Improve PEP8 adherance using flake8 linter

src/pg_rad/dataloader/dataloader.py

@@ -6,6 +6,7 @@ from pg_rad.exceptions import DataLoadError, InvalidCSVError
 
 logger = logging.getLogger(__name__)
 
+
 def load_data(filename: str) -> pd.DataFrame:
     logger.debug(f"Attempting to load file: {filename}")
 
@@ -25,4 +26,4 @@ def load_data(filename: str) -> pd.DataFrame:
         raise DataLoadError("Unexpected error while loading data") from e
 
     logger.debug(f"File loaded: {filename}")
-    return df
+    return df

src/pg_rad/exceptions/exceptions.py

@@ -1,8 +1,10 @@
 class ConvergenceError(Exception):
     """Raised when an algorithm fails to converge."""
 
+
 class DataLoadError(Exception):
     """Base class for data loading errors."""
 
+
 class InvalidCSVError(DataLoadError):
-    """Raised when a file is not a valid CSV."""
+    """Raised when a file is not a valid CSV."""

src/pg_rad/isotopes/isotope.py

@@ -5,7 +5,7 @@ class Isotope:
         name (str): Full name (e.g. Caesium-137).
         E (float): Energy of the primary gamma in keV.
         b (float): Branching ratio for the gamma at energy E.
-    """  
+    """
     def __init__(
             self,
             name: str,
@@ -20,4 +20,4 @@ class Isotope:
 
         self.name = name
         self.E = E
-        self.b = b
+        self.b = b

src/pg_rad/landscape/landscape.py

@@ -9,26 +9,29 @@ from pg_rad.objects import PointSource
 
 logger = logging.getLogger(__name__)
 
+
 class Landscape:
     """A generic Landscape that can contain a Path and sources.
 
     Args:
-        air_density (float, optional): Air density in kg / m^3. Defaults to 1.243.
+        air_density (float, optional): Air density, kg/m^3. Defaults to 1.243.
-        size (int | tuple[int, int, int], optional): Size of the world. Defaults to 500.
+        size (int | tuple[int, int, int], optional): Size of the world.
-        scale (str, optional): The scale of the size argument passed. Defaults to 'meters'.
+        Defaults to 500.
-    """    
+        scale (str, optional): The scale of the size argument passed.
+        Defaults to 'meters'.
+    """
     def __init__(
             self,
             air_density: float = 1.243,
             size: int | tuple[int, int, int] = 500,
-            scale = 'meters',
+            scale: str = 'meters'
-            ):    
+            ):
         if isinstance(size, int):
             self.world = np.zeros((size, size, size))
         elif isinstance(size, tuple) and len(size) == 3:
             self.world = np.zeros(size)
         else:
-            raise TypeError("size must be an integer or a tuple of 3 integers.")
+            raise TypeError("size must be integer or a tuple of 3 integers.")
 
         self.air_density = air_density
         self.scale = scale
@@ -36,8 +39,8 @@ class Landscape:
         self.path: Path = None
         self.sources: list[PointSource] = []
         logger.debug("Landscape initialized.")
-    
+
-    def plot(self, z = 0):
+    def plot(self, z: float | int = 0):
         """Plot a slice of the world at a height `z`.
 
         Args:
@@ -45,7 +48,7 @@ class Landscape:
 
         Returns:
             fig, ax: Matplotlib figure objects.
-        """        
+        """
         x_lim, y_lim, _ = self.world.shape
 
         fig, ax = plt.subplots()
@@ -54,9 +57,9 @@ class Landscape:
         ax.set_xlabel(f"X [{self.scale}]")
         ax.set_ylabel(f"Y [{self.scale}]")
 
-        if not self.path == None:
+        if self.path is not None:
             ax.plot(self.path.x_list, self.path.y_list, 'bo-')
-        
+
         for s in self.sources:
             if np.isclose(s.z, z):
                 dot = Circle(
@@ -78,19 +81,19 @@ class Landscape:
                 )
 
                 ax.add_patch(dot)
-                
+
         return fig, ax
 
     def add_sources(self, *sources: PointSource):
         """Add one or more point sources to the world.
 
         Args:
-            *sources (pg_rad.sources.PointSource): One or more sources, passed as
+            *sources (pg_rad.sources.PointSource): One or more sources,
-            Source1, Source2, ...
+            passed as Source1, Source2, ...
         Raises:
-            ValueError: If the source is outside the boundaries of the landscape.
+            ValueError: If the source is outside the boundaries of the
-        """        
+            landscape.
-
+        """
         max_x, max_y, max_z = self.world.shape[:3]
 
         if any(
@@ -108,24 +111,23 @@ class Landscape:
         Set the path in the landscape.
         """
         self.path = path
-    
+
-def create_landscape_from_path(path: Path, max_z = 500):
+
+def create_landscape_from_path(path: Path, max_z: float | int = 50):
     """Generate a landscape from a path, using its dimensions to determine
     the size of the landscape.
 
     Args:
         path (Path): A Path object describing the trajectory.
-        max_z (int, optional): Height of the world. Defaults to 500 meters.
+        max_z (int, optional): Height of the world. Defaults to 50 meters.
 
     Returns:
-        landscape (pg_rad.landscape.Landscape): A landscape with dimensions based on the provided Path.
+        landscape (pg_rad.landscape.Landscape): A landscape with dimensions
-    """    
+        based on the provided Path.
+    """
     max_x = np.ceil(max(path.x_list))
     max_y = np.ceil(max(path.y_list))
 
-    landscape = Landscape(
+    landscape = Landscape(size=(max_x, max_y, max_z))
-        size = (max_x, max_y, max_z)
-        )
-    
     landscape.path = path
-    return landscape
+    return landscape

src/pg_rad/logging/logger.py

@@ -3,18 +3,19 @@ import pathlib
 
 import yaml
 
+
 def setup_logger(log_level: str = "WARNING"):
     levels = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
-    
+
-    if not log_level in levels:
+    if log_level not in levels:
         raise ValueError(f"Log level must be one of {levels}.")
-    
+
     base_dir = pathlib.Path(__file__).resolve().parent
     config_file = base_dir / "configs" / "logging.yml"
 
     with open(config_file) as f:
         config = yaml.safe_load(f)
-    
+
     config["loggers"]["root"]["level"] = log_level
 
-    logging.config.dictConfig(config)
+    logging.config.dictConfig(config)

src/pg_rad/objects/objects.py

@@ -1,6 +1,7 @@
 import math
 from typing import Self
 
+
 class BaseObject:
     def __init__(
             self,
@@ -16,18 +17,20 @@ class BaseObject:
             x (float): X coordinate.
             y (float): Y coordinate.
             z (float): Z coordinate.
-            name (str, optional): Name for the object. Defaults to "Unnamed object".
+            name (str, optional): Name for the object.
-            color (str, optional): Matplotlib compatible color string. Defaults to "red".
+            Defaults to "Unnamed object".
+            color (str, optional): Matplotlib compatible color string.
+            Defaults to "red".
         """
-        
+
         self.x = x
         self.y = y
         self.z = z
         self.name = name
         self.color = color
-    
+
     def distance_to(self, other: Self) -> float:
         return math.dist(
             (self.x, self.y, self.z),
             (other.x, other.y, other.z),
-        )
+        )

src/pg_rad/objects/sources.py

@@ -5,8 +5,10 @@ from pg_rad.isotopes import Isotope
 
 logger = logging.getLogger(__name__)
 
+
 class PointSource(BaseObject):
     _id_counter = 1
+
     def __init__(
             self,
             x: float,
@@ -27,9 +29,10 @@ class PointSource(BaseObject):
             name (str | None, optional): Can give the source a unique name.
             Defaults to None, making the name sequential.
             (Source-1, Source-2, etc.).
-            color (str, optional): Matplotlib compatible color string. Defaults to "red".
+            color (str, optional): Matplotlib compatible color string.
+            Defaults to "red".
         """
-        
+
         self.id = PointSource._id_counter
         PointSource._id_counter += 1
 
@@ -42,8 +45,13 @@ class PointSource(BaseObject):
         self.activity = activity
         self.isotope = isotope
         self.color = color
-        
+
         logger.debug(f"Source created: {self.name}")
 
     def __repr__(self):
-        return f"PointSource(name={self.name}, pos={(self.x, self.y, self.z)}, isotope={self.isotope.name}, A={self.activity} MBq)"
+        repr_str = (f"PointSource(name={self.name}, "
+                    + f"pos={(self.x, self.y, self.z)}, "
+                    + f"A={self.activity} MBq), "
+                    + f"isotope={self.isotope.name}.")
+
+        return repr_str

src/pg_rad/path/path.py

@@ -11,6 +11,7 @@ from pg_rad.exceptions import ConvergenceError
 
 logger = logging.getLogger(__name__)
 
+
 class PathSegment:
     def __init__(self, a: tuple[float, float], b: tuple[float, float]):
         """A straight Segment of a Path, from (x_a, y_a) to (x_b, y_b).
@@ -18,18 +19,18 @@ class PathSegment:
         Args:
             a (tuple[float, float]): The starting point (x_a, y_a).
             b (tuple[float, float]): The final point (x_b, y_b).
-        """        
+        """
         self.a = a
         self.b = b
 
     def get_length(self) -> float:
         return math.dist(self.a, self.b)
-    
+
     length = property(get_length)
 
     def __str__(self) -> str:
         return str(f"({self.a}, {self.b})")
-    
+
     def __getitem__(self, index) -> float:
         if index == 0:
             return self.a
@@ -38,26 +39,30 @@ class PathSegment:
         else:
             raise IndexError
 
+
 class Path:
     def __init__(
             self,
             coord_list: Sequence[tuple[float, float]],
             z: float = 0,
-            path_simplify = False
+            path_simplify: bool = False
                  ):
         """Construct a path of sequences based on a list of coordinates.
 
         Args:
-            coord_list (Sequence[tuple[float, float]]): List of x,y coordinates.
+            coord_list (Sequence[tuple[float, float]]): List of x,y
+            coordinates.
             z (float, optional): Height of the path. Defaults to 0.
-            path_simplify (bool, optional): Whether to pg_rad.path.simplify_path(). Defaults to False.
+            path_simplify (bool, optional): Whether to
-        """        
+            pg_rad.path.simplify_path(). Defaults to False.
-        
+        """
+
         if len(coord_list) < 2:
-            raise ValueError("Must provide at least two coordinates as a list of tuples, e.g. [(x1, y1), (x2, y2)]")
+            raise ValueError("Must provide at least two coordinates as a \
+                of tuples, e.g. [(x1, y1), (x2, y2)]")
 
         x, y = tuple(zip(*coord_list))
-    
+
         if path_simplify:
             try:
                 x, y = simplify_path(list(x), list(y))
@@ -69,7 +74,11 @@ class Path:
 
         coord_list = list(zip(x, y))
 
-        self.segments = [PathSegment(i, ip1) for i, ip1 in zip(coord_list, coord_list[1:])]
+        self.segments = [
+            PathSegment(i, ip1)
+            for i, ip1 in
+            zip(coord_list, coord_list[1:])
+            ]
 
         self.z = z
 
@@ -77,7 +86,7 @@ class Path:
 
     def get_length(self) -> float:
         return sum([s.length for s in self.segments])
-    
+
     length = property(get_length)
 
     def __getitem__(self, index) -> PathSegment:
@@ -85,40 +94,43 @@ class Path:
 
     def __str__(self) -> str:
         return str([str(s) for s in self.segments])
-    
+
     def plot(self, **kwargs):
         """
         Plot the path using matplotlib.
-        """  
+        """
         plt.plot(self.x_list, self.y_list, **kwargs)
 
+
 def simplify_path(
         x: Sequence[float],
         y: Sequence[float],
         keep_endpoints_equal: bool = False,
         n_breakpoints: int = 3
         ):
-    """From full resolution x and y arrays, return a piecewise linearly approximated/simplified pair of x and y arrays.
+    """From full resolution x and y arrays, return a piecewise linearly
+    approximated/simplified pair of x and y arrays.
 
     This function uses the `piecewise_regression` package. From a full set of
     coordinate pairs, the function fits linear sections, automatically finding
     the number of breakpoints and their positions.
 
-    On why the default value of n_breakpoints is 3, from the `piecewise_regression`
+    On why the default value of n_breakpoints is 3, from the
-    docs:
+    `piecewise_regression` docs:
     "If you do not have (or do not want to use) initial guesses for the number
     of breakpoints, you can set it to n_breakpoints=3, and the algorithm will
     randomly generate start_values. With a 50% chance, the bootstrap restarting
     algorithm will either use the best currently converged breakpoints or
-    randomly generate new start_values, escaping the local optima in two ways in
+    randomly generate new start_values, escaping the local optima in two ways
-    order to find better global optima."
+    in order to find better global optima."
 
     Args:
         x (Sequence[float]): Full list of x coordinates.
         y (Sequence[float]): Full list of y coordinates.
         keep_endpoints_equal (bool, optional): Whether or not to force start
-        and end to be exactly equal to the original. This will worsen the linear
+        and end to be exactly equal to the original. This will worsen the
-        approximation at the beginning and end of path. Defaults to False.
+        linear approximation at the beginning and end of path. Defaults to
+        False.
         n_breakpoints (int, optional): Number of breakpoints. Defaults to 3.
 
     Returns:
@@ -129,25 +141,27 @@ def simplify_path(
         ConvergenceError: If the fitting algorithm failed to simplify the path.
 
     Reference:
-        Pilgrim, C., (2021). piecewise-regression (aka segmented regression) in Python. Journal of Open Source Software, 6(68), 3859, https://doi.org/10.21105/joss.03859.
+        Pilgrim, C., (2021). piecewise-regression (aka segmented regression)
+        in Python. Journal of Open Source Software,
+        6(68), 3859, https://doi.org/10.21105/joss.03859.
     """
-    
+
-    logger.debug(f"Attempting piecewise regression on path.")
+    logger.debug("Attempting piecewise regression on path.")
 
     pw_fit = piecewise_regression.Fit(x, y, n_breakpoints=n_breakpoints)
     pw_res = pw_fit.get_results()
 
-    if pw_res == None:
+    if pw_res is None:
         logger.warning("Piecewise regression failed to converge.")
-        raise ConvergenceError("Piecewise regression failed to converge.") 
+        raise ConvergenceError("Piecewise regression failed to converge.")
-    
+
     est = pw_res['estimates']
 
     # extract and sort breakpoints
     breakpoints_x = sorted(
         v['estimate'] for k, v in est.items() if k.startswith('breakpoint')
     )
- 
+
     x_points = [x[0]] + breakpoints_x + [x[-1]]
 
     y_points = pw_fit.predict(x_points)
@@ -158,28 +172,33 @@ def simplify_path(
         y_points[-1] = y[-1]
 
     logger.info(
-        f"Piecewise regression reduced path from {len(x)-1} to {len(x_points)-1} segments."
+        f"Piecewise regression reduced path from \
+            {len(x)-1} to {len(x_points)-1} segments."
     )
 
     return x_points, y_points
 
+
 def path_from_RT90(
         df: pd.DataFrame,
         east_col: str = "East",
         north_col: str = "North",
         **kwargs
         ) -> Path:
-    """Construct a path from East and North formatted coordinates (RT90) in a Pandas DataFrame.
+    """Construct a path from East and North formatted coordinates (RT90)
+    in a Pandas DataFrame.
 
     Args:
-        df (pandas.DataFrame): DataFrame containing at least the two columns noted in the cols argument.
+        df (pandas.DataFrame): DataFrame containing at least the two columns
+        noted in the cols argument.
         east_col (str): The column name for the East coordinates.
         north_col (str): The column name for the North coordinates.
 
     Returns:
-        Path: A Path object built from the aquisition coordinates in the DataFrame.
+        Path: A Path object built from the aquisition coordinates in the
-    """    
+        DataFrame.
-    
+    """
+
     east_arr = np.array(df[east_col]) - min(df[east_col])
     north_arr = np.array(df[north_col]) - min(df[north_col])
 
@@ -187,4 +206,4 @@ def path_from_RT90(
 
     path = Path(coord_pairs, **kwargs)
     logger.debug("Loaded path from provided RT90 coordinates.")
-    return path
+    return path