CLIReleases

CLI releases

What changed in each release of the biosimulant package, which provides both the Python runtime and the CLI. The desktop app bundles this same package, so its version moves with these.

To upgrade, see Install and upgrade. Released versions are on PyPI, and this page is generated from the changelog in the package repository.

0.0.36 (2026-09-20)

  • Labs are the only publishable and executable package resource. Standalone model packages and .bsimodel files are rejected; model components remain supported inside labs.

0.0.35 (2026-09-18)

Added

  • biosimulant auth login --web signs in through the browser. The console mints the key and hands it back over a loopback listener bound to a state this process generated, so no secret passes through a URL, a redirect or a shell history.
  • auth login resolves a token to an account before storing it, and auth status --verify does the same for one already stored. A registry with no identity endpoint reports that the check was skipped and stores the token anyway, so other Registry API v1 services keep working.
  • List the compatibility commands in commands list. They already ran, but the catalog the docs are generated from did not mention them.
  • commands list entries carry available, and unavailableReason when it is false.

Changed

  • biosimulant runs reuses the credential auth login stored when BIOSIMULANT_API_KEY is unset, so one account does not need signing in to twice. Only a developer API key is reused, and only against the default API host.
  • runs start, runs upload, jobs list and jobs get say what to use instead. None of them can succeed against the public API, and they are now listed as unavailable rather than published as working commands.
  • The labs serve UI points at runs create and the MCP server rather than another application, and its “Add to lab” dialog gives the add-model, vendor-model and pull commands with the lab’s own path filled in.

Fixed

  • Cancelling the sign-in prompt with Ctrl-C reports that it was cancelled instead of printing a traceback.
  • auth login names the registry it is signing in to, says the token is a developer API key and where to create one, and says that local runs and public pulls need no sign-in at all.

0.0.34 (2026-09-17)

Added

  • Record per-connection compatibility evidence. labs run results now carry a compatibility section with provenance (standard, catalogue, runtime version and profile digests), a record for every wire with its mode (verified, partial, structural or blocked), issues and live value-check counts, value-check counts for every profiled port, and a capped list of violations.
  • Report static wire modes from labs validate for source Labs, which now fails on wires whose declared profiles block.
  • Add CompatibilityRecorder, wire_mode, check_declared_contracts and CompatibilityError (a PackageError with code compatibility_blocked).

Changed

  • A blocked wire, initial input or emitted value raises CompatibilityError carrying the partial record. labs run, packages run and pack run exit 2 with a structured compatibility_blocked error, and labs run still writes --results-file as {"status": "failed", "error": …, "compatibility": …}. Managed Python child runs pass the same error back to the parent.
  • Check profiled output values when a module emits them, not only when a wire carries them. An unchanged output file is checked once.
  • Check each committed value once per wire instead of on every window it is read.

Fixed

  • Bind model.yaml port declarations, including contracts, for models that Labs load from directories, so profiles declared only in model.yaml are enforced in Lab runs. Lab initial inputs use those bound specs.
  • Stop a model’s biosimulant==… dependency pin from installing another runtime version into the interpreter that is running the Lab.

0.0.33 (2026-09-17)

Added

  • Accept an optional biosim.execution_policy in model.yaml that repeats the module’s execution policy for tools that can’t import model code. The Python attribute still decides when BioWorld invokes the module; loading a model whose declaration disagrees with the constructed module raises PackageError.
  • Add biosim.execution with lab execution profiles (finite, temporal, unknown), static execution-phase wiring rules, and a source reader that resolves a model’s policy without importing it.
  • Report execution timing from labs validate, which now fails on declarations the source contradicts and on backward phase wiring between declared modules, and warns on unverifiable or missing declarations.
  • Include the lab execution profile in labs serve /api/lab and resolved per-module policies in labs run results.

Changed

  • Hide duration, communication step and settle steps in the labs serve Run dialog for finite Labs, name the modules time settings apply to in mixed Labs, and send only runtime values the user changed.
  • Cross runs in a single step when no module runs each window instead of iterating empty communication windows.
  • Generate starter models that declare execution_policy: each_window in model.yaml.

Fixed

  • Apply Studio- and Desktop-shaped run input files: runtime overrides under simulation_config.runtime, initial inputs under simulation_config, and alias-keyed parameter overrides were previously ignored. Per-model parameter overrides now merge onto the Lab’s parameters.

0.0.32 (2026-09-17)

Changed

  • Relay a managed runtime child process’s output to stderr line by line while the lab runs, instead of only after it exits, so hosted runs show logs and progress for labs that need a different Python version.

0.0.31 (2026-09-17)

Fixed

  • Apply each model’s runtime.remote.init_kwargs when BIOSIM_REMOTE_EXECUTION=1, expanding ${REMOTE_EXECUTION_MOUNT_ROOT} from BIOSIM_REMOTE_EXECUTION_MOUNT_ROOT, so hosted runs use installed runtime dependencies and persistent caches as the hosted executor does.
  • Put the interpreter’s scripts directory on PATH before installing declared dependencies so models can invoke dependency console scripts such as boltz.

0.0.30 (2026-09-17)

Changed

  • Allow structurally valid connections when only one port declares a compatibility profile, reporting PROFILE_PARTIAL instead of blocking the wire. Live values are still checked against whichever profile is declared.
  • Report a partial-profile warning once when a connection is created instead of repeating it at every communication boundary.

0.0.28 (2026-09-13)

Added

  • Add biosimulant labs capabilities and labs run --require-local-capability for conservative, hardware-aware local-first execution on declared CPU, memory, CUDA, or Apple MPS resources.

Changed

  • Generate canonical execute(inputs, *, context) starter models with an explicit ExecutionPolicy.EACH_WINDOW from both Lab creation commands.
  • Route BioModule regression snapshots through BioWorld so canonical invocation policies, typed output normalization, and compatibility modules use the same execution path as Labs.
  • Lead active documentation and first-party examples with the canonical execution contract while retaining one explicit temporal compatibility path.

Removed

  • Remove obsolete audit and V1-to-V1.5 migration documents that described superseded execution signatures.

0.0.27 (2026-09-12)

Changed

  • Preserve every module’s typed terminal output signals in Lab run JSON and report results so managed and local runs retain inspectable scientific data.

0.0.26 (2026-09-10)

Added

  • Add ExecutionPolicy, immutable ExecutionContext, and the canonical execute(inputs, *, context) BioModule authoring contract for finite or temporal computation before, during, or after communication windows.
  • Add deterministic dependency draining for once-before and once-after modules.

Changed

  • Route standalone model-package execution through BioWorld so invocation policy, signal timestamps, and output validation match Lab execution.
  • Preserve existing temporal advance_window() behavior as the default while excluding canonical modules from zero-duration settle calls.
  • Validate canonical signatures at registration, warn when EACH_WINDOW is only inherited, and commit normalized canonical output caches atomically with world signals.

0.0.22 (2026-07-29)

Added

  • Generate a standalone HTML report for labs run --report-file, completing headless report parity for Studio, Desktop, local terminals, and CI.

0.0.21 (2026-07-29)

Added

  • Add the canonical headless CLI contract, schema-v1 JSON/JSONL output, standardized exit codes, portable doctor/runtime commands, and top-level validate and run aliases.
  • Add registry-qualified references, Registry API v1 discovery and publishing, registry-scoped credentials, and short-lived workspace token exchange.
  • Add headless runs, remote-runs, jobs capability reporting, lab publishing, sync status, and release publishing workflows.

Changed

  • Make the MIT PyPI package the sole public CLI implementation used by local, Desktop, Studio, CI, and server environments.

Removed

  • Remove the proprietary extension contract and Desktop-binary CLI delegation.

0.0.20 (2026-07-19)

Added

  • Add explicit biosimulant.hub.HubComposition for resolving exact, lockfile-pinned public Hub Labs into a caller-owned BioWorld.
  • Store composed Hub Lab payloads under the parent Lab’s .biosimulant/dependencies/ state instead of a shared machine cache.
  • Add biosimulant.lock validation for package-backed child Labs and --vendor-dependencies for fully self-contained archival .bsilab releases.
  • Add --dependency-root to biosimulant labs run for package-backed archives in read-only locations.

Changed

  • Keep ordinary Lab package payloads compact by preserving locked Hub package references; archive runtime state remains disposable and excluded from normal package output.

0.0.19 (2026-07-19)

Added

  • Add the open Client and AsyncClient interfaces for explicit managed, durable execution through the private Biosimulant developer API.
  • Add typed run, result, artifact, error, timeout, and webhook verification contracts while leaving BioWorld.run() local and unchanged.

0.0.18 (2026-06-05)

Added

  • Add managed runtime support for local lab execution and serving.
  • Add 3D Labs Serve visual support.
  • Add GPU accelerator warning detection.

Changed

  • Improve lab command progress messages during package resolution, dependency installation, and runtime preparation.
  • Add Python version validation and warnings for lab manifests.
  • Improve PublicRegistryClient request headers and Cloudflare error handling.
  • Disable uvicorn access logs for the Labs Serve API.

0.0.17 (2026-06-03)

Changed

  • Remove normal UI support for persistent manual input defaults while keeping runtime compatibility for existing runtime.initial_inputs.
  • Consolidate lab wiring authoring into the World inspector and simplify model inspectors to read-only interface summaries.
  • Keep run-modal input overrides ephemeral and prevent Save & Run from persisting input defaults.

0.0.16 (2026-06-03)

Added

  • Add root biosimulant --version output.
  • Add Labs Serve run progress metadata for active local runs.

Changed

  • Update Labs Serve desktop download links to https://www.biosimulant.com/download/desktop.
  • Avoid polling run results from the Labs Serve UI until a run reaches a terminal state.
  • Accept biosimulant labs run --no-open as a compatibility no-op flag.

0.0.15 (2026-06-02)

Added

  • Add the embedded open-source Labs Serve UI as the implementation behind biosimulant labs serve.
  • Add Labs Serve API endpoints for lab metadata, local run lifecycle, logs, results, cancellation, manifest edits, and layout persistence.
  • Add --no-open to suppress the default browser launch.

Changed

  • Serve the Labs Serve UI at the root URL (/) and report the root URL in JSON output.
  • Redirect /ui and /ui/ to / for one release.
  • Build the private React/Vite Labs Serve UI into the Python wheel so users do not install a separate UI package.

Removed

  • Remove the old Python-declared SimUI implementation and public biosim.simui / biosimulant.simui modules.
  • Remove the top-level --simui runner flag and the biosimulant[ui] extra.

0.0.14 (2026-06-02)

Changed

  • Move SimUI runtime dependencies into the default package install so pipx install biosimulant supports biosimulant labs serve without requiring the biosimulant[ui] extra.
  • Keep biosimulant[ui] as a backwards-compatible install extra while updating docs and stale-environment error messages to lead with the default install.
  • Update backend, desktop, sandbox, and web surfaces to target the next biosimulant runtime release (0.0.14).

0.0.13 (2026-06-02)

Added

  • Add shell completion support for the biosimulant CLI.
  • Add local lab identity handling improvements for source-tree lab workflows.

Changed

  • Focus release instructions and packaging language on the biosimulant distribution and CLI.
  • Split PyPI publishing workflows for clearer release automation.
  • Add archive messaging for the legacy biosim package.

0.0.12 (2026-06-02)

Added

  • Add product extension contracts and command routing for product-owned CLI surfaces.
  • Add broader registry, workspace, and package-management test coverage.

Changed

  • Rename public package and documentation language from BioSim/Biosim toward Biosimulant while preserving compatibility imports and commands.
  • Improve package validation and lab manifest package formatting.
  • Tighten the coverage gate and tidy wiring builder demo coverage.

0.0.11 (2026-05-30)

Added

  • Add the lab-scoped CLI surface for local lab initialization, validation, running, serving, packaging, registry lookup, and package repository release workflows.
  • Add package repository manifest validation/build support under biosimulant labs release.
  • Add input value type handling for SignalSpec.

Changed

  • Move public CLI guidance toward lab-scoped commands such as biosimulant labs package, biosimulant labs run, and biosimulant labs serve.

0.0.10 (2026-05-30)

Changed

  • Rename the Python distribution and primary CLI entrypoint to biosimulant.
  • Preserve the legacy biosim import path and python -m biosim compatibility command for existing model packages.
Biosimulant CLI