gbouvignies · gbouvignies · Dec 4, 2023 · Dec 4, 2023 · Dec 4, 2023 · Dec 4, 2023
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,48 @@
+# Contributing to ChemEx
+
+We welcome contributions to the ChemEx project! Whether you're interested in fixing bugs, adding new features, or improving documentation, your help is appreciated. This document provides guidelines for contributing to ChemEx.
+
+## Getting Started
+
+1. **Fork the Repository**: Start by forking the ChemEx repository on GitHub.
+2. **Clone Your Fork**: Clone the fork to your local machine.
+3. **Set Up Your Environment**: Make sure you have Python and other necessary tools installed.
+4. **Create a Branch**: Create a new branch for your work.
+
+## Making Contributions
+
+### Reporting Bugs
+
+-   **Use the GitHub Issue Tracker**: Report bugs by creating a new issue.
+-   **Describe the Bug**: Include detailed information about the bug and steps to reproduce it.
+-   **Screenshots and Logs**: If applicable, add screenshots and log files to help explain your problem.
+
+### Suggesting Enhancements
+
+-   **Use the GitHub Issue Tracker**: Suggest enhancements by opening a new issue.
+-   **Provide a Clear Description**: Explain why this enhancement would be useful, and propose a possible implementation if you can.
+
+### Pull Requests
+
+-   **Small and Focused**: Keep your pull requests small and focused on a single issue or feature.
+-   **Code Standards**: Follow the coding style of the project (PEP 8 for Python, for example).
+-   **Documentation**: Update the documentation accordingly.
+-   **Testing**: Add tests for new features or bug fixes.
+-   **Describe Your Changes**: In your pull request, clearly describe what you have done.
+
+## Code Review Process
+
+1. **Review by Maintainers**: The project maintainers will review your pull request.
+2. **Feedback**: Be open to feedback and make necessary changes.
+3. **Approval and Merge**: Once approved, your changes will be merged into the main branch.
+
+## Community Guidelines
+
+-   **Be Respectful**: Treat others as you would like to be treated.
+-   **Collaboration Over Competition**: We are all working towards the same goal.
+
+## Questions?
+
+If you have any questions, please don't hesitate to open a discussion in the GitHub repository.
+
+Thank you for considering contributing to ChemEx. Your efforts help make ChemEx a better tool for everyone!
diff --git a/README.md b/README.md
@@ -1,52 +1,73 @@
-# ChemEx
+# ChemEx: NMR Chemical Exchange Analysis Tool
 
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
-## Overview
+## Table of Contents
 
-ChemEx is an analysis program for chemical exchange detected by NMR. It is designed to analyze various types of NMR data, with a focus on CPMG relaxation dispersion and Chemical Exchange Saturation Transfer techniques.
+-   [About ChemEx](#about-chemex)
+-   [Quick Overview](#quick-overview)
+-   [Prerequisites](#prerequisites)
+-   [Installation](#installation)
+-   [Performance Optimization](#performance-optimization)
+-   [Contributing](#contributing)
+-   [Support and Documentation](#support-and-documentation)
+-   [License](#license)
+<!-- -   [Citing ChemEx](#citing-chemex) -->
 
-## Installation
+## About ChemEx
 
-You can install `chemex` using different methods:
+ChemEx is an advanced, open-source software specifically designed for analyzing NMR experimental data to characterize chemical exchange processes. Ideal for researchers and scientists in the field of biochemistry and molecular biology, ChemEx aids in the analysis of NMR experiments like Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion and Chemical Exchange Saturation Transfer (CEST).
 
-### Conda
+## Prerequisites
 
-The recommended way to install `chemex` is via [conda](http://conda.pydata.org):
+Before installing ChemEx, ensure you have Python installed on your system. For beginners and for a seamless setup, we recommend using the [Anaconda Distribution](https://www.anaconda.com/distribution/), which includes Python, Numpy, and other essential scientific computing tools.
 
-```bash
-conda install -c conda-forge chemex
-```
+## Installation
+
+ChemEx offers several installation methods to suit your specific setup:
 
-If your version of Python is less than 3.9, you can create a separate conda environment and enforce the use of Python 3.9+:
+### Using conda
 
-```bash
-conda create -c conda-forge -n chemex python=3.10 chemex
+```shell
+conda create -n chemex
 conda activate chemex
+conda install python=3.11
+conda config --env --add channels conda-forge
+conda install chemex
 ```
 
-### PyPI (Python Package Index)
+### Using pip
 
-`chemex` is also available on the [Python Package Index](https://pypi.python.org/pypi/chemex) and can be installed using `pip`:
-
-```bash
+```shell
 pip install chemex
 ```
 
-### Development Version
-
-To install the development version directly from GitHub, you can use `pip`:
+### From source
 
-```bash
-pip install git+https://github.com/gbouvignies/chemex.git
+```shell
+pip install git+https://github.com/gbouvignies/ChemEx.git
 ```
 
-Make sure you have Git installed and configured on your system before running this command.
+## Performance Optimization
+
+For the best performance, install [NumPy](https://numpy.org) and [SciPy](https://scipy.org) with Intel® Math Kernel Library (Intel® MKL), available via [Anaconda](https://www.anaconda.com/distribution/) or the [Intel® Distribution for Python](https://software.intel.com/en-us/distribution-for-python).
 
 ## Contributing
 
-Contributions are welcome! If you find any issues or have suggestions for improvements, please open an issue or a discussion on the [GitHub repository](https://github.com/gbouvignies/chemex). We appreciate your feedback and involvement in making ChemEx better.
+We encourage contributions from the community. Please see our [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines on how to make ChemEx better. For any issues or suggestions, please open an issue or a discussion on our [GitHub repository](https://github.com/gbouvignies/ChemEx).
+
+## Support and Documentation
+
+For additional support, tutorials, and detailed documentation, visit the [ChemEx Documentation](https://gbouvignies.github.io/ChemEx/).
 
 ## License
 
-ChemEx is released under the [MIT License](https://github.com/gbouvignies/chemex/blob/master/LICENSE). Please see the LICENSE file for more details.
+ChemEx is licensed under the [GPL-3.0](https://www.gnu.org/licenses/gpl-3.0.en.html). See the [LICENSE](LICENSE.md) file for more details.
+
+<!-- ## Citing ChemEx
+
+If you use ChemEx in your research, please cite it as follows: [Citation details](#). -->
+
+---
+
+Developed with ❤️ by the [ChemEx Contributors](https://github.com/gbouvignies/ChemEx/graphs/contributors)
diff --git a/website/docs/examples/binding.md b/website/docs/examples/binding.md
@@ -32,7 +32,7 @@ step, the major purpose is to obtain residue-specific parameters.
 
 Further analysis of the fitting results can be carried out with the aid of
 additional functions in ChemEx (refer to
-[`Plotting best-fit parameters`](user_guide/additional_modules.md#plotting-best-fit-parameters)
+[`Plotting best-fit parameters`](user_guide/additional_modules.mdx#plotting-best-fit-parameters)
 subsection). During the whole fitting process K<sub>d</sub> is fixed to the
 value obtained from ITC experiments, more details about this example can be
 found in the reference.[^1]

diff --git a/website/docs/examples/index.md → website/docs/examples/index.mdx b/website/docs/examples/index.md → website/docs/examples/index.mdx
diff --git a/website/docs/experiments/cest/cest_13c.md b/website/docs/experiments/cest/cest_13c.md
@@ -17,32 +17,32 @@ CEST block. This keeps the spin system purely in-phase throughout, and is
 calculated using the (3n)×(3n), single-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a),
-      Ix(b), Iy(b), Iz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a),
+      Ix(b), Iy(b), Iz(b), ... \}
 
 ## References
 
-- P. Vallurupalli, G. Bouvignies, and L.E. Kay. _ChemBioChem_ **14**, 1709-1713
-  (2014)
-- G. Bouvignies, P. Vallurupalli, and L.E. Kay. _J. Mol. Biol._ **426**, 763-774
-  (2014)
-- P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ **52**, 4156-4159
-  (2013)
-- D.F. Hansen, G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **55**, 279-289
-  (2013)
-- G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **53**, 303-310 (2012)
-- E. Rennella, R. Huang, A. Velyvis, and L.E. Kay. _J. Biomol. NMR_ **63**,
-  187-199 (2015)
+-   P. Vallurupalli, G. Bouvignies, and L.E. Kay. _ChemBioChem_ **14**, 1709-1713
+    (2014)
+-   G. Bouvignies, P. Vallurupalli, and L.E. Kay. _J. Mol. Biol._ **426**, 763-774
+    (2014)
+-   P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ **52**, 4156-4159
+    (2013)
+-   D.F. Hansen, G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **55**, 279-289
+    (2013)
+-   G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **53**, 303-310 (2012)
+-   E. Rennella, R. Huang, A. Velyvis, and L.E. Kay. _J. Biomol. NMR_ **63**,
+    187-199 (2015)
 
 ## Example
 
-- An example for studying side-chain methyl groups in selectively ¹³C-labeled
-  sample is available
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C/).
-- An example for studying
-  [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is
-  available
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C_LABEL_CN/).
+-   An example for studying side-chain methyl groups in selectively ¹³C-labeled
+    sample is available
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C/).
+-   An example for studying
+    [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is
+    available
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C_LABEL_CN/).
 
 ## Sample configuration file
 

diff --git a/website/docs/experiments/cest/cest_15n.md b/website/docs/experiments/cest/cest_15n.md
@@ -17,22 +17,22 @@ CEST block. This keeps the spin system purely in-phase throughout, and is
 calculated using the (3n)×(3n), single-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a),
-      Ix(b), Iy(b), Iz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a),
+      Ix(b), Iy(b), Iz(b), ... \}
 
 ## Reference
 
-- P. Vallurupalli, G. Bouvignies, and L.E. Kay. _J. Am. Chem. Soc._ **134**,
-  8148-8161 (2012)
+-   P. Vallurupalli, G. Bouvignies, and L.E. Kay. _J. Am. Chem. Soc._ **134**,
+    8148-8161 (2012)
 
 ## Examples
 
-- An example for studying ¹⁵N-labeled sample is available
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N/).
-- An example for studying
-  [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is
-  available
-  [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N_LABEL_CN/).
+-   An example for studying ¹⁵N-labeled sample is available
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N/).
+-   An example for studying
+    [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is
+    available
+    [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N_LABEL_CN/).
 
 ## Sample configuration file
 

diff --git a/website/docs/experiments/cest/cest_15n_cw.md b/website/docs/experiments/cest/cest_15n_cw.md
@@ -16,14 +16,14 @@ Analyzes chemical exchange in the presence of ¹H CW decoupling during the CEST
 block. Magnetization evolution is calculated using the (15n)×(15n), two-spin
 matrix, where n is the number of states:
 
-    {        Ix(a),   Iy(a),   Iz(a),   Sx(a), IxSx(a), IySx(a), IzSx(a),
+    \{        Ix(a),   Iy(a),   Iz(a),   Sx(a), IxSx(a), IySx(a), IzSx(a),
       Sy(a), IxSy(a), IySy(a), IzSy(a), Sz(a), IxSz(a), IySz(a), IzSz(a),
              Ix(b),   Iy(b),   Iz(b),   Sx(b), IxSx(b), IySx(b), IzSx(b),
-      Sy(b), IxSy(b), IySy(b), IzSy(b), Sz(b), IxSz(b), IySz(b), IzSz(b), ... }
+      Sy(b), IxSy(b), IySy(b), IzSy(b), Sz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## Reference
 
-- G. Bouvignies, and L.E. Kay. _J. Phys. Chem. B_ **116**, 14311-14317 (2012)
+-   G. Bouvignies, and L.E. Kay. _J. Phys. Chem. B_ **116**, 14311-14317 (2012)
 
 ## Example
 

diff --git a/website/docs/experiments/cest/cest_15n_tr.md b/website/docs/experiments/cest/cest_15n_tr.md
@@ -16,13 +16,13 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## Reference
 
-- D. Long, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci. USA_ **111**,
-  8820-8825 (2014)
+-   D. Long, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci. USA_ **111**,
+    8820-8825 (2014)
 
 ## Example
 

diff --git a/website/docs/experiments/cest/cest_1hn_ap.md b/website/docs/experiments/cest/cest_1hn_ap.md
@@ -16,13 +16,13 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## Reference
 
-- A. Sekhar, R. Rosenzweig, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci.
-  USA_ **113**, E2794-E2801 (2016)
+-   A. Sekhar, R. Rosenzweig, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci.
+    USA_ **113**, E2794-E2801 (2016)
 
 ## Example
 

diff --git a/website/docs/experiments/cest/cest_1hn_ip_ap.md b/website/docs/experiments/cest/cest_1hn_ip_ap.md
@@ -16,15 +16,15 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 ## References
 
-- T. Yuwen, A. Sekhar, and L.E. Kay. _Angew. Chem. Int. Ed._ **56**, 6122-6125
-  (2017)
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **67**, 295-307 (2017)
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018)
+-   T. Yuwen, A. Sekhar, and L.E. Kay. _Angew. Chem. Int. Ed._ **56**, 6122-6125
+    (2017)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **67**, 295-307 (2017)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018)
 
 ## Example
 

diff --git a/website/docs/experiments/cest/cest_ch3_1h_ip_ap.md b/website/docs/experiments/cest/cest_ch3_1h_ip_ap.md
@@ -16,8 +16,8 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is
 calculated using the (6n)×(6n), two-spin matrix, where n is the number of
 states:
 
-    { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
-      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a),
+      Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \}
 
 :::note
 
@@ -27,8 +27,8 @@ The same module works for both ¹³CH₃- and ¹³CHD₂-labeled methyl groups.
 
 ## References
 
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **68**, 215-224 (2017)
-- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **68**, 215-224 (2017)
+-   T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018)
 
 ## Example
 

diff --git a/website/docs/experiments/cest/index.md → website/docs/experiments/cest/index.mdx b/website/docs/experiments/cest/index.md → website/docs/experiments/cest/index.mdx
diff --git a/website/docs/experiments/cpmg/cpmg_13c_ip.md b/website/docs/experiments/cpmg/cpmg_13c_ip.md
@@ -17,18 +17,18 @@ during the CPMG block. This keeps the spin system purely in-phase throughout,
 and is calculated using the (3n)×(3n), single-spin matrix, where n is the number
 of states:
 
-    { Ix(a), Iy(a), Iz(a),
-      Ix(b), Iy(b), Iz(b), ... }
+    \{ Ix(a), Iy(a), Iz(a),
+      Ix(b), Iy(b), Iz(b), ... \}
 
 The CW decoupling on ¹H is assumed to be strong enough (> 15 kHz) such that
 perfect ¹H decoupling can be achieved. In the case of CHD2 experiment, CW
 decoupling on 2H should be applied properly.
 
 ## References
 
-- D.F. Hansen, P. Vallurupalli, Lundström, Neudecker, and L.E. Kay. _J. Am.
-  Chem. Soc._ **130**, 2667-2675 (2008)
-- E. Rennella, Schuetz, and L.E. Kay. _J. Biomol. NMR_ **65**, 59-64 (2016)
+-   D.F. Hansen, P. Vallurupalli, Lundström, Neudecker, and L.E. Kay. _J. Am.
+    Chem. Soc._ **130**, 2667-2675 (2008)
+-   E. Rennella, Schuetz, and L.E. Kay. _J. Biomol. NMR_ **65**, 59-64 (2016)
 
 ## Example
 

diff --git a/website/docs/experiments/cpmg/cpmg_13co_ap.md b/website/docs/experiments/cpmg/cpmg_13co_ap.md
@@ -17,8 +17,8 @@ magnetization throughout the CPMG block. This results in lower intrinsic
 relaxation rates and therefore better sensitivity. The calculations use a
 (6n)×(6n), two-spin matrix, where n is the number of states:
 
-    { COx(a), COy(a), COz(a), 2COxNz(a), 2COyNz(a), 2COzNz(a),
-      COx(b), COy(b), COz(b), 2COxNz(b), 2COyNz(b), 2COzNz(b), ... }
+    \{ COx(a), COy(a), COz(a), 2COxNz(a), 2COyNz(a), 2COzNz(a),
+      COx(b), COy(b), COz(b), 2COxNz(b), 2COyNz(b), 2COzNz(b), ... \}
 
 Because of the length of the shaped pulses used during the CPMG blocks,
 off-resonance effects are taken into account only for the 90-degree pulses that
@@ -29,7 +29,7 @@ the "refocusing" flag, with such option ncyc_cp should be set as even.
 
 # Reference:
 
-- Lundström, D.F. Hansen, and L.E. Kay. _J. Biomol. NMR_ **42**, 35-47 (2008)
+-   Lundström, D.F. Hansen, and L.E. Kay. _J. Biomol. NMR_ **42**, 35-47 (2008)
 
 ## Example