Build test suite

[davebridges]

✅ Add Test Suite for Core Modules (No Token Usage)

Overview

Set up a test framework using pytest to ensure core system components behave as expected without relying on OpenAI API calls. All model interactions (e.g. GPT completions and embeddings) will be mocked for speed, determinism, and zero token usage.

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📋 Plan of Action

1. Create /tests Directory

Structure tests by module:

/tests
test_indexing.py
test_query_zotero.py
test_query_pubmed.py
test_prompts.py
test_database.py
test_synthesis.py

2. Add Tests for Deterministic Components

• ✅ BibTeX parsing and metadata structure
• ✅ FAISS index and retrieval dimensions
• ✅ Prompt template loading and placeholders
• ✅ SQLite logging functions

3. Mock GPT Calls

Use unittest.mock or pytest-monkeypatch to override:

• client.chat.completions.create
• client.embeddings.create

This ensures tests:

• Use no tokens
• Run offline
• Are suitable for CI/CD (e.g., GitHub Actions)

4. Add pytest to Dev Requirements

If not already present:

# environment.yaml or requirements-dev.txt
- pytest

5. Optional: Add CI Hook

Later, set up GitHub Actions to run tests on push or PR:

# .github/workflows/test.yml
runs-on: ubuntu-latest
steps:
  - uses: actions/checkout@v2
  - uses: conda-incubator/setup-miniconda@v2
    with:
      environment-file: environment.yaml
  - run: pytest tests/