clear index page-installation instructions in docs and address review comments

Author: namiroues

package/doc/sphinx/source/index.rst

@@ -22,20 +22,20 @@ most of these formats, too, together with atom selections for use in
 Gromacs_, CHARMM_, VMD_ and PyMol_ (see :ref:`Selection exporters`).
 
 It allows one to read molecular dynamics trajectories and access the
-atomic coordinates through NumPy_ arrays. This provides a flexible and
+atomic coordinates through `NumPy`_ arrays. This provides a flexible and
 relatively fast framework for complex analysis tasks. Fairly complete
 atom :ref:`selection-commands-label` are implemented. Trajectories can
 also be manipulated (for instance, fit to a reference structure) and
 written out in a range of formats.
 
-.. _`www.mdanalysis.org`: https://www.mdanalysis.org
+.. _www.mdanalysis.org: https://www.mdanalysis.org
 .. _NumPy: https://numpy.org/
 .. _CHARMM:  http://www.charmm.org/
 .. _Amber:   http://ambermd.org/
 .. _LAMMPS:  http://lammps.sandia.gov/
 .. _NAMD:    http://www.ks.uiuc.edu/Research/namd/
 .. _Gromacs: http://www.gromacs.org/
-.. _`DL_POLY`: http://www.scd.stfc.ac.uk//44516.aspx
+.. _DL_POLY: http://www.scd.stfc.ac.uk//44516.aspx
 .. _VMD: http://www.ks.uiuc.edu/Research/vmd/
 .. _PyMol: http://www.pymol.org/
 .. _PDB: http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
@@ -48,37 +48,34 @@ Getting involved
 Please report **bugs** or **enhancement requests** through the `Issue
 Tracker`_. Questions can also be asked on the `GitHub Discussions`_.
 
-The MDAnalysis community subscribes to a `Code of Conduct`_ that all community
-members agree and adhere to --- please read it.
+The MDAnalysis community follows a `Code of Conduct`_ that all members are expected to adhere to. 
+Please take a moment to read it.
 
 .. _Issue Tracker: https://github.com/MDAnalysis/mdanalysis/issues
-.. _`GitHub Discussions`:
-   https://github.com/MDAnalysis/mdanalysis/discussions
-.. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/
+.. _GitHub Discussions: https://github.com/MDAnalysis/mdanalysis/discussions
+.. _Code of Conduct: https://www.mdanalysis.org/pages/conduct/
 
 
+.. _installation-instructions:
 
-Installing and Using MDAnalysis
+Installing and using MDAnalysis
 ===============================
 
-The MDAnalysis `User Guide`_ provides comprehensive information on how to `install <https://userguide.mdanalysis.org/stable/installation.html>`_
+The MDAnalysis `User Guide`_ provides comprehensive information on how to `install`_
 and use the library. We would recommend that new users have a look at the
 `Quick Start Guide`_. The User Guide also has a set of `examples`_ on how to
 use the MDAnalysis library which may be of interest.
 
-.. _`User Guide`: https://userguide.mdanalysis.org/stable/index.html
-.. _`Quick Start Guide`: https://userguide.mdanalysis.org/stable/examples/quickstart.html
-.. _`examples`: https://userguide.mdanalysis.org/stable/examples/README.html
-
+.. _User Guide: https://userguide.mdanalysis.org/stable/index.html
+.. _Quick Start Guide: https://userguide.mdanalysis.org/stable/examples/quickstart.html
+.. _examples: https://userguide.mdanalysis.org/stable/examples/README.html
+.. _install: https://userguide.mdanalysis.org/stable/installation.html 
 
-.. _installation-instructions:
-
-Source Code
+Source code
 ===========
 
-**Source code** is available from
-https://github.com/MDAnalysis/mdanalysis/ and is packaged under the
-`Lesser GNU Public Licence, version 3 or any later version`_. Individual components
+The MDAnalysis source code is available on [GitHub](https://github.com/MDAnalysis/mdanalysis/) and is 
+distributed under the `Lesser GNU Public Licence, version 3 or any later version`_. Individual components
 of the source code are provided under LGPL compatible licenses, details can be
 found in the `MDAnalysis license file`_. Obtain the sources with `git`_.
 
@@ -88,14 +85,12 @@ found in the `MDAnalysis license file`_. Obtain the sources with `git`_.
 
 
 The `User Guide`_ provides more information on how to
-`install the development version`_ of MDAnalysis.
+`install from source`_.
 
-.. _Lesser GNU Public Licence, version 3 or any later version:
-   https://www.gnu.org/licenses/lgpl-3.0.en.html
-.. _MDAnalysis license file:
-   https://github.com/MDAnalysis/mdanalysis/blob/develop/LICENSE
+.. _Lesser GNU Public Licence, version 3 or any later version: https://www.gnu.org/licenses/lgpl-3.0.en.html
+.. _MDAnalysis license file: https://github.com/MDAnalysis/mdanalysis/blob/develop/LICENSE
 .. _git: https://git-scm.com/
-.. _`install the development version`: https://userguide.mdanalysis.org/stable/installation.html#development-versions
+.. _install from source: https://userguide.mdanalysis.org/stable/installation.html
 
 
 Citation
@@ -104,14 +99,11 @@ Citation
 When using MDAnalysis in published work, please cite
 [Michaud-Agrawal2011]_ and [Gowers2016]_.
 
-MDAnalysis also contains specific algorithms and whole analysis
-modules whose algorithms have also been published in the scientific
-literature. Please make sure to also reference any
-:ref:`references-components` in published work.
+MDAnalysis includes specific algorithms and analysis modules, some of which have been published in the scientific literature.  
+Please ensure you cite the relevant :ref:`references-components` when using these features in your research.
 
 Thank you!
 
-
 .. Hide the contents from the front page because they are already in
 .. the side bar in the Alabaster sphinx style; requires Alabaster
 .. config sidebar_includehidden=True (default)