Update for amici>=1.0 (#663)

Update for amici>=1.0

Closes #661.

Author: dweindl

.github/workflows/install_deps.sh

@@ -70,7 +70,7 @@ install_r() {
 install_amici() {
   log_info "Installing AMICI dependencies..."
   if ! is_macos; then
-    apt_install swig libatlas-base-dev libhdf5-serial-dev libboost-all-dev
+    apt_install libhdf5-serial-dev libboost-all-dev
   fi
   log_info "Installing AMICI Python package..."
   python -m pip uninstall -y amici pyabc || true

.pre-commit-config.yaml

@@ -61,7 +61,7 @@ repos:
 
 # Configuration
 default_language_version:
-  python: python3.11
+  python: python3.13
 
 # Global exclusions
 exclude: |

doc/examples/petab_application.ipynb

@@ -31,7 +31,7 @@
    "outputs": [],
    "source": [
     "import petab.v1 as petab\n",
-    "from amici.petab import import_petab_problem\n",
+    "from amici.importers.petab.v1 import import_petab_problem\n",
     "\n",
     "from pyabc.petab import AmiciPetabImporter"
    ]
@@ -91,7 +91,7 @@
     "model = import_petab_problem(petab_problem)\n",
     "\n",
     "# the solver to numerically solve the ODE\n",
-    "solver = model.getSolver()\n",
+    "solver = model.create_solver()\n",
     "\n",
     "# import everything to pyABC\n",
     "importer = AmiciPetabImporter(petab_problem, model, solver)\n",
@@ -197,7 +197,7 @@
     "acceptor = pyabc.StochasticAcceptor(\n",
     "    pdf_norm_method = pyabc.ScaledPDFNorm())\n",
     "\n",
-    "abc = pyabc.ABCSMC(model, prior, kernel, \n",
+    "abc = pyabc.ABCSMC(model, prior, kernel,\n",
     "                   eps=temperature,\n",
     "                   acceptor=acceptor,\n",
     "                   sampler=sampler,\n",

doc/examples/petab_yaml2sbml.ipynb

@@ -36,7 +36,7 @@
     "\n",
     "import amici\n",
     "import numpy as np\n",
-    "from amici.petab import import_petab_problem\n",
+    "from amici.importers.petab.v1 import import_petab_problem\n",
     "\n",
     "import pyabc\n",
     "import pyabc.petab\n",
@@ -219,13 +219,13 @@
     "    sys.path.insert(0, os.path.abspath(amici_dir))\n",
     "model = import_petab_problem(\n",
     "    petab_problem,\n",
-    "    model_output_dir=amici_dir,\n",
+    "    output_dir=amici_dir,\n",
     "    verbose=False,\n",
     "    generate_sensitivity_code=False,\n",
     ")\n",
     "\n",
     "# the solver to numerically solve the ODE\n",
-    "solver = model.getSolver()\n",
+    "solver = model.create_solver()\n",
     "\n",
     "# import everything to pyABC\n",
     "importer = pyabc.petab.AmiciPetabImporter(petab_problem, model, solver)\n",
@@ -421,16 +421,16 @@
     "    if amici_dir not in sys.path:\n",
     "        sys.path.insert(0, os.path.abspath(amici_dir))\n",
     "    model_module = importlib.import_module(model_name)\n",
-    "    model = model_module.getModel()\n",
-    "    solver = model.getSolver()\n",
+    "    model = model_module.get_model()\n",
+    "    solver = model.create_solver()\n",
     "\n",
     "    # measurement times\n",
     "    n_time = 10\n",
     "    meas_times = np.linspace(0, 10, n_time)\n",
-    "    model.setTimepoints(meas_times)\n",
+    "    model.set_timepoints(meas_times)\n",
     "\n",
     "    # simulate with nominal parameters\n",
-    "    rdata = amici.runAmiciSimulation(model, solver)\n",
+    "    rdata = model.simulate(solver=solver)\n",
     "\n",
     "    # create noisy data\n",
     "    np.random.seed(2)\n",

pyabc/petab/amici.py

@@ -1,5 +1,7 @@
 """PEtab import with AMICI simulator."""
 
+from __future__ import annotations
+
 import copy
 import logging
 import os
@@ -18,18 +20,20 @@
 except ImportError:
     petab = C = None
     logger.error(
-        'Install PEtab (see https://github.com/icb-dcm/petab) to use '
+        'Install the PEtab library '
+        '(see https://github.com/PEtab-dev/libpetab-python/) to use '
         'the petab functionality, e.g. via `pip install pyabc[petab]`'
     )
 
 try:
     import amici
-    from amici.petab import petab_import as amici_petab_import
-    from amici.petab.simulations import LLH, RDATAS, simulate_petab
+    import amici.sim.sundials as asd
+    from amici.importers.petab.v1 import import_petab_problem
+    from amici.sim.sundials.petab.v1 import LLH, RDATAS, simulate_petab
 except ImportError:
-    amici = amici_petab_import = simulate_petab = LLH = RDATAS = None
+    amici = import_petab_problem = simulate_petab = LLH = RDATAS = None
     logger.error(
-        'Install amici (see https://github.com/icb-dcm/amici) to use '
+        'Install amici (see https://github.com/AMICI-dev/AMICI/) to use '
         'the amici functionality, e.g. via `pip install pyabc[amici]`'
     )
 
@@ -113,7 +117,7 @@ def __getstate__(self) -> dict:
         try:
             # write amici solver settings to file
             try:
-                amici.writeSolverSettingsToHDF5(self.amici_solver, _file)
+                asd.write_solver_settings_to_hdf5(self.amici_solver, _file)
             except AttributeError as e:
                 e.args += (
                     'Pickling the AmiciObjective requires an AMICI '
@@ -133,8 +137,8 @@ def __getstate__(self) -> dict:
     def __setstate__(self, state: dict):
         self.__dict__.update(state)
 
-        model = amici_petab_import.import_petab_problem(self.petab_problem)
-        solver = model.getSolver()
+        model = import_petab_problem(self.petab_problem)
+        solver = model.create_solver()
 
         _fd, _file = tempfile.mkstemp()
         try:
@@ -143,7 +147,7 @@ def __setstate__(self, state: dict):
                 f.write(state['amici_solver_settings'])
             # read in solver settings
             try:
-                amici.readSolverSettingsFromHDF5(_file, solver)
+                asd.read_solver_settings_from_hdf5(_file, solver)
             except AttributeError as err:
                 if not err.args:
                     err.args = ('',)
@@ -173,28 +177,26 @@ class AmiciPetabImporter(PetabImporter):
     amici_model:
         A corresponding compiled AMICI model that allows simulating data for
         parameters. If not provided, one is created using
-        `amici.petab_import.import_petab_problem`.
+        `amici.importers.petab.v1.import_petab_problem`.
     amici_solver:
         An AMICI solver to simulate the model. If not provided, one is created
-        using `amici_model.getSolver()`.
+        using `amici_model.create_solver()`.
     """
 
     def __init__(
         self,
         petab_problem: petab.Problem,
-        amici_model: 'amici.Model' = None,
-        amici_solver: 'amici.Solver' = None,
+        amici_model: amici.sim.sundials.Model = None,
+        amici_solver: amici.sim.sundials.Solver = None,
     ):
         super().__init__(petab_problem=petab_problem)
 
         if amici_model is None:
-            amici_model = amici_petab_import.import_petab_problem(
-                petab_problem
-            )
+            amici_model = import_petab_problem(petab_problem)
         self.amici_model = amici_model
 
         if amici_solver is None:
-            amici_solver = self.amici_model.getSolver()
+            amici_solver = self.amici_model.create_solver()
         self.amici_solver = amici_solver
 
     def create_model(
@@ -214,8 +216,8 @@ def create_model(
             Whether to return the simulations also (large, can be stored
             in database).
         return_rdatas:
-            Whether to return the full `List[amici.ExpData]` objects (large,
-            cannot be stored in database).
+            Whether to return the full `list[amici.sim.sundials.ExpData]`
+            objects (large, cannot be stored in database).
 
         Returns
         -------
@@ -237,7 +239,7 @@ def create_model(
             raise AssertionError('Parameter id mismatch')
 
         # no gradients for pyabc
-        self.amici_solver.setSensitivityOrder(0)
+        self.amici_solver.set_sensitivity_order(asd.SensitivityOrder.none)
 
         model = AmiciModel(
             petab_problem=self.petab_problem,

pyproject.toml

@@ -93,7 +93,7 @@ ot = [
 ]
 petab = ["petab>=0.2.0"]
 #petab-test = ["petabtests>=0.0.1"]  # problem with pysb
-amici = ["amici>=0.32.0,<1.0.0"]
+amici = ["amici>=1.0.0"]
 yaml2sbml = ["yaml2sbml>=0.2.1"]
 migrate = ["alembic>=1.5.4"]
 plotly = ["plotly>=5.3.1", "kaleido>=0.2.1"]

test/petab/test_petab.py

@@ -2,7 +2,6 @@
 import os
 import sys
 
-import amici.petab.petab_import
 import cloudpickle as pickle
 import git
 import matplotlib.pyplot as plt
@@ -12,6 +11,7 @@
 import petab.v1.C as C
 import pytest
 import scipy.stats
+from amici.importers.petab.v1 import import_petab_problem
 
 import pyabc.petab
 import pyabc.petab.base
@@ -322,12 +322,12 @@ def boehm_model_importer():
     output_folder = f'amici_models/{model_name}'
     if output_folder not in sys.path:
         sys.path.insert(0, output_folder)
-    model = amici.petab.petab_import.import_petab_problem(
+    model = import_petab_problem(
         petab_problem,
-        model_output_dir=output_folder,
+        output_dir=output_folder,
         generate_sensitivity_code=False,
     )
-    solver = model.getSolver()
+    solver = model.create_solver()
 
     # import to pyabc
     importer = pyabc.petab.AmiciPetabImporter(petab_problem, model, solver)

test/petab/test_petab_suite.py

@@ -9,10 +9,10 @@
 import pyabc
 
 try:
-    import amici.petab.petab_import
-    import amici.petab.simulations
     import petab.v1 as petab
     import petabtests
+    from amici.importers.petab.v1 import import_petab_problem
+    from amici.sim.sundials.petab.v1 import rdatas_to_measurement_df
 
     import pyabc.petab
 except ImportError:
@@ -104,13 +104,13 @@ def _execute_case(case):
     # models with the same name in a single python session
     model_name = f'petab_{MODEL_TYPE}_test_case_{case}_{PETAB_VERSION.replace(".", "_")}'
 
-    amici_model = amici.petab.petab_import.import_petab_problem(
+    amici_model = import_petab_problem(
         petab_problem=petab_problem,
         model_name=model_name,
-        model_output_dir=output_folder,
+        output_dir=output_folder,
         generate_sensitivity_code=False,
     )
-    solver = amici_model.getSolver()
+    solver = amici_model.create_solver()
 
     # import to pyabc
     importer = pyabc.petab.AmiciPetabImporter(
@@ -127,7 +127,7 @@ def _execute_case(case):
     # extract results
     rdatas = ret['rdatas']
     chi2 = sum(rdata['chi2'] for rdata in rdatas)
-    simulation_df = amici.petab.simulations.rdatas_to_measurement_df(
+    simulation_df = rdatas_to_measurement_df(
         rdatas, amici_model, importer.petab_problem.measurement_df
     )
     petab.check_measurement_df(

tox.ini

@@ -99,6 +99,9 @@ description =
     Test external model simulators (Julia, COPASI)
 
 [testenv:petab]
+deps =
+    git+https://github.com/PEtab-dev/petab_test_suite@main
+    git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master\#subdirectory=src/python&egg=benchmark_models_petab
 extras =
     test
     petab