Updating dependencies and documentation

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.12"]
 
     steps:
     - uses: actions/checkout@v4

CONTRIBUTING.md

@@ -3,23 +3,21 @@
 [apache]: https://opensource.org/licenses/Apache-2.0
 [apache-shield]: https://img.shields.io/badge/License-Apache_2.0-blue.svg
 
-# Welcome to the BibMon contributing guide
-
 Thank you for your interest in contributing to the BibMon project!
 
-We expect to receive various types of contributions from individuals, research institutions, startups, companies and oil operators partners.
+We expect to receive various types of contributions from individuals, research institutions, startups and companies.
 
 In this guide we present how the expected contributions might be proposed.
 
-# Getting started
+## Getting started
 
 The recommended first step is to read the project's [README](README.md) for an overview of what this repository contains.
 
-# Asking questions
+## Asking questions
 
 Please do not open issues to ask questions. Please use the Discussions section accessed through the link that appears in the top menu.
 
-# Before contributing
+## Before contributing
 
 Before you can contribute to this project, we require you read and agree to the following documents:
 
@@ -29,7 +27,7 @@ Before you can contribute to this project, we require you read and agree to the
 
 It is also very important to know, participate and follow the discussions. Click on the Discussions link that appears in the top menu.
 
-# BibMon architecture
+## BibMon architecture
 
 `BibMon` was designed with easy extensibility and maintenance in mind, even for users with little experience in software development. This was achieved through the use of the object-oriented paradigm, which allows for the pre-implementation of generic functionalities and enables new features to be quickly programmed by leveraging the original structure.
 
@@ -51,14 +49,14 @@ The following bulletpoints describe the library's architecture and provide instr
 * Additional Features
    * Additional features such as generating comparative tables, correlation analysis, etc., are programmed in the `_bibmon_tools.py` file.
 
-# Implementing New Functionalities
+## Implementing New Functionalities
 
 When implementing new functionalities, don't forget to:
 
 * Add the classes and functions to the library's namespace (in the `__init__.py` file).
 * Document the classes and functions using docstrings in the [NumPy format](https://numpydoc.readthedocs.io/en/latest/format.html).
 
-## Models
+### Models
 
 To implement a new model, create a .py file with the following import statement:
 
@@ -81,7 +79,7 @@ The functionality implemented in `train_core` is specific to the considered mode
 
 Optionally, implement an `__init__()` constructor or any other necessary methods.
 
-## Preprocessing Techniques
+### Preprocessing Techniques
 
 Preprocessing techniques should be implemented as methods of the `PreProcess` class following the pattern:
 
@@ -99,16 +97,16 @@ Use the `self.is_Y` and `train_or_test` flags to cover the possibilities regardi
 
 Even if not used, the `train_or_test` flag should be present in the input parameters.
 
-## Data
+### Data
 
 Add the new dataset to a specific subdirectory in the `bibmon` directory. Program the data loading function in the `_load_data.py` file.
 
-## Alarms
+### Alarms
 
 To program a new alarm logic, define a function in the `_alarms.py` file.
 
 To apply the new logic in the library, it will be necessary to implement the use of the functionality in the methods of the `GenericModel` class by creating a new key in the `self.alarms` dictionary. If necessary, window sizes and other parameters should be programmed in the method entries.
 
-## Additional Features
+### Additional Features
 
 Preferably, use the `_bibmon_tools.py` file to implement additional features.

docs/source/api.rst

@@ -0,0 +1,10 @@
+API Reference
+===================
+
+.. module:: bibmon
+
+.. automodule:: bibmon
+   :members:
+   :imported-members:
+   :inherited-members:
+   :show-inheritance:

docs/source/conf.py

@@ -18,29 +18,29 @@
 # -- Project information -----------------------------------------------------
 
 project = 'BibMon'
-copyright = '2022, Grupo EngePol'
-author = 'Grupo EngePol'
+copyright = '2024'
+author = 'BibMon devs'
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+#release = '1.0.0'
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc','sphinx.ext.napoleon']
+extensions = ['sphinx.ext.autodoc','sphinx.ext.napoleon','myst_nb']
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+#templates_path = ['_templates']
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'pt'
+#language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -58,4 +58,15 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+#html_static_path = ['_static']
+
+autosummary_ignore_module_all = False
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../bibmon/'))
+
+try:
+    jupyter_execute_notebooks = os.environ["EXECUTE_NOTEBOOKS"]
+except KeyError:
+    jupyter_execute_notebooks = "off"

docs/source/contributing.md

@@ -0,0 +1,4 @@
+# Contributing
+
+```{include} ../../CONTRIBUTING.md
+```

docs/source/index.rst

@@ -3,22 +3,53 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to BibMon's documentation!
+BibMon: Process Monitoring Library
 ==================================
 
+BibMon (from the Portuguese Biblioteca de Monitoramento de Processos, or Process Monitoring Library) is a Python package that provides deviation-based predictive models for fault detection, soft sensing, and process condition monitoring.
+
+Features
+----------------------
+
+The resources offered by `BibMon` are:
+
+* Application in online systems: a trained `BibMon` model can be used for online analysis with both individual samples and data windows. For each sample or window, a prediction is made, the model state is updated, and alarms are calculated.
+* Compatibility, within the same architecture, of regression models (i.e., virtual sensors, containing separate X and Y data, such as RandomForest) and reconstruction models (containing only X data, such as PCA).
+* Preprocessing pipelines that take into account the differences between X and Y data and between training and testing stages.
+* Possibility of programming different alarm logics.
+* Easy extensibility through inheritance (there is a class called `GenericModel` that implements all the common functionality for various models and can be used as a base for implementing new models). For details, consult the `CONTRIBUTING.md` file.
+* Convenience functions for performing automatic offline analysis and plotting control charts.
+* Real and simulated process datasets available for importing.
+* Comparative tables to automate the performance analysis of different models.
+* Automatic hyperparameter tuning using Optuna.
+
+Getting started
+-----------------------------
+
+.. toctree::
+   :maxdepth: 3
+
+   install
+   usage
+   tutorials
+   sci_article
+
+Contributing
+----------------------
+
+BibMon is an open-source project driven by the community. If you would like to contribute to the project, please refer to the following contributing page.
+
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
-   modules
 
-.. automodule:: bibmon
-   :members:
-   :inherited-members:
-   :show-inheritance:
+   contributing.md
 
-Indices and tables
-==================
+The API Documentation
+-----------------------------
+
+In this section you will find information about specific functions, classes, or methods.
+
+.. toctree::
+   :maxdepth: 3
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   api

docs/source/install.rst

@@ -0,0 +1,32 @@
+Installation
+========================
+
+This section covers the installation of BibMon.
+
+Installing from PyPI
+--------------------------------
+
+To install Requests, you can use pip::
+
+    $ pip install bimon
+
+Get the Source Code
+-------------------
+
+BibMon is developed on GitHub, where the code is
+`available at <https://github.com/petrobras/bibmon>`_.
+
+You can either clone the public repository::
+
+    $ git clone https://github.com/petrobras/bibmon.git
+
+Or, download the `tarball <https://github.com/petrobras/bibmon/tarball/main>`_::
+
+    $ curl -OL https://github.com/petrobras/bibmon/tarball/main
+    # optionally, zipball is also available (for Windows users).
+
+Once you have a copy of the source, you can embed it in your own Python
+package, or install it into your site-packages easily::
+
+    $ cd bibmon
+    $ python -m pip install .

docs/source/sci_article.rst

@@ -0,0 +1,4 @@
+Scientific article
+-----------------------------
+
+A scientific article detailing the package structure, design philosophy and main features can be accessed in `this link <https://drive.google.com/file/d/10DoNNA8gVeu2qtfjPuAbeFnwDWy_Xkzn/view?usp=sharing>`_.