links and documentation

CONTRIBUTING.md

@@ -18,28 +18,28 @@ Ideally, these contributions should use/implement methods that have already been
 
 # Opening issues
 
-We appreciate being notified of problems with the existing Systole code. We prefer that issues be filed on [Github Issue Tracker](https://github.com/embodied-computation-group/systole/issues), rather than on social media or by direct email to the developers.
+We appreciate being notified of problems with the existing Systole code. We prefer that issues be filed on [Github Issue Tracker](https://github.com/LegrandNico/systole/issues), rather than on social media or by direct email to the developers.
 
 Please verify that your issue is not being currently addressed by other issues or pull requests by using the GitHub search tool to look for keywords in the project issue tracker.
 
 # Contributing code via pull requests
 
 While issue reporting is valuable, we strongly encourage users who are inclined to do so to submit patches for new or existing issues via pull requests. This is particularly the case for simple fixes, such as typos or tweaks to documentation, which do not require a heavy investment of time and attention.
 
-Contributors are also encouraged to contribute new code to enhance Systole's functionality, also via pull requests. Please consult the [Systole documentation](https://embodied-computation-group.github.io/systole/#) to ensure that any new contribution does not strongly overlap with existing functionality.
+Contributors are also encouraged to contribute new code to enhance Systole's functionality, also via pull requests. Please consult the [Systole documentation](https://LegrandNico.github.io/systole/#) to ensure that any new contribution does not strongly overlap with existing functionality.
 
-The preferred workflow for contributing to Systole is to fork the [GitHub repository](https://github.com/embodied-computation-group/systole), clone it to your local machine, and develop on a feature branch.
+The preferred workflow for contributing to Systole is to fork the [GitHub repository](https://github.com/LegrandNico/systole), clone it to your local machine, and develop on a feature branch.
 
 ## Steps:
 
-1. Fork the [project repository](https://github.com/embodied-computation-group/systole) by clicking on the 'Fork' button near the top right of the main repository page. This creates a copy of the code under your GitHub user account.
+1. Fork the [project repository](https://github.com/LegrandNico/systole) by clicking on the 'Fork' button near the top right of the main repository page. This creates a copy of the code under your GitHub user account.
 
 2. Clone your fork of the Systole repo from your GitHub account to your local disk, and add the base repository as a remote:
 
    ```bash
    $ git clone [email protected]:<your GitHub handle>/systole.git
    $ cd systole
-   $ git remote add upstream [email protected]:embodied-computation-group/systole.git
+   $ git remote add upstream [email protected]:LegrandNico/systole.git
    ```
 
 3. Create a ``feature`` branch to hold your development changes:

README.rst

@@ -1,15 +1,15 @@
 
 .. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
-  :target: https://github.com/embodied-computation-group/systole/blob/master/LICENSE
+  :target: https://github.com/LegrandNico/systole/blob/master/LICENSE
 
 .. image:: https://badge.fury.io/py/systole.svg
     :target: https://badge.fury.io/py/systole
 
 .. image:: https://joss.theoj.org/papers/10.21105/joss.03832/status.svg
    :target: https://doi.org/10.21105/joss.03832
 
-.. image:: https://codecov.io/gh/embodied-computation-group/systole/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/embodied-computation-group/systole
+.. image:: https://codecov.io/gh/LegrandNico/systole/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/LegrandNico/systole
 
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/psf/black
@@ -28,7 +28,7 @@
 
 ================
 
-.. image:: https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/logo.png
+.. image:: https://github.com/LegrandNico/systole/blob/dev/docs/source/images/logo.png
    :align: center
 
 ================
@@ -38,9 +38,9 @@ This includes tools for data epoching, artefact detection, artefact correction,
 variability analyses, circular statistical approaches to analysing cardiac cycles, and synchronising stimulus 
 presentation with different cardiac phases via Psychopy.
 
-The documentation can be found under the following `link <https://embodied-computation-group.github.io/systole/#>`_.
+The documentation can be found under the following `link <https://LegrandNico.github.io/systole/#>`_.
 
-If you have questions, you can ask them in the `Gitter chat <https://gitter.im/ecg-systole/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge>`_.
+If you have questions, you can ask them in the discussion section of this repository.
 
 How to cite?
 ++++++++++++
@@ -100,22 +100,22 @@ For an introduction to Systole and cardiac signal analysis, you can refer to the
      - |Colab badge 6|
 
 .. |Colab badge 1| image:: https://colab.research.google.com/assets/colab-badge.svg
-  :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/dev/source/notebooks/1-PhysiologicalSignals.ipynb
+  :target: https://colab.research.google.com/github/LegrandNico/systole/blob/dev/source/notebooks/1-PhysiologicalSignals.ipynb
 
 .. |Colab badge 2| image:: https://colab.research.google.com/assets/colab-badge.svg
-  :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/dev/source/notebooks/2-DetectingCycles.ipynb
+  :target: https://colab.research.google.com/github/LegrandNico/systole/blob/dev/source/notebooks/2-DetectingCycles.ipynb
 
 .. |Colab badge 3| image:: https://colab.research.google.com/assets/colab-badge.svg
-  :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/dev/source/notebooks/3-DetectingAndCorrectingArtefacts.ipynb
+  :target: https://colab.research.google.com/github/LegrandNico/systole/blob/dev/source/notebooks/3-DetectingAndCorrectingArtefacts.ipynb
 
 .. |Colab badge 4| image:: https://colab.research.google.com/assets/colab-badge.svg
-  :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/dev/source/notebooks/4-HeartRateVariability.ipynb
+  :target: https://colab.research.google.com/github/LegrandNico/systole/blob/dev/source/notebooks/4-HeartRateVariability.ipynb
 
 .. |Colab badge 5| image:: https://colab.research.google.com/assets/colab-badge.svg
-  :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/dev/source/notebooks/5-InstantaneousHeartRate.ipynb
+  :target: https://colab.research.google.com/github/LegrandNico/systole/blob/dev/source/notebooks/5-InstantaneousHeartRate.ipynb
 
 .. |Colab badge 6| image:: https://colab.research.google.com/assets/colab-badge.svg
-  :target: https://colab.research.google.com/github/embodied-computation-group/systole/blob/dev/source/notebooks/6-WorkingWithBIDSFolders.ipynb
+  :target: https://colab.research.google.com/github/LegrandNico/systole/blob/dev/source/notebooks/6-WorkingWithBIDSFolders.ipynb
 
 
 Getting started
@@ -140,7 +140,7 @@ The package integrates a set of functions for interactive or non interactive dat
   plot_raw(signal[60000 : 120000], modality="ecg", backend="bokeh", 
               show_heart_rate=True, show_artefacts=True, figsize=300)
 
-.. image:: https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/raw.png
+.. image:: https://github.com/LegrandNico/systole/blob/dev/docs/source/images/raw.png
    :align: center
 
 
@@ -158,7 +158,7 @@ Artefacts can be detected and corrected in the RR interval time series or the pe
 
   plot_subspaces(peaks, input_type="peaks", backend="bokeh")
 
-.. image:: https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/subspaces.png
+.. image:: https://github.com/LegrandNico/systole/blob/dev/docs/source/images/subspaces.png
    :align: center
 
 
@@ -176,7 +176,7 @@ Systole implements time-domain, frequency-domain and non-linear HRV indices, as
       plot_poincare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
       )
 
-.. image:: https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/hrv.png
+.. image:: https://github.com/LegrandNico/systole/blob/dev/docs/source/images/hrv.png
    :align: center
 
 
@@ -201,25 +201,25 @@ Interactive visualization of BIDS structured datasets
       signal_type="ECG"
   )
 
-.. image:: https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/editor.gif
+.. image:: https://github.com/LegrandNico/systole/blob/dev/docs/source/images/editor.gif
    :align: center
 
 Inserting and removing peaks
 ============================
 
-.. image:: https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/peaks.gif
+.. image:: https://github.com/LegrandNico/systole/blob/dev/docs/source/images/peaks.gif
    :align: center
 
 Annotating bad segments
 =======================
 
-.. image:: https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/segments.gif
+.. image:: https://github.com/LegrandNico/systole/blob/dev/docs/source/images/segments.gif
    :align: center
 
 Development
 +++++++++++
 
-This module was created and is maintained by Nicolas Legrand and Micah Allen (ECG group, https://the-ecg.org/). If you want to contribute, feel free to contact one of the developers, open an issue or submit a pull request.
+This repository is a fork of the `original Systole repository <https://github.com/embodied-computation-group/systole>` and is maintained by Nicolas Legrand. If you want to contribute, feel free to contact one of the developers, open an issue or submit a pull request.
 
 This program is provided with NO WARRANTY OF ANY KIND.
 
@@ -246,11 +246,5 @@ Systole was largely inspired by pre-existing toolboxes dedicated to heartrate va
 
 |AU| |lundbeck| |lab|
 
-.. |AU| image::  https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/au_clinisk_logo.png
+.. |AU| image::  https://github.com/LegrandNico/systole/blob/dev/docs/source/images/au_clinisk_logo.png
    :width: 100%
-
-.. |lundbeck| image::  https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/lundbeckfonden_logo.png
-   :width: 10%
-
-.. |lab| image::  https://github.com/embodied-computation-group/systole/blob/dev/docs/source/images/LabLogo.png
-   :width: 20%

docs/source/conf.py

@@ -95,7 +95,7 @@
     "icon_links": [
         dict(
             name="GitHub",
-            url="https://github.com/embodied-computation-group/systole",
+            url="https://github.com/LegrandNico/systole",
             icon="fa-brands fa-square-github",
         ),
         dict(

docs/source/getting_started.rst

@@ -12,7 +12,7 @@ If you want to download the `dev` branch instead and try the last features that
 
 .. code-block:: shell
 
-  pip install “git+https://github.com/embodied-computation-group/systole.git@dev”
+  pip install “git+https://github.com/LegrandNico/systole.git@dev”
 
 The following packages are required to use Systole:
 

docs/source/index.rst

@@ -1,15 +1,15 @@
 
 .. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
-  :target: https://github.com/embodied-computation-group/systole/blob/master/LICENSE
+  :target: https://github.com/LegrandNico/systole/blob/master/LICENSE
 
 .. image:: https://badge.fury.io/py/systole.svg
     :target: https://badge.fury.io/py/systole
 
 .. image:: https://joss.theoj.org/papers/10.21105/joss.03832/status.svg
    :target: https://doi.org/10.21105/joss.03832
 
-.. image:: https://codecov.io/gh/embodied-computation-group/systole/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/embodied-computation-group/systole
+.. image:: https://codecov.io/gh/LegrandNico/systole/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/LegrandNico/systole
 
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/psf/black
@@ -28,7 +28,7 @@
 
 ================
 
-.. image:: https://raw.githubusercontent.com/embodied-computation-group/systole/dev/docs/source/images/logo.png
+.. image:: https://raw.githubusercontent.com/LegrandNico/systole/dev/docs/source/images/logo.png
    :align: center
 
 ================
@@ -38,7 +38,7 @@ This includes tools for data epoching, artefact detection, artefact correction,
 variability analyses, circular statistical approaches to analysing cardiac cycles, and synchronising stimulus 
 presentation with different cardiac phases via Psychopy.
 
-If you have questions, you can ask them in the `Gitter chat <https://gitter.im/ecg-systole/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge>`_.
+If you have questions, you can ask them in the discussion section of this repository.
 
 How to cite?
 ============
@@ -155,7 +155,7 @@ Systole was largely inspired by pre-existing toolboxes dedicated to heartrate va
 Development
 ===========
 
-This module was created and is maintained by Nicolas Legrand and Micah Allen (ECG group, https://the-ecg.org/). If you want to contribute, feel free to contact one of the developers, open an issue or submit a pull request.
+This repository is a fork of the `original Systole repository <https://github.com/embodied-computation-group/systole>` and is maintained by Nicolas Legrand. If you want to contribute, feel free to contact one of the developers, open an issue or submit a pull request.
 
 This program is provided with NO WARRANTY OF ANY KIND.
 
@@ -172,16 +172,9 @@ Contributors
 
 |AU| |lundbeck| |lab|
 
-.. |AU| image::  https://github.com/embodied-computation-group/systole/raw/dev/docs/source/images/au_clinisk_logo.png
+.. |AU| image::  https://github.com/LegrandNico/systole/raw/dev/docs/source/images/au_clinisk_logo.png
    :width: 100%
 
-.. |lundbeck| image::  https://github.com/embodied-computation-group/systole/raw/dev/docs/source/images/lundbeckfonden_logo.png
-   :width: 10%
-
-.. |lab| image::  https://github.com/embodied-computation-group/systole/raw/dev/docs/source/images/LabLogo.png
-   :width: 20%
-
-
 .. toctree::
    :maxdepth: 3
    :hidden: