Add comprehensive tests, documentation, and error handling improvements

.github/workflows/test.yml

@@ -0,0 +1,32 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+
+    - name: Install Poetry
+      run: pip install poetry
+
+    - name: Install dependencies
+      run: poetry install
+
+    - name: Run tests
+      run: poetry run pytest tests/ -v
+
+    - name: Run type checking
+      run: poetry run mypy --ignore-missing-imports src/
+      continue-on-error: true  # Don't fail build yet

.gitignore

@@ -1,14 +1,38 @@
 debug_log.txt
 
-# Ignore Python bytecode files
+# Python bytecode files
 __pycache__/
 *.pyc
 *.pyo
 *.pyd
+.Python
+*.egg-info/
 
+# Test artifacts
+.pytest_cache/
+.coverage
+htmlcov/
+*.coverage
 
-#output folder of results
+# IDE
+.vscode/
+.idea/
+*.swp
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Temporary files
+*.tmp
+*.bak
+
+# Output folder of results
 output
 
-#vim files
-*.swp
+# Generated data files
+db_id_to_name_mapping.tsv
+pathway_logic_network_*.csv
+reaction_connections_*.csv
+decomposed_uid_mapping_*.csv
+best_matches_*.csv