MALA for multiple elements #1183
Workflow file for this run
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name: CPU tests | |
on: | |
workflow_dispatch: | |
pull_request: | |
# Trigger on pull requests to master or develop that are | |
# marked as "ready for review" (non-draft PRs) | |
types: | |
- opened | |
- synchronize | |
- reopened | |
- ready_for_review | |
branches: | |
- master | |
- develop | |
push: | |
# Trigger on pushes to master or develop and for git tag pushes | |
branches: | |
- master | |
- develop | |
tags: | |
- v* | |
env: | |
IMAGE_NAME: mala_conda_cpu | |
IMAGE_REGISTRY: ghcr.io | |
DOCKER_CACHE_PATH: cache/docker | |
jobs: | |
build-docker-image-cpu: | |
# do not trigger on draft PRs | |
if: ${{ ! github.event.pull_request.draft }} | |
# Build and push temporary Docker image to GitHub's container registry | |
runs-on: ubuntu-22.04 | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: '1' | |
- name: Set environment variables | |
run: | | |
# Change all uppercase letters to lowercase | |
IMAGE_REPO=$IMAGE_REGISTRY/$(echo $GITHUB_REPOSITORY_OWNER | tr '[A-Z]' '[a-z]') | |
# Create environment variable to which any subsequent steps inside this workflow's job have access | |
echo "IMAGE_REPO=$IMAGE_REPO" >> $GITHUB_ENV | |
echo "IMAGE_REPO=$IMAGE_REPO" | |
- name: Restore cache | |
uses: actions/cache@v4 | |
id: cache-docker | |
with: | |
path: ${{ env.DOCKER_CACHE_PATH }} | |
key: ${{ github.run_id }} | |
- name: Check existence of Docker tar archive | |
id: check_file | |
run: | | |
if [[ -f "$DOCKER_CACHE_PATH/docker-image.tar.gz" ]]; then | |
echo "FILE_EXISTS=true" >> $GITHUB_OUTPUT | |
else | |
echo "FILE_EXISTS=false" >> $GITHUB_OUTPUT | |
fi | |
- name: Pull latest image from container registry | |
run: docker pull $IMAGE_REPO/$IMAGE_NAME --quiet || true | |
- name: Build temporary Docker image | |
run: | | |
if [[ "${{ steps.check_file.outputs.FILE_EXISTS }}" == 'true' ]] | |
then | |
docker load -i $DOCKER_CACHE_PATH/docker-image.tar.gz | |
CACHE=$IMAGE_NAME:$GITHUB_RUN_ID | |
else | |
CACHE=$IMAGE_REPO/$IMAGE_NAME:latest | |
fi | |
DOCKER_BUILDKIT=0 docker build . --file Dockerfile --tag $IMAGE_NAME:local --cache-from=$CACHE --build-arg DEVICE=cpu | |
# Show images | |
docker images --filter=reference=$IMAGE_NAME --filter=reference=$IMAGE_REPO/$IMAGE_NAME | |
# Get image IDs (hash of the local image JSON configuration) and check if images are equal | |
IMAGE_ID_OLD=$(docker images --format "{{.ID}}" --no-trunc --filter=reference=$IMAGE_REPO/$IMAGE_NAME:latest) | |
IMAGE_ID_NEW=$(docker images --format "{{.ID}}" --no-trunc --filter=reference=$IMAGE_NAME:local) | |
echo "IMAGE_ID_OLD=$IMAGE_ID_OLD" >> $GITHUB_ENV | |
echo "IMAGE_ID_NEW=$IMAGE_ID_NEW" >> $GITHUB_ENV | |
if [[ "$IMAGE_ID_OLD" == "$IMAGE_ID_NEW" ]] | |
then | |
echo "Image IDs are equal"; DOCKER_TAG=latest | |
else | |
echo "Image IDs are different"; DOCKER_TAG=$GITHUB_RUN_ID | |
fi | |
# Environment variable DOCKER_TAG references the image in subsequent jobs | |
echo "DOCKER_TAG=$DOCKER_TAG" >> $GITHUB_ENV | |
- name: Tag and save temporary built Docker image | |
# If temporary image is different from latest on ghcr.io | |
if: env.IMAGE_ID_OLD != env.IMAGE_ID_NEW | |
run: | | |
mkdir -p $DOCKER_CACHE_PATH | |
# Use GITHUB_RUN_ID, a unique number for each workflow run within a repository as a temporary Docker tag | |
docker tag $IMAGE_NAME:local $IMAGE_NAME:$GITHUB_RUN_ID | |
# Save Docker image locally | |
docker save $IMAGE_NAME:$GITHUB_RUN_ID -o $DOCKER_CACHE_PATH/docker-image.tar | |
pigz -f -v --fast $DOCKER_CACHE_PATH/docker-image.tar | |
outputs: | |
# Make variables available to all downstream jobs that depend on this job | |
image-repo: ${{ env.IMAGE_REPO }} | |
docker-tag: ${{ env.DOCKER_TAG }} | |
cpu-tests: | |
needs: build-docker-image-cpu | |
runs-on: ubuntu-20.04 | |
env: | |
IMAGE_REPO: ${{ needs.build-docker-image-cpu.outputs.image-repo }} | |
DOCKER_TAG: ${{ needs.build-docker-image-cpu.outputs.docker-tag }} | |
steps: | |
- name: "Prepare environment: Restore cache" | |
if: env.DOCKER_TAG != 'latest' | |
uses: actions/cache@v4 | |
id: cache-docker | |
with: | |
path: ${{ env.DOCKER_CACHE_PATH }} | |
key: ${{ github.run_id }} | |
- name: "Prepare environment: Load Docker image from cache" | |
if: env.DOCKER_TAG != 'latest' | |
run: docker load -i $DOCKER_CACHE_PATH/docker-image.tar.gz --quiet | |
- name: "Prepare environment: Pull latest image from container registry" | |
if: env.DOCKER_TAG == 'latest' | |
run: | | |
docker pull $IMAGE_REPO/$IMAGE_NAME:latest --quiet | |
docker image tag $IMAGE_REPO/$IMAGE_NAME:latest $IMAGE_NAME:latest | |
- name: "Prepare environment: Run Docker container" | |
run: | | |
# Make the github workspace (i.e. checked out mala repository) available inside Docker container by binding it to /home via -v | |
docker run -i -d --rm --name mala-cpu -v ${{ github.workspace }}:/home -w /home $IMAGE_NAME:$DOCKER_TAG /bin/bash & | |
# Wait for Docker container to come online | |
wait | |
# Check running docker container | |
docker ps | |
# Check if docker container is running | |
[[ $(docker inspect --format '{{json .State.Running}}' mala-cpu) == 'true' ]] | |
- name: Check out repository (mala) | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: '1' | |
- name: Install mala package | |
# Exec all commands inside the mala-cpu container | |
shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' | |
run: | | |
# export Docker image Conda environment for a later comparison | |
conda env export -n mala-cpu > env_before.yml | |
# install mala package | |
pip --no-cache-dir install -e .[opt,test] --no-build-isolation | |
- name: Check if Conda environment meets the specified requirements | |
shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' | |
run: | | |
# export Conda environment _with_ mala package installed in it (and extra dependencies) | |
conda env export -n mala-cpu > env_after.yml | |
# This command is necessary because conda includes even editable | |
# packages in an export, at least in the versions we recently used. | |
# That of course leads to the diff failing, since MALA can never | |
# be there before it has been installed. | |
sed -i '/materials-learning-algorithms/d' ./env_after.yml | |
# if comparison fails, `install/mala_cpu_[base]_environment.yml` needs to be aligned with | |
# `requirements.txt` and/or extra dependencies are missing in the Docker Conda environment | |
if diff --brief env_before.yml env_after.yml | |
then | |
echo "Files env_before.yml and env_after.yml do not differ." | |
else | |
diff --side-by-side env_before.yml env_after.yml | |
fi | |
- name: Download test data repository from RODARE | |
shell: 'bash -c "docker exec -i mala-cpu python < {0}"' | |
run: | | |
import requests, shutil, zipfile | |
# This DOI represents all versions, and will always resolve to the latest one | |
DOI = "https://doi.org/10.14278/rodare.2900" | |
# Resolve DOI and get record ID and the associated API URL | |
response = requests.get(DOI) | |
*_, record_id = response.url.split("/") | |
api_url = f"https://rodare.hzdr.de/api/records/{record_id}" | |
# Download record from API and get the first file | |
response = requests.get(api_url) | |
record = response.json() | |
size = record["files"][0]["size"] | |
download_link = record["files"][0]["links"]["self"] | |
print(size, "bytes", "--", download_link) | |
# TODO: implement some sort of auto retry for failed HTTP requests | |
response = requests.get(download_link) | |
# Saving downloaded content to a file | |
with open("test-data.zip", mode="wb") as file: | |
file.write(response.content) | |
# Get top level directory name | |
dir_name = zipfile.ZipFile("test-data.zip").namelist()[0] | |
shutil.unpack_archive("test-data.zip", ".") | |
print(f"Rename {dir_name} to mala_data") | |
shutil.move(dir_name, "mala_data") | |
- name: Test mala | |
shell: 'bash -c "docker exec -i mala-cpu bash < {0}"' | |
run: MALA_DATA_REPO=$(pwd)/mala_data pytest --cov=mala --cov-fail-under=60 -m "not examples" --disable-warnings | |
retag-docker-image-cpu: | |
needs: [cpu-tests, build-docker-image-cpu] | |
runs-on: ubuntu-22.04 | |
permissions: | |
packages: write | |
env: | |
IMAGE_REPO: ${{ needs.build-docker-image-cpu.outputs.image-repo }} | |
DOCKER_TAG: ${{ needs.build-docker-image-cpu.outputs.docker-tag }} | |
# Trigger on pushes to master or develop (this includes _merged_ PRs) only if Docker image has changed and on git tag pushes | |
# NOTE: The `env` context is not available for workflow key `jobs.<job_id>.if`. | |
if: | | |
((contains(github.ref_name, 'develop') || contains(github.ref_name, 'master')) && needs.build-docker-image-cpu.outputs.docker-tag != 'latest') | |
|| startsWith(github.ref, 'refs/tags/') | |
steps: | |
- name: "Prepare environment: Restore cache" | |
if: env.DOCKER_TAG != 'latest' | |
uses: actions/cache@v4 | |
id: cache-docker | |
with: | |
path: ${{ env.DOCKER_CACHE_PATH }} | |
key: ${{ github.run_id }} | |
- name: "Prepare environment: Load Docker image from cache" | |
if: env.DOCKER_TAG != 'latest' | |
run: docker load -i $DOCKER_CACHE_PATH/docker-image.tar.gz --quiet | |
- name: "Prepare environment: Pull latest image from container registry" | |
if: env.DOCKER_TAG == 'latest' | |
run: docker pull $IMAGE_REPO/$IMAGE_NAME:latest --quiet | |
- name: Tag Docker image | |
run: | | |
# Execute on change of Docker image | |
if [[ "$DOCKER_TAG" != 'latest' ]]; then | |
docker tag $IMAGE_NAME:$GITHUB_RUN_ID $IMAGE_REPO/$IMAGE_NAME:latest | |
docker tag $IMAGE_NAME:$GITHUB_RUN_ID $IMAGE_REPO/$IMAGE_NAME:${GITHUB_REF_NAME}-${GITHUB_SHA:0:7} | |
fi | |
# Execute on push of git tag | |
if ${{ startsWith(github.ref, 'refs/tags/') }}; then | |
GIT_TAG=$(echo "${{ github.ref_name }}" | sed -e 's/^v//') | |
echo "GIT_TAG=$GIT_TAG" | |
docker tag $IMAGE_REPO/$IMAGE_NAME:latest $IMAGE_REPO/$IMAGE_NAME:$GIT_TAG | |
fi | |
- name: Log into container registry | |
# Authentication required for pushing images | |
run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin | |
- name: Push Docker image | |
run: docker push $IMAGE_REPO/$IMAGE_NAME --all-tags | grep -v -E 'Waiting|Layer already|Preparing|Pushed' |