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simplify setup (./start.sh only script)
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‎README.md‎

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# pytc-client
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## Docker installation instructions
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## Quickstart (uv workflow)
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```bash
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# Pull the image (tag 0.0.1 -- subject to change in future versions)
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docker pull xbalbinus/pytc-client:0.0.1
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# Expose ports to run the backend servers on Docker
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docker run -it -p 4242:4242 -p 4243:4243 -p 4244:4244 -p 6006:6006 --shm-size=8g xbalbinus/pytc-client:0.0.1
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```
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**Prerequisites**
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- [git](https://git-scm.com/)
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- [uv](https://docs.astral.sh/uv/) (bundles Python and virtualenv management)
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- [Node.js](https://nodejs.org/) 18+ (includes npm)
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## Installation
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0. Create a Virtual Environment via. Conda
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Clone the repository and run the bootstrap script once to install everything (Python 3.11 environment, pytorch_connectomics checkout, npm packages):
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```bash
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conda create -n pytc python=3.9
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conda activate pytc
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conda install pytorch torchvision cudatoolkit=11.3 -c pytorch
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./scripts/bootstrap.sh # macOS / Linux
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scripts\bootstrap.ps1 # Windows (PowerShell)
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```
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Alternatively, dependencies can be installed with native Python via. the following:
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Launch the full stack (both FastAPI services + Electron client) with a single command:
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```bash
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# Create a venv
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python -m venv .venv
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# if running in windows, replace the line above with '.\.venv\Scripts\activate.bat'
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source .venv/bin/activate
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# Install dependencies
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pip install torch torchvision cuda-python
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./start.sh # macOS / Linux
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start.bat # Windows (CMD)
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```
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In the rare event that your device does not support CUDA, you may run the following respectively:
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```bash
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# If using a conda environment
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conda create -n pytc python=3.9
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conda activate pytc
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conda install pytorch torchvision
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# If installing via native python
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python -m venv .venv
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source .venv/bin/activate
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# if running in windows, replace the line above with '.\.venv\Scripts\activate.bat'
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pip install torch torchvision
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```
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1. Client
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```bash
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cd client
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npm install
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npm run build
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```
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2. API Server:
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```bash
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cd server_api
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pip install -r requirements.txt
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```
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The launcher keeps the API services running while Electron is open and cleans them up when you exit.
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3. Pytc-connectomics:
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## Alternate Setups
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In root folder,
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```bash
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# The setup script will automatically download pytorch_connectomics at commit 20ccfde (version 1.0)
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./setup_pytorch_connectomics.sh
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cd pytorch_connectomics
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pip install --editable .
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```
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Alternatively, you can run this manually:
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```bash
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git clone https://github.com/zudi-lin/pytorch_connectomics.git
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cd pytorch_connectomics
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git checkout 20ccfde
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pip install --editable .
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```
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## Run Project
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### To run
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```bash
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# if running on mac or linux:
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./start.sh
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# if running on windows:
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./start.bat
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```
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In a separate terminal
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```bash
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cd client
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npm run electron
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```
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- **Docker**: `docker pull xbalbinus/pytc-client:0.0.1` followed by `docker run -it -p 4242:4242 -p 4243:4243 -p 4244:4244 -p 6006:6006 --shm-size=8g xbalbinus/pytc-client:0.0.1`
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- **Manual Python environment**: still supported—create/activate your own virtualenv, run `pip install -r server_api/requirements.txt`, execute `setup_pytorch_connectomics.sh`, and install the package with `pip install -e pytorch_connectomics`.
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Below is a link to a video demo: showing how to set up and run the app:
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[video demo](https://www.loom.com/share/45c09b36bf37408fb3e5a9172e427deb?sid=2777bf8f-a705-4d47-b17a-adf882994168)
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## Video Demo
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[Video walkthrough](https://www.loom.com/share/45c09b36bf37408fb3e5a9172e427deb?sid=2777bf8f-a705-4d47-b17a-adf882994168)

‎pyproject.toml‎

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[project]
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name = "pytc-client"
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version = "0.1.0"
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description = "PyTC Client backend services"
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requires-python = ">=3.9,<3.12"
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dependencies = [
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"fastapi==0.119.0",
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"uvicorn==0.38.0",
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"python-multipart==0.0.20",
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"neuroglancer==2.38",
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"imageio==2.37.0",
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"tensorboard==2.20.0",
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"tensorboard-data-server==0.7.2",
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"psutil>=5.9.0",
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]

‎pytorch_connectomics‎

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Subproject commit 584129712da685d40b4c26ab9ca26f40802d7536
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Subproject commit 20ccfde6f85868351b00d7b795d4cf89a251d6be

‎scripts/bootstrap.ps1‎

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param()
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$ErrorActionPreference = 'Stop'
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$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Path
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$rootDir = Split-Path $scriptDir
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$clientDir = Join-Path $rootDir 'client'
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$pytcDir = Join-Path $rootDir 'pytorch_connectomics'
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function RequireCommand([string]$command, [string]$message) {
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if (-not (Get-Command $command -ErrorAction SilentlyContinue)) {
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Write-Error $message
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}
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}
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RequireCommand 'uv' 'uv is required. Install it from https://docs.astral.sh/uv/'
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RequireCommand 'npm' 'npm is required to install the Electron client.'
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RequireCommand 'git' 'git is required to download pytorch_connectomics.'
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Write-Host 'Synchronizing Python environment with uv...'
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uv sync --python 3.11 --directory $rootDir
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Write-Host 'Preparing pytorch_connectomics dependency...'
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if (Test-Path (Join-Path $pytcDir '.git')) {
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Push-Location $pytcDir
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git fetch origin *> $null
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$currentCommit = (git rev-parse HEAD) -replace '\s', ''
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$targetCommit = '20ccfde'
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if ($currentCommit -ne $targetCommit) {
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git checkout $targetCommit
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}
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Pop-Location
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} else {
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git clone 'https://github.com/zudi-lin/pytorch_connectomics.git' $pytcDir
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Push-Location $pytcDir
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git checkout '20ccfde'
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Pop-Location
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}
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Write-Host 'Installing pytorch_connectomics into the uv environment...'
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uv pip install --directory $rootDir --editable $pytcDir
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Write-Host 'Installing frontend dependencies...'
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Push-Location $clientDir
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npm install
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Pop-Location
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Write-Host 'Bootstrap complete. Use scripts\dev.ps1 or start.bat to launch the app.'

‎scripts/bootstrap.sh‎

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#!/usr/bin/env bash
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set -euo pipefail
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ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
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CLIENT_DIR="${ROOT_DIR}/client"
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if ! command -v uv >/dev/null 2>&1; then
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echo "uv is required. Install it from https://docs.astral.sh/uv/." >&2
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exit 1
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fi
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if ! command -v npm >/dev/null 2>&1; then
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echo "npm is required to install the Electron client." >&2
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exit 1
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fi
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echo "Synchronizing Python environment with uv..."
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uv sync --python 3.11 --directory "${ROOT_DIR}"
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echo "Preparing pytorch_connectomics dependency..."
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"${ROOT_DIR}/setup_pytorch_connectomics.sh"
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if [ -d "${ROOT_DIR}/pytorch_connectomics" ]; then
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echo "Installing pytorch_connectomics into the uv environment..."
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uv pip install --directory "${ROOT_DIR}" --editable "${ROOT_DIR}/pytorch_connectomics"
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fi
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echo "Installing frontend dependencies..."
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pushd "${CLIENT_DIR}" >/dev/null
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npm install
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popd >/dev/null
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echo "Bootstrap complete. Use ./scripts/dev.sh or ./start.sh to launch the app."

‎scripts/dev.ps1‎

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param()
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$ErrorActionPreference = 'Stop'
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$scriptDir = Split-Path -Parent $MyInvocation.MyCommand.Path
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$rootDir = Split-Path $scriptDir
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$clientDir = Join-Path $rootDir 'client'
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function RequireCommand([string]$command, [string]$message) {
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if (-not (Get-Command $command -ErrorAction SilentlyContinue)) {
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Write-Error $message
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}
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}
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RequireCommand 'uv' 'uv is required. Run scripts\bootstrap.ps1 first.'
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RequireCommand 'npm' 'npm is required to launch the Electron client.'
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Write-Host 'Starting API server...'
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$apiProcess = Start-Process uv -ArgumentList @('run','--directory', $rootDir, 'python', 'server_api/main.py') -NoNewWindow -PassThru
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Write-Host 'Starting PyTC server...'
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$pyProcess = Start-Process uv -ArgumentList @('run','--directory', $rootDir, 'python', 'server_pytc/main.py') -NoNewWindow -PassThru
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Push-Location $clientDir
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try {
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Write-Host 'Launching Electron client...'
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npm run electron
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} finally {
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Pop-Location
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if ($apiProcess -and -not $apiProcess.HasExited) {
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$apiProcess.Kill()
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}
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if ($pyProcess -and -not $pyProcess.HasExited) {
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$pyProcess.Kill()
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}
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}

‎scripts/dev.sh‎

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#!/usr/bin/env bash
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set -euo pipefail
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ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
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CLIENT_DIR="${ROOT_DIR}/client"
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if ! command -v uv >/dev/null 2>&1; then
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echo "uv is required. Run scripts/bootstrap.sh first." >&2
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exit 1
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fi
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if ! command -v npm >/dev/null 2>&1; then
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echo "npm is required to launch the Electron client." >&2
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exit 1
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fi
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cleanup() {
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local exit_code=$?
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if [[ -n "${API_PID:-}" ]] && ps -p "${API_PID}" >/dev/null 2>&1; then
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kill "${API_PID}" >/dev/null 2>&1 || true
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fi
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if [[ -n "${PYTC_PID:-}" ]] && ps -p "${PYTC_PID}" >/dev/null 2>&1; then
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kill "${PYTC_PID}" >/dev/null 2>&1 || true
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fi
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wait || true
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exit "${exit_code}"
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}
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trap cleanup EXIT INT TERM
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echo "Starting API server..."
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uv run --directory "${ROOT_DIR}" python server_api/main.py &
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API_PID=$!
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echo "Starting PyTC server..."
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uv run --directory "${ROOT_DIR}" python server_pytc/main.py &
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PYTC_PID=$!
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echo "Launching Electron client..."
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pushd "${CLIENT_DIR}" >/dev/null
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npm run electron
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popd >/dev/null

‎setup_pytorch_connectomics.sh‎

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#!/bin/bash
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#!/usr/bin/env bash
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# Setup script for pytorch_connectomics
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# Downloads the repository at commit 20ccfde (version 1.0)
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set -e
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set -euo pipefail
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PYTORCH_CONNECTOMICS_COMMIT="20ccfde"
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REPO_URL="https://github.com/zudi-lin/pytorch_connectomics.git"
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PYTORCH_CONNECTOMICS_DIR="pytorch_connectomics"
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echo "Setting up pytorch_connectomics at commit ${PYTORCH_CONNECTOMICS_COMMIT}"
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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cd "${SCRIPT_DIR}"
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# Remove existing directory if it exists
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if [ -d "${PYTORCH_CONNECTOMICS_DIR}" ]; then
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echo "Removing existing ${PYTORCH_CONNECTOMICS_DIR} directory"
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rm -rf "${PYTORCH_CONNECTOMICS_DIR}"
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if ! command -v git >/dev/null 2>&1; then
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echo "git is required to download pytorch_connectomics." >&2
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exit 1
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fi
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# Clone the repository
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echo "Cloning pytorch_connectomics repository..."
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git clone "${REPO_URL}" "${PYTORCH_CONNECTOMICS_DIR}"
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FORCE_REFRESH=0
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while [[ $# -gt 0 ]]; do
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case "$1" in
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--force)
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FORCE_REFRESH=1
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shift
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;;
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*)
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echo "Unknown argument: $1" >&2
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exit 1
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;;
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esac
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done
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# Change to the directory and checkout the specific commit
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cd "${PYTORCH_CONNECTOMICS_DIR}"
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echo "Checking out commit ${PYTORCH_CONNECTOMICS_COMMIT}..."
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git checkout "${PYTORCH_CONNECTOMICS_COMMIT}"
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echo "Ensuring pytorch_connectomics is available at commit ${PYTORCH_CONNECTOMICS_COMMIT}"
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# Return to parent directory
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cd ..
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if [ -d "${PYTORCH_CONNECTOMICS_DIR}/.git" ]; then
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echo "Existing pytorch_connectomics checkout detected."
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pushd "${PYTORCH_CONNECTOMICS_DIR}" >/dev/null
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echo "pytorch_connectomics setup complete!"
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echo "To install, run: cd ${PYTORCH_CONNECTOMICS_DIR} && pip install --editable ."
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if [ "${FORCE_REFRESH}" -eq 1 ]; then
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echo "Force refreshing repository..."
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git fetch origin
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git reset --hard "${PYTORCH_CONNECTOMICS_COMMIT}"
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else
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git fetch origin >/dev/null 2>&1 || true
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CURRENT_COMMIT="$(git rev-parse HEAD 2>/dev/null || echo "")"
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if [ "${CURRENT_COMMIT}" != "${PYTORCH_CONNECTOMICS_COMMIT}" ]; then
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echo "Checking out required commit ${PYTORCH_CONNECTOMICS_COMMIT}..."
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git checkout "${PYTORCH_CONNECTOMICS_COMMIT}"
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else
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echo "Repository already at required commit."
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fi
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fi
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popd >/dev/null
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else
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echo "Cloning pytorch_connectomics repository..."
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git clone "${REPO_URL}" "${PYTORCH_CONNECTOMICS_DIR}"
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pushd "${PYTORCH_CONNECTOMICS_DIR}" >/dev/null
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echo "Checking out commit ${PYTORCH_CONNECTOMICS_COMMIT}..."
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git checkout "${PYTORCH_CONNECTOMICS_COMMIT}"
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popd >/dev/null
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fi
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echo "pytorch_connectomics setup complete."
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echo "To install manually, run: pip install --editable ${PYTORCH_CONNECTOMICS_DIR}"

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