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Reorganized for fast info on if there will be a release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -69,39 +69,10 @@ jobs: | |
| python-version: "3.10" | ||
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| ############################################# | ||
| ## Lint and Test | ||
| ############################################# | ||
| - name: Lint the package | ||
| run: poetry run python -m flake8 | ||
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| - name: Run the tests | ||
| run: poetry run python -m pytest tests/ --cov=./biosimulators_copasi/ --cov-report=xml | ||
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| - name: Upload the coverage report to Codecov | ||
| uses: codecov/codecov-action@v2 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| flags: unittests | ||
| file: ./coverage.xml | ||
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| ## Check if we need to perform a release | ||
| ############################################# | ||
| ## Compile documentation | ||
| ############################################# | ||
| - name: Install the requirements for compiling the documentation | ||
| run: poetry install --with docs | ||
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| - name: Compile the documentation | ||
| run: | | ||
| poetry run sphinx-apidoc . pyproject.toml --output-dir docs-src/source --force --module-first --no-toc | ||
| mkdir -p docs-src/_static | ||
| poetry run sphinx-build docs-src docs | ||
| ############################################# | ||
| ## Apply the version of the simulator to `biosimulators.json` | ||
| ############################################# | ||
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| - id: update-simulator-version | ||
| name: Update the version of the simulator | ||
| - id: check-new-release | ||
| name: Check if we need to perform a release | ||
| run: | | ||
| # We version the containers with the `biosimulators_copasi` version, but list the version | ||
| # online as the COPASI version within the container. | ||
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@@ -131,12 +102,40 @@ jobs: | |
| fi | ||
| fi | ||
| ############################################# | ||
| ## Lint and Test | ||
| ############################################# | ||
| - name: Lint the package | ||
| run: poetry run python -m flake8 | ||
|
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||
| - name: Run the tests | ||
| run: poetry run python -m pytest tests/ --cov=./biosimulators_copasi/ --cov-report=xml | ||
|
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||
| - name: Upload the coverage report to Codecov | ||
| uses: codecov/codecov-action@v2 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| flags: unittests | ||
| file: ./coverage.xml | ||
|
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||
| ############################################# | ||
| ## Compile documentation | ||
| ############################################# | ||
| - name: Install the requirements for compiling the documentation | ||
| run: poetry install --with docs | ||
|
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||
| - name: Compile the documentation | ||
| run: | | ||
| poetry run sphinx-apidoc . pyproject.toml --output-dir docs-src/source --force --module-first --no-toc | ||
| mkdir -p docs-src/_static | ||
| poetry run sphinx-build docs-src docs | ||
| ############################################# | ||
| ## Check for Deploy, Stop if not Deploying (disabled due to the fact it cancels, not passes) | ||
| ############################################# | ||
| # - name: Cancel build if not for release | ||
| # uses: andymckay/[email protected] | ||
| # if: steps.update-simulator-version.outputs.needDeploy != 'true' | ||
| # if: steps.check-new-release.outputs.needDeploy != 'true' | ||
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| #*******************************************# | ||
| #* Release *# | ||
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@@ -146,14 +145,14 @@ jobs: | |
| # Give nice, clear heads up in GitHub Action that We are Deploying | ||
| ############################################# | ||
| - name: Start the Deploy Process | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| run: echo 'Beginning Deploy Steps | ||
| ############################################# | ||
| # If new tag, commit and push documentation | ||
| ############################################# | ||
| - id: commit-docs | ||
| name: Commit the compiled documentation | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| run: | | ||
| git config --local user.email "[email protected]" | ||
| git config --local user.name "biosimulatorsdaemon" | ||
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@@ -186,7 +185,7 @@ jobs: | |
| ############################################# | ||
| - name: Create GitHub release | ||
| uses: actions/create-release@v1 | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
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@@ -197,7 +196,7 @@ jobs: | |
| # Create PyPI release | ||
| ############################################# | ||
| - name: Create PyPI release | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| env: | ||
| POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }} | ||
| run: | | ||
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@@ -223,7 +222,7 @@ jobs: | |
| ## Form-fill the versions to the container and to `biosimulators.json` | ||
| ############################################# | ||
| - name: Update the version of the simulator | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| run: | | ||
| containerLabel=${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | ||
| docker pull $containerLabel | ||
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@@ -232,8 +231,8 @@ jobs: | |
| dockerDigest=docker inspect --format='{{index .RepoDigests 0}}' $imageId | cut -d '@' -f 2 | ||
| copasiVersion=${{ steps.update-simulator-version.outputs.copasiVersion }} | ||
| bioSimVersion=${{ steps.update-simulator-version.outputs.bioSimVersion }} | ||
| copasiVersion=${{ steps.check-new-release.outputs.copasiVersion }} | ||
| bioSimVersion=${{ steps.check-new-release.outputs.bioSimVersion }} | ||
| sed -i -e 's/__CONTAINER_DIGEST__/${dockerDigest}/g' biosimulators.json | ||
| sed -i -e 's/__COPASI_VERSION__/${copasiVersion}/g' biosimulators.json | ||
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@@ -246,7 +245,7 @@ jobs: | |
| ############################################# | ||
| - id: get-docker-image-tag | ||
| name: Determine Docker image tag | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| run: | | ||
| sudo apt-get update -y | ||
| sudo apt-get install -y --no-install-recommends jq | ||
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@@ -264,7 +263,7 @@ jobs: | |
| echo "::set-output name=dockerRegistry::${DOCKER_REGISTRY}" | ||
| - name: Build Docker image | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| run: | | ||
| REVISION=$(git rev-parse HEAD) | ||
| CREATED=$(date --rfc-3339=seconds | sed 's/ /T/') | ||
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@@ -274,27 +273,27 @@ jobs: | |
| --label org.opencontainers.image.created=${CREATED} \ | ||
| --build-arg VERSION=${{ steps.get-tagged-version.outputs.version }} \ | ||
| --build-arg SIMULATOR_VERSION=${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \ | ||
| --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.update-simulator-version.outputs.copasiVersion }} \ | ||
| --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.check-new-release.outputs.copasiVersion }} \ | ||
| --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest \ | ||
| . | ||
| - name: Push Docker image | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| run: | | ||
| docker login ${{ steps.get-docker-image-tag.outputs.dockerRegistry }} \ | ||
| --username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \ | ||
| --password ${{ secrets.DOCKER_REGISTRY_TOKEN }} | ||
| docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | ||
| if [[ "${{ github.ref }}" =~ ^refs/tags/ ]] || [ "${{ steps.update-simulator-version.outputs.simulatorVersionLatest }}" == "true" ]; then | ||
| if [[ "${{ github.ref }}" =~ ^refs/tags/ ]] || [ "${{ steps.check-new-release.outputs.simulatorVersionLatest }}" == "true" ]; then | ||
| docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest | ||
| fi | ||
| ############################################# | ||
| # Submit to BioSimulators registry | ||
| ############################################# | ||
| - name: Submit to BioSimulators registry | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| run: | | ||
| REVISION=$(git rev-parse HEAD) | ||
| IMAGE_DIGEST=$(docker image inspect ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | jq -r '.[0].RepoDigests[0]' | cut -d "@" -f 2-) | ||
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@@ -311,7 +310,7 @@ jobs: | |
| ############################################# | ||
| # # If new version of simulator, commit and push the new version | ||
| # - name: Commit the revised version of the simulator | ||
| # if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| # if: steps.check-new-release.outputs.needDeploy == 'true' | ||
| # run: | | ||
| # git config --local user.email "[email protected]" | ||
| # git config --local user.name "biosimulatorsdaemon" | ||
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@@ -325,7 +324,7 @@ jobs: | |
| # git commit -m "Updating version of simulator" | ||
| # | ||
| # - name: Push the revised version of the simulator | ||
| # if: steps.update-simulator-version.outputs.simulatorVersion && steps.update-simulator-version.outputs.simulatorVersionLatest == 'true' | ||
| # if: steps.check-new-release.outputs.simulatorVersion && steps.check-new-release.outputs.simulatorVersionLatest == 'true' | ||
| # uses: ad-m/github-push-action@master | ||
| # with: | ||
| # github_token: ${{ secrets.GITHUB_TOKEN }} | ||
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