Prepare for amici>=1.0.0

Author: dweindl

pypesto/hierarchical/inner_calculator_collector.py

@@ -225,7 +225,7 @@ def _get_quantitative_data_mask(
     ) -> list[np.ndarray]:
         # transform experimental data
         edatas = [
-            amici.numpy.ExpDataView(edata)["observedData"] for edata in edatas
+            amici.numpy.ExpDataView(edata)["observed_data"] for edata in edatas
         ]
 
         quantitative_data_mask = [

pypesto/hierarchical/relative/problem.py

@@ -123,7 +123,9 @@ def inner_problem_from_petab_problem(
     )
 
     # transform experimental data
-    data = [amici.numpy.ExpDataView(edata)["observedData"] for edata in edatas]
+    data = [
+        amici.numpy.ExpDataView(edata)["observed_data"] for edata in edatas
+    ]
 
     # matrixify
     ix_matrices = ix_matrices_from_arrays(ixs, data)
@@ -135,7 +137,7 @@ def inner_problem_from_petab_problem(
             meas_indices[2] for meas_indices in ixs[par.inner_parameter_id]
         ]
         par.observable_ids = [
-            amici_model.getObservableIds()[obs_idx]
+            amici_model.get_observable_ids()[obs_idx]
             for obs_idx in par.observable_indices
         ]
 
@@ -256,7 +258,7 @@ def ixs_for_measurement_specific_parameters(
     a sorted list of non-unique time points for which there are measurements.
     """
     ixs_for_par = {}
-    observable_ids = amici_model.getObservableIds()
+    observable_ids = amici_model.get_observable_ids()
 
     simulation_conditions = (
         petab_problem.get_simulation_conditions_from_measurement_df()

pypesto/objective/amici/amici.py

@@ -204,7 +204,7 @@ def __init__(
 
         if (
             self.guess_steadystate is not False
-            and self.amici_model.getSteadyStateSensitivityMode()
+            and self.amici_model.get_steady_state_sensitivity_mode()
             == amici.SteadyStateSensitivityMode.integrationOnly
         ):
             if self.guess_steadystate:
@@ -226,7 +226,7 @@ def __init__(
                 "data": {
                     iexp: {}
                     for iexp, edata in enumerate(self.edatas)
-                    if len(edata.fixedParametersPreequilibration)
+                    if len(edata.fixed_parameters_pre_equilibration)
                 },
             }
         # optimization parameter names
@@ -331,7 +331,7 @@ def __getstate__(self) -> dict:
         try:
             # write amici solver settings to file
             try:
-                amici.writeSolverSettingsToHDF5(self.amici_solver, _file)
+                amici.write_solver_settings_to_hdf5(self.amici_solver, _file)
             except AttributeError as e:
                 e.args += (
                     "Pickling the AmiciObjective requires an AMICI "
@@ -415,10 +415,10 @@ def check_sensi_orders(
         if max_sensi_order is None:
             max_sensi_order = 1
             # check whether it is ok to request 2nd order
-            sensi_mthd = self.amici_solver.getSensitivityMethod()
-            mthd_fwd = amici.SensitivityMethod_forward
+            sensi_mthd = self.amici_solver.get_sensitivity_method()
+            mthd_fwd = amici.SensitivityMethod.forward
             if mode == MODE_FUN and (
-                self.amici_model.o2mode
+                self.amici_model.get_second_order_mode()
                 or (sensi_mthd == mthd_fwd and self.fim_for_hess)
             ):
                 max_sensi_order = 2
@@ -469,7 +469,7 @@ def call_unprocessed(
                     if mode == MODE_FUN
                     else amici.RDataReporting.residuals
                 )
-        self.amici_solver.setReturnDataReportingMode(amici_reporting)
+        self.amici_solver.set_return_data_reporting_mode(amici_reporting)
 
         # update steady state
         if (
@@ -601,7 +601,9 @@ def apply_custom_timepoints(self) -> None:
         """
         if self.custom_timepoints is not None:
             for index in range(len(self.edatas)):
-                self.edatas[index].setTimepoints(self.custom_timepoints[index])
+                self.edatas[index].set_timepoints(
+                    self.custom_timepoints[index]
+                )
 
     def set_custom_timepoints(
         self,

pypesto/objective/amici/amici_calculator.py

@@ -96,9 +96,9 @@ def __call__(
 
         if sensi_order == 2 and fim_for_hess:
             # we use the FIM
-            amici_solver.setSensitivityOrder(sensi_order - 1)
+            amici_solver.set_sensitivity_order(sensi_order - 1)
         else:
-            amici_solver.setSensitivityOrder(sensi_order)
+            amici_solver.set_sensitivity_order(sensi_order)
 
         # fill in parameters
         amici.petab.conditions.fill_in_parameters(
@@ -110,7 +110,7 @@ def __call__(
         )
 
         # run amici simulation
-        rdatas = amici.runAmiciSimulations(
+        rdatas = amici.run_simulations(
             amici_model,
             amici_solver,
             edatas,
@@ -121,7 +121,7 @@ def __call__(
             and mode == MODE_RES
             and 1 in sensi_orders
         ):
-            if not amici_model.getAddSigmaResiduals() and any(
+            if not amici_model.get_add_sigma_residuals() and any(
                 (
                     (r["ssigmay"] is not None and np.any(r["ssigmay"]))
                     or (r["ssigmaz"] is not None and np.any(r["ssigmaz"]))
@@ -176,8 +176,8 @@ def calculate_function_values(
         sensi_orders, mode, dim
     )
 
-    par_sim_ids = list(amici_model.getParameterIds())
-    sensi_method = amici_solver.getSensitivityMethod()
+    par_sim_ids = list(amici_model.get_parameter_ids())
+    sensi_method = amici_solver.get_sensitivity_method()
 
     # iterate over return data
     for data_ix, rdata in enumerate(rdatas):
@@ -213,7 +213,7 @@ def calculate_function_values(
                 # Hessian
             if 2 in sensi_orders:
                 if (
-                    sensi_method != amici.SensitivityMethod_forward
+                    sensi_method != amici.SensitivityMethod.forward
                     or not fim_for_hess
                 ):
                     raise ValueError("AMICI cannot compute Hessians yet.")

pypesto/petab/objective_creator.py

@@ -170,7 +170,7 @@ def _create_model(self) -> amici.Model:
         module = amici.import_model_module(
             module_name=self.model_name, module_path=self.output_folder
         )
-        model = module.getModel()
+        model = module.get_model()
         check_model(
             amici_model=model,
             petab_problem=self.petab_problem,
@@ -238,7 +238,7 @@ def create_solver(
         if model is None:
             model = self.create_model(verbose=verbose)
 
-        solver = model.getSolver()
+        solver = model.create_solver()
         return solver
 
     def create_edatas(

pypesto/predict/amici_predictor.py

@@ -361,7 +361,7 @@ def _default_output(
             to AMICI was successful (``status == 0``), before writing the output.
             """
             amici_nt = [
-                len(edata.getTimepoints())
+                len(edata.get_timepoints())
                 for edata in self.amici_objective.edatas
             ]
             amici_ny = len(self.output_ids)

pypesto/visualize/model_fit.py

@@ -240,7 +240,7 @@ def time_trajectory_model(
         problem = result.problem
     # add timepoints as needed
     if timepoints is None:
-        end_time = max(problem.objective.edatas[0].getTimepoints())
+        end_time = max(problem.objective.edatas[0].get_timepoints())
         timepoints = np.linspace(start=0, stop=end_time, num=n_timepoints)
 
     # get rdatas
@@ -422,13 +422,13 @@ def _time_trajectory_model_with_states(
     axes = np.atleast_2d(axes)
 
     for i_cond, rdata in enumerate(rdatas):
-        amici.plotting.plotStateTrajectories(
+        amici.plotting.plot_state_trajectories(
             rdata=rdata,
             state_indices=state_indices,
             ax=axes[i_cond, 0],
             model=model,
         )
-        amici.plotting.plotObservableTrajectories(
+        amici.plotting.plot_observable_trajectories(
             rdata=rdata,
             observable_indices=observable_indices,
             ax=axes[i_cond, 1],
@@ -468,13 +468,14 @@ def _time_trajectory_model_without_states(
     observable_indices = None
     if observable_ids is not None:
         observable_indices = [
-            model.getObservableIds().index(obs_id) for obs_id in observable_ids
+            model.get_observable_ids().index(obs_id)
+            for obs_id in observable_ids
         ]
 
     fig, axes = plt.subplots(len(rdatas))
 
     for i_cond, rdata in enumerate(rdatas):
-        amici.plotting.plotObservableTrajectories(
+        amici.plotting.plot_observable_trajectories(
             rdata=rdata,
             observable_indices=observable_indices,
             ax=axes[i_cond] if len(rdatas) > 1 else axes,

test/petab/test_petab_import.py

@@ -56,7 +56,7 @@ def test_1_compile(self):
             )
 
             # observable ids
-            model_obs_ids = list(model.getObservableIds())
+            model_obs_ids = list(model.get_observable_ids())
             problem_obs_ids = list(petab_problem.get_observable_ids())
             self.assertEqual(set(model_obs_ids), set(problem_obs_ids))
 
@@ -123,11 +123,11 @@ def test_check_gradients(self):
         )
 
         objective = importer.create_problem().objective
-        objective.amici_solver.setSensitivityMethod(
-            amici.SensitivityMethod_forward
+        objective.amici_solver.set_sensitivity_method(
+            amici.SensitivityMethod.forward
         )
-        objective.amici_solver.setAbsoluteTolerance(1e-10)
-        objective.amici_solver.setRelativeTolerance(1e-12)
+        objective.amici_solver.set_absolute_tolerance(1e-10)
+        objective.amici_solver.set_relative_tolerance(1e-12)
 
         self.assertFalse(
             objective.check_gradients_match_finite_differences(
@@ -157,11 +157,11 @@ def test_plist_mapping():
         objective_creator.create_objective()
     )
     objective = problem.objective
-    objective.amici_solver.setSensitivityMethod(
+    objective.amici_solver.set_sensitivity_method(
         amici.SensitivityMethod.forward
     )
-    objective.amici_solver.setAbsoluteTolerance(1e-16)
-    objective.amici_solver.setRelativeTolerance(1e-15)
+    objective.amici_solver.set_absolute_tolerance(1e-16)
+    objective.amici_solver.set_relative_tolerance(1e-15)
 
     # slightly perturb the parameters to avoid vanishing gradients
     par = np.asarray(petab_importer.petab_problem.x_nominal_free_scaled) * 1.01
@@ -187,7 +187,7 @@ def test_plist_mapping():
     #  `plist` later on)
     fixed_model_par_ids = ["init_b10", "init_bcry"]
     fixed_model_par_idxs = [
-        objective.amici_model.getParameterIds().index(id)
+        objective.amici_model.get_parameter_ids().index(id)
         for id in fixed_model_par_ids
     ]
     fixed_idxs = [problem.x_names.index(id) for id in fixed_ids]
@@ -226,13 +226,13 @@ def test_max_sensi_order():
     hess = objective(par, sensi_orders=(2,))
     assert hess.shape == (npar, npar)
     assert (hess != 0).any()
-    objective.amici_solver.setSensitivityMethod(
-        amici.SensitivityMethod_adjoint
+    objective.amici_solver.set_sensitivity_method(
+        amici.SensitivityMethod.adjoint
     )
     with pytest.raises(ValueError):
         objective(par, sensi_orders=(2,))
-    objective.amici_solver.setSensitivityMethod(
-        amici.SensitivityMethod_forward
+    objective.amici_solver.set_sensitivity_method(
+        amici.SensitivityMethod.forward
     )
 
     # fix max_sensi_order to 1

test/visualize/test_visualize.py

@@ -1080,12 +1080,12 @@ def test_sampling_prediction_trajectories():
     post_processor_amici_x = functools.partial(
         post_processor,
         output_type=pypesto.C.AMICI_X,
-        output_ids=result.problem.objective.amici_model.getStateIds(),
+        output_ids=result.problem.objective.amici_model.get_state_ids(),
     )
     predictor = predict.AmiciPredictor(
         result.problem.objective,
         post_processor=post_processor_amici_x,
-        output_ids=result.problem.objective.amici_model.getStateIds(),
+        output_ids=result.problem.objective.amici_model.get_state_ids(),
     )
 
     sample_ensemble = ensemble.Ensemble.from_sample(

tox.ini

@@ -57,6 +57,9 @@ deps =
 #  with the pseudo-v2 format for pysb tests instead of `main`
 #    git+https://github.com/PEtab-dev/petab_test_suite@main
     git+https://github.com/PEtab-dev/petab_test_suite@10ffb050380933b60ac192962bf9550a9df65a9c
+commands_pre =
+    python3 -m pip uninstall -y amici
+    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@snakecase\#egg=amici&subdirectory=python/sdist
 commands =
     pytest --cov=pypesto --cov-report=xml --cov-append \
         test/base --durations=0 \
@@ -84,7 +87,7 @@ deps =
 #  to skip re-installation, run `tox -e petab --override testenv:petab.commands_pre=`
 commands_pre =
     python3 -m pip uninstall -y amici
-    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@main\#egg=amici&subdirectory=python/sdist
+    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@snakecase\#egg=amici&subdirectory=python/sdist
 commands =
 # FIXME: Until we have proper PEtab v2 import
 #  we need `10ffb050380933b60ac192962bf9550a9df65a9c`
@@ -125,6 +128,9 @@ commands =
     # workaround as ipopt has incomplete build
     pytest --cov=pypesto --cov-report=xml --cov-append \
         test/hierarchical
+commands_pre =
+    python3 -m pip uninstall -y amici
+    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@snakecase\#egg=amici&subdirectory=python/sdist
 description =
     Test hierarchical optimization module
 
@@ -135,6 +141,9 @@ commands =
         test/select
 description =
     Test model selection functionality
+commands_pre =
+    python3 -m pip uninstall -y amici
+    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@snakecase\#egg=amici&subdirectory=python/sdist
 
 [testenv:notebooks1]
 allowlist_externals = bash
@@ -143,6 +152,9 @@ commands =
     bash test/run_notebook.sh 1
 description =
     Run notebooks 1
+commands_pre =
+    python3 -m pip uninstall -y amici
+    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@snakecase\#egg=amici&subdirectory=python/sdist
 
 [testenv:notebooks2]
 allowlist_externals = bash
@@ -151,6 +163,9 @@ commands =
     bash test/run_notebook.sh 2
 description =
     Run notebooks 2
+commands_pre =
+    python3 -m pip uninstall -y amici
+    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@snakecase\#egg=amici&subdirectory=python/sdist
 
 # Management, docs
 
@@ -161,6 +176,9 @@ commands =
     sphinx-build -W -b html doc/ doc/_build/html
 description =
     Test whether docs build passes
+commands_pre =
+    python3 -m pip uninstall -y amici
+    python3 -m pip install git+https://github.com/AMICI-dev/amici.git@snakecase\#egg=amici&subdirectory=python/sdist
 
 [testenv:size]
 skip_install = true