[CI] Add Dockerfile and workflow to push to DockerHub (#150)

* add Dockerfile and wf for pushing to DockerHub

* add parent directory in Dockerfile to mount pre-loaded digest data

* update README

* fix sneaky typo detected by codespell

.github/workflows/build_docker.yml

@@ -0,0 +1,31 @@
+name: Build and push image to DockerHub
+
+on:
+  push:
+    branches:
+      - "main"
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ secrets.DOCKERHUB_USERNAME }}/digest:nightly

Dockerfile

@@ -0,0 +1,15 @@
+FROM python:3.10
+
+# Create parent directory to have a place to mount pre-loaded digest files (currently the nipoppy-qpn repo)
+# TODO: Revisit this with longer-term solution to handle available digests (e.g., QPN as submodule?)
+WORKDIR /app/code
+
+COPY ./requirements.txt /app/code/requirements.txt
+
+RUN pip install --upgrade pip
+RUN pip install --no-cache-dir --upgrade -r /app/code/requirements.txt
+
+COPY ./digest /app/code/digest
+COPY ./schemas /app/code/schemas
+
+CMD ["gunicorn", "digest.app:server", "-b", "0.0.0.0:8050", "--workers", "4", "--threads", "2"]

README.md

@@ -38,6 +38,25 @@ In brief, generating a `bagel.csv` for your dataset can be as simple as:
     - To see help text for this script: `python run_tracker.py --help`
     - This step can be repeated as needed to update the `bagel.csv` with newly processed subjects
 
+## Running in a Docker container
+
+1. To get the most recent changes, pull the `neurobagel/digest` docker image tagged `nightly`:
+```bash
+docker pull neurobagel/digest:nightly
+```
+
+2. Currently, `digest` also relies on a local copy of the [`nipoppy-qpn`](https://github.com/neurodatascience/nipoppy-qpn) repository, which contains ready-to-use `digest` files that are automatically generated for the Quebec Parkinson Network data.
+```
+git clone https://github.com/neurodatascience/nipoppy-qpn.git
+```
+
+3. Run `digest` and mount the `nipoppy-qpn` directory into the container:
+```bash
+docker run -d -p 8050:8050 -v ${PWD}/nipoppy-qpn:/app/nipoppy-qpn neurobagel/digest:nightly
+```
+
+Now, the dashboard can be accessed at http://127.0.0.1:8050 on your local machine.
+
 ## Local development
 To install `digest` from the source repository, run the following in a Python environment:
 ```bash

digest/app.py

@@ -59,7 +59,7 @@ def toggle_dataset_name_dialog(
             return not dialog_is_open, DEFAULT_DATASET_NAME, None
 
         # If the user loaded a preset file, do not open the dataset name modal, and get the name of the dataset
-        # from the preset dataset dictionary insteaad, based on the matching filename.
+        # from the preset dataset dictionary instead, based on the matching filename.
         for available_dataset in util.PUBLIC_DIGEST_FILE_PATHS.values():
             relevant_digest_path = available_dataset.get(
                 parsed_data.get("type")