llg3d 2.0.0__tar.gz → 2.0.1__tar.gz

{llg3d-2.0.0 → llg3d-2.0.1}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: llg3d
-Version: 2.0.0
-Summary: Solveur pour l'équation de Landau-Lifshitz-Gilbert stochastique en 3D
+Version: 2.0.1
+Summary: A solver for the stochastic Landau-Lifshitz-Gilbert equation in 3D
 Author-email: Clémentine Courtès <clementine.courtes@math.unistra.fr>, Matthieu Boileau <matthieu.boileau@math.unistra.fr>
 Project-URL: Homepage, https://gitlab.math.unistra.fr/llg3d/llg3d
 Classifier: Programming Language :: Python :: 3

{llg3d-2.0.0 → llg3d-2.0.1}/pyproject.toml

@@ -8,7 +8,7 @@ authors = [
     { name = "Clémentine Courtès", email = "clementine.courtes@math.unistra.fr" },
     { name = "Matthieu Boileau", email = "matthieu.boileau@math.unistra.fr" },
 ]
-description = "Solveur pour l'équation de Landau-Lifshitz-Gilbert stochastique en 3D"
+description = "A solver for the stochastic Landau-Lifshitz-Gilbert equation in 3D"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
@@ -78,3 +78,36 @@ doc = [
     "sphinxcontrib-bibtex",
     "ipython",
 ]
+
+[tool.ruff]
+# Set line length to 88 (compatible with Black)
+line-length = 88
+exclude = ["src/llg3d/process_tmp/"]
+
+[tool.ruff.lint.per-file-ignores]
+# Ignore all directories named `tests`.
+"tests/**" = ["D"]
+
+[tool.ruff.lint]
+# Enable pydocstyle (D) rules along with existing rules
+select = ["E", "F", "W", "D"]
+extend-select = ["D213"]
+ignore = [
+    "D107", # Missing docstring in __init__()
+    # Style preferences - ignore D212 to enable D213 (Google convention)
+    "D212", # Multi-line docstring summary should start at the first line (we prefer D213)
+]
+
+[tool.ruff.lint.pydocstyle]
+# Use Google convention for docstrings
+convention = "google"
+
+[tool.ruff.format]
+# Use double quotes for strings (compatible with Black)
+quote-style = "double"
+# Use 4 spaces for indentation (compatible with Black)
+indent-style = "space"
+# Respect magic trailing comma (compatible with Black)
+skip-magic-trailing-comma = false
+# Line length compatible with Black
+line-ending = "auto"

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/__init__.py

@@ -1,4 +1,6 @@
+"""Main llg3d package."""
+
 from .solver import LIB_AVAILABLE, rank, size, comm, status
 
-__version__ = "2.0.0"
+__version__ = "2.0.1"
 __all__ = ["LIB_AVAILABLE", "rank", "size", "comm", "status", "__version__"]

llg3d-2.0.1/src/llg3d/__main__.py

@@ -0,0 +1,6 @@
+"""Main entry point to execute the llg3d module."""
+
+from .main import main
+
+if __name__ == "__main__":
+    main()

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/element.py

@@ -1,6 +1,6 @@
-r"""
-Module containing the definition of the chemical elements
-"""
+"""Module containing the definition of the chemical elements."""
+
+from abc import ABC
 
 import numpy as np
 
@@ -11,8 +11,16 @@ mu_0 = 4 * np.pi * 1.0e-7  #: Vacuum permeability :math:`[H.m^{-1}]`
 gamma = 1.76e11  #: Gyromagnetic ratio :math:`[rad.s^{-1}.T^{-1}]`
 
 
-class Element:
-    """Abstract class for chemical elements"""
+class Element(ABC):
+    """
+    Abstract class for chemical elements.
+
+    Args:
+        T: Temperature in Kelvin
+        H_ext: External magnetic field strength
+        g: Grid object representing the simulation grid
+        dt: Time step for the simulation
+    """
 
     A = 0.0
     K = 0.0
@@ -22,14 +30,6 @@ class Element:
     anisotropy: str = ""
 
     def __init__(self, T: float, H_ext: float, g: Grid, dt: float) -> None:
-        """Initializes the Element class with given parameters
-
-        Args:
-            T: Temperature in Kelvin
-            H_ext: External magnetic field strength
-            g: Grid object representing the simulation grid
-            dt: Time step for the simulation
-        """
         self.H_ext = H_ext
         self.g = g
         self.dt = dt
@@ -52,16 +52,16 @@ class Element:
 
     def get_CFL(self) -> float:
         """
-        Returns the value of the CFL
+        Returns the value of the CFL.
 
         Returns:
-            float: The CFL value
+            The CFL value
         """
         return self.dt * self.coeff_1 / self.g.dx**2
 
     def to_dict(self) -> dict:
         """
-        Export element parameters to a dictionary for JAX JIT compatibility
+        Export element parameters to a dictionary for JAX JIT compatibility.
 
         Returns:
             Dictionary containing element parameters needed for computations
@@ -81,6 +81,8 @@ class Element:
 
 
 class Cobalt(Element):
+    """Cobalt element."""
+
     A = 30.0e-12  #: Exchange constant :math:`[J.m^{-1}]`
     K = 520.0e3  #: Anisotropy constant :math:`[J.m^{-3}]`
     lambda_G = 0.5  #: Damping parameter :math:`[1]`
@@ -90,6 +92,8 @@ class Cobalt(Element):
 
 
 class Iron(Element):
+    """Iron element."""
+
     A = 21.0e-12  #: Exchange constant :math:`[J.m^{-1}]`
     K = 48.0e3  #: Anisotropy constant :math:`[J.m^{-3}]`
     lambda_G = 0.5  #: Damping parameter :math:`[1]`
@@ -99,6 +103,8 @@ class Iron(Element):
 
 
 class Nickel(Element):
+    """Nickel element."""
+
     A = 9.0e-12  #: Exchange constant :math:`[J.m^{-1}]`
     K = -5.7e3  #: Anisotropy constant :math:`[J.m^{-3}]`
     lambda_G = 0.5  #: Damping parameter :math:`[1]`

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/grid.py

@@ -1,6 +1,4 @@
-"""
-Module to define the grid for the simulation
-"""
+"""Module to define the grid for the simulation."""
 
 from dataclasses import dataclass
 import numpy as np
@@ -10,7 +8,7 @@ from .solver import rank, size
 
 @dataclass
 class Grid:
-    """Stores grid data"""
+    """Stores grid data."""
 
     # Parameter values correspond to the global grid
     Jx: int  #: number of points in x direction
@@ -19,7 +17,7 @@ class Grid:
     dx: float  #: grid spacing in x direction
 
     def __post_init__(self) -> None:
-        """Compute grid characteristics"""
+        """Compute grid characteristics."""
         self.dy = self.dz = self.dx  # Setting dx = dy = dz
         self.Lx = (self.Jx - 1) * self.dx
         self.Ly = (self.Jy - 1) * self.dy
@@ -35,8 +33,7 @@ class Grid:
         self.ncell = (self.Jx - 1) * (self.Jy - 1) * (self.Jz - 1)
 
     def __str__(self) -> str:
-        """Print grid information"""
-
+        """Print grid information."""
         header = "\t\t".join(("x", "y", "z"))
         s = f"""\
 \t{header}
@@ -55,7 +52,7 @@ ncell = {self.ncell:d}
         self, T: float, name: str = "m1_mean", extension: str = "txt"
     ) -> str:
         """
-        Returns the output file name for a given temperature
+        Returns the output file name for a given temperature.
 
         Args:
             T: temperature
@@ -97,7 +94,7 @@ ncell = {self.ncell:d}
 
     def to_dict(self) -> dict:
         """
-        Export grid parameters to a dictionary for JAX JIT compatibility
+        Export grid parameters to a dictionary for JAX JIT compatibility.
 
         Returns:
             Dictionary containing grid parameters needed for computations
@@ -114,7 +111,7 @@ ncell = {self.ncell:d}
 
     def get_laplacian_coeff(self) -> tuple[float, float, float, float]:
         """
-        Returns the coefficients for the laplacian computation
+        Returns the coefficients for the laplacian computation.
 
         Returns:
             Tuple of coefficients (dx2_inv, dy2_inv, dz2_inv, center_coeff)

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/main.py

@@ -1,6 +1,4 @@
-"""
-Define a CLI for the llg3d package.
-"""
+"""Define a CLI for the llg3d package."""
 
 import argparse
 
@@ -20,6 +18,7 @@ else:
 def parse_args(args: list[str] | None) -> argparse.Namespace:
     """
     Argument parser for llg3d.
+
     Automatically adds arguments from the parameter dictionary.
 
     Returns:
@@ -44,9 +43,11 @@ def parse_args(args: list[str] | None) -> argparse.Namespace:
 
 def main(arg_list: list[str] = None):
     """
-    Evaluates the command line and runs the simulation
-    """
+    Evaluates the command line and runs the simulation.
 
+    Args:
+        arg_list: List of command line arguments
+    """
     args = parse_args(arg_list)
 
     if size > 1 and args.solver != "mpi":

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/output.py

@@ -1,6 +1,4 @@
-"""
-Utility functions for LLG3D
-"""
+"""Utility functions for LLG3D."""
 
 import json
 import sys
@@ -10,9 +8,11 @@ from .solver import rank
 from .grid import Grid
 
 
-def progress_bar(it: Iterable, prefix: str = "", size: int = 60, out: TextIO = sys.stdout):
+def progress_bar(
+    it: Iterable, prefix: str = "", size: int = 60, out: TextIO = sys.stdout
+):
     """
-    Displays a progress bar
+    Displays a progress bar.
 
     (Source: https://stackoverflow.com/a/34482761/16593179)
 
@@ -22,14 +22,13 @@ def progress_bar(it: Iterable, prefix: str = "", size: int = 60, out: TextIO = s
         size: Size of the progress bar (number of characters)
         out: Output stream (default is sys.stdout)
     """
-
     count = len(it)
 
     def show(j):
         x = int(size * j / count)
         if rank == 0:
             print(
-                f"{prefix}[{u'█'*x}{('.'*(size-x))}] {j}/{count}",
+                f"{prefix}[{'█' * x}{('.' * (size - x))}] {j}/{count}",
                 end="\r",
                 file=out,
                 flush=True,
@@ -48,7 +47,7 @@ def progress_bar(it: Iterable, prefix: str = "", size: int = 60, out: TextIO = s
 
 def write_json(json_file: str, run: dict):
     """
-    Writes the run dictionary to a JSON file
+    Writes the run dictionary to a JSON file.
 
     Args:
         json_file: Name of the JSON file
@@ -60,7 +59,7 @@ def write_json(json_file: str, run: dict):
 
 def get_output_files(g: Grid, T: float, n_mean: int, n_profile: int) -> tuple:
     """
-    Open files and list them
+    Open files and list them.
 
     Args:
         g: Grid object
@@ -95,7 +94,7 @@ def get_output_files(g: Grid, T: float, n_mean: int, n_profile: int) -> tuple:
 
 def close_output_files(f_mean: TextIO, f_profiles: list[TextIO] = None):
     """
-    Close all output files
+    Close all output files.
 
     Args:
         f_mean: file handler for storing m space integral over time

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/parameters.py

@@ -58,13 +58,13 @@ parameters: dict[str, Parameter] = {
 
 def get_parameter_list(parameters: dict) -> str:
     """
-    Returns parameter values as a string
+    Returns parameter values as a string.
 
     Args:
-        d: Dictionary of parameters parsed by argparse
+        parameters: Dictionary of parameters parsed by argparse
 
     Returns:
-        str: Formatted string of parameters
+        Formatted string of parameters
     """
     width = max([len(name) for name in parameters])
     s = ""

llg3d-2.0.1/src/llg3d/post/__init__.py

@@ -0,0 +1 @@
+"""Post-processing tools for LLG3D."""

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/post/plot_results.py

@@ -1,5 +1,5 @@
 """
-Plot 1D curves from several files
+Plot 1D curves from several files.
 
 Usage:
 
@@ -25,7 +25,6 @@ def plot(*files: tuple[str], output_file: str = DEFAULT_OUTPUT_FILE):
         files (tuple[str]): Paths to the result files.
         output_file (str): Path to the output image file.
     """
-
     fig, ax = plt.subplots()
     for file in files:
         if not file.endswith(".txt"):
@@ -43,12 +42,9 @@ def plot(*files: tuple[str], output_file: str = DEFAULT_OUTPUT_FILE):
 
 
 def main():
-    parser = argparse.ArgumentParser(
-        description="Plot results from one or more files."
-    )
-    parser.add_argument(
-        "files", nargs="+", type=str, help="Path to the result files."
-    )
+    """Main function to parse arguments and call the plot function."""
+    parser = argparse.ArgumentParser(description="Plot results from one or more files.")
+    parser.add_argument("files", nargs="+", type=str, help="Path to the result files.")
     parser.add_argument(
         "--output",
         "-o",

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/post/process.py

@@ -1,12 +1,14 @@
 #!/usr/bin/env python3
 """
-Post-processes a set of runs grouped into a `run.json` file or
-into a set of SLURM job arrays:
+Post-processes a set of runs.
+
+Runs are grouped into a `run.json` file or into a set of SLURM job arrays:
 
 1. Extracts result data,
 2. Plots the computed average magnetization against temperature,
 3. Interpolates the computed points using cubic splines,
-4. Determines the Curie temperature as the value corresponding to the minimal (negative) slope of the interpolated curve.
+4. Determines the Curie temperature as the value corresponding to the minimal (negative)
+    slope of the interpolated curve.
 """
 
 import json
@@ -17,14 +19,11 @@ from scipy.interpolate import interp1d
 
 
 class MagData:
-    """
-    Class to handle magnetization data and interpolation according to temperature
-    """
+    """Class to handle magnetization data and interpolation according to temperature."""
 
     n_interp = 200
 
     def __init__(self, job_dir: Path = None, run_file: Path = Path("run.json")) -> None:
-
         if job_dir:
             self.parentpath = job_dir
             data, self.run = self.process_slurm_jobs()
@@ -65,16 +64,18 @@ class MagData:
                     run = json.load(f)
                     # Adding temperature and averaging value to the data list
                     data.extend(
-                        [[float(T), res["m1_mean"]] for T, res in run["results"].items()]
+                        [
+                            [float(T), res["m1_mean"]]
+                            for T, res in run["results"].items()
+                        ]
                     )
             except FileNotFoundError:
-                print(f"Warning: {json_filename} file not found " f"in {jobdir.as_posix()}")
+                print(f"Warning: {json_filename} file not found in {jobdir.as_posix()}")
 
         data.sort()  # Sorting by increasing temperatures
 
         return np.array(data), run
 
-
     def process_json(json_filepath: Path) -> tuple[np.array, dict]:
         """
         Reads the run.json file and extracts result data.
@@ -98,8 +99,12 @@ class MagData:
     @property
     def T_Curie(self) -> float:
         """
-        Return the Curie temperature defined as the temperature at
-        which the magnetization is below 0.1
+        Return the Curie temperature.
+
+        It is defined as the temperature at which the magnetization is below 0.1.
+
+        Returns:
+            float: Curie temperature
         """
         i_max = np.where(0.1 - self.interp(self.T) > 0)[0].min()
-        return self.T[i_max]
+        return self.T[i_max]

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/post/temperature.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python3
-"""
-Plot the magnetization vs temperature and determine the Curie temperature.
-"""
+"""Plot the magnetization vs temperature and determine the Curie temperature."""
 
 import argparse
 from pathlib import Path
@@ -13,17 +11,14 @@ from .process import MagData
 
 def plot_m_vs_T(m: MagData, show: bool):
     """
-    Plots the data (T, <m>), interpolates the values,
-    calculates the Curie temperature.
-    Exports to PNG.
+    Plots the data (T, <m>).
+
+    Interpolates the values, calculates the Curie temperature, exports to PNG.
 
     Args:
-        data: numpy array (T, <m>)
-        parentdir: path to the directory containing the runs
-        run: descriptive dictionary of the run
+        m: Magnetization data object
         show: display the graph in a graphical window
     """
-
     print(f"T_Curie = {m.T_Curie:.0f} K")
 
     fig, ax = plt.subplots()
@@ -56,9 +51,7 @@ def plot_m_vs_T(m: MagData, show: bool):
 
 
 def main():
-    """
-    Parses the command line to execute processing functions
-    """
+    """Parses the command line to execute processing functions."""
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("--job_dir", type=Path, help="Slurm main job directory")
     parser.add_argument(

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/simulation.py

@@ -23,17 +23,14 @@ from .output import write_json
 class Simulation:
     """
     Class to encapsulate the simulation logic.
+
+    Args:
+        params: Dictionary of simulation parameters.
     """
 
     json_file = "run.json"  #: JSON file to store the results
 
     def __init__(self, params: dict[str, Parameter]):
-        """
-        Initializes the simulation with parameters.
-
-        Args:
-            params: Dictionary of simulation parameters.
-        """
         self.params: dict[str, Parameter] = params.copy()  #: simulation parameters
         self.simulate: callable = self._get_simulate_function_from_name(
             self.params["solver"]
@@ -46,9 +43,7 @@ class Simulation:
         self.params["element_class"] = get_element_class(params["element"])
 
     def run(self):
-        """
-        Runs the simulation and store the results.
-        """
+        """Runs the simulation and store the results."""
         self.total_time, self.filenames, self.m1_mean = self.simulate(**self.params)
 
     def _get_simulate_function_from_name(self, name: str) -> callable:
@@ -62,19 +57,15 @@ class Simulation:
             callable: The simulation function
 
         Example:
-
             >>> simulate = self.get_simulate_function_from_name("mpi")
 
             Will return the `simulate` function from the `llg3d.solver.mpi` module.
         """
-
         module = __import__(f"llg3d.solver.{name}", fromlist=["simulate"])
         return inspect.getattr_static(module, "simulate")
 
     def save(self):
-        """
-        Saves the results of the simulation to a JSON file.
-        """
+        """Saves the results of the simulation to a JSON file."""
         params = self.params.copy()  # save the parameters
         del params["element_class"]  # remove class object before serialization
         if rank == 0:

{llg3d-2.0.0 → llg3d-2.0.1}/src/llg3d/solver/__init__.py

@@ -1,5 +1,5 @@
 """
-Solver module for LLG3D
+Solver module for LLG3D.
 
 This module contains different solver implementations.
 """
@@ -42,4 +42,4 @@ else:
 
     status = DummyStatus()
 
-from . import numpy, solver
+from . import numpy, solver  # noqa: E402