biosimulant 0.0.10__tar.gz

biosimulant-0.0.10/.gitignore

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+# Byte-compiled / cache
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+coverage.xml
+htmlcov/
+
+node_modules/
+.venv/
+dist/
+build/
+src/biosim/simui/_frontend/dist/
+
+.DS_Store
+
+# SimUI UI build outputs (built automatically via prepare script)
+packages/simui-ui/dist/
+packages/simui-ui/dist-static/

biosimulant-0.0.10/LICENSE.txt

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+MIT License
+
+Copyright (c) 2026 BioSimulant
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

biosimulant-0.0.10/PKG-INFO

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+Metadata-Version: 2.4
+Name: biosimulant
+Version: 0.0.10
+Summary: Open-source local simulation runtime and CLI for Biosimulant
+Project-URL: Documentation, https://github.com/Biosimulant/biosim#readme
+Project-URL: Issues, https://github.com/Biosimulant/biosim/issues
+Project-URL: Source, https://github.com/Biosimulant/biosim
+Author-email: Demi <bjaiye1@gmail.com>
+License-Expression: MIT
+License-File: LICENSE.txt
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.26
+Provides-Extra: all
+Requires-Dist: fastapi<1,>=0.110; extra == 'all'
+Requires-Dist: httpx>=0.26; extra == 'all'
+Requires-Dist: libcellml<0.7,>=0.6.3; extra == 'all'
+Requires-Dist: onnxruntime>=1.18; extra == 'all'
+Requires-Dist: pytest-cov>=4; extra == 'all'
+Requires-Dist: pytest>=7; extra == 'all'
+Requires-Dist: pyyaml>=6; extra == 'all'
+Requires-Dist: scipy<2,>=1.11; extra == 'all'
+Requires-Dist: tomli>=2; (python_version < '3.11') and extra == 'all'
+Requires-Dist: uvicorn>=0.23; extra == 'all'
+Provides-Extra: cellml
+Requires-Dist: libcellml<0.7,>=0.6.3; extra == 'cellml'
+Requires-Dist: scipy<2,>=1.11; extra == 'cellml'
+Provides-Extra: dev
+Requires-Dist: httpx>=0.26; extra == 'dev'
+Requires-Dist: pytest-cov>=4; extra == 'dev'
+Requires-Dist: pytest>=7; extra == 'dev'
+Requires-Dist: pyyaml>=6; extra == 'dev'
+Requires-Dist: tomli>=2; (python_version < '3.11') and extra == 'dev'
+Provides-Extra: ml
+Requires-Dist: onnxruntime>=1.18; extra == 'ml'
+Provides-Extra: ui
+Requires-Dist: fastapi<1,>=0.110; extra == 'ui'
+Requires-Dist: uvicorn>=0.23; extra == 'ui'
+Description-Content-Type: text/markdown
+
+# biosimulant
+
+[![PyPI - Version](https://img.shields.io/pypi/v/biosimulant.svg)](https://pypi.org/project/biosimulant)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/biosimulant.svg)](https://pypi.org/project/biosimulant)
+
+Composable simulation runtime + UI layer for orchestrating runnable biomodules.
+
+`biosimulant` is the primary package and CLI name. The existing `biosim`
+Python import path and `python -m biosim` command remain supported for existing
+model packages during the migration.
+
+---
+
+## Executive Summary & System Goals
+
+### Vision
+
+Provide a small, stable composition layer for simulations: wire reusable components ("biomodules") into a `BioWorld`, run them with a single orchestration contract, and visualize/debug runs via a lightweight web UI (SimUI). Biomodules are self-contained Python packages that can wrap external simulators internally (SBML/NeuroML/CellML/etc.) without a separate adapter layer.
+
+### Core Mission
+
+- Compose simulations from reusable, interoperable biomodules.
+- Make "run + visualize + share a config" the default workflow (local-first; hosted later).
+- Keep the runtime small and predictable while letting biomodules embed their own simulator/tooling.
+
+### Primary Users
+
+- Developers and researchers who need composable simulation workflows and fast iteration.
+- Near-term beachhead: neuroscience demos (single neuron + small E/I microcircuits) with strong visuals and reproducible configs.
+
+---
+
+## Installation
+
+Preferred (pinned GitHub ref):
+
+```console
+pip install "biosimulant @ git+https://github.com/<org>/biosim.git@<ref>"
+```
+
+Alternative (package index):
+
+```console
+pip install biosimulant
+```
+
+For the shared ONNX biomodule helpers:
+
+```console
+pip install "biosimulant[ml]"
+```
+
+### Compatibility and command ownership
+
+The `biosimulant` package still ships the `biosim` Python import path so existing
+model packages keep working:
+
+```python
+import biosim
+```
+
+Use `biosimulant` for new CLI examples:
+
+```bash
+biosimulant --help
+python -m biosimulant --help
+```
+
+`python -m biosim` remains available as a compatibility command. If a machine
+also has the Desktop/product CLI installed, `PATH` decides which `biosimulant`
+binary runs. Use `python -m biosimulant ...` to force the Python package CLI.
+The Python package owns local open-source workflows; Desktop/product extensions
+own Hub, auth, cloud, app state, and managed-service workflows.
+
+## Publishing to PyPI
+
+See the release guide: [`docs/releasing.md`](docs/releasing.md).
+
+## Packaging Models And Labs
+
+`biosim` can package one model or one lab into a single archive for portability, upload, caching, and validation.
+
+Common commands:
+
+```bash
+# Build a package from a directory that contains model.yaml or lab.yaml
+biosimulant pack build path/to/model-or-lab
+
+# Validate an existing package file
+biosimulant pack validate dist/local__counter-1.0.0.bsimodel
+
+# Build a self-contained lab package (.bsilab)
+biosimulant pack build path/to/lab
+```
+
+Notes:
+- `build` prefers `package:` and `version:` from `model.yaml` or `lab.yaml` when present.
+- model dependencies in manifests must use exact `==` pins.
+- lab builds are always self-contained and preserve the full runnable source tree inside the `.bsilab`.
+- nested lab dependencies must use relative `path` refs and must already exist inside the packaged lab directory.
+- `validate` prints human-readable success or failure output by default; add `--json` for machine-readable output.
+
+See [`docs/packaging.md`](docs/packaging.md) for the full package layout, recommended authoring flow, and CLI examples.
+
+## Provisional Runtime Helpers
+
+`biosim.runtime` is the provisional public home for package interpretation helpers shared by the open-source CLI and Biosimulant platform executors. It owns entrypoint loading, typed `runtime.initial_inputs` coercion, communication-step resolution, and source-neutral lab flattening. Import these helpers from `biosim.runtime`; they are not exported from top-level `biosim` while the API settles.
+
+## BioModule Convenience Layers
+
+`BioModule` remains the minimal full-control runtime contract. For common model
+adapters, `biosim` also exports opt-in helpers:
+
+- `SignalEmitterBioModule`: output storage, source-name resolution, and raw
+  value to typed `BioSignal` wrapping.
+- `StatefulBioModule`: fixed-step window advancement, input override storage,
+  bounded history, and output publishing hooks.
+
+Signal helper functions are available from `biosim.signals` and top-level
+`biosim`: `unwrap_payload`, `coerce_float`, `scalar_or_record_input`, and
+`make_signal`.
+
+## Examples
+
+- See `examples/` for quick-start scripts. Try:
+
+```bash
+pip install -e .
+python examples/basic_usage.py
+```
+
+For advanced curated demos (neuro/ecology), wiring configs, and model-pack templates, see the companion repo:
+
+- https://github.com/Biosimulant/models
+
+### Quick Start: BioWorld
+
+Minimal usage:
+
+```python
+import biosim
+from biosim import ScalarSignal, SignalSpec
+
+
+class Counter(biosim.BioModule):
+    def __init__(self):
+        self.value = 0
+        self._t = 0.0
+
+    def outputs(self):
+        return {"count": SignalSpec.scalar(dtype="int64", emitted_unit="1")}
+
+    def advance_window(self, start: float, end: float) -> None:
+        _ = start
+        self.value += 1
+        self._t = end
+
+    def get_outputs(self):
+        return {
+            "count": ScalarSignal(
+                source="counter",
+                name="count",
+                value=self.value,
+                emitted_at=self._t,
+                spec=self.outputs()["count"],
+            )
+        }
+
+    def snapshot(self) -> dict:
+        return {"value": self.value, "t": self._t}
+
+    def restore(self, snapshot: dict) -> None:
+        self.value = int(snapshot.get("value", 0))
+        self._t = float(snapshot.get("t", 0.0))
+
+
+world = biosim.BioWorld(communication_step=0.1)
+world.add_biomodule("counter", Counter())
+world.run(duration=1.0)
+```
+
+Outputs produced during a communication window are committed at the end of that
+window and become visible to downstream modules on a later communication turn.
+For final report, export, or visualisation modules in workflow-style graphs, call
+`world.settle(steps=1)` after `world.run(...)` to propagate final outputs without
+advancing simulated time.
+
+### Visuals from Modules
+
+Modules may optionally expose visuals via `visualize()`, returning a dict or list of dicts with keys `render` and `data`. The world can collect them without any transport layer:
+
+```python
+class MyModule(biosim.BioModule):
+    def advance_window(self, start: float, end: float) -> None:
+        _ = start, end
+
+    def get_outputs(self):
+        return {}
+
+    def snapshot(self) -> dict:
+        return {}
+
+    def restore(self, snapshot: dict) -> None:
+        _ = snapshot
+
+    def visualize(self):
+        return {
+            "render": "timeseries",
+            "data": {"series": [{"name": "s", "points": [[0.0, 1.0]]}]},
+        }
+
+world = biosim.BioWorld(communication_step=0.1)
+world.add_biomodule("module", MyModule())
+world.run(duration=0.1)
+print(world.collect_visuals())  # [{"module": "module", "visuals": [...]}]
+```
+
+If visuals are generated by a separate downstream module wired to another
+producer's final outputs, run one or more settle turns before collecting visuals:
+`world.run(duration=...); world.settle(1); world.collect_visuals()`.
+
+See `examples/visuals_demo.py` for a minimal end-to-end example.
+
+### ONNX Modules
+
+`biosim` can host ONNX-backed modules without changing the core runtime. Install
+the ML extras and wrap the ONNX model behind the standard `BioModule`
+interface:
+
+```python
+from biosim import OnnxClassifierModule, ScalarSignal, SignalSpec
+
+classifier = OnnxClassifierModule(
+    model_path="artifacts/model.onnx",
+    class_labels=["quiescent", "subthreshold", "spiking"],
+    input_port="state_vector",
+    probabilities_port="state_probabilities",
+    predicted_port="predicted_state",
+    input_vector_length=4,
+)
+
+classifier.set_inputs(
+    {
+        "state_vector": ScalarSignal(
+            source="adapter",
+            name="state_vector",
+            value=-64.0,
+            emitted_at=0.0,
+            spec=SignalSpec.scalar(dtype="float64"),
+        )
+    }
+)
+classifier.advance_window(0.0, 0.001)
+print(classifier.get_outputs()["predicted_state"].value)
+```
+
+Model packs can subclass `OnnxClassifierModule` to set model-relative
+`model_path`, port names, and label sets while keeping the inference logic in
+the shared library.
+
+## SimUI (Python-Declared UI)
+
+SimUI lets you build and launch a small web UI entirely from Python (similar to Gradio's ergonomics), backed by FastAPI and a prebuilt React SPA that renders visuals from JSON. The frontend uses Server-Sent Events (SSE) for real-time updates.
+
+- User usage (no Node/npm required):
+  - Install UI extras: `pip install 'biosimulant[ui]'`
+  - Try the demo: `python examples/ui_demo.py` then open `http://127.0.0.1:7860/ui/`.
+  - From your own code:
+
+    ```python
+    from biosim.simui import Interface, Number, Button, EventLog, VisualsPanel
+    world = biosim.BioWorld(communication_step=0.1)
+    ui = Interface(
+        world,
+        controls=[Number("duration", 10), Button("Run")],
+        outputs=[EventLog(), VisualsPanel()],
+    )
+    ui.launch()
+    ```
+
+  - The UI provides endpoints under `/ui/api/...`:
+    - `GET /api/spec` – UI layout (controls, outputs, modules)
+    - `POST /api/run` – Start a simulation run
+    - `GET /api/status` – Runner status (running/paused/error + optional progress fields)
+    - `GET /api/state` – Full state (status + last step + modules)
+    - `GET /api/events` – Buffered world events (`?since_id=&limit=`)
+    - `GET /api/visuals` – Collected module visuals
+    - `GET /api/snapshot` – Full snapshot (status + visuals + events)
+    - `GET /api/stream` – SSE endpoint for real-time event streaming
+    - `POST /api/pause` – Pause running simulation
+    - `POST /api/resume` – Resume paused simulation
+    - `POST /api/reset` – Stop, reset, and clear buffers
+    - **Editor sub-API** (`/api/editor/...`): visual config editor for loading, saving, validating, and applying YAML wiring configs as node graphs. Endpoints include `modules`, `current`, `config`, `apply`, `validate`, `layout`, `to-yaml`, `from-yaml`, and `files`.
+
+Per-run resets for clean visuals
+- On each `Run`, the backend clears its event buffer and calls `reset()` on modules if they implement it.
+- The frontend clears visuals/events before posting `/api/run`.
+- To avoid overlapping charts across runs, add `reset()` to modules that accumulate history (e.g., time series points).
+
+- Maintainer flow (building the frontend SPA):
+  - Edit the React/Vite app under `src/biosim/simui/_frontend/`.
+  - Build via Python: `python -m biosim.simui.build` (requires Node/npm). This writes `src/biosim/simui/static/app.js`.
+  - Alternatively: `bash scripts/build_simui_frontend.sh`.
+  - Packaging includes `src/biosim/simui/static/**`, so end users never need npm.
+
+- CI packaging (recommended): run the frontend build before `python -m build` so wheels/sdists ship the bundled assets.
+
+Troubleshooting:
+- If you see `SimUI static bundle missing at .../static/app.js`, build the frontend with `python -m biosim.simui.build` (requires Node/npm) before launching. End users installing a release wheel won't see this.
+
+### SimUI Design Notes
+- Transport: SSE (Server-Sent Events). The SPA connects to `/api/stream` for real-time updates. Polling endpoints (`/api/status`, `/api/visuals`, `/api/events`) remain available for fallback/debugging.
+- Objective progress fields are based on simulation-time progress (`(sim_time - sim_start) / duration`), not wall-clock time.
+- `/api/status` may include: `sim_time`, `sim_start`, `sim_end`, `sim_remaining`, `progress`, `progress_pct` (all optional/additive).
+- Events API: `/api/events?since_id=<int>&limit=<int>` returns `{ events, next_since_id }` where `events` are appended world events and `next_since_id` is the cursor for subsequent calls.
+- VisualSpec types supported now:
+  - `timeseries`: `data = { "series": [{ "name": str, "points": [[x, y], ...] }, ...] }`
+  - `bar`: `data = { "items": [{ "label": str, "value": number }, ...] }`
+  - `scatter`: `data = { "points": [{ "x": number, "y": number, "label"?: str, "series"?: str }, ...] }`
+  - `heatmap`: `data = { "values": [[number, ...], ...], "x_labels"?: [str, ...], "y_labels"?: [str, ...] }`
+  - `table`: `data = { "columns": [..], "rows": [[..], ...] }` or `data = { "items": [{...}, ...] }`
+  - `image`: `data = { "src": str, "alt"?: str, "width"?: number, "height"?: number }`
+  - `graph`: simple node-edge graph renderer
+  - `structure3d`: `data = { "title"?: str, "source": { "kind": "url", "url": str } | { "kind": "artifact", "artifact_id": str }, "format": "mmcif" | "pdb", "annotations"?: [{ "label": str, "value": str|number|bool }], "initial_view"?: {...} }`
+- VisualSpec may also include an optional `description` (string) for hover text or captions.
+- SimUI serves artifact-backed `structure3d` files through `/api/artifacts/{artifact_id}` so browser clients do not receive raw local filesystem paths.
+
+## Terminology
+
+Understanding the core concepts is essential for working with biosim effectively.
+
+| Term | Description |
+|------|-------------|
+| **BioWorld** | Runtime container that orchestrates multi-rate biomodules, routes signals, and publishes lifecycle events. |
+| **BioModule** | Pluggable unit of behavior with local state. Implements the runnable contract (`setup/reset/advance_to/...`). |
+| **BioSignal** | Typed, versioned data payload exchanged between modules via named ports. |
+| **WorldEvent** | Runtime events emitted by the BioWorld (`STARTED`, `TICK`, `FINISHED`, etc.). |
+| **Wiring** | Module connection graph. Defined programmatically, via `WiringBuilder`, or loaded from YAML/TOML configs. |
+| **VisualSpec** | JSON structure returned by `module.visualize()` with `render` type and `data` payload. |
+
+### Event Lifecycle
+
+Every simulation follows this sequence:
+```
+STARTED -> TICK (xN) -> FINISHED
+```
+
+`PAUSED`, `RESUMED`, `STOPPED`, and `ERROR` may also be emitted depending on runtime control flow.
+
+## License
+
+MIT. See `LICENSE.txt`.