physiopy · tsalo · Nov 14, 2024 · Nov 14, 2024
diff --git a/.gitignore b/.gitignore
@@ -1 +1,3 @@
+.DS_Store
+site/
 env
diff --git a/docs/community/team.md b/docs/community/team.md
@@ -1,15 +1,15 @@
 ## Team
 
-**Project Leader(s):** 
+**Project Leader(s):**
 [Stefano Moia](https://github.com/smoia) - Postdoc researcher at the École Polytechnique Fédérale de Lausanne
 
 **Contributors:**
 Thanks goes to these wonderful people for all their help (see [emoji key](https://allcontributors.org/docs/en/emoji-key))!
 - [Phys2bids Contributors](https://github.com/physiopy/phys2bids#contributors-)
-- [Peakdet Contributors](https:https://hackmd.io/-M7a4dusTx6WBdN5WNaamg?both#//github.com/physiopy/peakdet#contributors-)
+- [Prep4Phys Contributors](https://github.com/physiopy/prep4phys#contributors-)
 - [Phys2denoise Contributors](https://github.com/physiopy/phys2denoise#contributors-)
 
-This could be you! We welcome all skill levels with an interest in physiological data collection. Join a meeting and figure out how you can get involved, or check out the contributions guide. 
+This could be you! We welcome all skill levels with an interest in physiological data collection. Join a meeting and figure out how you can get involved, or check out the contributions guide.
 
 This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification, meaning that contributions of any kind are recognized as such.
 
@@ -33,12 +33,12 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <td align="center"><a href="https://github.com/vinferrer"><img src="https://avatars2.githubusercontent.com/u/38909338?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Vicente Ferrer</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3Avinferrer" title="Bug reports">🐛</a> <a href="https://github.com/physiopy/phys2bids/commits?author=vinferrer" title="Code">💻</a> <a href="https://github.com/physiopy/phys2bids/commits?author=vinferrer" title="Documentation">📖</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Avinferrer" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/physiopy/phys2bids/commits?author=vinferrer" title="Tests">⚠️</a></td>
 </tr>
   <tr>
-    <td align="center"><a href="https://github.com/goodalse2019"><img src="https://avatars.githubusercontent.com/u/60117796?v=4" width="100px;" alt=""/><br /><sub><b>Sarah Goodale</b></sub></a><br /><a href="https://github.com/physiopy/physiopy.github.io/commits?author=goodalse2019" title="Documentation">📖</a><a href="#mentoring-goodalse2019" title="Mentoring">🧑‍🏫</a><a href="#eventOrganizing-goodalse2019" title="Mentoring">📋</a></td>   
+    <td align="center"><a href="https://github.com/goodalse2019"><img src="https://avatars.githubusercontent.com/u/60117796?v=4" width="100px;" alt=""/><br /><sub><b>Sarah Goodale</b></sub></a><br /><a href="https://github.com/physiopy/physiopy.github.io/commits?author=goodalse2019" title="Documentation">📖</a><a href="#mentoring-goodalse2019" title="Mentoring">🧑‍🏫</a><a href="#eventOrganizing-goodalse2019" title="Mentoring">📋</a></td>
     <td align="center"><a href="https://github.com/yarikoptic"><img src="https://avatars.githubusercontent.com/u/39889?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Yaroslav Halchenko</b></sub></a><br /><a href="#infra-yarikoptic" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
     <td align="center"><a href="http://soichi.us"><img src="https://avatars3.githubusercontent.com/u/923896?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Soichi Hayashi</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3Asoichih" title="Bug reports">🐛</a></td>
     <td align="center"><a href="https://github.com/viacovella"><img src="https://avatars1.githubusercontent.com/u/1639782?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Vittorio Iacovella</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=viacovella" title="Code">💻</a></td>
 </tr>
-  <tr>      
+  <tr>
       <td align="center"><a href="https://github.com/sangfrois"><img src="https://avatars0.githubusercontent.com/u/38385719?v=4?s=100" width="100px;" alt=""/><br /><sub><b>François Lespinasse</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=sangfrois" title="Code">💻</a> <a href="https://github.com/physiopy/phys2bids/commits?author=sangfrois" title="Tests">⚠️</a></td>
     <td align="center"><a href="https://github.com/NevMagi"><img src="https://avatars.githubusercontent.com/u/76997761?v=4" width="100px;" alt=""/><br /><sub><b>Neville Magielse</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=NevMagi" title="Documentation">📖</a></td>
     <td align="center"><a href="http://rossmarkello.com"><img src="https://avatars0.githubusercontent.com/u/14265705?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Ross Markello</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3Armarkello" title="Bug reports">🐛</a> <a href="https://github.com/physiopy/phys2bids/commits?author=rmarkello" title="Code">💻</a> <a href="#content-rmarkello" title="Content">🖋</a> <a href="#ideas-rmarkello" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-rmarkello" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Armarkello" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/physiopy/phys2bids/commits?author=rmarkello" title="Tests">⚠️</a> <a href="#mentoring-rmarkello" title="Mentoring">🧑‍🏫</a></td>

diff --git a/docs/contributors-guide/getting-started.md b/docs/contributors-guide/getting-started.md
@@ -9,7 +9,7 @@ up some guidelines for contributions - to help you get involved ASAP! If
 you lack knowledge in python development / github use / physiological
 data handling, don't be scared! Try to jump in anyway. Most of the
 original contributors learned these things exactly this way - jumping in
-and hoping to fall in the right way without breaking too many bones. 
+and hoping to fall in the right way without breaking too many bones.
 
 Contributions can be made in different ways, not only code! As we follow
 the
@@ -34,7 +34,7 @@ Follow these three simple steps to get started:
 Linux, Mac, and Windows developer installation
 ----------------------------------------------
 
-Note: 
+Note:
 The following instructions are provided assuming that python 3 is
 **not** your default version of python. If it is, you might need to use
 `pip` instead of `pip3`, although some OSs do adopt `pip3` anyway. If

diff --git a/docs/index.md b/docs/index.md
@@ -1,13 +1,13 @@
 # Home
-Welcome to the main documentation site for the physiopy community and python packages! Please also check out our [Github Page](https://github.com/physiopy). For questions, you can always contact the project manager at [[email protected]](mailto:[email protected]). 
+Welcome to the main documentation site for the physiopy community and python packages! Please also check out our [Github Page](https://github.com/physiopy). For questions, you can always contact the project manager at [[email protected]](mailto:[email protected]).
 
 <p align="center">
 <img src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/physiopy_logo_1280x640.png?raw=true" width="400">
 </p>
 
 ## Who are we?
-We are the physiopy development team consisting of an international group of volunteers. You can learn more about us and how to connect with us by visiting the [*Community*](/community) page. Contributions are also very much welcomed! Check out the [*Contributor Guide*](community/contributor-guide/) tab.
+We are the physiopy development team consisting of an international group of volunteers. You can learn more about us and how to connect with us by visiting the [*Community*](/community) page. Contributions are also very much welcomed! Check out the [*Contributor Guide*](/contributors-guide) tab.
 
 ## What is the importance of physiological data collection and its impact on MRI?
 
-Physiological data provides a rich representation of a research subject with respect to their bodily information (i.e., heart rate, respiratory rate and depth of breathing, skin conductance, etc.). Examining physiological activity helps us to understand the perception and embodied experience of cognition, emotion, motivation, and more. Additionaly, physiological data is a key component in understanding physiological sources of signal variance in fMRI data. Collecting these data helps to provide more accurate models of fMRI time-series. It also provides a real-time method to monitor subjects during scanning. See the [*Community Practices* documentation](https://physiopy-community-guidelines.readthedocs.io/en/latest/index.html) for recommendations from key personnel in the field on physiological data collection and analysis. 
+Physiological data provides a rich representation of a research subject with respect to their bodily information (i.e., heart rate, respiratory rate and depth of breathing, skin conductance, etc.). Examining physiological activity helps us to understand the perception and embodied experience of cognition, emotion, motivation, and more. Additionaly, physiological data is a key component in understanding physiological sources of signal variance in fMRI data. Collecting these data helps to provide more accurate models of fMRI time-series. It also provides a real-time method to monitor subjects during scanning. See the [*Community Practices* documentation](https://physiopy-community-guidelines.readthedocs.io/en/latest/index.html) for recommendations from key personnel in the field on physiological data collection and analysis.
diff --git a/docs/libraries/peakdet.md b/docs/libraries/peakdet.md
diff --git a/docs/libraries/prep4phys.md b/docs/libraries/prep4phys.md
@@ -0,0 +1,23 @@
+# Prep4Phys
+
+**Previously named Peakdet**
+
+### A toolbox for physiological peak detection analyses
+
+This package `prep4phys` is designed for use in the reproducible processing and analysis of physiological data, like those collected from respiratory belts, pulse photoplethysmography, or electrocardiogram (ECG/EKG) monitors. For github repository, follow this [link](https://github.com/physiopy/prep4phys)
+
+### Overview
+
+Physiological data are messy and prone to artifact (e.g., movement in respiration and pulse, ectopic beats in ECG). Despite leaps and bounds in recent algorithms for processing these data there still exists a need for manual inspection to ensure such artifacts have been appropriately removed. Because of this manual intervention step, understanding exactly what happened to go from "raw" data to "analysis-ready" data can often be difficult or impossible.
+
+This toolbox, `prep4phys`, aims to provide a set of tools that will work with a variety of input data to reproducibly generate manually-corrected, analysis- ready physiological data. If you'd like more information about the package, including how to install it and some example instructions on its use, check out our [documentation](https://prep4phys.readthedocs.io/en/latest/)
+
+### Installation and User Guide
+
+Follow this for more information on [installation and setup](https://prep4phys.readthedocs.io/en/latest/index.html) of `prep4phys` as well as ways to get involved in the development and testing of this package.
+
+The [user guide](https://prep4phys.readthedocs.io/en/latest/usage.html) also provided at the link above discusses the reproducibility of loading and saving data, as well as, the processing and editing of the physiological data.
+
+### License Information
+
+This codebase is licensed under the Apache License, Version 2.0. The full license can be found in the [LICENSE](https://github.com/physiopy/prep4phys/blob/master/LICENSE) file in the prep4phys distribution. You may also obtain a copy of the license [here](http://www.apache.org/licenses/LICENSE-2.0).
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -23,7 +23,7 @@ theme:
     # Palette toggle for light mode
     - scheme: default
       toggle:
-        icon: material/brightness-7 
+        icon: material/brightness-7
         name: Switch to dark mode
 
     # Palette toggle for dark mode
@@ -38,7 +38,7 @@ nav:
     - Libraries:
       - phys2bids: libraries/phys2bids.md
       - phys2denoise: libraries/phys2denoise.md
-      - peakdet: libraries/peakdet.md
+      - prep4phys: libraries/prep4phys.md
     - Contributor Guide:
       - Welcome: contributors-guide/index.md
       - Recognizing contributions: contributors-guide/recognition.md
@@ -58,7 +58,7 @@ nav:
         - Welcome: contributors-guide/documentation/index.md
         - Building documentation: contributors-guide/documentation/building.md
         - Adding to Community Practices: contributors-guide/documentation/community-practices.md
-    - Community Practices: 
+    - Community Practices:
       - Community Practices: https://physiopy-community-guidelines.readthedocs.io/en/latest/index.html
     - Community:
       - Welcome: community/index.md
@@ -69,6 +69,6 @@ nav:
     - Tutorials:
       - OHBM 2023 Tutorials: ohbm23_tutorials.md
       - ReproNim 2024 Tutorials: repronim24_tutorials.md
-      
+