Update pyproject.toml and README.md to reflect new conditions.

README.md

@@ -31,6 +31,14 @@ With the virtual environment activated, run:
 pip install -e .[dev]
 ```
 
+## Running example landscape
+
+The example landscape can be generated using the command-line interface. Still in the virtual environment, run
+
+```
+pgrad --test --loglevel DEBUG
+```
+
 ## Tests
 
 Tests can be run with `pytest` from the root directory of the repository. With the virtual environment activated, run:

pyproject.toml

@@ -7,6 +7,7 @@ where = ["src"]
 
 [tool.setuptools.package-data]
 "pg_rad.data" = ["*.csv"]
+"pg_rad.configs" = ["*.yml"]
 
 [project]
 name = "pg-rad"
@@ -26,6 +27,9 @@ dependencies = [
 license = "MIT"
 license-files = ["LICEN[CS]E*"]
 
+[project.scripts]
+pgrad = "pg_rad.main:main"
+
 [project.urls]
 Homepage = "https://github.com/pim-n/pg-rad"
 Issues = "https://github.com/pim-n/pg-rad/issues"

src/pg_rad/configs/filepaths.py

@@ -0,0 +1,3 @@
+ATTENUATION_TABLE = 'attenuation_table.csv'
+TEST_EXP_DATA = 'test_path_coords.csv'
+LOGGING_CONFIG = 'logging.yml'

src/pg_rad/isotopes/presets.py

@@ -3,7 +3,7 @@ from .isotope import Isotope
 
 class CS137(Isotope):
     def __init__(self):
-        super.__init__(
+        super().__init__(
             name="Cs-137",
             E=661.66,
             b=0.851

src/pg_rad/landscape/__init__.py

@@ -1,8 +1,11 @@
 # do not expose internal logger when running mkinit
 __ignore__ = ["logger"]
 
+from pg_rad.landscape import director
 from pg_rad.landscape import landscape
 
+from pg_rad.landscape.director import (LandscapeDirector,)
 from pg_rad.landscape.landscape import (Landscape, LandscapeBuilder,)
 
-__all__ = ['Landscape', 'LandscapeBuilder', 'landscape']
+__all__ = ['Landscape', 'LandscapeBuilder', 'LandscapeDirector', 'director',
+           'landscape']

src/pg_rad/landscape/director.py

@@ -0,0 +1,23 @@
+from importlib.resources import files
+import logging
+
+from pg_rad.configs.filepaths import TEST_EXP_DATA
+from pg_rad.isotopes import CS137
+from pg_rad.landscape.landscape import LandscapeBuilder
+from pg_rad.objects import PointSource
+
+
+class LandscapeDirector:
+    def __init__(self):
+        self.logger = logging.getLogger(__name__)
+        self.logger.debug("LandscapeDirector initialized.")
+
+    def build_test_landscape(self):
+        fp = files('pg_rad.data').joinpath(TEST_EXP_DATA)
+        source = PointSource(activity=100, isotope=CS137(), pos=(0, 0, 0))
+        lb = LandscapeBuilder("Test landscape")
+        lb.set_air_density(1.243)
+        lb.set_path_from_experimental_data(fp, z=0)
+        lb.set_point_sources(source)
+        landscape = lb.build()
+        return landscape

src/pg_rad/landscape/landscape.py

@@ -16,6 +16,7 @@ class Landscape:
     """
     def __init__(
             self,
+            name: str,
             path: Path,
             point_sources: list[PointSource] = [],
             size: tuple[int, int, int] = [500, 500, 50],
@@ -35,12 +36,13 @@ class Landscape:
             TypeError: _description_
         """
 
+        self.name = name
         self.path = path
         self.point_sources = point_sources
         self.size = size
         self.air_density = air_density
 
-        logger.debug("Landscape initialized.")
+        logger.debug(f"Landscape created: {self.name}")
 
     def calculate_fluence_at(self, pos: tuple):
         total_phi = 0.
@@ -61,12 +63,15 @@ class Landscape:
 
 
 class LandscapeBuilder:
-    def __init__(self):
+    def __init__(self, name: str = "Unnamed landscape"):
+        self.name = name
         self._path = None
         self._point_sources = []
         self._size = None
         self._air_density = None
 
+        logger.debug(f"LandscapeBuilder initialized: {self.name}")
+
     def set_air_density(self, air_density) -> Self:
         """Set the air density of the world."""
         self._air_density = air_density
@@ -95,7 +100,8 @@ class LandscapeBuilder:
         self._path = path_from_RT90(
             df=df,
             east_col=east_col,
-            north_col=north_col
+            north_col=north_col,
+            z=z
         )
 
         # The size of the landscape will be updated if
@@ -108,11 +114,12 @@ class LandscapeBuilder:
 
         if needs_resize:
             if not self._size:
-                logger.info("Landscape size set to path dimensions.")
+                logger.debug("Because no Landscape size was set, "
+                             "it will now set to path dimensions.")
             else:
                 logger.warning(
                     "Path exceeds current landscape size. "
-                    "Expanding landscape to accommodate it."
+                    "Landscape size will be expanded to accommodate path."
                 )
 
             self.set_landscape_size(self._path.size)
@@ -142,9 +149,13 @@ class LandscapeBuilder:
         self._point_sources = sources
 
     def build(self):
-        return Landscape(
+        landscape = Landscape(
+            name=self.name,
             path=self._path,
             point_sources=self._point_sources,
             size=self._size,
             air_density=self._air_density
         )
+
+        logger.info(f"Landscape built successfully: {landscape.name}")
+        return landscape

src/pg_rad/logger/__init__.py

@@ -0,0 +1,5 @@
+from pg_rad.logger import logger
+
+from pg_rad.logger.logger import (setup_logger,)
+
+__all__ = ['logger', 'setup_logger']

src/pg_rad/logger/logger.py

@@ -1,8 +1,10 @@
-import logging
-import pathlib
+import logging.config
+from importlib.resources import files
 
 import yaml
 
+from pg_rad.configs.filepaths import LOGGING_CONFIG
+
 
 def setup_logger(log_level: str = "WARNING"):
     levels = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
@@ -10,8 +12,7 @@ def setup_logger(log_level: str = "WARNING"):
     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"
+    config_file = files('pg_rad.configs').joinpath(LOGGING_CONFIG)
 
     with open(config_file) as f:
         config = yaml.safe_load(f)

src/pg_rad/logging/__init__.py

@@ -1,5 +0,0 @@
-from pg_rad.logging import logger
-
-from pg_rad.logging.logger import (setup_logger,)
-
-__all__ = ['logger', 'setup_logger']

src/pg_rad/main.py

@@ -0,0 +1,33 @@
+import argparse
+
+from pg_rad.logger import setup_logger
+from pg_rad.landscape import LandscapeDirector
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="pg-rad",
+        description="Primary Gamma RADiation landscape tool"
+    )
+
+    parser.add_argument(
+        "--test",
+        action="store_true",
+        help="Load and run the test landscape"
+    )
+    parser.add_argument(
+        "--loglevel",
+        default="INFO",
+        choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
+    )
+
+    args = parser.parse_args()
+    setup_logger(args.loglevel)
+
+    if args.test:
+        landscape = LandscapeDirector().build_test_landscape()
+        print(landscape.name)
+
+
+if __name__ == "__main__":
+    main()

src/pg_rad/objects/objects.py

@@ -6,7 +6,7 @@ import numpy as np
 class BaseObject:
     def __init__(
             self,
-            pos: tuple[float, float, float],
+            pos: tuple[float, float, float] = (0, 0, 0),
             name: str = "Unnamed object",
             color: str = 'grey'):
         """

src/pg_rad/objects/sources.py

@@ -11,22 +11,23 @@ class PointSource(BaseObject):
 
     def __init__(
             self,
-            pos: tuple,
             activity: int,
             isotope: Isotope,
+            pos: tuple[float, float, float] = (0, 0, 0),
             name: str | None = None,
-            color: str = "red"):
+            color: str = 'red'
+            ):
         """A point source.
 
         Args:
-            pos (tuple): a position vector of length 3 (x,y,z).
             activity (int): Activity A in MBq.
             isotope (Isotope): The isotope.
-            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".
+            pos (tuple[float, float, float], optional):
+                Position of the PointSource.
+            name (str, optional): Can give the source a unique name.
+                If not provided, point sources are sequentially
+                named: Source1, Source2, ...
+            color (str, optional): Matplotlib compatible color string
         """
 
         self.id = PointSource._id_counter

src/pg_rad/path/path.py

@@ -42,14 +42,18 @@ class Path:
     def __init__(
             self,
             coord_list: Sequence[tuple[float, float]],
-            z: float = 0
+            z: float = 0.,
+            z_box: float = 50.
                  ):
         """Construct a path of sequences based on a list of coordinates.
 
         Args:
             coord_list (Sequence[tuple[float, float]]): List of x,y
             coordinates.
-            z (float, optional): Height of the path. Defaults to 0.
+            z (float, optional): position of the path in z-direction in meters.
+                Defaults to 0 meters.
+            z_box (float, optional): How much empty space to set
+                above the path in meters. Defaults to 50 meters.
         """
 
         if len(coord_list) < 2:
@@ -73,7 +77,7 @@ class Path:
         self.size = (
             np.ceil(max(self.x_list)),
             np.ceil(max(self.y_list)),
-            z
+            z + z_box
         )
 
         logger.debug("Path created.")

src/pg_rad/physics/attenuation.py

@@ -3,11 +3,13 @@ from importlib.resources import files
 from pandas import read_csv
 from scipy.interpolate import interp1d
 
+from pg_rad.configs.filepaths import ATTENUATION_TABLE
+
 
 def get_mass_attenuation_coeff(
         *args
         ) -> float:
-    csv = files('pg_rad.data').joinpath('attenuation_table.csv')
+    csv = files('pg_rad.data').joinpath(ATTENUATION_TABLE)
     data = read_csv(csv)
     x = data["energy_mev"].to_numpy()
     y = data["mu"].to_numpy()