FIX broken links (#436)

* close #405
* FIX broken links
* add mamba instructions and refine installation quick start

Author: namiroues

_posts/2024-05-27-gsoc-outreachy-students.md

@@ -78,7 +78,7 @@ Adetutu is on GitHub as @adetutudeborah, and on Twitter as [@adetutuoluwa2](http
 She will be documenting her internship journey on her [Medium blog](https://medium.com/@adetutuoluwasanmi). Feel free to check it out for updates on her experience!
 
 
-— @BradyAJohnston @cbouy @hmacdope @IAlibay @jennaswa @micaela-matta @orbeckst @richardgowers @xhgchen @yuxuanzhuang (mentors and org admins)
+— @BradyAJohnston @cbouy @hmacdope @IAlibay @jennaswa @micaela-matta @orbeckst @richardjgowers @xhgchen @yuxuanzhuang (mentors and org admins)
 
 [gsoc]: https://summerofcode.withgoogle.com
 [outreachy]: https://www.outreachy.org/

_posts/2024-08-30-gsoc2024-final-sm.md

@@ -22,7 +22,7 @@ We have tremendously enjoyed working with Lawson and Valerij and wish them the b
 
 We also thank [Google](https://opensource.google/) for supporting the students and continuing to support MDAnalysis as a GSoC organization since 2016.
 
-— @cbouy @hmacdope @IAlibay @jennaswa @richardgowers @xhgchen @yuxuanzhuang (mentors and org admins)
+— @cbouy @hmacdope @IAlibay @jennaswa @richardjgowers @xhgchen @yuxuanzhuang (mentors and org admins)
 
 [blog-lawson]: {{ site.baseurl }}{% post_url 2024-08-03-gsoc2024_woods %}
 [blog-valerij]: {{ site.baseurl }}{% post_url 2024-08-02-gsoc2024_talagayev %}

_posts/2025-02-11-gsoc2024-final-lg.md

@@ -23,6 +23,6 @@ In the meantime, we welcome you to start [learning MDAnalysis](https://www.mdana
 
 Please note that in addition to code contributions, we highly value [participating in the MDAnalysis community](https://www.mdanalysis.org/#participating) in other ways, including submitting [general feedback](https://www.mdanalysis.org/about/#feedback) and [issues via the GitHub issue tracker](https://github.com/MDAnalysis/mdanalysis/issues) and/or engaging in discussions on the MDAnalysis [Discord server](https://discord.com/channels/807348386012987462/) (join using [this invite link](https://discord.com/invite/fXTSfDJyxE)) and [GitHub Discussions forum](https://github.com/MDAnalysis/mdanalysis/discussions).
 
-— @cbouy @hmacdope @IAlibay @jennaswa @richardgowers @xhgchen @yuxuanzhuang (GSoC 2024 mentors and org admins)
+— @cbouy @hmacdope @IAlibay @jennaswa @richardjgowers @xhgchen @yuxuanzhuang (GSoC 2024 mentors and org admins)
 
 [blog-luna]: {{ site.baseurl }}{% post_url 2025-02-09-Luna-Morrow-Final-Submission %}

about.md

@@ -206,7 +206,7 @@ The following contributors were sponsored to work on MDAnalysis through the [Goo
 - **2024**: @ljwoods2, @lunamorrow, @talagayev
 - **2023**: @marinegor, @xhgchen 
 - **2022**: @aya9aladdin, @BFedder
-- **2021**: @ojeda-e, @orioncohen
+- **2021**: @ojeda-e, @orionarcher
 - **2020**: @cbouy, @hmacdope, @yuxuanzhuang
 - **2019**: @NinadBhat
 - **2018**: @ayushsuhane, @davidercruz

index.md

@@ -17,7 +17,7 @@ suitable for visualization or native analysis tools.
 MDAnalysis allows one to read particle-based trajectories (including
 individual coordinate frames such as biomolecules in the PDB format)
 and access the atomic coordinates through
-[NumPy](https://numpy.scipy.org/) arrays. This provides a flexible and
+[NumPy](https://numpy.org/) arrays. This provides a flexible and
 relatively fast framework for complex analysis tasks. In addition,
 powerful atom
 [selection commands]({{site.pypi.docs}}/documentation_pages/selections.html)

pages/installation_quick_start.md

@@ -4,38 +4,41 @@ title: Installation Quick Start
 order: 2
 ---
 
-MDAnalysis offers two methods to install the released version. For most
-users we recommend the [*Conda*](#conda) installation method.
+MDAnalysis offers multiple installation methods. For most
+users we recommend [mamba][] installation method, a faster
+drop-in replacement for [conda][] .
 
-## Conda ##
+## Mamba ##
 
 If you don't have [conda][] installed yet, follow the [installation
-instructions for conda][].
+instructions for conda][]. Following that, install [mamba][] with:
 
-To install the lastest stable release with [conda][conda] do:
+{% highlight bash %}
+conda install -c conda-forge mamba
+{% endhighlight %}
+
+Then, install the latest stable release of MDAnalysis with:
 
 {% highlight bash %}
-conda config --add channels conda-forge
-conda install mdanalysis
+mamba install -c conda-forge mdanalysis
 {% endhighlight %}
 
-To upgrade to the latest stable release.
+To upgrade use:
 
 {% highlight bash %}
-conda update mdanalysis
+mamba update mdanalysis
 {% endhighlight %}
 
-To [run the test cases][run_tests] and examples, also install the unit tests (about 53 MiB
+To [run the test cases][run_tests] and examples, also install the unit tests (about 90 MB
 in size):
 
 {% highlight bash %}
-conda install MDAnalysisTests
+mamba install -c conda-forge MDAnalysisTests
 {% endhighlight %}
 
-The conda packages currently only support serial calculations. If you
-plan to use the parallel [OpenMP][OpenMP] algorithms you need to
-install MDAnalysis from the [Python Package
-Index](#python-package-index) and have a working OpenMP installation.
+MDAnalysis installed via mamba supports only serial calculations. 
+If you need OpenMP-based parallelism, install MDAnalysis via [pip](#python-package-index) 
+and ensure you have a working [OpenMP][] installation.
 
 ## Python Package Index ##
 
@@ -55,13 +58,14 @@ pip install --upgrade MDAnalysisTests
 
 ## More ##
 
-For more details on installation and alternative ways to install MDAnalysis see [Installing
+For more installation options and additional details see [Installing
 MDAnalysis in the {{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}/stable/installation.html).
 
 If you have questions with the installation, please ask on
 [{{site.mailinglists.discussion.name}}]({{site.mailinglists.discussion.url}}).
 
 [pip]: https://pip.pypa.io/en/latest/
+[mamba]:https://anaconda.org/conda-forge/mamba
 [conda]: https://conda.io/
 [installation instructions for conda]: https://conda.io/projects/conda/en/latest/user-guide/install/index.html
 [OpenMP]: https://www.openmp.org/

pages/learning_MDAnalysis.md

@@ -69,7 +69,7 @@ to use it in a research context.
 @lilyminium's talk at [PyCon AU 2019](https://2019.pycon-au.org/) *The universe as balls and
 springs: molecular dynamics in Python* gives a general introduction to
 molecular dynamics and shows how to use MDAnalysis (and other tools
-such as [OpenMM](http://openmm.org/), [nglviewer](nglviewer.org/nglview/latest/),
+such as [OpenMM](http://openmm.org/), [nglviewer](https://nglviewer.org/nglview/latest/),
 [pandas](https://pandas.pydata.org/),
 [plotly](https://pandas.pydata.org/)). If you want to better
 understand what MD simulations are and how scientists can make use of

pages/mdakits.md

@@ -19,7 +19,7 @@ MDAnalysis. Whilst we cannot guarantee the completeness of the MDAKit's test cov
 
 
 *If you have your own MDAKit and you would like to add it to the
-registry, please look at the [contribution instructions](https://mdakits.mdanalysis.org/add.html)
+registry, please look at the contribution [instructions](https://mdakits.mdanalysis.org/makingakit.html)
 or share it on [{{ site.mailinglists.discussion.name }}]({{ site.mailinglists.discussion.url }})!*