Skip to content

reorder pages in sidebar #458

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 6 commits into
base: master
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions _posts/2023-05-18-save-date-ugm2023.md
Original file line number Diff line number Diff line change
Expand Up @@ -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/
2 changes: 1 addition & 1 deletion _posts/2023-12-21-github-discussions.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions _posts/2024-01-15-mda_events.md
Original file line number Diff line number Diff line change
Expand Up @@ -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/
4 changes: 2 additions & 2 deletions _posts/2024-09-11-mda_2024events.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
8 changes: 4 additions & 4 deletions about.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
layout: page
title: About MDAnalysis
order: 10
order: 1
---

<img src="{{ site.baseurl }}/public/mdanalysis-logo_square.png"
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The Mission page feels like it goes missing to me being linked here. Thoughts on adding it back in as it's own section here on the About page (instead of as a separate Mission page)?

Expand All @@ -14,8 +14,8 @@ The MDAnalysis Project is committed to open-source, reproducible computational r
## Get Involved

- **Follow Our Code of Conduct:** We foster a welcoming, inclusive environment. Read our [Code of Conduct]({{ site.baseurl }}/conduct/) before participating.
- **Join the Community:** Connect with other users, report issues, and contribute through multiple channels. Learn more on our [Community]({{ site.baseurl }}/pages/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 }}/pages/contribute/) or [join a team]({{ site.baseurl }}/pages/team/) to support specific initiatives.
- **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.
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@namiroues - Have you built the page locally to see that the {{ site.baseurl }}blahblahblah/ pages render (as opposed to {{ site.baseurl }}/blahblahblah/ with a leading slash)? Just curious as I've always used the leading slash, and Oliver's comment from an old issue indicates there may have been a point that things broke without the leading slash.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes, links break without the leading slash. I am going through all links to update. Apologies for missing this.

- **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][].

Expand Down Expand Up @@ -46,7 +46,7 @@ MDAnalysis is:
- **Openly developed** &mdash; The [source code]({{ site.github.repo }}) is hosted on GitHub.
- **Regularly updated** &mdash; Official releases are distributed via [PyPI][].
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
- **Regularly updated** &mdash; Official releases are distributed via [PyPI][].
- **Regularly updated** &mdash; Official releases are distributed via [PyPI]({{ site.pypi.package }}).

There are several cases like this where we can (and should) pull from the _config file. I'll admit I haven't been diligent about this, and it may be worth just opening an issue (if we don't have one already) to update these links throughout the entire repo to be consistent.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks Jenna, sounds like a good idea. I will open a new issue about this and slowly update all links for consistency.


For full installation instructions and setup guides, visit our [Getting Started]({{ site.baseurl }}/pages/getting_started/) page.
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/
Expand Down
4 changes: 2 additions & 2 deletions blog/index.html
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
layout: page
title: Blog
order: 12
title: News
order: 2
---

<div class="posts">
Expand Down
2 changes: 1 addition & 1 deletion pages/citations.md → citations.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
layout: page
title: Citations
order: 9
order: 11
---

MDAnalysis and the included algorithms are scientific software that
Expand Down
8 changes: 4 additions & 4 deletions pages/community.md → community.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
layout: page
title: Community
order: 5
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&mdash;whether through GitHub Discussions, issue reports, or code contributions.
Expand All @@ -11,15 +11,15 @@ 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**.

## Stay Updated

Follow our official channels for news, updates, and major announcements:

- [Blog]({{ site.baseurl }}/blog/) &mdash; News, development highlights, tutorials, and releases.
- [News]({{ site.baseurl }}/blog/) &mdash; News, development highlights, tutorials, and releases.
- [LinkedIn](https://www.linkedin.com/company/mdanalysis/) &mdash; Professional networking, project updates, event announcements, and industry connections.
- [Bluesky](https://bsky.app/profile/mdanalysis.bsky.social) &mdash; Community-driven discussions and project insights.

Expand All @@ -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.



Expand Down
10 changes: 5 additions & 5 deletions pages/contribute.md → contribute.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
layout: page
title: Contribute
order: 6
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.
Expand All @@ -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).

Expand Down Expand Up @@ -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.
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looking at this again, this feels a bit out of place to me on the Contributing page; I think it might fit better on the Community page (but please remind me if we made a decision against that for some reason). In fact, earlier on this page we even redirect to Community and Events for more info on participating in mentoring programs:

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](https://www.mdanalysis.org/pages/community/) and [Events](https://www.mdanalysis.org/pages/events/) pages.


### 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:

Expand Down Expand Up @@ -110,7 +110,7 @@ MDAnalysis has participated in Google Summer of Code for several years, mentorin
- [GSoC 2016]({% post_url 2016-04-26-gsoc %})
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Rather than the announcement posts that we're participating as a host organization, I would link to the final project write-ups (where available) and/or student introductions. e.g.,

  • [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 %})

As an aside, this puts a lot of emphasis on GSoC, without linking to other projects that the team has mentored (e.g., https://github.com/MDAnalysis/MDAnalysis.github.io/blob/master/_posts/2023-08-17-sff-students.md, https://github.com/MDAnalysis/MDAnalysis.github.io/blob/master/_posts/2022-12-15-gsoc_outreachy2022-final.md, https://github.com/MDAnalysis/MDAnalysis.github.io/blob/master/_posts/2024-09-09-outreachy2024-final.md). We also track mentees on the Funding page for each mentorship program. Perhaps there's a way to combine this information so we only have to update it one place? (e.g., maybe instead of linking to GH profiles on the funding page, we link to each individual's final project write-up (when available)).


## 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 &mdash; 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 &mdash; 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.

Expand Down
2 changes: 1 addition & 1 deletion pages/documentation.md → documentation.md
Original file line number Diff line number Diff line change
@@ -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&mdash;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.
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
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&mdash;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&mdash;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.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@IAlibay - Are we cleared to say this, or should we be more specific that code contributions are under LGPLv2.1+, while the package itself is still under LGPLv3+?

Expand Down
6 changes: 3 additions & 3 deletions pages/events.md → events.md
Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
---
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.

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.

<!-- Uncomment the following section when new events are announced

Expand Down
2 changes: 1 addition & 1 deletion pages/getting_started.md → getting_started.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
layout: page
title: Getting Started
order: 1
order: 3
---

MDAnalysis is a Python library for analyzing molecular dynamics (MD) simulations. This page will guide you through quickly installing MDAnalysis, exploring a basic example, and accessing learning resources to get started.
Expand Down
Loading
Loading