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Refactor: Add JAX Hessian computation and correct Fitter.solve #2

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Refactor: Add JAX Hessian computation and correct Fitter.solve #2

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10 changes: 9 additions & 1 deletion src/freeflux/analysis/fit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -530,6 +530,7 @@ def solve(
max_iters = 400,
show_progress = True,
rng = None,
use_jax_experimental = False # Added parameter
):
'''
Parameters
Expand All @@ -546,11 +547,18 @@ def solve(
Maximum # of iterations.
show_progress: bool
Whether to show the progress bar.
use_jax_experimental: bool
Whether to attempt using the JAX-based calculation pathway.
'''

self._check_dependencies(fit_measured_fluxes)

optModel = MFAModel(self.model, fit_measured_fluxes, solver)
# Pass use_jax_experimental to MFAModel constructor
optModel = MFAModel(self.model,
fit_measured_fluxes,
solver,
use_jax=use_jax_experimental and hasattr(self.model, 'jax_prepared') and self.model.jax_prepared)

optModel.build_objective()
optModel.build_gradient()
optModel.build_flux_bound_constraints()
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30 changes: 30 additions & 0 deletions src/freeflux/analysis/inst_fit.py
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Expand Up @@ -340,6 +340,36 @@ def prepare(self, dilution_from = None, n_jobs = 1):
self._estimate_fluxes_range(self.model.unbalanced_metabolites)
self._set_default_concentration_bounds()
self._estimate_concentrations_range()

# --- JAX specific preparations for Instationary ---
if hasattr(self.model, 'use_jax_experimental') and self.model.use_jax_experimental:
# Ensure JAX is available (copied from Fitter.prepare)
try:
from ..utils.utils import JAX_INSTALLED as JAX_READY
except ImportError:
JAX_READY = False
if not JAX_READY:
raise RuntimeError("JAX features requested for InstFitter but JAX is not installed or not found.")

# Common JAX prep (already in Fitter.prepare, but if InstFitter.prepare is called directly)
self.calculator._lambdify_matrix_As_and_Bs_jax()
self.calculator._prepare_substrate_MDVs_jax()
self.calculator._prepare_matrix_derivatives_jax() # For A, B derivatives

# Instationary specific JAX prep
self.calculator._lambdify_matrix_Ms_jax()
self.calculator._prepare_matrix_Ms_derivatives_p_jax() # After matrix_Ms_der_p (numpy) is computed
self.calculator._prepare_initial_conditions_jax() # After initial_matrix_Xs/Ys etc (numpy) are computed

# Substrate derivatives for 'inst' kind need to be prepared for JAX
# This assumes self.model.substrate_MDVs_der_p was populated with 'inst' kind by the numpy path
self.calculator._prepare_substrate_MDVs_der_p_jax()

# For measured_fluxes_der_p_jax with 'inst' kind
self.model.jax_flux_derivatives_enabled = True
self.calculator._calculate_measured_fluxes_derivative_p('inst') # Ensure JAX version for 'inst' is populated

self.model.jax_prepared_inst = True # Signal that JAX data for instationary model is ready


def _check_dependencies(self, fit_measured_fluxes):
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