🚀 feat(docs): add Sphinx documentation to the project

The Sphinx documentation has been added to the project. This includes a Makefile, a make.bat file, and a conf.py file in the docs directory. The source directory contains the documentation files in reStructuredText format. The documentation includes an installation guide and an API reference. The utils package has been reorganized to be more modular and easier to document. The documentation can be built using the `make html` command in the docs directory.

🎉 feat(utils): add new modules and packages to the project
New modules and packages have been added to the project. The following packages have been added:
- utils.gui.pyqt.about
- utils.gui.pyqt.error_popup
- utils.gui.pyqt.main_window
- utils.gui.pyqt.settings
- utils.math
- utils.settings

The new packages contain modules that provide additional functionality to the project.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/_templates/custom-class-template.rst

@@ -0,0 +1,34 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+   :special-members: __call__, __add__, __mul__
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in methods %}
+      {%- if not item.startswith('_') %}
+      ~{{ name }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/source/_templates/custom-module-template.rst

@@ -0,0 +1,66 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+      :nosignatures:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/source/api.rst

@@ -0,0 +1,9 @@
+API
+===
+
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-module-template.rst
+   :recursive:
+
+   utils

docs/source/conf.py

@@ -0,0 +1,34 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import sys
+import os
+sys.path.insert(0, os.path.abspath('../..'))
+project = 'Analyse Morphologique'
+copyright = '2023, Djalim SIMAILA, Alexis DOGHMANE'
+author = 'Djalim SIMAILA, Alexis DOGHMANE'
+release = '1.2.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx_rtd_theme',
+    'sphinx.ext.autosummary'
+]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ['_static']

docs/source/index.rst

@@ -0,0 +1,31 @@
+.. Analyse Morphologique documentation master file, created by
+   sphinx-quickstart on Tue May 16 10:01:13 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Analyse Morphologique's documentation!
+=================================================
+
+"Analyse Morphologique" (Morphological Analysis) is a tool developed by the Geomechanics Laboratory of INRAE PACA Center. Its goal is to extract information about the morphology of 3D scans from HET (Hydraulic Erosion Test) tests.
+Check out the :doc:`installation` section for further information.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+Contents
+--------
+
+.. toctree::
+
+   installation
+   api

docs/source/installation.rst

@@ -0,0 +1,34 @@
+Installation
+=====
+
+Python Version
+--------------
+Analyse Morphologique is compatible with Python 3.10 and above.
+
+
+Install Analyse Morphologique
+------------
+
+To use Analyse Morphologique, first get a release tarball or clone the repository from `here https://forgemia.inra.fr/scanner3d/analysemorphologique`_.
+Then, install the dependencies with pip:
+
+.. code-block:: console
+   
+   $ pip install -r requirements.txt
+
+Once the dependencies installed, you can run Analyse Morphologique with
+
+.. code-block:: console
+
+   $ python main.py
+
+.. note::
+   If you have issues with the pyQt5 module, you can run Analyse Morphologique in a virtual envirenment.
+   To do so, run the following commands:
+
+   .. code-block:: console
+
+      $ python3 -m venv .venv
+      $ source .venv/bin/activate # on Windows, use .venv\Scripts\activate.bat instead
+      (.venv) $ pip install -r requirements.txt
+      (.venv) $ python main.py

utils/__init__.py

@@ -0,0 +1,7 @@
+import utils.data_processing as data_processing
+import utils.files as files
+import utils.graph2D as graph2D
+import utils.graph3D as graph3D
+import utils.math as math
+import utils.gui as gui
+import utils.settings as settings

utils/data_processing/__init__.py

@@ -0,0 +1 @@
+import utils.data_processing.data_processing as data_processing

utils/files/__init__.py

@@ -0,0 +1,3 @@
+import utils.files.input as input
+import utils.files.output as output
+import utils.files.norm as norm

utils/graph2D/__init__.py

@@ -0,0 +1,2 @@
+import utils.graph2D.mpl_render as mpl_render
+import utils.graph2D.visplot_render as visplot_render

utils/graph2D/mpl_render.py

@@ -1,8 +1,7 @@
 """
 Created on Fri Apr 21 2023
 @name:   mpl_render.py
-@desc:   A module to render a 2D data using matplotlib, 
-         thoses functions cant be integrated into pyqt gui yet
+@desc:   A module to render a 2D data using matplotlib, thoses functions cant be integrated into pyqt gui yet
 @auth:   Djalim Simaila
 @e-mail: djalim.simaila@inrae.fr
 """

utils/graph3D/__init__.py

@@ -0,0 +1,2 @@
+import utils.graph3D.mpl_render as mpl_render
+import utils.graph3D.visplot_render as visplot_render

utils/graph3D/mpl_render.py

@@ -1,8 +1,7 @@
 """
 Created on Fri Apr 21 2023
 @name:   mpl_render.py
-@desc:   A module to render a 3D data using matplotlib,
-         thoses functions cant be integrated into pyqt gui yet
+@desc:   A module to render a 3D data using matplotlib, thoses functions cant be integrated into pyqt gui yet
 @auth:   Djalim Simaila
 @e-mail: djalim.simaila@inrae.fr
 """

utils/gui/__init__.py

@@ -0,0 +1 @@
+import utils.gui.pyqt as pyqt

utils/gui/pyqt/__init__.py

@@ -0,0 +1,4 @@
+import utils.gui.pyqt.settings as settings
+import utils.gui.pyqt.main_window as main_window
+import utils.gui.pyqt.error_popup as error_popup
+import utils.gui.pyqt.about as about

utils/gui/pyqt/about/__init__.py

@@ -0,0 +1,2 @@
+import utils.gui.pyqt.about.AboutThis as AboutThis
+import utils.gui.pyqt.about.UI_AboutThis as UI_AboutThis

utils/gui/pyqt/error_popup/__init__.py

@@ -0,0 +1 @@
+import utils.gui.pyqt.error_popup.ErrorPopup as ErrorPopup

utils/gui/pyqt/main_window/Workers/__init__.py

@@ -0,0 +1,5 @@
+import utils.gui.pyqt.main_window.Workers.Worker as Worker
+import utils.gui.pyqt.main_window.Workers.AdvancedDataWorker as AdvancedDataWorker
+import utils.gui.pyqt.main_window.Workers.DiscreteDataWorker as DiscreteDataWorker
+import utils.gui.pyqt.main_window.Workers.PreProcessWorker as PreProcessWorker
+import utils.gui.pyqt.main_window.Workers.RawDataWorker as RawDataWorker    

utils/gui/pyqt/main_window/__init__.py

@@ -0,0 +1,3 @@
+import utils.gui.pyqt.main_window.MainWindow as MainWindow
+import utils.gui.pyqt.main_window.UI_MainWindow as UI_MainWindow
+import utils.gui.pyqt.main_window.Workers as Workers

utils/gui/pyqt/settings/__init__.py

@@ -0,0 +1,2 @@
+import utils.gui.pyqt.settings.Settings as Settings
+import utils.gui.pyqt.settings.UI_Settings as UI_Settings

utils/math/__init__.py

@@ -0,0 +1,2 @@
+import utils.math.data_extraction as data_extraction
+import utils.math.position_manipulation as position_manipulation 

utils/settings/__init__.py

@@ -0,0 +1 @@
+import utils.settings.SettingManager as SettingManager