added Runge Kutta integration methods #452
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| name: Release Linux | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - 'v**' | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| jobs: | |
| wheel: | |
| runs-on: ubuntu-latest | |
| env: | |
| SMOLDYN_PYPI_TOKEN: ${{ secrets.SMOLDYN_PYPI_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Building wheel in ManuLinux container | |
| run: | | |
| ls -ltR | |
| export PYPI_PASSWORD=$SMOLDYN_PYPI_TOKEN | |
| cd scripts && make wheels | |
| # BioSimulators | |
| - name: Build BioSimulators Docker image | |
| env: | |
| TAG: ${{ github.ref }} | |
| run: | | |
| cp ~/wheelhouse/smoldyn-*-cp39-*.whl scripts/ | |
| cd scripts | |
| if [[ "${TAG}" =~ ^refs/tags/ ]]; then | |
| VERSION="${TAG/refs\/tags\/v/}" | |
| else | |
| WHEEL_PATH=$(ls smoldyn*.whl) | |
| VERSION=$(echo $WHEEL_PATH | cut -d - -f 2- | cut -d . -f 1-2) | |
| fi | |
| REVISION=$(git rev-parse HEAD) | |
| CREATED=$(date --rfc-3339=seconds | sed 's/ /T/') | |
| docker build \ | |
| --file Dockerfile-BioSimulators \ | |
| --tag ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:${VERSION} \ | |
| --tag ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:latest \ | |
| --build-arg VERSION=${VERSION} \ | |
| --label org.opencontainers.image.revision=${REVISION} \ | |
| --label org.opencontainers.image.created=${CREATED} \ | |
| . | |
| - name: Push BioSimulators Docker image | |
| env: | |
| TAG: ${{ github.ref }} | |
| run: | | |
| cd scripts | |
| if [[ "${TAG}" =~ ^refs/tags/ ]]; then | |
| VERSION="${TAG/refs\/tags\/v/}" | |
| else | |
| WHEEL_PATH=$(ls smoldyn*.whl) | |
| VERSION=$(echo $WHEEL_PATH | cut -d - -f 2- | cut -d . -f 1-2) | |
| fi | |
| ( | |
| docker login ghcr.io \ | |
| --username ${{ secrets.BIOSIMULATORS_GH_USERNAME }} \ | |
| --password ${{ secrets.BIOSIMULATORS_GH_TOKEN }} | |
| docker push ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:${VERSION} | |
| docker push ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:latest | |
| ) || echo "The BioSimulators Docker image could not be pushed. Check that the BIOSIMULATORS_GH_USERNAME and BIOSIMULATORS_GH_TOKEN secrets are defined." | |
| - name: Submit Smoldyn to BioSimulators | |
| if: startsWith(github.ref, 'refs/tags/v') || github.event_name == 'workflow_dispatch' | |
| env: | |
| TAG: ${{ github.ref }} | |
| run: | | |
| cd scripts | |
| if [[ "${TAG}" =~ ^refs/tags/ ]]; then | |
| VERSION="${TAG/refs\/tags\/v/}" | |
| else | |
| WHEEL_PATH=$(ls smoldyn*.whl) | |
| VERSION=$(echo $WHEEL_PATH | cut -d - -f 2- | cut -d . -f 1-2) | |
| fi | |
| REVISION=$(git rev-parse HEAD) | |
| IMAGE_DIGEST=$(docker image inspect ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:${VERSION} | jq -r '.[0].RepoDigests[0]' | cut -d "@" -f 2-) | |
| ( | |
| curl \ | |
| -X POST \ | |
| -u ${{ secrets.BIOSIMULATORS_GH_USERNAME }}:${{ secrets.BIOSIMULATORS_GH_TOKEN }} \ | |
| -H "Accept: application/vnd.github.v3+json" \ | |
| https://api.github.com/repos/biosimulators/Biosimulators/issues \ | |
| -d "{\"labels\": [\"Validate/submit simulator\"], \"title\": \"Submit Smoldyn ${VERSION}\", \"body\": \"---\nid: smoldyn\nversion: \\\"${VERSION}\\\"\nspecificationsUrl: https://raw.githubusercontent.com/ssandrews/Smoldyn/${REVISION}/biosimulators.json\nspecificationsPatch:\n version: \\\"${VERSION}\\\"\n image:\n url: ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:${VERSION}\n digest: \\\"${IMAGE_DIGEST}\\\"\nvalidateImage: true\ncommitSimulator: true\n\n---\"}" | |
| ) || echo "Failed to create issue. Probably secrets are not available?" |