viva-copasi 0.1.2__tar.gz

viva_copasi-0.1.2/LICENSE

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+MIT License
+
+Copyright (c) 2026 Vivarium Collective
+
+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.

viva_copasi-0.1.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: viva-copasi
+Version: 0.1.2
+Summary: process-bigraph-compatible COPASI Steps and Processes (UTC + SteadyState)
+License: MIT
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: process-bigraph>=1.8.5
+Requires-Dist: bigraph-schema
+Requires-Dist: copasi-basico
+Requires-Dist: python-copasi
+Requires-Dist: viva-superpowers
+Requires-Dist: pyyaml
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: bigraph-viz; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Dynamic: license-file
+
+# viva-copasi
+
+process-bigraph-compatible COPASI Steps and Processes for SBML model simulation.
+
+Exposes any SBML kinetic model as a `process-bigraph` Step or Process so it can
+be composed with other simulators in a bigraph document, using
+[COPASI](https://copasi.org/) / [basico](https://basico.readthedocs.io/) as the
+simulation back-end.
+
+## Installation
+
+```bash
+uv venv .venv && source .venv/bin/activate
+uv pip install -e .
+```
+
+## Quick Start
+
+```python
+from importlib.resources import files
+from process_bigraph import Composite, gather_emitter_results
+from viva_copasi.composites import build_composite, register_copasi
+
+# Resolve the bundled Repressilator model
+model_path = str(files('viva_copasi.composites').joinpath('repressilator.xml'))
+
+# Build and run the incremental UTC process composite
+sim = build_composite('utc-process')
+for _ in range(10):
+    sim.update({}, 1.0)   # advance 1 time unit per step
+
+results = gather_emitter_results(sim)
+print(results[('emitter',)][-1])
+```
+
+## Classes
+
+- `CopasiUTCStep` — one-shot Uniform Time Course (UTC) trajectory (Step)
+- `CopasiUTCProcess` — incremental UTC simulation (Process)
+- `CopasiSteadyStateStep` — steady-state solve (Step)
+- `BaseCopasi` — shared model-load mixin (SBML parsing, species/reaction indexing)
+
+All classes accept a `model_source` config key pointing to an SBML or COPASI
+model file (path or URL).
+
+## Composites
+
+Three discoverable composites in `viva_copasi/composites/`:
+
+| Name | Type | Description |
+|---|---|---|
+| `utc-step` | Step | One-shot UTC trajectory; returns full time series in a single `update()` call |
+| `utc-process` | Process | Incremental UTC; advances one interval per `update()`, emitting concentrations + fluxes |
+| `steady-state` | Step | Steady-state solve; returns equilibrium concentrations and reaction fluxes |
+
+Each ships with the bundled SBML model
+[BIOMD0000000012](https://www.ebi.ac.uk/biomodels/BIOMD0000000012) — the Elowitz
+& Leibler 2000 Repressilator.
+
+Load a composite by name:
+
+```python
+from viva_copasi.composites import build_composite, list_composite_specs
+
+print(list_composite_specs())   # ['steady-state', 'utc-process', 'utc-step']
+sim = build_composite('utc-process')
+```
+
+Override the model or parameters:
+
+```python
+sim = build_composite('utc-step', overrides={
+    'model_source': '/path/to/my_model.xml',
+    'time': 50.0,
+    'n_points': 51,
+})
+```
+
+## API
+
+### `CopasiUTCStep` (Step)
+
+One-shot UTC trajectory.
+
+Config: `model_source` (str), `time` (float, default 1.0), `n_points` (int, default 2).
+
+Outputs: `result` — dict with keys `time` (list), `columns` (list), `values` (list of rows).
+
+### `CopasiUTCProcess` (Process)
+
+Incremental UTC simulation.
+
+Config: `model_source` (str), `time` (float, default 1.0), `intervals` (int, default 10).
+
+Outputs: `species_concentrations` (map[float]), `fluxes` (map[float]), `time` (list[float]).
+
+### `CopasiSteadyStateStep` (Step)
+
+Steady-state solve.
+
+Config: `model_source` (str).
+
+Outputs: `results` — dict with keys `time`, `species_concentrations`, `fluxes`.
+
+### `register_copasi(core=None)`
+
+Register all COPASI process classes, the RAM emitter, and the
+`SpeciesConcentrationsPlot` visualization into a bigraph core.
+
+### `make_copasi_utc_document(...)` / `make_copasi_utc_process_document(...)` / `make_copasi_steady_state_document(...)`
+
+Programmatic composite-document factories for callers that want full control
+over wiring without a YAML file.
+
+## Tests
+
+```bash
+python -m pytest tests/ -q
+```
+
+## Demos
+
+```bash
+python demo/demo_report.py       # runs all 3 classes; saves demo/report.html
+python demo/composite_report.py  # runs utc-process composite; saves demo/utc-process-report.html
+```

viva_copasi-0.1.2/README.md

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+# viva-copasi
+
+process-bigraph-compatible COPASI Steps and Processes for SBML model simulation.
+
+Exposes any SBML kinetic model as a `process-bigraph` Step or Process so it can
+be composed with other simulators in a bigraph document, using
+[COPASI](https://copasi.org/) / [basico](https://basico.readthedocs.io/) as the
+simulation back-end.
+
+## Installation
+
+```bash
+uv venv .venv && source .venv/bin/activate
+uv pip install -e .
+```
+
+## Quick Start
+
+```python
+from importlib.resources import files
+from process_bigraph import Composite, gather_emitter_results
+from viva_copasi.composites import build_composite, register_copasi
+
+# Resolve the bundled Repressilator model
+model_path = str(files('viva_copasi.composites').joinpath('repressilator.xml'))
+
+# Build and run the incremental UTC process composite
+sim = build_composite('utc-process')
+for _ in range(10):
+    sim.update({}, 1.0)   # advance 1 time unit per step
+
+results = gather_emitter_results(sim)
+print(results[('emitter',)][-1])
+```
+
+## Classes
+
+- `CopasiUTCStep` — one-shot Uniform Time Course (UTC) trajectory (Step)
+- `CopasiUTCProcess` — incremental UTC simulation (Process)
+- `CopasiSteadyStateStep` — steady-state solve (Step)
+- `BaseCopasi` — shared model-load mixin (SBML parsing, species/reaction indexing)
+
+All classes accept a `model_source` config key pointing to an SBML or COPASI
+model file (path or URL).
+
+## Composites
+
+Three discoverable composites in `viva_copasi/composites/`:
+
+| Name | Type | Description |
+|---|---|---|
+| `utc-step` | Step | One-shot UTC trajectory; returns full time series in a single `update()` call |
+| `utc-process` | Process | Incremental UTC; advances one interval per `update()`, emitting concentrations + fluxes |
+| `steady-state` | Step | Steady-state solve; returns equilibrium concentrations and reaction fluxes |
+
+Each ships with the bundled SBML model
+[BIOMD0000000012](https://www.ebi.ac.uk/biomodels/BIOMD0000000012) — the Elowitz
+& Leibler 2000 Repressilator.
+
+Load a composite by name:
+
+```python
+from viva_copasi.composites import build_composite, list_composite_specs
+
+print(list_composite_specs())   # ['steady-state', 'utc-process', 'utc-step']
+sim = build_composite('utc-process')
+```
+
+Override the model or parameters:
+
+```python
+sim = build_composite('utc-step', overrides={
+    'model_source': '/path/to/my_model.xml',
+    'time': 50.0,
+    'n_points': 51,
+})
+```
+
+## API
+
+### `CopasiUTCStep` (Step)
+
+One-shot UTC trajectory.
+
+Config: `model_source` (str), `time` (float, default 1.0), `n_points` (int, default 2).
+
+Outputs: `result` — dict with keys `time` (list), `columns` (list), `values` (list of rows).
+
+### `CopasiUTCProcess` (Process)
+
+Incremental UTC simulation.
+
+Config: `model_source` (str), `time` (float, default 1.0), `intervals` (int, default 10).
+
+Outputs: `species_concentrations` (map[float]), `fluxes` (map[float]), `time` (list[float]).
+
+### `CopasiSteadyStateStep` (Step)
+
+Steady-state solve.
+
+Config: `model_source` (str).
+
+Outputs: `results` — dict with keys `time`, `species_concentrations`, `fluxes`.
+
+### `register_copasi(core=None)`
+
+Register all COPASI process classes, the RAM emitter, and the
+`SpeciesConcentrationsPlot` visualization into a bigraph core.
+
+### `make_copasi_utc_document(...)` / `make_copasi_utc_process_document(...)` / `make_copasi_steady_state_document(...)`
+
+Programmatic composite-document factories for callers that want full control
+over wiring without a YAML file.
+
+## Tests
+
+```bash
+python -m pytest tests/ -q
+```
+
+## Demos
+
+```bash
+python demo/demo_report.py       # runs all 3 classes; saves demo/report.html
+python demo/composite_report.py  # runs utc-process composite; saves demo/utc-process-report.html
+```

viva_copasi-0.1.2/pbg_copasi/__init__.py

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+"""Back-compat shim: ``pbg_copasi`` was renamed to ``viva_copasi``.
+
+Part of the pbg -> viva rebrand (the GitHub repo is already
+``vivarium-collective/viva-copasi``). This shim keeps every existing consumer
+working during the deprecation window:
+
+  * ``import pbg_copasi`` / ``from pbg_copasi import X`` works (re-exports
+    the new package's top-level ``__all__``);
+  * ``import pbg_copasi.<sub>`` transparently resolves to
+    ``viva_copasi.<sub>`` via a meta-path finder (so
+    ``from pbg_copasi.simulators import ...`` still resolves); and
+  * ``python -m pbg_copasi.<sub>`` still executes.
+
+Importing anything under this package emits a one-time
+:class:`DeprecationWarning`. Update imports to ``viva_copasi``; this shim is
+removed in a future major release.
+"""
+from __future__ import annotations
+
+import importlib
+import importlib.abc
+import importlib.util
+import sys
+import warnings
+
+warnings.warn(
+    "pbg_copasi is renamed to viva_copasi; update your imports "
+    "(the pbg_copasi alias is removed in a future major release).",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
+_OLD = "pbg_copasi."
+_NEW = "viva_copasi."
+
+
+class _Redirect(importlib.abc.MetaPathFinder, importlib.abc.Loader):
+    """Forward ``pbg_copasi.<sub>`` imports to ``viva_copasi.<sub>``."""
+
+    def _target(self, name: str) -> str:
+        return _NEW + name[len(_OLD):]
+
+    def find_spec(self, name, path=None, target=None):
+        if not name.startswith(_OLD):
+            return None
+        real = importlib.util.find_spec(self._target(name))
+        if real is None:
+            return None
+        spec = importlib.util.spec_from_loader(
+            name,
+            self,
+            origin=real.origin,
+            is_package=real.submodule_search_locations is not None,
+        )
+        if real.submodule_search_locations is not None:
+            spec.submodule_search_locations = list(real.submodule_search_locations)
+        return spec
+
+    def create_module(self, spec):
+        # Alias the fully-initialized new-package module under BOTH names so
+        # `import a.b` and identity checks against either name agree.
+        mod = importlib.import_module(self._target(spec.name))
+        sys.modules[spec.name] = mod
+        return mod
+
+    def exec_module(self, module):  # already executed by import_module
+        pass
+
+    def get_code(self, name):
+        # Support `python -m pbg_copasi.<sub>`: runpy needs a code object.
+        target = self._target(name)
+        return importlib.util.find_spec(target).loader.get_code(target)
+
+
+sys.meta_path.insert(0, _Redirect())
+
+_new = importlib.import_module("viva_copasi")
+__version__ = getattr(_new, "__version__", "0.0.0")
+# Re-export the new package's public surface (if any is declared).
+globals().update({k: getattr(_new, k) for k in getattr(_new, "__all__", [])})

viva_copasi-0.1.2/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "viva-copasi"
+version = "0.1.2"
+description = "process-bigraph-compatible COPASI Steps and Processes (UTC + SteadyState)"
+readme = "README.md"
+license = { text = "MIT" }
+requires-python = ">=3.11"
+dependencies = [
+    "process-bigraph>=1.8.5",
+    "bigraph-schema",
+    "copasi-basico",
+    "python-copasi",
+    "viva-superpowers",
+    "pyyaml",
+]
+
+[project.optional-dependencies]
+dev = ["pytest", "bigraph-viz", "matplotlib"]
+
+[tool.uv.sources]
+# viva-superpowers (renamed from pbg-superpowers) is git-only, not on PyPI.
+viva-superpowers = { git = "https://github.com/vivarium-collective/viva-superpowers.git", branch = "main" }
+
+[tool.setuptools.packages.find]
+include = ["viva_copasi*", "pbg_copasi"]  # pbg_copasi = deprecation shim
+
+[tool.setuptools.package-data]
+"viva_copasi.composites" = ["*.xml", "*.yaml"]

viva_copasi-0.1.2/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

viva_copasi-0.1.2/tests/test_composites.py

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+"""Integration tests for viva-copasi composite specs.
+
+Tests cover:
+- Discovery: list_composite_specs() returns the three expected names.
+- Structural validity: each *.composite.yaml has the required top-level keys.
+- Instantiation: build_composite() produces a runnable process_bigraph.Composite.
+- Short run: the UTC process composite advances and emits data.
+
+Test model: Elowitz 2000 Repressilator (BIOMD0000000012), bundled at
+viva_copasi/composites/repressilator.xml.
+"""
+from pathlib import Path
+
+import pytest
+from process_bigraph import Composite, allocate_core, gather_emitter_results
+from process_bigraph.emitter import RAMEmitter
+
+from viva_copasi.composites import (
+    list_composite_specs,
+    load_composite_spec,
+    build_composite,
+    register_copasi,
+    make_copasi_utc_process_document,
+    make_copasi_steady_state_document,
+    _COMPOSITES_DIR,
+)
+from viva_copasi.processes import (
+    CopasiUTCStep,
+    CopasiSteadyStateStep,
+    CopasiUTCProcess,
+)
+
+# Repressilator model — same file bundled in the composites package dir.
+BUNDLED_MODEL = str(_COMPOSITES_DIR / "repressilator.xml")
+
+
+@pytest.fixture
+def core():
+    """Minimal core with all COPASI classes + RAM emitter registered."""
+    return register_copasi()
+
+
+# ---------------------------------------------------------------------------
+# Discovery
+# ---------------------------------------------------------------------------
+
+def test_list_composite_specs_returns_three():
+    """Discovery returns the three expected composite names."""
+    specs = list_composite_specs()
+    assert 'utc-step' in specs
+    assert 'utc-process' in specs
+    assert 'steady-state' in specs
+
+
+# ---------------------------------------------------------------------------
+# Structural validity
+# ---------------------------------------------------------------------------
+
+def test_utc_step_spec_well_formed():
+    """utc-step.composite.yaml has required top-level keys."""
+    spec = load_composite_spec('utc-step')
+    assert 'name' in spec
+    assert 'state' in spec
+    assert spec['name'] == 'utc-step'
+    assert 'copasi_utc' in spec['state']
+    assert spec['state']['copasi_utc']['address'] == 'local:CopasiUTCStep'
+
+
+def test_utc_process_spec_well_formed():
+    """utc-process.composite.yaml has required top-level keys."""
+    spec = load_composite_spec('utc-process')
+    assert 'name' in spec
+    assert 'state' in spec
+    assert spec['name'] == 'utc-process'
+    assert 'copasi_utc_process' in spec['state']
+    assert spec['state']['copasi_utc_process']['address'] == 'local:CopasiUTCProcess'
+
+
+def test_steady_state_spec_well_formed():
+    """steady-state.composite.yaml has required top-level keys."""
+    spec = load_composite_spec('steady-state')
+    assert 'name' in spec
+    assert 'state' in spec
+    assert spec['name'] == 'steady-state'
+    assert 'copasi_ss' in spec['state']
+    assert spec['state']['copasi_ss']['address'] == 'local:CopasiSteadyStateStep'
+
+
+# ---------------------------------------------------------------------------
+# build_composite — instantiation
+# ---------------------------------------------------------------------------
+
+def test_build_composite_utc_step(core):
+    """build_composite('utc-step') instantiates a Composite without error."""
+    sim = build_composite('utc-step', core=core)
+    assert sim is not None
+    assert isinstance(sim, Composite)
+
+
+def test_build_composite_utc_process(core):
+    """build_composite('utc-process') instantiates a Composite without error."""
+    sim = build_composite('utc-process', core=core)
+    assert sim is not None
+    assert isinstance(sim, Composite)
+
+
+def test_build_composite_steady_state(core):
+    """build_composite('steady-state') instantiates a Composite without error."""
+    sim = build_composite('steady-state', core=core)
+    assert sim is not None
+    assert isinstance(sim, Composite)
+
+
+# ---------------------------------------------------------------------------
+# End-to-end: UTC process composite — short run + emitter check
+# ---------------------------------------------------------------------------
+
+def test_utc_process_composite_short_run(core):
+    """CopasiUTCProcess composite runs 2 steps and emits species_concentrations."""
+    doc = make_copasi_utc_process_document(
+        model_source=BUNDLED_MODEL,
+        time=1.0,
+        intervals=5,
+    )
+    sim = Composite({'state': doc}, core=core)
+    sim.run(2.0)
+
+    stores = sim.state['stores']
+    assert 'species_concentrations' in stores
+    assert isinstance(stores['species_concentrations'], dict)
+    # Repressilator has 6 species
+    assert len(stores['species_concentrations']) >= 3
+
+
+def test_utc_process_composite_emitter(core):
+    """Emitter collects at least one record after a short run."""
+    doc = make_copasi_utc_process_document(
+        model_source=BUNDLED_MODEL,
+        time=1.0,
+        intervals=5,
+    )
+    sim = Composite({'state': doc}, core=core)
+    sim.run(2.0)
+
+    raw = gather_emitter_results(sim)
+    rows = raw[('emitter',)]
+    assert len(rows) >= 1
+    # Each row should have species_concentrations
+    row = rows[0]
+    assert 'species_concentrations' in row or 'fluxes' in row
+
+
+# ---------------------------------------------------------------------------
+# End-to-end: steady-state composite — single step
+# ---------------------------------------------------------------------------
+
+def test_steady_state_composite_runs(core):
+    """CopasiSteadyStateStep composite runs and populates results store."""
+    doc = make_copasi_steady_state_document(model_source=BUNDLED_MODEL)
+    sim = Composite({'state': doc}, core=core)
+    sim.run(1.0)
+
+    ss_stores = sim.state['ss_stores']
+    assert 'results' in ss_stores

viva_copasi-0.1.2/tests/test_model_loading.py

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+import pytest
+
+from viva_copasi.processes import _model_path_resolution
+
+
+def test_missing_relative_path_raises_with_context(tmp_path, monkeypatch):
+    monkeypatch.chdir(tmp_path)
+    with pytest.raises(FileNotFoundError) as e:
+        _model_path_resolution("does_not_exist.cps")
+    msg = str(e.value)
+    assert "does_not_exist.cps" in msg
+    assert str(tmp_path / "does_not_exist.cps") in msg
+    assert str(tmp_path) in msg
+
+
+def test_missing_absolute_path_raises(tmp_path):
+    with pytest.raises(FileNotFoundError):
+        _model_path_resolution(str(tmp_path / "nope.xml"))
+
+
+def test_url_passes_through():
+    url = "https://example.org/model.xml"
+    assert _model_path_resolution(url) == url
+
+
+def test_existing_absolute_path_unchanged(tmp_path):
+    f = tmp_path / "m.xml"
+    f.write_text("<sbml/>")
+    assert _model_path_resolution(str(f)) == str(f)