# CLI releases What changed in each release of the `biosimulant` package, which provides both the Python runtime and the [CLI](/cli). The desktop app bundles this same package, so its version moves with these. To upgrade, see [Install and upgrade](/cli#install-and-upgrade). Released versions are on [PyPI](https://pypi.org/project/biosimulant/), and this page is generated from the [changelog in the package repository](https://github.com/Biosimulant/biosimulant/blob/main/CHANGELOG.md). ## 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.