How ToPackage & Publish

Package & Publish with Biosimulant

Use the canonical biosimulant CLI for local validation and release work, or connect the Biosimulant GitHub App for push-to-deploy publishing from a branch.

GitHub App auto-deploy

Install the Biosimulant GitHub App from the Deployments screen. Pick one repository, one branch, and a lab manifest path such as labs/my-lab/lab.yaml, then link it to an existing lab or give a package name for a new one.

Each push to that branch validates the selected lab.yaml, builds one .bsilab archive, and publishes it to the Package Registry. Deployment history in the web app shows each stage, the commit SHA, and any failure reason. To deploy several labs from one branch, add one source per lab manifest path. Auto-deploy publishes Labs only.

CLI workflow

Use the CLI when you want to validate or publish locally, wire it into CI yourself, or test packages before enabling auto-deploy. For single-lab work, prefer the lab-centered flow:

biosimulant auth login
biosimulant labs init ./my-lab --name "My Lab"
biosimulant labs add-model ./models/my-model --lab ./my-lab --alias model
biosimulant labs validate ./my-lab
biosimulant labs serve ./my-lab
biosimulant labs run ./my-lab --results-file results.json --json
biosimulant labs publish ./my-lab --visibility private

Biosimulant Hub is the default registry. To publish to another Registry API v1 service, authenticate to its origin and pass a registry-qualified package reference:

printf '%s\n' "$TOKEN" | \
  biosimulant auth login registry.example.com --token-stdin
biosimulant labs publish ./my-lab registry.example.com/your-org/my-lab@1.0.0 --json

Registry credentials are stored separately by origin. Never place a token in a package reference, command history, or lab manifest.

Declare packages

Create a biosimulant-packages.yaml at the repository root:

schema_version: "1"
namespace: your-org
default_visibility: public
packages:
  - id: my-lab
    package: your-org/my-lab
    version: 1.0.0
    type: lab
    path: labs/my-lab
    visibility: public

Each package entry points to a lab source tree containing lab.yaml.

Validate

biosimulant labs release validate biosimulant-packages.yaml

Validation checks package names, exact SemVer versions, source paths, manifests, dependency pins, embedded paths, and duplicate package@version entries.

Build

biosimulant labs release build biosimulant-packages.yaml --out dist/biosimulant-packages

The build creates .bsilab archives under the output directory. Each archive contains package.yaml, payload/, and integrity/sha256sums.txt.

Publish

Publish builds, validates, uploads each artifact, and writes dist/package-report.json:

biosimulant labs release publish biosimulant-packages.yaml

Use --dry-run to validate and build locally without uploading:

biosimulant labs release publish biosimulant-packages.yaml --dry-run

Publishing the same package@version with different content fails on the backend. Re-uploading the same content reuses the existing artifact.

Pull and run versions

Consumers can use an exact package ref or leave the version out:

LAB_REF="your-org/my-lab@1.0.0"
 
biosimulant labs search "my lab"
biosimulant labs info "$LAB_REF"
biosimulant labs pull "$LAB_REF"
biosimulant labs run ./my-lab --results-file results.json --json

On the command line, namespace/name@x.y.z pins a version and namespace/name resolves the latest accessible version for labs pull and labs run. That only applies to CLI refs. Versions written in biosimulant-packages.yaml, model.yaml, and lab.yaml children must be exact.

Local CI

biosimulant labs release ci biosimulant-packages.yaml
biosimulant labs release ci biosimulant-packages.yaml --publish
biosimulant labs release ci biosimulant-packages.yaml --publish --json

The same command can run locally first and later move into GitHub Actions. All package commands exit non-zero on validation, build, or upload failure.

Use --json for one schema-v1 result or --json-stream for ordered progress followed by one terminal result. See Machine-readable output for the envelope and exit-code contract.

Compatibility Smoke

Before publishing a model or lab that should also run through the open-source Python package flow, build and run the package locally:

biosimulant labs package path/to/lab --out dist
biosimulant labs validate dist/your-package.bsilab --json
biosimulant labs run dist/your-package.bsilab --no-install-deps --json

This catches entrypoint loading, typed run input payloads, child-lab flattening, and io.maps_to remapping issues before the same package reaches remote execution. GPU or otherwise heavy packages can keep full execution in remote smoke tests, but should still validate manifests and entrypoints locally.

Next Steps

Add an ONNX ModelOverview