From 068801951c49f0a91f7cf4b023585c96d905afd0 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Thu, 27 Feb 2025 15:27:10 +0000 Subject: [PATCH 1/6] FIX broken links --- _posts/2024-05-27-gsoc-outreachy-students.md | 2 +- _posts/2024-08-30-gsoc2024-final-sm.md | 2 +- _posts/2025-02-11-gsoc2024-final-lg.md | 2 +- about.md | 2 +- index.md | 2 +- pages/learning_MDAnalysis.md | 2 +- pages/mdakits.md | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) 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/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 }})!* From 884c18e8533d41b444562b550b2bdf6a194d8f12 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Thu, 27 Feb 2025 18:53:06 +0000 Subject: [PATCH 2/6] add mamba instructions and refine installation quick start --- pages/installation_quick_start.md | 36 +++++++++++++++++-------------- 1 file changed, 20 insertions(+), 16 deletions(-) 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/ From 48bad024c427bef92c951925b0d40eb937283b7f Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 28 Feb 2025 12:43:17 +0000 Subject: [PATCH 3/6] add mamba instructions and refine installation quick start --- pages/installation_quick_start.md | 43 ++++++++++--------------------- 1 file changed, 13 insertions(+), 30 deletions(-) diff --git a/pages/installation_quick_start.md b/pages/installation_quick_start.md index daa8fafd..32e1b5dd 100644 --- a/pages/installation_quick_start.md +++ b/pages/installation_quick_start.md @@ -4,53 +4,37 @@ title: Installation Quick Start order: 2 --- -MDAnalysis offers multiple installation methods. For most -users we recommend [mamba][] installation method, a faster -drop-in replacement for [conda][] . +MDAnalysis can be installed using [mamba][] (recommended) or [pip][]. ## Mamba ## -If you don't have [conda][] installed yet, follow the [installation -instructions for conda][]. Following that, install [mamba][] with: +If you have [conda][] or [mamba][] installed, run: {% highlight bash %} conda install -c conda-forge mamba -{% endhighlight %} - -Then, install the latest stable release of MDAnalysis with: - -{% highlight bash %} mamba install -c conda-forge mdanalysis {% endhighlight %} -To upgrade use: - -{% highlight bash %} -mamba update mdanalysis -{% endhighlight %} - -To [run the test cases][run_tests] and examples, also install the unit tests (about 90 MB -in size): +To install [test cases][] cases (about 90 MB +in size) run: {% highlight bash %} mamba install -c conda-forge MDAnalysisTests {% endhighlight %} -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. +MDAnalysis via [mamba][] supports only serial calculations. +For OpenMP-based parallelism, use [pip][] and ensure you have +a working [OpenMP][] installation. ## Python Package Index ## -To install the latest stable release with -[pip][pip] (which should be available in all Python installations) do: +To install with [pip][] run: {% highlight bash %} pip install --upgrade MDAnalysis {% endhighlight %} -To [run the test cases][run_tests] and examples, also install the unit tests (about 53 MiB -in size): +To install [test cases][] run: {% highlight bash %} pip install --upgrade MDAnalysisTests @@ -58,15 +42,14 @@ pip install --upgrade MDAnalysisTests ## More ## -For more installation options and additional details see [Installing -MDAnalysis in the {{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}/stable/installation.html). +For detailed installation methods, including setting up [mamba][] from scratch, see the [Installation instuctions in the {{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}/stable/installation.html). -If you have questions with the installation, please ask on +If you have questions regarding 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 +[installation instuctions]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html [OpenMP]: https://www.openmp.org/ -[run_tests]: {{ site.docs.userguide.url }}/stable/installation.html#testing +[test cases]: {{ site.docs.userguide.url }}/stable/installation.html#testing From aef7dbc8950f2028e613ca2db3f3f59bd60f04e7 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 28 Feb 2025 19:02:57 +0000 Subject: [PATCH 4/6] address PR review comments --- pages/installation_quick_start.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/pages/installation_quick_start.md b/pages/installation_quick_start.md index 32e1b5dd..ed5b8aee 100644 --- a/pages/installation_quick_start.md +++ b/pages/installation_quick_start.md @@ -4,14 +4,14 @@ title: Installation Quick Start order: 2 --- -MDAnalysis can be installed using [mamba][] (recommended) or [pip][]. +MDAnalysis can be installed using [mamba][], a faster drop-in replacement for [conda][], or [pip][]. -## Mamba ## +## mamba/conda ## -If you have [conda][] or [mamba][] installed, run: +If you don't have [mamba][] installed you can follow the [mamba installation instructions][]. +To install MDAnalysis run: {% highlight bash %} -conda install -c conda-forge mamba mamba install -c conda-forge mdanalysis {% endhighlight %} @@ -28,7 +28,7 @@ a working [OpenMP][] installation. ## Python Package Index ## -To install with [pip][] run: +To install MDAnalysis with [pip][] run: {% highlight bash %} pip install --upgrade MDAnalysis @@ -42,7 +42,7 @@ pip install --upgrade MDAnalysisTests ## More ## -For detailed installation methods, including setting up [mamba][] from scratch, see the [Installation instuctions in the {{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}/stable/installation.html). +For more details about the installation see the [Installation instuctions in the {{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}/stable/installation.html). If you have questions regarding the installation, please ask on [{{site.mailinglists.discussion.name}}]({{site.mailinglists.discussion.url}}). @@ -50,6 +50,6 @@ If you have questions regarding the installation, please ask on [pip]: https://pip.pypa.io/en/latest/ [mamba]:https://anaconda.org/conda-forge/mamba [conda]: https://conda.io/ -[installation instuctions]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html +[mamba installation instructions]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html [OpenMP]: https://www.openmp.org/ [test cases]: {{ site.docs.userguide.url }}/stable/installation.html#testing From abd1307198a4f76505cd974c0c14e82483c75fac Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 7 Mar 2025 15:24:06 +0000 Subject: [PATCH 5/6] "create documentation page" --- pages/documentation.md | 26 ++++++++++++++++++++++++++ pages/installation_quick_start.md | 4 ---- 2 files changed, 26 insertions(+), 4 deletions(-) create mode 100644 pages/documentation.md diff --git a/pages/documentation.md b/pages/documentation.md new file mode 100644 index 00000000..d0683684 --- /dev/null +++ b/pages/documentation.md @@ -0,0 +1,26 @@ +--- +layout: page +title: Documentation +order: 3 +--- + +MDAnalysis is an open-source, available under the +[GNU General Public License, version 2](https://www.gnu.org/licenses/gpl-2.0.html). MDAnalysis provides **comprehensive documentation** to help users at all levels—whether you're just getting started, developing new tools, or contributing to the project. From **step-by-step tutorials** to an in-depth **API reference**, these resources will guide you through installing, using, and extending MDAnalysis. + +## User Guide +The [User Guide]({{ site.docs.userguide.url }}) is the best place for new users to start. It includes: + +- Installation instructions +- Tutorials and examples +- Detailed explanations of MDAnalysis functionalities + +## API Reference +The [API Reference]({{ site.docs.mdanalysis.url }}) offers detailed documentation on all MDAnalysis modules, classes, and functions—perfect for developers and advanced users. + +## MDAnalysis Paper +Learn about the design philosophy and scientific impact of MDAnalysis in the [MDAnalysis paper]({{ site.baseurl }}/pages/citations#Gowers2016). + +--- + +If you need help or have ideas, join the conversation in [GitHub Discussions]({{ site.mailinglists.discussion.url }}). If you found a bug, you can report it in the [Issue Tracker]({{ sitemap.github.issues }}). + diff --git a/pages/installation_quick_start.md b/pages/installation_quick_start.md index 7bc8de45..5362cfe8 100644 --- a/pages/installation_quick_start.md +++ b/pages/installation_quick_start.md @@ -4,14 +4,10 @@ title: Installation Quick Start order: 2 --- -MDAnalysis can be installed using [mamba][], a faster drop-in replacement for [conda][], or [pip][]. MDAnalysis can be installed using [mamba][], a faster drop-in replacement for [conda][], or [pip][]. -## mamba/conda ## ## mamba/conda ## -If you don't have [mamba][] installed you can follow the [mamba installation instructions][]. -To install MDAnalysis run: If you don't have [mamba][] installed you can follow the [mamba installation instructions][]. To install MDAnalysis run: From 3a649beeb8e455e55d1af6651bcbde8e5a1331d9 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Tue, 11 Mar 2025 12:06:05 +0000 Subject: [PATCH 6/6] address PR review comments --- pages/documentation.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/pages/documentation.md b/pages/documentation.md index d0683684..79bc6330 100644 --- a/pages/documentation.md +++ b/pages/documentation.md @@ -4,23 +4,22 @@ title: Documentation order: 3 --- -MDAnalysis is an open-source, available under the -[GNU General Public License, version 2](https://www.gnu.org/licenses/gpl-2.0.html). MDAnalysis provides **comprehensive documentation** to help users at all levels—whether you're just getting started, developing new tools, or contributing to the project. From **step-by-step tutorials** to an in-depth **API reference**, these resources will guide you through installing, using, and extending MDAnalysis. +MDAnalysis is an open-source, available under the [GNU Lesser General Public License, version 2.1 or later (LGPLv2.1+)](https://www.gnu.org/licenses/lgpl-2.1.html). MDAnalysis provides **comprehensive documentation** to help users at all levels—whether you're just getting started, developing new tools, or contributing to the project. From **step-by-step tutorials** to an in-depth **API reference**, these resources will guide you through installing, using, and extending MDAnalysis. ## User Guide The [User Guide]({{ site.docs.userguide.url }}) is the best place for new users to start. It includes: -- Installation instructions -- Tutorials and examples -- Detailed explanations of MDAnalysis functionalities +- [Installation instructions]({{ site.docs.userguide.url }}/stable/installation.html) +- Tutorials and [examples]({{ site.docs.userguide.url }}/stable/examples/README.html) +- Detailed explanations of MDAnalysis functionalities (see for example the [`AtomGroup`]({{ site.docs.userguide.url }}/stable/atomgroup.html)) ## API Reference -The [API Reference]({{ site.docs.mdanalysis.url }}) offers detailed documentation on all MDAnalysis modules, classes, and functions—perfect for developers and advanced users. +The [API Reference]({{ site.docs.mdanalysis.url }}) offers detailed documentation on all MDAnalysis modules, classes, and functions—perfect for developers and advanced users. ## MDAnalysis Paper Learn about the design philosophy and scientific impact of MDAnalysis in the [MDAnalysis paper]({{ site.baseurl }}/pages/citations#Gowers2016). --- -If you need help or have ideas, join the conversation in [GitHub Discussions]({{ site.mailinglists.discussion.url }}). If you found a bug, you can report it in the [Issue Tracker]({{ sitemap.github.issues }}). +If you need help or have ideas, visit our [Community]({{ site.baseurl }}/pages/community) page to learn about available discussion channels.