reorder pages in sb- rename blog to news - move core pages to top level

namiroues · namiroues · commit e3088b328d6c · 2025-04-05T09:43:58.000+01:00
diff --git 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
@@ -1,7 +1,7 @@
 ---
 layout: page
 title: About MDAnalysis
-order: 10
+order: 1
 ---
 
 <img src="{{ site.baseurl }}/public/mdanalysis-logo_square.png"
@@ -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. 
 - **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][].
 
@@ -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][].
 
-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/
diff --git a/blog/index.html b/blog/index.html
@@ -1,7 +1,7 @@
 ---
 layout: page
-title: Blog
-order: 12
+title: News
+order: 2
 ---
 
 <div class="posts">
diff --git a/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/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&mdash;whether through GitHub Discussions, issue reports, or code contributions.
@@ -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.
 
@@ -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/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 &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.
 
diff --git a/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&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.
diff --git a/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), and workshops** 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 
 
diff --git a/getting_started.md b/getting_started.md
@@ -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.
diff --git a/index.md b/index.md
@@ -21,34 +21,34 @@ Learn more about our **mission, development, team, and governance** on the [Abou
 
 If you're new to *MDAnalysis*, explore the following resources to install the `MDAnalysis` package, access tutorials, and dive into the documentation:
 
-- [Getting Started]({{ site.baseurl }}/pages/getting_started/)  
-- [Learning MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis)  
-- [Documentation]({{ site.baseurl }}/pages/documentation)  
+- [Getting Started]({{ site.baseurl }}/getting_started/)  
+- [Learning MDAnalysis]({{ site.baseurl }}/learning_MDAnalysis/)  
+- [Documentation]({{ site.baseurl }}/documentation/)  
 
 ## Community 
 
 MDAnalysis is driven by an active **community of users and contributors**. Stay updated and get involved through the following pages:  
 
 <!-- TODO: Add link [Get Involved]({{ site.baseurl }}/pages/about/#get-involved)
  -->
-- [Community]({{ site.baseurl }}/pages/community/) &mdash; Get involved, ask questions, and collaborate.
-- [Blog]({{ site.baseurl }}/blog) &mdash; Stay updated with development news and community highlights.
-- [Events]({{ site.baseurl }}/pages/events/) &mdash; Join workshops, conferences, and mentoring programs.
+- [Community]({{ site.baseurl }}/community/) &mdash; Get involved, ask questions, and collaborate.
+- [News]({{ site.baseurl }}/blog) &mdash; Stay updated with development news and community highlights.
+- [Events]({{ site.baseurl }}/events/) &mdash; Join workshops, conferences, and mentoring programs.
 
 ## Contributing 
 
 Want to contribute to MDAnalysis? Here’s how:  
 
-- [Contribute]({{ site.baseurl }}/pages/contribute/) &mdash; Learn how to help improve MDAnalysis through coding, documentation, or discussions.  
-- [MDAKits and MDA-based tools]({{ site.baseurl }}/pages/mdakits/) &mdash; Build and extend MDAnalysis with MDAKits.  
+- [Contribute]({{ site.baseurl }}/contribute/) &mdash; Learn how to help improve MDAnalysis through coding, documentation, or discussions.  
+- [MDAKits and MDA-based tools]({{ site.baseurl }}/mdakits/) &mdash; Build and extend MDAnalysis with MDAKits.  
 - [Support MDAnalysis financially](#funding--support) &mdash; 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/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/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/pages/conduct.md b/pages/conduct.md
diff --git a/pages/mission.md b/pages/mission.md
diff --git a/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/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.
