Revised documentation

COPYRIGHT

-"""
           ARIA -- Ambiguous Restraints for Iterative Assignment
 
                  A software for automated NOE assignment
@@ -19,9 +18,3 @@ a warranty of non-infringement.
 
 Distribution of substantively modified versions of this module is
 prohibited without the explicit permission of the copyright holders.
-
-$Author: bardiaux $
-$Revision: 1.1.1.1 $
-$Date: 2010/03/23 15:27:16 $
-"""
-

README.new.md

-# de Novo Ambiguous Restraints for Iterative Assignment
-
-**A pipeline for automated de novo contact map assignment**
-
-[![pipeline status](https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/pipeline.svg)](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
-[![coverage report](https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/coverage.svg)](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
-<!--[![DOI Status](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtl589-blue.svg)](https://doi.org/10.1093/bioinformatics/btl589)-->
-
-
-## Installation & usage
-
-Please refer to :
-
-* [Main ARIA documentation](http://aria.pasteur.fr/documentation)
-* [NARIA documentation](http://bis-aria.pages.pasteur.fr/ariaec)
-
-
-## Contributing
-
-Please refer to the [guidelines for contributing](CONTRIBUTING.md) for any 
-suggestions or bug report.
-
-<!--## Citation-->
-
-<!--If you use this software, please quote the following reference(s):-->
-
-<!--> Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,-->
-<!--Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR-->
-<!--structure calculation. Bioinformatics 23:381-382-->
\ No newline at end of file

docs/contents.rst

@@ -19,3 +19,5 @@
    :caption: Examples
 
    examples/index
+   examples/ec
+   examples/ecnmr
\ No newline at end of file

docs/installation.rst

@@ -63,7 +63,7 @@ allowing cross platform and legacy OS support.
 
     sudo singularity build aria.simg aria.shub
 
-The CLI:abbr:`Command Line Interface` described in :doc:`usage` section will
+The :abbr:`Command Line Interface (CLI)` described in :doc:`usage` section will
 then be accessible by calling the generated singularity image.
 
 .. code-block:: shell