Skip to content

README_SETUP.md

Latest commit

 

History

History
40 lines (33 loc) · 1.95 KB

README_SETUP.md

File metadata and controls

40 lines (33 loc) · 1.95 KB

Setup Guide

Use this checklist when provisioning an environment for the Tri-Channel OECT molecular communication simulator.

Requirements

  • Python 3.11 or newer
  • Recent pip, wheel, and setuptools
  • C/C++ build tools supplied by your OS package manager (SciPy wheels cover common platforms, but keeping compilers available helps with niche dependencies)

Standard Installation

python -m venv .venv
source .venv/bin/activate              # Windows PowerShell: .\.venv\Scripts\Activate.ps1
python -m pip install -U pip wheel setuptools
pip install -e ".[dev]"
python setup_project.py

setup_project.py validates the core Python packages and creates the expected results/ subdirectories. Re-run it anytime; use --reset cache or --reset all to clear cached data.

Guided Environment Creation

setup_env.py bootstraps a dedicated virtual environment and installs the manifests shipped with the repository:

# Latest versions from requirements.in + optional extras + editable install
python setup_env.py --extras dev --editable

# Frozen snapshot defined in requirements.latest.txt
python setup_env.py --use-freeze --editable

Supply --env <path> to customize the virtual environment location.

Post-Install Smoke Test

python analysis/run_final_analysis.py --mode CSK --num-seeds 4 --sequence-length 200 --recalibrate --resume --progress tqdm

Expect the run to create results/cache/, emit progress via tqdm, and write a log file under results/logs/.

Troubleshooting

  • Confirm python --version reports 3.11.x. Earlier interpreters lack ABI support for SciPy 1.16 and NumPy 2.x.
  • On macOS and Linux, ensure OPENBLAS_NUM_THREADS, MKL_NUM_THREADS, and related environment variables are set to one when running large Monte Carlo batches (the analysis scripts enforce this by default).
  • If pip cannot fetch wheels for SciPy or NumPy, upgrade pip first; fall back to conda (environment.yml) if your platform is exotic.