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add check_tool_compatibility helper #236

add check_tool_compatibility helper

add check_tool_compatibility helper #236

Workflow file for this run

name: test backoffice and build docs
on: push
concurrency:
group: test
cancel-in-progress: true
jobs:
initial-cleanup:
environment: testing
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: "3.12"
cache: "pip" # caching pip dependencies
- run: pip install .
- run: backoffice wipe
env:
S3_HOST: ${{vars.S3_HOST}}
S3_BUCKET: ${{vars.S3_BUCKET}}
S3_FOLDER: ${{vars.S3_FOLDER}}
S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
RUN_URL: ${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}}
BIOIMAGEIO_USER_ID: github|${{github.actor_id}}
generate-initial-collection-json:
needs: initial-cleanup
uses: bioimage-io/collection/.github/workflows/generate_collection_json_call.yaml@main
with:
environment_name: testing
secrets: inherit
test-stage:
needs: generate-initial-collection-json
uses: bioimage-io/collection/.github/workflows/stage_call.yaml@main
with:
concept_id: 'frank-water-buffalo'
package_url: 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/examples.bioimage.io/frank-water-buffalo_v1.zip'
environment_name: testing
secrets: inherit
test-publish:
needs: test-stage
uses: bioimage-io/collection/.github/workflows/publish_call.yaml@main
with:
concept_id: 'frank-water-buffalo'
reviewer: 'github|${{github.actor_id}}'
environment_name: testing
secrets: inherit
test-generate-collection-json:
needs: test-publish
uses: bioimage-io/collection/.github/workflows/generate_collection_json_call.yaml@main
with:
environment_name: testing
secrets: inherit
test-generate-collection-staged-json:
needs: test-publish
uses: bioimage-io/collection/.github/workflows/generate_collection_json_call.yaml@main
with:
mode: 'staged'
environment_name: testing
secrets: inherit
test-backup:
needs: test-generate-collection-json
uses: bioimage-io/collection/.github/workflows/backup_call.yaml@main
with:
environment_name: testing
secrets: inherit
build:
runs-on: ubuntu-latest
environment: testing
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: "3.12"
cache: "pip" # caching pip dependencies
- run: pip install -e .[dev]
- run: black . --check
- run: pyright -p pyproject.toml
- run: pytest
env:
S3_HOST: ${{vars.S3_HOST}}
S3_BUCKET: ${{vars.S3_BUCKET}}
S3_FOLDER: ${{vars.S3_FOLDER}}
S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
RUN_URL: ${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}}
ZENODO_URL: ${{vars.ZENODO_URL}}
ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}}
BIOIMAGEIO_USER_ID: github|${{github.actor_id}}
- name: export documentation
run: |
pdoc \
--mermaid \
--docformat google \
--logo https://bioimage.io/static/img/bioimage-io-logo.svg \
--logo-link https://bioimage.io/ \
--favicon https://bioimage.io/static/img/bioimage-io-icon-small.svg \
--footer-text 'bioimageio_collection_backoffice' \
-o ./docs bioimageio_collection_backoffice
- name: Deploy to gh-pages 🚀
if: ${{ github.ref == 'refs/heads/main' }}
uses: JamesIves/github-pages-deploy-action@v4
with:
folder: docs