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Module 2: Environment Setup and Sanity Checks

  • Objectives
    • Install/activate Mneme in a virtual environment
    • Verify core and optional dependencies
    • Run smoke tests on your machine
  • Time: 30–45 minutes

2.1 Install and activate

# From repo root
source venv/bin/activate
pip install -e .
# Optional dev tools
pip install -r requirements-dev.txt

2.2 Verify toolchain

mneme info

Check:

  • Python, NumPy, CUDA availability
  • Optional deps: gudhi, pysr, h5py, scipy, sklearn
  • Default topology backend (from config if provided)

2.3 Smoke tests

python -c "import mneme; print('OK')"
pytest -q  # optional dev

2.4 GPU optionality

  • GPU not required for MVP. Neural-field reconstructor is a placeholder; keep CPU for now.

Exercises

  1. Change verbosity: run mneme info -v and note any differences in logging
  2. Optional: install GUDHI if missing; confirm cubical backend will be used
  3. Optional: install PySR; run mneme info and confirm Julia availability status

Solutions (outline)

  • mneme info reports optional deps and default backend; with -v, console logging is verbose
  • With GUDHI installed, cubical/Rips/Alpha backends are available
  • PySR shows ✓; Julia may install lazily on first use