PyTC Client

A desktop client that interacts with the pytorch_connectomics library for connectomics workflows.

This file only contains instructions on running the application. For a high-level description of the project structure, see project-structure.md.

Set-up

Install uv and node:

brew install uv node                    # macOS / Linux
winget install Astral.uv OpenJS.NodeJS  # Windows

Install dependencies:

scripts/bootstrap.sh      # macOS / Linux
scripts\bootstrap.ps1     # Windows

Re-run the relevant bootstrap script when you need to update dependencies.

The bootstrap scripts fetch the legacy-compatible PyTorch Connectomics runtime from pytc-client-legacy-runtime and verify commit 04c2a35e78a1a7ca1138f83a98fc3ef27097abd4 before installation. The generated pytorch_connectomics/ checkout is intentionally not tracked by this repository.

Run the app

scripts/start.sh          # macOS / Linux
scripts\start.ps1         # Windows

Optional runtime environment variables:

PYTC_AUTH_SECRET=replace-me
PYTC_ALLOWED_ORIGINS=http://localhost:3000,http://127.0.0.1:3000,null
PYTC_NEUROGLANCER_PUBLIC_BASE=http://localhost:4244
OLLAMA_MODEL=qwen3.6:27b
PYTC_WORKFLOW_INTENT_MODEL=qwen3.6:27b
OLLAMA_EMBED_MODEL=qwen3-embedding:8b
PYTC_UNLOAD_OLLAMA_BEFORE_TRAINING=0  # set to 1 only on memory-constrained GPUs

Chatbot Docs Index

The chatbot's FAISS index is generated locally from the markdown files in server_api/chatbot/file_summaries/ and should not be committed to git.

When you update those markdown docs, rebuild the generated index with:

uv run python server_api/chatbot/update_faiss.py

You can override the embeddings endpoint if needed:

OLLAMA_BASE_URL=http://cscigpu08.bc.edu:4443 uv run python server_api/chatbot/update_faiss.py

The local assistant and workflow intent classifier default to qwen3.6:27b with qwen3-embedding:8b, matching the bundled FAISS index settings. For experimental local model upgrades, see docs/research/on-device-llm-options-2026-04-26.md.

If restarting after a crash or interrupted session, kill any lingering processes first:

lsof -ti:8000 | xargs kill -9   # macOS / Linux

Before pushing changes

Format most code with prettier:

npm install
npx prettier --write .

Format python code with black:

uv run black .

Format shell scripts with shfmt (macOS / Linux):

brew install shfmt
shfmt -w .