show distributions of unconfident predictions #112
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| # docker_action.yml | |
| name: Docker-ubuntu-build | |
| on: | |
| push: | |
| branches: | |
| - 'main' | |
| - 'develop' | |
| - 'releases/**' | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - 'main' | |
| - 'develop' | |
| - 'releases/**' | |
| env: | |
| # Use docker.io for Docker Hub if empty | |
| REGISTRY: ghcr.io | |
| # github.repository as <account>/<repo> | |
| IMAGE_NAME: ${{ github.repository }} | |
| DO_SIGNING: ${{ false }} | |
| jobs: | |
| build: | |
| name: docker_image_build | |
| runs-on: self-hosted | |
| steps: | |
| - name: Dump GitHub context | |
| env: | |
| GITHUB_CONTEXT: ${{ toJson(github) }} | |
| run: echo "$GITHUB_CONTEXT" | |
| - name: Dump job context | |
| env: | |
| JOB_CONTEXT: ${{ toJson(job) }} | |
| run: echo "$JOB_CONTEXT" | |
| - name: Dump steps context | |
| env: | |
| STEPS_CONTEXT: ${{ toJson(steps) }} | |
| run: echo "$STEPS_CONTEXT" | |
| - name: Dump runner context | |
| env: | |
| RUNNER_CONTEXT: ${{ toJson(runner) }} | |
| run: echo "$RUNNER_CONTEXT" | |
| # - name: Dump strategy context | |
| # env: | |
| # STRATEGY_CONTEXT: ${{ toJson(strategy) }} | |
| # run: echo "$STRATEGY_CONTEXT" | |
| # - name: Dump matrix context | |
| # env: | |
| # MATRIX_CONTEXT: ${{ toJson(matrix) }} | |
| # run: echo "$MATRIX_CONTEXT" | |
| - name: Show default environment variables | |
| run: | | |
| echo "The job_id is: $GITHUB_JOB" # reference the default environment variables | |
| echo "The id of this action is: $GITHUB_ACTION" # reference the default environment variables | |
| echo "The run id is: $GITHUB_RUN_ID" | |
| echo "The GitHub Actor's username is: $GITHUB_ACTOR" | |
| echo "GitHub SHA: $GITHUB_SHA" | |
| - name: Free Disk Space (Ubuntu) | |
| if: runner.environment != 'self-hosted' | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| # this might remove needed tools if set to "true" but frees about 6 GB | |
| tool-cache: false | |
| # all of these default to true | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: false | |
| docker-images: false | |
| swap-storage: true | |
| - name: Checkout just Dockerfile | |
| uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: | | |
| Dockerfile | |
| sparse-checkout-cone-mode: false | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| # Install the cosign tool except on PR | |
| # https://github.com/sigstore/cosign-installer | |
| # - name: Install cosign | |
| # if: ${{ env.DO_SIGNING }} && github.event_name != 'pull_request' | |
| # uses: sigstore/cosign-installer@v3.1.1 | |
| # with: | |
| # cosign-release: 'v2.1.1' | |
| # Login against a Docker registry except on PR | |
| # https://github.com/docker/login-action | |
| - name: Log into registry ${{ env.REGISTRY }} | |
| if: github.event_name != 'pull_request' | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} # aka ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| # Extract metadata (tags, labels) for Docker | |
| # https://github.com/docker/metadata-action | |
| - name: Extract Docker metadata | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| labels: | | |
| org.opencontainers.image.title=OpticalNet_ubuntu | |
| org.opencontainers.image.description=Docker image for a transformer network to perform sensorless detection of aberrations in adaptive optics. https://github.com/abcucberkeley/opticalaberrations | |
| org.opencontainers.image.vendor=Advanced Bioimaging Center at UC Berkeley and Janelia Research Campus | |
| # Load image for local test. | |
| - name: Build and load Docker image | |
| id: build-and-load | |
| continue-on-error: true | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| push: false | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| load: true | |
| - name: Retry Build and load Docker image with no-cache | |
| if: steps.build-and-load.outcome == 'failure' | |
| id: retry-build-and-load | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| push: false | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| no-cache: true | |
| cache-to: type=gha,mode=max | |
| load: true | |
| - name: Test IO | |
| run: | | |
| docker run --rm --gpus all ${{ steps.meta.outputs.tags }} "~/miniconda3/envs/ml/bin/python -m pytest -vvv --disable-warnings tests/test_io.py" | |
| - name: Test embeddings | |
| run: | | |
| docker run --rm --gpus all ${{ steps.meta.outputs.tags }} "~/miniconda3/envs/ml/bin/python -m pytest -vvv --disable-warnings tests/test_embeddings.py" | |
| - name: Test AO | |
| run: | | |
| docker run --rm --gpus all ${{ steps.meta.outputs.tags }} "~/miniconda3/envs/ml/bin/python -m pytest -vvv --disable-warnings tests/test_ao.py" | |
| - name: Test synthetic datasets | |
| run: | | |
| docker run --rm --gpus all ${{ steps.meta.outputs.tags }} "~/miniconda3/envs/ml/bin/python -m pytest -vvv --disable-warnings tests/test_datasets.py" | |
| - name: Build and push Docker image | |
| id: build-and-push | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| push: ${{ github.event_name != 'pull_request' }} | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| # Sign the resulting Docker image digest except on PRs. | |
| # This will only write to the public Rekor transparency log when the Docker | |
| # repository is public to avoid leaking data. If you would like to publish | |
| # transparency data even for private images, pass --force to cosign below. | |
| # https://github.com/sigstore/cosign | |
| # - name: Sign the published Docker image | |
| # if: ${{ env.DO_SIGNING }} && ${{ github.event_name != 'pull_request' }} | |
| # env: | |
| # # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable | |
| # TAGS: ${{ steps.meta.outputs.tags }} | |
| # DIGEST: ${{ steps.build-and-push.outputs.digest }} | |
| # # This step uses the identity token to provision an ephemeral certificate | |
| # # against the sigstore community Fulcio instance. | |
| # run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST} |