Add basic build/tests

This is taken directly from python-docker tests

We also synchronise the packages between them

.github/workflows/publish_docker.yaml

@@ -1,37 +1,19 @@
-name: Tag repo; build and publish assets
+name: Build and publish
 on:
   push:
-    branches:
-      - master
-  workflow_dispatch:
+    branches: [main]
 env:
   IMAGE_NAME: jupyter
 jobs:
-  tag-new-version:
-    runs-on: ubuntu-latest
-    outputs:
-      tag: ${{ steps.tag.outputs.new_version }}
-    steps:
-      - uses: actions/checkout@master
-        with:
-          fetch-depth: 0
-      - name: Bump version and push tag
-        id: tag
-        uses: mathieudutour/[email protected]
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          default_bump: false
-
-  build-and-publish-docker-image:
-    runs-on: ubuntu-latest
-    name: Build and publish docker image
-    needs: tag-new-version
-    if: needs.tag-new-version.outputs.tag
+  build:
+    runs-on: ubuntu-20.04
     steps:
     - name: Checkout
-      uses: actions/checkout@v1
+      uses: actions/checkout@master
     - name: Build image
-      run: docker build . --file Dockerfile --tag $IMAGE_NAME
+      run: make build
+    - name: Run tests
+      run: make test
     - name: Log into GitHub Container Registry
       run: docker login https://ghcr.io -u ${{ github.actor }} --password ${{ secrets.DOCKER_RW_TOKEN }}
     - name: Push image to GitHub Container Registry

.github/workflows/tests.yaml

@@ -0,0 +1,15 @@
+name: Run tests
+on:
+  pull_request:
+env:
+  IMAGE_NAME: jupyter
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+    - name: Checkout
+      uses: actions/checkout@master
+    - name: Build image
+      run: make build
+    - name: Run tests
+      run: make test

.gitignore

@@ -1 +1,3 @@
-*~
+*~
+__pycache__
+.venv

Makefile

@@ -1,3 +1,32 @@
+IMAGE_NAME ?= docker-jupyter-test
+INTERACTIVE:=$(shell [ -t 0 ] && echo 1)
+export DOCKER_BUILDKIT=1
+
+.PHONY: build
+build: BUILD_DATE=$(shell date +'%y-%m-%dT%H:%M:%S.%3NZ')
+build: GITREF=$(shell git rev-parse --short HEAD)
+build:
+	docker build . --tag $(IMAGE_NAME) --progress=plain \
+		--build-arg BUILDKIT_INLINE_CACHE=1 --cache-from ghcr.io/opensafely-core/jupyter \
+		--build-arg BUILD_DATE=$(BUILD_DATE) --build-arg GITREF=$(GITREF)
+
+
+.PHONY: test
+ifdef INTERACTIVE
+test: RUN_ARGS=-it
+else
+test: RUN_ARGS=
+endif
+test:
+	docker run $(RUN_ARGS) --rm -v $(PWD):/tests -w /tests $(IMAGE_NAME) pytest tests -v
+
+
+.PHONY: lint
+lint:
+	@docker pull hadolint/hadolint
+	@docker run --rm -i hadolint/hadolint < Dockerfile
+
+
 
 requirements.txt: requirements.in .venv/bin/pip-compile
 	.venv/bin/pip-compile requirements.in

requirements.in

@@ -6,14 +6,22 @@ jupyterlab
 jupytext
 bash_kernel
 nbval
+opensafely-matching
 
 # Commonly-used packages provided in base docker image
 pandas-gbq
 pandas
 numpy
 ebmdatalab
 matplotlib
+scipy
 tqdm
+numba
+opensafely-cohort-extractor
+pyarrow
+venn
+kaleido
+scikit-learn
 
 # Both these required for plotly+notebooks
 plotly
@@ -23,5 +31,11 @@ ipywidgets
 py-spy
 
 # Add extra per-notebook packages here
-pyodbc
 pillow
+
+# Allow for projects to run tests inside the container
+pytest
+
+
+# interactive use on level 3
+pyodbc