Optional BNGsim integration: in-process simulation + multi-format input

README.md

@@ -18,6 +18,12 @@ You will need both python (3.7 and above) and perl installed. Once both are avai
 $ pip install bionetgen
 ```
 
+### Optional: in-process simulation with BNGsim
+
+PyBioNetGen can optionally use [BNGsim](https://github.com/RuleWorld/bngsim) as an in-process simulation engine (ODE/SSA/NFsim, multi-format input). This is fully opt-in: if BNGsim is not installed, every simulation uses the existing subprocess `BNG2.pl` path and behavior is unchanged. BNGsim is never a required dependency.
+
+BNGsim is a compiled extension and is not on PyPI yet, so `pip install bionetgen[bngsim]` will not resolve until it is published. To try it now, install a prebuilt wheel from the [release assets](https://github.com/wshlavacek/PyBioNetGen/releases/tag/bngsim-wheels-0.9.10) (macOS / Python 3.12; build from source on other platforms). PyBioNetGen requires BNGsim `0.9.10` or newer. Set `BIONETGEN_NO_BNGSIM=1` to force the legacy subprocess path even when BNGsim is installed. See the [BNGsim documentation page](https://pybionetgen.readthedocs.io/en/latest/bngsim.html) for details.
+
 ### Features 
 
 PyBioNetGen comes with a command line interface (CLI), based on [cement framework](https://builtoncement.com/), as well as a functional library that can be imported. The CLI can be used to run BNGL models, generate Jupyter notebooks and do rudimentary plotting. 

bionetgen/__init__.py

@@ -1,4 +1,5 @@
 from .core.defaults import defaults
+from .core.tools.bngsim_bridge import BNGSIM_AVAILABLE, BNGSIM_VERSION
 from .modelapi import bngmodel
 from .modelapi.runner import run
 from .simulator import sim_getter
@@ -8,6 +9,8 @@
 
 __all__ = [
     "defaults",
+    "BNGSIM_AVAILABLE",
+    "BNGSIM_VERSION",
     "bngmodel",
     "run",
     "sim_getter",

bionetgen/core/tools/__init__.py

@@ -7,3 +7,16 @@
 from .cli import BNGCLI
 from .visualize import BNGVisualize
 from .gdiff import BNGGdiff
+from .bngsim_bridge import (
+    BNGSIM_AVAILABLE,
+    BNGSIM_HAS_NFSIM,
+    BNGSIM_VERSION,
+    detect_input_format,
+    run_bngl_with_bngsim,
+    run_bngl_with_bngsim_backend_hook,
+    run_nfsim,
+    run_with_bngsim,
+)
+from .bngsim_backend_helper import (
+    execute_backend_payload as execute_bngsim_backend_payload,
+)