From 3bb4a039f008f5f4bdf2ac4ca8a6aef8bc9f2328 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 4 Apr 2025 09:25:44 +0100 Subject: [PATCH 1/7] reorder pages in sidebar --- pages/citations.md | 2 +- pages/contribute.md | 2 +- pages/events.md | 2 +- pages/learning_MDAnalysis.md | 2 +- pages/mdakits.md | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/pages/citations.md b/pages/citations.md index 1a83683d..774db111 100644 --- a/pages/citations.md +++ b/pages/citations.md @@ -1,7 +1,7 @@ --- layout: page title: Citations -order: 9 +order: 8 --- MDAnalysis and the included algorithms are scientific software that diff --git a/pages/contribute.md b/pages/contribute.md index 1ed24c0f..d1b34bd9 100644 --- a/pages/contribute.md +++ b/pages/contribute.md @@ -1,7 +1,7 @@ --- layout: page title: Contribute -order: 6 +order: 5 --- 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. diff --git a/pages/events.md b/pages/events.md index 4fa68e53..8a99ccbb 100644 --- a/pages/events.md +++ b/pages/events.md @@ -1,7 +1,7 @@ --- layout: page title: Events -order: 4 +order: 7 --- MDAnalysis hosts and participates in various **community-driven events, user group meetings (UGMs), workshops, and hackathons** to foster collaboration and learning. diff --git a/pages/learning_MDAnalysis.md b/pages/learning_MDAnalysis.md index 073c5974..baa4f8d0 100644 --- a/pages/learning_MDAnalysis.md +++ b/pages/learning_MDAnalysis.md @@ -1,7 +1,7 @@ --- layout: page title: Learning MDAnalysis -order: 3 +order: 2 --- MDAnalysis is a powerful Python library for analyzing MD simulations. While primarily designed to help you build custom analysis tools, it also supports interactive data exploration in environments like [IPython](http://ipython.org/) and [Jupyter notebooks](https://jupyter.org/), especially when combined with [pandas](http://pandas.pydata.org/). This makes MDAnalysis an excellent choice for rapid prototyping and exploratory analysis. diff --git a/pages/mdakits.md b/pages/mdakits.md index 6c432661..dccf3cb6 100644 --- a/pages/mdakits.md +++ b/pages/mdakits.md @@ -1,7 +1,7 @@ --- layout: page title: MDAKits and MDA-based tools -order: 5 +order: 4 --- MDAnalysis is developed with extensibility in mind, allowing From d43d9351b6fd38142b13b97a4dbf8ca25fca432a Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Sat, 5 Apr 2025 09:43:58 +0100 Subject: [PATCH 2/7] reorder pages in sb- rename blog to news - move core pages to top level --- _posts/2023-12-21-github-discussions.md | 2 +- about.md | 8 ++++---- blog/index.html | 4 ++-- pages/citations.md => citations.md | 2 +- pages/community.md => community.md | 8 ++++---- pages/contribute.md => contribute.md | 10 +++++----- pages/documentation.md => documentation.md | 2 +- pages/events.md => events.md | 6 +++--- .../getting_started.md => getting_started.md | 2 +- index.md | 20 +++++++++---------- ...ng_MDAnalysis.md => learning_MDAnalysis.md | 8 ++++---- pages/mdakits.md => mdakits.md | 4 ++-- conduct.md => pages/conduct.md | 0 mission.md => pages/mission.md | 0 pages/privacy.md => privacy.md | 2 +- pages/team.md => team.md | 2 +- 16 files changed, 40 insertions(+), 40 deletions(-) rename pages/citations.md => citations.md (99%) rename pages/community.md => community.md (85%) rename pages/contribute.md => contribute.md (96%) rename pages/documentation.md => documentation.md (99%) rename pages/events.md => events.md (97%) rename pages/getting_started.md => getting_started.md (99%) rename pages/learning_MDAnalysis.md => learning_MDAnalysis.md (95%) rename pages/mdakits.md => mdakits.md (99%) rename conduct.md => pages/conduct.md (100%) rename mission.md => pages/mission.md (100%) rename pages/privacy.md => privacy.md (99%) rename pages/team.md => team.md (99%) diff --git a/_posts/2023-12-21-github-discussions.md b/_posts/2023-12-21-github-discussions.md index 9978a473..574d328a 100644 --- a/_posts/2023-12-21-github-discussions.md +++ b/_posts/2023-12-21-github-discussions.md @@ -22,7 +22,7 @@ The mailing lists will remain open for a bit longer to finish off open discussio \- Rocco Meli, on behalf of the [MDAnalysis Team][] -[MDAnalysis Team]: {{ site.url }}{% link pages/team.md %} +[MDAnalysis Team]: {{ site.url }}{% link team.md %} [GitHub Discussions]: https://github.com/MDAnalysis/mdanalysis/discussions [Q&A]: https://github.com/MDAnalysis/mdanalysis/discussions/categories/q-a [mdnalysis-devel]: https://groups.google.com/g/mdnalysis-devel diff --git a/about.md b/about.md index 865056fb..29d048fe 100644 --- a/about.md +++ b/about.md @@ -1,7 +1,7 @@ --- layout: page title: About MDAnalysis -order: 10 +order: 1 --- diff --git a/pages/citations.md b/citations.md similarity index 99% rename from pages/citations.md rename to citations.md index 774db111..7a76fabd 100644 --- a/pages/citations.md +++ b/citations.md @@ -1,7 +1,7 @@ --- layout: page title: Citations -order: 8 +order: 11 --- MDAnalysis and the included algorithms are scientific software that diff --git a/pages/community.md b/community.md similarity index 85% rename from pages/community.md rename to community.md index 37ad7821..85eb4024 100644 --- a/pages/community.md +++ b/community.md @@ -1,7 +1,7 @@ --- layout: page title: Community -order: 5 +order: 7 --- MDAnalysis is developed and maintained as a freely available, open-source project by a global community of scientists. Our community adheres to our [Code of Conduct]({{ site.baseurl }}/pages/conduct/) and welcomes everyone to participate—whether through GitHub Discussions, issue reports, or code contributions. @@ -11,7 +11,7 @@ in a file called `AUTHORS` in each source code repository and in the list of contributions; for example, see the [`AUTHORS` file for mdanalysis](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/AUTHORS) and the [contributors for mdanalysis](https://github.com/MDAnalysis/mdanalysis/graphs/contributors). -MDAnalysis is widely used in scientific research and is described in various [academic publications]({{site.baseurl}}/pages/citations/). It also serves as the foundation for several other [molecular dynamics tools]({{site.baseurl}}/pages/mdakits/). +MDAnalysis is widely used in scientific research and is described in various [academic publications]({{site.baseurl}}/pages/citations/). It also serves as the foundation for several other [molecular dynamics tools]({{site.baseurl}}/mdakits/). This page provides an overview of **how you can engage with the MDAnalysis community, where to seek support, and how to participate**. @@ -19,7 +19,7 @@ This page provides an overview of **how you can engage with the MDAnalysis commu Follow our official channels for news, updates, and major announcements: -- [Blog]({{ site.baseurl }}/blog/) — News, development highlights, tutorials, and releases. +- [News]({{ site.baseurl }}/blog/) — News, development highlights, tutorials, and releases. - [LinkedIn](https://www.linkedin.com/company/mdanalysis/) — Professional networking, project updates, event announcements, and industry connections. - [Bluesky](https://bsky.app/profile/mdanalysis.bsky.social) — Community-driven discussions and project insights. @@ -33,7 +33,7 @@ Need help with MDAnalysis? Choose the right platform for your needs: ## Contribute -If you are interested in contributing to MDAnalysis, visit our [Contribute]({{ site.baseurl }}/pages/contribute/) page for guidelines on how to get involved. Whether it’s improving documentation, fixing bugs, or adding new features, every contribution helps strengthen the project and its community. +If you are interested in contributing to MDAnalysis, visit our [Contribute]({{ site.baseurl }}/contribute/) page for guidelines on how to get involved. Whether it’s improving documentation, fixing bugs, or adding new features, every contribution helps strengthen the project and its community. diff --git a/pages/contribute.md b/contribute.md similarity index 96% rename from pages/contribute.md rename to contribute.md index d1b34bd9..4180c530 100644 --- a/pages/contribute.md +++ b/contribute.md @@ -1,7 +1,7 @@ --- layout: page title: Contribute -order: 5 +order: 8 --- 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. @@ -10,13 +10,13 @@ You can contribute by **developing new features, fixing bugs, improving document 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. +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 }}/community/) and [Events]({{ site.baseurl }}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. +- Contact maintainers via [GitHub discussions][] or MDAnalysis [Community]({{ site.baseurl }}/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). @@ -74,7 +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 -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 [News]({{ site.baseurl }}/blog/) where we share updates on participation and application guidelines. We have been involved in several mentoring initiatives: @@ -110,7 +110,7 @@ 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 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 }}/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. diff --git a/pages/documentation.md b/documentation.md similarity index 99% rename from pages/documentation.md rename to documentation.md index 6cf96629..a2653e88 100644 --- a/pages/documentation.md +++ b/documentation.md @@ -1,7 +1,7 @@ --- layout: page title: Documentation -order: 3 +order: 5 --- The MDAnalysis library (`import MDAnalysis`) is open-source code, 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. diff --git a/pages/events.md b/events.md similarity index 97% rename from pages/events.md rename to events.md index 8a99ccbb..1edb151e 100644 --- a/pages/events.md +++ b/events.md @@ -1,16 +1,16 @@ --- layout: page title: Events -order: 7 +order: 6 --- MDAnalysis hosts and participates in various **community-driven events, user group meetings (UGMs), workshops, and hackathons** to foster collaboration and learning. This page provides information on **upcoming and past events**, including **UGMs, workshops, and talks**. Whether you're a developer, researcher, or new to the field, these events provide opportunities to engage with and contribute to the MDAnalysis ecosystem. -For the latest discussions, **join the MDAnalysis community channels** by visiting our [Community]({{ site.baseurl }}/pages/community/) page. +For the latest discussions, **join the MDAnalysis community channels** by visiting our [Community]({{ site.baseurl }}/community/) page. -For mentoring programs and outreach opportunities, please visit the [Contribute]({{ site.baseurl }}/pages/contribute/) page. +For mentoring programs and outreach opportunities, please visit the [Contribute]({{ site.baseurl }}/contribute/) page. -- [Community]({{ site.baseurl }}/pages/community/) — Get involved, ask questions, and collaborate. -- [Blog]({{ site.baseurl }}/blog) — Stay updated with development news and community highlights. -- [Events]({{ site.baseurl }}/pages/events/) — Join workshops, conferences, and mentoring programs. +- [Community]({{ site.baseurl }}/community/) — Get involved, ask questions, and collaborate. +- [News]({{ site.baseurl }}/blog) — Stay updated with development news and community highlights. +- [Events]({{ site.baseurl }}/events/) — Join workshops, conferences, and mentoring programs. ## Contributing Want to contribute to MDAnalysis? Here’s how: -- [Contribute]({{ site.baseurl }}/pages/contribute/) — Learn how to help improve MDAnalysis through coding, documentation, or discussions. -- [MDAKits and MDA-based tools]({{ site.baseurl }}/pages/mdakits/) — Build and extend MDAnalysis with MDAKits. +- [Contribute]({{ site.baseurl }}/contribute/) — Learn how to help improve MDAnalysis through coding, documentation, or discussions. +- [MDAKits and MDA-based tools]({{ site.baseurl }}/mdakits/) — Build and extend MDAnalysis with MDAKits. - [Support MDAnalysis financially](#funding--support) — Donate via NumFOCUS to sustain the project. ## Citing MDAnalysis -If you use MDAnalysis in your research, please cite it appropriately and consider displaying our MDAnalysis badge in your projects. All citation formats and badge instructions are available in our [Citation guidelines]({{ site.baseurl }}/pages/citations/). +If you use MDAnalysis in your research, please cite it appropriately and consider displaying our MDAnalysis badge in your projects. All citation formats and badge instructions are available in our [Citation guidelines]({{ site.baseurl }}/citations/). -Additionally, consider displaying our badge in your projects that use MDAnalysis. We provide several [embedding markup examples]({{ site.baseurl }}/pages/citations/#powered-by-mdanalysis). +Additionally, consider displaying our badge in your projects that use MDAnalysis. We provide several [embedding markup examples]({{ site.baseurl }}/citations/#powered-by-mdanalysis). [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org) diff --git a/pages/learning_MDAnalysis.md b/learning_MDAnalysis.md similarity index 95% rename from pages/learning_MDAnalysis.md rename to learning_MDAnalysis.md index baa4f8d0..cf7d8af0 100644 --- a/pages/learning_MDAnalysis.md +++ b/learning_MDAnalysis.md @@ -1,7 +1,7 @@ --- layout: page title: Learning MDAnalysis -order: 2 +order: 4 --- MDAnalysis is a powerful Python library for analyzing MD simulations. While primarily designed to help you build custom analysis tools, it also supports interactive data exploration in environments like [IPython](http://ipython.org/) and [Jupyter notebooks](https://jupyter.org/), especially when combined with [pandas](http://pandas.pydata.org/). This makes MDAnalysis an excellent choice for rapid prototyping and exploratory analysis. @@ -13,7 +13,7 @@ Whether you're new to MDAnalysis or looking to deepen your expertise, this page ## Step-by-Step Guide to Learning MDAnalysis 1. **Install MDAnalysis** - Follow the instructions in [Getting Started]({{ site.baseurl }}/pages/getting_started/) to install MDAnalysis. + Follow the instructions in [Getting Started]({{ site.baseurl }}/getting_started/) to install MDAnalysis. 2. **Quickstart Tutorial** Begin with the [{{ site.docs.quickstart.name }}]({{ site.docs.quickstart.url }}) tutorial to write and run your first MDAnalysis script. @@ -25,12 +25,12 @@ Whether you're new to MDAnalysis or looking to deepen your expertise, this page Browse additional learning resources and code examples in our Tutorials repository. 5. **Full Documentation** - For in-depth technical details, visit the [Documentation]({{ site.baseurl }}/pages/documentation/) page. + For in-depth technical details, visit the [Documentation]({{ site.baseurl }}/documentation/) page. 6. **Watch MDAnalysis videos** Learn from conference talks, workshops, and webinars presented by core developers. Explore the [Videos](#videos) section below and our [YouTube channel](https://www.youtube.com/channel/UC3TCuK-z_bJNdwWCvsH9D3Q). -If you need help, check out our [Community]({{ site.baseurl }}/pages/community/) page. +If you need help, check out our [Community]({{ site.baseurl }}/community/) page. ## Videos diff --git a/pages/mdakits.md b/mdakits.md similarity index 99% rename from pages/mdakits.md rename to mdakits.md index dccf3cb6..4a822331 100644 --- a/pages/mdakits.md +++ b/mdakits.md @@ -1,7 +1,7 @@ --- layout: page -title: MDAKits and MDA-based tools -order: 4 +title: MDAKits +order: 10 --- MDAnalysis is developed with extensibility in mind, allowing diff --git a/conduct.md b/pages/conduct.md similarity index 100% rename from conduct.md rename to pages/conduct.md diff --git a/mission.md b/pages/mission.md similarity index 100% rename from mission.md rename to pages/mission.md diff --git a/pages/privacy.md b/privacy.md similarity index 99% rename from pages/privacy.md rename to privacy.md index a3f94317..332ad768 100644 --- a/pages/privacy.md +++ b/privacy.md @@ -1,7 +1,7 @@ --- layout: page title: Privacy Policy -order: 13 +order: 12 --- MDAnalysis is a [fiscally sponsored diff --git a/pages/team.md b/team.md similarity index 99% rename from pages/team.md rename to team.md index 46a3ac53..70e6b21a 100644 --- a/pages/team.md +++ b/team.md @@ -1,7 +1,7 @@ --- layout: page title: MDAnalysis team -order: 11 +order: 9 --- MDAnalysis is a community-driven project that is made possible through the efforts of many members who contribute in numerous and diverse ways, ranging from direct package development, maintenance, documentation, communication, and managerial responsibilities. On this page we list identified project roles and team members for each of those roles. We note that the listed roles on this page can differ significantly in scope and required effort. From b3fea3f6a11d50643fdbacc9e3cef9cefff9fa95 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Sat, 5 Apr 2025 09:59:55 +0100 Subject: [PATCH 3/7] fix capitalisation consistency and rename Blog to News pages --- _posts/2023-05-18-save-date-ugm2023.md | 4 ++-- _posts/2024-01-15-mda_events.md | 4 ++-- _posts/2024-09-11-mda_2024events.md | 4 ++-- team.md | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/_posts/2023-05-18-save-date-ugm2023.md b/_posts/2023-05-18-save-date-ugm2023.md index b9fa5187..6d1bc466 100644 --- a/_posts/2023-05-18-save-date-ugm2023.md +++ b/_posts/2023-05-18-save-date-ugm2023.md @@ -20,10 +20,10 @@ Whether you are a new MDAnalysis contributor, an MDAnalysis core developer, or a * Networking opportunities to foster new collaborations * Hackathon and other social outings -Additional details of the schedule and call for proposals will be communicated soon. In the meantime, save the date and keep an eye out for additional announcements on our [blog][blog] and [UGM website page][ugmPage], as well as on our [Twitter][twitter] and [LinkedIn][linkedin] accounts. +Additional details of the schedule and call for proposals will be communicated soon. In the meantime, save the date and keep an eye out for additional announcements on our [News] and [UGM website page][ugmPage], as well as on our [Twitter][twitter] and [LinkedIn][linkedin] accounts. [uniL]: https://www.ulisboa.pt/en/unidade-organica/faculty-sciences -[blog]: https://www.mdanalysis.org/blog/ +[News]: https://www.mdanalysis.org/blog/ [ugmPage]: https://www.mdanalysis.org/pages/ugm2023/ [twitter]: https://twitter.com/mdanalysis [linkedin]: https://www.linkedin.com/company/mdanalysis/ diff --git a/_posts/2024-01-15-mda_events.md b/_posts/2024-01-15-mda_events.md index a373bfbd..d4aec5df 100644 --- a/_posts/2024-01-15-mda_events.md +++ b/_posts/2024-01-15-mda_events.md @@ -46,10 +46,10 @@ Additional details about registration and a call for proposals will be communica More than 70 people joined us live on October 25, 2023 for a free online workshop, during which 4 instructors (@fiona-naughton, @ianmkenney, @micaela-matta, @richardjgowers) introduced the MDAnalysis package and demonstrated use cases through interactive tutorials; the [recording](https://www.youtube.com/watch?v=njzoNzOwR78) is now available on our [YouTube](https://www.youtube.com/@mdanalysis3040) channel. @micaela-matta led the first lecture/tutorial on the Basics of MDAnalysis, and @richardjgowers led a lecture/tutorial on positions, distances, and trajectories; all instructors helped answer participant questions throughout the workshop. Prior to the workshop, @ianmkenney answered participant questions during an optional installation troubleshooting block. All workshop materials and installation instructions are publicly available on the [MDAnalysis/MDAnalysisWorkshop2023](https://github.com/MDAnalysis/MDAnalysisWorkshop2023/) GitHub repository. -We will soon be announcing a series of additional workshops taking place in 2024. These workshops are planned to accommodate both beginner and more advanced MDAnalysis users across differing time zones. We are also working on some exciting collaborations to offer workshops on more specialized topics! Stay tuned for updates on our [blog][], [X][], and [LinkedIn][] pages. +We will soon be announcing a series of additional workshops taking place in 2024. These workshops are planned to accommodate both beginner and more advanced MDAnalysis users across differing time zones. We are also working on some exciting collaborations to offer workshops on more specialized topics! Stay tuned for updates on our [News][], [X][], and [LinkedIn][] pages. ![Workshop Instructors Present MDAnalysis Tutorial](/public/images/20231025_Online_Workshop.png) -[blog]: https://www.mdanalysis.org/blog/ +[News]: https://www.mdanalysis.org/blog/ [X]: https://twitter.com/mdanalysis [LinkedIn]: https://www.linkedin.com/company/mdanalysis/ diff --git a/_posts/2024-09-11-mda_2024events.md b/_posts/2024-09-11-mda_2024events.md index 059b0adb..c7bcb40a 100644 --- a/_posts/2024-09-11-mda_2024events.md +++ b/_posts/2024-09-11-mda_2024events.md @@ -145,9 +145,9 @@ style="float: left; height: 5em; " /> We would like to again thank everyone who helped us make these workshops a success, including the participants, instructors, teaching assistants, and workshop organizers! If you or your organization are interested in partnering with MDAnalysis to organize future workshops, you are always welcome to fill out our [Google form](https://docs.google.com/forms/d/e/1FAIpQLSf5-c4kE_trtA1ciSFcLLRsiFASHY-rXuFu7y902pqUgPDppg/viewform?usp=sf_link) to discuss further. -To stay up-to-date on all MDAnalysis event offerings, be sure to follow our [blog][], [X][], [LinkedIn][], and [Bluesky][] pages. +To stay up-to-date on all MDAnalysis event offerings, be sure to follow our [News][], [X][], [LinkedIn][], and [Bluesky][] pages. -[blog]: https://www.mdanalysis.org/blog/ +[News]: https://www.mdanalysis.org/blog/ [X]: https://twitter.com/mdanalysis [LinkedIn]: https://www.linkedin.com/company/mdanalysis/ [Bluesky]: https://bsky.app/profile/mdanalysis.bsky.social diff --git a/team.md b/team.md index 70e6b21a..10211bd1 100644 --- a/team.md +++ b/team.md @@ -1,6 +1,6 @@ --- layout: page -title: MDAnalysis team +title: MDAnalysis Team order: 9 --- From 6b6f8b901e4fb2d8d784a75f4e0fe82d0b8f3f8d Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Mon, 7 Apr 2025 15:33:59 +0100 Subject: [PATCH 4/7] swap order between community and events pages --- community.md | 2 +- events.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/community.md b/community.md index 85eb4024..377b14b8 100644 --- a/community.md +++ b/community.md @@ -1,7 +1,7 @@ --- layout: page title: Community -order: 7 +order: 6 --- MDAnalysis is developed and maintained as a freely available, open-source project by a global community of scientists. Our community adheres to our [Code of Conduct]({{ site.baseurl }}/pages/conduct/) and welcomes everyone to participate—whether through GitHub Discussions, issue reports, or code contributions. diff --git a/events.md b/events.md index 1edb151e..3de42ae2 100644 --- a/events.md +++ b/events.md @@ -1,7 +1,7 @@ --- layout: page title: Events -order: 6 +order: 7 --- MDAnalysis hosts and participates in various **community-driven events, user group meetings (UGMs), workshops, and hackathons** to foster collaboration and learning. From 86f33bbc151eefb479114aa5f0b3d7560212336c Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Mon, 14 Jul 2025 07:32:08 +0100 Subject: [PATCH 5/7] address PR review comments --- _config.yml | 2 +- _posts/2024-11-22-release-2.8.0.md | 4 ++-- _posts/2025-02-14-new_coredevs.md | 2 +- _posts/2025-03-11-release-2.9.0.md | 4 ++-- about.md | 11 +++++------ community.md | 3 ++- contribute.md | 24 ++++++++++++------------ documentation.md | 6 +++--- events.md | 10 ++++++---- getting_started.md | 4 ++-- index.md | 3 ++- learning_MDAnalysis.md | 2 +- pages/ugm2024.md | 2 +- pages/ugm2025.md | 2 +- team.md | 2 +- 15 files changed, 42 insertions(+), 39 deletions(-) diff --git a/_config.yml b/_config.yml index 8f8b860f..fcd14995 100644 --- a/_config.yml +++ b/_config.yml @@ -24,7 +24,7 @@ url: https://www.mdanalysis.org baseurl: author: name: The MDAnalysis Team - url: https://www.mdanalysis.org/pages/team/ + url: https://www.mdanalysis.org/team/ email: mdanalysis@numfocus.org images: /public/images diff --git a/_posts/2024-11-22-release-2.8.0.md b/_posts/2024-11-22-release-2.8.0.md index e35b3313..3c62186f 100644 --- a/_posts/2024-11-22-release-2.8.0.md +++ b/_posts/2024-11-22-release-2.8.0.md @@ -281,8 +281,8 @@ the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under EOSS4 and EOS [CHANGELOG]: https://github.com/MDAnalysis/mdanalysis/blob/release-2.8.0/package/CHANGELOG [Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ [licensing update]: {{ site.baseurl }}{% post_url 2023-09-22-licensing-update %} -[roles]: {{ site.baseurl }}/pages/team/#roles -[MDAnalysis Team]: {{ site.baseurl }}/pages/team +[roles]: {{ site.baseurl }}/team/#roles +[MDAnalysis Team]: ({{ site.baseurl }}/team/) [MDAKits]: https://mdakits.mdanalysis.org/ [roadmap]: {{ site.baseurl }}{% post_url 2023-10-25-towards_3.0 %}#a-trimmed-down-core-library [mdaencore]: https://mdakits.mdanalysis.org/mdaencore.html diff --git a/_posts/2025-02-14-new_coredevs.md b/_posts/2025-02-14-new_coredevs.md index 858d8777..89844da1 100644 --- a/_posts/2025-02-14-new_coredevs.md +++ b/_posts/2025-02-14-new_coredevs.md @@ -55,7 +55,7 @@ If a candidate has shown a history of participating in these activities, they ar Finally, being an active Core Developer requires some amount of active participation in meetings, decisions, and other administrative business. As MDAnalysis does not have any guaranteed long-term funding, this work is usually unpaid. Therefore, the final decision to accept or decline the election is left to the developers themselves: do they have the time and willingness to keep contributing? -If you are interested in becoming a Core Developer, we highly encourage you to [participate]({{ site.baseurl }}/#participating) in some of the activities listed above, especially reviewing pull requests and mentoring other developers. Learn more about the many roles MDAnalysis community members take on to move the project forward on our [MDAnalysis team]({{ site.baseurl }}/pages/team) page, and reach out to us on our [GitHub discussions forum]({{ site.mailinglists.discussion.url }}) or [Discord server]({{ site.discord.url }}) (join the server using the invitation link, [{{ site.discord.invite }}]({{ site.discord.invite }}). On our end, the MDAnalysis Core Developer team will, to the best of its abilities, aim to offer mentorship and other opportunities to people who express an interest in becoming a Core Developer. +If you are interested in becoming a Core Developer, we highly encourage you to [participate]({{ site.baseurl }}/#participating) in some of the activities listed above, especially reviewing pull requests and mentoring other developers. Learn more about the many roles MDAnalysis community members take on to move the project forward on our [MDAnalysis team]({{ site.baseurl }}/team) page, and reach out to us on our [GitHub discussions forum]({{ site.mailinglists.discussion.url }}) or [Discord server]({{ site.discord.url }}) (join the server using the invitation link, [{{ site.discord.invite }}]({{ site.discord.invite }}). On our end, the MDAnalysis Core Developer team will, to the best of its abilities, aim to offer mentorship and other opportunities to people who express an interest in becoming a Core Developer. Being a Core Developer is work, but it’s also a fantastic opportunity to work with and for a wonderful and welcoming community. As part of [our mission]({{ site.baseurl }}/about/#mission), we welcome anyone who cares for this community and wants to help it grow. diff --git a/_posts/2025-03-11-release-2.9.0.md b/_posts/2025-03-11-release-2.9.0.md index bbeb18bb..f2848e53 100644 --- a/_posts/2025-03-11-release-2.9.0.md +++ b/_posts/2025-03-11-release-2.9.0.md @@ -129,7 +129,7 @@ the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under EOSS4 and EOS [NumFOCUS]: https://www.numfocus.org [CHANGELOG]: https://github.com/MDAnalysis/mdanalysis/blob/release-2.9.0/package/CHANGELOG [Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ -[roles]: {{ site.baseurl }}/pages/team/#roles -[MDAnalysis Team]: {{ site.baseurl }}/pages/team +[roles]: {{ site.baseurl }}/team/#roles +[MDAnalysis Team]: {{ site.baseurl }}/team [MDAKits]: https://mdakits.mdanalysis.org/ [distopia]: https://github.com/MDAnalysis/distopia diff --git a/about.md b/about.md index 29d048fe..b3cd31b7 100644 --- a/about.md +++ b/about.md @@ -9,13 +9,13 @@ style="float: right" alt="MDAnalysis" width="30%"/> MDAnalysis is an open-source project dedicated to advancing molecular dynamics analysis through a robust software library, an active community, and sustainable governance. Our tools enable high-performance, reproducible computational studies supporting researchers across academia and industry. -The MDAnalysis Project is committed to open-source, reproducible computational research. Our [Mission]({{ site.baseurl }}/mission/) guides our efforts in developing robust tools, fostering an inclusive community, and supporting scientists worldwide. +The MDAnalysis Project is committed to open-source, reproducible computational research. Our [Mission]({{ site.baseurl }}/pages/mission/) guides our efforts in developing robust tools, fostering an inclusive community, and supporting scientists worldwide. ## Get Involved -- **Follow Our Code of Conduct:** We foster a welcoming, inclusive environment. Read our [Code of Conduct]({{ site.baseurl }}/conduct/) before participating. +- **Follow Our Code of Conduct:** We foster a welcoming, inclusive environment. Read our [Code of Conduct]({{ site.baseurl }}/pages/conduct/) before participating. - **Join the Community:** Connect with other users, report issues, and contribute through multiple channels. Learn more on our [Community]({{ site.baseurl }}/community/) page. -- **Contribute:** Whether through coding, documentation, community support, or event organization, you can help shape the MDAnalysis ecosystem. Get started with our [Contributing Guide]({{ site.baseurl }}contribute/) or [join a team]({{ site.baseurl }}team/) to support specific initiatives. +- **Contribute:** Whether through coding, documentation, community support, or event organization, you can help shape the MDAnalysis ecosystem. Get started with our [Contributing Guide]({{ site.baseurl }}/contribute/) or [join a team]({{ site.baseurl }}/team/) to support specific initiatives. - **Support MDAnalysis:** MDAnalysis relies on grants, sponsorships, and donations to sustain development and community events. Your support helps fund maintenance, development, UGMs (User Group Meetings), workshops, and more. Learn more on our [Funding]({{ site.baseurl }}/pages/funding/) page. - **Share your Feedback:** MDAnalysis welcomes feedback for improvement from its users and community. Share your thoughts on MDAnalysis, the community, or events by filling out [this feedback form][]. @@ -23,7 +23,7 @@ The MDAnalysis Project is committed to open-source, reproducible computational r MDAnalysis is maintained by the [Core Developers]({{ site.baseurl }}/pages/governance/#mdanalysis-core-developers) who lead the project and make key decisions regarding its development. Past contributors who've stepped back become Emeriti Core Developers. -Our governance structure ensures transparency and sustainability. See our [Governance]({{ site.baseurl }}/pages/governance/) and [Team]({{ site.baseurl }}/pages/team/) pages for more details. +Our governance structure ensures transparency and sustainability. See our [Governance]({{ site.baseurl }}/pages/governance/) and [Team]({{ site.baseurl }}/team/) pages for more details. ## Funding & Sponsors @@ -44,12 +44,11 @@ MDAnalysis is: - **Easy to install** — Available via `pip`, `conda/mamba` and `conda-forge`. - **Openly developed** — The [source code]({{ site.github.repo }}) is hosted on GitHub. -- **Regularly updated** — Official releases are distributed via [PyPI][]. +- **Regularly updated** — Official releases are distributed via [PyPI]({{ site.pypi.package }}). For full installation instructions and setup guides, visit our [Getting Started]({{ site.baseurl }}/getting_started/) page. [GNU Lesser General Public License, version 2.1 or later (LGPLv2.1+)]: https://www.gnu.org/licenses/lgpl-2.1.html -[PyPI]: https://pypi.org/project/MDAnalysis/ [this feedback form]: https://docs.google.com/forms/d/e/1FAIpQLScAjjI730i63LbyVkk_tuZ1-FCXUkg6xFugw_gmcsqUvBUtnw/viewform?usp=sf_link [NumFOCUS]: https://www.numfocus.org diff --git a/community.md b/community.md index 377b14b8..b8057504 100644 --- a/community.md +++ b/community.md @@ -11,7 +11,7 @@ in a file called `AUTHORS` in each source code repository and in the list of contributions; for example, see the [`AUTHORS` file for mdanalysis](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/AUTHORS) and the [contributors for mdanalysis](https://github.com/MDAnalysis/mdanalysis/graphs/contributors). -MDAnalysis is widely used in scientific research and is described in various [academic publications]({{site.baseurl}}/pages/citations/). It also serves as the foundation for several other [molecular dynamics tools]({{site.baseurl}}/mdakits/). +MDAnalysis is widely used in scientific research and is described in various [academic publications]({{site.baseurl}}/citations/). It also serves as the foundation for several other [molecular dynamics tools]({{site.baseurl}}/mdakits/). This page provides an overview of **how you can engage with the MDAnalysis community, where to seek support, and how to participate**. @@ -22,6 +22,7 @@ Follow our official channels for news, updates, and major announcements: - [News]({{ site.baseurl }}/blog/) — News, development highlights, tutorials, and releases. - [LinkedIn](https://www.linkedin.com/company/mdanalysis/) — Professional networking, project updates, event announcements, and industry connections. - [Bluesky](https://bsky.app/profile/mdanalysis.bsky.social) — Community-driven discussions and project insights. +- [Events]({{ site.baseurl }}/events/) — Upcoming (and past) user group meetings, workshops, and hackathons. ## Ask Questions & Get Help diff --git a/contribute.md b/contribute.md index 4180c530..ab3b160a 100644 --- a/contribute.md +++ b/contribute.md @@ -10,7 +10,7 @@ You can contribute by **developing new features, fixing bugs, improving document 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 }}/community/) and [Events]({{ site.baseurl }}events) pages. +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 }}/community/) and [Events]({{ site.baseurl }}/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: @@ -93,24 +93,24 @@ 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]({{ site.baseurl }}/governance/#mdanalysis-core-developers) started through these programs — consider joining and becoming part of the MDAnalysis community! +Many of our [core developers]({{ site.baseurl }}/pages/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 %}) -- [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 2025]({% post_url 2025-05-23-gsoc-students %}) +- GSoC 2024 — [Small Projects]({% post_url 2024-08-30-gsoc2024-final-sm %}); [Large Projects]({% post_url 2025-02-11-gsoc2024-final-lg %}) +- [GSoC 2023]({% post_url 2024-01-18-gsoc2023-final %}) +- [GSoC 2022]({% post_url 2022-12-15-gsoc_outreachy2022-final %}) +- [GSoC 2021]({% post_url 2021-9-14-gsoc2021-final %}) +- [GSoC 2020]({% post_url 2020-09-10-gsoc2020-final %}) +- [GSoC 2019]({% post_url 2019-05-24-gsoc-students %}) +- [GSoC 2018]({% post_url 2018-04-26-gsoc-students %}) +- [GSoC 2017]({% post_url 2017-06-04-gsoc-students %}) - [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 }}/community/) page for guidance on submitting a post. +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 user group meeting, or working on a project. Feel free to reach out via the [Community]({{ site.baseurl }}/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. diff --git a/documentation.md b/documentation.md index a2653e88..81e50199 100644 --- a/documentation.md +++ b/documentation.md @@ -4,7 +4,7 @@ title: Documentation order: 5 --- -The MDAnalysis library (`import MDAnalysis`) is open-source code, 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. +The [MDAnalysis library]({{ site.github.repo }}) (`import MDAnalysis`) is open-source code, 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. The MDAnalysis Project maintains many other software projects related to working with data in the molecular sciences, which can be found under the [MDAnalysis GitHub organization](https://github.com/MDAnalysis). @@ -19,9 +19,9 @@ The [User Guide]({{ site.docs.userguide.url }}) is the best place for new 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). +Learn about the design philosophy and scientific impact of MDAnalysis in the [MDAnalysis paper]({{ site.baseurl }}/citations#Gowers2016). --- -If you need help or have ideas, visit our [Community]({{ site.baseurl }}/pages/community) page to learn about available discussion channels. +If you need help or have ideas, visit our [Community]({{ site.baseurl }}/community) page to learn about available discussion channels. diff --git a/events.md b/events.md index 3de42ae2..b8bdaf43 100644 --- a/events.md +++ b/events.md @@ -13,11 +13,13 @@ For the latest discussions, **join the MDAnalysis community channels** by visiti For mentoring programs and outreach opportunities, please visit the [Contribute]({{ site.baseurl }}/contribute/) page. +## Upcoming Events + +| **Title and Website** | **Date(s)** | **Format** | **Additional Links** | +| ----- | ------- | ------ | -------------- | +| [UGM 2025]({{ site.baseurl }}/pages/ugm2025/) | Nov 9-11, 2025 | Hybrid | [Announcement]({% post_url 2025-04-13-ugm2025 %}) | ## User Group Meetings (UGMs) @@ -70,7 +72,7 @@ Workshop materials are made publicly available under open source licenses. Recor ## Hosting Your Own MDAnalysis Workshops **Have you previously hosted/Are you already organizing an MDAnalysis workshop?** [Let us know][partner-workshops], as we would love to help you spread the word and share information about your event. -**Would you like to host your own MDAnalysis workshop**, but don't know where to get started, have questions on available workshop materials, or would like to seek other support from the [MDAnalysis workshop team]({{ site.baseurl }}/pages/team/)? [Get in touch][partner-workshops] to let us know how we can best support you. +**Would you like to host your own MDAnalysis workshop**, but don't know where to get started, have questions on available workshop materials, or would like to seek other support from the [MDAnalysis workshop team]({{ site.baseurl }}/team/)? [Get in touch][partner-workshops] to let us know how we can best support you. [YouTube channel]: https://www.youtube.com/@mdanalysis3040 diff --git a/getting_started.md b/getting_started.md index 580ab69d..00fdbba5 100644 --- a/getting_started.md +++ b/getting_started.md @@ -46,8 +46,8 @@ In the following example, the end-to-end distance of a protein and the radius of ## Learning Resources To find out what else you can do, head over to [Learning -MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis) to explore +MDAnalysis]({{ site.baseurl }}/learning_MDAnalysis/) to explore tutorials and documentation. -If you have questions, visit our [Community]({{ site.baseurl }}/pages/community) page to learn about available discussion channels. Happy coding! +If you have questions, visit our [Community]({{ site.baseurl }}/community/) page to learn about available discussion channels. Happy coding! diff --git a/index.md b/index.md index 925c54d7..07bd37d7 100644 --- a/index.md +++ b/index.md @@ -31,8 +31,8 @@ MDAnalysis is driven by an active **community of users and contributors**. Stay -- [Community]({{ site.baseurl }}/community/) — Get involved, ask questions, and collaborate. - [News]({{ site.baseurl }}/blog) — Stay updated with development news and community highlights. +- [Community]({{ site.baseurl }}/community/) — Get involved, ask questions, and collaborate. - [Events]({{ site.baseurl }}/events/) — Join workshops, conferences, and mentoring programs. ## Contributing @@ -40,6 +40,7 @@ MDAnalysis is driven by an active **community of users and contributors**. Stay Want to contribute to MDAnalysis? Here’s how: - [Contribute]({{ site.baseurl }}/contribute/) — Learn how to help improve MDAnalysis through coding, documentation, or discussions. +- Join a [Team]({{ site.baseurl}}/team/) — Express your interest in contributing to any of the roles related to sustaining the MDAnalysis project. - [MDAKits and MDA-based tools]({{ site.baseurl }}/mdakits/) — Build and extend MDAnalysis with MDAKits. - [Support MDAnalysis financially](#funding--support) — Donate via NumFOCUS to sustain the project. diff --git a/learning_MDAnalysis.md b/learning_MDAnalysis.md index cf7d8af0..149362e0 100644 --- a/learning_MDAnalysis.md +++ b/learning_MDAnalysis.md @@ -6,7 +6,7 @@ order: 4 MDAnalysis is a powerful Python library for analyzing MD simulations. While primarily designed to help you build custom analysis tools, it also supports interactive data exploration in environments like [IPython](http://ipython.org/) and [Jupyter notebooks](https://jupyter.org/), especially when combined with [pandas](http://pandas.pydata.org/). This makes MDAnalysis an excellent choice for rapid prototyping and exploratory analysis. -MDAnalysis is an academic software package, and if you use it in your research, please cite the relevant publications. For details on how to cite MDAnalysis, visit our [Citations]({{ site.baseurl }}/pages/citations/) page. +MDAnalysis is an academic software package, and if you use it in your research, please cite the relevant publications. For details on how to cite MDAnalysis, visit our [Citations]({{ site.baseurl }}/citations/) page. Whether you're new to MDAnalysis or looking to deepen your expertise, this page will guide you through our learning resources. diff --git a/pages/ugm2024.md b/pages/ugm2024.md index 86b8132b..5553630d 100644 --- a/pages/ugm2024.md +++ b/pages/ugm2024.md @@ -110,7 +110,7 @@ While we will be unable to enforce social distancing guidelines during the UGM, ## Code of Conduct All members of the MDAnalysis community and participants in this UGM are expected to abide by the MDAnalysis [Code of Conduct][coc] (CoC). -If you are attending the UGM and wish to make a report, you may contact the [CoC Committee members](https://www.mdanalysis.org/pages/team/#roles) or other event staff/organizers so that they can take any appropriate immediate response. If you would prefer not to do that, please [submit a report][coc_report] to MDAnalysis. +If you are attending the UGM and wish to make a report, you may contact the [CoC Committee members](https://www.mdanalysis.org/team/#roles) or other event staff/organizers so that they can take any appropriate immediate response. If you would prefer not to do that, please [submit a report][coc_report] to MDAnalysis. ## Who to Contact If you have any questions or special requests related to the UGM, you may [contact the organizing committee][ugm_email]. diff --git a/pages/ugm2025.md b/pages/ugm2025.md index 79b0b2cb..42b74bb1 100644 --- a/pages/ugm2025.md +++ b/pages/ugm2025.md @@ -202,7 +202,7 @@ You can find the [long version of the Code of Conduct](https://numfocus.org/code ### How to report -If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://numfocus.typeform.com/to/ynjGdT?typeform-source=numfocus.org). For an [appropriate *immediate* response](https://numfocus.org/code-of-conduct-archive/response-and-enforcement-events-meetups), you may contact the [CoC Committee members](https://www.mdanalysis.org/pages/team/#roles) or other event staff/organizers, who will introduce themselves to you at the event. +If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://numfocus.typeform.com/to/ynjGdT?typeform-source=numfocus.org). For an [appropriate *immediate* response](https://numfocus.org/code-of-conduct-archive/response-and-enforcement-events-meetups), you may contact the [CoC Committee members](https://www.mdanalysis.org/team/#roles) or other event staff/organizers, who will introduce themselves to you at the event. ### Who will receive your report Your report will be received and handled by the NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds. The group is making decisions independently from the MDAnalysis project, PyData, NumFOCUS or any other organization. diff --git a/team.md b/team.md index 10211bd1..abc64b8c 100644 --- a/team.md +++ b/team.md @@ -10,7 +10,7 @@ We also invite community members to reach out to [mdanalysis@numfocus.org](mailt ## Roles -In this section we list major contributors who are currently devoting substantial effort to the roles listed below. This team organisation structure was started in November 2023; many people contributed to these tasks before then and may not appear in this table, in particular the [emeritus core developers]({{ site.url }}{% link about.md %}#mdanalysis-emeriti-core-developers). +In this section we list major contributors who are currently devoting substantial effort to the roles listed below. This team organisation structure was started in November 2023; many people contributed to these tasks before then and may not appear in this table, in particular the [emeritus core developers]({{ site.baseurl }}/pages/governance/#mdanalysis-emeriti-core-developers). Names are listed in *alphabetical* order. From 44e988f1858c05efc521ee25778ec0a42f7cf610 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Mon, 11 Aug 2025 09:15:33 +0100 Subject: [PATCH 6/7] address PR review comment about licence --- documentation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/documentation.md b/documentation.md index 81e50199..8159a9d4 100644 --- a/documentation.md +++ b/documentation.md @@ -4,7 +4,7 @@ title: Documentation order: 5 --- -The [MDAnalysis library]({{ site.github.repo }}) (`import MDAnalysis`) is open-source code, 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. +The [MDAnalysis library]({{ site.github.repo }}) (`import MDAnalysis`) is open-source code, available under the [GNU Lesser General Public License, version 3 or later (LGPLv3+)](https://www.gnu.org/licenses/lgpl-3.0.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. The MDAnalysis Project maintains many other software projects related to working with data in the molecular sciences, which can be found under the [MDAnalysis GitHub organization](https://github.com/MDAnalysis). From aadde387353b3c7a8995d0f125853e06be3197f6 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Mon, 27 Oct 2025 15:42:49 +0000 Subject: [PATCH 7/7] resolve conflicts for mdakits page --- pages/mdakits.md | 93 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 pages/mdakits.md diff --git a/pages/mdakits.md b/pages/mdakits.md new file mode 100644 index 00000000..6c432661 --- /dev/null +++ b/pages/mdakits.md @@ -0,0 +1,93 @@ +--- +layout: page +title: MDAKits and MDA-based tools +order: 5 +--- + +MDAnalysis is developed with extensibility in mind, allowing +scientists to create various tools with the components +that the library provides. To help developers in this process, +and to advertise these wonderful tools to the MDAnalysis user community, +we have created an ecosystem of [MDAnalysis Toolkits, or "MDAKits"](https://mdakits.mdanalysis.org/about.html). + +## MDAKits + +Please look at the [registry of MDAKits](https://mdakits.mdanalysis.org/mdakits.html) +for a list of toolkits that [meet the minimum MDAKit requirements](https://mdakits.mdanalysis.org/about.html#requirements). +These are regularly tested against the latest and development versions of +MDAnalysis. Whilst we cannot guarantee the completeness of the MDAKit's test coverage, if you see a green badge, the code should be minimally behaving as the MDAKit authors intended it! + + +*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/makingakit.html) +or share it on [{{ site.mailinglists.discussion.name }}]({{ site.mailinglists.discussion.url }})!* + + +## Other (non-MDAKit registered) tools using MDAnalysis + +Below we list projects that use MDAnalysis and are not (yet) registered as MDAKits: + +### Visualization tools + +- [nglview](https://github.com/arose/nglview): nglview is a tool to visualize + trajectories in jupyter notebooks. +- [MDSrv](https://github.com/nglviewer/mdsrv) streams and visualizes MD trajectories interactively within web browsers +- [MD Trajectories in + PyMOL](https://nms.kcl.ac.uk/lorenz.lab/wp/?p=1768): MDAnalysis has + been embedded into Open Source PyMOL to read many different MD formats + directly. Source code is available from + [bieniekmateusz/pymol-mdanalysis](https://github.com/bieniekmateusz/pymol-mdanalysis) on GitHub. +- [MolecularNodes](https://github.com/BradyAJohnston/MolecularNodes) plugin for the [Blender](https://www.blender.org/) rendering package; the plugin provides a convenient method for importing structural biology files, including MD trajectories, into Blender, and several nodes for working with atomic data inside of Blender's Geometry Nodes. + +### Analysis tools + +- [pydiffusion](https://github.com/bio-phys/pydiffusion): Analyze the + rotational diffusion of your molecules. +- [pycontact](https://github.com/maxscheurer/pycontact): Analysis of + non-covalent interactions in MD trajectories. +- [RotamerConvolveMD](https://github.com/MDAnalysis/RotamerConvolveMD): + Analysis of molecular dynamics trajectories or conformational ensembles in + terms of spin-label distances as probed in double electron-electron resonance + (DEER) experiments. +- [PBxplore](https://github.com/pierrepo/PBxplore): PBxplore is a suite of + tools dedicated to Protein Block (PB) analysis. +- [cgheliparm](https://github.com/ifaust83/cgheliparm): Scripts used to analyze + dsDNA structures from Martini MD simulations. +- [accelerated_sampling_with_autoencoder](https://github.com/weiHelloWorld/accelerated_sampling_with_autoencoder): + This is the framework for running accelerated sampling with data-augmented + autoencoders. +- [BioEn](https://github.com/bio-phys/BioEn): BioEn integrates a broad range of experimental data to refine ensembles of structures. +- [kugupu](https://github.com/kugupu/kugupu): A molecular network generator to study charge transport pathways in amorphous materials +- [PyInteraph](https://github.com/ELELAB/pyinteraph): A software tool + for the analysis of structural communication in protein ensembles, + including a PyMOL plugin and an InteractionPlotter. +- [taurenmd](https://taurenmd.readthedocs.io/en/latest/): A command-line interface for analysis of Molecular Dynamics simulations. +- [PENSA](https://github.com/drorlab/pensa): A toolkit for exploratory analysis and comparison of protein structural ensembles +- [LiPyphilic](https://lipyphilic.readthedocs.io/en/latest/): A Python package for the analysis of lipid membrane simulations. +- [MDVoxelSegmentation](https://github.com/marrink-lab/MDVoxelSegmentation): A voxel-based approach for dynamic cluster analysis of molecular dynamics trajectories. + +### Molecular modeling tools + +- [Swarm-CG](https://github.com/GMPavanLab/Swarm-CG): Automatically optimizes the bonded terms of a MARTINI-like coarse-grained (CG) molecular model with respect to its reference all-atom (AA) trajectory, via [FST-PSO](https://github.com/aresio/fst-pso). + +### Simulation packages +- [ESPResSo](http://espressomd.org/) is a software package for + performing and analyzing Molecular Dynamics many-particle + simulations of coarse-grained atomistic or bead-spring models as + they are used in soft matter research in physics, chemistry and + molecular biology. + +### Distributions + +MDAnalysis is included in [NMRBox](https://nmrbox.org/) a distribution of +common software to analyze NMR measurements. + +Some generic distributions such as [MacPorts: +py-MDAnalysis](https://ports.macports.org/port/py-MDAnalysis/summary) +(macOS), [Fedora: +python-MDAnalysis](https://src.fedoraproject.org/rpms/python-MDAnalysis/) +and [archlinux: +python-mdanalysis](https://aur.archlinux.org/packages/python-mdanalysis/) +(Linux) maintain packages of MDAnalysis. + +