rename Object to BaseObject

Fix imports and refactor

.github/workflows/ci-docs.yml

@@ -17,7 +17,7 @@ jobs:
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: 3.12.9
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
       - uses: actions/cache@v4
         with:

.gitignore

@@ -1,3 +1,6 @@
+# Custom
+dev-tools/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[codz]

README.md

@@ -23,13 +23,27 @@ With Python verion `>=3.12.4` and `<3.13`, create a virtual environment and inst
 ```
 python3 -m venv .venv
 source .venv/bin/activate
-(venv) pip install -e .[dev]
+```
+
+With the virtual environment activated, run:
+
+```
+pip install -e .[dev]
 ```
 
 ## Tests
 
-Tests can be run with `pytest` from the root directory of the repository.
+Tests can be run with `pytest` from the root directory of the repository. With the virtual environment activated, run:
 
 ```
-(venv) pytest
+pytest
 ```
+
+## Local viewing of documentation
+
+PG-RAD uses [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) for generating documentation. It can be locally viewed by (in the venv) running:
+```
+mkdocs serve
+```
+
+where you can add the `--livereload` flag to automatically update the documentation as you write to the Markdown files.

docs/javascripts/mathjax.js

@@ -0,0 +1,18 @@
+window.MathJax = {
+  tex: {
+    inlineMath: [['$', '$'], ["\\(", "\\)"]],
+    displayMath: [['$$', '$$'], ["\\[", "\\]"]],
+    processEscapes: true,
+    processEnvironments: true
+  },
+  options: {
+    processHtmlClass: "arithmatex"
+  }
+};
+
+document$.subscribe(() => { 
+  MathJax.startup.output.clearCache()
+  MathJax.typesetClear()
+  MathJax.texReset()
+  MathJax.typesetPromise()
+})

docs/pg-rad-in-python.md

@@ -1,5 +0,0 @@
----
-title: Using PG-RAD as a module
----
-
-Consult the API documentation in the side bar.

mkdocs.yml

@@ -28,8 +28,16 @@ markdown_extensions:
   - pymdownx.inlinehilite
   - pymdownx.snippets
   - pymdownx.superfences
+  - pymdownx.arithmatex:
+      generic: true
+
+extra_javascript:
+  - javascripts/mathjax.js
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
 
 plugins:
+- mkdocs-jupyter:
+    execute: false
 - mkdocstrings:
     enabled: !ENV [ENABLE_MKDOCSTRINGS, true]
     default_handler: python

pyproject.toml

@@ -7,7 +7,7 @@ where = ["src"]
 
 [project]
 name = "pg-rad"
-version = "0.2.0"
+version = "0.2.1"
 authors = [
   { name="Pim Nelissen", email="pi0274ne-s@student.lu.se" },
 ]
@@ -29,4 +29,4 @@ Homepage = "https://github.com/pim-n/pg-rad"
 Issues = "https://github.com/pim-n/pg-rad/issues"
 
 [project.optional-dependencies]
-dev = ["pytest", "notebook", "mkdocs-material", "mkdocstrings-python"]
+dev = ["pytest", "mkinit", "notebook", "mkdocs-material", "mkdocstrings-python", "mkdocs-jupyter"]

src/pg_rad/dataloader/__init__.py

@@ -0,0 +1,8 @@
+# do not expose internal logger when running mkinit
+__ignore__ = ["logger"]
+
+from pg_rad.dataloader import dataloader
+
+from pg_rad.dataloader.dataloader import (load_data,)
+
+__all__ = ['dataloader', 'load_data']

src/pg_rad/dataloader/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/exceptions/__init__.py

@@ -0,0 +1,10 @@
+# do not expose internal logger when running mkinit
+__ignore__ = ["logger"]
+
+from pg_rad.exceptions import exceptions
+
+from pg_rad.exceptions.exceptions import (ConvergenceError, DataLoadError,
+                                          InvalidCSVError,)
+
+__all__ = ['ConvergenceError', 'DataLoadError', 'InvalidCSVError',
+           'exceptions']

src/pg_rad/isotopes/__init__.py

@@ -0,0 +1,8 @@
+# do not expose internal logger when running mkinit
+__ignore__ = ["logger"]
+
+from pg_rad.isotopes import isotope
+
+from pg_rad.isotopes.isotope import (Isotope,)
+
+__all__ = ['Isotope', 'isotope']

src/pg_rad/landscape/__init__.py

@@ -0,0 +1,8 @@
+# do not expose internal logger when running mkinit
+__ignore__ = ["logger"]
+
+from pg_rad.landscape import landscape
+
+from pg_rad.landscape.landscape import (Landscape, create_landscape_from_path,)
+
+__all__ = ['Landscape', 'create_landscape_from_path', 'landscape']

src/pg_rad/landscape/landscape.py

@@ -1,9 +1,13 @@
+import logging
+
 from matplotlib import pyplot as plt
 from matplotlib.patches import Circle
 import numpy as np
 
 from pg_rad.path import Path
-from pg_rad.sources import PointSource
+from pg_rad.objects 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

@@ -1,17 +0,0 @@
-import logging
-import logging.config
-import pathlib
-
-import yaml
-
-def setup_logger(name):
-    logger = logging.getLogger(name)
-
-    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)
-    return logger

src/pg_rad/logging/__init__.py

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

src/pg_rad/logging/logger.py

@@ -0,0 +1,20 @@
+import logging
+import pathlib
+
+import yaml
+
+def setup_logger(log_level: str = "WARNING"):
+    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)
+    
+    config["loggers"]["root"]["level"] = log_level
+
+    logging.config.dictConfig(config)

src/pg_rad/objects/__init__.py

@@ -0,0 +1,13 @@
+# do not expose internal logger when running mkinit
+__ignore__ = ["logger"]
+
+from pg_rad.objects import detectors
+from pg_rad.objects import objects
+from pg_rad.objects import sources
+
+from pg_rad.objects.detectors import (Detector,)
+from pg_rad.objects.objects import (Object,)
+from pg_rad.objects.sources import (PointSource,)
+
+__all__ = ['Detector', 'Object', 'PointSource', 'detectors', 'objects',
+           'sources']

src/pg_rad/objects/objects.py

@@ -1,7 +1,7 @@
 import math
 from typing import Self
 
-class Object:
+class BaseObject:
     def __init__(
             self,
             x: float,

src/pg_rad/objects/sources.py

@@ -1,7 +1,11 @@
-from pg_rad.objects import Object
-from pg_rad.isotope import Isotope
+import logging
 
-class PointSource(Object):
+from .objects import BaseObject
+from pg_rad.isotopes import Isotope
+
+logger = logging.getLogger(__name__)
+
+class PointSource(BaseObject):
     _id_counter = 1
     def __init__(
             self,
@@ -39,5 +43,7 @@ class PointSource(Object):
         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)"

src/pg_rad/path/__init__.py

@@ -0,0 +1,9 @@
+# do not expose internal logger when running mkinit
+__ignore__ = ["logger"]
+
+from pg_rad.path import path
+
+from pg_rad.path.path import (Path, PathSegment, path_from_RT90,
+                              simplify_path,)
+
+__all__ = ['Path', 'PathSegment', 'path', 'path_from_RT90', 'simplify_path']

src/pg_rad/path/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

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)
-    b = Source(*tuple(pos_b), strength = None)
+    a = PointSource(*tuple(pos_a), 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) 
-    is calculated correctly._"""
+    """Verify whether distance between two PointSources is calculated correctly."""
 
     pos_a, pos_b, a, b = test_sources