physioblocks 1.0.0__tar.gz → 1.0.2__tar.gz

{physioblocks-1.0.0 → physioblocks-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: physioblocks
-Version: 1.0.0
+Version: 1.0.2
 Dynamic: Author
 Dynamic: Author-email
 Dynamic: License
@@ -124,4 +124,7 @@ python -m physioblocks.launcher references/spherical_heart_sim.jsonc -v -t -s Qu
 ```
 
 
-Results will be available in the `$LAUNCHER_FOLDER_PATH$/simulations/QuickStart` series folder.
+Results will be available in the `$LAUNCHER_FOLDER_PATH$/simulations/QuickStart` series folder:
+* the csv file contains the simulation results.
+* the html allows you to visualize the results.
+* the log and json files are here for debug purposes.

{physioblocks-1.0.0 → physioblocks-1.0.2}/README.md

@@ -76,4 +76,7 @@ python -m physioblocks.launcher references/spherical_heart_sim.jsonc -v -t -s Qu
 ```
 
 
-Results will be available in the `$LAUNCHER_FOLDER_PATH$/simulations/QuickStart` series folder.
+Results will be available in the `$LAUNCHER_FOLDER_PATH$/simulations/QuickStart` series folder:
+* the csv file contains the simulation results.
+* the html allows you to visualize the results.
+* the log and json files are here for debug purposes.

{physioblocks-1.0.0 → physioblocks-1.0.2}/doc/source/library/configuration/simulation.rst

@@ -133,6 +133,13 @@ Solvers Configuration
 
 Description of available configuration item to build :class:`~physioblocks.simulation.solvers.AbstractSolver` object from a configuration file.
 
+
+Linear Solver
+-------------
+
+* **Class:** :class:`~physioblocks.simulation.solvers.LinearSolver`
+* **Type name:** ``linear_solver``
+
 Newton Solver
 -------------
 

{physioblocks-1.0.0 → physioblocks-1.0.2}/doc/source/user_guide/level_2/create_simulation.rst

@@ -89,8 +89,7 @@ Solver
 
 This field define the solver implementation used to run a single simulation step.
 
-For now, only the :class:`~physioblocks.simulation.solvers.NewtonSolver` object is implemented in the current API.
-Its ``type`` is found in the :ref:`configuration section <library_configuration_simulation_solvers>` of the library
+The ``type`` parameters of available solver are found in the :ref:`configuration section <library_configuration_simulation_solvers>` of the library.
 
 .. code:: json
 
@@ -111,6 +110,7 @@ In this case, we set two parameters to the solver:
     Concerning our simple example the problem is **linear**, so a **Newton method is not adapted**.
     Still, we should be able to solve the system in two iterations, so ``iteration_max`` is set to 2.
 
+    A better choice would have been the ``linear_solver``, but we wanted to show the Newton solver in the example because it will be useful for most nets.
 
 Time
 ^^^^
@@ -135,7 +135,7 @@ It needs :
     }
 
 Here we set a 30 seconds simulation starting at 0.0.
-The simulation gives the state each 1ms and can divide a time step in parts of minimum lenght 62.5us before considering it can not solve the global system for the step.
+The simulation gives the state each 1ms and can divide a time step in parts of minimum length 62.5us before considering it can not solve the global system for the step.
 
 Net
 ^^^

{physioblocks-1.0.0 → physioblocks-1.0.2}/physioblocks/__init__.py

@@ -26,7 +26,7 @@
 
 """Physioblocks package definition"""
 
-__version__ = "1.0.0"
+__version__ = "1.0.2"
 __copyright__ = "INRIA"
 __license__ = "LGPL-3.0-only"
 __authors__ = [

{physioblocks-1.0.0 → physioblocks-1.0.2}/physioblocks/library/aliases/simulations/circulation_alone_forward_simulation.jsonc

@@ -49,7 +49,5 @@
             "inverses": ["aorta_distal.resistance"]
         }
     },
-    "solver": {
-        "iteration_max": 2 // This problem is linear
-    }
+    "solver": {"type": "linear_solver"}
 }

{physioblocks-1.0.0 → physioblocks-1.0.2}/physioblocks/simulation/solvers.py

@@ -114,6 +114,36 @@ class AbstractSolver(ABC):
         """
 
 
+LINEAR_SOLVER = "linear_solver"
+
+
+@register_type(LINEAR_SOLVER)
+class LinearSolver(AbstractSolver):
+    """
+    Implementation of the :class:`~.AbstractSolver` class for linear problems.
+    """
+
+    def solve(
+        self,
+        state: State,
+        system: EqSystem,
+        magnitudes: dict[str, float] | None = None,
+    ) -> Solution:
+        """
+        Solve the equation system directly
+
+        :return: the solution
+        :rtype: Solution
+        """
+        res = system.compute_residual()
+        grad = system.compute_gradient()
+
+        xn = np.linalg.solve(grad, res)
+        x = state.state_vector - xn
+
+        return Solution(x, True)
+
+
 # Type id for the Newton Solver
 NEWTON_SOLVER_TYPE_ID = "newton_solver"
 

{physioblocks-1.0.0 → physioblocks-1.0.2}/tests/tests_simulation/test_solvers.py

@@ -28,9 +28,10 @@ from unittest.mock import Mock, patch
 
 import numpy as np
 import pytest
+from numpy.linalg import LinAlgError
 
 from physioblocks.computing.assembling import EqSystem
-from physioblocks.simulation.solvers import AbstractSolver, NewtonSolver
+from physioblocks.simulation.solvers import AbstractSolver, LinearSolver, NewtonSolver
 from physioblocks.simulation.state import State
 
 
@@ -68,6 +69,12 @@ def mock_gradient():
     )
 
 
+def mock_singular_gradient():
+    return np.array(
+        [[0, 0], [0, 0]],
+    )
+
+
 @pytest.fixture
 def system() -> EqSystem:
     return EqSystem(2)
@@ -94,6 +101,31 @@ class TestAbstractSolver:
         assert solver_mag.tolerance == pytest.approx(1e-12)
 
 
+class TestLinearSolver:
+    @patch.multiple(
+        EqSystem,
+        compute_residual=Mock(return_value=mock_residual_converge()),
+        compute_gradient=Mock(return_value=mock_gradient()),
+    )
+    def test_run(self, state, system):
+        solver = LinearSolver()
+        sol = solver.solve(state, system)
+
+        assert sol.converged is True
+        assert sol.x == pytest.approx([0, 0])
+
+    @patch.multiple(
+        EqSystem,
+        compute_residual=Mock(return_value=mock_residual_converge()),
+        compute_gradient=Mock(return_value=mock_singular_gradient()),
+    )
+    def test_singular_matrix(self, state, system):
+        solver = LinearSolver()
+
+        with pytest.raises(LinAlgError):
+            solver.solve(state, system)
+
+
 class TestNewtonSolver:
     @patch.multiple(
         EqSystem,

physioblocks-1.0.0/doc/build/html/.buildinfo

@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: efd432c11c801e0d2c433b68089ef1c3
-tags: 645f666f9bcd5a90fca523b33c5a78b7

physioblocks-1.0.0/doc/build/html/_sources/api_reference/base.rst.txt

@@ -1,45 +0,0 @@
-.. 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/>.
-
-***********
-Base Module
-***********
-
-.. automodule:: physioblocks.base
-    :members:
-
-Operators
-=========
-
-.. automodule:: physioblocks.base.operators
-    :members:
-
-
-Registers
-=========
-
-.. automodule:: physioblocks.base.registers
-    :members:

physioblocks-1.0.0/doc/build/html/_sources/api_reference/computing.rst.txt

@@ -1,55 +0,0 @@
-.. 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/>.
-
-****************
-Computing Module
-****************
-
-The computing module declares functions and classes to:
-
-    * Hold numerical values for model quantities.
-    * Declare **Expressions** to define the **Blocks** and **ModelComponents** Flux, InternalExpressions and SavedQuantities
-    * Assemble the global **System** from those declaration.
-
-.. _quantity_ref:
-
-Quantities
-==========
-
-.. automodule:: physioblocks.computing.quantities
-    :members:
-
-Models
-======
-
-.. automodule:: physioblocks.computing.models
-    :members:
-
-Assembling
-==========
-
-.. automodule:: physioblocks.computing.assembling
-    :members:

physioblocks-1.0.0/doc/build/html/_sources/api_reference/configuration.rst.txt

@@ -1,50 +0,0 @@
-.. 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/>.
-
-********************
-Configuration Module
-********************
-
-Defines classes and functions to turn PhysioBlocks objects into a generic configuration that can
-be saved or loaded.
-
-Configuration
-=============
-
-.. automodule:: physioblocks.configuration.base
-    :members:
-
-Load ans save functions
-=======================
-
-.. automodule:: physioblocks.configuration.functions
-    :members:
-
-Aliases
-=======
-
-.. automodule:: physioblocks.configuration.aliases
-    :members:

physioblocks-1.0.0/doc/build/html/_sources/api_reference/description.rst.txt

@@ -1,51 +0,0 @@
-.. 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/>.
-
-******************
-Description Module
-******************
-
-Declares objects and functions to describe **Nets**.
-
-Flux
-====
-
-.. automodule:: physioblocks.description.flux
-    :members:
-
-Blocks
-======
-
-.. _api_reference_blocks:
-
-.. automodule:: physioblocks.description.blocks
-    :members:
-
-Nets
-====
-
-.. automodule:: physioblocks.description.nets
-    :members:

physioblocks-1.0.0/doc/build/html/_sources/api_reference/io.rst.txt

@@ -1,44 +0,0 @@
-.. 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/>.
-
-*********
-IO Module
-*********
-
-.. automodule:: physioblocks.io
-    :members:
-
-Configuration
-=============
-
-.. automodule:: physioblocks.io.configuration
-    :members:
-
-Aliases
-=======
-
-.. automodule:: physioblocks.io.aliases
-    :members:

physioblocks-1.0.0/doc/build/html/_sources/api_reference/registers.rst.txt

@@ -1,51 +0,0 @@
-.. 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/>.
-
-***************
-Register Module
-***************
-
-Declares decorators to register types or functions for a specific use.
-
-Type register
-=============
-
-.. automodule:: physioblocks.registers.type_register
-    :members:
-
-
-Load functions register
-=======================
-
-.. automodule:: physioblocks.registers.load_function_register
-    :members:
-
-
-Save functions register
-=======================
-
-.. automodule:: physioblocks.registers.save_function_register
-    :members: