[FIX] Make pipeline-catalog submodule available to built Docker ima…

…ge (#373)

* check out submodules before building Docker image
- CLI functionality now depends on a submodule (pipeline-catalog)

* expand ignore patterns in .dockerignore
- only copy required files into Docker image

.dockerignore

@@ -13,20 +13,31 @@ bagelbids.egg-info
 .eggs/**/*
 .eggs
 
+.editorconfig
 **/.git
+**/.github
 **/.gitignore
 **/.vscode
 **/coverage
 **/.env
 **/.aws
 **/.ssh
-Dockerfile
-README.md
-docker-compose.yml
 **/.DS_Store
 **/venv
 **/env
+Dockerfile
 
-bids-examples
+# other configuration files and scripts
+.autorc
+.pre-commit-config.yaml
+generate_nb_vocab_file.py
 
+# documentation
+CHANGELOG.md
+CITATION.cff
+LICENSE
+README.md
 
+# submodules used for testing
+bids-examples
+neurobagel_examples

.github/workflows/build_docker_nightly.yml

@@ -12,6 +12,8 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Login to Docker Hub
         uses: docker/login-action@v3

.github/workflows/build_docker_on_release.yml

@@ -11,6 +11,8 @@ jobs:
       -
         name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
       - 
         # The release event is a superset of the push tag event, 
         # so we expect two tags to be generated by docker/metadata-action 

Dockerfile

@@ -3,6 +3,7 @@ FROM python:3.10-slim-buster
 
 WORKDIR /app
 COPY . /app/src
+
 # To have a deterministic build, we
 # 1. install the environment from our lockfile
 RUN pip install -r /app/src/requirements.txt