Merge pull request #13 from fedepup/main

Several addition for version 0.2.0

.gitignore

@@ -5,6 +5,9 @@
 Data/
 Simulated_EEG/
 
+# Directory with all generated rst files from autosummary
+docs/api/
+
 ### Linux ###
 *~
 

.pre-commit-config.yaml

@@ -11,10 +11,10 @@ repos:
     -   id: check-added-large-files
         args: [-- maxkb=5000]
 
--   repo: https://gitlab.com/iamlikeme/nbhooks
-    rev: 1.0.0
+-   repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
     hooks:
-    -   id: nb-ensure-clean
+    -   id: nbstripout
         exclude: ^docs/
 
 -   repo: https://github.com/PyCQA/bandit

CONTRIBUTING.md

@@ -1,10 +1,14 @@
 # Contributing
 
-Thank you for considering contributing to our project! We highly appreciate your effort towards enhancing our project.
+Thank you for considering contributing to our project! We highly appreciate your
+effort towards enhancing our project.
 
-SelfEEG is designed to help building self-supervised learning (SSL) experiments on electroencephalography (EEG) data, hoping that various teams working on this or related areas will find this project useful for their research purposes.
+SelfEEG is designed to help building self-supervised learning (SSL) experiments on
+electroencephalography (EEG) data, hoping that various teams working on this or
+related areas will find this project useful for their research purposes.
 
-Before getting started, please take a moment to review the following guidelines to ensure a smooth collaboration.
+Before getting started, please take a moment to review the following guidelines to
+ensure a smooth collaboration.
 
 ## Table of Contents
 * [Before you start](#Before-you-start)
@@ -18,26 +22,38 @@ Before getting started, please take a moment to review the following guidelines
 
 ## Before you start
 
-If you are new to selfEEG or self-supervised learning in general, we recommend you do the following before start working on the code:
+If you are new to selfEEG or self-supervised learning in general, we recommend you
+do the following before start working on the code:
 
  * Read the [Code of Conduct](https://github.com/MedMaxLab/selfEEG)
- * Familiarize yourself with the library. Introductory notebooks in the [Notebooks](https://github.com/MedMaxLab/selfEEG/Notebooks) folder are a good starting point.
- * Read about the self-supervised learning paradigm. The literature offers many review papers about this topic. Our recent [review](https://www.techrxiv.org/articles/preprint/Applications_of_Self-Supervised_Learning_to_Biomedical_Signals_where_are_we_now/22567021) can be a good starting point.
+ * Familiarize yourself with the library. Introductory notebooks in the
+   [Notebooks](https://github.com/MedMaxLab/selfEEG/Notebooks) folder are a
+   good starting point.
+ * Read about the self-supervised learning paradigm. The literature offers many
+   review papers about this topic. Our recent
+   [review](https://doi.org/10.1109/ACCESS.2023.3344531) can be a good
+   starting point.
 
 ## How to contribute
 
-You can contribute to this library by reporting and/or solving issues, or by proposing and/or implementing novel features. Both contributions are very welcome.
+You can contribute to this library by reporting and/or solving issues, or by
+proposing and/or implementing novel features. Both contributions are very welcome.
 
 
 ### Reporting issues
 
-If you come across any issues or bugs in the project, you can report them via our [issue](https://github.com/MedMaxLab/selfEEG/issues) section. Please ensure that you provide sufficient information to reproduce the issue.
+If you come across any issues or bugs in the project, you can report them via our
+[issue](https://github.com/MedMaxLab/selfEEG/issues) section.
+Please ensure that you provide sufficient information to reproduce the issue.
 
 ### Suggesting enhancements
 
-If you have any suggestions for new features, improvements or enhancements, you can either open a new issue detailing your proposal or write directly to our group. We highly value your input and will gladly review your suggestions.
+If you have any suggestions for new features, improvements or enhancements,
+you can either open a new issue detailing your proposal or write directly to our
+group. We highly value your input and will gladly review your suggestions.
 
-The following (not exhaustive) list of possible additions, sorted by priority order, can be used as a reference:
+The following (not exhaustive) list of possible additions,
+sorted by priority order, can be used as a reference:
 
 * add novel self-supervised learning algorithms
 * add novel reproducibility features
@@ -58,53 +74,87 @@ To start contributing, follow these simple steps:
 8. Open a pull request to our repository, describing your changes and their benefits.
 9. Wait for our review and discuss together with us how to merge your additions.
 
-More details about setting your working environment and how to prepare your pulling request can be found in the next sections
+More details about setting your working environment and how to prepare your pulling
+request can be found in the next sections.
 
 
 ## Set up a Python virtual environment
 
 To work on your changes you first need to setup a virtual environment.
-Just create a fresh environment, activate it and pip install the library with its dependencies.
+Just create a fresh environment, activate it and pip install the library with its
+dependencies.
 
-We suggest working with conda (or miniconda), where a new environment can be easily created with the following commands:
+We suggest working with conda (or miniconda), where a new environment can be easily
+created with the following commands:
 
 ```
-conda create -n selfeegDev python=3
+conda create -n selfeegDev python=3.11
 conda activate selfeegDev
 ```
-To install the library with its dependencies, run the following command using the project main directory as the working directory:
+To install the library with its dependencies, run the following command using the
+project main directory as the working directory:
 ```
 pip install -e .
 ```
-this will install all the selfeeg main dependencies. As reported in the [README.md](README.md) file, we suggest to also add jupyter-lab, matplotib, and scikit-learn, which can facilitate the development and testing of novel features.
+this will install all the selfeeg main dependencies. As reported in the
+[README.md](README.md) file, we suggest to also add jupyter-lab, matplotib,
+and scikit-learn, which can facilitate the development and testing of
+novel features.
 
 ## testing
 
-It is important to ensure that all the implemented changes will not break any existing library functionality. The [test](/test) folder provides an automatic way to check all the library functionalities. Tests will be performed automatically via GitHub Actions whenever changes to the test, selfeeg, or . github/workflows folders are pushed to the remote repository. However, these tests are performed only on a CPU device. For this reason, it is strongly suggested to perform tests locally before any push in order to evaluate the functionalities of selfEEG also on a GPU device.
-Local tests can be performed with unittest by simply running the following command using the main repository directory as the working directory:
+It is important to ensure that all the implemented changes will not break any
+existing library functionality. The [test](/test) folder provides an automatic
+way to check all the library functionalities. Tests will be performed automatically
+via GitHub Actions whenever changes to the test, selfeeg, or .github/workflows
+folders are pushed to the remote repository. However, these tests are performed
+only on a CPU device. For this reason, it is strongly suggested to perform tests
+locally before any push in order to evaluate the functionalities of selfEEG also on
+a GPU device.
+Local tests can be performed with unittest by simply running the following command
+using the main repository directory as the working directory:
 
 ```
 python3 -m unittest discover test "*_test.py"
 ```
+If you want to run only a specific test and not the entire battery, you can run
+the following command, changing the syntax according to the specific test
+```
+python3 -m unittest test.EEGself.module.python_filename.UnittestClass.test_function
+
+for example
+
+python3 -m unittest test.EEGself.ssl.ssl_test.TestSSL.test_BYOL
+```
 
-Remember to add test functionalities if you are working on novel features. More detail about tests can be found in the readme file in the test folder.
+Remember to add test functionalities if you are working on novel features.
+More detail about tests can be found in the readme file in the test folder.
 
 
 ## Submitting Pull Requests
 
-If you believe that your changes are ready for possible merging with our main branch, it is time to send us a pull request, clearly explaining your changes and their purpose. Before submitting a pull request we kindly ask you to ensure that:
+If you believe that your changes are ready for possible merging with our main
+branch, it is time to send us a pull request, clearly explaining your changes and
+their purpose. Before submitting a pull request we kindly ask you to ensure that:
 
 1. Existing tests can be run without errors
-2. Novel tests were added to check that an issue is solved or a novel feature works correctly.
-3. Additions are properly documented and ready to be included without errors in our API documentation.
-4. The code style follow that of the project. In particular, check that:
-   * indentations follow a 4 space rule.
-   * comments are provided wherever necessary for clarity.
+2. Novel tests were added to check that an issue is solved or a novel feature works
+   correctly.
+4. Additions are properly documented and ready to be included without errors in our
+   API documentation.
+6. The code style follow that of the project. In particular, check that:
+   * Indentations follow a 4 space rule.
+   * Comments are provided wherever necessary for clarity.
    * The input arguments order is similar to that of other similar functions.
-5. commit messages are clear, descriptive, and provide concise summaries that conveys its purpose.
+   * Functions follow the `lower_case_with_underscores` name format.
+   * Classes follow the `CapitalizedWords` name format.
+7. commit messages are clear, descriptive, and provide concise summaries that
+   conveys its purpose.
 
-After submitting a pull request, rest assured that everything will be done to provide a response as soon as possible.
+After submitting a pull request, rest assured that everything will be done to
+provide a response as soon as possible.
 
 ## License
 
-By contributing to this project, you agree that your contributions will be licensed under the project's [license](LICENSE.md) (MIT License).
+By contributing to this project, you agree that your contributions will be licensed
+under the project's [license](LICENSE.md) (MIT License).