Add build and push step to GH Actions

.github/workflows/build.yml

@@ -0,0 +1,44 @@
+name: Build image
+
+on:
+  push:
+    branches:
+      - 'master'
+    tags:
+      - 'v*'
+  pull_request:
+    branches:
+      - 'master'
+
+jobs:
+  build-and-push-docker-image:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/neuroscout/neuroscout
+
+      - name: Login to Github Packages
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build image and push to Docker Hub and GitHub Container Registry
+        uses: docker/build-push-action@v3
+        with:
+          context: ./neuroscout
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

README.md

@@ -29,10 +29,10 @@ For single sign on using Google, a [sign-in project](https://developers.google.c
 ## Initalizing backend
 Build the containers and start services using the development configuration:
 
-    docker-compose build
+    docker-compose -f docker-compose.yml -f docker-compose.dev.yml build
     docker-compose -f docker-compose.yml -f docker-compose.dev.yml up -d
 
-The server should now be running at http://localhost/
+The server should now be running at http://localhost/ 
 
 Next, initialize, migrate and upgrade the database migrations.
 If you have a database file, load it using `pg_restore`. Otherwise, delete the migrations folder,
@@ -45,6 +45,20 @@ initalize the database and add a test user.
     python manage.py db upgrade
     python manage.py add_user useremail password
 
+### Staging & production server
+
+For the staging server, you can trigger a manual build as follows:
+
+    docker-compose -f docker-compose.yml -f docker-compose.build.yml build
+    docker-compose -f docker-compose.yml -f docker-compose.build.yml up -d
+
+For the staging or production server, you can trigger pull a pre-built image from GHCR:
+First set the variable `IMAGE_TAG` to the apprioriate image tag
+
+    docker-compose -f docker-compose.yml -f docker-compose.image.yml build
+    docker-compose -f docker-compose.yml -f docker-compose.image.yml up -d
+
+
 ## Setting up front end
 The frontend dependencies are managed using `yarn`
 

docker-compose.build.yml

@@ -0,0 +1,4 @@
+version: "2"
+services:
+  neuroscout:
+    build: ./neuroscout

docker-compose.dev.yml

@@ -7,5 +7,6 @@ services:
   neuroscout:
     command: /usr/local/bin/gunicorn -w 2 -b :8000 neuroscout.core:app --log-level debug --timeout 120 --reload
     restart: "no"
+    build: ./neuroscout
     ports:
       - "4000:4000"

docker-compose.image.yml

@@ -0,0 +1,4 @@
+version: "2"
+services:
+  neuroscout:
+    image: ghcr.io/neuroscout/neuroscout:${IMAGE_TAG}

docker-compose.yml

@@ -1,8 +1,8 @@
 version: "2"
 services:
   neuroscout:
+    image: neuroscout_neuroscout
     restart: always
-    build: ./neuroscout
     expose:
       - "8000"
     volumes:

neuroscout/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.7-buster
+FROM python:3.8-bullseye
 ARG DEBIAN_FRONTEND=noninteractive
 
 RUN mkdir -p /usr/src/app
@@ -7,10 +7,12 @@ WORKDIR /usr/src/app
 RUN apt-get -qq update
 RUN apt-get install -yq ffmpeg tesseract-ocr apt-transport-https libnss3 xvfb
 RUN pip install -e git+https://github.com/PsychoinformaticsLab/pliers.git#egg=pliers
-RUN pip install clarifai duecredit google-api-python-client IndicoIo librosa>=0.6.3 pysrt pytesseract spacy rev_ai
+RUN pip install clarifai duecredit google-api-python-client librosa>=0.6.3 pysrt pytesseract spacy rev_ai
 
-RUN wget -O- http://neuro.debian.net/lists/buster.us-nh.libre | tee /etc/apt/sources.list.d/neurodebian.sources.list && apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
-RUN apt-get update && apt-get install -yq datalad && pip install datalad
+RUN wget -O- http://neuro.debian.net/lists/bullseye.us-tn.libre | tee /etc/apt/sources.list.d/neurodebian.sources.list 
+RUN apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
+RUN apt-get update
+RUN apt-get install -yq datalad-container
 
 RUN curl -sSL https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add -
 RUN echo "deb https://deb.nodesource.com/node_12.x buster main" | tee /etc/apt/sources.list.d/nodesource.list

neuroscout/populate/setup.py

@@ -10,7 +10,7 @@
 from .utils import add_to_bibliography
 from pathlib import Path
 from datalad.api import install, get
-from datalad.distribution.utils import _get_installationpath_from_url
+from datalad.core.distributed.clone import _get_installationpath_from_url
 from bids.layout import BIDSLayout
 from ..models import Dataset
 

neuroscout/requirements.txt

@@ -6,14 +6,14 @@ blinker==1.4
 celery
 citeproc-py==0.4.0
 citeproc-py-styles==0.1.1
-datalad==0.10.2
+datalad
 dataclasses==0.6
 decorator==4.0.11
 docopt==0.6.2
 duecredit==0.6.1
 -e git+https://github.com/adelavega/pybids@0.13.1-patch#egg=pybids
 pynv==0.2
-Flask==1.1.1
+Flask==1.1.4
 flask-apispec==0.10.0
 Flask-Caching==1.10.1
 Flask-cors==3.0.9
@@ -66,6 +66,7 @@ scipy
 sentry-sdk[flask]==0.13
 soundfile
 pytesseract
+werkzeug<2.0
 SQLAlchemy==1.3.0
 shortuuid==1.0.1
 webargs==6.1.1

postgres/Dockerfile

@@ -1,6 +1,6 @@
 FROM postgres:12
 RUN apt-get update && apt-get install -y dos2unix
-RUN apt-get install -yq python-pip python-dev build-essential
+RUN apt-get install -yq python3-pip python-dev build-essential
 RUN apt-get install -yq cron
 RUN pip install awscli
 COPY pg_dump-to-s3 /home