diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..2afde73 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,5 @@ +.git +.gitignore +old +LICENSE +Dockerfile diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml new file mode 100644 index 0000000..8aa3abe --- /dev/null +++ b/.github/workflows/docker-publish.yml @@ -0,0 +1,105 @@ +name: Docker + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +on: [push] + #release: + # types: published + #pull_request: + # branches: ["main"] + + +# schedule: +# - cron: '1 * * * *' +# push: +# branches: [ "main" ] + # Publish semver tags as releases. +# tags: [ 'v*.*.*' ] +# pull_request: +# branches: [ "main" ] + +env: + # Use docker.io for Docker Hub if empty + REGISTRY: ghcr.io + # github.repository as / + IMAGE_NAME: ${{ github.repository }} + + +jobs: + build: + + runs-on: ubuntu-latest + permissions: + contents: read + packages: write + # This is used to complete the identity challenge + # with sigstore/fulcio when running outside of PRs. + id-token: write + + steps: + - name: Checkout repository + uses: actions/checkout@v4 + + # Install the cosign tool except on PR + # https://github.com/sigstore/cosign-installer + - name: Install cosign + if: github.event_name != 'pull_request' + uses: sigstore/cosign-installer@v3.5.0 #v3.1.1 + with: + cosign-release: 'v2.2.4' + + # Set up BuildKit Docker container builder to be able to build + # multi-platform images and export cache + # https://github.com/docker/setup-buildx-action + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0 + + # 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@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0 + with: + registry: ${{ env.REGISTRY }} + 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@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0 + with: + images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} + + # Build and push Docker image with Buildx (don't push on PR) + # https://github.com/docker/build-push-action + - name: Build and push Docker image + id: build-and-push + uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0 + with: + context: . + platforms: linux/amd64,linux/arm64 + 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: ${{ 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 {}@${DIGEST} diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..8df3acc --- /dev/null +++ b/Dockerfile @@ -0,0 +1,7 @@ +FROM mambaorg/micromamba:latest +COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yaml +RUN micromamba install -y -n base -f /tmp/env.yaml && \ + micromamba clean --all --yes +ENV PATH="${PATH}:/opt/conda/bin" +WORKDIR /scripts +COPY /scripts/ill_correction.py . \ No newline at end of file diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..a52c965 --- /dev/null +++ b/environment.yml @@ -0,0 +1,11 @@ +name: staging_env +channels: + - defaults +dependencies: + - python=3.12 + - conda-forge::ome-types=0.5.2 + - numpy + - conda-forge::tifffile + - pandas + - conda-forge::beautifulsoup4 +prefix: C:\Users\VictorP\anaconda3\envs\staging_env diff --git a/scripts/ill_correction.py b/scripts/ill_correction.py index cefc574..24ab564 100644 --- a/scripts/ill_correction.py +++ b/scripts/ill_correction.py @@ -75,9 +75,8 @@ def ill_correction(img_path,ffp_path): def apply_correction(img_path,out_dir): - img_name=img_path.stem + img_path.suffix img_corr=ill_correction(img_path,ill_profile(img_path)) - output_img_path=out_dir / img_name + output_img_path=out_dir / '{stem}_{tag}_{file_format}'.format(stem=img_path.stem ,file_format=img_path.suffix,tag='corr') ome_metadata=tifff.tiffcomment(img_path) tifff.imwrite( output_img_path ,img_corr ) tifff.tiffcomment(output_img_path,ome_metadata)