bug: Missing automated test suite causes undetected regressions across critical modules

[bhavyakeerthi3]

Problem

The reactome_chatbot repository currently has no automated test suite and no CI testing infrastructure. This creates several risks as the project scales:

• Contributors cannot easily verify their changes don't break existing behaviour
• Regressions in critical paths (config loading, retrieval logic) go undetected until runtime
• The absence of a test gate makes it harder to confidently merge PRs

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Proposed Solution

Introduce a lightweight testing foundation using pytest, targeting the core modules most critical to chatbot operation:

1. util.config_yml — Validate that config.yml (and default fallbacks) parse correctly into Pydantic models, and that feature flags / usage limits evaluate as expected
2. retrievers.csv_chroma — Unit test utility helpers such as ChromaDB subdirectory discovery, ensuring retrieval scaffolding behaves correctly under edge cases

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Implementation Plan

• Add a tests/ directory at the project root
• Add pytest and pytest-mock to pyproject.toml under [tool.poetry.group.dev.dependencies]
• Add a GitHub Actions workflow at .github/workflows/tests.yml that triggers on push and pull requests
• Write initial test coverage for the two modules above as a foundation others can build on

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Example Test Structure

tests/
├── __init__.py
├── test_config_yml.py       # Config loading, defaults, validation
└── test_csv_chroma.py       # ChromaDB subdir discovery, edge cases

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Impact

Area	Benefit
Maintainability	Contributors can verify changes without manual testing
Stability	Prevents silent regressions in retrieval and config pipelines
CI Gate	PRs blocked from merging if tests fail
Onboarding	New contributors have a clear, testable contract for each module

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Related

This complements ongoing work in:

• feat: make LLM and embedding model configurable via YAML config #112 (configurable LLM/embedding via YAML — config tests will validate this)
• fix: replace mutable default arguments in Config methods #131 (mutable default args in Config — tests will catch this class of bug going forward)

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Opening a PR with the initial tests/ scaffolding and GitHub Actions workflow.