Refactor codebase extensively; add input validation.

.gitignore

@@ -78,3 +78,5 @@ target/
 make_env.sh
 
 FauxPyReport*
+
+.DS_Store

CHANGELOG.md

@@ -1,6 +1,9 @@
 # FauxPy Changelog
 
-## Unreleased
+## FauxPy 0.2.0
+- Add entry for Analysis Mode.
+- Refactor code structure.
+- Add input validation for command-line arguments.
 - Improve the Read the Docs
 documentation.
 - Update the README files in the
@@ -9,7 +12,6 @@ directory.
 - Add `version.py` file to manage FauxPy's versioning.
 
 ## FauxPy 0.1.1
-
 - Remove tests depending on FauxPy.
 - Add Read the Docs documentation.
 - Fix a bug in ST.

README.md

@@ -15,9 +15,14 @@ FauxPy's source code and
 instructions to install 
 and use the tool.
 
-*For comprehensive documentation, visit
-[FauxPy 
-documentation](https://fauxpy.readthedocs.io/).*
+- For comprehensive documentation, visit
+[FauxPy documentation](https://fauxpy.readthedocs.io/).
+- You can also participate in our 
+[Discussions section](https://github.com/mohrez86/fauxpy/discussions) 
+for questions, feedback, and more. 
+- If you encounter any issues, feel free
+to open an issue on our 
+[GitHub repository](https://github.com/mohrez86/fauxpy/issues).
 
 ## Features
 

docs/source/conf.py

@@ -1,10 +1,14 @@
 # Configuration file for the Sphinx documentation builder.
 import datetime
+import os
+import sys
 from pathlib import Path
 
+sys.path.insert(0, os.path.abspath("../../."))
+
 # Load version
 root_path = Path(__file__).parents[2]
-version_file_path = root_path / "fauxpy" / 'version.py'
+version_file_path = root_path / "fauxpy" / "version.py"
 __version__ = ""
 exec(version_file_path.read_text())
 assert __version__ != ""
@@ -27,6 +31,7 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
 ]
 
 intersphinx_mapping = {

docs/source/developer/entry_points.rst

@@ -0,0 +1,55 @@
+=========================
+Entry Points and Handlers
+=========================
+
+FauxPy can work in two different modes: **Pytest Mode** and **Analysis Mode**.
+
+- **Pytest Mode** is activated when FauxPy is used with commands like
+  ``pytest tests --src my_code``. In this mode, FauxPy runs as a Pytest
+  plugin, integrating itself into the test execution pipeline to gather
+  information about the tests being run.
+
+- **Analysis Mode** is activated when FauxPy is used with commands like
+  ``fauxpy -v``. In this mode, FauxPy runs as a standalone application,
+  independently of Pytest.
+
+Module ``main.py`` is the main entry point for FauxPy, determining
+FauxPy's mode based on how FauxPy is executed.
+
+Module ``main.py``
+==================
+
+This module is the main entry point for FauxPy, containing six functions.
+The function ``fauxpy_analysis_mode`` is called when FauxPy starts in Analysis Mode.
+It creates an instance of the ``FauxpyAnalysisModeHandler`` class, which manages
+the whole Analysis Mode.
+
+The other five functions in ``main.py`` are Pytest hooks executed in Pytest Mode.
+Module ``main.py`` instantiates a ``FauxpyPytestModeHandler`` object as a global variable.
+These hooks call corresponding methods in the object, delegating control
+of Pytest Mode to class ``FauxpyPytestModeHandler``.
+
+Below are the details of these six functions in ``main.py``.
+
+.. automodule:: fauxpy.main
+    :members:
+
+Pytest Mode Handler
+===================
+
+Class ``FauxpyPytestModeHandler`` is responsible for managing Pytest Mode.
+Details of this class are provided below.
+
+.. automodule:: fauxpy.command_line.pytest_mode.handler
+    :members:
+
+Analysis Mode Handler
+=====================
+
+Class ``FauxpyAnalysisModeHandler`` manages Analysis Mode.
+Details of this class are provided below. Currently, Analysis Mode
+supports only one command, ``fauxpy --version``, which shows
+the current version of FauxPy.
+
+.. automodule:: fauxpy.command_line.analysis_mode.handler
+    :members:

docs/source/developer/sbfl.rst

@@ -0,0 +1,6 @@
+===================================
+Spectrum-Based Fault Localization
+===================================
+
+.. automodule:: fauxpy.fault_localization.sbfl.session_lib
+    :members:

docs/source/index.rst

@@ -22,26 +22,18 @@ FauxPy documentation
 .. image:: https://img.shields.io/github/stars/atom-sw/fauxpy?style=social
    :target: https://github.com/atom-sw/fauxpy
 
+.. image:: https://img.shields.io/github/stars/mohrez86/fauxpy?style=social
+   :target: https://github.com/mohrez86/fauxpy
+
 FauxPy (pronounced: "foh pie") is an automated fault localization tool for Python programs,
 `available as open-source software on GitHub <https://github.com/atom-sw/fauxpy>`_.
 This documentation includes instructions to install and use FauxPy.
 
-.. note::
-   We are improving FauxPy as we continue our
-   research, and we value your **feedback and suggestions**.
-   Whether it's regarding the user interface, new features,
-   or any other aspect of FauxPy,
-   your input can be incredibly helpful.
-   Please send your suggestions or feedback to us at:
-
-   **rezaalipour [dot] mohammad [at] gmail [dot] com**
-
-   If you enjoy using FauxPy and find it useful, giving us
-   a `star on GitHub <https://github.com/atom-sw/fauxpy>`_ would greatly encourage us
-   and make us happy. Your support means a lot to us!
-
-   .. image:: https://img.shields.io/github/stars/atom-sw/fauxpy?style=social
-      :target: https://github.com/atom-sw/fauxpy
+.. tip::
+   We are constantly improving FauxPy and
+   welcome your **feedback and suggestions**.
+   Share your ideas in our
+   `Discussions section <https://github.com/mohrez86/fauxpy/discussions>`_.
 
 
 Features
@@ -77,15 +69,27 @@ at
    :target: https://www.youtube.com/watch?v=6ooPPiwd79g
 
 
-Contents
-========
-
 .. toctree::
    :maxdepth: 1
+   :caption: User Guide
 
    user/installation
    user/getting_started
    user/using_fauxpy
    user/limitations
    user/test_repo
    user/citing_fauxpy_and_references
+
+.. toctree::
+   :maxdepth: 1
+   :caption: API Documentation
+
+   developer/entry_points
+..   developer/sbfl
+
+.. API Indices and tables
+.. ======================
+
+.. * :ref:`genindex`
+.. * :ref:`modindex`
+.. * :ref:`search`

docs/source/user/test_repo.rst

@@ -69,12 +69,11 @@ projects can be used for further research
 in the software analysis domain.
 
 If you discover any case where FauxPy
-does not work
-with a project, whether it's one
+does not work with a project, whether it's one
 of the included ones or a different
-real-world project,
-please let us know so that
+real-world project, please let us know
+via our
+`Discussions section <https://github.com/mohrez86/fauxpy/discussions>`_
+so that
 we can fix bugs, improve FauxPy, and add
 new projects to our test repository.
-
-Email: **rezaalipour [dot] mohammad [at] gmail [dot] com**

examples/triangle_area/README.md

@@ -1,35 +1,15 @@
 # Triangle Area Example
 
 This directory contains an 
-example project demonstrating 
-the use of FauxPy to perform 
-fault localization on a simple 
-Python program that 
-calculates the area 
-of a triangle.
-
-## Getting Started
+example project to demonstrate 
+the use of FauxPy.
 
 To get started with this example,
-please refer to the detailed 
-walkthrough available in the 
-FauxPy documentation on 
-Read the Docs:
-
-[Read the Docs: FauxPy 
-Usage Example](https://fauxpy.readthedocs.io/en/latest/user/getting_started.html)
+please refer to the 
+[Usage Example](https://fauxpy.readthedocs.io/en/latest/user/getting_started.html) 
+page on FauxPy documentation.
 
 The documentation provides step-by-step
 instructions on setting up the 
 environment, running the example, and 
 understanding the results.
-
-## Additional Resources
-
-- [FauxPy Repository](https://github.com/atom-sw/fauxpy)
-- [FauxPy Documentation](https://fauxpy.readthedocs.io)
-
-For any further assistance or 
-questions, feel free to open an 
-issue on our 
-[GitHub repository](https://github.com/atom-sw/fauxpy/issues).