Verifying installation..."
+	@$(PYTHON) --version
+	@$(PYTHON) -c "import sys; print(f'Python executable: {sys.executable}')"
+	@echo "Testing module imports..."
+	@cd /home/will/Code/thechart && $(PYTHON) -c "import sys; sys.path.insert(0, 'src'); import main; print('✅ Main module imports successfully')"
+	@echo "Development environment setup complete!"
+	@echo ""
+	@echo "🐟 For Fish shell users:"
+	@echo "  source $(VENV_DIR)/bin/activate.fish"
+	@echo ""
+	@echo "🐚 For Bash/Zsh shell users:"
+	@echo "  source $(VENV_ACTIVATE)"
+	@echo ""
+	@echo "To run the application: make run"
+	@echo "To run tests: make test"
 build: ## Build the Docker image
 	@echo "Building the Docker image..."
 	docker buildx build --platform linux/amd64,linux/arm64 -t ${IMAGE} --push .
 deploy: ## Deploy the application as a standalone executable
 	@echo "Deploying the application..."
-	pyinstaller --name ${TARGET} --optimize 2 --onefile --windowed --hidden-import='PIL._tkinter_finder' --icon='${ICON}' --add-data="./.env:." --add-data='./chart-671.png:.' --add-data='./thechart_data.csv:.' src/main.py
+	pyinstaller --name ${TARGET} --optimize 2 --onefile --windowed --hidden-import='PIL._tkinter_finder' --icon='${ICON}' --add-data="./.env:." --add-data='./chart-671.png:.' --add-data='./thechart_data.csv:.' --log-level=DEBUG src/main.py
 	cp -f ./thechart_data.csv ${ROOT}/Documents/
 	cp -f ./dist/${TARGET} ${ROOT}/Applications/
 	cp -f ./deploy/${TARGET}.desktop ${ROOT}/.local/share/applications/
 	desktop-file-validate ${ROOT}/.local/share/applications/${TARGET}.desktop
-run: ## Run the application
+run: $(VENV_ACTIVATE) ## Run the application
 	@echo "Running the application..."
-	python src/main.py
+	@bash -c 'if [ ! -f "$(VENV_ACTIVATE)" ]; then \
+		echo "❌ Virtual environment not found. Run \"make install\" first."; \
+		exit 1; \
+	fi'
+	$(PYTHON) src/main.py
 start: ## Start the application
 	@echo "Starting the application..."
 	docker-compose up -d --build
@@ -35,7 +108,34 @@ stop: ## Stop the application
 	docker-compose down
 test: ## Run the tests
 	@echo "Running the tests..."
-	docker-compose exec ${TARGET} pipenv run pytest -v --tb=short
+	.venv/bin/python -m pytest tests/ -v --cov=src --cov-report=term-missing --cov-report=html:htmlcov
+test-unit: ## Run unit tests only
+	@echo "Running unit tests..."
+	.venv/bin/python -m pytest tests/ -v --tb=short
+test-coverage: ## Run tests with detailed coverage report
+	@echo "Running tests with coverage..."
+	.venv/bin/python -m pytest tests/ --cov=src --cov-report=html:htmlcov --cov-report=xml --cov-report=term-missing
+test-watch: ## Run tests in watch mode
+	@echo "Running tests in watch mode..."
+	.venv/bin/python -m pytest-watch tests/ -- -v --cov=src
+test-debug: ## Run tests with debug output
+	@echo "Running tests with debug output..."
+	.venv/bin/python -m pytest tests/ -v -s --tb=long --cov=src
+test-dose-tracking: ## Test the dose tracking functionality
+	@echo "Testing dose tracking functionality..."
+	.venv/bin/python scripts/test_dose_tracking.py
+test-scrollable-input: ## Test the scrollable input frame UI
+	@echo "Testing scrollable input frame..."
+	.venv/bin/python scripts/test_scrollable_input.py
+test-edit-functionality: ## Test the enhanced edit functionality
+	@echo "Testing edit functionality..."
+	.venv/bin/python scripts/test_edit_functionality.py
+test-edit-window: $(VENV_ACTIVATE)  ## Test edit window functionality (save and delete)
+	@echo "Running edit window functionality test..."
+	$(PYTHON) scripts/test_edit_window_functionality.py
+test-dose-editing: $(VENV_ACTIVATE)  ## Test dose editing functionality in edit window
+	@echo "Running dose editing functionality test..."
+	$(PYTHON) scripts/test_dose_editing_functionality.py
 lint: ## Run the linter
 	@echo "Running the linter..."
 	docker-compose exec ${TARGET} pipenv run pre-commit run --all-files
@@ -47,8 +147,14 @@ attach: ## Open a shell in the container
 	docker-compose exec -it ${TARGET} /bin/bash
 shell: ## Open a shell in the local environment
 	@echo "Opening a shell in the local environment..."
-	${SHELL} -c "eval (poetry env activate)"
+	source .venv/bin/activate.${SHELL}; /bin/${SHELL}
 requirements: ## Export the requirements to a file
 	@echo "Exporting requirements to requirements.txt..."
 	poetry export --without-hashes -f requirements.txt -o requirements.txt
-.PHONY: install build attach deploy run start stop test lint format shell requirements help
+commit-emergency: ## Emergency commit (bypasses pre-commit hooks) - USE SPARINGLY
+	@echo "⚠️  WARNING: Emergency commit bypasses all pre-commit checks!"
+	@echo "This should only be used in true emergencies."
+	@read -p "Enter commit message: " msg; \
+	git add . && git commit --no-verify -m "$$msg"
+	@echo "✅ Emergency commit completed. Please run tests manually when possible."
+.PHONY: install clean reinstall check-env build attach deploy run start stop test lint format shell requirements commit-emergency test-dose-tracking test-scrollable-input test-edit-functionality test-edit-window test-dose-editing migrate-csv help

README.md

@@ -1,72 +1,497 @@
-# 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)
+- [Quick Reference](#quick-reference)
+
+## Prerequisites
+
+Before installing Thechart, ensure you have the following installed on your system:
+
+### Required Software
+- **Python 3.13 or higher** - The application requires Python 3.13+
+- **uv** - For fast dependency management and virtual environment handling
+- **Git** - For version control (if cloning from repository)
+
+### Installing Prerequisites
+
+#### Install Python 3.13
+**Ubuntu/Debian:**
+```shell
+sudo apt update
+sudo apt install python3.13 python3.13-venv python3.13-dev
+```
+
+**macOS (using Homebrew):**
+```shell
+brew install python@3.13
+```
+
+**Windows:**
+Download and install from [python.org](https://www.python.org/downloads/)
+
+#### Install uv
+**All Platforms:**
+```shell
+curl -LsSf https://astral.sh/uv/install.sh | sh
+```
+
+**macOS (using Homebrew):**
+```shell
+brew install uv
+```
+
+**Windows (using PowerShell):**
+```shell
+powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
+```
+
+**Alternative (using pip):**
+```shell
+pip install uv
+```
+
+Add uv to your PATH (usually done automatically by the installer):
+```shell
+export PATH="$HOME/.local/bin:$PATH"
+```
+
+#### Verify Installation
+```shell
+python3.13 --version
+uv --version
+```
 
 ## Installation
 
-### Install dev environment and dependencies
-The Makefile is set to use the fish shell by default, see the section on [`bash/zsh/csh`](#bash/zsh/csh). The environment will be activated as well, therefore the next section can be skiped, and you can jump to [`run the app`](#Run%20the%20app).
+### Quick Setup (Recommended)
+The Makefile is configured to use the fish shell by default. For other shells, see the [shell-specific instructions](#shell-specific-activation) below.
+
+**Note:** The current Makefile still uses Poetry commands. If you've switched to uv, you may need to update the Makefile or use the manual installation method below.
+
 ```shell
 make install
 ```
 
-### Activate the environment according to your shell
+This command will:
+- Set up the Python virtual environment using uv
+- Install all required dependencies
+- Install development dependencies
+- Set up pre-commit hooks for code quality
+- Run initial code formatting and linting
 
-#### bash/zsh/csh
+### Manual Installation
+If you prefer to set up the environment manually:
+
+1. **Clone the repository** (if not already done):
 ```shell
-eval $(poetry env activate)
+git clone <repository-url>
+cd thechart
 ```
 
-#### fish
+2. **Create and activate virtual environment:**
 ```shell
-eval (poetry env activate)
+uv venv --python 3.13
+uv sync
 ```
-or
+
+3. **Install pre-commit hooks** (for development):
+```shell
+uv run pre-commit install --install-hooks --overwrite
+uv run pre-commit autoupdate
+```
+
+### Migrating from Poetry to uv
+
+If you have an existing Poetry setup and want to migrate to uv:
+
+1. **Remove Poetry environment** (optional):
+```shell
+poetry env remove python
+```
+
+2. **Create new uv environment:**
+```shell
+uv venv --python 3.13
+uv sync
+```
+
+3. **Update your workflow:** Replace `poetry run` with `uv run` in your commands.
+
+The `pyproject.toml` file remains compatible between Poetry and uv, so no changes are needed there.
+
+### Shell-Specific Activation
+
+If the automatic environment activation doesn't work or you're using a different shell, manually activate the environment:
+
+#### fish shell (default)
+```shell
+source .venv/bin/activate.fish
+```
+or use the convenience command:
 ```shell
 make shell
 ```
 
-## Run the app
+#### bash/zsh
+```shell
+source .venv/bin/activate
+```
+
+#### PowerShell (Windows)
+```shell
+.venv\Scripts\Activate.ps1
+```
+
+#### Using uv run (recommended)
+For any command, you can use `uv run` to automatically use the virtual environment:
+```shell
+uv run python src/main.py
+uv run pre-commit run --all-files
+```
+
+## Running the Application
+
+### Quick Start
+After installation, run the application with:
 ```shell
 make run
 ```
 
-## Build container image
+### Manual Run
+Alternatively, you can run the application directly:
 ```shell
-make build
+uv run python src/main.py
+```
+or if you have activated the virtual environment:
+```shell
+python src/main.py
 ```
 
-## Run unit tests
-```shell
+### First-Time Setup
+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
+- 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
+
+### Testing Framework
+TheChart includes a comprehensive testing suite with **93% code coverage**:
+
+```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
 ```
 
-## Deploy the app
-### Linux / Unix
-The app will be deployed in **~/Applications**, the CSV data file *thechart_data.csv* will be store in **~/Documents**.
+**Testing Statistics:**
+- **112 total tests** across 6 test modules
+- **93% overall coverage** (482 statements, 33 missed)
+- **Pre-commit testing** prevents broken commits
+
+### Code Quality
+```bash
+# Format code
+make format
+
+# Check code quality
+make lint
+
+# Run pre-commit checks
+pre-commit run --all-files
+```
+
+### Package Management with uv
+```bash
+# Add dependencies
+uv add package-name
+
+# Add development dependencies
+uv add --dev package-name
+
+# Update dependencies
+uv sync --upgrade
+
+# Remove dependencies
+uv remove package-name
+```
+
+For detailed development information, see **[docs/DEVELOPMENT.md](docs/DEVELOPMENT.md)**.
+
+## Deployment
+
+### Creating a Standalone Executable
+
+#### Linux/Unix Deployment
+Deploy the application as a standalone executable that can run without Python installed:
+
 ```shell
 make deploy
 ```
-### MacOS / Windows
-TODO: use OS specific flags with *pyinstaller*.
 
-## Make options
-Show the help menu:
+This command will:
+1. **Create a standalone executable** using PyInstaller
+2. **Install the executable** to `~/Applications/`
+3. **Copy data file** to `~/Documents/thechart_data.csv`
+4. **Create desktop entry** for easy access from the applications menu
+5. **Validate desktop file** to ensure proper integration
+
+#### Manual Deployment Steps
+If you prefer to deploy manually:
+
+1. **Build the executable:**
 ```shell
-make help
+pyinstaller --name thechart \
+    --optimize 2 \
+    --onefile \
+    --windowed \
+    --hidden-import='PIL._tkinter_finder' \
+    --icon='chart-671.png' \
+    --add-data="./.env:." \
+    --add-data='./chart-671.png:.' \
+    --add-data='./thechart_data.csv:.' \
+    src/main.py
 ```
-Sub-commands listed below:
+
+2. **Install files:**
+```shell
+# Copy executable
+cp ./dist/thechart ~/Applications/
+
+# Copy data file
+cp ./thechart_data.csv ~/Documents/
+
+# Install desktop entry (Linux)
+cp ./deploy/thechart.desktop ~/.local/share/applications/
+desktop-file-validate ~/.local/share/applications/thechart.desktop
 ```
-attach               Open a shell in the container
-build                Build the Docker image
-deploy               Deploy standalone app executable
-format               Format the code
-help                 Show this help
-install              Set up the development environment
-lint                 Run the linter
-requirements         Export the requirements to a file
-run                  Run the application
-shell                Open a shell in the local environment
-start                Start the app
-stop                 Stop the app
-test                 Run the tests
+
+#### macOS/Windows Deployment
+**Note:** macOS and Windows deployment is planned for future releases. Currently, you can run the application using Python directly on these platforms.
+
+For now, use:
+```shell
+python src/main.py
 ```
+
+### Deployment Requirements
+- **PyInstaller** (included in dev dependencies)
+- **Icon file** (`chart-671.png`)
+- **Desktop file** (`deploy/thechart.desktop` for Linux)
+
+## Docker Usage
+
+### Quick Start with Docker
+```bash
+# Build and start the application
+make build
+make start
+
+# Stop the application
+make stop
+
+# Access container shell
+make attach
+```
+
+### Manual Docker Commands
+```bash
+# Build image
+docker build -t 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
+
+#### Python Version Conflicts
+**Problem:** `uv sync` fails with Python version errors.
+**Solution:** Ensure Python 3.13+ is installed and specify the correct version:
+```shell
+uv venv --python 3.13
+uv sync
+```
+
+#### Permission Denied During Deployment
+**Problem:** Cannot copy files to `~/Applications/` or `~/Documents/`.
+**Solution:** Ensure directories exist and have proper permissions:
+```shell
+mkdir -p ~/Applications ~/Documents
+chmod 755 ~/Applications ~/Documents
+```
+
+#### Missing System Dependencies
+**Problem:** Application fails to start due to missing system libraries.
+**Solution:** Install required system packages:
+
+**Ubuntu/Debian:**
+```shell
+sudo apt install python3-tk python3-dev build-essential
+```
+
+**macOS:**
+```shell
+brew install tcl-tk
+```
+
+#### Virtual Environment Issues
+**Problem:** Environment activation fails or commands not found.
+**Solution:** Rebuild the virtual environment:
+```shell
+rm -rf .venv
+uv venv --python 3.13
+uv sync
+```
+
+### Logs and Debugging
+Application logs are stored in the `logs/` directory:
+- `app.log` - General application logs
+- `app.error.log` - Error messages
+- `app.warning.log` - Warning messages
+
+To enable debug logging, modify the logging configuration in `src/logger.py`.
+
+### Getting Help
+If you encounter issues not covered here:
+1. Check the application logs in the `logs/` directory
+2. Ensure all prerequisites are properly installed
+3. Try rebuilding the virtual environment
+4. Verify file permissions for deployment directories
+
+## Quick Reference
+
+### Essential Commands
+```bash
+# Development workflow
+make install    # One-time setup
+make run        # Run application
+make test       # Run tests
+make format     # Format code
+make lint       # Check code quality
+
+# Deployment
+make deploy     # Create standalone executable
+
+# Docker
+make build      # Build container image
+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?
+
+**uv** is a fast Python package installer and resolver, written in Rust. It offers several advantages over Poetry:
+
+- **Speed**: 10-100x faster than pip and Poetry
+- **Compatibility**: Drop-in replacement for pip with Poetry-like project management
+- **Simplicity**: Unified tool for package management and virtual environments
+- **Standards**: Follows Python packaging standards (PEP 621, etc.)
+
+### Key uv Commands vs Poetry
+
+| Task | uv Command | Poetry Equivalent |
+|------|------------|-------------------|
+| Create virtual environment | `uv venv` | `poetry env use` |
+| Install dependencies | `uv sync` | `poetry install` |
+| Add package | `uv add package` | `poetry add package` |
+| Run command | `uv run command` | `poetry run command` |
+| Activate environment | `source .venv/bin/activate` | `poetry shell` |

docs/CHANGELOG.md

@@ -0,0 +1,200 @@
+# Changelog
+
+All notable changes to TheChart project are 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).
+
+## [1.6.1] - 2025-07-31
+
+### 📚 Documentation Overhaul
+- **BREAKING**: Consolidated scattered documentation into organized structure
+- **Added**: Comprehensive `docs/FEATURES.md` with complete feature documentation
+- **Added**: Detailed `docs/DEVELOPMENT.md` with testing and development guide
+- **Updated**: Streamlined `README.md` with quick-start focus and navigation
+- **Removed**: 10 redundant/outdated markdown files
+- **Improved**: Clear separation between user and developer documentation
+
+### 🏗️ Documentation Structure
+```
+docs/
+├── FEATURES.md     # Complete feature guide (new)
+├── DEVELOPMENT.md  # Development & testing guide (new)
+└── CHANGELOG.md    # This changelog (new)
+
+README.md          # Streamlined quick-start guide (updated)
+```
+
+## [1.3.3] - Previous Releases
+
+### 🏥 Modular Medicine System
+- **Added**: Dynamic medicine management system
+- **Added**: JSON-based medicine configuration (`medicines.json`)
+- **Added**: Medicine management UI (`Tools` → `Manage Medicines...`)
+- **Added**: Configurable medicine properties (colors, doses, names)
+- **Added**: Automatic UI updates when medicines change
+- **Added**: Backward compatibility with existing data
+
+### 💊 Advanced Dose Tracking System
+- **Added**: Precise timestamp recording for medicine doses
+- **Added**: Multiple daily dose support for same medicine
+- **Added**: Comprehensive dose tracking interface in edit windows
+- **Added**: Quick-dose buttons for common amounts
+- **Added**: Real-time dose display and feedback
+- **Added**: Historical dose data persistence in CSV
+- **Improved**: Dose format parsing with robust error handling
+
+#### Punch Button Redesign
+- **Moved**: Dose tracking from main input to edit window
+- **Added**: Individual dose entry fields per medicine
+- **Added**: "Take [Medicine]" buttons with immediate recording
+- **Added**: Editable dose display areas with history
+- **Improved**: User experience with centralized dose management
+
+### 📊 Enhanced Graph Visualization
+- **Added**: Medicine dose bar charts with distinct colors
+- **Added**: Interactive toggle controls for symptoms and medicines
+- **Added**: Enhanced legend with multi-column layout
+- **Added**: Average dosage calculations and displays
+- **Added**: Professional styling with transparency and shadows
+- **Improved**: Graph layout with dynamic positioning
+
+#### Medicine Dose Plotting
+- **Added**: Visual representation of daily medication intake
+- **Added**: Scaled dose display (mg/10) for chart compatibility
+- **Added**: Color-coded bars for each medicine
+- **Added**: Semi-transparent rendering to preserve symptom visibility
+- **Fixed**: Dose calculation logic for complex timestamp formats
+
+#### Legend Enhancements
+- **Added**: Multi-column legend layout (2 columns)
+- **Added**: Average dosage information per medicine
+- **Added**: Tracking status for medicines without current doses
+- **Added**: Frame, shadow, and transparency effects
+- **Improved**: Space utilization and readability
+
+### 🧪 Comprehensive Testing Framework
+- **Added**: Professional testing infrastructure with pytest
+- **Added**: 93% code coverage across 112 tests
+- **Added**: Coverage reporting (HTML, XML, terminal)
+- **Added**: Pre-commit testing hooks
+- **Added**: Comprehensive dose calculation testing
+- **Added**: UI component testing with mocking
+- **Added**: Medicine plotting and legend testing
+
+#### Test Infrastructure
+- **Added**: `tests/conftest.py` with shared fixtures
+- **Added**: Sample data generators for realistic testing
+- **Added**: Mock loggers and temporary file management
+- **Added**: Environment variable mocking
+
+#### Pre-commit Testing
+- **Added**: Automated testing before commits
+- **Added**: Core functionality validation (3 essential tests)
+- **Added**: Commit blocking on test failures
+- **Configured**: `.pre-commit-config.yaml` with testing hooks
+
+### 🏗️ Technical Architecture Improvements
+- **Added**: Modular component architecture
+- **Added**: MedicineManager and PathologyManager classes
+- **Added**: Dynamic UI generation based on configuration
+- **Improved**: Separation of concerns across modules
+- **Enhanced**: Error handling and logging throughout
+
+### 📈 Data Management Enhancements
+- **Added**: Automatic data migration and backup system
+- **Added**: Dynamic CSV column management
+- **Added**: Robust dose string parsing
+- **Improved**: Data validation and error handling
+- **Enhanced**: Backward compatibility preservation
+
+### 🔧 Development Tools & Workflow
+- **Added**: uv integration for fast package management
+- **Added**: Comprehensive Makefile with development commands
+- **Added**: Docker support with multi-platform builds
+- **Added**: Pre-commit hooks for code quality
+- **Added**: Ruff for fast Python formatting and linting
+- **Improved**: Virtual environment management
+
+### 🚀 Deployment & Distribution
+- **Added**: PyInstaller integration for standalone executables
+- **Added**: Linux desktop integration
+- **Added**: Automatic file installation and desktop entries
+- **Added**: Docker containerization support
+- **Improved**: Build and deployment automation
+
+## Technical Details
+
+### Dependencies
+- **Runtime**: Python 3.13+, matplotlib, pandas, tkinter, colorlog
+- **Development**: pytest, pytest-cov, ruff, pre-commit, pyinstaller
+- **Package Management**: uv (Rust-based, 10-100x faster than pip/Poetry)
+
+### Architecture
+- **Frontend**: Tkinter-based GUI with dynamic component generation
+- **Backend**: Pandas for data manipulation, Matplotlib for visualization
+- **Storage**: CSV-based with JSON configuration files
+- **Testing**: pytest with comprehensive mocking and coverage
+
+### File Structure
+```
+src/                    # Main application code
+├── main.py            # Application entry point
+├── ui_manager.py      # User interface management
+├── data_manager.py    # CSV operations and data persistence
+├── graph_manager.py   # Visualization and plotting
+├── medicine_manager.py # Medicine system management
+└── pathology_manager.py # Symptom tracking
+
+tests/                 # Comprehensive test suite (112 tests, 93% coverage)
+docs/                  # Organized documentation
+├── FEATURES.md        # Complete feature documentation
+├── DEVELOPMENT.md     # Development and testing guide
+└── CHANGELOG.md       # This changelog
+
+Configuration Files:
+├── medicines.json     # Medicine definitions (auto-generated)
+├── pathologies.json   # Symptom categories (auto-generated)
+├── pyproject.toml     # Project configuration
+└── uv.lock           # Dependency lock file
+```
+
+## Migration Notes
+
+### From Previous Versions
+- **Data Compatibility**: All existing CSV data continues to work
+- **Automatic Migration**: Data structure updates handled automatically
+- **Backup Creation**: Automatic backups before major changes
+- **No Data Loss**: Existing functionality preserved during updates
+
+### Configuration Migration
+- **Medicine System**: Hard-coded medicines converted to JSON configuration
+- **UI Updates**: Interface automatically adapts to new medicine definitions
+- **Graph Integration**: Visualization system updated for dynamic medicines
+
+## Future Roadmap
+
+### Planned Features (v2.0)
+- **Mobile App**: Companion mobile application for dose tracking
+- **Cloud Sync**: Multi-device data synchronization
+- **Advanced Analytics**: Machine learning-based trend analysis
+- **Reminder System**: Intelligent medication reminders
+- **Doctor Integration**: Healthcare provider report generation
+
+### Platform Expansion
+- **macOS Support**: Native macOS application
+- **Windows Support**: Windows executable and installer
+- **Web Interface**: Browser-based version for universal access
+
+### API Development
+- **REST API**: External system integration
+- **Plugin Architecture**: Third-party extension support
+- **Data Export**: Multiple format support (JSON, XML, etc.)
+
+---
+
+## Contributing
+
+This project follows semantic versioning and maintains comprehensive documentation.
+For development guidelines, see [docs/DEVELOPMENT.md](docs/DEVELOPMENT.md).
+For feature information, see [docs/FEATURES.md](docs/FEATURES.md).

docs/DEVELOPMENT.md

@@ -0,0 +1,340 @@
+# TheChart - Development Documentation
+
+## Development Environment Setup
+
+### Prerequisites
+- **Python 3.13+**: Required for the application
+- **uv**: Fast Python package manager (10-100x faster than pip/Poetry)
+- **Git**: Version control
+
+### Quick Setup
+```bash
+# Clone and setup
+git clone <repository-url>
+cd thechart
+
+# Install with uv (recommended)
+make install
+
+# Or manual setup
+uv venv --python 3.13
+uv sync
+uv run pre-commit install --install-hooks --overwrite
+```
+
+### Environment Activation
+```bash
+# fish shell (default)
+source .venv/bin/activate.fish
+# or
+make shell
+
+# bash/zsh
+source .venv/bin/activate
+
+# Using uv run (recommended)
+uv run python src/main.py
+```
+
+## Testing Framework
+
+### Test Infrastructure
+Professional testing setup with comprehensive coverage and automation.
+
+#### Testing Tools
+- **pytest**: Modern Python testing framework
+- **pytest-cov**: Coverage reporting (HTML, XML, terminal)
+- **pytest-mock**: Mocking support for isolated testing
+- **coverage**: Detailed coverage analysis
+
+#### Test Statistics
+- **93% Overall Code Coverage** (482 total statements, 33 missed)
+- **112 Total Tests** across 6 test modules
+- **80 Tests Passing** (71.4% pass rate)
+
+#### Coverage by Module
+| Module | Coverage | Status |
+|--------|----------|--------|
+| constants.py | 100% | ✅ Complete |
+| logger.py | 100% | ✅ Complete |
+| graph_manager.py | 97% | ✅ Excellent |
+| init.py | 95% | ✅ Excellent |
+| ui_manager.py | 93% | ✅ Very Good |
+| main.py | 91% | ✅ Very Good |
+| data_manager.py | 87% | ✅ Good |
+
+### Test Structure
+
+#### Test Files
+- **`tests/test_data_manager.py`** (16 tests): CSV operations, validation, error handling
+- **`tests/test_graph_manager.py`** (14 tests): Matplotlib integration, dose calculations
+- **`tests/test_ui_manager.py`** (21 tests): Tkinter UI components, user interactions
+- **`tests/test_main.py`** (18 tests): Application integration, workflow testing
+- **`tests/test_constants.py`** (12 tests): Configuration validation
+- **`tests/test_logger.py`** (8 tests): Logging functionality
+- **`tests/test_init.py`** (23 tests): Initialization and setup
+
+#### Test Fixtures (`tests/conftest.py`)
+- **Temporary Files**: Safe testing without affecting real data
+- **Sample Data**: Comprehensive test datasets with realistic dose information
+- **Mock Loggers**: Isolated logging for testing
+- **Environment Mocking**: Controlled test environments
+
+### Running Tests
+
+#### Basic Testing
+```bash
+# Run all tests
+make test
+# or
+uv run pytest
+
+# Run specific test file
+uv run pytest tests/test_graph_manager.py -v
+
+# Run tests with specific pattern
+uv run pytest -k "dose_calculation" -v
+```
+
+#### Coverage Testing
+```bash
+# Generate coverage report
+uv run pytest --cov=src --cov-report=html
+
+# Coverage with specific module
+uv run pytest tests/test_graph_manager.py --cov=src.graph_manager --cov-report=term-missing
+```
+
+#### Continuous Testing
+```bash
+# Watch for changes and re-run tests
+uv run pytest --watch
+
+# Quick test runner script
+./scripts/run_tests.py
+```
+
+### Pre-commit Testing
+Automated testing prevents commits when core functionality is broken.
+
+#### Configuration
+Located in `.pre-commit-config.yaml`:
+- **Core Tests**: 3 essential tests run before each commit
+- **Fast Execution**: Only critical functionality tested
+- **Commit Blocking**: Prevents commits when tests fail
+
+#### Core Tests
+1. **`test_init`**: DataManager initialization
+2. **`test_initialize_csv_creates_file_with_headers`**: CSV file creation
+3. **`test_load_data_with_valid_data`**: Data loading functionality
+
+#### Usage
+```bash
+# Automatic on commit
+git commit -m "Your changes"
+
+# Manual pre-commit check
+pre-commit run --all-files
+
+# Run just test check
+pre-commit run pytest-check --all-files
+```
+
+### Dose Calculation Testing
+Comprehensive testing for the complex dose parsing and calculation system.
+
+#### Test Categories
+- **Standard Format**: `2025-07-28 18:59:45:150mg` → 150.0mg
+- **Multiple Doses**: `2025-07-28 18:59:45:150mg|2025-07-28 19:34:19:75mg` → 225.0mg
+- **With Symbols**: `• • • • 2025-07-30 07:50:00:300` → 300.0mg
+- **Decimal Values**: `2025-07-28 18:59:45:12.5mg|2025-07-28 19:34:19:7.5mg` → 20.0mg
+- **No Timestamps**: `100mg|50mg` → 150.0mg
+- **Mixed Formats**: `• 2025-07-30 22:50:00:10|75mg` → 85.0mg
+- **Edge Cases**: Empty strings, NaN values, malformed data → 0.0mg
+
+#### Test Implementation
+```python
+# Example test case
+def test_calculate_daily_dose_standard_format(self, graph_manager):
+    dose_str = "2025-07-28 18:59:45:150mg|2025-07-28 19:34:19:75mg"
+    result = graph_manager._calculate_daily_dose(dose_str)
+    assert result == 225.0
+```
+
+### Medicine Plotting Tests
+Testing for the enhanced graph functionality with medicine dose visualization.
+
+#### Test Areas
+- **Toggle Functionality**: Medicine show/hide controls
+- **Dose Plotting**: Bar chart generation for medicine doses
+- **Color Coding**: Proper color assignment and consistency
+- **Legend Enhancement**: Multi-column layout and average calculations
+- **Data Integration**: Proper data flow from CSV to visualization
+
+### UI Testing Strategy
+Testing user interface components with mock frameworks to avoid GUI dependencies.
+
+#### UI Test Coverage
+- **Component Creation**: Widget creation and configuration
+- **Event Handling**: User interactions and callbacks
+- **Data Binding**: Variable synchronization and updates
+- **Layout Management**: Grid and frame arrangements
+- **Error Handling**: User input validation and error messages
+
+#### Mocking Strategy
+```python
+# Example UI test with mocking
+@patch('tkinter.Tk')
+def test_create_input_frame(self, mock_tk, ui_manager):
+    parent = Mock()
+    result = ui_manager.create_input_frame(parent, {}, {})
+    assert result is not None
+    assert isinstance(result, dict)
+```
+
+## Code Quality
+
+### Tools and Standards
+- **ruff**: Fast Python linter and formatter (Rust-based)
+- **pre-commit**: Git hook management for code quality
+- **Type Hints**: Comprehensive type annotations
+- **Docstrings**: Detailed function and class documentation
+
+### Code Formatting
+```bash
+# Format code
+make format
+# or
+uv run ruff format .
+
+# Check formatting
+make lint
+# or
+uv run ruff check .
+```
+
+### Pre-commit Hooks
+Automatically installed hooks ensure code quality:
+- **Code Formatting**: ruff formatting
+- **Linting Checks**: Code quality validation
+- **Import Sorting**: Consistent import organization
+- **Basic File Checks**: Trailing whitespace, file endings
+
+## Development Workflow
+
+### Feature Development
+1. **Create Feature Branch**: `git checkout -b feature/new-feature`
+2. **Implement Changes**: Follow existing patterns and architecture
+3. **Add Tests**: Ensure new functionality is tested
+4. **Run Tests**: `make test` to verify functionality
+5. **Code Quality**: `make format && make lint`
+6. **Commit Changes**: Pre-commit hooks run automatically
+7. **Create Pull Request**: For code review
+
+### Medicine System Development
+Adding new medicines or modifying the medicine system:
+
+```python
+# Example: Adding a new medicine programmatically
+from medicine_manager import MedicineManager, Medicine
+
+medicine_manager = MedicineManager()
+new_medicine = Medicine(
+    key="sertraline",
+    display_name="Sertraline",
+    dosage_info="50mg",
+    quick_doses=["25", "50", "100"],
+    color="#9B59B6",
+    default_enabled=False
+)
+medicine_manager.add_medicine(new_medicine)
+```
+
+### Testing New Features
+1. **Unit Tests**: Add tests for new functionality
+2. **Integration Tests**: Test feature integration with existing system
+3. **UI Tests**: Test user interface changes
+4. **Dose Calculation Tests**: If affecting dose calculations
+5. **Regression Tests**: Ensure existing functionality still works
+
+## Debugging and Troubleshooting
+
+### Logging
+Application logs are stored in `logs/` directory:
+- **`app.log`**: General application logs
+- **`app.error.log`**: Error messages only
+- **`app.warning.log`**: Warning messages only
+
+### Debug Mode
+Enable debug logging by modifying `src/logger.py` configuration.
+
+### Common Issues
+
+#### Test Failures
+- **Matplotlib Mocking**: Ensure proper matplotlib component mocking
+- **Tkinter Dependencies**: Use headless testing for UI components
+- **File Path Issues**: Use absolute paths in tests
+- **Mock Configuration**: Proper mock setup for external dependencies
+
+#### Development Environment
+- **Python Version**: Ensure Python 3.13+ is used
+- **Virtual Environment**: Always work within the virtual environment
+- **Dependencies**: Keep dependencies up to date with `uv sync --upgrade`
+
+### Performance Testing
+- **Dose Calculation Performance**: Test with large datasets
+- **UI Responsiveness**: Test with extensive medicine lists
+- **Memory Usage**: Monitor memory consumption with large CSV files
+- **Graph Rendering**: Test graph performance with large datasets
+
+## Architecture Documentation
+
+### Core Components
+- **MedTrackerApp**: Main application class
+- **MedicineManager**: Medicine CRUD operations
+- **PathologyManager**: Pathology/symptom management
+- **GraphManager**: Visualization and plotting
+- **UIManager**: User interface creation
+- **DataManager**: Data persistence and CSV operations
+
+### Data Flow
+1. **User Input** → UIManager → DataManager → CSV
+2. **Data Loading** → DataManager → pandas DataFrame → GraphManager
+3. **Visualization** → GraphManager → matplotlib → UI Display
+
+### Extension Points
+- **Medicine System**: Add new medicine properties
+- **Graph Types**: Add new visualization types
+- **Export Formats**: Add new data export options
+- **UI Components**: Add new interface elements
+
+## Deployment Testing
+
+### Standalone Executable
+```bash
+# Build executable
+make deploy
+
+# Test deployment
+./dist/thechart
+```
+
+### Docker Testing
+```bash
+# Build container
+make build
+
+# Test container
+make start
+make attach
+```
+
+### Cross-platform Testing
+- **Linux**: Primary development and testing platform
+- **macOS**: Planned support (testing needed)
+- **Windows**: Planned support (testing needed)
+
+---
+
+For user documentation, see [README.md](../README.md).
+For feature details, see [docs/FEATURES.md](FEATURES.md).

docs/FEATURES.md

@@ -0,0 +1,232 @@
+# TheChart - Features Documentation
+
+## Overview
+TheChart is a comprehensive medication tracking application that allows users to monitor medication intake, symptom tracking, and visualize treatment progress over time.
+
+## Core Features
+
+### 🏥 Modular Medicine System
+TheChart features a dynamic medicine management system that allows complete customization without code modifications.
+
+#### Features:
+- **Dynamic Medicine Management**: Add, edit, and remove medicines through the UI
+- **Configurable Properties**: Each medicine has customizable display names, dosages, colors, and quick-dose options
+- **Automatic UI Updates**: All interface elements update automatically when medicines change
+- **JSON Configuration**: Human-readable `medicines.json` file for easy management
+
+#### Medicine Configuration:
+Each medicine includes:
+- **Key**: Internal identifier (e.g., "bupropion")
+- **Display Name**: User-friendly name (e.g., "Bupropion")
+- **Dosage Info**: Dosage information (e.g., "150/300 mg")
+- **Quick Doses**: Common dose amounts for quick selection
+- **Color**: Hex color for graph display (e.g., "#FF6B6B")
+- **Default Enabled**: Whether to show in graphs by default
+
+#### Default Medicines:
+| Medicine | Dosage | Default Graph | Color |
+|----------|--------|---------------|--------|
+| Bupropion | 150/300 mg | ✅ | Red (#FF6B6B) |
+| Hydroxyzine | 25 mg | ❌ | Teal (#4ECDC4) |
+| Gabapentin | 100 mg | ❌ | Blue (#45B7D1) |
+| Propranolol | 10 mg | ✅ | Green (#96CEB4) |
+| Quetiapine | 25 mg | ❌ | Yellow (#FFEAA7) |
+
+#### Usage:
+1. **Through UI**: Go to `Tools` → `Manage Medicines...`
+2. **Manual Configuration**: Edit `medicines.json` directly
+3. **Programmatically**: Use the MedicineManager API
+
+### 💊 Advanced Dose Tracking
+Comprehensive dose tracking system that records exact timestamps and dosages throughout the day.
+
+#### Core Capabilities:
+- **Timestamp Recording**: Exact time when medicine is taken
+- **Dose Amount Tracking**: Record specific doses (150mg, 10mg, etc.)
+- **Multiple Doses Per Day**: Take the same medicine multiple times
+- **Real-time Display**: See today's doses immediately
+- **Data Persistence**: All doses saved to CSV with full history
+
+#### Dose Management Interface:
+Located in the edit window (double-click any entry):
+- **Individual Dose Entry Fields**: For each medicine
+- **"Take [Medicine]" Buttons**: Immediate dose recording with timestamps
+- **Editable Dose Display Areas**: View and modify existing doses
+- **Quick Dose Buttons**: Pre-configured common dose amounts
+- **Format Consistency**: All doses displayed in HH:MM: dose format
+
+#### Data Format:
+- **Timestamp Format**: `YYYY-MM-DD HH:MM:SS`
+- **Dose Separator**: `|` (pipe) for multiple doses
+- **Dose Format**: `timestamp:dose`
+- **CSV Storage**: Additional columns in existing CSV file
+
+#### Example CSV Format:
+```csv
+date,depression,anxiety,sleep,appetite,bupropion,bupropion_doses,hydroxyzine,hydroxyzine_doses,propranolol,propranolol_doses,note
+07/28/2025,4,5,3,3,1,"2025-07-28 14:30:00:150mg|2025-07-28 18:30:00:150mg",0,"",1,"2025-07-28 12:30:00:10mg","Multiple doses today"
+```
+
+### 📊 Enhanced Graph Visualization
+Advanced graphing system with comprehensive data visualization and interactive controls.
+
+#### Medicine Dose Visualization:
+- **Colored Bar Charts**: Each medicine has distinct colors
+- **Daily Dose Totals**: Automatically calculated from individual doses
+- **Scaled Display**: Doses scaled by 1/10 for better visibility (labeled as "mg/10")
+- **Dynamic Positioning**: Bars positioned below main chart area
+- **Semi-transparent Bars**: Alpha=0.6 to avoid overwhelming symptom data
+
+#### Interactive Controls:
+- **Toggle Buttons**: Independent show/hide for each medicine and symptom
+- **Organized Sections**: "Symptoms" and "Medicines" sections
+- **Real-time Updates**: Changes take effect immediately
+
+#### Enhanced Legend:
+- **Multi-column Layout**: Efficient use of graph space (2 columns)
+- **Average Dosage Display**: Shows average dose for each medicine
+- **Color Coding**: Consistent color scheme matching graph elements
+- **Professional Styling**: Frame, shadow, and transparency effects
+- **Tracking Status**: Shows medicines being monitored but without current dose data
+
+#### Dose Calculation Features:
+- **Multiple Format Support**: Handles various dose string formats
+- **Robust Parsing**: Handles timestamps, symbols (•), and mixed formats
+- **Edge Case Handling**: Manages empty strings, NaN values, malformed data
+- **Daily Totals**: Sums all individual doses for comprehensive daily tracking
+
+### 🏥 Pathology Management
+Comprehensive symptom tracking with configurable pathologies.
+
+#### Features:
+- **Dynamic Pathology System**: Similar to medicine management
+- **Configurable Symptoms**: Add, edit, and remove symptom categories
+- **Scale-based Rating**: 0-10 rating system for symptom severity
+- **Historical Tracking**: Full symptom history with trend analysis
+
+### 📝 Data Management
+Robust data handling with comprehensive backup and migration support.
+
+#### Data Features:
+- **CSV-based Storage**: Human-readable and portable data format
+- **Automatic Backups**: Created before major migrations
+- **Backward Compatibility**: Existing data continues to work with updates
+- **Dynamic Column Management**: Automatically adapts to new medicines/pathologies
+- **Data Validation**: Ensures data integrity and handles edge cases
+
+#### Migration Support:
+- **Automatic Migration**: Data structure updates handled automatically
+- **Backup Creation**: `thechart_data.csv.backup_YYYYMMDD_HHMMSS` format
+- **No Data Loss**: All existing functionality and data preserved
+- **Version Compatibility**: Seamless updates across application versions
+
+### 🧪 Comprehensive Testing Framework
+Professional testing infrastructure with high code coverage.
+
+#### Testing Statistics:
+- **93% Overall Code Coverage** (482 total statements, 33 missed)
+- **112 Total Tests** across 6 test modules
+- **80 Tests Passing** (71.4% pass rate)
+- **Pre-commit Testing**: Core functionality tests run before each commit
+
+#### Test Coverage by Module:
+- **100% Coverage**: constants.py, logger.py
+- **97% Coverage**: graph_manager.py
+- **95% Coverage**: init.py
+- **93% Coverage**: ui_manager.py
+- **91% Coverage**: main.py
+- **87% Coverage**: data_manager.py
+
+#### Testing Tools:
+- **pytest**: Modern Python testing framework
+- **pytest-cov**: Coverage reporting with HTML, XML, and terminal output
+- **pytest-mock**: Mocking support for isolated testing
+- **pre-commit hooks**: Automated testing before commits
+
+## User Interface Features
+
+### 🖥️ Intuitive Design
+- **Clean Main Interface**: Simplified new entry form focused on essential inputs
+- **Organized Edit Windows**: Comprehensive dose management in dedicated edit interface
+- **Scrollable Interface**: Vertical scrollbar for expanded UI components
+- **Responsive Design**: Interface adapts to window size and content
+- **Visual Feedback**: Success messages and clear status indicators
+
+### 🎯 User Experience Improvements
+- **Centralized Dose Management**: All dose operations consolidated in edit windows
+- **Quick Entry Options**: Pre-configured dose buttons for common amounts
+- **Format Guidance**: Clear instructions and format examples
+- **Real-time Updates**: Immediate feedback and data updates
+- **Error Handling**: Comprehensive error messages and recovery options
+
+## Technical Architecture
+
+### 🏗️ Modular Design
+- **MedicineManager**: Core medicine CRUD operations
+- **PathologyManager**: Symptom and pathology management
+- **GraphManager**: All graph-related operations and visualizations
+- **UIManager**: User interface creation and management
+- **DataManager**: CSV operations and data persistence
+
+### 🔧 Configuration Management
+- **JSON-based Configuration**: `medicines.json` and `pathologies.json`
+- **Dynamic Loading**: Runtime configuration updates
+- **Validation**: Input validation and error handling
+- **Backward Compatibility**: Seamless updates and migrations
+
+### 📈 Data Processing
+- **Pandas Integration**: Efficient data manipulation and analysis
+- **Matplotlib Visualization**: Professional graph rendering
+- **Robust Parsing**: Handles various data formats and edge cases
+- **Real-time Calculations**: Dynamic dose totals and averages
+
+## Deployment and Distribution
+
+### 📦 Standalone Executable
+- **PyInstaller Integration**: Creates self-contained executables
+- **Cross-platform Support**: Linux deployment with desktop integration
+- **Automatic Installation**: Installs to `~/Applications/` with desktop entry
+- **Data Migration**: Copies data files to appropriate user directories
+
+### 🐳 Docker Support
+- **Multi-platform Images**: Docker container support
+- **Docker Compose**: Easy container management
+- **Development Environment**: Consistent development setup across platforms
+
+### 🔄 Package Management
+- **UV Integration**: Fast Python package management with Rust performance
+- **Virtual Environment**: Isolated dependency management
+- **Lock Files**: Reproducible builds with `uv.lock`
+- **Development Dependencies**: Separate dev dependencies for clean production builds
+
+## Integration Features
+
+### 🔄 Import/Export
+- **CSV Import**: Import existing medication data
+- **Data Export**: Export data for backup or analysis
+- **Format Compatibility**: Standard CSV format for portability
+
+### 🔌 API Integration
+- **Extensible Architecture**: Plugin system for future enhancements
+- **Medicine API**: Programmatic medicine management
+- **Data API**: Direct data access and manipulation
+
+## Future Enhancements
+
+### 🚀 Planned Features
+- **Mobile Companion App**: Mobile dose tracking and reminders
+- **Cloud Synchronization**: Multi-device data synchronization
+- **Advanced Analytics**: Machine learning-based trend analysis
+- **Reminder System**: Intelligent dose reminders and scheduling
+- **Doctor Integration**: Export reports for healthcare providers
+
+### 🎯 Development Roadmap
+- **macOS/Windows Support**: Extended platform support
+- **Plugin Architecture**: Third-party extension support
+- **API Development**: RESTful API for external integrations
+- **Advanced Visualizations**: Additional chart types and analysis tools
+
+---
+
+For detailed usage instructions, see the main [README.md](../README.md).
+For development information, see [DEVELOPMENT.md](DEVELOPMENT.md).

docs/README.md

@@ -0,0 +1,76 @@
+# TheChart Documentation
+
+Welcome to TheChart documentation! This guide will help you navigate the available documentation.
+
+## 📖 Documentation Index
+
+### For Users
+- **[README.md](../README.md)** - Quick start guide and installation
+- **[Features Guide](FEATURES.md)** - Complete feature documentation
+  - Modular Medicine System
+  - Advanced Dose Tracking
+  - Graph Visualizations
+  - Data Management
+
+### For Developers
+- **[Development Guide](DEVELOPMENT.md)** - Development setup and testing
+  - Testing Framework (93% coverage)
+  - Code Quality Tools
+  - Architecture Overview
+  - Debugging Guide
+
+### Project History
+- **[Changelog](CHANGELOG.md)** - Version history and feature evolution
+  - Recent updates and improvements
+  - Migration notes
+  - Future roadmap
+
+## 🚀 Quick Navigation
+
+### Getting Started
+1. **Installation**: See [README.md - Installation](../README.md#installation)
+2. **First Run**: See [README.md - Running the Application](../README.md#running-the-application)
+3. **Key Features**: See [FEATURES.md](FEATURES.md)
+
+### Development
+1. **Setup**: See [DEVELOPMENT.md - Development Environment Setup](DEVELOPMENT.md#development-environment-setup)
+2. **Testing**: See [DEVELOPMENT.md - Testing Framework](DEVELOPMENT.md#testing-framework)
+3. **Contributing**: See [DEVELOPMENT.md - Development Workflow](DEVELOPMENT.md#development-workflow)
+
+### Advanced Usage
+1. **Medicine Management**: See [FEATURES.md - Modular Medicine System](FEATURES.md#-modular-medicine-system)
+2. **Dose Tracking**: See [FEATURES.md - Advanced Dose Tracking](FEATURES.md#-advanced-dose-tracking)
+3. **Visualizations**: See [FEATURES.md - Enhanced Graph Visualization](FEATURES.md#-enhanced-graph-visualization)
+
+## 📋 Documentation Standards
+
+All documentation follows these principles:
+- **Clear Structure**: Hierarchical organization with clear headings
+- **Practical Examples**: Code snippets and usage examples
+- **Up-to-date**: Synchronized with current codebase
+- **Comprehensive**: Covers all major features and workflows
+- **Cross-referenced**: Links between related sections
+
+## 🔍 Finding Information
+
+### By Topic
+- **Installation & Setup** → [README.md](../README.md)
+- **Feature Usage** → [FEATURES.md](FEATURES.md)
+- **Development** → [DEVELOPMENT.md](DEVELOPMENT.md)
+- **Version History** → [CHANGELOG.md](CHANGELOG.md)
+
+### By User Type
+- **End Users** → Start with [README.md](../README.md), then [FEATURES.md](FEATURES.md)
+- **Developers** → [DEVELOPMENT.md](DEVELOPMENT.md) and [CHANGELOG.md](CHANGELOG.md)
+- **Contributors** → All documentation, especially [DEVELOPMENT.md](DEVELOPMENT.md)
+
+### By Task
+- **Install TheChart** → [README.md - Installation](../README.md#installation)
+- **Add New Medicine** → [FEATURES.md - Modular Medicine System](FEATURES.md#-modular-medicine-system)
+- **Track Doses** → [FEATURES.md - Advanced Dose Tracking](FEATURES.md#-advanced-dose-tracking)
+- **Run Tests** → [DEVELOPMENT.md - Testing Framework](DEVELOPMENT.md#testing-framework)
+- **Deploy Application** → [README.md - Deployment](../README.md#deployment)
+
+---
+
+**Need help?** Check the troubleshooting sections in [README.md](../README.md#troubleshooting) and [DEVELOPMENT.md](DEVELOPMENT.md#debugging-and-troubleshooting).

medicines.json

@@ -0,0 +1,62 @@
+{
+  "medicines": [
+    {
+      "key": "bupropion",
+      "display_name": "Bupropion",
+      "dosage_info": "150/300 mg",
+      "quick_doses": [
+        "150",
+        "300"
+      ],
+      "color": "#FF6B6B",
+      "default_enabled": false
+    },
+    {
+      "key": "hydroxyzine",
+      "display_name": "Hydroxyzine",
+      "dosage_info": "25 mg",
+      "quick_doses": [
+        "25",
+        "50"
+      ],
+      "color": "#4ECDC4",
+      "default_enabled": false
+    },
+    {
+      "key": "gabapentin",
+      "display_name": "Gabapentin",
+      "dosage_info": "100 mg",
+      "quick_doses": [
+        "100",
+        "300",
+        "600"
+      ],
+      "color": "#45B7D1",
+      "default_enabled": false
+    },
+    {
+      "key": "propranolol",
+      "display_name": "Propranolol",
+      "dosage_info": "10 mg",
+      "quick_doses": [
+        "10",
+        "20",
+        "40"
+      ],
+      "color": "#96CEB4",
+      "default_enabled": false
+    },
+    {
+      "key": "quetiapine",
+      "display_name": "Quetiapine",
+      "dosage_info": "25 mg",
+      "quick_doses": [
+        "25",
+        "50",
+        "100"
+      ],
+      "color": "#FFEAA7",
+      "default_enabled": false
+    }
+  ]
+}

nonexistent.csv

@@ -0,0 +1 @@
+date,depression,anxiety,sleep,appetite,bupropion,bupropion_doses,hydroxyzine,hydroxyzine_doses,gabapentin,gabapentin_doses,propranolol,propranolol_doses,quetiapine,quetiapine_doses,note

pathologies.json

@@ -0,0 +1,44 @@
+{
+    "pathologies": [
+        {
+            "key": "depression",
+            "display_name": "Depression",
+            "scale_info": "0:good, 10:bad",
+            "color": "#FF6B6B",
+            "default_enabled": true,
+            "scale_min": 0,
+            "scale_max": 10,
+            "scale_orientation": "normal"
+        },
+        {
+            "key": "anxiety",
+            "display_name": "Anxiety",
+            "scale_info": "0:good, 10:bad",
+            "color": "#FFA726",
+            "default_enabled": true,
+            "scale_min": 0,
+            "scale_max": 10,
+            "scale_orientation": "normal"
+        },
+        {
+            "key": "sleep",
+            "display_name": "Sleep Quality",
+            "scale_info": "0:bad, 10:good",
+            "color": "#66BB6A",
+            "default_enabled": true,
+            "scale_min": 0,
+            "scale_max": 10,
+            "scale_orientation": "inverted"
+        },
+        {
+            "key": "appetite",
+            "display_name": "Appetite",
+            "scale_info": "0:bad, 10:good",
+            "color": "#42A5F5",
+            "default_enabled": true,
+            "scale_min": 0,
+            "scale_max": 10,
+            "scale_orientation": "inverted"
+        }
+    ]
+}

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "thechart"
-version = "1.0.1"
+version = "1.6.1"
 description = "Chart to monitor your medication intake over time."
 readme = "README.md"
 requires-python = ">=3.13"
@@ -13,7 +13,47 @@ dependencies = [
 ]
 
 [dependency-groups]
-dev = ["pre-commit>=4.2.0", "pyinstaller>=6.14.2", "ruff>=0.12.5"]
+dev = [
+    "pre-commit>=4.2.0",
+    "pyinstaller>=6.14.2",
+    "ruff>=0.12.5",
+    "pytest>=8.0.0",
+    "pytest-cov>=4.0.0",
+    "pytest-mock>=3.12.0",
+    "coverage>=7.3.0",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py", "*_test.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "--verbose",
+    "--cov=src",
+    "--cov-report=term-missing",
+    "--cov-report=html:htmlcov",
+    "--cov-report=xml",
+]
+minversion = "8.0"
+
+[tool.coverage.run]
+source = ["src"]
+omit = ["tests/*", "*/test_*", "*/__pycache__/*", ".venv/*"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "if self.debug:",
+    "if settings.DEBUG",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if 0:",
+    "if __name__ == .__main__.:",
+    "class .*\\bProtocol\\):",
+    "@(abc\\.)?abstractmethod",
+]
 
 [tool.ruff]
 target-version = "py313" # Target Python 3.13

requirements-dev.in

@@ -3,3 +3,7 @@
 
 pre-commit
 pyinstaller
+pytest>=8.0.0
+pytest-cov>=4.0.0
+pytest-mock>=3.12.0
+coverage>=7.3.0

scripts/run_tests.py

@@ -0,0 +1,45 @@
+#!/usr/bin/env python3
+"""
+Test runner script for TheChart application.
+Run this script to execute all tests with coverage reporting.
+"""
+
+import os
+import subprocess
+import sys
+
+
+def run_tests():
+    """Run all tests with coverage reporting."""
+
+    # Change to project root directory
+    project_root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+    os.chdir(project_root)
+
+    print("Running TheChart tests with coverage...")
+    print(f"Project root: {project_root}")
+
+    # Run pytest with coverage
+    cmd = [
+        sys.executable,
+        "-m",
+        "pytest",
+        "tests/",
+        "--verbose",
+        "--cov=src",
+        "--cov-report=term-missing",
+        "--cov-report=html:htmlcov",
+        "--cov-report=xml",
+    ]
+
+    try:
+        result = subprocess.run(cmd, check=False)
+        return result.returncode
+    except Exception as e:
+        print(f"Error running tests: {e}")
+        return 1
+
+
+if __name__ == "__main__":
+    exit_code = run_tests()
+    sys.exit(exit_code)

src/constants.py

@@ -1,8 +1,12 @@
 import os
+import sys
 
 from dotenv import load_dotenv
 
-load_dotenv(override=True)
+extDataDir = os.getcwd()
+if getattr(sys, "frozen", False):
+    extDataDir = sys._MEIPASS
+load_dotenv(dotenv_path=os.path.join(extDataDir, ".env"))
 
 LOG_LEVEL = os.getenv("LOG_LEVEL", "INFO").upper()
 LOG_PATH = os.getenv("LOG_PATH", "/tmp/logs/thechart")

src/data_manager.py

@@ -4,58 +4,129 @@ import os
 
 import pandas as pd
 
+from medicine_manager import MedicineManager
+from pathology_manager import PathologyManager
+
 
 class DataManager:
-    """Handle all data operations for the application."""
+    """Handle all data operations for the application with performance optimizations."""
 
-    def __init__(self, filename: str, logger: logging.Logger) -> None:
+    def __init__(
+        self,
+        filename: str,
+        logger: logging.Logger,
+        medicine_manager: MedicineManager,
+        pathology_manager: PathologyManager,
+    ) -> None:
         self.filename: str = filename
         self.logger: logging.Logger = logger
-        self.initialize_csv()
+        self.medicine_manager = medicine_manager
+        self.pathology_manager = pathology_manager
 
-    def initialize_csv(self) -> None:
-        """Create CSV file with headers if it doesn't exist."""
-        if not os.path.exists(self.filename):
+        # Cache for loaded data to avoid repeated file I/O
+        self._data_cache: pd.DataFrame | None = None
+        self._cache_timestamp: float = 0
+        self._headers_cache: tuple[str, ...] | None = None
+        self._dtype_cache: dict[str, type] | None = None
+
+        self._initialize_csv_file()
+
+    def _get_csv_headers(self) -> tuple[str, ...]:
+        """Get CSV headers based on current pathology and medicine configuration.
+        Cached to avoid repeated computation."""
+        if self._headers_cache is not None:
+            return self._headers_cache
+
+        # Start with date
+        headers = ["date"]
+
+        # Add pathology headers
+        for pathology_key in self.pathology_manager.get_pathology_keys():
+            headers.append(pathology_key)
+
+        # Add medicine headers
+        for medicine_key in self.medicine_manager.get_medicine_keys():
+            headers.extend([medicine_key, f"{medicine_key}_doses"])
+
+        result = tuple(headers + ["note"])
+        self._headers_cache = result
+        return result
+
+    def _initialize_csv_file(self) -> None:
+        """Create CSV file with headers if it doesn't exist or is empty."""
+        if not os.path.exists(self.filename) or os.path.getsize(self.filename) == 0:
             with open(self.filename, mode="w", newline="") as file:
                 writer = csv.writer(file)
-                writer.writerow(
-                    [
-                        "date",
-                        "depression",
-                        "anxiety",
-                        "sleep",
-                        "appetite",
-                        "bupropion",
-                        "hydroxyzine",
-                        "gabapentin",
-                        "propranolol",
-                        "note",
-                    ]
-                )
+                writer.writerow(self._get_csv_headers())
+
+    def _invalidate_cache(self) -> None:
+        """Invalidate the data cache when data changes."""
+        self._data_cache = None
+        self._cache_timestamp = 0
+
+    def _should_reload_data(self) -> bool:
+        """Check if data should be reloaded based on file modification time."""
+        if self._data_cache is None:
+            return True
+
+        try:
+            file_mtime = os.path.getmtime(self.filename)
+            return file_mtime > self._cache_timestamp
+        except OSError:
+            return True
+
+    def _get_dtype_dict(self) -> dict[str, type]:
+        """Get pandas dtype dictionary for efficient reading.
+        Cached to avoid recreation."""
+        if self._dtype_cache is not None:
+            return self._dtype_cache
+
+        dtype_dict = {"date": str, "note": str}
+
+        # Add pathology types
+        for pathology_key in self.pathology_manager.get_pathology_keys():
+            dtype_dict[pathology_key] = int
+
+        # Add medicine types
+        for medicine_key in self.medicine_manager.get_medicine_keys():
+            dtype_dict[medicine_key] = int
+            dtype_dict[f"{medicine_key}_doses"] = str
+
+        self._dtype_cache = dtype_dict
+        return dtype_dict
 
     def load_data(self) -> pd.DataFrame:
-        """Load data from CSV file."""
+        """Load data from CSV file with caching for better performance."""
         if not os.path.exists(self.filename) or os.path.getsize(self.filename) == 0:
             self.logger.warning("CSV file is empty or doesn't exist. No data to load.")
             return pd.DataFrame()
 
+        # Use cached data if available and file hasn't changed
+        if not self._should_reload_data():
+            return self._data_cache.copy()
+
         try:
+            # Use pre-built dtype dictionary for faster parsing
+            dtype_dict = self._get_dtype_dict()
+
+            # Read with optimized settings
             df: pd.DataFrame = pd.read_csv(
                 self.filename,
-                dtype={
-                    "depression": int,
-                    "anxiety": int,
-                    "sleep": int,
-                    "appetite": int,
-                    "bupropion": int,
-                    "hydroxyzine": int,
-                    "gabapentin": int,
-                    "propranolol": int,
-                    "note": str,
-                    "date": str,
-                },
-            ).fillna("")
-            return df.sort_values(by="date").reset_index(drop=True)
+                dtype=dtype_dict,
+                na_filter=False,  # Don't convert to NaN, keep as empty strings
+                engine="c",  # Use faster C engine
+            )
+
+            # Sort only if needed (check if already sorted)
+            if len(df) > 1 and not df["date"].is_monotonic_increasing:
+                df = df.sort_values(by="date").reset_index(drop=True)
+
+            # Cache the data and timestamp
+            self._data_cache = df.copy()
+            self._cache_timestamp = os.path.getmtime(self.filename)
+
+            return df.copy()
+
         except pd.errors.EmptyDataError:
             self.logger.warning("CSV file is empty. No data to load.")
             return pd.DataFrame()
@@ -64,51 +135,142 @@ class DataManager:
             return pd.DataFrame()
 
     def add_entry(self, entry_data: list[str | int]) -> bool:
-        """Add a new entry to the CSV file."""
+        """Add a new entry to the CSV file with optimized duplicate checking."""
         try:
+            # Quick duplicate check using cached data if available
+            date_to_add: str = str(entry_data[0])
+
+            if self._data_cache is not None:
+                # Use cached data for duplicate check
+                if date_to_add in self._data_cache["date"].values:
+                    self.logger.warning(
+                        f"Entry with date {date_to_add} already exists."
+                    )
+                    return False
+            else:
+                # Fallback to loading data if no cache
+                df: pd.DataFrame = self.load_data()
+                if not df.empty and date_to_add in df["date"].values:
+                    self.logger.warning(
+                        f"Entry with date {date_to_add} already exists."
+                    )
+                    return False
+
+            # Write to file
             with open(self.filename, mode="a", newline="") as file:
                 writer = csv.writer(file)
                 writer.writerow(entry_data)
+
+            # Invalidate cache since data changed
+            self._invalidate_cache()
             return True
+
         except Exception as e:
             self.logger.error(f"Error adding entry: {str(e)}")
             return False
 
-    def update_entry(self, date: str, values: list[str | int]) -> bool:
-        """Update an existing entry identified by date."""
+    def update_entry(self, original_date: str, values: list[str | int]) -> bool:
+        """Update an existing entry identified by original_date
+        with optimized processing."""
         try:
             df: pd.DataFrame = self.load_data()
-            # Find the row to update using date as a unique identifier
-            df.loc[
-                df["date"] == date,
-                [
-                    "date",
-                    "depression",
-                    "anxiety",
-                    "sleep",
-                    "appetite",
-                    "bupropion",
-                    "hydroxyzine",
-                    "gabapentin",
-                    "propranolol",
-                    "note",
-                ],
-            ] = values
-            df.to_csv(self.filename, index=False)
-            return True
+            new_date: str = str(values[0])
+
+            # Optimized duplicate check
+            if original_date != new_date:
+                date_exists = (df["date"] == new_date).any()
+                if date_exists:
+                    self.logger.warning(
+                        f"Cannot update: entry with date {new_date} already exists."
+                    )
+                    return False
+
+            # Get current CSV headers to match with values
+            headers = list(self._get_csv_headers())
+
+            # Ensure we have the right number of values with optimized padding
+            if len(values) < len(headers):
+                # Pad with defaults efficiently
+                padding_needed = len(headers) - len(values)
+                for i in range(padding_needed):
+                    header_idx = len(values) + i
+                    if header_idx < len(headers):
+                        header = headers[header_idx]
+                        if header == "note" or header.endswith("_doses"):
+                            values.append("")
+                        else:
+                            values.append(0)
+
+            # Use vectorized update for better performance
+            mask = df["date"] == original_date
+            if mask.any():
+                df.loc[mask, headers] = values
+                # Write back to CSV with optimized method
+                df.to_csv(self.filename, index=False, mode="w")
+                self._invalidate_cache()
+                return True
+            else:
+                self.logger.warning(
+                    f"Entry with date {original_date} not found for update."
+                )
+                return False
+
         except Exception as e:
             self.logger.error(f"Error updating entry: {str(e)}")
             return False
 
     def delete_entry(self, date: str) -> bool:
-        """Delete an entry identified by date."""
+        """Delete an entry identified by date with optimized processing."""
         try:
             df: pd.DataFrame = self.load_data()
-            # Remove the row with the matching date
+            original_len = len(df)
+
+            # Use vectorized filtering for better performance
             df = df[df["date"] != date]
-            # Write the updated dataframe back to the CSV
-            df.to_csv(self.filename, index=False)
+
+            # Only write if something was actually deleted
+            if len(df) < original_len:
+                df.to_csv(self.filename, index=False, mode="w")
+                self._invalidate_cache()
+
             return True
         except Exception as e:
             self.logger.error(f"Error deleting entry: {str(e)}")
             return False
+
+    def get_today_medicine_doses(
+        self, date: str, medicine_name: str
+    ) -> list[tuple[str, str]]:
+        """Get list of (timestamp, dose) tuples for a medicine on a given date
+        with caching."""
+        try:
+            df: pd.DataFrame = self.load_data()
+            if df.empty:
+                return []
+
+            # Use vectorized filtering for better performance
+            date_mask = df["date"] == date
+            if not date_mask.any():
+                return []
+
+            dose_column = f"{medicine_name}_doses"
+            if dose_column not in df.columns:
+                return []
+
+            doses_str = df.loc[date_mask, dose_column].iloc[0]
+
+            if not doses_str:
+                return []
+
+            # Optimized dose parsing
+            doses = []
+            for dose_entry in doses_str.split("|"):
+                if ":" in dose_entry:
+                    parts = dose_entry.split(":", 1)
+                    if len(parts) == 2:
+                        doses.append((parts[0], parts[1]))
+
+            return doses
+        except Exception as e:
+            self.logger.error(f"Error getting medicine doses: {str(e)}")
+            return []

src/graph_manager.py

@@ -7,125 +7,286 @@ import pandas as pd
 from matplotlib.axes import Axes
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 
+from medicine_manager import MedicineManager
+from pathology_manager import PathologyManager
+
 
 class GraphManager:
-    """Handle all graph-related operations for the application."""
+    """Optimized version - Handle all graph-related operations for the
+    application with performance improvements."""
 
-    def __init__(self, parent_frame: ttk.LabelFrame) -> None:
+    def __init__(
+        self,
+        parent_frame: ttk.LabelFrame,
+        medicine_manager: MedicineManager,
+        pathology_manager: PathologyManager,
+    ) -> None:
         self.parent_frame: ttk.LabelFrame = parent_frame
+        self.medicine_manager = medicine_manager
+        self.pathology_manager = pathology_manager
 
-        # Configure graph frame to expand
-        self.parent_frame.grid_rowconfigure(0, weight=1)
-        self.parent_frame.grid_columnconfigure(0, weight=1)
+        # Initialize matplotlib with optimized settings
+        self.fig: matplotlib.figure.Figure = plt.figure(figsize=(10, 6), dpi=80)
+        self.ax: Axes = self.fig.add_subplot(111)
 
-        # Initialize toggle variables for chart elements
-        self.toggle_vars: dict[str, tk.BooleanVar] = {
-            "depression": tk.BooleanVar(value=True),
-            "anxiety": tk.BooleanVar(value=True),
-            "sleep": tk.BooleanVar(value=True),
-            "appetite": tk.BooleanVar(value=True),
-        }
-
-        # Create control frame for toggles
-        self.control_frame: ttk.Frame = ttk.Frame(self.parent_frame)
-        self.control_frame.grid(row=0, column=0, sticky="ew", padx=5, pady=5)
-
-        # Create toggle checkboxes
-        self._create_toggle_controls()
-
-        # Create graph frame
-        self.graph_frame: ttk.Frame = ttk.Frame(self.parent_frame)
-        self.graph_frame.grid(row=1, column=0, sticky="nsew", padx=5, pady=5)
-
-        # Reconfigure parent frame for new layout
-        self.parent_frame.grid_rowconfigure(1, weight=1)
-        self.parent_frame.grid_columnconfigure(0, weight=1)
-
-        # Initialize matplotlib figure and canvas
-        self.fig: matplotlib.figure.Figure
-        self.ax: Axes
-        self.fig, self.ax = plt.subplots()
-        self.canvas: FigureCanvasTkAgg = FigureCanvasTkAgg(
-            figure=self.fig, master=self.graph_frame
-        )
-        self.canvas.get_tk_widget().pack(fill="both", expand=True)
-
-        # Store current data for replotting
+        # Cache for current data to avoid reprocessing
         self.current_data: pd.DataFrame = pd.DataFrame()
+        self._last_plot_hash: str = ""
 
-    def _create_toggle_controls(self) -> None:
-        """Create toggle controls for chart elements."""
-        ttk.Label(self.control_frame, text="Show/Hide Elements:").pack(
-            side="left", padx=5
+        # Initialize UI components
+        self.toggle_vars: dict[str, tk.IntVar] = {}
+        self._setup_ui()
+        self._initialize_toggle_vars()
+        self._create_chart_toggles()
+
+    def _initialize_toggle_vars(self) -> None:
+        """Initialize toggle variables for chart elements with optimization."""
+        # Initialize pathology toggles
+        for pathology_key in self.pathology_manager.get_pathology_keys():
+            self.toggle_vars[pathology_key] = tk.IntVar(value=1)
+
+        # Initialize medicine toggles (unchecked by default)
+        for medicine_key in self.medicine_manager.get_medicine_keys():
+            self.toggle_vars[medicine_key] = tk.IntVar(value=0)
+
+    def _setup_ui(self) -> None:
+        """Set up the UI components with performance optimizations."""
+        # Create canvas with optimized settings
+        self.canvas = FigureCanvasTkAgg(self.fig, master=self.parent_frame)
+        self.canvas.draw_idle()  # Use draw_idle for better performance
+
+        # Pack canvas
+        canvas_widget = self.canvas.get_tk_widget()
+        canvas_widget.pack(side=tk.TOP, fill=tk.BOTH, expand=True)
+
+        # Create control frame
+        self.control_frame = ttk.Frame(self.parent_frame)
+        self.control_frame.pack(side=tk.BOTTOM, fill=tk.X, padx=5, pady=2)
+
+    def _create_chart_toggles(self) -> None:
+        """Create toggle controls for chart elements with improved layout."""
+        # Pathology toggles
+        pathology_frame = ttk.LabelFrame(
+            self.control_frame, text="Pathologies", padding="5"
         )
+        pathology_frame.pack(side=tk.LEFT, fill=tk.X, expand=True, padx=2)
 
-        toggle_configs = [
-            ("depression", "Depression"),
-            ("anxiety", "Anxiety"),
-            ("sleep", "Sleep"),
-            ("appetite", "Appetite"),
-        ]
+        # Use grid for better layout
+        row, col = 0, 0
+        for pathology_key in self.pathology_manager.get_pathology_keys():
+            pathology = self.pathology_manager.get_pathology(pathology_key)
+            if pathology:
+                display_name = pathology.display_name
+                text = (
+                    display_name[:10] + "..."
+                    if len(display_name) > 10
+                    else display_name
+                )
+                cb = ttk.Checkbutton(
+                    pathology_frame,
+                    text=text,
+                    variable=self.toggle_vars[pathology_key],
+                    command=self._handle_toggle_changed,
+                )
+                cb.grid(row=row, column=col, sticky="w", padx=2)
+                col += 1
+                if col > 1:  # 2 columns max
+                    col = 0
+                    row += 1
 
-        for key, label in toggle_configs:
-            checkbox = ttk.Checkbutton(
-                self.control_frame,
-                text=label,
-                variable=self.toggle_vars[key],
-                command=self._on_toggle_changed,
-            )
-            checkbox.pack(side="left", padx=5)
+        # Medicine toggles
+        medicine_frame = ttk.LabelFrame(
+            self.control_frame, text="Medicines", padding="5"
+        )
+        medicine_frame.pack(side=tk.RIGHT, fill=tk.X, expand=True, padx=2)
 
-    def _on_toggle_changed(self) -> None:
-        """Handle toggle changes by replotting the graph."""
+        # Use grid for medicines too
+        row, col = 0, 0
+        for medicine_key in self.medicine_manager.get_medicine_keys():
+            medicine = self.medicine_manager.get_medicine(medicine_key)
+            if medicine:
+                med_name = medicine.display_name
+                text = med_name[:10] + "..." if len(med_name) > 10 else med_name
+                cb = ttk.Checkbutton(
+                    medicine_frame,
+                    text=text,
+                    variable=self.toggle_vars[medicine_key],
+                    command=self._handle_toggle_changed,
+                )
+                cb.grid(row=row, column=col, sticky="w", padx=2)
+                col += 1
+                if col > 2:  # 3 columns max for medicines
+                    col = 0
+                    row += 1
+
+    def _handle_toggle_changed(self) -> None:
+        """Handle toggle changes by replotting the graph with optimization."""
         if not self.current_data.empty:
             self._plot_graph_data(self.current_data)
 
     def update_graph(self, df: pd.DataFrame) -> None:
-        """Update the graph with new data."""
-        self.current_data = df.copy() if not df.empty else pd.DataFrame()
-        self._plot_graph_data(df)
+        """Update the graph with new data using optimization checks."""
+        # Create hash of data to avoid unnecessary redraws
+        data_hash = str(hash(str(df.values.tobytes()) if not df.empty else "empty"))
+
+        # Only update if data actually changed
+        if data_hash != self._last_plot_hash or self.current_data.empty:
+            self.current_data = df.copy() if not df.empty else pd.DataFrame()
+            self._last_plot_hash = data_hash
+            self._plot_graph_data(df)
 
     def _plot_graph_data(self, df: pd.DataFrame) -> None:
-        """Plot the graph data with current toggle settings."""
-        self.ax.clear()
-        if not df.empty:
-            # Convert dates and sort
-            df = df.copy()  # Create a copy to avoid modifying the original
-            df["date"] = pd.to_datetime(df["date"])
-            df = df.sort_values(by="date")
-            df.set_index(keys="date", inplace=True)
+        """Plot the graph data with current toggle settings using optimizations."""
+        # Use batch updates to reduce redraws
+        with plt.ioff():  # Turn off interactive mode for batch updates
+            self.ax.clear()
 
-            # Track if any series are plotted
-            has_plotted_series = False
+            if not df.empty:
+                # Optimize data processing
+                df_processed = self._preprocess_data(df)
 
-            # Plot data series based on toggle states
-            if self.toggle_vars["depression"].get():
-                self._plot_series(
-                    df, "depression", "Depression (0:good, 10:bad)", "o", "-"
-                )
-                has_plotted_series = True
-            if self.toggle_vars["anxiety"].get():
-                self._plot_series(df, "anxiety", "Anxiety (0:good, 10:bad)", "o", "-")
-                has_plotted_series = True
-            if self.toggle_vars["sleep"].get():
-                self._plot_series(df, "sleep", "Sleep (0:bad, 10:good)", "o", "dashed")
-                has_plotted_series = True
-            if self.toggle_vars["appetite"].get():
-                self._plot_series(
-                    df, "appetite", "Appetite (0:bad, 10:good)", "o", "dashed"
+                # Track if any series are plotted
+                has_plotted_series = self._plot_pathology_data(df_processed)
+                medicine_data = self._plot_medicine_data(df_processed)
+
+                if has_plotted_series or medicine_data["has_plotted"]:
+                    self._configure_graph_appearance(medicine_data)
+
+        # Single draw call at the end
+        self.canvas.draw_idle()
+
+    def _preprocess_data(self, df: pd.DataFrame) -> pd.DataFrame:
+        """Preprocess data for plotting with optimizations."""
+        df = df.copy()
+        # Batch convert dates and sort
+        df["date"] = pd.to_datetime(df["date"], cache=True)
+        df = df.sort_values(by="date")
+        df.set_index(keys="date", inplace=True)
+        return df
+
+    def _plot_pathology_data(self, df: pd.DataFrame) -> bool:
+        """Plot pathology data series with optimizations."""
+        has_plotted_series = False
+
+        # Batch plot pathology data
+        pathology_keys = self.pathology_manager.get_pathology_keys()
+        active_pathologies = [
+            key
+            for key in pathology_keys
+            if self.toggle_vars[key].get() and key in df.columns
+        ]
+
+        for pathology_key in active_pathologies:
+            pathology = self.pathology_manager.get_pathology(pathology_key)
+            if pathology:
+                label = f"{pathology.display_name} ({pathology.scale_info})"
+                linestyle = (
+                    "dashed" if pathology.scale_orientation == "inverted" else "-"
                 )
+                self._plot_series(df, pathology_key, label, "o", linestyle)
                 has_plotted_series = True
 
-            # Configure graph appearance
-            if has_plotted_series:
-                self.ax.legend()
-            self.ax.set_title("Medication Effects Over Time")
-            self.ax.set_xlabel("Date")
-            self.ax.set_ylabel("Rating (0-10)")
-            self.fig.autofmt_xdate()
+        return has_plotted_series
 
-        # Redraw the canvas
-        self.canvas.draw()
+    def _plot_medicine_data(self, df: pd.DataFrame) -> dict:
+        """Plot medicine data with optimizations."""
+        result = {"has_plotted": False, "with_data": [], "without_data": []}
+
+        # Get medicine colors and keys in batch
+        medicine_colors = self.medicine_manager.get_graph_colors()
+        medicines = self.medicine_manager.get_medicine_keys()
+
+        # Pre-calculate daily doses for all medicines to avoid repeated computation
+        medicine_doses = {}
+        for medicine in medicines:
+            dose_column = f"{medicine}_doses"
+            if dose_column in df.columns:
+                daily_doses = [
+                    self._calculate_daily_dose(dose_str) for dose_str in df[dose_column]
+                ]
+                medicine_doses[medicine] = daily_doses
+
+        # Plot medicines with data
+        for medicine in medicines:
+            if self.toggle_vars[medicine].get() and medicine in medicine_doses:
+                daily_doses = medicine_doses[medicine]
+
+                # Check if there's any data to plot
+                if any(dose > 0 for dose in daily_doses):
+                    result["with_data"].append(medicine)
+
+                    # Optimize dose scaling and bar plotting
+                    scaled_doses = [dose / 10 for dose in daily_doses]
+
+                    # Calculate statistics more efficiently
+                    non_zero_doses = [d for d in daily_doses if d > 0]
+                    if non_zero_doses:
+                        avg_dose = sum(daily_doses) / len(non_zero_doses)
+                        label = f"{medicine.capitalize()} (avg: {avg_dose:.1f}mg)"
+
+                        # Single bar plot call
+                        self.ax.bar(
+                            df.index,
+                            scaled_doses,
+                            alpha=0.6,
+                            color=medicine_colors.get(medicine, "#DDA0DD"),
+                            label=label,
+                            width=0.6,
+                            bottom=-max(scaled_doses) * 1.1 if scaled_doses else -1,
+                        )
+                        result["has_plotted"] = True
+                else:
+                    # Medicine is toggled on but has no dose data
+                    if self.toggle_vars[medicine].get():
+                        result["without_data"].append(medicine)
+
+        return result
+
+    def _configure_graph_appearance(self, medicine_data: dict) -> None:
+        """Configure graph appearance with optimizations."""
+        # Get legend data in batch
+        handles, labels = self.ax.get_legend_handles_labels()
+
+        # Add information about medicines without data if any are toggled on
+        if medicine_data["without_data"]:
+            med_list = ", ".join(medicine_data["without_data"])
+            info_text = f"Tracked (no doses): {med_list}"
+            labels.append(info_text)
+
+            # Create dummy handle more efficiently
+            from matplotlib.patches import Rectangle
+
+            dummy_handle = Rectangle(
+                (0, 0), 1, 1, fc="w", fill=False, edgecolor="none", linewidth=0
+            )
+            handles.append(dummy_handle)
+
+        # Create legend with optimized settings
+        if handles and labels:
+            self.ax.legend(
+                handles,
+                labels,
+                loc="upper left",
+                bbox_to_anchor=(0, 1),
+                ncol=2,
+                fontsize="small",
+                frameon=True,
+                fancybox=True,
+                shadow=True,
+                framealpha=0.9,
+            )
+
+        # Set titles and labels
+        self.ax.set_title("Medication Effects Over Time")
+        self.ax.set_xlabel("Date")
+        self.ax.set_ylabel("Rating (0-10) / Dose (mg)")
+
+        # Optimize y-axis configuration
+        current_ylim = self.ax.get_ylim()
+        self.ax.set_ylim(bottom=current_ylim[0], top=max(10, current_ylim[1]))
+
+        # Optimize date formatting
+        self.fig.autofmt_xdate()
 
     def _plot_series(
         self,
@@ -135,15 +296,59 @@ class GraphManager:
         marker: str,
         linestyle: str,
     ) -> None:
-        """Helper method to plot a data series."""
+        """Helper method to plot a data series with optimizations."""
+        # Use more efficient plotting parameters
         self.ax.plot(
             df.index,
             df[column],
             marker=marker,
             linestyle=linestyle,
             label=label,
+            markersize=4,  # Smaller markers for better performance
+            linewidth=1.5,  # Optimized line width
         )
 
+    def _calculate_daily_dose(self, dose_str: str) -> float:
+        """Calculate total daily dose from dose string format with optimizations."""
+        if not dose_str or pd.isna(dose_str) or str(dose_str).lower() == "nan":
+            return 0.0
+
+        total_dose = 0.0
+        # Optimize string processing
+        dose_str = str(dose_str).replace("•", "").strip()
+
+        # More efficient splitting and processing
+        dose_entries = dose_str.split("|") if "|" in dose_str else [dose_str]
+
+        for entry in dose_entries:
+            entry = entry.strip()
+            if not entry:
+                continue
+
+            try:
+                # More efficient dose extraction
+                dose_part = entry.split(":")[-1] if ":" in entry else entry
+
+                # Optimized numeric extraction
+                dose_value = ""
+                for char in dose_part:
+                    if char.isdigit() or char == ".":
+                        dose_value += char
+                    elif dose_value:
+                        break
+
+                if dose_value:
+                    total_dose += float(dose_value)
+            except (ValueError, IndexError):
+                continue
+
+        return total_dose
+
     def close(self) -> None:
-        """Clean up resources."""
-        plt.close(self.fig)
+        """Clean up resources with proper optimization."""
+        try:
+            # Clear the plot before closing
+            self.ax.clear()
+            plt.close(self.fig)
+        except Exception:
+            pass  # Ignore cleanup errors

src/main.py

@@ -2,7 +2,7 @@ import os
 import sys
 import tkinter as tk
 from collections.abc import Callable
-from tkinter import messagebox
+from tkinter import messagebox, ttk
 from typing import Any
 
 import pandas as pd
@@ -11,6 +11,10 @@ from constants import LOG_LEVEL, LOG_PATH
 from data_manager import DataManager
 from graph_manager import GraphManager
 from init import logger
+from medicine_management_window import MedicineManagementWindow
+from medicine_manager import MedicineManager
+from pathology_management_window import PathologyManagementWindow
+from pathology_manager import PathologyManager
 from ui_manager import UIManager
 
 
@@ -19,7 +23,7 @@ class MedTrackerApp:
         self.root: tk.Tk = root
         self.root.resizable(True, True)
         self.root.title("Thechart - medication tracker")
-        self.root.protocol("WM_DELETE_WINDOW", self.on_closing)
+        self.root.protocol("WM_DELETE_WINDOW", self.handle_window_closing)
 
         # Set up data file
         self.filename: str = "thechart_data.csv"
@@ -42,18 +46,50 @@ class MedTrackerApp:
             logger.debug(f"First argument: {first_argument}")
 
         # Initialize managers
-        self.ui_manager: UIManager = UIManager(root, logger)
-        self.data_manager: DataManager = DataManager(self.filename, logger)
+        self.medicine_manager: MedicineManager = MedicineManager(logger=logger)
+        self.pathology_manager: PathologyManager = PathologyManager(logger=logger)
+        self.ui_manager: UIManager = UIManager(
+            root, logger, self.medicine_manager, self.pathology_manager
+        )
+        self.data_manager: DataManager = DataManager(
+            self.filename, logger, self.medicine_manager, self.pathology_manager
+        )
 
         # Set up application icon
         icon_path: str = "chart-671.png"
         if not os.path.exists(icon_path) and os.path.exists("./chart-671.png"):
             icon_path = "./chart-671.png"
-        self.ui_manager.setup_icon(img_path=icon_path)
+        self.ui_manager.setup_application_icon(img_path=icon_path)
 
         # Set up the main application UI
         self._setup_main_ui()
 
+        # Add menu bar
+        self._setup_menu()
+
+        # Center the window on screen
+        self._center_window()
+
+    def _center_window(self) -> None:
+        """Center the main window on the screen."""
+        # Update the window to get accurate dimensions
+        self.root.update_idletasks()
+
+        # Get window dimensions
+        window_width = self.root.winfo_reqwidth()
+        window_height = self.root.winfo_reqheight()
+
+        # Get screen dimensions
+        screen_width = self.root.winfo_screenwidth()
+        screen_height = self.root.winfo_screenheight()
+
+        # Calculate position to center the window
+        x = (screen_width // 2) - (window_width // 2)
+        y = (screen_height // 2) - (window_height // 2)
+
+        # Set the window geometry
+        self.root.geometry(f"{window_width}x{window_height}+{x}+{y}")
+
     def _setup_main_ui(self) -> None:
         """Set up the main UI components."""
         import tkinter.ttk as ttk
@@ -74,41 +110,110 @@ class MedTrackerApp:
 
         # --- Create Graph Frame ---
         graph_frame: ttk.Frame = self.ui_manager.create_graph_frame(main_frame)
-        self.graph_manager: GraphManager = GraphManager(graph_frame)
+        self.graph_manager: GraphManager = GraphManager(
+            graph_frame, self.medicine_manager, self.pathology_manager
+        )
 
         # --- Create Input Frame ---
         input_ui: dict[str, Any] = self.ui_manager.create_input_frame(main_frame)
         self.input_frame: ttk.Frame = input_ui["frame"]
-        self.symptom_vars: dict[str, tk.IntVar] = input_ui["symptom_vars"]
-        self.medicine_vars: dict[str, list[tk.IntVar | ttk.Spinbox]] = input_ui[
-            "medicine_vars"
-        ]
+        self.pathology_vars: dict[str, tk.IntVar] = input_ui["pathology_vars"]
+        self.medicine_vars: dict[str, tuple[tk.IntVar, str]] = input_ui["medicine_vars"]
         self.note_var: tk.StringVar = input_ui["note_var"]
         self.date_var: tk.StringVar = input_ui["date_var"]
 
         # Add buttons to input frame
-        self.ui_manager.add_buttons(
+        self.ui_manager.add_action_buttons(
             self.input_frame,
             [
                 {
                     "text": "Add Entry",
-                    "command": self.add_entry,
+                    "command": self.add_new_entry,
                     "fill": "both",
                     "expand": True,
                 },
-                {"text": "Quit", "command": self.on_closing},
+                {"text": "Quit", "command": self.handle_window_closing},
             ],
         )
 
         # --- Create Table Frame ---
         table_ui: dict[str, Any] = self.ui_manager.create_table_frame(main_frame)
         self.tree: ttk.Treeview = table_ui["tree"]
-        self.tree.bind("<Double-1>", self.on_double_click)
+        self.tree.bind("<Double-1>", self.handle_double_click)
 
         # Load data
-        self.load_data()
+        self.refresh_data_display()
 
-    def on_double_click(self, event: tk.Event) -> None:
+    def _setup_menu(self) -> None:
+        """Set up the menu bar."""
+        menubar = tk.Menu(self.root)
+        self.root.config(menu=menubar)
+
+        # Tools menu
+        tools_menu = tk.Menu(menubar, tearoff=0)
+        menubar.add_cascade(label="Tools", menu=tools_menu)
+        tools_menu.add_command(
+            label="Manage Pathologies...", command=self._open_pathology_manager
+        )
+        tools_menu.add_command(
+            label="Manage Medicines...", command=self._open_medicine_manager
+        )
+
+    def _open_pathology_manager(self) -> None:
+        """Open the pathology management window."""
+        PathologyManagementWindow(
+            self.root, self.pathology_manager, self._refresh_ui_after_config_change
+        )
+
+    def _open_medicine_manager(self) -> None:
+        """Open the medicine management window."""
+        MedicineManagementWindow(
+            self.root, self.medicine_manager, self._refresh_ui_after_config_change
+        )
+
+    def _refresh_ui_after_config_change(self) -> None:
+        """Refresh UI components after pathology or medicine configuration changes."""
+        # Clear caches in optimized data manager
+        if hasattr(self.data_manager, "_invalidate_cache"):
+            self.data_manager._invalidate_cache()
+            self.data_manager._headers_cache = None
+            self.data_manager._dtype_cache = None
+
+        # Recreate the input frame with new pathologies and medicines
+        self.input_frame.destroy()
+        input_ui: dict[str, Any] = self.ui_manager.create_input_frame(
+            self.input_frame.master
+        )
+        self.input_frame: ttk.Frame = input_ui["frame"]
+        self.pathology_vars: dict[str, tk.IntVar] = input_ui["pathology_vars"]
+        self.medicine_vars: dict[str, tuple[tk.IntVar, str]] = input_ui["medicine_vars"]
+
+        # Add buttons to input frame
+        self.ui_manager.add_action_buttons(
+            self.input_frame,
+            [
+                {
+                    "text": "Add Entry",
+                    "command": self.add_new_entry,
+                    "fill": "both",
+                    "expand": True,
+                },
+                {"text": "Quit", "command": self.handle_window_closing},
+            ],
+        )
+
+        # Recreate the table with new columns
+        self.tree.destroy()
+        table_ui: dict[str, Any] = self.ui_manager.create_table_frame(
+            self.tree.master.master
+        )
+        self.tree: ttk.Treeview = table_ui["tree"]
+        self.tree.bind("<Double-1>", self.handle_double_click)
+
+        # Refresh data display
+        self.refresh_data_display()
+
+    def handle_double_click(self, event: tk.Event) -> None:
         """Handle double-click event to edit an entry."""
         logger.debug("Double-click event triggered on treeview.")
         if len(self.tree.get_children()) > 0:
@@ -119,84 +224,187 @@ class MedTrackerApp:
 
     def _create_edit_window(self, item_id: str, values: tuple[str, ...]) -> None:
         """Create a new Toplevel window for editing an entry."""
+        original_date = values[0]  # Store the original date
+
+        # Get the full row data from the CSV (including dose columns)
+        df = self.data_manager.load_data()
+        if not df.empty and original_date in df["date"].values:
+            full_row = df[df["date"] == original_date].iloc[0]
+            # Convert to tuple in the expected order for the edit window
+            full_values = [full_row["date"]]
+
+            # Add pathology data dynamically
+            for pathology_key in self.pathology_manager.get_pathology_keys():
+                if pathology_key in full_row:
+                    full_values.append(full_row[pathology_key])
+                else:
+                    full_values.append(0)
+
+            # Add medicine data dynamically
+            for medicine_key in self.medicine_manager.get_medicine_keys():
+                if medicine_key in full_row:
+                    full_values.append(full_row[medicine_key])
+                    full_values.append(full_row.get(f"{medicine_key}_doses", ""))
+                else:
+                    full_values.extend([0, ""])
+
+            full_values.append(full_row["note"])
+            full_values = tuple(full_values)
+        else:
+            # Fallback to the table values if full data not found
+            full_values = values
+
         # Define callbacks for edit window buttons
         callbacks: dict[str, Callable] = {
-            "save": self._save_edit,
+            "save": lambda win, *args: self._save_edit(win, original_date, *args),
             "delete": lambda win: self._delete_entry(win, item_id),
         }
 
-        # Create edit window using UI manager
-        _: tk.Toplevel = self.ui_manager.create_edit_window(values, callbacks)
+        # Create edit window using UI manager with full data
+        _: tk.Toplevel = self.ui_manager.create_edit_window(full_values, callbacks)
 
     def _save_edit(
         self,
         edit_win: tk.Toplevel,
-        date: str,
-        dep: int,
-        anx: int,
-        slp: int,
-        app: int,
-        bup: int,
-        hydro: int,
-        gaba: int,
-        prop: int,
-        note: str,
+        original_date: str,
+        *args,
     ) -> None:
-        """Save the edited data to the CSV file."""
-        values: list[str | int] = [
-            date,
-            dep,
-            anx,
-            slp,
-            app,
-            bup,
-            hydro,
-            gaba,
-            prop,
-            note,
-        ]
+        """Save edited data to CSV file with dynamic pathology/medicine support."""
+        # Parse dynamic arguments
+        # Format: date, pathology1, pathology2, ..., medicine1, medicine2,
+        # ..., note, dose_data
 
-        if self.data_manager.update_entry(date, values):
+        if len(args) < 2:  # At minimum need date and note
+            messagebox.showerror("Error", "Invalid save data format", parent=edit_win)
+            return
+
+        # Extract arguments
+        date = args[0]
+
+        # Get pathology count to extract values
+        pathology_keys = self.pathology_manager.get_pathology_keys()
+        medicine_keys = self.medicine_manager.get_medicine_keys()
+
+        # Expected format: date, pathology_values..., medicine_values...,
+        # note, dose_data
+        expected_pathology_count = len(pathology_keys)
+        expected_medicine_count = len(medicine_keys)
+
+        # Extract pathology values
+        pathology_values = []
+        for i in range(expected_pathology_count):
+            if i + 1 < len(args):
+                pathology_values.append(args[i + 1])
+            else:
+                pathology_values.append(0)
+
+        # Extract medicine values
+        medicine_values = []
+        medicine_start_idx = 1 + expected_pathology_count
+        for i in range(expected_medicine_count):
+            if medicine_start_idx + i < len(args):
+                medicine_values.append(args[medicine_start_idx + i])
+            else:
+                medicine_values.append(0)
+
+        # Extract note and dose data (last two arguments)
+        note = args[-2] if len(args) >= 2 else ""
+        dose_data = args[-1] if len(args) >= 1 else {}
+
+        # Build the values list for data manager
+        values = [date]
+        values.extend(pathology_values)
+
+        # Add medicine data dynamically
+        for i, medicine_key in enumerate(medicine_keys):
+            values.append(medicine_values[i] if i < len(medicine_values) else 0)
+            values.append(dose_data.get(medicine_key, ""))
+
+        values.append(note)
+
+        if self.data_manager.update_entry(original_date, values):
             edit_win.destroy()
             messagebox.showinfo(
                 "Success", "Entry updated successfully!", parent=self.root
             )
             self._clear_entries()
-            self.load_data()
+            self.refresh_data_display()
         else:
-            messagebox.showerror("Error", "Failed to save changes", parent=edit_win)
+            # Check if it's a duplicate date issue
+            df = self.data_manager.load_data()
+            if original_date != date and not df.empty and date in df["date"].values:
+                messagebox.showerror(
+                    "Error",
+                    f"An entry for date '{date}' already exists. "
+                    "Please use a different date.",
+                    parent=edit_win,
+                )
+            else:
+                messagebox.showerror("Error", "Failed to save changes", parent=edit_win)
 
-    def on_closing(self) -> None:
+    def handle_window_closing(self) -> None:
         if messagebox.askokcancel(
             "Quit", "Do you want to quit the application?", parent=self.root
         ):
             self.graph_manager.close()
             self.root.destroy()
 
-    def add_entry(self) -> None:
+    def add_new_entry(self) -> None:
         """Add a new entry to the CSV file."""
-        entry: list[str | int] = [
-            self.date_var.get(),
-            self.symptom_vars["depression"].get(),
-            self.symptom_vars["anxiety"].get(),
-            self.symptom_vars["sleep"].get(),
-            self.symptom_vars["appetite"].get(),
-            self.medicine_vars["bupropion"][0].get(),
-            self.medicine_vars["hydroxyzine"][0].get(),
-            self.medicine_vars["gabapentin"][0].get(),
-            self.medicine_vars["propranolol"][0].get(),
-            self.note_var.get(),
-        ]
+        # Get current doses for today
+        today = self.date_var.get()
+        dose_values = {}
+
+        if today:
+            # Get doses for all medicines dynamically
+            for medicine_key in self.medicine_manager.get_medicine_keys():
+                doses = self.data_manager.get_today_medicine_doses(today, medicine_key)
+                dose_values[f"{medicine_key}_doses"] = "|".join(
+                    [f"{ts}:{dose}" for ts, dose in doses]
+                )
+        else:
+            # Set empty doses for all medicines
+            for medicine_key in self.medicine_manager.get_medicine_keys():
+                dose_values[f"{medicine_key}_doses"] = ""
+
+        # Build entry dynamically
+        entry: list[str | int] = [self.date_var.get()]
+
+        # Add pathology data dynamically
+        for pathology_key in self.pathology_manager.get_pathology_keys():
+            entry.append(self.pathology_vars[pathology_key].get())
+
+        # Add medicine data
+        for medicine_key in self.medicine_manager.get_medicine_keys():
+            entry.append(self.medicine_vars[medicine_key][0].get())
+            entry.append(dose_values[f"{medicine_key}_doses"])
+
+        entry.append(self.note_var.get())
         logger.debug(f"Adding entry: {entry}")
 
+        # Check if date is empty
+        if not self.date_var.get().strip():
+            messagebox.showerror("Error", "Please enter a date.", parent=self.root)
+            return
+
         if self.data_manager.add_entry(entry):
             messagebox.showinfo(
                 "Success", "Entry added successfully!", parent=self.root
             )
             self._clear_entries()
-            self.load_data()
+            self.refresh_data_display()
         else:
-            messagebox.showerror("Error", "Failed to add entry", parent=self.root)
+            # Check if it's a duplicate date by trying to load existing data
+            df = self.data_manager.load_data()
+            if not df.empty and self.date_var.get() in df["date"].values:
+                messagebox.showerror(
+                    "Error",
+                    f"An entry for date '{self.date_var.get()}' already exists. "
+                    "Please use a different date or edit the existing entry.",
+                    parent=self.root,
+                )
+            else:
+                messagebox.showerror("Error", "Failed to add entry", parent=self.root)
 
     def _delete_entry(self, edit_win: tk.Toplevel, item_id: str) -> None:
         """Delete the selected entry from the CSV file."""
@@ -213,9 +421,9 @@ class MedTrackerApp:
             if self.data_manager.delete_entry(date):
                 edit_win.destroy()
                 messagebox.showinfo(
-                    "Success", "Entry deleted successfully!", parent=edit_win
+                    "Success", "Entry deleted successfully!", parent=self.root
                 )
-                self.load_data()
+                self.refresh_data_display()
             else:
                 messagebox.showerror("Error", "Failed to delete entry", parent=edit_win)
 
@@ -223,28 +431,50 @@ class MedTrackerApp:
         """Clear all input fields."""
         logger.debug("Clearing input fields.")
         self.date_var.set("")
-        for key in self.symptom_vars:
-            self.symptom_vars[key].set(0)
+        for key in self.pathology_vars:
+            self.pathology_vars[key].set(0)
         for key in self.medicine_vars:
             self.medicine_vars[key][0].set(0)
         self.note_var.set("")
 
-    def load_data(self) -> None:
+    def refresh_data_display(self) -> None:
         """Load data from the CSV file into the table and graph."""
         logger.debug("Loading data from CSV.")
 
-        # Clear existing data in the treeview
-        for i in self.tree.get_children():
-            self.tree.delete(i)
+        # Clear existing data in the treeview efficiently
+        children = self.tree.get_children()
+        if children:
+            self.tree.delete(*children)
 
         # Load data from the CSV file
         df: pd.DataFrame = self.data_manager.load_data()
 
         # Update the treeview with the data
         if not df.empty:
-            for _index, row in df.iterrows():
+            # Build display columns dynamically (exclude dose columns for table view)
+            display_columns = ["date"]
+
+            # Add pathology columns
+            for pathology_key in self.pathology_manager.get_pathology_keys():
+                display_columns.append(pathology_key)
+
+            # Add medicine columns (without dose columns)
+            for medicine_key in self.medicine_manager.get_medicine_keys():
+                display_columns.append(medicine_key)
+
+            display_columns.append("note")
+
+            # Filter to only the columns we want to display
+            if all(col in df.columns for col in display_columns):
+                display_df = df[display_columns]
+            else:
+                # Fallback - just use all columns
+                display_df = df
+
+            # Batch insert for better performance
+            for _index, row in display_df.iterrows():
                 self.tree.insert(parent="", index="end", values=list(row))
-            logger.debug(f"Loaded {len(df)} entries into treeview.")
+            logger.debug(f"Loaded {len(display_df)} entries into treeview.")
 
         # Update the graph
         self.graph_manager.update_graph(df)

src/medicine_management_window.py

@@ -0,0 +1,401 @@
+"""
+Medicine management window for adding, editing, and removing medicines.
+"""
+
+import tkinter as tk
+from tkinter import messagebox, ttk
+
+from medicine_manager import Medicine, MedicineManager
+
+
+class MedicineManagementWindow:
+    """Window for managing medicine configurations."""
+
+    def __init__(
+        self, parent: tk.Tk, medicine_manager: MedicineManager, refresh_callback
+    ):
+        self.parent = parent
+        self.medicine_manager = medicine_manager
+        self.refresh_callback = refresh_callback
+
+        # Create the window
+        self.window = tk.Toplevel(parent)
+        self.window.title("Manage Medicines")
+        self.window.geometry("600x500")
+        self.window.resizable(True, True)
+
+        # Make window modal
+        self.window.transient(parent)
+        self.window.grab_set()
+
+        self._setup_ui()
+        self._populate_medicine_list()
+
+        # Center window
+        self.window.update_idletasks()
+        x = (self.window.winfo_screenwidth() // 2) - (600 // 2)
+        y = (self.window.winfo_screenheight() // 2) - (500 // 2)
+        self.window.geometry(f"600x500+{x}+{y}")
+
+    def _setup_ui(self):
+        """Set up the user interface."""
+        main_frame = ttk.Frame(self.window, padding="10")
+        main_frame.grid(row=0, column=0, sticky="nsew")
+
+        self.window.grid_rowconfigure(0, weight=1)
+        self.window.grid_columnconfigure(0, weight=1)
+        main_frame.grid_rowconfigure(1, weight=1)
+        main_frame.grid_columnconfigure(0, weight=1)
+
+        # Title
+        title_label = ttk.Label(
+            main_frame, text="Medicine Management", font=("Arial", 14, "bold")
+        )
+        title_label.grid(row=0, column=0, columnspan=2, pady=(0, 10))
+
+        # Medicine list
+        list_frame = ttk.LabelFrame(main_frame, text="Current Medicines")
+        list_frame.grid(row=1, column=0, columnspan=2, sticky="nsew", pady=(0, 10))
+        list_frame.grid_rowconfigure(0, weight=1)
+        list_frame.grid_columnconfigure(0, weight=1)
+
+        # Treeview for medicines
+        columns = ("key", "name", "dosage", "quick_doses", "color", "default")
+        self.tree = ttk.Treeview(list_frame, columns=columns, show="headings")
+
+        # Column headings
+        self.tree.heading("key", text="Key")
+        self.tree.heading("name", text="Name")
+        self.tree.heading("dosage", text="Dosage Info")
+        self.tree.heading("quick_doses", text="Quick Doses")
+        self.tree.heading("color", text="Color")
+        self.tree.heading("default", text="Default Enabled")
+
+        # Column widths
+        self.tree.column("key", width=80)
+        self.tree.column("name", width=100)
+        self.tree.column("dosage", width=100)
+        self.tree.column("quick_doses", width=120)
+        self.tree.column("color", width=70)
+        self.tree.column("default", width=100)
+
+        self.tree.grid(row=0, column=0, sticky="nsew", padx=5, pady=5)
+
+        # Scrollbar for treeview
+        scrollbar = ttk.Scrollbar(
+            list_frame, orient="vertical", command=self.tree.yview
+        )
+        scrollbar.grid(row=0, column=1, sticky="ns")
+        self.tree.configure(yscrollcommand=scrollbar.set)
+
+        # Buttons
+        button_frame = ttk.Frame(main_frame)
+        button_frame.grid(row=2, column=0, columnspan=2, pady=(10, 0))
+
+        ttk.Button(button_frame, text="Add Medicine", command=self._add_medicine).grid(
+            row=0, column=0, padx=(0, 5)
+        )
+
+        ttk.Button(
+            button_frame, text="Edit Medicine", command=self._edit_medicine
+        ).grid(row=0, column=1, padx=5)
+
+        ttk.Button(
+            button_frame, text="Remove Medicine", command=self._remove_medicine
+        ).grid(row=0, column=2, padx=5)
+
+        ttk.Button(button_frame, text="Close", command=self._close_window).grid(
+            row=0, column=3, padx=(5, 0)
+        )
+
+    def _populate_medicine_list(self):
+        """Populate the medicine list."""
+        # Clear existing items
+        for item in self.tree.get_children():
+            self.tree.delete(item)
+
+        # Add medicines
+        for medicine in self.medicine_manager.get_all_medicines().values():
+            self.tree.insert(
+                "",
+                "end",
+                values=(
+                    medicine.key,
+                    medicine.display_name,
+                    medicine.dosage_info,
+                    ", ".join(medicine.quick_doses),
+                    medicine.color,
+                    "Yes" if medicine.default_enabled else "No",
+                ),
+            )
+
+    def _add_medicine(self):
+        """Add a new medicine."""
+        MedicineEditDialog(
+            self.window, self.medicine_manager, None, self._on_medicine_changed
+        )
+
+    def _edit_medicine(self):
+        """Edit selected medicine."""
+        selection = self.tree.selection()
+        if not selection:
+            messagebox.showwarning("No Selection", "Please select a medicine to edit.")
+            return
+
+        item = self.tree.item(selection[0])
+        medicine_key = item["values"][0]
+        medicine = self.medicine_manager.get_medicine(medicine_key)
+
+        if medicine:
+            MedicineEditDialog(
+                self.window, self.medicine_manager, medicine, self._on_medicine_changed
+            )
+
+    def _remove_medicine(self):
+        """Remove selected medicine."""
+        selection = self.tree.selection()
+        if not selection:
+            messagebox.showwarning(
+                "No Selection", "Please select a medicine to remove."
+            )
+            return
+
+        item = self.tree.item(selection[0])
+        medicine_key = item["values"][0]
+        medicine_name = item["values"][1]
+
+        if messagebox.askyesno(
+            "Confirm Removal",
+            f"Are you sure you want to remove '{medicine_name}'?\n\n"
+            "This will also remove all associated data from your records!",
+        ):
+            if self.medicine_manager.remove_medicine(medicine_key):
+                messagebox.showinfo(
+                    "Success", f"'{medicine_name}' removed successfully!"
+                )
+                self._populate_medicine_list()
+                self._refresh_main_app()
+            else:
+                messagebox.showerror("Error", f"Failed to remove '{medicine_name}'.")
+
+    def _on_medicine_changed(self):
+        """Called when a medicine is added or edited."""
+        self._populate_medicine_list()
+        self._refresh_main_app()
+
+    def _refresh_main_app(self):
+        """Refresh the main application after medicine changes."""
+        if self.refresh_callback:
+            self.refresh_callback()
+
+    def _close_window(self):
+        """Close the window."""
+        self.window.destroy()
+
+
+class MedicineEditDialog:
+    """Dialog for adding/editing a medicine."""
+
+    def __init__(
+        self,
+        parent: tk.Toplevel,
+        medicine_manager: MedicineManager,
+        medicine: Medicine | None,
+        callback,
+    ):
+        self.parent = parent
+        self.medicine_manager = medicine_manager
+        self.medicine = medicine
+        self.callback = callback
+        self.is_edit = medicine is not None
+
+        # Create dialog
+        self.dialog = tk.Toplevel(parent)
+        self.dialog.title("Edit Medicine" if self.is_edit else "Add Medicine")
+        self.dialog.geometry("400x350")
+        self.dialog.resizable(False, False)
+
+        # Make modal
+        self.dialog.transient(parent)
+        self.dialog.grab_set()
+
+        self._setup_dialog()
+        self._populate_fields()
+
+        # Center dialog
+        self.dialog.update_idletasks()
+        x = parent.winfo_x() + (parent.winfo_width() // 2) - (400 // 2)
+        y = parent.winfo_y() + (parent.winfo_height() // 2) - (350 // 2)
+        self.dialog.geometry(f"400x350+{x}+{y}")
+
+    def _setup_dialog(self):
+        """Set up the dialog UI."""
+        main_frame = ttk.Frame(self.dialog, padding="15")
+        main_frame.grid(row=0, column=0, sticky="nsew")
+
+        self.dialog.grid_rowconfigure(0, weight=1)
+        self.dialog.grid_columnconfigure(0, weight=1)
+
+        # Fields
+        fields_frame = ttk.Frame(main_frame)
+        fields_frame.grid(row=0, column=0, sticky="ew", pady=(0, 15))
+        fields_frame.grid_columnconfigure(1, weight=1)
+
+        row = 0
+
+        # Key
+        ttk.Label(fields_frame, text="Key:").grid(row=row, column=0, sticky="w", pady=5)
+        self.key_var = tk.StringVar()
+        key_entry = ttk.Entry(fields_frame, textvariable=self.key_var)
+        key_entry.grid(row=row, column=1, sticky="ew", padx=(10, 0), pady=5)
+        if self.is_edit:
+            key_entry.configure(state="readonly")
+        row += 1
+
+        # Display Name
+        ttk.Label(fields_frame, text="Display Name:").grid(
+            row=row, column=0, sticky="w", pady=5
+        )
+        self.name_var = tk.StringVar()
+        ttk.Entry(fields_frame, textvariable=self.name_var).grid(
+            row=row, column=1, sticky="ew", padx=(10, 0), pady=5
+        )
+        row += 1
+
+        # Dosage Info
+        ttk.Label(fields_frame, text="Dosage Info:").grid(
+            row=row, column=0, sticky="w", pady=5
+        )
+        self.dosage_var = tk.StringVar()
+        ttk.Entry(fields_frame, textvariable=self.dosage_var).grid(
+            row=row, column=1, sticky="ew", padx=(10, 0), pady=5
+        )
+        row += 1
+
+        # Quick Doses
+        ttk.Label(fields_frame, text="Quick Doses:").grid(
+            row=row, column=0, sticky="w", pady=5
+        )
+        self.doses_var = tk.StringVar()
+        ttk.Entry(fields_frame, textvariable=self.doses_var).grid(
+            row=row, column=1, sticky="ew", padx=(10, 0), pady=5
+        )
+        ttk.Label(
+            fields_frame, text="(comma-separated, e.g. 25,50,100)", font=("Arial", 8)
+        ).grid(row=row + 1, column=1, sticky="w", padx=(10, 0))
+        row += 2
+
+        # Color
+        ttk.Label(fields_frame, text="Graph Color:").grid(
+            row=row, column=0, sticky="w", pady=5
+        )
+        self.color_var = tk.StringVar()
+        ttk.Entry(fields_frame, textvariable=self.color_var).grid(
+            row=row, column=1, sticky="ew", padx=(10, 0), pady=5
+        )
+        ttk.Label(
+            fields_frame, text="(hex color, e.g. #FF6B6B)", font=("Arial", 8)
+        ).grid(row=row + 1, column=1, sticky="w", padx=(10, 0))
+        row += 2
+
+        # Default Enabled
+        self.default_var = tk.BooleanVar()
+        ttk.Checkbutton(
+            fields_frame,
+            text="Show in graph by default",
+            variable=self.default_var,
+        ).grid(row=row, column=0, columnspan=2, sticky="w", pady=5)
+
+        # Buttons
+        button_frame = ttk.Frame(main_frame)
+        button_frame.grid(row=1, column=0)
+
+        ttk.Button(button_frame, text="Save", command=self._save_medicine).grid(
+            row=0, column=0, padx=(0, 10)
+        )
+
+        ttk.Button(button_frame, text="Cancel", command=self.dialog.destroy).grid(
+            row=0, column=1
+        )
+
+    def _populate_fields(self):
+        """Populate fields if editing."""
+        if self.medicine:
+            self.key_var.set(self.medicine.key)
+            self.name_var.set(self.medicine.display_name)
+            self.dosage_var.set(self.medicine.dosage_info)
+            self.doses_var.set(",".join(self.medicine.quick_doses))
+            self.color_var.set(self.medicine.color)
+            self.default_var.set(self.medicine.default_enabled)
+
+    def _save_medicine(self):
+        """Save the medicine."""
+        # Validate fields
+        key = self.key_var.get().strip()
+        name = self.name_var.get().strip()
+        dosage = self.dosage_var.get().strip()
+        doses_str = self.doses_var.get().strip()
+        color = self.color_var.get().strip()
+
+        if not all([key, name, dosage, doses_str, color]):
+            messagebox.showerror("Error", "All fields are required.")
+            return
+
+        # Validate key format (alphanumeric and underscores only)
+        if not key.replace("_", "").replace("-", "").isalnum():
+            messagebox.showerror(
+                "Error",
+                "Key must contain only letters, numbers, underscores, and hyphens.",
+            )
+            return
+
+        # Parse quick doses
+        try:
+            quick_doses = [dose.strip() for dose in doses_str.split(",")]
+            quick_doses = [dose for dose in quick_doses if dose]  # Remove empty strings
+            if not quick_doses:
+                raise ValueError("At least one quick dose is required.")
+        except Exception:
+            messagebox.showerror("Error", "Quick doses must be comma-separated values.")
+            return
+
+        # Validate color format
+        if not color.startswith("#") or len(color) != 7:
+            messagebox.showerror(
+                "Error", "Color must be in hex format (e.g., #FF6B6B)."
+            )
+            return
+
+        try:
+            int(color[1:], 16)  # Validate hex color
+        except ValueError:
+            messagebox.showerror("Error", "Invalid hex color format.")
+            return
+
+        # Create medicine object
+        new_medicine = Medicine(
+            key=key,
+            display_name=name,
+            dosage_info=dosage,
+            quick_doses=quick_doses,
+            color=color,
+            default_enabled=self.default_var.get(),
+        )
+
+        # Save medicine
+        success = False
+        if self.is_edit:
+            success = self.medicine_manager.update_medicine(
+                self.medicine.key, new_medicine
+            )
+        else:
+            success = self.medicine_manager.add_medicine(new_medicine)
+
+        if success:
+            action = "updated" if self.is_edit else "added"
+            messagebox.showinfo("Success", f"Medicine {action} successfully!")
+            self.callback()
+            self.dialog.destroy()
+        else:
+            action = "update" if self.is_edit else "add"
+            messagebox.showerror("Error", f"Failed to {action} medicine.")

src/medicine_manager.py

@@ -0,0 +1,195 @@
+"""
+Medicine configuration manager for the MedTracker application.
+Handles dynamic loading and saving of medicine configurations.
+"""
+
+import json
+import logging
+import os
+from dataclasses import asdict, dataclass
+from typing import Any
+
+
+@dataclass
+class Medicine:
+    """Data class representing a medicine."""
+
+    key: str  # Internal key (e.g., "bupropion")
+    display_name: str  # Display name (e.g., "Bupropion")
+    dosage_info: str  # Dosage information (e.g., "150/300 mg")
+    quick_doses: list[str]  # Common dose amounts for quick selection
+    color: str  # Color for graph display
+    default_enabled: bool = False  # Whether to show in graph by default
+
+
+class MedicineManager:
+    """Manages medicine configurations and provides access to medicine data."""
+
+    def __init__(
+        self, config_file: str = "medicines.json", logger: logging.Logger = None
+    ):
+        self.config_file = config_file
+        self.logger = logger or logging.getLogger(__name__)
+        self.medicines: dict[str, Medicine] = {}
+        self._load_medicines()
+
+    def _get_default_medicines(self) -> list[Medicine]:
+        """Get the default medicine configuration."""
+        return [
+            Medicine(
+                key="bupropion",
+                display_name="Bupropion",
+                dosage_info="150/300 mg",
+                quick_doses=["150", "300"],
+                color="#FF6B6B",
+                default_enabled=True,
+            ),
+            Medicine(
+                key="hydroxyzine",
+                display_name="Hydroxyzine",
+                dosage_info="25 mg",
+                quick_doses=["25", "50"],
+                color="#4ECDC4",
+                default_enabled=False,
+            ),
+            Medicine(
+                key="gabapentin",
+                display_name="Gabapentin",
+                dosage_info="100 mg",
+                quick_doses=["100", "300", "600"],
+                color="#45B7D1",
+                default_enabled=False,
+            ),
+            Medicine(
+                key="propranolol",
+                display_name="Propranolol",
+                dosage_info="10 mg",
+                quick_doses=["10", "20", "40"],
+                color="#96CEB4",
+                default_enabled=True,
+            ),
+            Medicine(
+                key="quetiapine",
+                display_name="Quetiapine",
+                dosage_info="25 mg",
+                quick_doses=["25", "50", "100"],
+                color="#FFEAA7",
+                default_enabled=False,
+            ),
+        ]
+
+    def _load_medicines(self) -> None:
+        """Load medicines from configuration file."""
+        if os.path.exists(self.config_file):
+            try:
+                with open(self.config_file) as f:
+                    data = json.load(f)
+
+                self.medicines = {}
+                for medicine_data in data.get("medicines", []):
+                    medicine = Medicine(**medicine_data)
+                    self.medicines[medicine.key] = medicine
+
+                self.logger.info(
+                    f"Loaded {len(self.medicines)} medicines from {self.config_file}"
+                )
+            except Exception as e:
+                self.logger.error(f"Error loading medicines config: {e}")
+                self._create_default_config()
+        else:
+            self._create_default_config()
+
+    def _create_default_config(self) -> None:
+        """Create default medicine configuration."""
+        default_medicines = self._get_default_medicines()
+        self.medicines = {med.key: med for med in default_medicines}
+        self.save_medicines()
+        self.logger.info("Created default medicine configuration")
+
+    def save_medicines(self) -> bool:
+        """Save current medicines to configuration file."""
+        try:
+            data = {
+                "medicines": [asdict(medicine) for medicine in self.medicines.values()]
+            }
+
+            with open(self.config_file, "w") as f:
+                json.dump(data, f, indent=2)
+
+            self.logger.info(
+                f"Saved {len(self.medicines)} medicines to {self.config_file}"
+            )
+            return True
+        except Exception as e:
+            self.logger.error(f"Error saving medicines config: {e}")
+            return False
+
+    def get_all_medicines(self) -> dict[str, Medicine]:
+        """Get all medicines."""
+        return self.medicines.copy()
+
+    def get_medicine(self, key: str) -> Medicine | None:
+        """Get a specific medicine by key."""
+        return self.medicines.get(key)
+
+    def add_medicine(self, medicine: Medicine) -> bool:
+        """Add a new medicine."""
+        if medicine.key in self.medicines:
+            self.logger.warning(f"Medicine with key '{medicine.key}' already exists")
+            return False
+
+        self.medicines[medicine.key] = medicine
+        return self.save_medicines()
+
+    def update_medicine(self, key: str, medicine: Medicine) -> bool:
+        """Update an existing medicine."""
+        if key not in self.medicines:
+            self.logger.warning(f"Medicine with key '{key}' does not exist")
+            return False
+
+        # If key is changing, remove old entry
+        if key != medicine.key:
+            del self.medicines[key]
+
+        self.medicines[medicine.key] = medicine
+        return self.save_medicines()
+
+    def remove_medicine(self, key: str) -> bool:
+        """Remove a medicine."""
+        if key not in self.medicines:
+            self.logger.warning(f"Medicine with key '{key}' does not exist")
+            return False
+
+        del self.medicines[key]
+        return self.save_medicines()
+
+    def get_medicine_keys(self) -> list[str]:
+        """Get list of all medicine keys."""
+        return list(self.medicines.keys())
+
+    def get_display_names(self) -> dict[str, str]:
+        """Get mapping of keys to display names."""
+        return {key: med.display_name for key, med in self.medicines.items()}
+
+    def get_quick_doses(self, key: str) -> list[str]:
+        """Get quick dose options for a medicine."""
+        medicine = self.medicines.get(key)
+        return medicine.quick_doses if medicine else ["25", "50"]
+
+    def get_graph_colors(self) -> dict[str, str]:
+        """Get mapping of medicine keys to graph colors."""
+        return {key: med.color for key, med in self.medicines.items()}
+
+    def get_default_enabled_medicines(self) -> list[str]:
+        """Get list of medicines that should be enabled by default in graphs."""
+        return [key for key, med in self.medicines.items() if med.default_enabled]
+
+    def get_medicine_vars_dict(self) -> dict[str, tuple[Any, str]]:
+        """Get medicine variables dictionary for UI compatibility."""
+        # This maintains compatibility with existing UI code
+        import tkinter as tk
+
+        return {
+            key: (tk.IntVar(value=0), f"{med.display_name} {med.dosage_info}")
+            for key, med in self.medicines.items()
+        }

src/pathology_management_window.py

@@ -0,0 +1,425 @@
+"""
+Pathology management window for adding, editing, and removing pathologies.
+"""
+
+import tkinter as tk
+from tkinter import messagebox, ttk
+
+from pathology_manager import Pathology, PathologyManager
+
+
+class PathologyManagementWindow:
+    """Window for managing pathology configurations."""
+
+    def __init__(
+        self, parent: tk.Tk, pathology_manager: PathologyManager, refresh_callback
+    ):
+        self.parent = parent
+        self.pathology_manager = pathology_manager
+        self.refresh_callback = refresh_callback
+
+        # Create the window
+        self.window = tk.Toplevel(parent)
+        self.window.title("Manage Pathologies")
+        self.window.geometry("800x500")
+        self.window.resizable(True, True)
+
+        # Make window modal
+        self.window.transient(parent)
+        self.window.grab_set()
+
+        self._setup_ui()
+        self._populate_pathology_list()
+
+        # Center window
+        self.window.update_idletasks()
+        x = (self.window.winfo_screenwidth() // 2) - (800 // 2)
+        y = (self.window.winfo_screenheight() // 2) - (500 // 2)
+        self.window.geometry(f"800x500+{x}+{y}")
+
+    def _setup_ui(self):
+        """Set up the UI components."""
+        # Main frame
+        main_frame = ttk.Frame(self.window, padding="10")
+        main_frame.grid(row=0, column=0, sticky="nsew")
+        self.window.grid_rowconfigure(0, weight=1)
+        self.window.grid_columnconfigure(0, weight=1)
+
+        # Pathology list
+        list_frame = ttk.LabelFrame(main_frame, text="Pathologies", padding="5")
+        list_frame.grid(row=0, column=0, sticky="nsew", pady=(0, 10))
+        main_frame.grid_rowconfigure(0, weight=1)
+        main_frame.grid_columnconfigure(0, weight=1)
+
+        # Treeview for pathology list
+        columns = (
+            "Key",
+            "Display Name",
+            "Scale Info",
+            "Color",
+            "Default Enabled",
+            "Scale Range",
+        )
+        self.tree = ttk.Treeview(list_frame, columns=columns, show="headings")
+
+        # Configure columns
+        self.tree.heading("Key", text="Key")
+        self.tree.heading("Display Name", text="Display Name")
+        self.tree.heading("Scale Info", text="Scale Info")
+        self.tree.heading("Color", text="Color")
+        self.tree.heading("Default Enabled", text="Default Enabled")
+        self.tree.heading("Scale Range", text="Scale Range")
+
+        self.tree.column("Key", width=120)
+        self.tree.column("Display Name", width=150)
+        self.tree.column("Scale Info", width=150)
+        self.tree.column("Color", width=80)
+        self.tree.column("Default Enabled", width=100)
+        self.tree.column("Scale Range", width=100)
+
+        # Scrollbar for treeview
+        scrollbar = ttk.Scrollbar(
+            list_frame, orient="vertical", command=self.tree.yview
+        )
+        self.tree.configure(yscrollcommand=scrollbar.set)
+
+        self.tree.grid(row=0, column=0, sticky="nsew")
+        scrollbar.grid(row=0, column=1, sticky="ns")
+
+        list_frame.grid_rowconfigure(0, weight=1)
+        list_frame.grid_columnconfigure(0, weight=1)
+
+        # Buttons frame
+        button_frame = ttk.Frame(main_frame)
+        button_frame.grid(row=1, column=0, sticky="ew")
+
+        ttk.Button(
+            button_frame, text="Add Pathology", command=self._add_pathology
+        ).pack(side="left", padx=(0, 5))
+        ttk.Button(
+            button_frame, text="Edit Pathology", command=self._edit_pathology
+        ).pack(side="left", padx=(0, 5))
+        ttk.Button(
+            button_frame, text="Remove Pathology", command=self._remove_pathology
+        ).pack(side="left", padx=(0, 5))
+        ttk.Button(button_frame, text="Close", command=self.window.destroy).pack(
+            side="right"
+        )
+
+    def _populate_pathology_list(self):
+        """Populate the pathology list."""
+        # Clear existing items
+        for item in self.tree.get_children():
+            self.tree.delete(item)
+
+        # Add pathologies
+        for pathology in self.pathology_manager.get_all_pathologies().values():
+            scale_range = f"{pathology.scale_min}-{pathology.scale_max}"
+            self.tree.insert(
+                "",
+                "end",
+                values=(
+                    pathology.key,
+                    pathology.display_name,
+                    pathology.scale_info,
+                    pathology.color,
+                    "Yes" if pathology.default_enabled else "No",
+                    scale_range,
+                ),
+            )
+
+    def _add_pathology(self):
+        """Add a new pathology."""
+        PathologyEditDialog(
+            self.window, self.pathology_manager, None, self._on_pathology_changed
+        )
+
+    def _edit_pathology(self):
+        """Edit selected pathology."""
+        selection = self.tree.selection()
+        if not selection:
+            messagebox.showwarning("No Selection", "Please select a pathology to edit.")
+            return
+
+        item = self.tree.item(selection[0])
+        pathology_key = item["values"][0]
+        pathology = self.pathology_manager.get_pathology(pathology_key)
+
+        if pathology:
+            PathologyEditDialog(
+                self.window,
+                self.pathology_manager,
+                pathology,
+                self._on_pathology_changed,
+            )
+
+    def _remove_pathology(self):
+        """Remove selected pathology."""
+        selection = self.tree.selection()
+        if not selection:
+            messagebox.showwarning(
+                "No Selection", "Please select a pathology to remove."
+            )
+            return
+
+        item = self.tree.item(selection[0])
+        pathology_key = item["values"][0]
+        pathology_name = item["values"][1]
+
+        if messagebox.askyesno(
+            "Confirm Removal",
+            f"Are you sure you want to remove '{pathology_name}'?\n\n"
+            "This will also remove all associated data from your records!",
+        ):
+            if self.pathology_manager.remove_pathology(pathology_key):
+                messagebox.showinfo(
+                    "Success", f"'{pathology_name}' removed successfully!"
+                )
+                self._populate_pathology_list()
+                self._refresh_main_app()
+            else:
+                messagebox.showerror("Error", f"Failed to remove '{pathology_name}'.")
+
+    def _on_pathology_changed(self):
+        """Handle pathology changes."""
+        self._populate_pathology_list()
+        self._refresh_main_app()
+
+    def _refresh_main_app(self):
+        """Refresh the main application."""
+        if self.refresh_callback:
+            self.refresh_callback()
+
+
+class PathologyEditDialog:
+    """Dialog for adding/editing a pathology."""
+
+    def __init__(
+        self,
+        parent: tk.Toplevel,
+        pathology_manager: PathologyManager,
+        pathology: Pathology | None,
+        callback,
+    ):
+        self.parent = parent
+        self.pathology_manager = pathology_manager
+        self.pathology = pathology
+        self.callback = callback
+        self.is_edit = pathology is not None
+
+        # Create dialog
+        self.dialog = tk.Toplevel(parent)
+        self.dialog.title("Edit Pathology" if self.is_edit else "Add Pathology")
+        self.dialog.geometry("450x400")
+        self.dialog.resizable(False, False)
+
+        # Make modal
+        self.dialog.transient(parent)
+        self.dialog.grab_set()
+
+        self._setup_dialog()
+        self._populate_fields()
+
+        # Center dialog
+        self.dialog.update_idletasks()
+        x = parent.winfo_x() + (parent.winfo_width() // 2) - (450 // 2)
+        y = parent.winfo_y() + (parent.winfo_height() // 2) - (400 // 2)
+        self.dialog.geometry(f"450x400+{x}+{y}")
+
+    def _setup_dialog(self):
+        """Set up the dialog UI."""
+        # Main frame
+        main_frame = ttk.Frame(self.dialog, padding="15")
+        main_frame.grid(row=0, column=0, sticky="nsew")
+        self.dialog.grid_rowconfigure(0, weight=1)
+        self.dialog.grid_columnconfigure(0, weight=1)
+
+        # Form fields
+        self.key_var = tk.StringVar()
+        self.name_var = tk.StringVar()
+        self.scale_info_var = tk.StringVar()
+        self.color_var = tk.StringVar()
+        self.default_var = tk.BooleanVar()
+        self.scale_min_var = tk.IntVar(value=0)
+        self.scale_max_var = tk.IntVar(value=10)
+        self.orientation_var = tk.StringVar(value="normal")
+
+        # Key field
+        ttk.Label(main_frame, text="Key:").grid(
+            row=0, column=0, sticky="w", pady=(0, 5)
+        )
+        key_entry = ttk.Entry(main_frame, textvariable=self.key_var, width=40)
+        key_entry.grid(row=0, column=1, sticky="ew", pady=(0, 5))
+        ttk.Label(main_frame, text="(alphanumeric, underscores, hyphens only)").grid(
+            row=0, column=2, sticky="w", padx=(5, 0), pady=(0, 5)
+        )
+
+        # Display name field
+        ttk.Label(main_frame, text="Display Name:").grid(
+            row=1, column=0, sticky="w", pady=(0, 5)
+        )
+        ttk.Entry(main_frame, textvariable=self.name_var, width=40).grid(
+            row=1, column=1, sticky="ew", pady=(0, 5)
+        )
+
+        # Scale info field
+        ttk.Label(main_frame, text="Scale Info:").grid(
+            row=2, column=0, sticky="w", pady=(0, 5)
+        )
+        ttk.Entry(main_frame, textvariable=self.scale_info_var, width=40).grid(
+            row=2, column=1, sticky="ew", pady=(0, 5)
+        )
+        ttk.Label(main_frame, text='(e.g., "0:good, 10:bad")').grid(
+            row=2, column=2, sticky="w", padx=(5, 0), pady=(0, 5)
+        )
+
+        # Scale range
+        scale_frame = ttk.Frame(main_frame)
+        scale_frame.grid(row=3, column=1, sticky="ew", pady=(0, 5))
+
+        ttk.Label(main_frame, text="Scale Range:").grid(
+            row=3, column=0, sticky="w", pady=(0, 5)
+        )
+        ttk.Label(scale_frame, text="Min:").grid(row=0, column=0, sticky="w")
+        ttk.Entry(scale_frame, textvariable=self.scale_min_var, width=5).grid(
+            row=0, column=1, padx=(5, 10)
+        )
+        ttk.Label(scale_frame, text="Max:").grid(row=0, column=2, sticky="w")
+        ttk.Entry(scale_frame, textvariable=self.scale_max_var, width=5).grid(
+            row=0, column=3, padx=5
+        )
+
+        # Scale orientation
+        ttk.Label(main_frame, text="Scale Orientation:").grid(
+            row=4, column=0, sticky="w", pady=(0, 5)
+        )
+        orientation_frame = ttk.Frame(main_frame)
+        orientation_frame.grid(row=4, column=1, sticky="ew", pady=(0, 5))
+
+        ttk.Radiobutton(
+            orientation_frame,
+            text="Normal (0=good)",
+            variable=self.orientation_var,
+            value="normal",
+        ).grid(row=0, column=0, sticky="w")
+        ttk.Radiobutton(
+            orientation_frame,
+            text="Inverted (0=bad)",
+            variable=self.orientation_var,
+            value="inverted",
+        ).grid(row=0, column=1, sticky="w", padx=(20, 0))
+
+        # Color field
+        ttk.Label(main_frame, text="Color:").grid(
+            row=5, column=0, sticky="w", pady=(0, 5)
+        )
+        ttk.Entry(main_frame, textvariable=self.color_var, width=40).grid(
+            row=5, column=1, sticky="ew", pady=(0, 5)
+        )
+        ttk.Label(main_frame, text="(hex format, e.g., #FF6B6B)").grid(
+            row=5, column=2, sticky="w", padx=(5, 0), pady=(0, 5)
+        )
+
+        # Default enabled checkbox
+        ttk.Checkbutton(
+            main_frame, text="Show in graph by default", variable=self.default_var
+        ).grid(row=6, column=1, sticky="w", pady=(10, 15))
+
+        # Buttons
+        button_frame = ttk.Frame(main_frame)
+        button_frame.grid(row=7, column=0, columnspan=3, sticky="ew", pady=(10, 0))
+
+        ttk.Button(button_frame, text="Save", command=self._save_pathology).pack(
+            side="right", padx=(5, 0)
+        )
+        ttk.Button(button_frame, text="Cancel", command=self.dialog.destroy).pack(
+            side="right"
+        )
+
+        # Configure column weights
+        main_frame.grid_columnconfigure(1, weight=1)
+
+        # Focus on first field
+        key_entry.focus()
+
+    def _populate_fields(self):
+        """Populate fields if editing."""
+        if self.pathology:
+            self.key_var.set(self.pathology.key)
+            self.name_var.set(self.pathology.display_name)
+            self.scale_info_var.set(self.pathology.scale_info)
+            self.color_var.set(self.pathology.color)
+            self.default_var.set(self.pathology.default_enabled)
+            self.scale_min_var.set(self.pathology.scale_min)
+            self.scale_max_var.set(self.pathology.scale_max)
+            self.orientation_var.set(self.pathology.scale_orientation)
+
+    def _save_pathology(self):
+        """Save the pathology."""
+        # Validate fields
+        key = self.key_var.get().strip()
+        name = self.name_var.get().strip()
+        scale_info = self.scale_info_var.get().strip()
+        color = self.color_var.get().strip()
+        scale_min = self.scale_min_var.get()
+        scale_max = self.scale_max_var.get()
+
+        if not all([key, name, scale_info, color]):
+            messagebox.showerror("Error", "All fields are required.")
+            return
+
+        # Validate key format (alphanumeric and underscores only)
+        if not key.replace("_", "").replace("-", "").isalnum():
+            messagebox.showerror(
+                "Error",
+                "Key must contain only letters, numbers, underscores, and hyphens.",
+            )
+            return
+
+        # Validate scale range
+        if scale_min >= scale_max:
+            messagebox.showerror("Error", "Scale minimum must be less than maximum.")
+            return
+
+        # Validate color format
+        if not color.startswith("#") or len(color) != 7:
+            messagebox.showerror(
+                "Error", "Color must be in hex format (e.g., #FF6B6B)."
+            )
+            return
+
+        try:
+            int(color[1:], 16)  # Validate hex color
+        except ValueError:
+            messagebox.showerror("Error", "Invalid hex color format.")
+            return
+
+        # Create pathology object
+        new_pathology = Pathology(
+            key=key,
+            display_name=name,
+            scale_info=scale_info,
+            color=color,
+            default_enabled=self.default_var.get(),
+            scale_min=scale_min,
+            scale_max=scale_max,
+            scale_orientation=self.orientation_var.get(),
+        )
+
+        # Save pathology
+        success = False
+        if self.is_edit:
+            success = self.pathology_manager.update_pathology(
+                self.pathology.key, new_pathology
+            )
+        else:
+            success = self.pathology_manager.add_pathology(new_pathology)
+
+        if success:
+            action = "updated" if self.is_edit else "added"
+            messagebox.showinfo("Success", f"Pathology {action} successfully!")
+            self.callback()
+            self.dialog.destroy()
+        else:
+            action = "update" if self.is_edit else "add"
+            messagebox.showerror("Error", f"Failed to {action} pathology.")

src/pathology_manager.py

@@ -0,0 +1,199 @@
+"""
+Pathology configuration manager for the MedTracker application.
+Handles dynamic loading and saving of pathology/symptom configurations.
+"""
+
+import json
+import logging
+import os
+from dataclasses import asdict, dataclass
+from typing import Any
+
+
+@dataclass
+class Pathology:
+    """Data class representing a pathology/symptom."""
+
+    key: str  # Internal key (e.g., "depression")
+    display_name: str  # Display name (e.g., "Depression")
+    scale_info: str  # Scale information (e.g., "0:good, 10:bad")
+    color: str  # Color for graph display
+    default_enabled: bool = True  # Whether to show in graph by default
+    scale_min: int = 0  # Minimum scale value
+    scale_max: int = 10  # Maximum scale value
+    scale_orientation: str = "normal"  # "normal" (0=good) or "inverted" (0=bad)
+
+
+class PathologyManager:
+    """Manages pathology configurations and provides access to pathology data."""
+
+    def __init__(
+        self, config_file: str = "pathologies.json", logger: logging.Logger = None
+    ):
+        self.config_file = config_file
+        self.logger = logger or logging.getLogger(__name__)
+        self.pathologies: dict[str, Pathology] = {}
+        self._load_pathologies()
+
+    def _get_default_pathologies(self) -> list[Pathology]:
+        """Get the default pathology configuration."""
+        return [
+            Pathology(
+                key="depression",
+                display_name="Depression",
+                scale_info="0:good, 10:bad",
+                color="#FF6B6B",
+                default_enabled=True,
+                scale_orientation="normal",
+            ),
+            Pathology(
+                key="anxiety",
+                display_name="Anxiety",
+                scale_info="0:good, 10:bad",
+                color="#FFA726",
+                default_enabled=True,
+                scale_orientation="normal",
+            ),
+            Pathology(
+                key="sleep",
+                display_name="Sleep Quality",
+                scale_info="0:bad, 10:good",
+                color="#66BB6A",
+                default_enabled=True,
+                scale_orientation="inverted",
+            ),
+            Pathology(
+                key="appetite",
+                display_name="Appetite",
+                scale_info="0:bad, 10:good",
+                color="#42A5F5",
+                default_enabled=True,
+                scale_orientation="inverted",
+            ),
+        ]
+
+    def _load_pathologies(self) -> None:
+        """Load pathologies from configuration file."""
+        if os.path.exists(self.config_file):
+            try:
+                with open(self.config_file) as f:
+                    data = json.load(f)
+
+                self.pathologies = {}
+                for pathology_data in data.get("pathologies", []):
+                    pathology = Pathology(**pathology_data)
+                    self.pathologies[pathology.key] = pathology
+
+                self.logger.info(
+                    f"Loaded {len(self.pathologies)} pathologies from "
+                    f"{self.config_file}"
+                )
+            except Exception as e:
+                self.logger.error(f"Error loading pathologies config: {e}")
+                self._create_default_config()
+        else:
+            self._create_default_config()
+
+    def _create_default_config(self) -> None:
+        """Create default pathology configuration."""
+        default_pathologies = self._get_default_pathologies()
+        self.pathologies = {path.key: path for path in default_pathologies}
+        self.save_pathologies()
+        self.logger.info("Created default pathology configuration")
+
+    def save_pathologies(self) -> bool:
+        """Save current pathologies to configuration file."""
+        try:
+            data = {
+                "pathologies": [
+                    asdict(pathology) for pathology in self.pathologies.values()
+                ]
+            }
+
+            with open(self.config_file, "w") as f:
+                json.dump(data, f, indent=2)
+
+            self.logger.info(
+                f"Saved {len(self.pathologies)} pathologies to {self.config_file}"
+            )
+            return True
+        except Exception as e:
+            self.logger.error(f"Error saving pathologies config: {e}")
+            return False
+
+    def get_all_pathologies(self) -> dict[str, Pathology]:
+        """Get all pathologies."""
+        return self.pathologies.copy()
+
+    def get_pathology(self, key: str) -> Pathology | None:
+        """Get a specific pathology by key."""
+        return self.pathologies.get(key)
+
+    def add_pathology(self, pathology: Pathology) -> bool:
+        """Add a new pathology."""
+        if pathology.key in self.pathologies:
+            self.logger.warning(f"Pathology with key '{pathology.key}' already exists")
+            return False
+
+        self.pathologies[pathology.key] = pathology
+        return self.save_pathologies()
+
+    def update_pathology(self, key: str, pathology: Pathology) -> bool:
+        """Update an existing pathology."""
+        if key not in self.pathologies:
+            self.logger.warning(f"Pathology with key '{key}' does not exist")
+            return False
+
+        # If key is changing, remove old entry
+        if key != pathology.key:
+            del self.pathologies[key]
+
+        self.pathologies[pathology.key] = pathology
+        return self.save_pathologies()
+
+    def remove_pathology(self, key: str) -> bool:
+        """Remove a pathology."""
+        if key not in self.pathologies:
+            self.logger.warning(f"Pathology with key '{key}' does not exist")
+            return False
+
+        del self.pathologies[key]
+        return self.save_pathologies()
+
+    def get_pathology_keys(self) -> list[str]:
+        """Get list of all pathology keys."""
+        return list(self.pathologies.keys())
+
+    def get_display_names(self) -> dict[str, str]:
+        """Get mapping of keys to display names."""
+        return {key: path.display_name for key, path in self.pathologies.items()}
+
+    def get_graph_colors(self) -> dict[str, str]:
+        """Get mapping of pathology keys to graph colors."""
+        return {key: path.color for key, path in self.pathologies.items()}
+
+    def get_default_enabled_pathologies(self) -> list[str]:
+        """Get list of pathologies that should be enabled by default in graphs."""
+        return [key for key, path in self.pathologies.items() if path.default_enabled]
+
+    def get_pathology_vars_dict(self) -> dict[str, tuple[Any, str]]:
+        """Get pathology variables dictionary for UI compatibility."""
+        # This maintains compatibility with existing UI code
+        import tkinter as tk
+
+        return {
+            key: (tk.IntVar(value=0), path.display_name)
+            for key, path in self.pathologies.items()
+        }
+
+    def get_scale_info(self, key: str) -> tuple[int, int, str, str]:
+        """Get scale information for a pathology."""
+        pathology = self.get_pathology(key)
+        if pathology:
+            return (
+                pathology.scale_min,
+                pathology.scale_max,
+                pathology.scale_info,
+                pathology.scale_orientation,
+            )
+        return (0, 10, "0-10", "normal")

tests/__init__.py

@@ -0,0 +1 @@
+# Tests for TheChart application

tests/conftest.py

@@ -0,0 +1,196 @@
+"""
+Fixtures and configuration for pytest tests.
+"""
+import os
+import tempfile
+import pytest
+import pandas as pd
+from unittest.mock import Mock
+import logging
+
+# Add src to path for imports
+import sys
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'src'))
+
+from src.medicine_manager import MedicineManager, Medicine
+
+
+@pytest.fixture
+def temp_csv_file():
+    """Create a temporary CSV file for testing."""
+    fd, path = tempfile.mkstemp(suffix='.csv')
+    os.close(fd)
+    yield path
+    # Cleanup
+    if os.path.exists(path):
+        os.unlink(path)
+
+
+@pytest.fixture
+def mock_medicine_manager():
+    """Create a mock medicine manager with default medicines for testing."""
+    mock_manager = Mock(spec=MedicineManager)
+
+    # Default medicines matching the original system
+    default_medicines = {
+        "bupropion": Medicine(
+            key="bupropion",
+            display_name="Bupropion",
+            dosage_info="150/300 mg",
+            quick_doses=["150", "300"],
+            color="#FF6B6B",
+            default_enabled=True
+        ),
+        "hydroxyzine": Medicine(
+            key="hydroxyzine",
+            display_name="Hydroxyzine",
+            dosage_info="25 mg",
+            quick_doses=["25", "50"],
+            color="#4ECDC4",
+            default_enabled=False
+        ),
+        "gabapentin": Medicine(
+            key="gabapentin",
+            display_name="Gabapentin",
+            dosage_info="100 mg",
+            quick_doses=["100", "300", "600"],
+            color="#45B7D1",
+            default_enabled=False
+        ),
+        "propranolol": Medicine(
+            key="propranolol",
+            display_name="Propranolol",
+            dosage_info="10 mg",
+            quick_doses=["10", "20", "40"],
+            color="#96CEB4",
+            default_enabled=True
+        ),
+        "quetiapine": Medicine(
+            key="quetiapine",
+            display_name="Quetiapine",
+            dosage_info="25 mg",
+            quick_doses=["25", "50", "100"],
+            color="#FFEAA7",
+            default_enabled=False
+        )
+    }
+
+    mock_manager.get_medicine_keys.return_value = list(default_medicines.keys())
+    mock_manager.get_all_medicines.return_value = default_medicines
+    mock_manager.get_medicine.side_effect = lambda key: default_medicines.get(key)
+    mock_manager.get_graph_colors.return_value = {k: v.color for k, v in default_medicines.items()}
+    mock_manager.get_quick_doses.side_effect = lambda key: default_medicines.get(key, Medicine("", "", "", [], "", False)).quick_doses
+
+    return mock_manager
+
+
+@pytest.fixture
+def mock_pathology_manager():
+    """Create a mock pathology manager with default pathologies for testing."""
+    mock_manager = Mock()
+
+    # Default pathologies matching the original system
+    mock_manager.get_pathology_keys.return_value = ["depression", "anxiety", "sleep", "appetite"]
+
+    return mock_manager
+
+
+@pytest.fixture
+def sample_data():
+    """Sample data for testing."""
+    return [
+        ["2024-01-01", 3, 2, 4, 3, 1, "", 0, "", 2, "", 1, "", 0, "", "Test note 1"],
+        ["2024-01-02", 2, 3, 3, 4, 1, "", 1, "", 2, "", 0, "", 1, "", "Test note 2"],
+        ["2024-01-03", 4, 1, 5, 2, 0, "", 0, "", 1, "", 1, "", 0, "", ""],
+    ]
+
+
+@pytest.fixture
+def sample_dataframe():
+    """Sample DataFrame for testing."""
+    return pd.DataFrame({
+        'date': ['2024-01-01', '2024-01-02', '2024-01-03'],
+        'depression': [3, 2, 4],
+        'anxiety': [2, 3, 1],
+        'sleep': [4, 3, 5],
+        'appetite': [3, 4, 2],
+        'bupropion': [1, 1, 0],
+        'bupropion_doses': ['2024-01-01 08:00:00:150mg', '2024-01-02 08:00:00:300mg', ''],
+        'hydroxyzine': [0, 1, 0],
+        'hydroxyzine_doses': ['', '2024-01-02 20:00:00:25mg', ''],
+        'gabapentin': [2, 2, 1],
+        'gabapentin_doses': ['2024-01-01 12:00:00:100mg|2024-01-01 20:00:00:100mg',
+                            '2024-01-02 12:00:00:100mg|2024-01-02 20:00:00:100mg',
+                            '2024-01-03 12:00:00:100mg'],
+        'propranolol': [1, 0, 1],
+        'propranolol_doses': ['2024-01-01 12:00:00:10mg', '', '2024-01-03 12:00:00:20mg'],
+        'quetiapine': [0, 1, 0],
+        'quetiapine_doses': ['', '2024-01-02 22:00:00:50mg', ''],
+        'note': ['Test note 1', 'Test note 2', '']
+    })
+
+
+@pytest.fixture
+def mock_logger():
+    """Mock logger for testing."""
+    return Mock(spec=logging.Logger)
+
+
+@pytest.fixture
+def temp_log_dir():
+    """Create a temporary directory for log files."""
+    with tempfile.TemporaryDirectory() as temp_dir:
+        yield temp_dir
+
+
+@pytest.fixture
+def mock_env_vars(monkeypatch):
+    """Mock environment variables."""
+    monkeypatch.setenv("LOG_LEVEL", "DEBUG")
+    monkeypatch.setenv("LOG_PATH", "/tmp/test_logs")
+    monkeypatch.setenv("LOG_CLEAR", "False")
+
+
+@pytest.fixture
+def sample_dose_data():
+    """Sample dose data for testing dose calculation."""
+    return {
+        'standard_format': '2025-07-28 18:59:45:150mg|2025-07-28 19:34:19:75mg',  # Should sum to 225
+        'with_bullets': '• • • • 2025-07-30 07:50:00:300',  # Should be 300
+        'decimal_doses': '2025-07-28 18:59:45:12.5mg|2025-07-28 19:34:19:7.5mg',  # Should sum to 20
+        'no_timestamp': '100mg|50mg',  # Should sum to 150
+        'mixed_format': '• 2025-07-30 22:50:00:10|75mg',  # Should sum to 85
+        'empty_string': '',  # Should be 0
+        'nan_value': 'nan',  # Should be 0
+        'no_units': '2025-07-28 18:59:45:10|2025-07-28 19:34:19:5',  # Should sum to 15
+    }
+
+
+@pytest.fixture
+def legend_test_dataframe():
+    """DataFrame specifically designed for testing legend functionality."""
+    return pd.DataFrame({
+        'date': ['2024-01-01', '2024-01-02', '2024-01-03'],
+        'depression': [3, 2, 4],
+        'anxiety': [2, 3, 1],
+        'sleep': [4, 3, 5],
+        'appetite': [3, 4, 2],
+        # Medicine with consistent doses for average testing
+        'bupropion': [1, 1, 1],
+        'bupropion_doses': ['2024-01-01 08:00:00:100mg',
+                           '2024-01-02 08:00:00:200mg',
+                           '2024-01-03 08:00:00:150mg'],  # Average: 150mg
+        # Medicine with varying doses
+        'propranolol': [1, 1, 0],
+        'propranolol_doses': ['2024-01-01 12:00:00:10mg',
+                             '2024-01-02 12:00:00:20mg',
+                             ''],  # Average: 15mg (10+20)/2
+        # Medicines without dose data
+        'hydroxyzine': [0, 0, 0],
+        'hydroxyzine_doses': ['', '', ''],
+        'gabapentin': [0, 0, 0],
+        'gabapentin_doses': ['', '', ''],
+        'quetiapine': [0, 0, 0],
+        'quetiapine_doses': ['', '', ''],
+        'note': ['Test note 1', 'Test note 2', 'Test note 3']
+    })

tests/test_constants.py

@@ -0,0 +1,129 @@
+"""
+Tests for constants module.
+"""
+import os
+from unittest.mock import patch
+
+import sys
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'src'))
+
+
+class TestConstants:
+    """Test cases for the constants module."""
+
+    def test_default_log_level(self):
+        """Test default LOG_LEVEL when not set in environment."""
+        with patch.dict(os.environ, {}, clear=True):
+            # Re-import to get fresh values
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            assert src.constants.LOG_LEVEL == "INFO"
+
+    def test_custom_log_level(self):
+        """Test custom LOG_LEVEL from environment."""
+        with patch.dict(os.environ, {'LOG_LEVEL': 'debug'}, clear=True):
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            assert src.constants.LOG_LEVEL == "DEBUG"
+
+    def test_default_log_path(self):
+        """Test default LOG_PATH when not set in environment."""
+        with patch.dict(os.environ, {}, clear=True):
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            assert src.constants.LOG_PATH == "/tmp/logs/thechart"
+
+    def test_custom_log_path(self):
+        """Test custom LOG_PATH from environment."""
+        with patch.dict(os.environ, {'LOG_PATH': '/custom/log/path'}, clear=True):
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            assert src.constants.LOG_PATH == "/custom/log/path"
+
+    def test_default_log_clear(self):
+        """Test default LOG_CLEAR when not set in environment."""
+        with patch.dict(os.environ, {}, clear=True):
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            assert src.constants.LOG_CLEAR == "False"
+
+    def test_custom_log_clear_true(self):
+        """Test LOG_CLEAR when set to true in environment."""
+        with patch.dict(os.environ, {'LOG_CLEAR': 'true'}, clear=True):
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            assert src.constants.LOG_CLEAR == "True"
+
+    def test_custom_log_clear_false(self):
+        """Test LOG_CLEAR when set to false in environment."""
+        with patch.dict(os.environ, {'LOG_CLEAR': 'false'}, clear=True):
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            assert src.constants.LOG_CLEAR == "False"
+
+    def test_log_level_case_insensitive(self):
+        """Test that LOG_LEVEL is converted to uppercase."""
+        with patch.dict(os.environ, {'LOG_LEVEL': 'warning'}, clear=True):
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            assert src.constants.LOG_LEVEL == "WARNING"
+
+    def test_dotenv_override(self):
+        """Test that dotenv override parameter is set to True."""
+        # This is a structural test since dotenv is loaded during import
+        with patch('constants.load_dotenv') as mock_load_dotenv:
+            import importlib
+            if 'constants' in sys.modules:
+                importlib.reload(sys.modules['constants'])
+            else:
+                import src.constants
+
+            mock_load_dotenv.assert_called_once_with(override=True)
+
+    def test_all_constants_are_strings(self):
+        """Test that all constants are string type."""
+        import src.constants
+
+        assert isinstance(src.constants.LOG_LEVEL, str)
+        assert isinstance(src.constants.LOG_PATH, str)
+        assert isinstance(src.constants.LOG_CLEAR, str)
+
+    def test_constants_not_empty(self):
+        """Test that constants are not empty strings."""
+        import src.constants
+
+        assert src.constants.LOG_LEVEL != ""
+        assert src.constants.LOG_PATH != ""
+        assert src.constants.LOG_CLEAR != ""

tests/test_data_manager.py

@@ -0,0 +1,303 @@
+"""
+Tests for the DataManager class.
+"""
+import os
+import csv
+from unittest.mock import patch
+
+import sys
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'src'))
+
+from src.data_manager import DataManager
+
+
+class TestDataManager:
+    """Test cases for the DataManager class."""
+
+    def test_init(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test DataManager initialization."""
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        assert dm.filename == temp_csv_file
+        assert dm.logger == mock_logger
+        assert dm.medicine_manager == mock_medicine_manager
+        assert os.path.exists(temp_csv_file)
+
+    def test_initialize_csv_creates_file_with_headers(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test that initialize_csv creates a file with proper headers."""
+        # Remove the file if it exists
+        if os.path.exists(temp_csv_file):
+            os.unlink(temp_csv_file)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+
+        # Check file exists and has correct headers
+        assert os.path.exists(temp_csv_file)
+        with open(temp_csv_file, 'r') as f:
+            reader = csv.reader(f)
+            headers = next(reader)
+            expected_headers = [
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ]
+            assert headers == expected_headers
+
+    def test_initialize_csv_does_not_overwrite_existing_file(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test that initialize_csv does not overwrite existing file."""
+        # Write some data to the file first
+        with open(temp_csv_file, 'w') as f:
+            f.write("existing,data\n1,2\n")
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+
+        # Check that existing data is preserved
+        with open(temp_csv_file, 'r') as f:
+            content = f.read()
+            assert "existing,data" in content
+
+    def test_load_data_empty_file(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test loading data from an empty file."""
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        df = dm.load_data()
+        assert df.empty
+
+    def test_load_data_nonexistent_file(self, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test loading data from a nonexistent file."""
+        dm = DataManager("nonexistent.csv", mock_logger, mock_medicine_manager, mock_pathology_manager)
+        df = dm.load_data()
+        assert df.empty
+        mock_logger.warning.assert_called()
+
+    def test_load_data_with_valid_data(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager, sample_data):
+        """Test loading valid data from CSV file."""
+        # Write sample data to file
+        with open(temp_csv_file, 'w', newline='') as f:
+            writer = csv.writer(f)
+            # Write headers first
+            writer.writerow([
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ])
+            # Write sample data
+            writer.writerows(sample_data)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        df = dm.load_data()
+
+        assert not df.empty
+        assert len(df) == 3
+        assert list(df.columns) == [
+            "date", "depression", "anxiety", "sleep", "appetite",
+            "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+            "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+            "quetiapine", "quetiapine_doses", "note"
+        ]
+        # Check data types
+        assert df["depression"].dtype == int
+        assert df["anxiety"].dtype == int
+        assert df["note"].dtype == object
+
+    def test_load_data_sorted_by_date(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test that loaded data is sorted by date."""
+        # Write data in random order
+        unsorted_data = [
+            ["2024-01-03", 1, 1, 1, 1, 1, "", 1, "", 1, "", 1, "", 0, "", "third"],
+            ["2024-01-01", 2, 2, 2, 2, 2, "", 2, "", 2, "", 2, "", 1, "", "first"],
+            ["2024-01-02", 3, 3, 3, 3, 3, "", 3, "", 3, "", 3, "", 0, "", "second"],
+        ]
+
+        with open(temp_csv_file, 'w', newline='') as f:
+            writer = csv.writer(f)
+            writer.writerow([
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ])
+            writer.writerows(unsorted_data)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        df = dm.load_data()
+
+        # Check that data is sorted by date
+        assert df.iloc[0]["note"] == "first"
+        assert df.iloc[1]["note"] == "second"
+        assert df.iloc[2]["note"] == "third"
+
+    def test_add_entry_success(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test successfully adding an entry."""
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        entry = ["2024-01-01", 3, 2, 4, 3, 1, "", 0, "", 2, "", 1, "", 0, "", "Test note"]
+
+        result = dm.add_entry(entry)
+        assert result is True
+
+        # Verify entry was added
+        df = dm.load_data()
+        assert len(df) == 1
+        assert df.iloc[0]["date"] == "2024-01-01"
+        assert df.iloc[0]["note"] == "Test note"
+
+    def test_add_entry_duplicate_date(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager, sample_data):
+        """Test adding entry with duplicate date."""
+        # Add initial data
+        with open(temp_csv_file, 'w', newline='') as f:
+            writer = csv.writer(f)
+            writer.writerow([
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ])
+            writer.writerows(sample_data)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        # Try to add entry with existing date
+        duplicate_entry = ["2024-01-01", 5, 5, 5, 5, 1, "", 1, "", 1, "", 1, "", 0, "", "Duplicate"]
+
+        result = dm.add_entry(duplicate_entry)
+        assert result is False
+        mock_logger.warning.assert_called_with("Entry with date 2024-01-01 already exists.")
+
+    def test_update_entry_success(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager, sample_data):
+        """Test successfully updating an entry."""
+        # Add initial data
+        with open(temp_csv_file, 'w', newline='') as f:
+            writer = csv.writer(f)
+            writer.writerow([
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ])
+            writer.writerows(sample_data)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        updated_values = ["2024-01-01", 5, 5, 5, 5, 2, "", 2, "", 2, "", 2, "", 1, "", "Updated note"]
+
+        result = dm.update_entry("2024-01-01", updated_values)
+        assert result is True
+
+        # Verify entry was updated
+        df = dm.load_data()
+        updated_row = df[df["date"] == "2024-01-01"].iloc[0]
+        assert updated_row["depression"] == 5
+        assert updated_row["note"] == "Updated note"
+
+    def test_update_entry_change_date(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager, sample_data):
+        """Test updating an entry with a date change."""
+        # Add initial data
+        with open(temp_csv_file, 'w', newline='') as f:
+            writer = csv.writer(f)
+            writer.writerow([
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ])
+            writer.writerows(sample_data)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        updated_values = ["2024-01-05", 5, 5, 5, 5, 2, "", 2, "", 2, "", 2, "", 1, "", "Updated note"]
+
+        result = dm.update_entry("2024-01-01", updated_values)
+        assert result is True
+
+        # Verify old date is gone and new date exists
+        df = dm.load_data()
+        assert not any(df["date"] == "2024-01-01")
+        assert any(df["date"] == "2024-01-05")
+
+    def test_update_entry_duplicate_date(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager, sample_data):
+        """Test updating entry to a date that already exists."""
+        # Add initial data
+        with open(temp_csv_file, 'w', newline='') as f:
+            writer = csv.writer(f)
+            writer.writerow([
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ])
+            writer.writerows(sample_data)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        # Try to change date to one that already exists
+        updated_values = ["2024-01-02", 5, 5, 5, 5, 2, "", 2, "", 2, "", 2, "", 1, "", "Updated note"]
+
+        result = dm.update_entry("2024-01-01", updated_values)
+        assert result is False
+        mock_logger.warning.assert_called_with(
+            "Cannot update: entry with date 2024-01-02 already exists."
+        )
+
+    def test_delete_entry_success(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager, sample_data):
+        """Test successfully deleting an entry."""
+        # Add initial data
+        with open(temp_csv_file, 'w', newline='') as f:
+            writer = csv.writer(f)
+            writer.writerow([
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ])
+            writer.writerows(sample_data)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+
+        result = dm.delete_entry("2024-01-02")
+        assert result is True
+
+        # Verify entry was deleted
+        df = dm.load_data()
+        assert len(df) == 2
+        assert not any(df["date"] == "2024-01-02")
+
+    def test_delete_entry_nonexistent(self, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager, sample_data):
+        """Test deleting a nonexistent entry."""
+        # Add initial data
+        with open(temp_csv_file, 'w', newline='') as f:
+            writer = csv.writer(f)
+            writer.writerow([
+                "date", "depression", "anxiety", "sleep", "appetite",
+                "bupropion", "bupropion_doses", "hydroxyzine", "hydroxyzine_doses",
+                "gabapentin", "gabapentin_doses", "propranolol", "propranolol_doses",
+                "quetiapine", "quetiapine_doses", "note"
+            ])
+            writer.writerows(sample_data)
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+
+        result = dm.delete_entry("2024-01-10")
+        assert result is True  # Should return True even if no matching entry
+
+        # Verify no data was lost
+        df = dm.load_data()
+        assert len(df) == 3
+
+    @patch('pandas.read_csv')
+    def test_load_data_exception_handling(self, mock_read_csv, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test exception handling in load_data."""
+        mock_read_csv.side_effect = Exception("Test error")
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        df = dm.load_data()
+
+        assert df.empty
+        mock_logger.error.assert_called_with("Error loading data: Test error")
+
+    @patch('builtins.open')
+    def test_add_entry_exception_handling(self, mock_open, temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager):
+        """Test exception handling in add_entry."""
+        mock_open.side_effect = Exception("Test error")
+
+        dm = DataManager(temp_csv_file, mock_logger, mock_medicine_manager, mock_pathology_manager)
+        entry = ["2024-01-01", 3, 2, 4, 3, 1, 0, 2, 1, "Test note"]
+
+        result = dm.add_entry(entry)
+        assert result is False
+        mock_logger.error.assert_called_with("Error adding entry: Test error")

tests/test_dose_parsing.py

@@ -0,0 +1,50 @@
+import pytest
+import tkinter as tk
+from src.ui_manager import UIManager
+
+@pytest.fixture
+def root_window():
+    root = tk.Tk()
+    yield root
+    root.destroy()
+
+@pytest.fixture
+def ui_manager(root_window):
+    class DummyLogger:
+        def debug(self, *a, **k): pass
+        def warning(self, *a, **k): pass
+        def error(self, *a, **k): pass
+    return UIManager(root_window, DummyLogger())
+
+def test_parse_dose_history_for_saving_bullet_and_delete(ui_manager):
+    # Simulate user editing: add, delete, and custom lines
+    date_str = "07/30/2025"
+    # User deletes one line, adds a custom one
+    text = """
+• 09:00 AM - 150mg
+• 06:00 PM - 150mg
+Custom note
+""".strip()
+    result = ui_manager._parse_dose_history_for_saving(text, date_str)
+    # Should parse both bullets and keep the custom line
+    assert "2025-07-30 09:00:00:150mg" in result
+    assert "2025-07-30 18:00:00:150mg" in result
+    assert "Custom note" in result
+    # If user deletes all, should return empty string
+    assert ui_manager._parse_dose_history_for_saving("", date_str) == ""
+    assert ui_manager._parse_dose_history_for_saving("No doses recorded today", date_str) == ""
+
+def test_parse_dose_history_for_saving_simple_time(ui_manager):
+    date_str = "07/30/2025"
+    text = "09:00 150mg\n18:00 150mg"
+    result = ui_manager._parse_dose_history_for_saving(text, date_str)
+    assert "2025-07-30 09:00:00:150mg" in result
+    assert "2025-07-30 18:00:00:150mg" in result
+
+def test_parse_dose_history_for_saving_mixed(ui_manager):
+    date_str = "07/30/2025"
+    text = "• 09:00 AM - 150mg\n18:00 150mg\nJust a note"
+    result = ui_manager._parse_dose_history_for_saving(text, date_str)
+    assert "2025-07-30 09:00:00:150mg" in result
+    assert "2025-07-30 18:00:00:150mg" in result
+    assert "Just a note" in result

tests/test_graph_manager.py

@@ -0,0 +1,788 @@
+"""
+Tests for the GraphManager class.
+"""
+import os
+import pytest
+import pandas as pd
+import tkinter as tk
+from tkinter import ttk
+from unittest.mock import Mock, patch
+
+import sys
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'src'))
+
+from src.graph_manager import GraphManager
+
+
+class TestGraphManager:
+    """Test cases for the GraphManager class."""
+
+    @pytest.fixture
+    def root_window(self):
+        """Create a root window for testing."""
+        root = tk.Tk()
+        yield root
+        root.destroy()
+
+    @pytest.fixture
+    def parent_frame(self, root_window):
+        """Create a parent frame for testing."""
+        frame = ttk.LabelFrame(root_window, text="Test Frame")
+        frame.pack()
+        return frame
+
+    def test_init(self, parent_frame):
+        """Test GraphManager initialization."""
+        gm = GraphManager(parent_frame)
+
+        assert gm.parent_frame == parent_frame
+        assert isinstance(gm.toggle_vars, dict)
+
+        # Check symptom toggles
+        assert "depression" in gm.toggle_vars
+        assert "anxiety" in gm.toggle_vars
+        assert "sleep" in gm.toggle_vars
+        assert "appetite" in gm.toggle_vars
+
+        # Check medicine toggles
+        assert "bupropion" in gm.toggle_vars
+        assert "hydroxyzine" in gm.toggle_vars
+        assert "gabapentin" in gm.toggle_vars
+        assert "propranolol" in gm.toggle_vars
+        assert "quetiapine" in gm.toggle_vars
+
+        # Check that symptom toggles are initially True
+        for symptom in ["depression", "anxiety", "sleep", "appetite"]:
+            assert gm.toggle_vars[symptom].get() is True
+
+        # Check that some medicine toggles are True by default
+        assert gm.toggle_vars["bupropion"].get() is True
+        assert gm.toggle_vars["propranolol"].get() is True
+
+        # Check that some medicine toggles are False by default
+        assert gm.toggle_vars["hydroxyzine"].get() is False
+        assert gm.toggle_vars["gabapentin"].get() is False
+        assert gm.toggle_vars["quetiapine"].get() is False
+
+    def test_toggle_controls_creation(self, parent_frame):
+        """Test that toggle controls are created properly."""
+        gm = GraphManager(parent_frame)
+
+        # Check that control frame exists
+        assert hasattr(gm, 'control_frame')
+        assert isinstance(gm.control_frame, ttk.Frame)
+
+        # Check that all toggle variables exist
+        expected_toggles = ["depression", "anxiety", "sleep", "appetite",
+                           "bupropion", "hydroxyzine", "gabapentin", "propranolol", "quetiapine"]
+        for toggle in expected_toggles:
+            assert toggle in gm.toggle_vars
+            assert isinstance(gm.toggle_vars[toggle], tk.BooleanVar)
+
+    def test_graph_frame_creation(self, parent_frame):
+        """Test that graph frame is created properly."""
+        gm = GraphManager(parent_frame)
+
+        assert hasattr(gm, 'graph_frame')
+        assert isinstance(gm.graph_frame, ttk.Frame)
+
+    @patch('matplotlib.pyplot.subplots')
+    def test_matplotlib_initialization(self, mock_subplots, parent_frame):
+        """Test matplotlib figure and canvas initialization."""
+        mock_fig = Mock()
+        mock_ax = Mock()
+        mock_subplots.return_value = (mock_fig, mock_ax)
+
+        with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+            mock_canvas = Mock()
+            mock_canvas_class.return_value = mock_canvas
+
+            gm = GraphManager(parent_frame)
+
+            assert gm.fig == mock_fig
+            assert gm.ax == mock_ax
+            assert gm.canvas == mock_canvas
+            mock_canvas_class.assert_called_once_with(figure=mock_fig, master=gm.graph_frame)
+
+    def test_update_graph_empty_dataframe(self, parent_frame):
+        """Test updating graph with empty DataFrame."""
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg'):
+                gm = GraphManager(parent_frame)
+
+                # Test with empty DataFrame
+                empty_df = pd.DataFrame()
+                gm.update_graph(empty_df)
+
+                # Verify ax.clear() was called
+                mock_ax.clear.assert_called()
+
+    def test_update_graph_with_data(self, parent_frame, sample_dataframe):
+        """Test updating graph with valid data."""
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+                gm.update_graph(sample_dataframe)
+
+                # Verify methods were called
+                mock_ax.clear.assert_called()
+                mock_canvas.draw.assert_called()
+
+    def test_toggle_functionality(self, parent_frame, sample_dataframe):
+        """Test that toggle variables affect graph display."""
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+
+                # Turn off depression toggle
+                gm.toggle_vars["depression"].set(False)
+                gm.update_graph(sample_dataframe)
+
+                # The graph should still update (specific plotting logic would need more detailed testing)
+                mock_ax.clear.assert_called()
+                mock_canvas.draw.assert_called()
+
+    def test_close_method(self, parent_frame):
+        """Test the close method."""
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                with patch('matplotlib.pyplot.close') as mock_plt_close:
+                    gm = GraphManager(parent_frame)
+                    gm.close()
+
+                    mock_plt_close.assert_called_once_with(mock_fig)
+
+    def test_date_parsing_in_update_graph(self, parent_frame):
+        """Test that date parsing works correctly in update_graph."""
+        # Create a DataFrame with date strings
+        df_with_dates = pd.DataFrame({
+            'date': ['2024-01-01', '2024-01-02', '2024-01-03'],
+            'depression': [3, 2, 4],
+            'anxiety': [2, 3, 1],
+            'sleep': [4, 3, 5],
+            'appetite': [3, 4, 2],
+            'bupropion': [1, 1, 0],
+            'hydroxyzine': [0, 1, 0],
+            'gabapentin': [2, 2, 1],
+            'propranolol': [1, 0, 1],
+            'note': ['Test note 1', 'Test note 2', '']
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                with patch('pandas.to_datetime') as mock_to_datetime:
+                    gm = GraphManager(parent_frame)
+                    gm.update_graph(df_with_dates)
+
+                    # Verify pandas.to_datetime was called
+                    mock_to_datetime.assert_called()
+
+    @patch('matplotlib.pyplot.subplots')
+    def test_exception_handling_in_update_graph(self, mock_subplots, parent_frame, sample_dataframe):
+        """Test exception handling in update_graph method."""
+        mock_fig = Mock()
+        mock_ax = Mock()
+        mock_ax.plot.side_effect = Exception("Plot error")
+        mock_subplots.return_value = (mock_fig, mock_ax)
+
+        with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+            mock_canvas = Mock()
+            mock_canvas_class.return_value = mock_canvas
+
+            gm = GraphManager(parent_frame)
+
+            # This should not raise an exception, but handle it gracefully
+            try:
+                gm.update_graph(sample_dataframe)
+            except Exception as e:
+                pytest.fail(f"update_graph should handle exceptions gracefully, but raised: {e}")
+
+    def test_grid_configuration(self, parent_frame):
+        """Test that grid configuration is set up correctly."""
+        gm = GraphManager(parent_frame)
+
+        # The parent frame should have grid configuration
+        # Note: In a real test, you might need to check grid_info() or similar
+        # This is a basic structure test
+        assert hasattr(gm, 'parent_frame')
+        assert hasattr(gm, 'control_frame')
+        assert hasattr(gm, 'graph_frame')
+
+    def test_canvas_widget_packing(self, parent_frame):
+        """Test that canvas widget is properly packed."""
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas.get_tk_widget.return_value = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+
+                # Verify get_tk_widget was called (for packing)
+                mock_canvas.get_tk_widget.assert_called()
+
+    def test_multiple_toggle_combinations(self, parent_frame, sample_dataframe):
+        """Test various combinations of toggle states."""
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+
+                # Test all toggles off
+                for toggle in gm.toggle_vars.values():
+                    toggle.set(False)
+                gm.update_graph(sample_dataframe)
+
+                # Test mixed toggles
+                gm.toggle_vars["depression"].set(True)
+                gm.toggle_vars["anxiety"].set(False)
+                gm.update_graph(sample_dataframe)
+
+                # Verify the graph was updated in each case
+                assert mock_ax.clear.call_count >= 2
+                assert mock_canvas.draw.call_count >= 2
+
+    def test_calculate_daily_dose_empty_input(self, parent_frame):
+        """Test dose calculation with empty/invalid input."""
+        gm = GraphManager(parent_frame)
+
+        # Test empty string
+        assert gm._calculate_daily_dose("") == 0.0
+
+        # Test NaN values
+        assert gm._calculate_daily_dose("nan") == 0.0
+        assert gm._calculate_daily_dose("NaN") == 0.0
+
+        # Test None (will be converted to string)
+        assert gm._calculate_daily_dose(None) == 0.0
+
+    def test_calculate_daily_dose_standard_format(self, parent_frame):
+        """Test dose calculation with standard timestamp:dose format."""
+        gm = GraphManager(parent_frame)
+
+        # Single dose
+        dose_str = "2025-07-28 18:59:45:150mg"
+        assert gm._calculate_daily_dose(dose_str) == 150.0
+
+        # Multiple doses
+        dose_str = "2025-07-28 18:59:45:150mg|2025-07-28 19:34:19:75mg"
+        assert gm._calculate_daily_dose(dose_str) == 225.0
+
+        # Doses without units
+        dose_str = "2025-07-28 18:59:45:10|2025-07-28 19:34:19:5"
+        assert gm._calculate_daily_dose(dose_str) == 15.0
+
+    def test_calculate_daily_dose_with_symbols(self, parent_frame):
+        """Test dose calculation with bullet symbols."""
+        gm = GraphManager(parent_frame)
+
+        # With bullet symbols
+        dose_str = "• • • • 2025-07-30 07:50:00:300"
+        assert gm._calculate_daily_dose(dose_str) == 300.0
+
+        # Multiple bullets
+        dose_str = "• 2025-07-30 22:50:00:10|• 2025-07-30 23:50:00:5"
+        assert gm._calculate_daily_dose(dose_str) == 15.0
+
+    def test_calculate_daily_dose_no_timestamp(self, parent_frame):
+        """Test dose calculation without timestamp."""
+        gm = GraphManager(parent_frame)
+
+        # Just dose value
+        dose_str = "150mg"
+        assert gm._calculate_daily_dose(dose_str) == 150.0
+
+        # Multiple values without timestamp
+        dose_str = "100|50"
+        assert gm._calculate_daily_dose(dose_str) == 150.0
+
+    def test_calculate_daily_dose_decimal_values(self, parent_frame):
+        """Test dose calculation with decimal values."""
+        gm = GraphManager(parent_frame)
+
+        # Decimal dose
+        dose_str = "2025-07-28 18:59:45:12.5mg"
+        assert gm._calculate_daily_dose(dose_str) == 12.5
+
+        # Multiple decimal doses
+        dose_str = "2025-07-28 18:59:45:12.5mg|2025-07-28 19:34:19:7.5mg"
+        assert gm._calculate_daily_dose(dose_str) == 20.0
+
+    def test_medicine_dose_plotting(self, parent_frame):
+        """Test that medicine doses are plotted correctly."""
+        # Create a DataFrame with dose data
+        df_with_doses = pd.DataFrame({
+            'date': ['2024-01-01', '2024-01-02', '2024-01-03'],
+            'depression': [3, 2, 4],
+            'anxiety': [2, 3, 1],
+            'sleep': [4, 3, 5],
+            'appetite': [3, 4, 2],
+            'bupropion': [1, 1, 0],
+            'bupropion_doses': ['2024-01-01 08:00:00:150mg', '2024-01-02 08:00:00:300mg', ''],
+            'hydroxyzine': [0, 1, 0],
+            'hydroxyzine_doses': ['', '2024-01-02 20:00:00:25mg', ''],
+            'gabapentin': [0, 0, 0],
+            'gabapentin_doses': ['', '', ''],
+            'propranolol': [1, 0, 1],
+            'propranolol_doses': ['2024-01-01 12:00:00:10mg', '', '2024-01-03 12:00:00:20mg'],
+            'quetiapine': [0, 0, 0],
+            'quetiapine_doses': ['', '', ''],
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+                gm.update_graph(df_with_doses)
+
+                # Verify that bar plots were called (for medicines with doses)
+                mock_ax.bar.assert_called()
+
+                # Verify canvas was redrawn
+                mock_canvas.draw.assert_called()
+
+    def test_medicine_toggle_functionality(self, parent_frame):
+        """Test that medicine toggles affect dose display."""
+        df_with_doses = pd.DataFrame({
+            'date': ['2024-01-01'],
+            'depression': [3],
+            'anxiety': [2],
+            'sleep': [4],
+            'appetite': [3],
+            'bupropion': [1],
+            'bupropion_doses': ['2024-01-01 08:00:00:150mg'],
+            'hydroxyzine': [0],
+            'hydroxyzine_doses': [''],
+            'gabapentin': [0],
+            'gabapentin_doses': [''],
+            'propranolol': [1],
+            'propranolol_doses': ['2024-01-01 12:00:00:10mg'],
+            'quetiapine': [0],
+            'quetiapine_doses': [''],
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+
+                # Turn off bupropion toggle
+                gm.toggle_vars["bupropion"].set(False)
+                gm.update_graph(df_with_doses)
+
+                # Turn on hydroxyzine toggle (though it has no doses)
+                gm.toggle_vars["hydroxyzine"].set(True)
+                gm.update_graph(df_with_doses)
+
+                # Verify the graph was updated
+                assert mock_ax.clear.call_count >= 2
+                assert mock_canvas.draw.call_count >= 2
+
+    def test_enhanced_legend_functionality(self, parent_frame):
+        """Test that the enhanced legend displays correctly with medicine data."""
+        df_with_doses = pd.DataFrame({
+            'date': ['2024-01-01', '2024-01-02'],
+            'depression': [3, 2],
+            'anxiety': [2, 3],
+            'sleep': [4, 3],
+            'appetite': [3, 4],
+            'bupropion': [1, 1],
+            'bupropion_doses': ['2024-01-01 08:00:00:150mg', '2024-01-02 08:00:00:200mg'],
+            'hydroxyzine': [0, 0],
+            'hydroxyzine_doses': ['', ''],
+            'gabapentin': [0, 0],
+            'gabapentin_doses': ['', ''],
+            'propranolol': [1, 1],
+            'propranolol_doses': ['2024-01-01 12:00:00:10mg', '2024-01-02 12:00:00:15mg'],
+            'quetiapine': [0, 0],
+            'quetiapine_doses': ['', ''],
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_ax.get_legend_handles_labels.return_value = ([], [])
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+
+                # Enable some medicine toggles
+                gm.toggle_vars["bupropion"].set(True)
+                gm.toggle_vars["propranolol"].set(True)
+                gm.toggle_vars["hydroxyzine"].set(True)  # No dose data
+
+                gm.update_graph(df_with_doses)
+
+                # Verify that legend is called with enhanced parameters
+                mock_ax.legend.assert_called()
+                legend_call = mock_ax.legend.call_args
+
+                # Check that enhanced legend parameters are used
+                assert 'ncol' in legend_call.kwargs
+                assert legend_call.kwargs['ncol'] == 2
+                assert 'fontsize' in legend_call.kwargs
+                assert legend_call.kwargs['fontsize'] == 'small'
+                assert 'frameon' in legend_call.kwargs
+                assert legend_call.kwargs['frameon'] is True
+
+    def test_legend_with_medicines_without_data(self, parent_frame):
+        """Test that medicines without dose data are properly tracked in legend."""
+        df_with_partial_doses = pd.DataFrame({
+            'date': ['2024-01-01'],
+            'depression': [3],
+            'anxiety': [2],
+            'sleep': [4],
+            'appetite': [3],
+            'bupropion': [1],
+            'bupropion_doses': ['2024-01-01 08:00:00:150mg'],
+            'hydroxyzine': [0],
+            'hydroxyzine_doses': [''],  # No dose data
+            'gabapentin': [0],
+            'gabapentin_doses': [''],  # No dose data
+            'propranolol': [0],
+            'propranolol_doses': [''],
+            'quetiapine': [0],
+            'quetiapine_doses': [''],
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+
+            # Mock the legend handles and labels
+            original_handles = [Mock()]
+            original_labels = ['Bupropion (avg: 150.0mg)']
+            mock_ax.get_legend_handles_labels.return_value = (original_handles, original_labels)
+
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+
+                # Enable medicines with and without data
+                gm.toggle_vars["bupropion"].set(True)  # Has data
+                gm.toggle_vars["hydroxyzine"].set(True)  # No data
+                gm.toggle_vars["gabapentin"].set(True)  # No data
+
+                gm.update_graph(df_with_partial_doses)
+
+                # Verify legend was called
+                mock_ax.legend.assert_called()
+
+                # Check that the legend call includes additional handles/labels
+                legend_call = mock_ax.legend.call_args
+                handles, labels = legend_call.args[:2]
+
+                # Should have more labels than just the original ones
+                assert len(labels) > len(original_labels)
+
+    def test_average_dose_calculation_in_legend(self, parent_frame):
+        """Test that average doses are correctly calculated and displayed in legend."""
+        df_with_varying_doses = pd.DataFrame({
+            'date': ['2024-01-01', '2024-01-02', '2024-01-03'],
+            'depression': [3, 2, 4],
+            'anxiety': [2, 3, 1],
+            'sleep': [4, 3, 5],
+            'appetite': [3, 4, 2],
+            'bupropion': [1, 1, 1],
+            'bupropion_doses': ['2024-01-01 08:00:00:100mg',
+                               '2024-01-02 08:00:00:200mg',
+                               '2024-01-03 08:00:00:150mg'],  # Average should be 150mg
+            'propranolol': [1, 1, 0],
+            'propranolol_doses': ['2024-01-01 12:00:00:10mg',
+                                 '2024-01-02 12:00:00:20mg',
+                                 ''],  # Average should be 15mg
+            'hydroxyzine': [0, 0, 0],
+            'hydroxyzine_doses': ['', '', ''],
+            'gabapentin': [0, 0, 0],
+            'gabapentin_doses': ['', '', ''],
+            'quetiapine': [0, 0, 0],
+            'quetiapine_doses': ['', '', ''],
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+
+                # Test the average calculation directly
+                bup_avg = gm._calculate_daily_dose('2024-01-01 08:00:00:100mg')
+                assert bup_avg == 100.0
+
+                prop_avg = gm._calculate_daily_dose('2024-01-01 12:00:00:10mg')
+                assert prop_avg == 10.0
+
+                # Test with full data
+                gm.toggle_vars["bupropion"].set(True)
+                gm.toggle_vars["propranolol"].set(True)
+                gm.update_graph(df_with_varying_doses)
+
+                # Verify that bars were plotted (indicating dose data was processed)
+                mock_ax.bar.assert_called()
+
+    def test_legend_positioning_and_styling(self, parent_frame):
+        """Test that legend positioning and styling parameters are correctly applied."""
+        df_simple = pd.DataFrame({
+            'date': ['2024-01-01'],
+            'depression': [3],
+            'anxiety': [2],
+            'sleep': [4],
+            'appetite': [3],
+            'bupropion': [1],
+            'bupropion_doses': ['2024-01-01 08:00:00:150mg'],
+            'hydroxyzine': [0],
+            'hydroxyzine_doses': [''],
+            'gabapentin': [0],
+            'gabapentin_doses': [''],
+            'propranolol': [0],
+            'propranolol_doses': [''],
+            'quetiapine': [0],
+            'quetiapine_doses': [''],
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_ax.get_legend_handles_labels.return_value = ([Mock()], ['Test Label'])
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+                gm.update_graph(df_simple)
+
+                # Verify legend styling parameters
+                mock_ax.legend.assert_called()
+                legend_call = mock_ax.legend.call_args
+
+                expected_params = {
+                    'loc': 'upper left',
+                    'bbox_to_anchor': (0, 1),
+                    'ncol': 2,
+                    'fontsize': 'small',
+                    'frameon': True,
+                    'fancybox': True,
+                    'shadow': True,
+                    'framealpha': 0.9
+                }
+
+                for param, expected_value in expected_params.items():
+                    assert param in legend_call.kwargs
+                    assert legend_call.kwargs[param] == expected_value
+
+    def test_medicine_tracking_lists(self, parent_frame):
+        """Test that medicines are correctly categorized into with_data and without_data lists."""
+        df_mixed_data = pd.DataFrame({
+            'date': ['2024-01-01', '2024-01-02'],
+            'depression': [3, 2],
+            'anxiety': [2, 3],
+            'sleep': [4, 3],
+            'appetite': [3, 4],
+            # Medicines with data
+            'bupropion': [1, 1],
+            'bupropion_doses': ['2024-01-01 08:00:00:150mg', '2024-01-02 08:00:00:200mg'],
+            'propranolol': [1, 1],
+            'propranolol_doses': ['2024-01-01 12:00:00:10mg', '2024-01-02 12:00:00:15mg'],
+            # Medicines without data (but toggled on)
+            'hydroxyzine': [0, 0],
+            'hydroxyzine_doses': ['', ''],
+            'gabapentin': [0, 0],
+            'gabapentin_doses': ['', ''],
+            'quetiapine': [0, 0],
+            'quetiapine_doses': ['', ''],
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_ax.get_legend_handles_labels.return_value = ([], [])
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+
+                # Enable all medicines
+                gm.toggle_vars["bupropion"].set(True)      # Has data
+                gm.toggle_vars["propranolol"].set(True)    # Has data
+                gm.toggle_vars["hydroxyzine"].set(True)    # No data
+                gm.toggle_vars["gabapentin"].set(True)     # No data
+                gm.toggle_vars["quetiapine"].set(False)    # Disabled
+
+                gm.update_graph(df_mixed_data)
+
+                # Verify that the method was called and plotting occurred
+                mock_ax.bar.assert_called()  # Should be called for medicines with data
+                mock_ax.legend.assert_called()  # Legend should be created
+
+    def test_legend_dummy_handle_creation(self, parent_frame):
+        """Test that dummy handles are created for medicines without data."""
+        df_no_dose_data = pd.DataFrame({
+            'date': ['2024-01-01'],
+            'depression': [3],
+            'anxiety': [2],
+            'sleep': [4],
+            'appetite': [3],
+            'bupropion': [0],
+            'bupropion_doses': [''],
+            'hydroxyzine': [0],
+            'hydroxyzine_doses': [''],
+            'gabapentin': [0],
+            'gabapentin_doses': [''],
+            'propranolol': [0],
+            'propranolol_doses': [''],
+            'quetiapine': [0],
+            'quetiapine_doses': [''],
+        })
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_ax.get_legend_handles_labels.return_value = ([Mock()], ['Depression'])
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                # Mock Rectangle import for dummy handle creation
+                with patch('matplotlib.patches.Rectangle') as mock_rectangle:
+                    mock_dummy_handle = Mock()
+                    mock_rectangle.return_value = mock_dummy_handle
+
+                    gm = GraphManager(parent_frame)
+
+                    # Enable some medicines without data
+                    gm.toggle_vars["hydroxyzine"].set(True)
+                    gm.toggle_vars["gabapentin"].set(True)
+
+                    gm.update_graph(df_no_dose_data)
+
+                    # If there are medicines without data, Rectangle should be called
+                    # to create dummy handles
+                    if gm.toggle_vars["hydroxyzine"].get() or gm.toggle_vars["gabapentin"].get():
+                        mock_rectangle.assert_called()
+
+    def test_empty_dataframe_legend_handling(self, parent_frame):
+        """Test that legend is handled correctly with empty DataFrame."""
+        empty_df = pd.DataFrame()
+
+        with patch('matplotlib.pyplot.subplots') as mock_subplots:
+            mock_fig = Mock()
+            mock_ax = Mock()
+            mock_subplots.return_value = (mock_fig, mock_ax)
+
+            with patch('graph_manager.FigureCanvasTkAgg') as mock_canvas_class:
+                mock_canvas = Mock()
+                mock_canvas_class.return_value = mock_canvas
+
+                gm = GraphManager(parent_frame)
+                gm.update_graph(empty_df)
+
+                # With empty data, legend should not be called
+                mock_ax.legend.assert_not_called()
+                mock_ax.clear.assert_called()
+                mock_canvas.draw.assert_called()
+
+    def test_dose_calculation_comprehensive(self, parent_frame, sample_dose_data):
+        """Test dose calculation with comprehensive test cases."""
+        gm = GraphManager(parent_frame)
+
+        # Test all sample dose data cases
+        assert gm._calculate_daily_dose(sample_dose_data['standard_format']) == 225.0
+        assert gm._calculate_daily_dose(sample_dose_data['with_bullets']) == 300.0
+        assert gm._calculate_daily_dose(sample_dose_data['decimal_doses']) == 20.0
+        assert gm._calculate_daily_dose(sample_dose_data['no_timestamp']) == 150.0
+        assert gm._calculate_daily_dose(sample_dose_data['mixed_format']) == 85.0
+        assert gm._calculate_daily_dose(sample_dose_data['empty_string']) == 0.0
+        assert gm._calculate_daily_dose(sample_dose_data['nan_value']) == 0.0
+        assert gm._calculate_daily_dose(sample_dose_data['no_units']) == 15.0
+
+    def test_dose_calculation_edge_cases(self, parent_frame):
+        """Test dose calculation with edge cases."""
+        gm = GraphManager(parent_frame)
+
+        # Test with malformed data
+        assert gm._calculate_daily_dose("malformed:data") == 0.0
+        assert gm._calculate_daily_dose("::::") == 0.0
+        assert gm._calculate_daily_dose("2025-07-28:") == 0.0
+        assert gm._calculate_daily_dose("2025-07-28::mg") == 0.0
+
+        # Test with partial data
+        assert gm._calculate_daily_dose("2025-07-28 18:59:45:150") == 150.0  # no units
+        assert gm._calculate_daily_dose("150mg") == 150.0  # no timestamp
+
+        # Test with spaces and special characters
+        assert gm._calculate_daily_dose("  2025-07-28 18:59:45:150mg  ") == 150.0
+        assert gm._calculate_daily_dose("••• 2025-07-28 18:59:45:150mg •••") == 150.0

tests/test_init.py

@@ -0,0 +1,257 @@
+"""
+Tests for init module.
+"""
+import os
+import pytest
+from unittest.mock import patch, Mock
+
+import sys
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'src'))
+
+
+class TestInit:
+    """Test cases for the init module."""
+
+    def test_log_directory_creation(self, temp_log_dir):
+        """Test that log directory is created if it doesn't exist."""
+        with patch('init.LOG_PATH', temp_log_dir + '/new_dir'), \
+             patch('os.path.exists', return_value=False), \
+             patch('os.mkdir') as mock_mkdir:
+
+            # Re-import to trigger the directory creation logic
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            mock_mkdir.assert_called_once()
+
+    def test_log_directory_exists(self, temp_log_dir):
+        """Test behavior when log directory already exists."""
+        with patch('init.LOG_PATH', temp_log_dir), \
+             patch('os.path.exists', return_value=True), \
+             patch('os.mkdir') as mock_mkdir:
+
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            mock_mkdir.assert_not_called()
+
+    def test_log_directory_creation_error(self, temp_log_dir):
+        """Test handling of errors during log directory creation."""
+        with patch('init.LOG_PATH', '/invalid/path'), \
+             patch('os.path.exists', return_value=False), \
+             patch('os.mkdir', side_effect=PermissionError("Permission denied")), \
+             patch('builtins.print') as mock_print:
+
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            mock_print.assert_called()
+
+    def test_logger_initialization(self, temp_log_dir):
+        """Test that logger is initialized correctly."""
+        with patch('init.LOG_PATH', temp_log_dir), \
+             patch('init.LOG_LEVEL', 'INFO'), \
+             patch('init.init_logger') as mock_init_logger:
+
+            mock_logger = Mock()
+            mock_init_logger.return_value = mock_logger
+
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            mock_init_logger.assert_called_once_with('init', testing_mode=False)
+
+    def test_logger_initialization_debug_mode(self, temp_log_dir):
+        """Test logger initialization in debug mode."""
+        with patch('init.LOG_PATH', temp_log_dir), \
+             patch('init.LOG_LEVEL', 'DEBUG'), \
+             patch('init.init_logger') as mock_init_logger:
+
+            mock_logger = Mock()
+            mock_init_logger.return_value = mock_logger
+
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            mock_init_logger.assert_called_once_with('init', testing_mode=True)
+
+    def test_log_files_definition(self, temp_log_dir):
+        """Test that log files tuple is defined correctly."""
+        with patch('init.LOG_PATH', temp_log_dir):
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            expected_files = (
+                f"{temp_log_dir}/thechart.log",
+                f"{temp_log_dir}/thechart.warning.log",
+                f"{temp_log_dir}/thechart.error.log",
+            )
+
+            assert src.init.log_files == expected_files
+
+    def test_testing_mode_detection(self, temp_log_dir):
+        """Test that testing mode is detected correctly."""
+        with patch('init.LOG_PATH', temp_log_dir):
+            # Test with DEBUG level
+            with patch('init.LOG_LEVEL', 'DEBUG'):
+                import importlib
+                if 'init' in sys.modules:
+                    importlib.reload(sys.modules['init'])
+                else:
+                    import src.init
+
+                assert src.init.testing_mode is True
+
+            # Test with non-DEBUG level
+            with patch('init.LOG_LEVEL', 'INFO'):
+                importlib.reload(sys.modules['init'])
+                assert src.init.testing_mode is False
+
+    def test_log_clear_true(self, temp_log_dir):
+        """Test log file clearing when LOG_CLEAR is True."""
+        # Create some test log files
+        log_files = [
+            os.path.join(temp_log_dir, "thechart.log"),
+            os.path.join(temp_log_dir, "thechart.warning.log"),
+            os.path.join(temp_log_dir, "thechart.error.log"),
+        ]
+
+        for log_file in log_files:
+            with open(log_file, 'w') as f:
+                f.write("Old log content")
+
+        with patch('init.LOG_PATH', temp_log_dir), \
+             patch('init.LOG_CLEAR', 'True'), \
+             patch('init.log_files', log_files):
+
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            # Check that files were truncated
+            for log_file in log_files:
+                with open(log_file, 'r') as f:
+                    assert f.read() == ""
+
+    def test_log_clear_false(self, temp_log_dir):
+        """Test that log files are not cleared when LOG_CLEAR is False."""
+        # Create some test log files
+        log_files = [
+            os.path.join(temp_log_dir, "thechart.log"),
+            os.path.join(temp_log_dir, "thechart.warning.log"),
+            os.path.join(temp_log_dir, "thechart.error.log"),
+        ]
+
+        original_content = "Original log content"
+        for log_file in log_files:
+            with open(log_file, 'w') as f:
+                f.write(original_content)
+
+        with patch('init.LOG_PATH', temp_log_dir), \
+             patch('init.LOG_CLEAR', 'False'), \
+             patch('init.log_files', log_files):
+
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            # Check that files were not truncated
+            for log_file in log_files:
+                with open(log_file, 'r') as f:
+                    assert f.read() == original_content
+
+    def test_log_clear_nonexistent_files(self, temp_log_dir):
+        """Test log clearing when some log files don't exist."""
+        log_files = [
+            os.path.join(temp_log_dir, "thechart.log"),
+            os.path.join(temp_log_dir, "nonexistent.log"),
+        ]
+
+        # Create only one of the files
+        with open(log_files[0], 'w') as f:
+            f.write("Content")
+
+        with patch('init.LOG_PATH', temp_log_dir), \
+             patch('init.LOG_CLEAR', 'True'), \
+             patch('init.log_files', log_files):
+
+            # This should not raise an exception
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+    def test_log_clear_permission_error(self, temp_log_dir):
+        """Test handling of permission errors during log clearing."""
+        log_files = [os.path.join(temp_log_dir, "thechart.log")]
+
+        with open(log_files[0], 'w') as f:
+            f.write("Content")
+
+        with patch('init.LOG_PATH', temp_log_dir), \
+             patch('init.LOG_CLEAR', 'True'), \
+             patch('init.log_files', log_files), \
+             patch('builtins.open', side_effect=PermissionError("Permission denied")), \
+             patch('init.logger') as mock_logger:
+
+            mock_logger.error = Mock()
+
+            # Should raise the exception after logging
+            with pytest.raises(PermissionError):
+                import importlib
+                if 'init' in sys.modules:
+                    importlib.reload(sys.modules['init'])
+                else:
+                    import src.init
+
+    def test_module_exports(self, temp_log_dir):
+        """Test that module exports expected objects."""
+        with patch('init.LOG_PATH', temp_log_dir):
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            # Check that expected objects are available
+            assert hasattr(src.init, 'logger')
+            assert hasattr(src.init, 'log_files')
+            assert hasattr(src.init, 'testing_mode')
+
+    def test_log_path_printing(self, temp_log_dir):
+        """Test that LOG_PATH is printed when directory is created."""
+        with patch('init.LOG_PATH', temp_log_dir + '/new_dir'), \
+             patch('os.path.exists', return_value=False), \
+             patch('os.mkdir'), \
+             patch('builtins.print') as mock_print:
+
+            import importlib
+            if 'init' in sys.modules:
+                importlib.reload(sys.modules['init'])
+            else:
+                import src.init
+
+            mock_print.assert_called_with(temp_log_dir + '/new_dir')

tests/test_logger.py

@@ -0,0 +1,179 @@
+"""
+Tests for logger module.
+"""
+import os
+import logging
+import pytest
+from unittest.mock import patch
+
+import sys
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'src'))
+
+from src.logger import init_logger
+
+
+class TestLogger:
+    """Test cases for the logger module."""
+
+    def test_init_logger_basic(self, temp_log_dir):
+        """Test basic logger initialization."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=False)
+
+            assert isinstance(logger, logging.Logger)
+            assert logger.name == "test_logger"
+            assert logger.level == logging.INFO
+
+    def test_init_logger_testing_mode(self, temp_log_dir):
+        """Test logger initialization in testing mode."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=True)
+
+            assert logger.level == logging.DEBUG
+
+    def test_init_logger_production_mode(self, temp_log_dir):
+        """Test logger initialization in production mode."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=False)
+
+            assert logger.level == logging.INFO
+
+    def test_file_handlers_created(self, temp_log_dir):
+        """Test that file handlers are created correctly."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=False)
+
+            # Check that handlers were added
+            assert len(logger.handlers) >= 3  # At least 3 file handlers
+
+    def test_file_handler_levels(self, temp_log_dir):
+        """Test that file handlers have correct log levels."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=False)
+
+            handler_levels = [handler.level for handler in logger.handlers if isinstance(handler, logging.FileHandler)]
+
+            # Should have handlers for DEBUG, WARNING, and ERROR levels
+            assert logging.DEBUG in handler_levels
+            assert logging.WARNING in handler_levels
+            assert logging.ERROR in handler_levels
+
+    def test_log_file_paths(self, temp_log_dir):
+        """Test that log files are created with correct paths."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=False)
+
+            # Log something to trigger file creation
+            logger.debug("Test debug message")
+            logger.warning("Test warning message")
+            logger.error("Test error message")
+
+            # Check that log files would be created (paths are correct)
+            expected_files = [
+                os.path.join(temp_log_dir, "app.log"),
+                os.path.join(temp_log_dir, "app.warning.log"),
+                os.path.join(temp_log_dir, "app.error.log")
+            ]
+
+            # The files should exist or be ready to be created
+            for handler in logger.handlers:
+                if isinstance(handler, logging.FileHandler):
+                    assert handler.baseFilename in expected_files
+
+    def test_formatter_format(self, temp_log_dir):
+        """Test that formatters are set correctly."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=False)
+
+            expected_format = "%(asctime)s - %(name)s - %(funcName)s - %(levelname)s - %(message)s"
+
+            for handler in logger.handlers:
+                if isinstance(handler, logging.FileHandler):
+                    assert handler.formatter._fmt == expected_format
+
+    @patch('colorlog.basicConfig')
+    def test_colorlog_configuration(self, mock_basicConfig, temp_log_dir):
+        """Test that colorlog is configured correctly."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            init_logger("test_logger", testing_mode=False)
+
+            mock_basicConfig.assert_called_once()
+
+            # Check that format includes color and bold formatting
+            call_args = mock_basicConfig.call_args
+            assert 'format' in call_args[1]
+            format_string = call_args[1]['format']
+            assert '%(log_color)s' in format_string
+            assert '\033[1m' in format_string  # Bold sequence
+
+    def test_multiple_logger_instances(self, temp_log_dir):
+        """Test creating multiple logger instances."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger1 = init_logger("logger1", testing_mode=False)
+            logger2 = init_logger("logger2", testing_mode=True)
+
+            assert logger1.name == "logger1"
+            assert logger2.name == "logger2"
+            assert logger1.level == logging.INFO
+            assert logger2.level == logging.DEBUG
+
+    def test_logger_inheritance(self, temp_log_dir):
+        """Test that logger follows Python logging hierarchy."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test.module.logger", testing_mode=False)
+
+            assert logger.name == "test.module.logger"
+
+    @patch('logging.FileHandler')
+    def test_file_handler_error_handling(self, mock_file_handler, temp_log_dir):
+        """Test error handling when file handler creation fails."""
+        mock_file_handler.side_effect = PermissionError("Cannot create log file")
+
+        with patch('logger.LOG_PATH', temp_log_dir):
+            # Should not raise an exception, but handle gracefully
+            try:
+                logger = init_logger("test_logger", testing_mode=False)
+                # Logger should still be created, just without file handlers
+                assert isinstance(logger, logging.Logger)
+            except PermissionError:
+                pytest.fail("init_logger should handle file creation errors gracefully")
+
+    def test_logger_name_parameter(self, temp_log_dir):
+        """Test that logger name is set correctly from parameter."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            test_name = "my.custom.logger.name"
+            logger = init_logger(test_name, testing_mode=False)
+
+            assert logger.name == test_name
+
+    def test_testing_mode_boolean(self, temp_log_dir):
+        """Test that testing_mode parameter accepts boolean values."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger_true = init_logger("test1", testing_mode=True)
+            logger_false = init_logger("test2", testing_mode=False)
+
+            assert logger_true.level == logging.DEBUG
+            assert logger_false.level == logging.INFO
+
+    def test_log_format_contains_required_fields(self, temp_log_dir):
+        """Test that log format contains all required fields."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=False)
+
+            log_format = "%(asctime)s - %(name)s - %(funcName)s - %(levelname)s - %(message)s"
+
+            # Check that format contains all expected fields
+            expected_fields = ['%(asctime)s', '%(name)s', '%(funcName)s', '%(levelname)s', '%(message)s']
+            for field in expected_fields:
+                assert field in log_format
+
+    def test_handler_file_mode(self, temp_log_dir):
+        """Test that file handlers use append mode by default."""
+        with patch('logger.LOG_PATH', temp_log_dir):
+            logger = init_logger("test_logger", testing_mode=False)
+
+            # File handlers should be in append mode by default
+            for handler in logger.handlers:
+                if isinstance(handler, logging.FileHandler):
+                    # FileHandler uses 'a' mode by default
+                    assert hasattr(handler, 'mode')  # Basic check that it's a file handler

tests/test_main.py

@@ -0,0 +1,411 @@
+"""
+Tests for the main application and MedTrackerApp class.
+"""
+import os
+import pytest
+import tkinter as tk
+from unittest.mock import Mock, patch
+import pandas as pd
+
+import sys
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'src'))
+
+from src.main import MedTrackerApp
+
+
+class TestMedTrackerApp:
+    """Test cases for the MedTrackerApp class."""
+
+    @pytest.fixture
+    def root_window(self):
+        """Create a root window for testing."""
+        root = tk.Tk()
+        yield root
+        root.destroy()
+
+    @pytest.fixture
+    def mock_managers(self):
+        """Mock the manager classes."""
+        with patch('main.UIManager') as mock_ui, \
+             patch('main.DataManager') as mock_data, \
+             patch('main.GraphManager') as mock_graph:
+            yield {
+                'ui': mock_ui,
+                'data': mock_data,
+                'graph': mock_graph
+            }
+
+    def test_init_default_filename(self, root_window, mock_managers):
+        """Test initialization with default filename."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            assert app.filename == "thechart_data.csv"
+            assert app.root == root_window
+            assert root_window.title() == "Thechart - medication tracker"
+
+    def test_init_custom_filename_exists(self, root_window, mock_managers):
+        """Test initialization with custom filename that exists."""
+        with patch('sys.argv', ['main.py', 'custom_data.csv']), \
+             patch('os.path.exists', return_value=True):
+
+            app = MedTrackerApp(root_window)
+
+            assert app.filename == "custom_data.csv"
+
+    def test_init_custom_filename_not_exists(self, root_window, mock_managers):
+        """Test initialization with custom filename that doesn't exist."""
+        with patch('sys.argv', ['main.py', 'nonexistent.csv']), \
+             patch('os.path.exists', return_value=False):
+
+            app = MedTrackerApp(root_window)
+
+            assert app.filename == "thechart_data.csv"
+
+    @patch('main.LOG_LEVEL', 'DEBUG')
+    def test_debug_logging(self, root_window, mock_managers):
+        """Test debug logging when LOG_LEVEL is DEBUG."""
+        with patch('sys.argv', ['main.py', 'test.csv']), \
+             patch('os.path.exists', return_value=True), \
+             patch('main.logger') as mock_logger:
+
+            app = MedTrackerApp(root_window)
+
+            # Check that debug messages were logged
+            mock_logger.debug.assert_called()
+
+    def test_setup_main_ui_components(self, root_window, mock_managers):
+        """Test that main UI components are set up correctly."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            # Check that managers were instantiated
+            mock_managers['ui'].assert_called()
+            mock_managers['data'].assert_called()
+
+    def test_icon_setup(self, root_window, mock_managers):
+        """Test icon setup functionality."""
+        with patch('sys.argv', ['main.py']), \
+             patch('os.path.exists', return_value=True):
+
+            app = MedTrackerApp(root_window)
+
+            # Check that setup_application_icon was called on UI manager
+            app.ui_manager.setup_application_icon.assert_called()
+
+    def test_icon_setup_fallback_path(self, root_window, mock_managers):
+        """Test icon setup with fallback path."""
+        def mock_exists(path):
+            return path == "./chart-671.png"
+
+        with patch('sys.argv', ['main.py']), \
+             patch('os.path.exists', side_effect=mock_exists):
+
+            app = MedTrackerApp(root_window)
+
+            # Check that setup_application_icon was called with fallback path
+            app.ui_manager.setup_application_icon.assert_called_with(img_path="./chart-671.png")
+
+    def test_add_new_entry_success(self, root_window, mock_managers):
+        """Test successful entry addition."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            # Mock the UI variables
+            app.date_var = Mock()
+            app.date_var.get.return_value = "2024-01-01"
+            app.symptom_vars = {
+                "depression": Mock(), "anxiety": Mock(),
+                "sleep": Mock(), "appetite": Mock()
+            }
+            for var in app.symptom_vars.values():
+                var.get.return_value = 3
+
+            app.medicine_vars = {
+                "bupropion": [Mock()], "hydroxyzine": [Mock()],
+                "gabapentin": [Mock()], "propranolol": [Mock()]
+            }
+            for med_var in app.medicine_vars.values():
+                med_var[0].get.return_value = 1
+
+            app.note_var = Mock()
+            app.note_var.get.return_value = "Test note"
+
+            # Mock data manager to return success
+            app.data_manager.add_entry.return_value = True
+
+            with patch('tkinter.messagebox.showinfo') as mock_info, \
+                 patch.object(app, '_clear_entries') as mock_clear, \
+                 patch.object(app, 'refresh_data_display') as mock_load:
+
+                app.add_new_entry()
+
+                mock_info.assert_called_once()
+                mock_clear.assert_called_once()
+                mock_load.assert_called_once()
+
+    def test_add_new_entry_empty_date(self, root_window, mock_managers):
+        """Test adding entry with empty date."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            app.date_var = Mock()
+            app.date_var.get.return_value = "   "  # Empty/whitespace date
+
+            with patch('tkinter.messagebox.showerror') as mock_error:
+                app.add_new_entry()
+
+                mock_error.assert_called_once_with(
+                    "Error", "Please enter a date.", parent=app.root
+                )
+
+    def test_add_new_entry_duplicate_date(self, root_window, mock_managers):
+        """Test adding entry with duplicate date."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            # Set up UI variables
+            app.date_var = Mock()
+            app.date_var.get.return_value = "2024-01-01"
+            app.symptom_vars = {"depression": Mock(), "anxiety": Mock(),
+                              "sleep": Mock(), "appetite": Mock()}
+            for var in app.symptom_vars.values():
+                var.get.return_value = 3
+            app.medicine_vars = {"bupropion": [Mock()], "hydroxyzine": [Mock()],
+                               "gabapentin": [Mock()], "propranolol": [Mock()]}
+            for med_var in app.medicine_vars.values():
+                med_var[0].get.return_value = 1
+            app.note_var = Mock()
+            app.note_var.get.return_value = "Test"
+
+            # Mock data manager to return failure (duplicate)
+            app.data_manager.add_entry.return_value = False
+
+            # Mock load_data to return DataFrame with existing date
+            mock_df = pd.DataFrame({'date': ['2024-01-01']})
+            app.data_manager.load_data.return_value = mock_df
+
+            with patch('tkinter.messagebox.showerror') as mock_error:
+                app.add_new_entry()
+
+                mock_error.assert_called_once()
+                assert "already exists" in mock_error.call_args[0][1]
+
+    def test_handle_double_click(self, root_window, mock_managers):
+        """Test double-click event handling."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            # Mock tree with selection
+            app.tree = Mock()
+            app.tree.get_children.return_value = ['item1']
+            app.tree.selection.return_value = ['item1']
+            app.tree.item.return_value = {'values': ('2024-01-01', '3', '2', '4', '3', '1', '0', '2', '1', 'Note')}
+
+            mock_event = Mock()
+
+            with patch.object(app, '_create_edit_window') as mock_create_edit:
+                app.handle_double_click(mock_event)
+
+                mock_create_edit.assert_called_once()
+
+    def test_handle_double_click_empty_tree(self, root_window, mock_managers):
+        """Test double-click when tree is empty."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            app.tree = Mock()
+            app.tree.get_children.return_value = []
+
+            mock_event = Mock()
+
+            with patch.object(app, '_create_edit_window') as mock_create_edit:
+                app.handle_double_click(mock_event)
+
+                mock_create_edit.assert_not_called()
+
+    def test_save_edit_success(self, root_window, mock_managers):
+        """Test successful save edit operation."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            # Mock edit window
+            mock_edit_win = Mock()
+
+            # Mock data manager to return success
+            app.data_manager.update_entry.return_value = True
+
+            with patch('tkinter.messagebox.showinfo') as mock_info, \
+                 patch.object(app, '_clear_entries') as mock_clear, \
+                 patch.object(app, 'refresh_data_display') as mock_load:
+
+                app._save_edit(
+                    mock_edit_win, "2024-01-01", "2024-01-01",
+                    3, 2, 4, 3, 1, 0, 2, 1, "Updated note"
+                )
+
+                mock_edit_win.destroy.assert_called_once()
+                mock_info.assert_called_once()
+                mock_clear.assert_called_once()
+                mock_load.assert_called_once()
+
+    def test_save_edit_duplicate_date(self, root_window, mock_managers):
+        """Test save edit with duplicate date."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            mock_edit_win = Mock()
+
+            # Mock data manager to return failure
+            app.data_manager.update_entry.return_value = False
+
+            # Mock load_data to return DataFrame with existing date
+            mock_df = pd.DataFrame({'date': ['2024-01-02']})
+            app.data_manager.load_data.return_value = mock_df
+
+            with patch('tkinter.messagebox.showerror') as mock_error:
+                app._save_edit(
+                    mock_edit_win, "2024-01-01", "2024-01-02",  # Different dates
+                    3, 2, 4, 3, 1, 0, 2, 1, "Updated note"
+                )
+
+                mock_error.assert_called_once()
+                assert "already exists" in mock_error.call_args[0][1]
+
+    def test_delete_entry_success(self, root_window, mock_managers):
+        """Test successful entry deletion."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            mock_edit_win = Mock()
+            app.tree = Mock()
+            app.tree.item.return_value = {'values': ['2024-01-01']}
+
+            # Mock data manager to return success
+            app.data_manager.delete_entry.return_value = True
+
+            with patch('tkinter.messagebox.askyesno', return_value=True) as mock_confirm, \
+                 patch('tkinter.messagebox.showinfo') as mock_info, \
+                 patch.object(app, 'refresh_data_display') as mock_load:
+
+                app._delete_entry(mock_edit_win, 'item1')
+
+                mock_confirm.assert_called_once()
+                mock_edit_win.destroy.assert_called_once()
+                mock_info.assert_called_once()
+                mock_load.assert_called_once()
+
+    def test_delete_entry_cancelled(self, root_window, mock_managers):
+        """Test deletion when user cancels."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            mock_edit_win = Mock()
+
+            with patch('tkinter.messagebox.askyesno', return_value=False) as mock_confirm:
+                app._delete_entry(mock_edit_win, 'item1')
+
+                mock_confirm.assert_called_once()
+                mock_edit_win.destroy.assert_not_called()
+
+    def test_clear_entries(self, root_window, mock_managers):
+        """Test clearing input entries."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            # Mock variables
+            app.date_var = Mock()
+            app.symptom_vars = {"depression": Mock(), "anxiety": Mock()}
+            app.medicine_vars = {"bupropion": [Mock()], "hydroxyzine": [Mock()]}
+            app.note_var = Mock()
+
+            app._clear_entries()
+
+            app.date_var.set.assert_called_with("")
+            app.note_var.set.assert_called_with("")
+            for var in app.symptom_vars.values():
+                var.set.assert_called_with(0)
+            for med_var in app.medicine_vars.values():
+                med_var[0].set.assert_called_with(0)
+
+    def test_refresh_data_display(self, root_window, mock_managers):
+        """Test loading data into tree and graph."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            # Mock tree
+            app.tree = Mock()
+            app.tree.get_children.return_value = ['item1', 'item2']
+
+            # Mock data
+            mock_df = pd.DataFrame({
+                'date': ['2024-01-01', '2024-01-02'],
+                'depression': [3, 2],
+                'note': ['Note1', 'Note2']
+            })
+            app.data_manager.load_data.return_value = mock_df
+
+            app.refresh_data_display()
+
+            # Check that tree was cleared and populated
+            app.tree.delete.assert_called()
+            app.tree.insert.assert_called()
+
+            # Check that graph was updated
+            app.graph_manager.update_graph.assert_called_with(mock_df)
+
+    def test_refresh_data_display_empty_dataframe(self, root_window, mock_managers):
+        """Test loading empty data."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            app.tree = Mock()
+            app.tree.get_children.return_value = []
+
+            # Mock empty DataFrame
+            empty_df = pd.DataFrame()
+            app.data_manager.load_data.return_value = empty_df
+
+            app.refresh_data_display()
+
+            # Graph should still be updated even with empty data
+            app.graph_manager.update_graph.assert_called_with(empty_df)
+
+    def test_handle_window_closing_confirmed(self, root_window, mock_managers):
+        """Test application closing when confirmed."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            with patch('tkinter.messagebox.askokcancel', return_value=True) as mock_confirm:
+                app.handle_window_closing()
+
+                mock_confirm.assert_called_once()
+                app.graph_manager.close.assert_called_once()
+
+    def test_handle_window_closing_cancelled(self, root_window, mock_managers):
+        """Test application closing when cancelled."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            with patch('tkinter.messagebox.askokcancel', return_value=False) as mock_confirm:
+                app.handle_window_closing()
+
+                mock_confirm.assert_called_once()
+                app.graph_manager.close.assert_not_called()
+
+    def test_protocol_handler_setup(self, root_window, mock_managers):
+        """Test that window close protocol is set up."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            # The protocol should be set during initialization
+            # This is more of a structural test
+            assert app.root is root_window
+
+    def test_window_properties(self, root_window, mock_managers):
+        """Test window properties are set correctly."""
+        with patch('sys.argv', ['main.py']):
+            app = MedTrackerApp(root_window)
+
+            assert root_window.title() == "Thechart - medication tracker"
+            # Note: Testing resizable would require more complex mocking

tests/test_ui_manager.py

@@ -0,0 +1,293 @@
+"""
+Tests for the UIManager class.
+"""
+import os
+import pytest
+import tkinter as tk
+from tkinter import ttk
+from unittest.mock import Mock, patch
+
+import sys
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'src'))
+
+from src.ui_manager import UIManager
+
+
+class TestUIManager:
+    """Test cases for the UIManager class."""
+
+    @pytest.fixture
+    def root_window(self):
+        """Create a root window for testing."""
+        root = tk.Tk()
+        yield root
+        root.destroy()
+
+    @pytest.fixture
+    def ui_manager(self, root_window, mock_logger):
+        """Create a UIManager instance for testing."""
+        return UIManager(root_window, mock_logger)
+
+    def test_init(self, root_window, mock_logger):
+        """Test UIManager initialization."""
+        ui = UIManager(root_window, mock_logger)
+        assert ui.root == root_window
+        assert ui.logger == mock_logger
+
+    @patch('os.path.exists')
+    @patch('PIL.Image.open')
+    def test_setup_application_icon_success(self, mock_image_open, mock_exists, ui_manager):
+        """Test successful icon setup."""
+        mock_exists.return_value = True
+        mock_image = Mock()
+        mock_image.resize.return_value = mock_image
+        mock_image_open.return_value = mock_image
+
+        with patch('PIL.ImageTk.PhotoImage') as mock_photo:
+            mock_photo_instance = Mock()
+            mock_photo.return_value = mock_photo_instance
+
+            with patch.object(ui_manager.root, 'iconphoto') as mock_iconphoto, \
+                 patch.object(ui_manager.root, 'wm_iconphoto') as mock_wm_iconphoto:
+
+                result = ui_manager.setup_application_icon("test_icon.png")
+
+                assert result is True
+                mock_image_open.assert_called_once_with("test_icon.png")
+                mock_image.resize.assert_called_once()
+                ui_manager.logger.info.assert_called_with("Trying to load icon from: test_icon.png")
+
+    @patch('os.path.exists')
+    def test_setup_application_icon_file_not_found(self, mock_exists, ui_manager):
+        """Test icon setup when file is not found."""
+        mock_exists.return_value = False
+
+        result = ui_manager.setup_application_icon("nonexistent_icon.png")
+
+        assert result is False
+        ui_manager.logger.warning.assert_called_with("Icon file not found at nonexistent_icon.png")
+
+    @patch('os.path.exists')
+    @patch('PIL.Image.open')
+    def test_setup_application_icon_exception(self, mock_image_open, mock_exists, ui_manager):
+        """Test icon setup with exception."""
+        mock_exists.return_value = True
+        mock_image_open.side_effect = Exception("Test error")
+
+        result = ui_manager.setup_application_icon("test_icon.png")
+
+        assert result is False
+        ui_manager.logger.error.assert_called_with("Error setting icon: Test error")
+
+    @patch('sys._MEIPASS', '/test/bundle/path', create=True)
+    @patch('os.path.exists')
+    @patch('PIL.Image.open')
+    def test_setup_application_icon_pyinstaller_bundle(self, mock_image_open, mock_exists, ui_manager):
+        """Test icon setup in PyInstaller bundle."""
+        # Mock exists to return False for original path, True for bundle path
+        def mock_exists_side_effect(path):
+            if 'test_icon.png' in path and '/test/bundle/path' in path:
+                return True
+            return False
+
+        mock_exists.side_effect = mock_exists_side_effect
+        mock_image = Mock()
+        mock_image.resize.return_value = mock_image
+        mock_image_open.return_value = mock_image
+
+        with patch('PIL.ImageTk.PhotoImage') as mock_photo:
+            mock_photo_instance = Mock()
+            mock_photo.return_value = mock_photo_instance
+
+            with patch.object(ui_manager.root, 'iconphoto') as mock_iconphoto, \
+                 patch.object(ui_manager.root, 'wm_iconphoto') as mock_wm_iconphoto:
+
+                result = ui_manager.setup_application_icon("test_icon.png")
+
+                assert result is True
+            ui_manager.logger.info.assert_called_with("Found icon in PyInstaller bundle: /test/bundle/path/test_icon.png")
+
+    def test_create_graph_frame(self, ui_manager, root_window):
+        """Test creation of graph frame."""
+        main_frame = ttk.Frame(root_window)
+
+        graph_frame = ui_manager.create_graph_frame(main_frame)
+
+        assert isinstance(graph_frame, ttk.LabelFrame)
+        assert graph_frame.winfo_parent() == str(main_frame)
+
+    def test_create_input_frame(self, ui_manager, root_window):
+        """Test creation of input frame."""
+        main_frame = ttk.Frame(root_window)
+
+        input_ui = ui_manager.create_input_frame(main_frame)
+
+        assert isinstance(input_ui, dict)
+        assert "frame" in input_ui
+        assert "symptom_vars" in input_ui
+        assert "medicine_vars" in input_ui
+        assert "note_var" in input_ui
+        assert "date_var" in input_ui
+
+        assert isinstance(input_ui["frame"], ttk.LabelFrame)
+        assert isinstance(input_ui["symptom_vars"], dict)
+        assert isinstance(input_ui["medicine_vars"], dict)
+        assert isinstance(input_ui["note_var"], tk.StringVar)
+        assert isinstance(input_ui["date_var"], tk.StringVar)
+
+    def test_create_input_frame_symptom_vars(self, ui_manager, root_window):
+        """Test that symptom variables are created correctly."""
+        main_frame = ttk.Frame(root_window)
+
+        input_ui = ui_manager.create_input_frame(main_frame)
+        symptom_vars = input_ui["symptom_vars"]
+
+        expected_symptoms = ["depression", "anxiety", "sleep", "appetite"]
+        for symptom in expected_symptoms:
+            assert symptom in symptom_vars
+            assert isinstance(symptom_vars[symptom], tk.IntVar)
+
+    def test_create_input_frame_medicine_vars(self, ui_manager, root_window):
+        """Test that medicine variables are created correctly."""
+        main_frame = ttk.Frame(root_window)
+
+        input_ui = ui_manager.create_input_frame(main_frame)
+        medicine_vars = input_ui["medicine_vars"]
+
+        expected_medicines = ["bupropion", "hydroxyzine", "gabapentin", "propranolol", "quetiapine"]
+        for medicine in expected_medicines:
+            assert medicine in medicine_vars
+            assert isinstance(medicine_vars[medicine], tuple)
+            assert len(medicine_vars[medicine]) == 2  # IntVar and display text
+            assert isinstance(medicine_vars[medicine][0], tk.IntVar)
+            assert isinstance(medicine_vars[medicine][1], str)
+
+    @patch('src.ui_manager.datetime')
+    def test_create_input_frame_default_date(self, mock_datetime, ui_manager, root_window):
+        """Test that default date is set to today."""
+        mock_datetime.now.return_value.strftime.return_value = "07/30/2025"
+
+        main_frame = ttk.Frame(root_window)
+        input_ui = ui_manager.create_input_frame(main_frame)
+
+        # The actual date will be today's date, not the mocked value
+        # because the datetime import is within the function
+        assert input_ui["date_var"].get() == "07/30/2025"
+
+    def test_create_table_frame(self, ui_manager, root_window):
+        """Test creation of table frame."""
+        main_frame = ttk.Frame(root_window)
+
+        table_ui = ui_manager.create_table_frame(main_frame)
+
+        assert isinstance(table_ui, dict)
+        assert "tree" in table_ui
+        assert isinstance(table_ui["tree"], ttk.Treeview)
+
+    def test_create_table_frame_columns(self, ui_manager, root_window):
+        """Test that table columns are set up correctly."""
+        main_frame = ttk.Frame(root_window)
+
+        table_ui = ui_manager.create_table_frame(main_frame)
+        tree = table_ui["tree"]
+
+        expected_columns = [
+            "Date", "Depression", "Anxiety", "Sleep", "Appetite",
+            "Bupropion", "Hydroxyzine", "Gabapentin", "Propranolol", "Quetiapine", "Note"
+        ]
+
+        # Check that columns are configured
+        assert tree["columns"] == tuple(expected_columns)
+
+    def test_add_buttons(self, ui_manager, root_window):
+        """Test adding buttons to a frame."""
+        frame = ttk.Frame(root_window)
+
+        buttons_config = [
+            {"text": "Test Button 1", "command": lambda: None},
+            {"text": "Test Button 2", "command": lambda: None, "fill": "x"},
+        ]
+
+        ui_manager.add_buttons(frame, buttons_config)
+
+        # Check that a button frame was added
+        children = frame.winfo_children()
+        assert len(children) >= 1  # At least the button frame should be added
+
+    def test_create_edit_window(self, ui_manager):
+        """Test creation of edit window."""
+        values = ("2024-01-01", "3", "2", "4", "3", "1", "0", "2", "1", "Test note")
+        callbacks = {
+            "save": lambda win, *args: None,
+            "delete": lambda win: None
+        }
+
+        edit_window = ui_manager.create_edit_window(values, callbacks)
+
+        assert isinstance(edit_window, tk.Toplevel)
+        assert edit_window.title() == "Edit Entry"
+
+    def test_create_edit_window_widgets(self, ui_manager):
+        """Test that edit window contains expected widgets."""
+        values = ("2024-01-01", "3", "2", "4", "3", "1", "0", "2", "1", "Test note")
+        callbacks = {
+            "save": lambda win, *args: None,
+            "delete": lambda win: None
+        }
+
+        edit_window = ui_manager.create_edit_window(values, callbacks)
+
+        # Check that window has children (widgets)
+        children = edit_window.winfo_children()
+        assert len(children) > 0
+
+    def test_create_edit_window_initial_values(self, ui_manager):
+        """Test that edit window is populated with initial values."""
+        values = ("2024-01-01", "3", "2", "4", "3", "1", "0", "2", "1", "Test note")
+        callbacks = {
+            "save": lambda win, *args: None,
+            "delete": lambda win: None
+        }
+
+        edit_window = ui_manager.create_edit_window(values, callbacks)
+
+        # The window should be created successfully
+        assert edit_window is not None
+        # More detailed testing would require examining the internal widgets
+
+    def test_frame_positioning(self, ui_manager, root_window):
+        """Test that frames are positioned correctly."""
+        main_frame = ttk.Frame(root_window)
+
+        # Create multiple frames
+        graph_frame = ui_manager.create_graph_frame(main_frame)
+        input_ui = ui_manager.create_input_frame(main_frame)
+        table_ui = ui_manager.create_table_frame(main_frame)
+
+        # All frames should be created successfully
+        assert graph_frame is not None
+        assert input_ui["frame"] is not None
+        assert table_ui["tree"] is not None
+
+    def test_widget_configuration(self, ui_manager, root_window):
+        """Test that widgets are configured with appropriate properties."""
+        main_frame = ttk.Frame(root_window)
+        input_ui = ui_manager.create_input_frame(main_frame)
+
+        # Check that variables have default values
+        for var in input_ui["symptom_vars"].values():
+            assert var.get() == 0
+
+        for medicine_data in input_ui["medicine_vars"].values():
+            assert medicine_data[0].get() == 0  # IntVar should be 0
+
+    @patch('tkinter.messagebox.showerror')
+    def test_error_handling_in_setup_application_icon(self, mock_showerror, ui_manager):
+        """Test error handling in setup_application_icon method."""
+        with patch('PIL.Image.open') as mock_open:
+            mock_open.side_effect = Exception("Image error")
+
+            result = ui_manager.setup_application_icon("test.png")
+
+            assert result is False
+            ui_manager.logger.error.assert_called()

uv.lock

@@ -96,6 +96,59 @@ wheels = [
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