enhancement #37: generate doc with pdoc

.github/workflows/docs.yml

@@ -0,0 +1,45 @@
+name: Generate Python Documentation
+
+on: [pull_request]
+
+jobs:
+  check-docstrings:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: 'pip' # caching pip dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name : Check docstrings
+        run : pydocstyle src/ --convention google --count
+
+  build-docs:
+    runs-on: ubuntu-22.04
+    steps:
+    - name: Checkout Repository
+      uses: actions/checkout@v3
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[dev]
+
+    - name: Generate Documentation
+      run: pdoc example --output-dir docs
+
+    - name: Archive Documentation
+      uses: actions/upload-artifact@v4
+      with:
+        name: documentation
+        path: docs/

.gitignore

@@ -163,3 +163,8 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# generate documentation
+docs/*.html
+docs/*.js
+docs/example/

README.md

@@ -143,4 +143,17 @@ Then, if all tests are sucessful:
  The main guidelines for the coding style is defined by [PEP8](https://peps.python.org/pep-0008/). You can directly refer to the examples in the code.
 
  Specific choices are detailed in dedicated document:
- - for the mathematical notation please refer to [Coding convention for Maths](docs/convention_maths.md)
+ - for the mathematical notation please refer to [Coding convention for Maths](docs/convention_maths.md)
+
+ ## Documentation
+
+The documentation is generated with [pdoc](https://pdoc.dev), automatically with the CI. To generate it locally you can run:
+
+```
+ pdoc example --output-dir docs --logo https://www.pollen-robotics.com/wp-content/themes/bambi-theme-main/assets/images/pollen_robotics_logo.webp --logo-link https://www.pollen-robotics.com --docformat google
+ ```
+
+ The documentation relies on the provided docstings with the google style. [pydocstyle](http://www.pydocstyle.org/en/stable/) is used to enforced this style.
+ ```
+ pydocstyle src/ --convention google --count
+ ```

scripts/git_hooks/pre-commit

@@ -24,3 +24,6 @@ echo "-------> Flake8 passed!"
 mypy .
 echo "-------> Mypy passed!"
 
+# Run pydocstring against all code in the `source_code` directory
+pydocstyle --convention google src/
+echo "-------> pydocstring passed!"

setup.cfg

@@ -32,6 +32,8 @@ dev = black==24.10.0
       coverage==7.3.2
       mypy==1.8.0
       isort==5.13.2
+      pdoc==14.7.0
+      pydocstyle==6.3.0
 
 [options.entry_points]
 console_scripts = 

src/config_files/__init__.py

@@ -0,0 +1,4 @@
+"""config_files module.
+
+Contains example of config files that are accessible by the modules.
+"""

src/example/__init__.py

@@ -0,0 +1,4 @@
+"""Example module.
+
+Illustrates various use cases.
+"""

src/example/cam_config.py

@@ -1,22 +1,50 @@
+"""Camera Configuration Management.
+
+This module provides classes and functions for managing camera configuration data stored in JSON
+files. It includes a class for reading and displaying camera configuration data, as well as
+functions for retrieving the names of available configuration files and their paths.
+"""
+
 import json
 from importlib.resources import files
 from typing import Any, List
 
 
 class CamConfig:
-    def __init__(
-        self,
-        cam_config_json: str,
-    ) -> None:
+    """A class to manage camera configuration data from a JSON file.
+
+    This class reads a JSON file containing camera configuration data and provides methods to
+    access and display the information.
+
+    Attributes:
+        cam_config_json (str): The path to the JSON file containing the camera configuration data.
+        socket_to_name (dict): A dictionary mapping socket IDs to camera names.
+        inverted (bool): A boolean indicating whether the camera is inverted.
+        fisheye (bool): A boolean indicating whether the camera is a fisheye camera.
+        mono (bool): A boolean indicating whether the camera is a monochrome camera.
+    """
+
+    def __init__(self, cam_config_json: str) -> None:
+        """Initialize the camera configuration data from the given JSON file.
+
+        Args:
+            cam_config_json (str): The path to the JSON file containing the camera configuration data.
+        """
         self.cam_config_json = cam_config_json
 
-        config = json.load(open(self.cam_config_json, "rb"))
-        self.socket_to_name = config["socket_to_name"]
-        self.inverted = config["inverted"]
-        self.fisheye = config["fisheye"]
-        self.mono = config["mono"]
+        with open(self.cam_config_json, "rb") as f:
+            config = json.load(f)
+            self.socket_to_name = config["socket_to_name"]
+            self.inverted = config["inverted"]
+            self.fisheye = config["fisheye"]
+            self.mono = config["mono"]
 
     def to_string(self) -> str:
+        """Return a string representation of the camera configuration data.
+
+        Returns:
+            str: A string containing the camera configuration data in a human-readable format.
+        """
         ret_string = "Camera Config: \n"
         ret_string += "Inverted: {}\n".format(self.inverted)
         ret_string += "Fisheye: {}\n".format(self.fisheye)
@@ -26,11 +54,25 @@ def to_string(self) -> str:
 
 
 def get_config_files_names() -> List[str]:
+    """Return a list of the names of the JSON configuration files in the config_files package.
+
+    Returns:
+        List[str]: A list of the names of the JSON configuration files in the config_files package.
+    """
     path = files("config_files")
     return [file.stem for file in path.glob("**/*.json")]  # type: ignore[attr-defined]
 
 
 def get_config_file_path(name: str) -> Any:
+    """Return the path to the JSON configuration file with the given name in the config_files package.
+
+    Args:
+        name (str): The name of the JSON configuration file.
+
+    Returns:
+        Any: The path to the JSON configuration file with the given name in the config_files package.
+            If the file is not found, returns None.
+    """
     path = files("config_files")
     for file in path.glob("**/*"):  # type: ignore[attr-defined]
         if file.stem == name:

src/example/celcius.py

@@ -1,30 +1,81 @@
+"""Celsius Temperature Conversion and Management.
+
+This module provides a class for managing Celsius temperatures and converting them to Fahrenheit.
+It also includes a main function that demonstrates the usage of the class.
+"""
+
 import logging
 
 
 class Celsius:
-    """Manage celcius temperature and other format."""
+    """A class to manage Celsius temperature and convert it to other formats.
+
+    This class provides a way to store and manipulate Celsius temperatures, as well as convert
+    them to Fahrenheit. It also includes a check to ensure that the temperature is not below
+    absolute zero (-273.15°C).
+
+    Attributes:
+        _temperature (float): The current temperature in Celsius.
+    """
 
     def __init__(self, temperature: float = 0):
+        """Initialize the logger and the temperature attribute.
+
+        Args:
+            temperature (float, optional): The initial temperature in Celsius. Defaults to 0.
+        """
         self._logger = logging.getLogger(__name__)
         self._temperature = temperature
 
     def to_fahrenheit(self) -> float:
+        """Convert the current temperature from Celsius to Fahrenheit.
+
+        Returns:
+            float: The temperature in Fahrenheit.
+        """
         return (self._temperature * 1.8) + 32
 
     @property
     def temperature(self) -> float:
+        """A property decorator that allows access to the temperature attribute.
+
+        This property decorator provides a way to access the temperature attribute from outside
+        the class. It also logs a message indicating that the value is being retrieved.
+
+        Returns:
+            float: The current temperature in Celsius.
+        """
         self._logger.info("Getting value...")
         return self._temperature
 
     @temperature.setter
     def temperature(self, value: float) -> None:
+        """A setter for the temperature property.
+
+        This method allows the value of the temperature attribute to be changed from outside the
+        class. It also logs a message indicating that the value is being set and checks that the
+        temperature is not below absolute zero.
+
+        Args:
+            value (float): The new temperature in Celsius.
+
+        Raises:
+            ValueError: If the temperature is below -273.15°C.
+        """
         self._logger.info("Setting value...")
         if value < -273.15:
             raise ValueError("Temperature below -273 is not possible")
         self._temperature = value
 
 
 def main() -> None:
+    """The main function that demonstrates the usage of the Celsius class.
+
+    This function creates an instance of the Celsius class, sets its temperature, and prints
+    the equivalent temperature in Fahrenheit. It also activates logging at the INFO level.
+    """
+    logging.basicConfig(level=logging.INFO)
+
     print("Test entry point")
     temp = Celsius(37)
     temp.temperature = -30

src/example/foo.py

@@ -5,24 +5,43 @@
 
 
 class Foo:
-    """This is a template class"""
+    """This is a template class."""
 
     def __init__(self) -> None:
-        """Set up empty slots."""
+        """Set up empty slots and initialize the logger and private variable.
+
+        This method is called when an object of the class is created. It sets up the logger and
+        initializes the private variable.
+        """
         self._logger = logging.getLogger(__name__)
         self._logger.info("Constructor")
         self._private_variable = "private"
         self.public_variable = "public"
 
     @property
     def private_variable(self) -> str:
+        """A property decorator that allows access to the private variable.
+
+        This property decorator provides a way to access the private variable from outside
+        the class. It returns the value of the private variable.
+        """
         return self._private_variable
 
     @private_variable.setter
     def private_variable(self, value: str) -> None:
+        """A setter for the private_variable property.
+
+        This method allows the value of the private variable to be changed from outside the
+        class. It sets the value of the private variable to the provided argument.
+        """
         self._private_variable = value
 
     def __del__(self) -> None:
+        """The destructor method called when the object is about to be destroyed.
+
+        This method is called when an object of the class is about to be destroyed. It logs a
+        message indicating that the destructor has been called.
+        """
         self._logger.info("Destructor")
 
     @overload
@@ -32,6 +51,12 @@ def doingstuffs(self, var: int, var2: float) -> None: ...
     def doingstuffs(self, var: int) -> None: ...
 
     def doingstuffs(self, var: Any = None, var2: Any = None) -> None:
+        """An overloaded method that takes one or two arguments and logs their values and types.
+
+        This method demonstrates the use of overloading in Python. It takes one or two arguments
+        and logs their values and types using the logger. If no arguments are provided, it does
+        nothing.
+        """
         if var is not None:
             self._logger.info(f"{var} {type(var)} ")
         if var2 is not None:

src/example/xterrabot.py

@@ -1,15 +1,31 @@
+"""XTerraBot.
+
+Illustrate Maths notation based on
+    https://www.mecharithm.com/
+    homogenous-transformation-matrices-configurations-in-robotics/.
+"""
+
 import logging
 
 import numpy as np
 import numpy.typing as npt
 
 
 class XTerraBot:
-    """Illustrate Maths notation based on
-    https://www.mecharithm.com/
-    homogenous-transformation-matrices-configurations-in-robotics/."""
+    """XTerraBot class.
+
+    This class illustrates the use of homogeneous transformation matrices to represent the
+    configuration of a robot in the context of robotics. It demonstrates the calculation of
+    the transformation matrix of an object with respect to the gripper frame using matrix
+    multiplication and inversion.
+    """
 
     def __init__(self) -> None:
+        """Constructor.
+
+        Initialize the logger and the homogeneous transformation matrices representing the
+        configuration of the robot.
+        """
         self._logger = logging.getLogger(__name__)
         # b is the mobile base
         # d is the camera
@@ -27,6 +43,19 @@ def __init__(self) -> None:
         self._T_a_d = np.array([[0, 0, -1, 400], [0, -1, 0, 50], [-1, 0, 0, 300], [0, 0, 0, 1]])  # a is the root
 
     def get_object_in_gripper_frame(self) -> npt.NDArray[np.float64]:
+        """Get the object in the gripper frame.
+
+        Calculate and return the homogeneous transformation matrix representing the
+        configuration of the object with respect to the gripper frame.
+
+        This method calculates the transformation matrix (T_c_e) by performing matrix
+        multiplication and inversion on the given transformation matrices. It returns the
+        resulting matrix as a NumPy array.
+
+        Returns:
+            np.ndarray: The homogeneous transformation matrix representing the configuration
+                of the object with respect to the gripper frame.
+        """
         T_c_e = (
             np.linalg.inv(self._T_b_c)
             @ np.linalg.inv(self._T_d_b)