Change default units when reading from cube files #1093
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 | |
| # 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 --color-always 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 -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' |