From 068801951c49f0a91f7cf4b023585c96d905afd0 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Thu, 27 Feb 2025 15:27:10 +0000 Subject: [PATCH 01/14] 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 02/14] 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 03/14] 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 04/14] 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 0dd030c96d536555fe1e13fa1e4417e81433b638 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 7 Mar 2025 15:22:57 +0000 Subject: [PATCH 05/14] Add contribute page Add contribute page Add contribute page --- _config.yml | 2 ++ pages/contribute.md | 63 +++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 pages/contribute.md diff --git a/_config.yml b/_config.yml index c2c59b08..a09151ee 100644 --- a/_config.yml +++ b/_config.yml @@ -90,6 +90,8 @@ docs: userguide: name: User Guide url: https://userguide.mdanalysis.org + repo: https://github.com/MDAnalysis/UserGuide + issues: https://github.com/MDAnalysis/UserGuide/issues quickstart: name: Quick Start Guide url: https://userguide.mdanalysis.org/stable/examples/quickstart.html diff --git a/pages/contribute.md b/pages/contribute.md new file mode 100644 index 00000000..440c1236 --- /dev/null +++ b/pages/contribute.md @@ -0,0 +1,63 @@ +--- +layout: page +title: Contribute +order: 6 +--- + +MDAnalysis is an open-source project that welcomes contributions from the community. Whether you're a developer, documentation writer, or interested in improving the website, there are many ways to get involved. + +You can contribute by **developing new features, fixing bugs, improving documentation, enhancing tutorials, or engaging in discussions**. If you're new, you can start by participating in community conversations and mentoring programs. For more information on how you can participate, check out the [Community]({{ site.baseurl }}/pages/community/) and [Events]({{ site.baseurl }}/pages/events/) pages. + +This page provides an overview of how you can contribute to the [Code](#contributing-to-the-code) or [Documentation](#contributing-to-documentation). + +MDAnalysis maintains **three GitHub repositories**, each dedicated to a specific area of contribution: + +- [Main Code Repository]({{ site.github.repo }}): for code development and API documentation. +- [User Guide Repository]({{ site.docs.userguide.repo }}): containing installation instructions, tutorials and learning resources. +- [Website Repository][]: Hosts the website and blog. + +--- + +## Contributing to the Code + +If you're interested in developing new features, fixing bugs, or improving performance, contributing to the MDAnalysis codebase is a great way to get involved. + +To get started: +- Read the [Contributing to the Main Codebase]({{ site.docs.userguide.url }}/stable/contributing_code.html#working-with-mdanalysis-code) guide, which outlines all the necessary steps. +- Browse [GitHub Issues]({{ site.github.issues }}) to find open tasks (look for "good first issue" if you're a beginner). You can also report bugs or suggest improvements there. +- Follow best practices, including [writing and running tests]({{ site.docs.userguide.url }}/stable/testing.html#testing) and [updating the documentation]({{ site.docs.userguide.url }}/stable/contributing_code.html#building-code-documentation) for any changes. + +--- + +## Contributing to Documentation + +Good documentation is essential to making MDAnalysis accessible to users and developers. MDAnalysis maintains two types of documentation: the [User Guide]({{ site.docs.userguide.url }}) and the [API Reference]({{ site.docs.mdanalysis.url }}/stable/index.html). + +### User Guide + +The [User Guide]({{ site.docs.userguide.url }}/stable/index.html) provides tutorials and explanatory content to help users install and learn MDAnalysis. You can contribute by updating unclear explanations or adding new tutorials or examples. + +To get started: +- Follow the [Contributing to the User Guide]({{ site.docs.userguide.url }}/stable/contributing_docs.html). +- Check for open documentation-related issues in the [User Guide GitHub Issues]({{ site.docs.userguide.issues }}). + +### API Reference + +The [API reference]({{ site.docs.mdanalysis.url }}/stable/index.html) is **automatically generated** from *docstrings* in the codebase and serves as a reference for developers. You can contribute by improving *docstrings* for functions, classes, and modules or updating outdated documentation. + +To get started: +- Follow the [API Documentation Contribution Guide]({{ site.docs.userguide.url }}/stable/contributing_code.html#working-with-mdanalysis-docs). +- Browse open API documentation issues in [GitHub Issues]({{ site.github.issues }}). + +--- + +## Other Contributions + +If you are interested in contributing in other ways, such as improving the website or blog, you can refer to the [README file][] in the [Website Repository][]. While the website is already maintained by the MDAnalysis team, minor fixes and updates are always welcome. + +If you'd like to write a **blog post**, feel free to reach out via the [Community]({{ site.baseurl }}/pages/community/) page. + +[Website Repository]: https://github.com/MDAnalysis/MDAnalysis.github.io +[README file]: https://github.com/namiroues/MDAnalysis.github.io/blob/master/README.md + + From 06d4f66afe430665ab2ef1c186dcd2c5789f8bd5 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Tue, 11 Mar 2025 16:37:48 +0000 Subject: [PATCH 06/14] Revert unintended changes to installation_quick_start.md --- pages/installation_quick_start.md | 4 ---- 1 file changed, 4 deletions(-) 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 2e89f10cf90744f33cad52cfb109defabd7d69c2 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Wed, 12 Mar 2025 11:49:16 +0000 Subject: [PATCH 07/14] address PR review comments --- _config.yml | 4 ++++ pages/contribute.md | 56 +++++++++++++++++++++++++++++---------------- 2 files changed, 40 insertions(+), 20 deletions(-) diff --git a/_config.yml b/_config.yml index 0773d7ac..65d0023e 100644 --- a/_config.yml +++ b/_config.yml @@ -68,6 +68,10 @@ pypi: package: https://pypi.org/project/MDAnalysis tests: https://pypi.org/project/MDAnalysisTests docs: https://docs.mdanalysis.org +mdakits: + registry: https://mdakits.mdanalysis.org/mdakits.html + guide: https://mdakits.mdanalysis.org/makingakit.html + issues: https://github.com/MDAnalysis/MDAKits/issues mailinglists: discussion: name: GitHub Discussions diff --git a/pages/contribute.md b/pages/contribute.md index 440c1236..846b297c 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -4,53 +4,69 @@ title: Contribute order: 6 --- -MDAnalysis is an open-source project that welcomes contributions from the community. Whether you're a developer, documentation writer, or interested in improving the website, there are many ways to get involved. +MDAnalysis is an open-source project that welcomes and encourages contributions from the community. Whether you're a developer, documentation writer, or interested in improving the website, there are many ways to get involved. -You can contribute by **developing new features, fixing bugs, improving documentation, enhancing tutorials, or engaging in discussions**. If you're new, you can start by participating in community conversations and mentoring programs. For more information on how you can participate, check out the [Community]({{ site.baseurl }}/pages/community/) and [Events]({{ site.baseurl }}/pages/events/) pages. +You can contribute by **developing new features, fixing bugs, improving documentation, enhancing tutorials, contributing to MDAKits, improving the website, or engaging in discussions**. -This page provides an overview of how you can contribute to the [Code](#contributing-to-the-code) or [Documentation](#contributing-to-documentation). +If you're new, you can start by participating in community conversations and mentoring programs. For more information on how you can participate, check out the [Community]({{ site.baseurl }}/pages/community/) and [Events]({{ site.baseurl }}/pages/events/) pages. -MDAnalysis maintains **three GitHub repositories**, each dedicated to a specific area of contribution: +This page provides an overview of how you can contribute to the [Codebase](#contributing-to-the-codebase), [MDAKits](#contributing-to-mdakits) or [Documentation](#contributing-to-the-documentation). -- [Main Code Repository]({{ site.github.repo }}): for code development and API documentation. -- [User Guide Repository]({{ site.docs.userguide.repo }}): containing installation instructions, tutorials and learning resources. -- [Website Repository][]: Hosts the website and blog. +## Contributing to the Codebase ---- +If you are interested in developing new features, fixing bugs, or improving performance, contributing to the MDAnalysis main codebase is a great way to get involved. -## Contributing to the Code +### Main Codebase Repository +MDAnalysis is developed and maintained in the [MDAnalysis Main Code Repository]({{ site.github.repo }}), which contains: -If you're interested in developing new features, fixing bugs, or improving performance, contributing to the MDAnalysis codebase is a great way to get involved. +- The core library for molecular dynamics analysis. +- The [API documentation]({{ site.docs.mdanalysis.url }}/stable/index.html), generated from in-code docstrings. +- [Open issues]({{ site.github.issues }}), where contributions such as bug fixes and feature implementations are tracked. -To get started: +### How to Get Started - Read the [Contributing to the Main Codebase]({{ site.docs.userguide.url }}/stable/contributing_code.html#working-with-mdanalysis-code) guide, which outlines all the necessary steps. -- Browse [GitHub Issues]({{ site.github.issues }}) to find open tasks (look for "good first issue" if you're a beginner). You can also report bugs or suggest improvements there. -- Follow best practices, including [writing and running tests]({{ site.docs.userguide.url }}/stable/testing.html#testing) and [updating the documentation]({{ site.docs.userguide.url }}/stable/contributing_code.html#building-code-documentation) for any changes. +- Browse [GitHub Issues]({{ site.github.issues }}) to find open tasks. Look for "good first issue" if you're a beginner. You can also report bugs or suggest improvements there. +- Follow best practices, including + - [Writing and Running Tests]({{ site.docs.userguide.url }}/stable/testing.html#testing) to ensure your changes work correctly. + - [Updating the Documentation]({{ site.docs.userguide.url }}/stable/contributing_code.html#building-code-documentation) when making modifications. ---- +## Contributing to MDAKits + +[MDAKits]({{ site.mdakits.registry }}) are **community-driven projects** that extend MDAnalysis functionality. They allow researchers and developers to build tools tailored for specific workflows while staying within the MDAnalysis ecosystem. + +### MDAKits Registry +The [MDAKits Registry]({{ site.mdakits.registry }}) lists active projects contributed by the community. These projects cover various applications, such as enhanced trajectory analysis, molecular simulations, and integration with machine learning frameworks. -## Contributing to Documentation +### How to Get Started +- **Explore existing MDAKits** in the [MDAKits Registry]({{ site.mdakits.registry }}) to find projects that match your interests. Each entry includes functionality, installation instructions, and contribution guidelines. +- **Find open issues** in [MDAKits GitHub Issues]({{ site.mdakits.issues }}). +- **Propose a new MDAKit** by following the [MDAKits Guide]({{ site.mdakits.guide }}). +- **Contribute to an existing MDAKit** by collaborating with maintainers to improve functionality, fix bugs, or add new features. + +MDAKits follow MDAnalysis coding standards but operate independently. Contributions to these projects are highly encouraged and help expand the MDAnalysis ecosystem. + +## Contributing to the Documentation Good documentation is essential to making MDAnalysis accessible to users and developers. MDAnalysis maintains two types of documentation: the [User Guide]({{ site.docs.userguide.url }}) and the [API Reference]({{ site.docs.mdanalysis.url }}/stable/index.html). ### User Guide -The [User Guide]({{ site.docs.userguide.url }}/stable/index.html) provides tutorials and explanatory content to help users install and learn MDAnalysis. You can contribute by updating unclear explanations or adding new tutorials or examples. +The [User Guide]({{ site.docs.userguide.url }}/stable/index.html) provides tutorials and explanatory content to help users install and learn MDAnalysis. You can contribute by updating unclear explanations, adding new tutorials or examples, or fixing outdated information. -To get started: +### How to Get Started +- Work on the [User Guide Repository]({{ site.docs.userguide.repo }}). - Follow the [Contributing to the User Guide]({{ site.docs.userguide.url }}/stable/contributing_docs.html). - Check for open documentation-related issues in the [User Guide GitHub Issues]({{ site.docs.userguide.issues }}). ### API Reference -The [API reference]({{ site.docs.mdanalysis.url }}/stable/index.html) is **automatically generated** from *docstrings* in the codebase and serves as a reference for developers. You can contribute by improving *docstrings* for functions, classes, and modules or updating outdated documentation. +The [API reference]({{ site.docs.mdanalysis.url }}/stable/index.html) is **automatically generated** from *docstrings* in the codebase. It provides a structured reference for developers working with MDAnalysis. You can contribute by improving *docstrings* for functions, classes, and modules or updating outdated documentation. To get started: +- Work on the [MDAnalysis Main Code Repository]({{ site.github.repo }}). - Follow the [API Documentation Contribution Guide]({{ site.docs.userguide.url }}/stable/contributing_code.html#working-with-mdanalysis-docs). - Browse open API documentation issues in [GitHub Issues]({{ site.github.issues }}). ---- - ## Other Contributions If you are interested in contributing in other ways, such as improving the website or blog, you can refer to the [README file][] in the [Website Repository][]. While the website is already maintained by the MDAnalysis team, minor fixes and updates are always welcome. From e05ac73cfeca5aba147a48f831544a70e0e1dd59 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Sat, 15 Mar 2025 09:46:37 +0100 Subject: [PATCH 08/14] add 'mentorship & outreach programs' to contribute page --- pages/contribute.md | 61 +++++++++++++++++++++++++++++++++++---------- 1 file changed, 48 insertions(+), 13 deletions(-) diff --git a/pages/contribute.md b/pages/contribute.md index 846b297c..3da6d59e 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -6,14 +6,13 @@ order: 6 MDAnalysis is an open-source project that welcomes and encourages contributions from the community. Whether you're a developer, documentation writer, or interested in improving the website, there are many ways to get involved. -You can contribute by **developing new features, fixing bugs, improving documentation, enhancing tutorials, contributing to MDAKits, improving the website, or engaging in discussions**. +You can contribute by **developing new features, fixing bugs, improving documentation, enhancing tutorials, contributing to MDAKits, improving the website, or engaging in discussions**. Contributions also extend to our **mentoring and outreach programs**, where participants gain hands-on experience in open-source development and scientific software. If you're new, you can start by participating in community conversations and mentoring programs. For more information on how you can participate, check out the [Community]({{ site.baseurl }}/pages/community/) and [Events]({{ site.baseurl }}/pages/events/) pages. -This page provides an overview of how you can contribute to the [Codebase](#contributing-to-the-codebase), [MDAKits](#contributing-to-mdakits) or [Documentation](#contributing-to-the-documentation). +This page provides an overview of how you can contribute to the [Codebase](#contributing-to-the-codebase), [MDAKits](#contributing-to-mdakits), [Documentation](#contributing-to-the-documentation), or [Mentoring & Outreach Programs](#mentoring--outreach-programs). ## Contributing to the Codebase - If you are interested in developing new features, fixing bugs, or improving performance, contributing to the MDAnalysis main codebase is a great way to get involved. ### Main Codebase Repository @@ -31,26 +30,23 @@ MDAnalysis is developed and maintained in the [MDAnalysis Main Code Repository]( - [Updating the Documentation]({{ site.docs.userguide.url }}/stable/contributing_code.html#building-code-documentation) when making modifications. ## Contributing to MDAKits - [MDAKits]({{ site.mdakits.registry }}) are **community-driven projects** that extend MDAnalysis functionality. They allow researchers and developers to build tools tailored for specific workflows while staying within the MDAnalysis ecosystem. ### MDAKits Registry The [MDAKits Registry]({{ site.mdakits.registry }}) lists active projects contributed by the community. These projects cover various applications, such as enhanced trajectory analysis, molecular simulations, and integration with machine learning frameworks. ### How to Get Started -- **Explore existing MDAKits** in the [MDAKits Registry]({{ site.mdakits.registry }}) to find projects that match your interests. Each entry includes functionality, installation instructions, and contribution guidelines. -- **Find open issues** in [MDAKits GitHub Issues]({{ site.mdakits.issues }}). -- **Propose a new MDAKit** by following the [MDAKits Guide]({{ site.mdakits.guide }}). -- **Contribute to an existing MDAKit** by collaborating with maintainers to improve functionality, fix bugs, or add new features. +- Explore existing MDAKits in the [MDAKits Registry]({{ site.mdakits.registry }}) to find projects that match your interests. Each entry includes functionality, installation instructions, and contribution guidelines. +- Find open issues in [MDAKits GitHub Issues]({{ site.mdakits.issues }}). +- Propose a new MDAKit by following the [MDAKits Guide]({{ site.mdakits.guide }}). +- Contribute to an existing MDAKit by collaborating with maintainers to improve functionality, fix bugs, or add new features. MDAKits follow MDAnalysis coding standards but operate independently. Contributions to these projects are highly encouraged and help expand the MDAnalysis ecosystem. ## Contributing to the Documentation - Good documentation is essential to making MDAnalysis accessible to users and developers. MDAnalysis maintains two types of documentation: the [User Guide]({{ site.docs.userguide.url }}) and the [API Reference]({{ site.docs.mdanalysis.url }}/stable/index.html). ### User Guide - The [User Guide]({{ site.docs.userguide.url }}/stable/index.html) provides tutorials and explanatory content to help users install and learn MDAnalysis. You can contribute by updating unclear explanations, adding new tutorials or examples, or fixing outdated information. ### How to Get Started @@ -59,7 +55,6 @@ The [User Guide]({{ site.docs.userguide.url }}/stable/index.html) provides tutor - Check for open documentation-related issues in the [User Guide GitHub Issues]({{ site.docs.userguide.issues }}). ### API Reference - The [API reference]({{ site.docs.mdanalysis.url }}/stable/index.html) is **automatically generated** from *docstrings* in the codebase. It provides a structured reference for developers working with MDAnalysis. You can contribute by improving *docstrings* for functions, classes, and modules or updating outdated documentation. To get started: @@ -67,13 +62,53 @@ To get started: - Follow the [API Documentation Contribution Guide]({{ site.docs.userguide.url }}/stable/contributing_code.html#working-with-mdanalysis-docs). - Browse open API documentation issues in [GitHub Issues]({{ site.github.issues }}). +## Mentoring & Outreach Programs +MDAnalysis actively participates in various mentoring and outreach programs **to help students, researchers, and early-career contributors gain experience in open-source development and scientific software**. Through these programs, participants receive mentorship, contribute to real-world projects, and develop valuable skills in computational science and software engineering. + +### Available Programs +We have been involved in several mentoring initiatives: + +- **[Google Summer of Code (GSoC)](https://summerofcode.withgoogle.com/)** \ + A global, remote program where students contribute to open-source projects under mentorship, enhancing their programming skills while engaging with the open-source community. + +- **[Google Season of Docs](https://developers.google.com/season-of-docs)** \ + A program that connects technical writers with open-source projects to improve documentation quality and accessibility. + +- **[Outreachy](https://www.outreachy.org/)** \ + A diversity-focused program offering paid remote internships to individuals underrepresented in tech, providing opportunities to contribute to open-source software. + +- **[Station1 Frontiers Fellowship](https://www.station1.org/sff)** \ + A unique research and internship program designed for students in science and technology, promoting inclusive and socially impactful research. + +- **[CompChemURG](https://www.bindingsites.co.uk/home)** \ + A mentoring initiative focused on computational chemistry, supporting undergraduates and early-career researchers in gaining expertise in the field. + +Many of our [core developers][] started through these programs — consider joining and becoming part of the MDAnalysis community! + +### Upcoming Opportunities + +Applications for [Google Summer of Code 2025][] are open! If you're interested in participating, check out our project ideas and application guidelines. + +For additional updates on upcoming events, visit our [Community]({{ site.baseurl }}/pages/community/) page. + +### Past GSoC + +MDAnalysis has participated in Google Summer of Code for several years, mentoring students on a variety of open-source projects. Explore our past projects: + +- [GSoC 2024][] +- [GSoC 2023][] +- [GSoC 2022][] + ## Other Contributions If you are interested in contributing in other ways, such as improving the website or blog, you can refer to the [README file][] in the [Website Repository][]. While the website is already maintained by the MDAnalysis team, minor fixes and updates are always welcome. If you'd like to write a **blog post**, feel free to reach out via the [Community]({{ site.baseurl }}/pages/community/) page. +[core developers]: https://github.com/orgs/MDAnalysis/teams/coredevs/members [Website Repository]: https://github.com/MDAnalysis/MDAnalysis.github.io [README file]: https://github.com/namiroues/MDAnalysis.github.io/blob/master/README.md - - +[Google Summer of Code 2025]: https://www.mdanalysis.org/2025/02/28/gsoc2025/ +[GSoC 2024]: https://www.mdanalysis.org/2024/02/27/gsoc2024/ +[GSoC 2023]: https://www.mdanalysis.org/2023/02/22/gsoc2023/ +[GSoC 2022]: https://www.mdanalysis.org/2022/03/07/gsoc2022/ From 99786a30b2d10dbf2025f59a29b9288eacce28f1 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Tue, 18 Mar 2025 21:05:11 +0000 Subject: [PATCH 09/14] address PR review comments --- pages/contribute.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/pages/contribute.md b/pages/contribute.md index 3da6d59e..6dc7d184 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -6,7 +6,9 @@ order: 6 MDAnalysis is an open-source project that welcomes and encourages contributions from the community. Whether you're a developer, documentation writer, or interested in improving the website, there are many ways to get involved. -You can contribute by **developing new features, fixing bugs, improving documentation, enhancing tutorials, contributing to MDAKits, improving the website, or engaging in discussions**. Contributions also extend to our **mentoring and outreach programs**, where participants gain hands-on experience in open-source development and scientific software. +You can contribute by **developing new features, fixing bugs, improving documentation, enhancing tutorials, contributing to MDAKits, improving the website, or engaging in discussions**. + +Contributions also extend to our **mentoring and outreach programs**, where participants gain hands-on experience in open-source development and scientific software. You can also contribute by **mentoring new contributors**, helping them navigate MDAnalysis, review their work, and share best practices. If you're new, you can start by participating in community conversations and mentoring programs. For more information on how you can participate, check out the [Community]({{ site.baseurl }}/pages/community/) and [Events]({{ site.baseurl }}/pages/events/) pages. @@ -63,7 +65,7 @@ To get started: - Browse open API documentation issues in [GitHub Issues]({{ site.github.issues }}). ## Mentoring & Outreach Programs -MDAnalysis actively participates in various mentoring and outreach programs **to help students, researchers, and early-career contributors gain experience in open-source development and scientific software**. Through these programs, participants receive mentorship, contribute to real-world projects, and develop valuable skills in computational science and software engineering. +MDAnalysis has actively participated in various mentoring and outreach programs **to help students, researchers, and early-career contributors gain experience in open-source development and scientific software**. Through these programs, participants receive mentorship, contribute to real-world projects, and develop valuable skills in computational science and software engineering. ### Available Programs We have been involved in several mentoring initiatives: @@ -103,7 +105,7 @@ MDAnalysis has participated in Google Summer of Code for several years, mentorin If you are interested in contributing in other ways, such as improving the website or blog, you can refer to the [README file][] in the [Website Repository][]. While the website is already maintained by the MDAnalysis team, minor fixes and updates are always welcome. -If you'd like to write a **blog post**, feel free to reach out via the [Community]({{ site.baseurl }}/pages/community/) page. +If you'd like to write a **blog post**, we welcome contributions that document your experience with MDAnalysis—whether it's learning the software, participating in a UGM, or working on a project. Feel free to reach out via the [Community]({{ site.baseurl }}/pages/community/) page for guidance on submitting a post. [core developers]: https://github.com/orgs/MDAnalysis/teams/coredevs/members [Website Repository]: https://github.com/MDAnalysis/MDAnalysis.github.io From 7e1f993ea29578ab0aa98210895c9c25251e9982 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Thu, 20 Mar 2025 09:43:58 +0000 Subject: [PATCH 10/14] address PR review comments --- pages/contribute.md | 30 +++++++++++++++++++++++++----- 1 file changed, 25 insertions(+), 5 deletions(-) diff --git a/pages/contribute.md b/pages/contribute.md index 6dc7d184..bb26758f 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -12,6 +12,12 @@ Contributions also extend to our **mentoring and outreach programs**, where part If you're new, you can start by participating in community conversations and mentoring programs. For more information on how you can participate, check out the [Community]({{ site.baseurl }}/pages/community/) and [Events]({{ site.baseurl }}/pages/events/) pages. +The [MDAnalysis Project][] hosts several open-source repositories beyond the main library and MDAKits. You are welcome to contribute to any of them! Each repository typically has a `CONTRIBUTING.md` file to help you get started. If you’re unsure where to begin, you can: + +- Check the repository’s issue tracker for open tasks. +- Submit a pull request for improvements. +- Contact maintainers via [GitHub discussions][] or MDAnalysis [Community]({{ site.baseurl }}/pages/community/) forums. + This page provides an overview of how you can contribute to the [Codebase](#contributing-to-the-codebase), [MDAKits](#contributing-to-mdakits), [Documentation](#contributing-to-the-documentation), or [Mentoring & Outreach Programs](#mentoring--outreach-programs). ## Contributing to the Codebase @@ -89,17 +95,22 @@ Many of our [core developers][] started through these programs — consider ### Upcoming Opportunities -Applications for [Google Summer of Code 2025][] are open! If you're interested in participating, check out our project ideas and application guidelines. +Stay informed about upcoming opportunities such as **Google Summer of Code, Outreachy, and other mentoring programs**. For the latest announcements, deadlines, and project ideas, check out our [blog]({{ site.baseurl }}/blog/) where we share updates on participation and application guidelines. -For additional updates on upcoming events, visit our [Community]({{ site.baseurl }}/pages/community/) page. - -### Past GSoC +### GSoC MDAnalysis has participated in Google Summer of Code for several years, mentoring students on a variety of open-source projects. Explore our past projects: +- [GSoC 2025][] - [GSoC 2024][] - [GSoC 2023][] - [GSoC 2022][] +- [GSoC 2021][] +- [GSoC 2020][] +- [GSoC 2019][] +- [GSoC 2018][] +- [GSoC 2017][] +- [GSoC 2016][] ## Other Contributions @@ -107,10 +118,19 @@ If you are interested in contributing in other ways, such as improving the websi If you'd like to write a **blog post**, we welcome contributions that document your experience with MDAnalysis—whether it's learning the software, participating in a UGM, or working on a project. Feel free to reach out via the [Community]({{ site.baseurl }}/pages/community/) page for guidance on submitting a post. +[MDAnalysis Project]: https://github.com/MDAnalysis/ +[GitHub discussions]: https://github.com/MDAnalysis/mdanalysis/discussions [core developers]: https://github.com/orgs/MDAnalysis/teams/coredevs/members [Website Repository]: https://github.com/MDAnalysis/MDAnalysis.github.io [README file]: https://github.com/namiroues/MDAnalysis.github.io/blob/master/README.md -[Google Summer of Code 2025]: https://www.mdanalysis.org/2025/02/28/gsoc2025/ +[GSoC 2025]: https://www.mdanalysis.org/2025/02/28/gsoc2025/ [GSoC 2024]: https://www.mdanalysis.org/2024/02/27/gsoc2024/ [GSoC 2023]: https://www.mdanalysis.org/2023/02/22/gsoc2023/ [GSoC 2022]: https://www.mdanalysis.org/2022/03/07/gsoc2022/ +[GSoC 2021]: https://www.mdanalysis.org/2021/03/09/gsoc2021/ +[GSoC 2020]: https://www.mdanalysis.org/2020/02/22/gsoc2020/ +[GSoC 2019]: https://www.mdanalysis.org/2019/03/04/gsoc2019/ +[GSoC 2018]: https://www.mdanalysis.org/2018/02/14/gsoc2018/ +[GSoC 2017]: https://www.mdanalysis.org/2017/03/02/gsoc2017/ +[GSoC 2016]: https://www.mdanalysis.org/2016/04/26/gsoc/ + From 18728ca080dd9d80833fa33dd4898882c3326081 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 21 Mar 2025 17:34:09 +0000 Subject: [PATCH 11/14] address PR review comments --- pages/contribute.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/pages/contribute.md b/pages/contribute.md index bb26758f..81fe6aa3 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -73,7 +73,10 @@ To get started: ## Mentoring & Outreach Programs MDAnalysis has actively participated in various mentoring and outreach programs **to help students, researchers, and early-career contributors gain experience in open-source development and scientific software**. Through these programs, participants receive mentorship, contribute to real-world projects, and develop valuable skills in computational science and software engineering. -### Available Programs +### Stay informed + +Stay informed about upcoming opportunities such as **Google Summer of Code, Outreachy, and other mentoring programs**. For the latest announcements, deadlines, and project ideas, check out our [blog]({{ site.baseurl }}/blog/) where we share updates on participation and application guidelines. + We have been involved in several mentoring initiatives: - **[Google Summer of Code (GSoC)](https://summerofcode.withgoogle.com/)** \ @@ -93,10 +96,6 @@ We have been involved in several mentoring initiatives: Many of our [core developers][] started through these programs — consider joining and becoming part of the MDAnalysis community! -### Upcoming Opportunities - -Stay informed about upcoming opportunities such as **Google Summer of Code, Outreachy, and other mentoring programs**. For the latest announcements, deadlines, and project ideas, check out our [blog]({{ site.baseurl }}/blog/) where we share updates on participation and application guidelines. - ### GSoC MDAnalysis has participated in Google Summer of Code for several years, mentoring students on a variety of open-source projects. Explore our past projects: From 12dfbd38efa88f43f9619c5ef3b5590432479369 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 21 Mar 2025 19:13:47 +0000 Subject: [PATCH 12/14] address PR review comments --- pages/contribute.md | 44 +++++++++++++++++--------------------------- 1 file changed, 17 insertions(+), 27 deletions(-) diff --git a/pages/contribute.md b/pages/contribute.md index 81fe6aa3..b5a65342 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -30,7 +30,7 @@ MDAnalysis is developed and maintained in the [MDAnalysis Main Code Repository]( - The [API documentation]({{ site.docs.mdanalysis.url }}/stable/index.html), generated from in-code docstrings. - [Open issues]({{ site.github.issues }}), where contributions such as bug fixes and feature implementations are tracked. -### How to Get Started +#### How to Get Started - Read the [Contributing to the Main Codebase]({{ site.docs.userguide.url }}/stable/contributing_code.html#working-with-mdanalysis-code) guide, which outlines all the necessary steps. - Browse [GitHub Issues]({{ site.github.issues }}) to find open tasks. Look for "good first issue" if you're a beginner. You can also report bugs or suggest improvements there. - Follow best practices, including @@ -43,7 +43,8 @@ MDAnalysis is developed and maintained in the [MDAnalysis Main Code Repository]( ### MDAKits Registry The [MDAKits Registry]({{ site.mdakits.registry }}) lists active projects contributed by the community. These projects cover various applications, such as enhanced trajectory analysis, molecular simulations, and integration with machine learning frameworks. -### How to Get Started +#### How to Get Started + - Explore existing MDAKits in the [MDAKits Registry]({{ site.mdakits.registry }}) to find projects that match your interests. Each entry includes functionality, installation instructions, and contribution guidelines. - Find open issues in [MDAKits GitHub Issues]({{ site.mdakits.issues }}). - Propose a new MDAKit by following the [MDAKits Guide]({{ site.mdakits.guide }}). @@ -57,7 +58,7 @@ Good documentation is essential to making MDAnalysis accessible to users and dev ### User Guide The [User Guide]({{ site.docs.userguide.url }}/stable/index.html) provides tutorials and explanatory content to help users install and learn MDAnalysis. You can contribute by updating unclear explanations, adding new tutorials or examples, or fixing outdated information. -### How to Get Started +#### How to Get Started - Work on the [User Guide Repository]({{ site.docs.userguide.repo }}). - Follow the [Contributing to the User Guide]({{ site.docs.userguide.url }}/stable/contributing_docs.html). - Check for open documentation-related issues in the [User Guide GitHub Issues]({{ site.docs.userguide.issues }}). @@ -65,7 +66,7 @@ The [User Guide]({{ site.docs.userguide.url }}/stable/index.html) provides tutor ### API Reference The [API reference]({{ site.docs.mdanalysis.url }}/stable/index.html) is **automatically generated** from *docstrings* in the codebase. It provides a structured reference for developers working with MDAnalysis. You can contribute by improving *docstrings* for functions, classes, and modules or updating outdated documentation. -To get started: +#### How to Get Started - Work on the [MDAnalysis Main Code Repository]({{ site.github.repo }}). - Follow the [API Documentation Contribution Guide]({{ site.docs.userguide.url }}/stable/contributing_code.html#working-with-mdanalysis-docs). - Browse open API documentation issues in [GitHub Issues]({{ site.github.issues }}). @@ -94,42 +95,31 @@ We have been involved in several mentoring initiatives: - **[CompChemURG](https://www.bindingsites.co.uk/home)** \ A mentoring initiative focused on computational chemistry, supporting undergraduates and early-career researchers in gaining expertise in the field. -Many of our [core developers][] started through these programs — consider joining and becoming part of the MDAnalysis community! +Many of our [core developers]({{ site.baseurl }}/governance/#mdanalysis-core-developers) started through these programs — consider joining and becoming part of the MDAnalysis community! ### GSoC MDAnalysis has participated in Google Summer of Code for several years, mentoring students on a variety of open-source projects. Explore our past projects: -- [GSoC 2025][] -- [GSoC 2024][] -- [GSoC 2023][] -- [GSoC 2022][] -- [GSoC 2021][] -- [GSoC 2020][] -- [GSoC 2019][] -- [GSoC 2018][] -- [GSoC 2017][] -- [GSoC 2016][] +- [GSoC 2025]({% post_url 2025-02-28-gsoc2025 %}) +- [GSoC 2024]({% post_url 2024-02-27-gsoc2024 %}) +- [GSoC 2023]({% post_url 2023-02-22-gsoc2023 %}) +- [GSoC 2022]({% post_url 2022-03-07-gsoc2022 %}) +- [GSoC 2021]({% post_url 2021-03-09-gsoc2021 %}) +- [GSoC 2020]({% post_url 2020-02-22-gsoc2020 %}) +- [GSoC 2019]({% post_url 2019-03-04-gsoc2019 %}) +- [GSoC 2018]({% post_url 2018-02-14-gsoc2018 %}) +- [GSoC 2017]({% post_url 2017-03-02-gsoc2017 %}) +- [GSoC 2016]({% post_url 2016-04-26-gsoc %}) ## Other Contributions -If you are interested in contributing in other ways, such as improving the website or blog, you can refer to the [README file][] in the [Website Repository][]. While the website is already maintained by the MDAnalysis team, minor fixes and updates are always welcome. +If you are interested in contributing in other ways, such as improving the website or blog, you can refer to the [README file][] in the [Website Repository][]. While the website is already maintained by the MDAnalysis team, any fixes and updates are always welcome. If you'd like to write a **blog post**, we welcome contributions that document your experience with MDAnalysis—whether it's learning the software, participating in a UGM, or working on a project. Feel free to reach out via the [Community]({{ site.baseurl }}/pages/community/) page for guidance on submitting a post. [MDAnalysis Project]: https://github.com/MDAnalysis/ [GitHub discussions]: https://github.com/MDAnalysis/mdanalysis/discussions -[core developers]: https://github.com/orgs/MDAnalysis/teams/coredevs/members [Website Repository]: https://github.com/MDAnalysis/MDAnalysis.github.io [README file]: https://github.com/namiroues/MDAnalysis.github.io/blob/master/README.md -[GSoC 2025]: https://www.mdanalysis.org/2025/02/28/gsoc2025/ -[GSoC 2024]: https://www.mdanalysis.org/2024/02/27/gsoc2024/ -[GSoC 2023]: https://www.mdanalysis.org/2023/02/22/gsoc2023/ -[GSoC 2022]: https://www.mdanalysis.org/2022/03/07/gsoc2022/ -[GSoC 2021]: https://www.mdanalysis.org/2021/03/09/gsoc2021/ -[GSoC 2020]: https://www.mdanalysis.org/2020/02/22/gsoc2020/ -[GSoC 2019]: https://www.mdanalysis.org/2019/03/04/gsoc2019/ -[GSoC 2018]: https://www.mdanalysis.org/2018/02/14/gsoc2018/ -[GSoC 2017]: https://www.mdanalysis.org/2017/03/02/gsoc2017/ -[GSoC 2016]: https://www.mdanalysis.org/2016/04/26/gsoc/ From 7e792a9f3c1aec2da43898471cfd5125b129a30b Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Sun, 23 Mar 2025 09:44:11 +0000 Subject: [PATCH 13/14] address PR review comments --- pages/contribute.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/contribute.md b/pages/contribute.md index b5a65342..8c276232 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -45,10 +45,10 @@ The [MDAKits Registry]({{ site.mdakits.registry }}) lists active projects contri #### How to Get Started -- Explore existing MDAKits in the [MDAKits Registry]({{ site.mdakits.registry }}) to find projects that match your interests. Each entry includes functionality, installation instructions, and contribution guidelines. - Find open issues in [MDAKits GitHub Issues]({{ site.mdakits.issues }}). - Propose a new MDAKit by following the [MDAKits Guide]({{ site.mdakits.guide }}). - Contribute to an existing MDAKit by collaborating with maintainers to improve functionality, fix bugs, or add new features. +- Explore existing MDAKits in the [MDAKits Registry]({{ site.mdakits.registry }}) to find projects that match your interests. Each entry includes functionality, installation instructions, and contribution guidelines. MDAKits follow MDAnalysis coding standards but operate independently. Contributions to these projects are highly encouraged and help expand the MDAnalysis ecosystem. From 2b345939d7c0a9f55c2924a24c4f337b1f2fbef3 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Tue, 25 Mar 2025 19:48:33 +0000 Subject: [PATCH 14/14] address PR review comments --- pages/contribute.md | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/pages/contribute.md b/pages/contribute.md index 8c276232..1ed24c0f 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -44,7 +44,6 @@ MDAnalysis is developed and maintained in the [MDAnalysis Main Code Repository]( The [MDAKits Registry]({{ site.mdakits.registry }}) lists active projects contributed by the community. These projects cover various applications, such as enhanced trajectory analysis, molecular simulations, and integration with machine learning frameworks. #### How to Get Started - - Find open issues in [MDAKits GitHub Issues]({{ site.mdakits.issues }}). - Propose a new MDAKit by following the [MDAKits Guide]({{ site.mdakits.guide }}). - Contribute to an existing MDAKit by collaborating with maintainers to improve functionality, fix bugs, or add new features. @@ -75,8 +74,7 @@ The [API reference]({{ site.docs.mdanalysis.url }}/stable/index.html) is **autom MDAnalysis has actively participated in various mentoring and outreach programs **to help students, researchers, and early-career contributors gain experience in open-source development and scientific software**. Through these programs, participants receive mentorship, contribute to real-world projects, and develop valuable skills in computational science and software engineering. ### Stay informed - -Stay informed about upcoming opportunities such as **Google Summer of Code, Outreachy, and other mentoring programs**. For the latest announcements, deadlines, and project ideas, check out our [blog]({{ site.baseurl }}/blog/) where we share updates on participation and application guidelines. +For the latest announcements, deadlines, and project ideas, check out our [blog]({{ site.baseurl }}/blog/) where we share updates on participation and application guidelines. We have been involved in several mentoring initiatives: @@ -98,7 +96,6 @@ We have been involved in several mentoring initiatives: Many of our [core developers]({{ site.baseurl }}/governance/#mdanalysis-core-developers) started through these programs — consider joining and becoming part of the MDAnalysis community! ### GSoC - MDAnalysis has participated in Google Summer of Code for several years, mentoring students on a variety of open-source projects. Explore our past projects: - [GSoC 2025]({% post_url 2025-02-28-gsoc2025 %}) @@ -113,10 +110,9 @@ MDAnalysis has participated in Google Summer of Code for several years, mentorin - [GSoC 2016]({% post_url 2016-04-26-gsoc %}) ## Other Contributions +If you are interested in contributing in other ways, such as writing a **blog post**, we welcome contributions that document your experience with MDAnalysis — whether it's learning the software, participating in a UGM, or working on a project. Feel free to reach out via the [Community]({{ site.baseurl }}/pages/community/) page for guidance on submitting a post. -If you are interested in contributing in other ways, such as improving the website or blog, you can refer to the [README file][] in the [Website Repository][]. While the website is already maintained by the MDAnalysis team, any fixes and updates are always welcome. - -If you'd like to write a **blog post**, we welcome contributions that document your experience with MDAnalysis—whether it's learning the software, participating in a UGM, or working on a project. Feel free to reach out via the [Community]({{ site.baseurl }}/pages/community/) page for guidance on submitting a post. +If you are interested in improving our website, you can refer to the [README file][] in the [Website Repository][]. While the website is already maintained by the MDAnalysis team, any fixes and updates are always welcome. [MDAnalysis Project]: https://github.com/MDAnalysis/ [GitHub discussions]: https://github.com/MDAnalysis/mdanalysis/discussions