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

[wshlavacek]

Summary

Adds BNGsim as an optional in-process simulation engine for PyBioNetGen.
The integration is a pure soft-import: if bngsim is not installed, every
simulation routes through the existing subprocess BNG2.pl / run_network / NFsim
path exactly as today. With bngsim absent, behavior is unchanged — the
contract this PR is built around.

bngsim is never an install dependency. It is offered as an optional extra
(pip install bionetgen[bngsim], floor bngsim>=0.9.10) and gated at runtime
by a single BNGSIM_AVAILABLE flag; a BIONETGEN_NO_BNGSIM=1 kill-switch and a
version floor (MINIMUM_BNGSIM_VERSION = 0.9.10) force the legacy path when set
or when an older bngsim is present.

New capabilities (only active when bngsim is installed)

• In-process ODE, SSA, and NFsim simulation via bngsim (no Perl subprocess
  for the simulation step).
• Multi-format input with auto-detection — .bngl, .net, SBML (.xml),
  and Antimony (.ant) — plus an explicit override (--format / format=).
• tfun (inline tabulated functions): models using tfun(...) run correctly
  in-process (the bridge routes them to the interpreted RHS, since bngsim
  codegen + tfun is not yet stable).
• Codegen (compiled C RHS) for accelerated ODE simulation, with automatic
  fallback to the interpreted RHS where codegen is unsafe.
• Threaded parameter scanning and steady-state solving, with an optional
  persistent helper process to amortize bngsim import cost across scan points.
• New CLI flags on run: --method, --format, --timeout, --no-bngsim.
• New bionetgen.run(...) kwargs: simulator= (default "auto"), method=,
  format=, t_span=, n_points=, timeout=.

Issues addressed

Closes #66 — BNGsim integration: in-process simulation + multi-format support.
Closes #65 — tfun (inline tabulated functions) now run in-process.

Addresses #6 — input-format auto-detection removes the hard file-extension
requirement (with an explicit --format/format= hint).
Addresses #22 — the in-process engine removes Perl from the simulation step
(a different mechanism than the py-perl5 suggestion, but the same goal); left
open for the remaining broader work.

Scope of the diff

Purely additive against upstream/main — 20 files, +7976/−53 (the deletions are
re-routings inside three existing entry points, not feature removals):

• 3 new modules: core/tools/bngsim_bridge.py (the soft-import + routing
  core), core/tools/bngsim_backend_helper.py, core/tools/bngsim_parameter_scan.py.
• 3 pure-additive touchpoints: __init__.py (+3, export BNGSIM_AVAILABLE),
  core/tools/__init__.py (+13), core/tools/info.py (+16, banner line).
• 3 routing touchpoints (route through the bridge iff available, else legacy):
  main.py (the new CLI flags), core/tools/cli.py, modelapi/runner.py.
• Packaging: setup.py (+9) — adds only extras_require={"bngsim": [...]};
  bngsim stays out of install_requires.
• Tests: tests/conftest.py (+34, require_bng2/require_atomizer fixtures)
  and 9 new tests/test_bngsim_*.py files.

Test plan / verification

• With bngsim 0.9.10 installed: 248 bngsim tests pass; a model runs through
  the in-process path and produces output.
• With bngsim genuinely uninstalled: the bngsim test files give
  239 passed / 9 skipped / 0 errors (the 9 skips are the real-engine paths,
  guarded by skipif(not BNGSIM_AVAILABLE)); no collection-time import bngsim.
• Legacy-path equivalence: test_model_running_CLI is identical on this branch
  with bngsim disabled vs. pristine upstream/main (same pre-existing results) —
  i.e. zero regression on the no-bngsim path.
• black --check clean on all added/changed files; Python 3.8–3.12 safe.

Trying the optional engine (not required to use this PR)

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 the in-process
engine now, install a prebuilt wheel from the release:

• macOS / Python 3.12 wheels (arm64 + x86_64): https://github.com/wshlavacek/PyBioNetGen/releases/tag/bngsim-wheels-0.9.10
• Other platforms / Python versions: build from source (scikit-build-core).

CI does not install bngsim, so none of this affects the green-checks contract.