How ToLibraryPackage & 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

The hosted workflow is the simplest path for teams:

  1. Install the Biosimulant GitHub App from the Deployments screen.
  2. Select one repository, one branch, and the path to a lab manifest such as labs/my-lab/lab.yaml.
  3. Link the source to an existing lab, or provide a package name when creating a new lab.
  4. Push to that branch.

Each push runs the same backend stages used by package upload:

  • clone repository archive
  • validate the selected lab.yaml
  • build one .bsilab archive from that lab folder
  • publish and materialize the Lab into the Package Registry

Deployment history stays visible in the web app with stage-by-stage status, commit SHA, published lab rows, and failure reasons for validation, build, or publish issues. A single repository branch can deploy multiple labs by creating one source per lab manifest path.

The GitHub App should be granted:

  • repository contents: read
  • metadata: read
  • commit statuses: write
  • webhooks for push events

V1 GitHub auto-deploy publishes Labs only. Preview environments and smoke tests are not part of this flow yet.

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 ./my-lab ./models/my-model --as 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

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 exact package refs, or omit the version to resolve the latest accessible package:

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

Exact package refs use namespace/name@x.y.z; namespace/name resolves latest for pull and run commands.

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.

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 runtime.initial_inputs, child-lab flattening, and io.maps_to remapping issues before the same package reaches Desktop or 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

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