Merge pull request #2 from andreped/demo

Added workflows, shell scripts, and README

.github/workflows/deploy.yml

@@ -0,0 +1,20 @@
+name: Deploy
+on:
+  push:
+    branches: [ main ]
+
+  # to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  sync-to-hub:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          lfs: true
+      - name: Push to hub
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: git push https://andreped:[email protected]/spaces/andreped/LyNoS main

.github/workflows/filesize.yml

@@ -0,0 +1,16 @@
+name: Check file size
+on:               # or directly `on: [push]` to run the action on every push on any branch
+  pull_request:
+    branches: [ main ]
+
+  # to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  check-filesize:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check large files
+        uses: ActionsDesk/[email protected]
+        with:
+          filesizelimit: 10485760 # this is 10MB so we can sync to HF Spaces

.github/workflows/linting.yml

@@ -0,0 +1,26 @@
+name: Linting
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      
+      - name: Install lint dependencies
+        run: pip install wheel setuptools black==22.3.0 isort==5.10.1 flake8==4.0.1
+
+      - name: Lint the code
+        run: sh shell/lint.sh

README.md

@@ -1 +1,24 @@
-# LyNoS
+---
+title: 'AeroPath: automatic airway segmentation using deep learning'
+colorFrom: indigo
+colorTo: indigo
+sdk: docker
+app_port: 7860
+emoji: 🫁
+pinned: false
+license: mit
+app_file: demo/app.py
+---
+
+<div align="center">
+<h1 align="center">🫁 LyNoS 🤗</h1>
+<h3 align="center">A lymph node segmentation benchmark from contrast CT</h3>
+
+[![license](https://img.shields.io/github/license/DAVFoundation/captain-n3m0.svg?style=flat-square)](https://github.com/raidionics/LyNoS/blob/main/LICENSE.md)
+[![CI/CD](https://github.com/raidionics/LyNoS/actions/workflows/deploy.yml/badge.svg)](https://github.com/raidionics/LyNoS/actions/workflows/deploy.yml)
+<a target="_blank" href="https://huggingface.co/spaces/andreped/LyNoS"><img src="https://img.shields.io/badge/🤗%20Hugging%20Face-Spaces-yellow.svg"></a>
+[![paper](https://img.shields.io/badge/arXiv-preprint-D12424)](https://arxiv.org/abs/2311.01138)
+
+**LyNoS** was developed by SINTEF Medical Image Analysis to accelerate medical AI research.
+
+</div>

shell/format.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+isort --sl demo/src/ demo/app.py
+black --line-length 160 demo/src/ demo/app.py
+flake8 demo/src/ demo/app.py

shell/lint.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+isort --check --sl -c demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please run \"sh shell/format.sh\" to format the code."
+  exit 1
+fi
+echo "no issues with isort"
+flake8 demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please fix the code style issue."
+  exit 1
+fi
+echo "no issues with flake8"
+black --check --line-length 160 demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please run \"sh shell/format.sh\" to format the code."
+    exit 1
+fi
+echo "no issues with black"
+echo "linting success!"