physioblocks 1.0.0__py3-none-any.whl

physioblocks/registers/type_register.py

@@ -0,0 +1,97 @@
+# SPDX-FileCopyrightText: Copyright INRIA
+#
+# SPDX-License-Identifier: LGPL-3.0-only
+#
+# Copyright INRIA
+#
+# This file is part of PhysioBlocks, a library mostly developed by the
+# [Ananke project-team](https://team.inria.fr/ananke) at INRIA.
+#
+# Authors:
+# - Colin Drieu
+# - Dominique Chapelle
+# - François Kimmig
+# - Philippe Moireau
+#
+# PhysioBlocks is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free Software
+# Foundation, version 3 of the License.
+#
+# PhysioBlocks is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License along with
+# PhysioBlocks. If not, see <https://www.gnu.org/licenses/>.
+
+"""
+Define decorators to register any type with a name in a dedicated register.
+"""
+
+from collections.abc import Callable
+from typing import Any, TypeVar
+
+from physioblocks.base.registers import check_key_value_type, register
+
+__type_register: dict[Any, Any] = {}
+
+
+T = TypeVar("T")
+
+
+def register_type(type_id: str) -> Callable[[T], T]:
+    """
+    Class decorator to register the class type with the given name.
+
+    :param type_id: the defined type id for the class type
+    :type type_id: str
+
+    :return: the class decorator
+    :rtype: Callable
+    """
+
+    def class_decorator(registered_type: T) -> T:
+        check_key_value_type(type_id, str, registered_type, type)
+        register(__type_register, type_id, registered_type)
+        return registered_type
+
+    return class_decorator
+
+
+def get_registered_type(type_id: str) -> Any:
+    """
+    Get a registered type.
+
+    :param type_id: the registered type id
+    :type type_id: str
+
+    :return: the registered type
+    :rtype: type
+    """
+    return __type_register[type_id]
+
+
+def get_registered_type_id(registered_type: type) -> Any:
+    """
+    Get a registered type name for the matching type.
+
+    :param registered_type: the registered type id
+    :type registered_type: type
+
+    :return: the registered type id
+    :rtype: str
+    """
+    return __type_register[registered_type]
+
+
+def is_registered(key: Any) -> bool:
+    """
+    Get if the given value is registered as a type or type id.
+
+    :param key: the key to test
+    :type key: Any
+
+    :return: True if the key is registered, False otherwise
+    :rtype: bool
+    """
+    return key in __type_register

physioblocks/simulation/__init__.py

@@ -0,0 +1,48 @@
+# SPDX-FileCopyrightText: Copyright INRIA
+#
+# SPDX-License-Identifier: LGPL-3.0-only
+#
+# Copyright INRIA
+#
+# This file is part of PhysioBlocks, a library mostly developed by the
+# [Ananke project-team](https://team.inria.fr/ananke) at INRIA.
+#
+# Authors:
+# - Colin Drieu
+# - Dominique Chapelle
+# - François Kimmig
+# - Philippe Moireau
+#
+# PhysioBlocks is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free Software
+# Foundation, version 3 of the License.
+#
+# PhysioBlocks is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License along with
+# PhysioBlocks. If not, see <https://www.gnu.org/licenses/>.
+
+"""
+Define methods to setup a simulation and run it.
+"""
+
+__all__ = [
+    "AbstractFunction",
+    "AbstractSimulation",
+    "ForwardSimulation",
+    "SimulationError",
+    "SimulationFactory",
+    "State",
+    "Time",
+]
+from physioblocks.simulation.functions import AbstractFunction
+from physioblocks.simulation.runtime import (
+    AbstractSimulation,
+    ForwardSimulation,
+    SimulationError,
+)
+from physioblocks.simulation.setup import SimulationFactory
+from physioblocks.simulation.state import State
+from physioblocks.simulation.time_manager import Time

physioblocks/simulation/constants.py

@@ -0,0 +1,30 @@
+# SPDX-FileCopyrightText: Copyright INRIA
+#
+# SPDX-License-Identifier: LGPL-3.0-only
+#
+# Copyright INRIA
+#
+# This file is part of PhysioBlocks, a library mostly developed by the
+# [Ananke project-team](https://team.inria.fr/ananke) at INRIA.
+#
+# Authors:
+# - Colin Drieu
+# - Dominique Chapelle
+# - François Kimmig
+# - Philippe Moireau
+#
+# PhysioBlocks is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free Software
+# Foundation, version 3 of the License.
+#
+# PhysioBlocks is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License along with
+# PhysioBlocks. If not, see <https://www.gnu.org/licenses/>.
+
+"""Define constants in the simulation module"""
+
+SCHEME_TIME_SHIFT_PREFIX = "scheme_ts"
+"""Prefix for time shift quantities ids."""

physioblocks/simulation/functions.py

@@ -0,0 +1,71 @@
+# SPDX-FileCopyrightText: Copyright INRIA
+#
+# SPDX-License-Identifier: LGPL-3.0-only
+#
+# Copyright INRIA
+#
+# This file is part of PhysioBlocks, a library mostly developed by the
+# [Ananke project-team](https://team.inria.fr/ananke) at INRIA.
+#
+# Authors:
+# - Colin Drieu
+# - Dominique Chapelle
+# - François Kimmig
+# - Philippe Moireau
+#
+# PhysioBlocks is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free Software
+# Foundation, version 3 of the License.
+#
+# PhysioBlocks is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License along with
+# PhysioBlocks. If not, see <https://www.gnu.org/licenses/>.
+
+"""Declare base functions to write functions used during the simulation."""
+
+from abc import ABC, abstractmethod
+from inspect import signature
+from typing import Any
+
+from physioblocks.simulation.state import STATE_NAME_ID
+from physioblocks.simulation.time_manager import TIME_QUANTITY_ID
+
+
+class AbstractFunction(ABC):
+    """Base class for functions that update quantities during the simulation."""
+
+    @abstractmethod
+    def eval(self, *args: Any, **kwargs: Any) -> Any:
+        """Child Functions have to overwrite this method to compute the
+        function result."""
+
+
+def is_time_function(tested_function: AbstractFunction) -> bool:
+    """Test if the simulation function needs simulation time parameter.
+
+    :param tested_function: the function
+    :type tested_function: AbstractFunction
+
+    :return: True if the function needs time, False otherwise
+    :rtype: bool
+    """
+
+    sig = signature(tested_function.eval)
+    return TIME_QUANTITY_ID in sig.parameters
+
+
+def is_state_function(tested_function: AbstractFunction) -> bool:
+    """Test if the simulation function needs the state.
+
+    :param function: the simulation function
+    :type function: AbstractFunction
+
+    :return: True if the function needs the state, False otherwise
+    :rtype: bool
+    """
+
+    sig = signature(tested_function.eval)
+    return STATE_NAME_ID in sig.parameters