PySCeS is available for simulation online through BioSimulators/RunBioSimulations. To keep the version of PySCeS in BioSimulators up to date, we recommend automating the release of new versions to BioSimulators.
This can be done using the GitHub API.
An easy way to do this is with the GitHub action below. This would automatically push PySCeS to BioSimulators when releases are published to GitHub. Note, this must be run a few minutes after PySCeS is released to PyPI. To use the action:
Save the YAML below to .github/workflows/release-biosimulators.yml
BIOSIMULATORS_GH_USERNAME: the name of the GitHub user who pushes PySCeS to BioSimulators (e.g., bgoli). bgoli and jmrohwer already have permissions for this.
BIOSIMULATORS_GH_TOKEN: token for BIOSIMULATORS_GH_USERNAME
name: Update BioSimulators command-line interface and Docker image
on:
release:
types:
- published
jobs:
updateBioSimulatorsCliAndDockerImage:
name: Trigger the building and release of the BioSimulators version of PySCeS
runs-on: ubuntu-latest
env:
# Owner/repository-id for the GitHub repository for the downstream
# command-line interface and Docker image.
DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_PySCeS
# Username/token to use the GitHub API to trigger an action on the GitHub
# repository for the downstream command line interface and Docker image.
# Tokens can be generated at https://github.com/settings/tokens and should
# have the scope "repo".
BIOSIMULATORS_GH_USERNAME: ${{ secrets.BIOSIMULATORS_GH_USERNAME }}
BIOSIMULATORS_GH_TOKEN: ${{ secrets.BIOSIMULATORS_GH_TOKEN }}
steps:
- name: Trigger a GitHub action that will build and release the BioSimulators version of PySCeS
run: |
PACKAGE_VERSION="${GITHUB_REF/refs\/tags\//}"
WORKFLOW_FILE=ci.yml
curl -X POST \
-u ${BIOSIMULATORS_GH_USERNAME}:${BIOSIMULATORS_GH_TOKEN} \
-H "Accept: application/vnd.github.v3+json" https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
-d "{\"ref\": \"dev\", \"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"
PySCeS is available for simulation online through BioSimulators/RunBioSimulations. To keep the version of PySCeS in BioSimulators up to date, we recommend automating the release of new versions to BioSimulators.
This can be done using the GitHub API.
An easy way to do this is with the GitHub action below. This would automatically push PySCeS to BioSimulators when releases are published to GitHub. Note, this must be run a few minutes after PySCeS is released to PyPI. To use the action:
.github/workflows/release-biosimulators.yml
BIOSIMULATORS_GH_USERNAME
: the name of the GitHub user who pushes PySCeS to BioSimulators (e.g.,bgoli
).bgoli
andjmrohwer
already have permissions for this.BIOSIMULATORS_GH_TOKEN
: token forBIOSIMULATORS_GH_USERNAME
BIOSIMULATORS_GH_USERNAME
can be created a https://github.com/settings/tokensrepo