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Disentangle amici and roadrunner #1429

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merged 6 commits into from
Jul 18, 2024
Merged

Disentangle amici and roadrunner #1429

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63d4761
Removed amici not installed warning, as we specifically moved the ami…
PaulJonasJost Jul 15, 2024
2afb99a
Added petab and libsbml dependency to roadrunner.
PaulJonasJost Jul 15, 2024
f02d733
Fixed import errors i stumbled across hierarchical when only installi…
PaulJonasJost Jul 15, 2024
9d3ec7e
Merge branch 'develop' into fix_amici_dependencies
PaulJonasJost Jul 15, 2024
eb0e989
Fixed rather through `from __future__ import annotations`
PaulJonasJost Jul 15, 2024
0b044b1
Update setup.cfg
PaulJonasJost Jul 15, 2024
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15 changes: 7 additions & 8 deletions pypesto/hierarchical/base_problem.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
"""Inner optimization problem in hierarchical optimization."""

from __future__ import annotations

import copy
import logging
from typing import Union

import numpy as np
import pandas as pd
Expand Down Expand Up @@ -60,10 +61,10 @@ def __init__(self, xs: list[InnerParameter], data: list[np.ndarray]):

@staticmethod
def from_petab_amici(
petab_problem: "petab.Problem",
amici_model: "amici.Model",
edatas: list["amici.ExpData"],
) -> "InnerProblem":
petab_problem: petab.Problem,
amici_model: amici.Model,
edatas: list[amici.ExpData],
) -> InnerProblem:
"""Create an InnerProblem from a PEtab problem and AMICI objects."""

def get_x_ids(self) -> list[str]:
Expand Down Expand Up @@ -219,9 +220,7 @@ def scale_value_dict(
return scaled_dct


def scale_value(
val: Union[float, np.array], scale: str
) -> Union[float, np.array]:
def scale_value(val: float | np.array, scale: str) -> float | np.array:
"""Scale a single value."""
if scale == "lin":
return val
Expand Down
6 changes: 4 additions & 2 deletions pypesto/hierarchical/ordinal/calculator.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
"""Definition of an optimal scaling calculator class."""

from __future__ import annotations

import copy
from collections.abc import Sequence

Expand Down Expand Up @@ -86,12 +88,12 @@ def __call__(
mode: str,
amici_model: AmiciModel,
amici_solver: AmiciSolver,
edatas: list["amici.ExpData"],
edatas: list[amici.ExpData],
n_threads: int,
x_ids: Sequence[str],
parameter_mapping: ParameterMapping,
fim_for_hess: bool,
rdatas: list["amici.ReturnData"] = None,
rdatas: list[amici.ReturnData] = None,
):
"""Perform the actual AMICI call.

Expand Down
18 changes: 10 additions & 8 deletions pypesto/hierarchical/ordinal/problem.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
"""Definition of an optimal scaling parameter class."""

from __future__ import annotations

import numpy as np
import pandas as pd

Expand Down Expand Up @@ -172,10 +174,10 @@ def initialize(self) -> None:
@staticmethod
def from_petab_amici(
petab_problem: petab.Problem,
amici_model: "amici.Model",
edatas: list["amici.ExpData"],
amici_model: amici.Model,
edatas: list[amici.ExpData],
method: str = None,
) -> "OrdinalProblem":
) -> OrdinalProblem:
"""Construct the inner problem from the `petab_problem`."""
if not method:
method = REDUCED
Expand Down Expand Up @@ -475,8 +477,8 @@ def get_inner_parameter_dictionary(self) -> dict:

def optimal_scaling_inner_problem_from_petab_problem(
petab_problem: petab.Problem,
amici_model: "amici.Model",
edatas: list["amici.ExpData"],
amici_model: amici.Model,
edatas: list[amici.ExpData],
method: str,
):
"""Construct the inner problem from the `petab_problem`."""
Expand Down Expand Up @@ -511,7 +513,7 @@ def optimal_scaling_inner_problem_from_petab_problem(
def optimal_scaling_inner_parameters_from_measurement_df(
df: pd.DataFrame,
method: str,
amici_model: "amici.Model",
amici_model: amici.Model,
) -> list[OrdinalParameter]:
"""Create list of inner free parameters from PEtab measurement table dependent on the method provided."""
df = df.reset_index()
Expand Down Expand Up @@ -611,8 +613,8 @@ def get_estimate_for_method(method: str) -> tuple[bool, bool]:


def optimal_scaling_ixs_for_measurement_specific_parameters(
petab_problem: "petab.Problem",
amici_model: "amici.Model",
petab_problem: petab.Problem,
amici_model: amici.Model,
inner_parameters: list[OrdinalParameter],
) -> dict[str, list[tuple[int, int, int]]]:
"""Create mapping of parameters to measurements.
Expand Down
2 changes: 1 addition & 1 deletion pypesto/hierarchical/ordinal/solver.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@
try:
from amici.petab.parameter_mapping import ParameterMapping
except ImportError:
pass
ParameterMapping = None


class OrdinalInnerSolver(InnerSolver):
Expand Down
2 changes: 2 additions & 0 deletions pypesto/hierarchical/relative/solver.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
from __future__ import annotations

import copy
from typing import Any

Expand Down
6 changes: 4 additions & 2 deletions pypesto/hierarchical/semiquantitative/calculator.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
from __future__ import annotations

import copy
from collections.abc import Sequence

Expand Down Expand Up @@ -79,12 +81,12 @@ def __call__(
mode: str,
amici_model: AmiciModel,
amici_solver: AmiciSolver,
edatas: list["amici.ExpData"],
edatas: list[amici.ExpData],
n_threads: int,
x_ids: Sequence[str],
parameter_mapping: ParameterMapping,
fim_for_hess: bool,
rdatas: list["amici.ReturnData"] = None,
rdatas: list[amici.ReturnData] = None,
):
"""Perform the actual AMICI call.

Expand Down
22 changes: 12 additions & 10 deletions pypesto/hierarchical/semiquantitative/problem.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
from __future__ import annotations

import numpy as np
import pandas as pd

Expand Down Expand Up @@ -124,10 +126,10 @@ def initialize(self) -> None:
@staticmethod
def from_petab_amici(
petab_problem: petab.Problem,
amici_model: "amici.Model",
edatas: list["amici.ExpData"],
amici_model: amici.Model,
edatas: list[amici.ExpData],
spline_ratio: float = None,
) -> "SemiquantProblem":
) -> SemiquantProblem:
"""Construct the inner problem from the `petab_problem`."""
if spline_ratio is None:
spline_ratio = get_default_options()
Expand Down Expand Up @@ -289,8 +291,8 @@ def get_default_options() -> dict:

def spline_inner_problem_from_petab_problem(
petab_problem: petab.Problem,
amici_model: "amici.Model",
edatas: list["amici.ExpData"],
amici_model: amici.Model,
edatas: list[amici.ExpData],
spline_ratio: float = None,
):
"""Construct the inner problem from the `petab_problem`."""
Expand Down Expand Up @@ -336,7 +338,7 @@ def spline_inner_problem_from_petab_problem(
def spline_inner_parameters_from_measurement_df(
df: pd.DataFrame,
spline_ratio: float,
amici_model: "amici.Model",
amici_model: amici.Model,
) -> list[SplineInnerParameter]:
"""Create list of inner free spline parameters from PEtab measurement table."""
df = df.reset_index()
Expand Down Expand Up @@ -382,8 +384,8 @@ def spline_inner_parameters_from_measurement_df(


def noise_inner_parameters_from_parameter_df(
petab_problem: "petab.Problem",
amici_model: "amici.Model",
petab_problem: petab.Problem,
amici_model: amici.Model,
) -> list[SplineInnerParameter]:
"""Create list of inner free noise parameters from PEtab parameter table."""
# Select the semiquantitative measurements.
Expand Down Expand Up @@ -432,8 +434,8 @@ def noise_inner_parameters_from_parameter_df(


def spline_ixs_for_measurement_specific_parameters(
petab_problem: "petab.Problem",
amici_model: "amici.Model",
petab_problem: petab.Problem,
amici_model: amici.Model,
inner_parameters: list[SplineInnerParameter],
) -> dict[str, list[tuple[int, int, int]]]:
"""Create mapping of parameters to measurements.
Expand Down
2 changes: 2 additions & 0 deletions pypesto/hierarchical/semiquantitative/solver.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
from __future__ import annotations
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unused?

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@PaulJonasJost PaulJonasJost Jul 15, 2024 •
edited
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needed for the ParameterMapping (l168)


import warnings

import numpy as np
Expand Down
7 changes: 1 addition & 6 deletions pypesto/petab/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,4 @@
try:
import amici
except ImportError:
warnings.warn(
"PEtab import requires an installation of amici "
"(https://github.com/AMICI-dev/AMICI). "
"Install via `pip3 install amici`.",
stacklevel=1,
)
amici = None
2 changes: 2 additions & 0 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,8 @@ amici =
amici >= 0.21.0
roadrunner =
libroadrunner >= 2.7.0
petab >= 0.4.0
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python-libsbml >= 5.20.2
petab =
petab >= 0.4.0
ipopt =
Expand Down
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