diff --git a/_posts/2024-05-27-gsoc-outreachy-students.md b/_posts/2024-05-27-gsoc-outreachy-students.md index 542a50fa..5e88162c 100644 --- a/_posts/2024-05-27-gsoc-outreachy-students.md +++ b/_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/ diff --git a/_posts/2024-08-30-gsoc2024-final-sm.md b/_posts/2024-08-30-gsoc2024-final-sm.md index 4e46cc5d..385c7537 100644 --- a/_posts/2024-08-30-gsoc2024-final-sm.md +++ b/_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 %} diff --git a/_posts/2025-02-11-gsoc2024-final-lg.md b/_posts/2025-02-11-gsoc2024-final-lg.md index 6005bb76..0edbf3f5 100644 --- a/_posts/2025-02-11-gsoc2024-final-lg.md +++ b/_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 %} diff --git a/about.md b/about.md index b4cc393c..8f71cbc5 100644 --- a/about.md +++ b/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 diff --git a/index.md b/index.md index 1f969ef0..91ff8485 100644 --- a/index.md +++ b/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) diff --git a/pages/installation_quick_start.md b/pages/installation_quick_start.md index 5b39f166..daa8fafd 100644 --- a/pages/installation_quick_start.md +++ b/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/ diff --git a/pages/learning_MDAnalysis.md b/pages/learning_MDAnalysis.md index 94b68229..23a52a27 100644 --- a/pages/learning_MDAnalysis.md +++ b/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 diff --git a/pages/mdakits.md b/pages/mdakits.md index 54e76273..6c432661 100644 --- a/pages/mdakits.md +++ b/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 }})!*