diff --git a/package/AUTHORS b/package/AUTHORS index a09b9dc1829..72e98d6c6e8 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -247,7 +247,8 @@ Chronological list of authors - Jia-Xin Zhu - Tanish Yelgoe 2025 - - Joshua Raphael Uy + - Joshua Raphael Uy + - Namir Oues External code ------------- diff --git a/package/doc/sphinx/source/index.rst b/package/doc/sphinx/source/index.rst index d9fd61df14e..adee0e6ece9 100644 --- a/package/doc/sphinx/source/index.rst +++ b/package/doc/sphinx/source/index.rst @@ -22,13 +22,13 @@ 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/ @@ -48,100 +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: -User Guide -========== +Installing and using MDAnalysis +=============================== -The MDAnalysis `User Guide`_ provides comprehensive information on how to -use the library. We would recommend that new users have a look at the +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 - - -.. _installation-instructions: - -Installing MDAnalysis -===================== - -The easiest approach to `install the latest release`_ is to use a package that -can be installed either with conda_ or pip_. - -conda ------ - -First installation with conda_: - -.. code-block:: bash - - conda config --add channels conda-forge - conda install mdanalysis - -which will automatically install a *full set of dependencies*. - -To upgrade later: - -.. code-block:: bash - - conda update mdanalysis - -pip ---- - -Installation with `pip`_ and a *minimal set of dependencies*: +.. _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 -.. code-block:: bash - - pip install --upgrade MDAnalysis - -To install with a *full set of dependencies* (which includes everything needed -for :mod:`MDAnalysis.analysis`), add the ``[analysis]`` tag: - -.. code-block:: bash - - pip install --upgrade MDAnalysis[analysis] - - -Tests ------ - -If you want to `run the tests`_ or use example files to follow some of the -examples in the documentation or the tutorials_, also install the -``MDAnalysisTests`` package: - -.. code-block:: bash - - conda install mdanalysistests # with conda - pip install --upgrade MDAnalysisTests # with pip - -.. _install the latest release: - https://userguide.mdanalysis.org/stable/installation.html#installation -.. _pip: - http://www.pip-installer.org/en/latest/index.html -.. _conda: - http://conda.pydata.org/docs/ -.. _run the tests: https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests -.. _tutorials: https://www.mdanalysis.org/pages/learning_MDAnalysis/ - - -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 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`_. @@ -151,14 +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 @@ -167,14 +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) @@ -185,7 +114,7 @@ Thank you! .. toctree:: :maxdepth: 4 :caption: Documentation - :numbered: + :numbered: :hidden: ./documentation_pages/overview @@ -214,3 +143,4 @@ Indices and tables * :ref:`genindex` * :ref:`modindex` * :ref:`search` +