improving logging setup

docs/javascripts/mathjax.js

@@ -1,12 +1,11 @@
 window.MathJax = {
   tex: {
-    inlineMath: [["\\(", "\\)"]],
+    inlineMath: [['$', '$'], ["\\(", "\\)"]],
-    displayMath: [["\\[", "\\]"]],
+    displayMath: [['$$', '$$'], ["\\[", "\\]"]],
     processEscapes: true,
     processEnvironments: true
   },
   options: {
-    ignoreHtmlClass: ".*|",
     processHtmlClass: "arithmatex"
   }
 };

mkdocs.yml

@@ -33,10 +33,11 @@ markdown_extensions:
 
 extra_javascript:
   - javascripts/mathjax.js
-  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
 
 plugins:
-- mkdocs-jupyter
+- mkdocs-jupyter:
+    execute: false
 - mkdocstrings:
     enabled: !ENV [ENABLE_MKDOCSTRINGS, true]
     default_handler: python

src/pg_rad/dataloader.py

@@ -1,12 +1,13 @@
+import logging
+
 import pandas as pd
 
-from pg_rad.logger import setup_logger
 from pg_rad.exceptions import DataLoadError, InvalidCSVError
 
-logger = setup_logger(__name__)
+logger = logging.getLogger(__name__)
 
 def load_data(filename: str) -> pd.DataFrame:
-    logger.debug(f"Attempting to load data from {filename}")
+    logger.debug(f"Attempting to load file: {filename}")
 
     try:
         df = pd.read_csv(filename, delimiter=',')
@@ -23,4 +24,5 @@ def load_data(filename: str) -> pd.DataFrame:
         logger.exception(f"Unexpected error while loading {filename}")
         raise DataLoadError("Unexpected error while loading data") from e
 
+    logger.debug(f"File loaded: {filename}")
     return df

src/pg_rad/landscape.py

@@ -1,3 +1,5 @@
+import logging
+
 from matplotlib import pyplot as plt
 from matplotlib.patches import Circle
 import numpy as np
@@ -5,6 +7,8 @@ import numpy as np
 from pg_rad.path import Path
 from pg_rad.sources import PointSource
 
+logger = logging.getLogger(__name__)
+
 class Landscape:
     """A generic Landscape that can contain a Path and sources.
 
@@ -31,6 +35,7 @@ class Landscape:
 
         self.path: Path = None
         self.sources: list[PointSource] = []
+        logger.debug("Landscape initialized.")
     
     def plot(self, z = 0):
         """Plot a slice of the world at a height `z`.

src/pg_rad/logger.py

@@ -4,14 +4,18 @@ import pathlib
 
 import yaml
 
-def setup_logger(name):
+def setup_logger(log_level: str = "WARNING"):
-    logger = logging.getLogger(name)
+    levels = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
-
+    
+    if not log_level 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)
     
-    logging.config.dictConfig(config)
+    config["loggers"]["root"]["level"] = log_level
-    return logger
+
+    logging.config.dictConfig(config)

src/pg_rad/path.py

@@ -1,4 +1,5 @@
 from collections.abc import Sequence
+import logging
 import math
 
 from matplotlib import pyplot as plt
@@ -7,9 +8,8 @@ import pandas as pd
 import piecewise_regression
 
 from pg_rad.exceptions import ConvergenceError
-from pg_rad.logger import setup_logger
 
-logger = setup_logger(__name__)
+logger = logging.getLogger(__name__)
 
 class PathSegment:
     def __init__(self, a: tuple[float, float], b: tuple[float, float]):
@@ -73,6 +73,8 @@ class Path:
 
         self.z = z
 
+        logger.debug("Path created.")
+
     def get_length(self) -> float:
         return sum([s.length for s in self.segments])
     
@@ -136,7 +138,7 @@ def simplify_path(
     pw_res = pw_fit.get_results()
 
     if pw_res == None:
-        logger.error("Piecewise regression failed to converge.")
+        logger.warning("Piecewise regression failed to converge.")
         raise ConvergenceError("Piecewise regression failed to converge.") 
     
     est = pw_res['estimates']
@@ -184,4 +186,5 @@ def path_from_RT90(
     coord_pairs = list(zip(east_arr, north_arr))
 
     path = Path(coord_pairs, **kwargs)
+    logger.debug("Loaded path from provided RT90 coordinates.")
     return path

src/pg_rad/sources.py

@@ -1,6 +1,10 @@
+import logging
+
 from pg_rad.objects import Object
 from pg_rad.isotope import Isotope
 
+logger = logging.getLogger(__name__)
+
 class PointSource(Object):
     _id_counter = 1
     def __init__(
@@ -38,6 +42,8 @@ class PointSource(Object):
         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)"

tests/test_sources.py

@@ -1,28 +1,27 @@
 import numpy as np
 import pytest
 
-from pg_rad.objects import Source
+from pg_rad.sources import PointSource
 
 @pytest.fixture
 def test_sources():
     pos_a = np.random.rand(3)
     pos_b = np.random.rand(3)
 
-    a = Source(*tuple(pos_a), strength = None)
+    a = PointSource(*tuple(pos_a), strength = None)
-    b = Source(*tuple(pos_b), strength = None)
+    b = PointSource(*tuple(pos_b), strength = None)
 
     return pos_a, pos_b, a, b
 
 def test_if_distances_equal(test_sources):
-    """_Verify whether from object A to object B is the same as B to A._"""
+    """Verify whether from PointSource A to PointSource B is the same as B to A."""
 
     _, _, a, b = test_sources
 
     assert a.distance_to(b) == b.distance_to(a)
 
 def test_distance_calculation(test_sources):
-    """_Verify whether distance between two static objects (e.g. sources) 
+    """Verify whether distance between two PointSources is calculated correctly."""
-    is calculated correctly._"""
 
     pos_a, pos_b, a, b = test_sources