Merge pull request #54 from DynamicsAndNeuralSystems/jmoo2880-update-…

…readme

Update pyspi README

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,127 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge 🤝
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards 🌟
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities 🛡️
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope 🌐
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement 👮🏻
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement [here]([email protected]).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines 📋
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction ✔️
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning ❗
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban ⏳
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban ❌
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution 👍
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

.github/SECURITY.md

@@ -0,0 +1,18 @@
+# Reporting Security Issues 🛡️
+
+The _pyspi_ team and community take security bugs in _pyspi_ seriously. We appreciate your efforts to responsibly disclose your findings, and will make every effort to acknowledge your contributions.
+
+To report a security issue, please use the GitHub Security Advisory tab.
+
+The _pyspi_ team will send a response indicating the next steps in handling your report. After the initial reply to your report, the security team will keep you informed of the progress towards a fix and full announcement, and may ask for additional information or guidance.
+
+## Supported Versions
+
+The following versions of _pyspi_ are
+currently being supported with security updates.
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 0.4   | :white_check_mark: |
+
+

README.md

@@ -2,11 +2,14 @@
 
 <h1 align="center"><em>pyspi</em>: Python Toolkit of Statistics for Pairwise Interactions</h1>
 
+
+
 <p align="center">
  	<a href="https://zenodo.org/badge/latestdoi/601919618"><img src="https://zenodo.org/badge/601919618.svg" height="20"/></a>
     <a href="https://www.gnu.org/licenses/gpl-3.0"><img src="https://img.shields.io/badge/License-GPLv3-blue.svg" height="20"/></a>
     <a href="https://github.com/DynamicsAndNeuralSystems/pyspi/actions/workflows/run_unit_tests.yaml"><img src="https://github.com/DynamicsAndNeuralSystems/pyspi/actions/workflows/run_unit_tests.yaml/badge.svg" height="20"/></a>
     <a href="https://twitter.com/compTimeSeries"><img src="https://img.shields.io/twitter/url/https/twitter.com/compTimeSeries.svg?style=social&label=Follow%20%40compTimeSeries" height="20"/></a>
+
 </p>
 
 _pyspi_ is a comprehensive python library for computing statistics of pairwise interactions (SPIs) from multivariate time-series (MTS) data.
@@ -16,32 +19,153 @@ The code is licensed under the [GNU GPL v3 license](http://www.gnu.org/licenses/
 **Feel free to reach out for help with real-world applications.**
 Feedback is much appreciated through [issues](https://github.com/DynamicsAndNeuralSystems/pyspi/issues), or [pull requests](https://github.com/DynamicsAndNeuralSystems/pyspi/pulls).
 
-## Acknowledgement :+1:
+| Section       | Description           |
+|:--------------|:----------------------|
+| [Installation](#installation-)       | Installing _pyspi_ and its dependencies                      |
+| [Getting Started](#getting-started-) | A quick introduction on how to get started with _pyspi_      |
+| [SPI Descriptions](#spi-descriptions-) | A link to the full table of SPIs and detailed descriptions   |
+| [Documentation](#documentation)     | A link to our API reference and full documentation on GitBooks |
+| [Contributing to _pyspi_](#contributing-to-pyspi-) | A guide for community members willing to contribute to _pyspi_ |
+| [Acknowledgement](#acknowledgement-) | A citation for _pyspi_ for scholarly articles                |
+| [Our Contributors](#our-contributors-) | A summary of our primary contributors                        |
+<hr style="border-top: 3px solid #bbb;">
 
-If you use this software, please read and cite this article:
+## Installation 📥
+The simplest way to get the _pyspi_ package up and running is to install the package locally using `pip`. 
+For access to the full library of SPIs, the code requires GNU's [Octave](https://octave.org/download) to be installed on your system.
 
-- &#x1F4D7; O.M. Cliff, A.G. Bryant, J.T. Lizier, N. Tsuchiya, B.D. Fulcher. [Unifying pairwise interactions in complex dynamics](https://doi.org/10.1038/s43588-023-00519-x), _Nature Computational Science_ (2023).
+#### 1. Pre-Install Octave (Optional)
+While you can safely install _pyspi_ without first installing `Octave`, you will not have access to the full library of SPIs
 
-Note that [preprint](https://arxiv.org/abs/2201.11941) and [free-to-read](https://rdcu.be/dn3JB) versions of this article are available.
+#### 2. Create a conda environment (Optional, Recommended)
+While you can also install _pyspi_ outside of a conda environment, it depends on a lot of user packages that may make managing dependencies quite difficult. 
+So, we would also recommend installing pyspi in a conda environment. Firstly, create a fresh conda environment:
+```
+conda create -n pyspi python=3.9.0
+```
+Once you have created the environment, activate it using `conda activate pyspi`.
+
+#### 3. Install with _pip_
+To install _pyspi_ using a local pip install, download or clone the latest version from the repository:
+```
+git clone https://github.com/DynamicsAndNeuralSystems/pyspi
+```
+
+Once you have navigated to the main folder (`pyspi`), you can install using:
+```
+pip install .
+```
+
+
+For a more detailed guide on how to install _pyspi_, as well as how you can use _pyspi_ without first installing Octave, 
+please see the [full documentation](https://time-series-features.gitbook.io/pyspi/installation/installing-pyspi).
+Additionally, we provide a comprehensive [troubleshooting guide](https://time-series-features.gitbook.io/pyspi/installation/troubleshooting) for users who encounter issues installing _pyspi_ on their system,
+as well as [alternative installation options](https://time-series-features.gitbook.io/pyspi/installation/alternative-installation-options). 
+
+## Getting Started 🚀
+
+Once you have installed _pyspi_, you can learn how to apply the package by checking out the [walkthrough tutorials](https://time-series-features.gitbook.io/pyspi/usage/walkthrough-tutorials) in our documentation.  Click any of the examples below to access the tutorials in our full documentation:
+
+- [Simple demonstration](https://time-series-features.gitbook.io/pyspi/usage/walkthrough-tutorials/getting-started-a-simple-demonstration)
+
+- [Finance: stock price time series](https://time-series-features.gitbook.io/pyspi/usage/walkthrough-tutorials/finance-stock-price-time-series)
+
+
+- [Neuroimaging: fMRI time series)](https://time-series-features.gitbook.io/pyspi/usage/walkthrough-tutorials/neuroimaging-fmri-time-series)
 
-## Getting Started
+### Advanced Usage
+For advanced users, we offer several additional guides in the [full documentation](https://time-series-features.gitbook.io/pyspi/usage/advanced-usage) on how you can distribute your _pyspi_ jobs across PBS clusters, as well as how you can construct your own subsets of SPIs. 
+Click one of the following dropdowns for more information:
 
-See the [documentation](https://time-series-features.gitbook.io/pyspi/) for installing and setting up _pyspi_.
-Once you're done, you can learn how to use the package by checking out the:
+<details closed>
+<summary>Distributing pyspi calculations</summary>
+<p>If you have access to a PBS cluster and are processing MTS with many processes (or are analyzing many MTS), then you may find the <a href="https://github.com/DynamicsAndNeuralSystems/pyspi-distribute"><em>pyspi distribute</em></a> repository helpful.
+In the full <a href="https://time-series-features.gitbook.io/pyspi/usage/advanced-usage/distributing-calculations-on-a-cluster">documentation </a>, we provide a comprehensive guide on how you can distribute <em>pyspi</em> calculations on a PBS cluster, along with the necessary scripts and commands to get started!</p>
+</details>
 
-- [Simple demo](https://time-series-features.gitbook.io/pyspi/usage/walkthrough-tutorials/getting-started-a-simple-demonstration)
-- [Tutorial (finance: stock price time series)](https://time-series-features.gitbook.io/pyspi/usage/walkthrough-tutorials/finance-stock-price-time-series)
-- [Tutorial (neuroimaging: fMRI time series)](https://time-series-features.gitbook.io/pyspi/usage/walkthrough-tutorials/neuroimaging-fmri-time-series).
+<details closed>
+<summary>Reduced subsets</summary>
+<p>If your dataset is large (containing many processes and/or observations), you can use a pre-configured set of reduced statistics or create your own subsets.
+Follow the guide in the <a href="https://time-series-features.gitbook.io/pyspi/usage/advanced-usage/using-a-reduced-spi-set">documentation </a> to learn how you can create your own reduced subsets.</p>
+</details>
 
-If you have access to a PBS cluster and are processing MTS with many processes (or are analyzing many MTS), then you may find the [_pyspi_ distribute](https://github.com/DynamicsAndNeuralSystems/pyspi-distribute) repository helpful.
 
-If your dataset is large (containing many processes and/or observations), you can use a pre-configured set of reduced statistics or create your own subsets (cf. the [documentation guide](https://time-series-features.gitbook.io/pyspi/usage/advanced-usage/using-a-reduced-spi-set)).
 
-## Other highly comparative toolboxes
+## SPI Descriptions 📋
+To access a table with a high-level overview of the _pyspi_ library of SPIs, including their associated identifiers, see the [table of SPIs](https://time-series-features.gitbook.io/pyspi/spis/table-of-spis) in the full documentation.
+For detailed descriptions of each SPI, as well as its associated estimators, we provide a full breakdown in the [SPI descriptions](https://time-series-features.gitbook.io/pyspi/spis/spi-descriptions) page of our documentation. 
+
+## Documentation
+The full documentation is hosted on [GitBooks](https://time-series-features.gitbook.io/pyspi/). 
+Use the following links to quickly access some of the key sections:
+
+- [Full installation guide](https://time-series-features.gitbook.io/pyspi/installation)
+- [Troubleshooting](https://time-series-features.gitbook.io/pyspi/installation/troubleshooting)
+- [Alternative installation options](https://time-series-features.gitbook.io/pyspi/installation/alternative-installation-options)
+- [Usage guide](https://time-series-features.gitbook.io/pyspi/usage)
+- [Distributing _pyspi_ computations](https://time-series-features.gitbook.io/pyspi/usage/advanced-usage/distributing-calculations-on-a-cluster)
+- [Table of SPIs and descriptions](https://time-series-features.gitbook.io/pyspi/spis)
+- [FAQ](https://time-series-features.gitbook.io/pyspi/usage/faq)
+- [API Reference](https://time-series-features.gitbook.io/pyspi/api-reference)
+- [Development guide](https://time-series-features.gitbook.io/pyspi/development)
+
+## Contributing to _pyspi_ 👨‍👨‍👦‍👦
+Contributions play a vital role in the continual development and enhancement of _pyspi_, a project built and enriched through community collaboration.
+If you would like to contribute to _pyspi_, or explore the many ways in which you can participate in the project, please have a look at our 
+detailed [contribution guidelines](https://time-series-features.gitbook.io/pyspi/development/contributing-to-pyspi) about how to proceed.
+In contributing to _pyspi_, all participants are expected to adhere to our [code of conduct](https://time-series-features.gitbook.io/pyspi/development/code-of-conduct).
+
+### SPI Wishlist
+We strive to provide the most comprehensive toolkit of SPIs. If you have ideas for new SPIs or suggestions for improvements to existing ones, we are eager to hear from and collaborate with you! 
+Any pairwise dependence measure, provided it is accompanied by a published research paper, typically falls within the scope for consideration in the 
+_pyspi_ library.
+You can access our SPI wishlist via the [projects tab](https://github.com/DynamicsAndNeuralSystems/pyspi/projects) in this repo to open a request.
+
+## Acknowledgement 👍
+
+If you use this software, please read and cite this article:
+
+- &#x1F4D7; O.M. Cliff, A.G. Bryant, J.T. Lizier, N. Tsuchiya, B.D. Fulcher. [Unifying pairwise interactions in complex dynamics](https://doi.org/10.1038/s43588-023-00519-x), _Nature Computational Science_ (2023).
+
+Note that [preprint](https://arxiv.org/abs/2201.11941) and [free-to-read](https://rdcu.be/dn3JB) versions of this article are available.
+
+<details closed>
+    <summary>Click here for a BibTex reference:</summary>
+
+```
+@article{Cliff2023:UnifyingPairwiseInteractions,
+	title = {Unifying pairwise interactions in complex dynamics},
+	volume = {3},
+	issn = {2662-8457},
+	url = {https://www.nature.com/articles/s43588-023-00519-x},
+	doi = {10.1038/s43588-023-00519-x},
+	number = {10},
+	journal = {Nature Computational Science},
+	author = {Cliff, Oliver M. and Bryant, Annie G. and Lizier, Joseph T. and Tsuchiya, Naotsugu and Fulcher, Ben D.},
+	month = oct,
+	year = {2023},
+	pages = {883--893},
+}
+```
+
+</details>
+
+## Other highly comparative toolboxes 🧰
+If you are interested in trying other highly comparative toolboxes like _pyspi_, see the below list:
 
 - [_hctsa_](https://github.com/benfulcher/hctsa), the _highly comparative time-series analysis_ toolkit, computes over 7000 time-series features from univariate time series.
 - [_hcga_](https://github.com/barahona-research-group/hcga), a _highly comparative graph analysis_ toolkit, computes several thousands of graph features directly from any given network.
 
-## SPI Wishlist
 
-As _pyspi_ is under active development, we are always open to suggestions for new SPIs to be added via the [projects tab](https://github.com/DynamicsAndNeuralSystems/pyspi/projects) in this repo.
+## Our Contributors 🌟
+We are thankful for the contributions of each and everyone who has helped make this project better. 
+Whether you've added a line of code, improved our documentation, or reported an issue, your contributions are greatly appreciated! 
+Below are some of the leading contributors to _pyspi_:
+
+<a href="https://github.com/DynamicsAndNeuralSystems/pyspi/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=DynamicsAndNeuralSystems/pyspi" />
+</a>
+
+## License 🧾
+_pyspi_ is released under the [GNU General Public License](https://www.gnu.org/licenses/gpl-3.0).
+