capytaine 2.3__cp312-cp312-macosx_14_0_arm64.whl → 3.0.0a1__cp312-cp312-macosx_14_0_arm64.whl

capytaine/tools/memory_monitor.py

@@ -0,0 +1,45 @@
+import logging
+import time
+from threading import Thread
+
+from capytaine.tools.optional_imports import silently_import_optional_dependency
+
+LOG = logging.getLogger(__name__)
+
+class MemoryMonitor(Thread):
+    """Monitor the memory usage in a separate thread.
+    from : https://joblib.readthedocs.io/en/stable/auto_examples/parallel_generator.html#sphx-glr-auto-examples-parallel-generator-py
+    """
+
+    def __init__(self):
+        super().__init__()
+        self.stop = False
+        self.memory_buffer = [0]
+        self.psutil = silently_import_optional_dependency("psutil")
+        self.start()
+
+    def get_memory(self):
+        "Get memory of a process and its children."
+        p = self.psutil.Process()
+        memory = p.memory_info().rss
+        for c in p.children():
+            try:
+                memory += c.memory_info().rss
+            except self.psutil.NoSuchProcess:
+                pass
+        return memory
+
+    def run(self):
+        if self.psutil is not None:
+            memory_start = self.get_memory()
+            while not self.stop:
+                self.memory_buffer.append(self.get_memory() - memory_start)
+                time.sleep(0.2)
+
+    def get_memory_peak(self):
+        self.stop = True 
+        super().join()
+        if self.psutil is None:
+            return None
+        else:
+            return round(max(self.memory_buffer) / 1e9, 2)

capytaine/tools/symbolic_multiplication.py

@@ -11,7 +11,6 @@ output of the form `SymbolicMultiplication("0", np.array(...))`
 import numpy as np
 from functools import wraps, total_ordering
 
-@total_ordering
 class SymbolicMultiplication:
     def __init__(self, symbol, value=1.0):
         self.symbol = symbol
@@ -25,11 +24,23 @@ class SymbolicMultiplication:
     __array_priority__ = 1.0
 
     def __array_function__(self, func, types, *args, **kwargs):
-        if func in {np.real, np.imag, np.sum}:
+        actual_args = args[0]  # args = (actual_args, kwargs) for some reason
+        if func in {np.real, np.imag, np.sum} and len(actual_args) == 1 and len(kwargs) == 0:
             return SymbolicMultiplication(self.symbol, func(self.value))
+        elif (
+                func in {np.einsum} and
+                len([a for a in actual_args if isinstance(a, SymbolicMultiplication)]) == 1 and
+                "out" not in kwargs
+                ):
+            # Einsum with one of the array being wrapped in SymbolicMultiplication
+            unwrapped = [a.value if isinstance(a, SymbolicMultiplication) else a for a in actual_args]
+            return SymbolicMultiplication(self.symbol, func(*unwrapped, **kwargs))
         else:
             return NotImplemented
 
+    def astype(self, proper_type):
+        return SymbolicMultiplication(self.symbol, proper_type(self.value))
+
     def __str__(self):
         return f"{self.symbol}×{self.value}"
 
@@ -82,11 +93,26 @@ class SymbolicMultiplication:
     def __getitem__(self, item):
         return SymbolicMultiplication(self.symbol, self.value[item])
 
-    def __eq__(self, x):
-        return float(self) == x
+    def __setitem__(self, item, val):
+        if isinstance(val, SymbolicMultiplication) and self.symbol == val.symbol:
+            self.value.__setitem__(item, val.value)
+        else:
+            raise NotImplementedError
 
     def __lt__(self, x):
-        return float(self) < x
+        return self._concretize() < x
+
+    def __le__(self, x):
+        return self._concretize() <= x
+
+    def __eq__(self, x):
+        return self._concretize() == x
+
+    def __ge__(self, x):
+        return self._concretize() >= x
+
+    def __gt__(self, x):
+        return self._concretize() > x
 
     def __hash__(self):
         return hash((self.symbol, self.value))

capytaine/tools/timer.py

@@ -2,63 +2,89 @@
 
 from functools import wraps
 import time
+import contextlib
+
+import pandas as pd
 
 class Timer:
-    """A simple timer class that can be used as context manager or as decorator using `wraps_function` method
+    """A timer class that can be used as context manager or as decorator using `wraps_function` method.
+    Several timing measurement can be nested.
+
+    Attributes
+    ----------
+    timings: List[Dict]]
+        List of records of each timing measurement.
+        The record is a dict with a 'timing' key and any number of other metadata keys.
+    default_tags: Optional[Dict]
+        Tags added to all the timing measurements.
+    _start_times: List[float]
+        Start times of the ongoing timing measurements.
 
     Example
     -------
-    timer = Timer()
-    with timer:
-        sleep(1.0)
+    ::
+        from time import sleep  # For testing
 
-    print(timer.total)  # 1.0...
+        timer = Timer()
 
-    @timer.wraps_function
-    def my_function():
-        sleep(0.5)
+        with timer(tag="run 1"):
+            sleep(1.0)
 
-    my_function()
-    print(timer.total)  # 1.5...
-    my_function()
-    print(timer.total)  # 2.0...
+        print(timer.total)  # 1.0...
 
-    print(timer.timings)  # [1.0, 0.5, 0.5]
-    """
+        @timer.wraps_function(tag="run function")
+        def my_function():
+            sleep(0.5)
 
-    def __init__(self, timings=None):
-        if timings is None:
-            self.timings = []
-        else:
-            self.timings = timings
+        my_function()
+        print(timer.total)  # 1.5...
+        my_function()
+        print(timer.total)  # 2.0...
+
+        with timer(tag="outer"):
+            sleep(0.3)
+            with timer(tag="inner"):
+                sleep(0.3)
+            sleep(0.3)
+    """
+    def __init__(self, *, default_tags=None):
+        self.timings = []
+        if default_tags is None:
+            default_tags = {}
+        self.default_tags = default_tags
+        self._start_times = []  # Starting time of ongoing sub-timers
 
     def __repr__(self):
         return f"Timer({self.timings})"
 
-    @property
-    def nb_timings(self):
-        return len(self.timings)
+    def add_data_from_other_timer(self, other, **supplementary_tags):
+        self.timings.extend([{**t, **supplementary_tags} for t in other.timings])
 
-    @property
-    def total(self):
-        return sum(self.timings)
-
-    @property
-    def mean(self):
-        if self.nb_timings == 0:
-            return float('nan')
-        else:
-            return self.total/self.nb_timings
+    @contextlib.contextmanager
+    def __call__(self, **tags):
+        self._start_times.append(time.perf_counter())
+        try:
+            yield
+        finally:
+            timing = time.perf_counter() - self._start_times.pop()
+            self.timings.append({'timing': timing, **tags, **self.default_tags})
 
-    def __enter__(self):
-        self.start_time = time.perf_counter()
+    def wraps_function(self, **tags):
+        def wrapper(f):
+            @wraps(f)
+            def wrapped_f(*args, **kwargs):
+                with self(**tags):
+                    out = f(*args, **kwargs)
+                return out
+            return wrapped_f
+        return wrapper
 
-    def __exit__(self, *exc):
-        self.timings.append(time.perf_counter() - self.start_time)
+    def as_dataframe(self):
+        if len(self.timings) == 0:
+            return pd.DataFrame([{'timing': 0.0}])
+        else:
+            return pd.DataFrame(self.timings)
 
-    def wraps_function(self, f):
-        @wraps(f)
-        def wrapped_f(*args, **kwargs):
-            with self:
-                return f(*args, **kwargs)
-        return wrapped_f
+    @property
+    def total(self):
+        return self.as_dataframe()['timing'].sum()

{capytaine-2.3.dist-info → capytaine-3.0.0a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: capytaine
-Version: 2.3
+Version: 3.0.0a1
 Summary: Python BEM solver for linear potential flow, based on Nemoh
 Author-Email: Matthieu Ancellin <matthieu.ancellin@mews-labs.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -689,26 +689,20 @@ Requires-Python: >=3.8
 Requires-Dist: numpy>=1.20; python_version >= "3.9"
 Requires-Dist: numpy>=1.24; python_version == "3.8"
 Requires-Dist: scipy
-Requires-Dist: pandas>=1.3
+Requires-Dist: pandas<3,>=1.3
 Requires-Dist: xarray
 Requires-Dist: rich
 Provides-Extra: optional
 Requires-Dist: matplotlib; extra == "optional"
+Requires-Dist: vtk; extra == "optional"
+Requires-Dist: pyvista; extra == "optional"
+Requires-Dist: psutil; extra == "optional"
 Requires-Dist: joblib>=1.3; extra == "optional"
+Requires-Dist: threadpoolctl; extra == "optional"
 Requires-Dist: meshio; extra == "optional"
+Requires-Dist: trimesh; extra == "optional"
+Requires-Dist: h5py; extra == "optional"
 Requires-Dist: netcdf4; extra == "optional"
-Requires-Dist: vtk; extra == "optional"
-Provides-Extra: more-optional
-Requires-Dist: pygmsh; extra == "more-optional"
-Requires-Dist: gmsh; extra == "more-optional"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: capytaine[optional]; extra == "test"
-Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
-Requires-Dist: sphinx-toolbox; extra == "docs"
-Requires-Dist: sphinxcontrib-proof; extra == "docs"
-Requires-Dist: sphinxcontrib-mermaid; extra == "docs"
 Description-Content-Type: text/markdown
 
 # Capytaine: a linear potential flow BEM solver with Python.

capytaine-3.0.0a1.dist-info/RECORD

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capytaine-3.0.0a1.dist-info/WHEEL

@@ -0,0 +1,6 @@
+Wheel-Version: 1.0
+Generator: meson
+Root-Is-Purelib: false
+Tag: cp312-cp312-macosx_14_0_arm64
+Generator: delocate 0.13.0
+

capytaine/bodies/predefined/__init__.py

@@ -1,6 +0,0 @@
-# Copyright (C) 2017-2019 Matthieu Ancellin
-# See LICENSE file at <https://github.com/mancellin/capytaine>
-
-from capytaine.bodies.predefined.spheres import Sphere
-from capytaine.bodies.predefined.cylinders import HorizontalCylinder, VerticalCylinder
-from capytaine.bodies.predefined.rectangles import Rectangle, RectangularParallelepiped

capytaine/bodies/predefined/cylinders.py

@@ -1,151 +0,0 @@
-"""Legacy interfaces to predefined meshes"""
-# Copyright (C) 2017-2022 Matthieu Ancellin
-# See LICENSE file at <https://github.com/capytaine/capytaine>
-
-import logging
-import numpy as np
-
-from capytaine.meshes.predefined import mesh_disk, mesh_vertical_cylinder, mesh_horizontal_cylinder
-from capytaine.meshes.meshes import Mesh
-from capytaine.bodies.bodies import FloatingBody
-
-LOG = logging.getLogger(__name__)
-
-
-##########
-#  Disk  #
-##########
-
-class Disk(FloatingBody):
-    """(One-sided) disk.
-    Deprecated: please prefer capytaine.meshes.predefined.mesh_disk()
-
-    Parameters
-    ----------
-    radius : float, optional
-        radius of the disk
-    resolution : 2-ple of int, optional
-        number of panels along a radius and around the disk
-    center : 3-ple or array of shape (3,), optional
-        position of the geometric center of the disk
-    normal: 3-ple of floats, optional
-        normal vector, default: along x axis
-    axial_symmetry : bool, optional
-        if True, use the axial symmetry to speed up the computations
-    reflection_symmetry : bool, optional
-        if True, use the reflection symmetry to speed up the computations
-    name : str, optional
-        a string naming the floating body
-    """
-
-    def __init__(self, radius=1.0, resolution=(3, 5),
-                 center=(0, 0, 0), normal=(1, 0, 0),
-                 reflection_symmetry=False, axial_symmetry=False,
-                 name=None):
-        LOG.warning("Deprecation warning: The class Disk() is deprecated. "
-                "Please prefer the function capytaine.meshes.predefined.mesh_disk()")
-
-        if name is None:
-            name = f"disk_{next(Mesh._ids)}"
-
-        self.radius = float(radius)
-        self.geometric_center = np.asarray(center, dtype=float)
-        mesh = mesh_disk(radius=radius, center=center, normal=normal, resolution=resolution,
-                reflection_symmetry=reflection_symmetry, axial_symmetry=axial_symmetry, name=f"{name}_mesh")
-        FloatingBody.__init__(self, mesh=mesh, name=name)
-
-
-##############
-#  Cylinder  #
-##############
-
-class HorizontalCylinder(FloatingBody):
-    """Horizontal cylinder
-    Deprecated: please prefer capytaine.meshes.predefined.mesh_horizontal_cylinder()
-
-    Parameters
-    ----------
-    length : float, optional
-        length of the cylinder
-    radius : float, optional
-        radius of the cylinder
-    center : 3-ple or array of shape (3,), optional
-        position of the geometric center of the cylinder
-    nx : int, optional
-        number of circular slices
-    ntheta : int, optional
-        number of panels along a circular slice of the cylinder
-    nr : int, optional
-        number of panels along a radius on the extremities of the cylinder
-    reflection_symmetry : bool, optional
-        if True, returns a ReflectionSymmetricMesh
-    translation_symmetry : bool, optional
-        if True, uses a TranslationalSymmetricMesh internally for the main part of the cylinder
-    name : str, optional
-        a string naming the floating body
-    """
-
-    def __init__(self, length=10.0, radius=1.0, center=(0, 0, 0),
-                 nx=10, ntheta=10, nr=2,
-                 reflection_symmetry=True, translation_symmetry=False,
-                 clever=None,
-                 name=None):
-
-        LOG.warning("Deprecation warning: The class HorizontalCylinder() is deprecated. "
-                "Please prefer the function capytaine.meshes.predefined.mesh_horizontal_cylinder()")
-
-        self.length = length
-        self.radius = radius
-        self.geometric_center = np.asarray(center, dtype=float)
-
-        if name is None:
-            name = f"cylinder_{next(Mesh._ids)}"
-
-        mesh = mesh_horizontal_cylinder(length=length, radius=radius, center=center,
-                resolution=(nr, ntheta, nx), reflection_symmetry=reflection_symmetry,
-                translation_symmetry=translation_symmetry, name=f"{name}_mesh")
-        FloatingBody.__init__(self, mesh=mesh, name=name)
-
-
-class VerticalCylinder(FloatingBody):
-    """Vertical cylinder.
-    Deprecated: please prefer capytaine.meshes.predefined.mesh_vertical_cylinder()
-
-    Parameters
-    ----------
-    length : float, optional
-        length of the cylinder
-    radius : float, optional
-        radius of the cylinder
-    center : 3-ple or array of shape (3,), optional
-        position of the geometric center of the cylinder
-    nx : int, optional
-        number of circular slices
-    ntheta : int, optional
-        number of panels along a circular slice of the cylinder
-    nr : int, optional
-        number of panels along a radius on the extremities of the cylinder
-    clever : bool, optional
-        if True, uses the mesh symmetries
-    name : str, optional
-        a string naming the floating body
-    """
-
-    def __init__(self, length=10.0, radius=1.0, center=(0, 0, 0),
-                 nx=10, ntheta=10, nr=2,
-                 clever=True, name=None):
-        LOG.warning("Deprecation warning: The class VerticalCylinder() is deprecated. "
-                "Please prefer the function capytaine.meshes.predefined.mesh_vertical_cylinder()")
-
-        self.length = length
-        self.radius = radius
-        self.geometric_center = np.asarray(center, dtype=float)
-
-        if name is None:
-            name = f"cylinder_{next(Mesh._ids)}"
-
-        mesh = mesh_vertical_cylinder(length=length, radius=radius, center=center,
-                resolution=(nr, ntheta, nx), reflection_symmetry=False,
-                axial_symmetry=clever, name=f"{name}_mesh")
-
-        FloatingBody.__init__(self, mesh=mesh, name=name)

capytaine/bodies/predefined/rectangles.py

@@ -1,111 +0,0 @@
-"""Legacy interfaces to predefined meshes"""
-# Copyright (C) 2017-2022 Matthieu Ancellin
-# See LICENSE file at <https://github.com/capytaine/capytaine>
-
-import logging
-import numpy as np
-
-from capytaine.meshes.predefined import mesh_rectangle, mesh_parallelepiped
-from capytaine.meshes.meshes import Mesh
-from capytaine.bodies.bodies import FloatingBody
-
-LOG = logging.getLogger(__name__)
-
-
-class Rectangle(FloatingBody):
-    """One-sided vertical rectangle (along y and z).
-
-    By default, the normals are oriented in the positive y direction.
-
-    Parameters
-    ----------
-    size : couple of floats, optional
-        dimensions of the rectangle (width and height)
-    resolution : couple of ints, optional
-        number of faces along each of the two directions
-    center : 3-ple of floats, optional
-        position of the geometric center of the rectangle, default: (0, 0, 0)
-    normal: 3-ple of floats, optional
-        normal vector, default: along x axis
-    translational_symmetry : bool, optional
-        if True, use the translation symmetry to speed up the computations
-    reflection_symmetry : bool, optional
-        if True, use the reflection symmetry to speed up the computations
-    name : string, optional
-        a name for the body
-    """
-
-    def __init__(self, size=(5.0, 5.0), resolution=(5, 5),
-                 center=(0, 0, 0), normal=(1, 0, 0),
-                 translational_symmetry=False, reflection_symmetry=False, name=None):
-
-        LOG.warning("Deprecation warning: The class Rectangle() is deprecated. "
-                    "Please prefer the function capytaine.meshes.predefined.mesh_rectangle()")
-
-        self.size = np.asarray(size, dtype=float)
-        self.geometric_center = np.asarray(center, dtype=float)
-
-        if name is None:
-            name = f"rectangle_{next(Mesh._ids)}"
-
-        mesh = mesh_rectangle(size=size, resolution=resolution, center=center, normal=normal,
-                translation_symmetry=translational_symmetry, reflection_symmetry=reflection_symmetry,
-                name=f"{name}_mesh")
-        FloatingBody.__init__(self, mesh=mesh, name=name)
-
-
-class RectangularParallelepiped(FloatingBody):
-    """Six rectangles forming a parallelepiped.
-
-    Parameters
-    ----------
-    size : 3-ple of floats, optional
-        dimensions of the parallelepiped (width, thickness, height) for coordinates (x, y, z).
-    resolution : 3-ple of ints, optional
-        number of faces along the three directions
-    center : 3-ple of floats, optional
-        coordinates of the geometric center of the parallelepiped
-    top: bool, optional
-        whether or not to close the parallelepiped on the top
-    bottom: bool, optional
-        whether or not to close the parallelepiped on the bottom
-    reflection_symmetry : bool, optional
-        use xOz and yOz symmetry plane to generate the mesh
-    translational_symmetry : bool, optional
-        if True, use the translation symmetry in the x direction to speed up the computations.
-        To use the translation symmetry in the y direction, create a x-symmetric body and then rotate it by pi/2.
-    name : string, optional
-        a name for the body
-    """
-
-    def __init__(self,
-                 size=(1.0, 1.0, 1.0), resolution=(4, 4, 4),
-                 center=(0, 0, 0),
-                 top=True, bottom=True,
-                 reflection_symmetry=False,
-                 translational_symmetry=False,
-                 name=None):
-
-        LOG.warning("Deprecation warning: The class RectangularParallelepiped() is deprecated. "
-                    "Please prefer the function capytaine.meshes.predefined.mesh_parallelepiped()")
-
-        if name is None:
-            name = f"rectangular_parallelepiped_{next(Mesh._ids)}"
-
-        missing_sides = set()
-        if not top: missing_sides.add("top")
-        if not bottom: missing_sides.add("bottom")
-
-        mesh = mesh_parallelepiped(size=size, resolution=resolution, center=center,
-                missing_sides=missing_sides,
-                translation_symmetry=translational_symmetry, reflection_symmetry=reflection_symmetry,
-                name=f"{name}_mesh")
-
-        self.geometric_center = np.asarray(center, dtype=float)
-
-        FloatingBody.__init__(self, mesh=mesh, name=name)
-
-class OpenRectangularParallelepiped(RectangularParallelepiped):
-    def __init__(self, *args, **kwargs):
-        RectangularParallelepiped.__init__(self, top=False, bottom=False, *args, **kwargs)
-        # Kept mostly for legacy