Merge pull request #7 from opensafely-core/initial-setup

Initial setup

.github/workflows/main.yml

@@ -1,40 +1,74 @@
 ---
 name: CI
 
+env:
+  IMAGE_NAME: research-template
+  PUBLIC_IMAGE_NAME: ghcr.io/opensafely/research-template
+  REGISTRY: ghcr.io
+
 on:
+  workflow_dispatch:
+  pull_request:
   push:
+    branches: [main]
 
 jobs:
-  check:
+  build-and-test:
     runs-on: ubuntu-latest
-
     steps:
       - uses: actions/checkout@v4
+      - uses: hadolint/hadolint-action@54c9adbab1582c2ef04b2016b760714a4bfde3cf  # v3.1.0
+        # Lint the dockerfile before building
+        with:
+          failure-threshold: error
       - uses: "opensafely-core/setup-action@v1"
         with:
-          python-version: "3.11"
           install-just: true
-      - name: Check formatting, linting and import sorting
-        run: just check
 
-  test:
-    runs-on: ubuntu-latest
+      - name: Build docker image
+        run: just build
+
+      - name: Test docker image
+        run: just smoke-test
+
+      - name: Save docker image
+        run: |
+          docker save research-template | gzip > /tmp/research-template.tar.gz
+
+      - name: Upload docker image
+        uses: actions/upload-artifact@v4
+        with:
+            name: research-template-image
+            path: /tmp/research-template.tar.gz
+
+  publish:
+    needs: [build]
+
+    runs-on: ubuntu-22.04
+
+    permissions:
+      contents: read
+      packages: write
+
+    if: github.ref == 'refs/heads/main'
 
     steps:
       - uses: actions/checkout@v4
       - uses: "opensafely-core/setup-action@v1"
         with:
-          python-version: "3.11"
           install-just: true
-      - name: Run tests
-#       env:  # Add environment variables required for tests
-        run: |
-          just test
 
-  lint-dockerfile:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: hadolint/hadolint-action@54c9adbab1582c2ef04b2016b760714a4bfde3cf  # v3.1.0
+      - name: Download docker image
+        uses: actions/download-artifact@v4
         with:
-          failure-threshold: error
+            name: research-template-image
+            path: /tmp/image
+
+      - name: Import docker image
+        run: gunzip -c /tmp/image/research-template.tar.gz | docker load
+
+      - name: Publish image
+        run: |
+            echo ${{ secrets.GITHUB_TOKEN }} | docker login $REGISTRY -u ${{ github.actor }} --password-stdin
+            docker tag $IMAGE_NAME $PUBLIC_IMAGE_NAME:latest
+            docker push $PUBLIC_IMAGE_NAME:latest

DEVELOPERS.md

@@ -18,17 +18,6 @@ source <(just --completions bash)
 just #  shortcut for just --list
 ```
 
+## Build instructions
 
-## Local development environment
-
-
-Set up a local development environment with:
-```
-just dev_setup
-```
-
-## Tests
-Run the tests with:
-```
-just test <args>
-```
+Run `just build` to build the Docker image.

Dockerfile

@@ -1,3 +1,51 @@
-# All Dockerfiles should start from this base image
-# Provide the TAG environment variable, or replace with the image version required
-FROM ghcr.io/opensafely-core/base-docker:$TAG
+FROM rocker/rstudio:4.0.5
+
+LABEL org.opencontainers.image.source https://github.com/opensafely/research-template
+
+# we are going to use an apt cache on the host, so disable the default debian
+# docker clean up that deletes that cache on every apt install
+RUN rm -f /etc/apt/apt.conf.d/docker-clean
+
+# Install python 3.10. This is the version used by the python-docker 
+# image, used for analyses using the OpenSAFELY pipeline.
+#
+# DL3042: we always want latest package versions when we rebuild
+# DL3013: using an apt cache on the host instead
+# hadolint ignore=DL3042,DL3013
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+RUN --mount=type=cache,target=/var/cache/apt \
+    echo "deb http://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu focal main" > /etc/apt/sources.list.d/deadsnakes-ppa.list &&\
+    /usr/lib/apt/apt-helper download-file 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xf23c5a6cf475977595c89f51ba6932366a755776' /etc/apt/trusted.gpg.d/deadsnakes.asc &&\
+    apt-get update &&\
+    apt-get install -y --no-install-recommends curl python3.10 python3.10-distutils python3.10-venv &&\
+    # Pip for Python 3.10 isn't included in deadsnakes, so install separately
+    curl https://bootstrap.pypa.io/get-pip.py | python3.10 &&\
+    # Set default python, so that the Python virtualenv works as expected
+    rm /usr/bin/python3 &&\
+    ln -s /usr/bin/python3.10 /usr/bin/python3
+
+# install renv
+RUN --mount=type=cache,target=/cache,id=/cache-2004 R -e 'install.packages("renv", destdir="/cache"); renv::init(bare = TRUE)'
+
+# copy the renv directory from the OpenSAFELY R action image
+#
+# DL3022: hadolint can't access a network and doesn't behave
+# as expected when a reference is made to an external image.
+# hadolint ignore=DL3022
+COPY --from=ghcr.io/opensafely-core/r /renv/ /renv/
+
+# Copy the Python virtualenv from OpenSAFELY Python action image
+#
+# DL3022: hadolint can't access a network and doesn't behave
+# as expected when a reference is made to an external image.
+# hadolint ignore=DL3022
+COPY --from=ghcr.io/opensafely-core/python:v2 /opt/venv /opt/venv
+
+# Create a local user and give it sudo (aka root) permissions
+RUN usermod -aG sudo rstudio &&\
+    echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+
+# Required for installing opensafely cli
+ENV PATH="/home/rstudio/.local/bin:${PATH}"
+
+USER rstudio

README.md

@@ -1,28 +1,6 @@
-# research-template-docker
-
-This is a template for an OpenSAFELY Core repository.
-
-Put your project description here.
-
-New repo checklist:
-- [ ] Does the repo require a Dockerfile?
-  If not, delete:
-  - Dockerfile -
-  - .dockerignore
-  - hadolint pre-commit hook from `.pre-commit-config.yaml`
-  - `lint-dockerfile` action from `.github/workflows/main.yml`
-- [ ] Is this a Django project?
-  If so, you probably need to add the following per-file ignores to `.flake8`
-  ```
-  per-file-ignores =
-    manage.py:INP001
-    gunicorn.conf.py:INP001
-  ```
-- [ ] Will this project be installed with pip?
-  If so, delete `requirements.prod.in` and switch references in the `justfile` to `pyproject.toml`
-- [ ] Update DEVELOPERS.md with any project-specific requirements and commands
-- [ ] Update commands in `justfile`
+# Research Template Docker
 
+This provides the devcontainer Docker image used by repos created from the OpenSAFELY [research template](https://github.com/opensafely/research-template).
 
 ## Developer docs
 

docs/adr/0000-record-architecture-decisions.md

@@ -0,0 +1,19 @@
+# 0. Record architecture decisions
+
+Date: 2024-04-29
+
+## Status
+
+Accepted
+
+## Context
+
+We need to record the architectural decisions made on this project.
+
+## Decision
+
+We will use Architecture Decision Records, as [described by Michael Nygard](http://thinkrelevance.com/blog/2011/11/15/documenting-architecture-decisions).
+
+## Consequences
+
+See Michael Nygard's article, linked above. For a lightweight ADR toolset, see Nat Pryce's [adr-tools](https://github.com/npryce/adr-tools).