From 314e7ff5ce2daeec834e07e3d413a3a22412d152 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Mon, 10 Mar 2025 12:27:19 +0000 Subject: [PATCH 1/4] add icons and reorder pages on sidebar --- _config.yml | 6 +- _includes/head.html | 4 + _includes/sidebar.html | 37 +++- _posts/2022-11-07-relicensing.md | 2 +- _posts/2023-09-22-licensing-update.md | 2 +- _posts/2023-10-25-towards_3.0.md | 2 +- pages/about.md | 300 ++++++++++++++++++++++++++ pages/blog/index.html | 38 ++++ pages/citations.md | 2 +- pages/privacy.md | 2 +- pages/team.md | 4 +- public/css/local.css | 77 ++++++- public/images/bluesky.svg | 1 + 13 files changed, 451 insertions(+), 26 deletions(-) create mode 100644 pages/about.md create mode 100644 pages/blog/index.html create mode 100644 public/images/bluesky.svg diff --git a/_config.yml b/_config.yml index 188f2028..53e0574e 100644 --- a/_config.yml +++ b/_config.yml @@ -9,7 +9,7 @@ permalink: pretty title: MDAnalysis name: MDAnalysis tagline: molecular simulations data analysis -description: working with data in the molecular sciences +description: working with data in molecular sciences # long_description is not currently used by the theme long_description: | MDAnalysis is a Python library which enables the handling and @@ -40,8 +40,8 @@ plugins: - jekyll-feed # Blog pagination -paginate_path: "/blog/page:num/" -paginate: 3 +paginate_path: "/pages/blog/page:num/" +paginate: 12 # jekyll-feed # - our previous feed was called atom.xml so we use it instead diff --git a/_includes/head.html b/_includes/head.html index c9a893e2..59ef45e4 100644 --- a/_includes/head.html +++ b/_includes/head.html @@ -39,4 +39,8 @@ anchors.add('h1, h2, h3, h4, h5, h6'); }); + + + + diff --git a/_includes/sidebar.html b/_includes/sidebar.html index 19dab458..0e0a3f6a 100644 --- a/_includes/sidebar.html +++ b/_includes/sidebar.html @@ -9,8 +9,29 @@

{{ site.description }}

-
Enable javascript for search.
- + +
+ + + + + Bluesky + + + + + + + +
+ + +
+
+
Enable javascript for search.
+
+
+

© {{ site.time | date: '%Y' }}. All rights reserved.

diff --git a/_posts/2022-11-07-relicensing.md b/_posts/2022-11-07-relicensing.md index 034442fa..41f7f1d2 100644 --- a/_posts/2022-11-07-relicensing.md +++ b/_posts/2022-11-07-relicensing.md @@ -203,4 +203,4 @@ fiscal sponsor, [NumFOCUS][]. [contributors]: https://github.com/MDAnalysis/mdanalysis/blob/develop/package/AUTHORS [faq wiki]: https://github.com/MDAnalysis/mdanalysis/wiki/GPLv2--to-LGPLv3--relicensing-summary-and-FAQ [NumFOCUS]: https://www.numfocus.org -[Core Developers]: {% link about.md %}#mdanalysis-core-developers +[Core Developers]: {% link pages/about.md %}#mdanalysis-core-developers diff --git a/_posts/2023-09-22-licensing-update.md b/_posts/2023-09-22-licensing-update.md index c97d274e..64f22290 100644 --- a/_posts/2023-09-22-licensing-update.md +++ b/_posts/2023-09-22-licensing-update.md @@ -324,4 +324,4 @@ an advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/1000 [consultation]: {{ site.baseurl }}{% post_url 2022-11-07-relicensing %}#consultation-period-7th-november-until-5th-december-2022 [release 2.6]: {{ site.baseurl }}{% post_url 2023-09-02-release-2.6.1 %} [release 2.5]: {{ site.baseurl }}{% post_url 2023-06-05-releases-2.4.x-2.5.0 %} -[Core Developers]: {% link about.md %}#mdanalysis-core-developers +[Core Developers]: {% link pages/about.md %}#mdanalysis-core-developers diff --git a/_posts/2023-10-25-towards_3.0.md b/_posts/2023-10-25-towards_3.0.md index fc3d8e22..3642efe4 100644 --- a/_posts/2023-10-25-towards_3.0.md +++ b/_posts/2023-10-25-towards_3.0.md @@ -64,7 +64,7 @@ If you have any feedback on this roadmap or would like to discuss our future pla – Hugo MacDermott-Opeskin on behalf of the MDAnalysis [Core Developers][] -[Core Developers]: {{ site.baseurl }}{% link about.md %}#mdanalysis-core-developers +[Core Developers]: {{ site.baseurl }}{% link pages/about.md %}#mdanalysis-core-developers [Discord]: {{ site.discord.url }} [distopia]: https://github.com/MDAnalysis/distopia [EOSS4]: {{ site.baseurl }}{% post_url 2021-08-31-CZI-EOSS4 %} diff --git a/pages/about.md b/pages/about.md new file mode 100644 index 00000000..a411bf18 --- /dev/null +++ b/pages/about.md @@ -0,0 +1,300 @@ +--- +layout: page +title: About MDAnalysis +order: 10 +--- + +MDAnalysis + +## Mission + +The MDAnalysis [Community](#community) is interested in all facets of **working +with data in the computational molecular sciences**. We welcome everyone. **We all follow our +[Code of Conduct] and strive to create an environment that is welcoming to +all.** Our primary purpose is to produce software that scientists in academia and +industry will trust to use in their research. + +We develop and maintain projects related to the broader goal of processing and +analyzing data in the computational molecular sciences. We aim to empower users/developers to +work with our packages following [FAIR principles]. Our central package is the +[MDAnalysis library] for the analysis of computer simulations of many-body +systems at the molecular scale. + +We believe that scientific software should be open to all while using best +practices to maintain high standards of correctness and reproducibility. We +emphasize educating our users to make best use of the tools that we produce, to +enable them to become contributors to our community and code bases. + + + +## Community + +**MDAnalysis** is developed and maintained as a freely available, open-source +project by a global community of scientists. The MDAnalysis community adheres +to our [Code of Conduct]({{site.baseurl}}/pages/conduct/) and invites everyone +to [participate]({{site.baseurl}}/#participating) --- be it on GitHub Discussions, +through issue reports, or code contributions. + +All *contributors* to the MDAnalysis library and its subprojects are acknowledged +in a file called `AUTHORS` in each source code repository and in the list of +contributions; as examples see the [`AUTHORS` file for +mdanalysis](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/AUTHORS) +and the [contributors for +MDAnalysis/mdanalysis](https://github.com/MDAnalysis/mdanalysis/graphs/contributors). + +MDAnalysis and the algorithms implemented in the library and the subprojects are +scientific software that are described in [academic +publications]({{site.baseurl}}/pages/citations/). + +MDAnalysis is used in a variety of [other molecular dynamics tools]({{site.baseurl}}/pages/mdakits/). + + +## Open source + +All our [code]({{site.baseurl}}/#availability) and our [teaching +materials]({{site.baseurl}}/pages/learning_MDAnalysis/) are available +under open source licenses from repositories at +[https://github.com/MDAnalysis/](https://github.com/MDAnalysis/). The +MDAnalysis library itself is published under the [GNU General Public +License, version 2](https://www.gnu.org/licenses/gpl-2.0.html); other +supporting libraries are published under the MIT or the BSD-3 clause +licence. + +Installable packages are available through the popular ``pip`` and +``conda`` package managers as well as some Linux distributions. + + +## Governance + +Project leadership is provided by a subset of contributors, the +*MDAnalysis Core Developers* +([@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs)) +who have produced substantial contributions over extended lengths of +time and who remain active in reviewing issues and discussions on +GitHub Discussions and our Discord server. + +### MDAnalysis Core Developers + +The **Core Developers** lead the MDAnalysis project and are responsible to +the community and to NumFOCUS, our fiscal sponsor. They **represent +the project publicly** and **vote to make decisions for the project**. + +PIs on a grant submitted by MDAnalysis via NumFOCUS must be Core Developers +while co-PIs do not have to be Core Developers. + +Core Developers are granted commit rights (write access) to the [GitHub source +code repositories][orgrepo] and thus can approve pull requests for merges. + +The current +[@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs/members) +team ("MDAnalysis Core Developers") consists of: + +- @BradyAJohnston +- @fiona-naughton +- @hmacdope +- @IAlibay +- @jennaswa +- @lilyminium +- @marinegor +- @micaela-matta +- @orbeckst +- @p-j-smith +- @richardjgowers +- @RMeli +- @tylerjereddy +- @yuxuanzhuang + +### MDAnalysis Emeriti Core Developers + +**Emerita/Emeritus Core Developers** are former Core Developers who remain +connected to the project but have stepped back from the day-to-day +decision making. Emeriti Core Developers can reinstate themselves to +Core Developer status. + +Emeriti Core Developers maintain commit rights (write access) to the +[GitHub source code repositories][orgrepo] and can approve pull requests for +merges. + +The current *Emeriti Core Developers* are: + +- @dotsdl +- Elizabeth Denning +- @jandom +- @jbarnoud +- @kain88-de +- @mnmelo +- @mtiberti +- @nmichaud +- @PicoCentauri +- @seb-buch +- @zemanj + +### Decision Making Process and Membership + +1. All decisions are made by *simple majority*[^1] of the [MDAnalysis Core + Developers](#mdanalysis-core-developers). +2. New *Core Developers* are elected with a simple majority of current + MDAnalysis Core Developers. +3. Current Core Developers are polled annually to *opt-in* to remain + a Core Developer; otherwise they transition to [Emerita/Emeritus + Core Developer](#mdanalysis-emeriti-core-developers) status. + +[^1]: A [simple majority][] is defined as *more than half the votes + cast*. Abstentions or blanks are excluded in calculating a + majority vote. Totals do not include votes cast by someone not + entitled to vote[^2] or improper multiple votes by a single + member. Illegal votes[^3] are counted as votes cast; + if only two choices (such as a binary "yes"/"no" vote) are + possible, a majority vote is more "yes" than "no" votes. + +[^2]: See [MDAnalysis Core Developers](#mdanalysis-core-developers) + for the list of *individuals entitled to vote*. + +[^3]: *Illegal votes* are votes that were cast for ineligible choices. + +### Code of Conduct + +Everyone in the MDAnalysis community adheres to our [Code of +Conduct]({{site.baseurl}}/pages/conduct/). A rotating subset of three +MDAnalysis Core Developers is tasked to respond to and to investigate +[Code of Conduct]({{site.baseurl}}/pages/conduct/) violations. + + +## Partners + +MDAnalysis is a [fiscally sponsored +project]({{site.numfocus.sponsored_project}}) of [NumFOCUS][], a nonprofit +dedicated to supporting the open source scientific computing +community. + +If you like MDAnalysis and want to support our mission, please +consider making a [donation]({{site.numfocus.donate}}) to support our +efforts. NumFOCUS is a 501(c)(3) non-profit charity in the United +States; as such, donations to NumFOCUS are tax-deductible as allowed +by law. As with any donation, you should consult with your personal +tax adviser or the IRS about your particular tax situation. + +{{ site.numfocus.donate_button }} + + +## Funding + +We are grateful for financial support from the following organizations, which have supported MDAnalysis either through direct funding or indirectly by funding MDAnalysis contributors. + +### [Chan Zuckerberg Initiative][] (CZI) + +Chan Zuckerberg Initiative + +MDAnalysis has been supported by the [Essential Open Source for Science](https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/) (EOSS) program from the CZI Donor-Advised Fund (DAF), an advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989) + +- EOSS5, 2022-253062 (**2022**): [MDAnalysis: Outreach and Project Manager](https://chanzuckerberg.com/eoss/proposals/mdanalysis-outreach-and-project-manager/) (**Personnel**: @IAlibay, @jennaswa, @micaela-matta, @orbeckst, @richardjgowers (*PI*)) +- EOSS4, DAF2021-237663, DOI [https://doi.org/10.37921/426590wiobus](https://doi.org/10.37921/426590wiobus) (**2021**): [MDAnalysis: Faster, Extensible Molecular Analysis for Reproducible Science](https://chanzuckerberg.com/eoss/proposals/mdanalysis-faster-extensible-molecular-analysis-for-reproducible-science/) (**Personnel**: @fiona-naughton, @hmacdope, @IAlibay, @ianmkenney, @lilyminium, @orbeckst (*PI*), @richardjgowers) + +### [Google](https://opensource.google/) + + Google Summer of Code + +The following contributors were sponsored to work on MDAnalysis through the [Google Summer of Code](https://summerofcode.withgoogle.com/) program. + +- **2024**: @ljwoods2, @lunamorrow, @talagayev +- **2023**: @marinegor, @xhgchen +- **2022**: @aya9aladdin, @BFedder +- **2021**: @ojeda-e, @orionarcher +- **2020**: @cbouy, @hmacdope, @yuxuanzhuang +- **2019**: @NinadBhat +- **2018**: @ayushsuhane, @davidercruz +- **2017**: @utkbansal +- **2016**: @fiona-naughton, @jdetle + + Google Season of Docs + +The following technical writers were sponsored to work on MDAnalysis through the [Google Season of Docs](https://developers.google.com/season-of-docs) program. + +- **2019**: @lilyminium + +### [National Science Foundation](https://www.nsf.gov/) + + +National Science Foundation + +Earlier work was partially supported by the NSF (as part of award ACI-1443054). + +- NSF DIBBS award, ACI-1443054 (**2014**): [CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1443054) (**MDAnalysis Personnel**: @orbeckst) + +The following students were sponsored to work on MDAnalysis through the [NSF Research Experience for Undergraduates](https://www.nsf.gov/crssprgm/reu/) (REU) program. + +- **2021**: @ALescoulie, @edisj +- **2020**: @edisj +- **2019**: @nawtrey +- **2018**: @hfmull +- **2017**: @kaceyaurum +- **2016**: @rbrtdlgd +- **2015**: @ianmkenney + +### [NumFOCUS][] + +NumFOCUS Sponsored + +MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor, as well as through its [Small Development Grants](https://numfocus.org/programs/small-development-grants) (SDG) program. + +- SDG Round 3 (**2024**): Customizable and automated scientific molecular rendering with Molecular Nodes (**Personnel**: @yuxuanzhuang, @BradyAJohnston) +- SDG Round 2 (**2023**): Unified and comprehensive documentation and learning resources for MDAnalysis (**Personnel**: @IAlibay, @jennaswa, @lilyminium, @micaela-matta, @orbeckst) +- SDG Round 2 (**2022**): Improving the organization and content of MDAnalysis teaching materials (**Personnel**: @micaela-matta, @pgbarletta) +- SDG Round 1 (**2020**): Periodic boundary handling and on the fly transformations +- SDG Round 2 (**2018**): MDAnalysis tutorial and hackathon +- SDG Round 1 (**2017**): Widening platform availability for MDAnalysis: Full Python 3 Support + +### [Outreachy](https://www.outreachy.org/) + +Outreachy + +The following contributors were sponsored to work on MDAnalysis through the [Outreachy](https://www.outreachy.org/) program. + +- **2024**: @adetutudeborah +- **2022**: @umak1106 + +### [Station1](https://www.station1.org/) + +Station1 Logo + +The following contributors were sponsored to work on MDAnalysis through the [Station1 Frontiers Fellowship](https://www.station1.org/sff) program. + +- **2023**: @jong9559, @KarenBekhazi + +
+ +## Feedback + +MDAnalysis welcomes feedback for improvement from its users and community. If you have any general feedback or comments to make about MDAnalysis, the community, events, or other aspects, please [let us know in this form here](https://forms.gle/n8GLe2QsL2hW2QiDA)! + +------ + +[Code of Conduct]: {{ site.baseurl }}/pages/conduct/ +[MDAnalysis library]: {{ site.github.repo }} +[FAIR principles]: https://www.go-fair.org/fair-principles/ +[NumFOCUS]: https://www.numfocus.org +[simple majority]: https://en.wikipedia.org/wiki/Majority#Majority_vote +[orgrepo]: https://github.com/MDAnalysis +[Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ diff --git a/pages/blog/index.html b/pages/blog/index.html new file mode 100644 index 00000000..91142459 --- /dev/null +++ b/pages/blog/index.html @@ -0,0 +1,38 @@ +--- +layout: page +title: Blog +order: 12 +--- + +
+ {% for post in paginator.posts %} +
+

+ + {{ post.title }} + +

+ + {{ post.date | date_to_string }} + + {{ post.content }} +
+ {% endfor %} +
+ + diff --git a/pages/citations.md b/pages/citations.md index 39b9de29..1a83683d 100644 --- a/pages/citations.md +++ b/pages/citations.md @@ -1,7 +1,7 @@ --- layout: page title: Citations -order: 100 +order: 9 --- MDAnalysis and the included algorithms are scientific software that diff --git a/pages/privacy.md b/pages/privacy.md index 7cdcab05..a3f94317 100644 --- a/pages/privacy.md +++ b/pages/privacy.md @@ -1,7 +1,7 @@ --- layout: page title: Privacy Policy -order: 10 +order: 13 --- MDAnalysis is a [fiscally sponsored diff --git a/pages/team.md b/pages/team.md index fae0891e..cd07f8fe 100644 --- a/pages/team.md +++ b/pages/team.md @@ -1,7 +1,7 @@ --- layout: page title: MDAnalysis team -order: 4 +order: 11 --- 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. @@ -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 contributing 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 contributing 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 pages/about.md %}#mdanalysis-emeriti-core-developers). Names are listed in *alphabetical* order. diff --git a/public/css/local.css b/public/css/local.css index 41f13308..f0f3749f 100644 --- a/public/css/local.css +++ b/public/css/local.css @@ -45,11 +45,78 @@ but our YouTube videos seem to be natively widescreen. position: absolute; } -.wide-code pre { - white-space: pre; - overflow-x: auto; - display: block; - max-width: 100%; +/* Sidebar Social Media Icons */ + +.sidebar-social-icons { + display: flex; + justify-content: flex-start; + align-items: center; + gap: 15px; + margin-top: 20px; + margin-bottom: 20px; + width: 100%; + text-align: left; +} + +/* Ensure sidebar social icons override sidebar link styles */ +.sidebar .sidebar-social-icons a { + font-size: 24px !important; + text-decoration: none !important; +} + +/* Apply white color to icons */ +.sidebar .sidebar-social-icons a[href*="linkedin.com"], +.sidebar .sidebar-social-icons a[href*="discord.com"], +.sidebar .sidebar-social-icons a[href*="github.com"] { + color: #ffffff !important; +} + +/* Hover effect for icons */ +.sidebar .sidebar-social-icons a:hover { + opacity: 0.8 !important; +} + +/* Fix Bluesky Icon Alignment */ +.sidebar-social-icons img { + width: 24px; + height: 24px; + margin-bottom: -2px; + object-fit: contain; + transition: opacity 0.3s ease; +} + +.sidebar-social-icons img[src*="bluesky"] { + filter: brightness(0) invert(1); +} + +.sidebar-social-icons img:hover { + opacity: 0.8; +} + +.sidebar-search { + display: flex; + justify-content: flex-start; + align-items: center; width: 100%; + padding-left: 0; + margin-left: -20px; + margin-bottom: 20px; } +.sidebar-search-box { + display: flex; + align-items: center; + width: 100%; + max-width: 100%; + text-align: left; + margin-left: 0; + padding-left: 0; +} + +#docsearch { + width: 100%; + max-width: 100%; + text-align: left; + margin-left: 0 !important; + padding-left: 5px; +} diff --git a/public/images/bluesky.svg b/public/images/bluesky.svg new file mode 100644 index 00000000..0f25b8b8 --- /dev/null +++ b/public/images/bluesky.svg @@ -0,0 +1 @@ + \ No newline at end of file From 8cfe66c5e435cba0ae208c3a8d9f32f7292d88a4 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Tue, 11 Mar 2025 10:42:23 +0000 Subject: [PATCH 2/4] address PR review comments --- _config.yml | 9 +- _includes/sidebar.html | 8 +- _posts/2022-11-07-relicensing.md | 2 +- _posts/2023-09-22-licensing-update.md | 2 +- _posts/2023-10-25-towards_3.0.md | 2 +- about.md | 1 + blog/index.html | 1 + pages/about.md | 300 -------------------------- pages/blog/index.html | 38 ---- pages/team.md | 2 +- 10 files changed, 17 insertions(+), 348 deletions(-) delete mode 100644 pages/about.md delete mode 100644 pages/blog/index.html diff --git a/_config.yml b/_config.yml index 53e0574e..637d7c67 100644 --- a/_config.yml +++ b/_config.yml @@ -9,7 +9,7 @@ permalink: pretty title: MDAnalysis name: MDAnalysis tagline: molecular simulations data analysis -description: working with data in molecular sciences +description: working with data in the molecular sciences # long_description is not currently used by the theme long_description: | MDAnalysis is a Python library which enables the handling and @@ -40,7 +40,7 @@ plugins: - jekyll-feed # Blog pagination -paginate_path: "/pages/blog/page:num/" +paginate_path: "/blog/page:num/" paginate: 12 # jekyll-feed @@ -123,3 +123,8 @@ numfocus: sponsored_project: https://numfocus.org/project/mdanalysis donate_button: Donate Now +social: + linkedin: "https://www.linkedin.com/company/mdanalysis/" + bsky: "https://bsky.app/profile/mdanalysis.bsky.social" + discord: "https://discord.com/invite/fXTSfDJyxE" + github: "https://github.com/MDAnalysis/mdanalysis" diff --git a/_includes/sidebar.html b/_includes/sidebar.html index 0e0a3f6a..a3804fc8 100644 --- a/_includes/sidebar.html +++ b/_includes/sidebar.html @@ -11,16 +11,16 @@

- + - + Bluesky - + - +
diff --git a/_posts/2022-11-07-relicensing.md b/_posts/2022-11-07-relicensing.md index 41f7f1d2..034442fa 100644 --- a/_posts/2022-11-07-relicensing.md +++ b/_posts/2022-11-07-relicensing.md @@ -203,4 +203,4 @@ fiscal sponsor, [NumFOCUS][]. [contributors]: https://github.com/MDAnalysis/mdanalysis/blob/develop/package/AUTHORS [faq wiki]: https://github.com/MDAnalysis/mdanalysis/wiki/GPLv2--to-LGPLv3--relicensing-summary-and-FAQ [NumFOCUS]: https://www.numfocus.org -[Core Developers]: {% link pages/about.md %}#mdanalysis-core-developers +[Core Developers]: {% link about.md %}#mdanalysis-core-developers diff --git a/_posts/2023-09-22-licensing-update.md b/_posts/2023-09-22-licensing-update.md index 64f22290..c97d274e 100644 --- a/_posts/2023-09-22-licensing-update.md +++ b/_posts/2023-09-22-licensing-update.md @@ -324,4 +324,4 @@ an advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/1000 [consultation]: {{ site.baseurl }}{% post_url 2022-11-07-relicensing %}#consultation-period-7th-november-until-5th-december-2022 [release 2.6]: {{ site.baseurl }}{% post_url 2023-09-02-release-2.6.1 %} [release 2.5]: {{ site.baseurl }}{% post_url 2023-06-05-releases-2.4.x-2.5.0 %} -[Core Developers]: {% link pages/about.md %}#mdanalysis-core-developers +[Core Developers]: {% link about.md %}#mdanalysis-core-developers diff --git a/_posts/2023-10-25-towards_3.0.md b/_posts/2023-10-25-towards_3.0.md index 3642efe4..fc3d8e22 100644 --- a/_posts/2023-10-25-towards_3.0.md +++ b/_posts/2023-10-25-towards_3.0.md @@ -64,7 +64,7 @@ If you have any feedback on this roadmap or would like to discuss our future pla – Hugo MacDermott-Opeskin on behalf of the MDAnalysis [Core Developers][] -[Core Developers]: {{ site.baseurl }}{% link pages/about.md %}#mdanalysis-core-developers +[Core Developers]: {{ site.baseurl }}{% link about.md %}#mdanalysis-core-developers [Discord]: {{ site.discord.url }} [distopia]: https://github.com/MDAnalysis/distopia [EOSS4]: {{ site.baseurl }}{% post_url 2021-08-31-CZI-EOSS4 %} diff --git a/about.md b/about.md index 54b5ad6c..865056fb 100644 --- a/about.md +++ b/about.md @@ -1,6 +1,7 @@ --- layout: page title: About MDAnalysis +order: 10 --- diff --git a/pages/about.md b/pages/about.md deleted file mode 100644 index a411bf18..00000000 --- a/pages/about.md +++ /dev/null @@ -1,300 +0,0 @@ ---- -layout: page -title: About MDAnalysis -order: 10 ---- - -MDAnalysis - -## Mission - -The MDAnalysis [Community](#community) is interested in all facets of **working -with data in the computational molecular sciences**. We welcome everyone. **We all follow our -[Code of Conduct] and strive to create an environment that is welcoming to -all.** Our primary purpose is to produce software that scientists in academia and -industry will trust to use in their research. - -We develop and maintain projects related to the broader goal of processing and -analyzing data in the computational molecular sciences. We aim to empower users/developers to -work with our packages following [FAIR principles]. Our central package is the -[MDAnalysis library] for the analysis of computer simulations of many-body -systems at the molecular scale. - -We believe that scientific software should be open to all while using best -practices to maintain high standards of correctness and reproducibility. We -emphasize educating our users to make best use of the tools that we produce, to -enable them to become contributors to our community and code bases. - - - -## Community - -**MDAnalysis** is developed and maintained as a freely available, open-source -project by a global community of scientists. The MDAnalysis community adheres -to our [Code of Conduct]({{site.baseurl}}/pages/conduct/) and invites everyone -to [participate]({{site.baseurl}}/#participating) --- be it on GitHub Discussions, -through issue reports, or code contributions. - -All *contributors* to the MDAnalysis library and its subprojects are acknowledged -in a file called `AUTHORS` in each source code repository and in the list of -contributions; as examples see the [`AUTHORS` file for -mdanalysis](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/AUTHORS) -and the [contributors for -MDAnalysis/mdanalysis](https://github.com/MDAnalysis/mdanalysis/graphs/contributors). - -MDAnalysis and the algorithms implemented in the library and the subprojects are -scientific software that are described in [academic -publications]({{site.baseurl}}/pages/citations/). - -MDAnalysis is used in a variety of [other molecular dynamics tools]({{site.baseurl}}/pages/mdakits/). - - -## Open source - -All our [code]({{site.baseurl}}/#availability) and our [teaching -materials]({{site.baseurl}}/pages/learning_MDAnalysis/) are available -under open source licenses from repositories at -[https://github.com/MDAnalysis/](https://github.com/MDAnalysis/). The -MDAnalysis library itself is published under the [GNU General Public -License, version 2](https://www.gnu.org/licenses/gpl-2.0.html); other -supporting libraries are published under the MIT or the BSD-3 clause -licence. - -Installable packages are available through the popular ``pip`` and -``conda`` package managers as well as some Linux distributions. - - -## Governance - -Project leadership is provided by a subset of contributors, the -*MDAnalysis Core Developers* -([@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs)) -who have produced substantial contributions over extended lengths of -time and who remain active in reviewing issues and discussions on -GitHub Discussions and our Discord server. - -### MDAnalysis Core Developers - -The **Core Developers** lead the MDAnalysis project and are responsible to -the community and to NumFOCUS, our fiscal sponsor. They **represent -the project publicly** and **vote to make decisions for the project**. - -PIs on a grant submitted by MDAnalysis via NumFOCUS must be Core Developers -while co-PIs do not have to be Core Developers. - -Core Developers are granted commit rights (write access) to the [GitHub source -code repositories][orgrepo] and thus can approve pull requests for merges. - -The current -[@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs/members) -team ("MDAnalysis Core Developers") consists of: - -- @BradyAJohnston -- @fiona-naughton -- @hmacdope -- @IAlibay -- @jennaswa -- @lilyminium -- @marinegor -- @micaela-matta -- @orbeckst -- @p-j-smith -- @richardjgowers -- @RMeli -- @tylerjereddy -- @yuxuanzhuang - -### MDAnalysis Emeriti Core Developers - -**Emerita/Emeritus Core Developers** are former Core Developers who remain -connected to the project but have stepped back from the day-to-day -decision making. Emeriti Core Developers can reinstate themselves to -Core Developer status. - -Emeriti Core Developers maintain commit rights (write access) to the -[GitHub source code repositories][orgrepo] and can approve pull requests for -merges. - -The current *Emeriti Core Developers* are: - -- @dotsdl -- Elizabeth Denning -- @jandom -- @jbarnoud -- @kain88-de -- @mnmelo -- @mtiberti -- @nmichaud -- @PicoCentauri -- @seb-buch -- @zemanj - -### Decision Making Process and Membership - -1. All decisions are made by *simple majority*[^1] of the [MDAnalysis Core - Developers](#mdanalysis-core-developers). -2. New *Core Developers* are elected with a simple majority of current - MDAnalysis Core Developers. -3. Current Core Developers are polled annually to *opt-in* to remain - a Core Developer; otherwise they transition to [Emerita/Emeritus - Core Developer](#mdanalysis-emeriti-core-developers) status. - -[^1]: A [simple majority][] is defined as *more than half the votes - cast*. Abstentions or blanks are excluded in calculating a - majority vote. Totals do not include votes cast by someone not - entitled to vote[^2] or improper multiple votes by a single - member. Illegal votes[^3] are counted as votes cast; - if only two choices (such as a binary "yes"/"no" vote) are - possible, a majority vote is more "yes" than "no" votes. - -[^2]: See [MDAnalysis Core Developers](#mdanalysis-core-developers) - for the list of *individuals entitled to vote*. - -[^3]: *Illegal votes* are votes that were cast for ineligible choices. - -### Code of Conduct - -Everyone in the MDAnalysis community adheres to our [Code of -Conduct]({{site.baseurl}}/pages/conduct/). A rotating subset of three -MDAnalysis Core Developers is tasked to respond to and to investigate -[Code of Conduct]({{site.baseurl}}/pages/conduct/) violations. - - -## Partners - -MDAnalysis is a [fiscally sponsored -project]({{site.numfocus.sponsored_project}}) of [NumFOCUS][], a nonprofit -dedicated to supporting the open source scientific computing -community. - -If you like MDAnalysis and want to support our mission, please -consider making a [donation]({{site.numfocus.donate}}) to support our -efforts. NumFOCUS is a 501(c)(3) non-profit charity in the United -States; as such, donations to NumFOCUS are tax-deductible as allowed -by law. As with any donation, you should consult with your personal -tax adviser or the IRS about your particular tax situation. - -{{ site.numfocus.donate_button }} - - -## Funding - -We are grateful for financial support from the following organizations, which have supported MDAnalysis either through direct funding or indirectly by funding MDAnalysis contributors. - -### [Chan Zuckerberg Initiative][] (CZI) - -Chan Zuckerberg Initiative - -MDAnalysis has been supported by the [Essential Open Source for Science](https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/) (EOSS) program from the CZI Donor-Advised Fund (DAF), an advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989) - -- EOSS5, 2022-253062 (**2022**): [MDAnalysis: Outreach and Project Manager](https://chanzuckerberg.com/eoss/proposals/mdanalysis-outreach-and-project-manager/) (**Personnel**: @IAlibay, @jennaswa, @micaela-matta, @orbeckst, @richardjgowers (*PI*)) -- EOSS4, DAF2021-237663, DOI [https://doi.org/10.37921/426590wiobus](https://doi.org/10.37921/426590wiobus) (**2021**): [MDAnalysis: Faster, Extensible Molecular Analysis for Reproducible Science](https://chanzuckerberg.com/eoss/proposals/mdanalysis-faster-extensible-molecular-analysis-for-reproducible-science/) (**Personnel**: @fiona-naughton, @hmacdope, @IAlibay, @ianmkenney, @lilyminium, @orbeckst (*PI*), @richardjgowers) - -### [Google](https://opensource.google/) - - Google Summer of Code - -The following contributors were sponsored to work on MDAnalysis through the [Google Summer of Code](https://summerofcode.withgoogle.com/) program. - -- **2024**: @ljwoods2, @lunamorrow, @talagayev -- **2023**: @marinegor, @xhgchen -- **2022**: @aya9aladdin, @BFedder -- **2021**: @ojeda-e, @orionarcher -- **2020**: @cbouy, @hmacdope, @yuxuanzhuang -- **2019**: @NinadBhat -- **2018**: @ayushsuhane, @davidercruz -- **2017**: @utkbansal -- **2016**: @fiona-naughton, @jdetle - - Google Season of Docs - -The following technical writers were sponsored to work on MDAnalysis through the [Google Season of Docs](https://developers.google.com/season-of-docs) program. - -- **2019**: @lilyminium - -### [National Science Foundation](https://www.nsf.gov/) - - -National Science Foundation - -Earlier work was partially supported by the NSF (as part of award ACI-1443054). - -- NSF DIBBS award, ACI-1443054 (**2014**): [CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1443054) (**MDAnalysis Personnel**: @orbeckst) - -The following students were sponsored to work on MDAnalysis through the [NSF Research Experience for Undergraduates](https://www.nsf.gov/crssprgm/reu/) (REU) program. - -- **2021**: @ALescoulie, @edisj -- **2020**: @edisj -- **2019**: @nawtrey -- **2018**: @hfmull -- **2017**: @kaceyaurum -- **2016**: @rbrtdlgd -- **2015**: @ianmkenney - -### [NumFOCUS][] - -NumFOCUS Sponsored - -MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor, as well as through its [Small Development Grants](https://numfocus.org/programs/small-development-grants) (SDG) program. - -- SDG Round 3 (**2024**): Customizable and automated scientific molecular rendering with Molecular Nodes (**Personnel**: @yuxuanzhuang, @BradyAJohnston) -- SDG Round 2 (**2023**): Unified and comprehensive documentation and learning resources for MDAnalysis (**Personnel**: @IAlibay, @jennaswa, @lilyminium, @micaela-matta, @orbeckst) -- SDG Round 2 (**2022**): Improving the organization and content of MDAnalysis teaching materials (**Personnel**: @micaela-matta, @pgbarletta) -- SDG Round 1 (**2020**): Periodic boundary handling and on the fly transformations -- SDG Round 2 (**2018**): MDAnalysis tutorial and hackathon -- SDG Round 1 (**2017**): Widening platform availability for MDAnalysis: Full Python 3 Support - -### [Outreachy](https://www.outreachy.org/) - -Outreachy - -The following contributors were sponsored to work on MDAnalysis through the [Outreachy](https://www.outreachy.org/) program. - -- **2024**: @adetutudeborah -- **2022**: @umak1106 - -### [Station1](https://www.station1.org/) - -Station1 Logo - -The following contributors were sponsored to work on MDAnalysis through the [Station1 Frontiers Fellowship](https://www.station1.org/sff) program. - -- **2023**: @jong9559, @KarenBekhazi - -
- -## Feedback - -MDAnalysis welcomes feedback for improvement from its users and community. If you have any general feedback or comments to make about MDAnalysis, the community, events, or other aspects, please [let us know in this form here](https://forms.gle/n8GLe2QsL2hW2QiDA)! - ------- - -[Code of Conduct]: {{ site.baseurl }}/pages/conduct/ -[MDAnalysis library]: {{ site.github.repo }} -[FAIR principles]: https://www.go-fair.org/fair-principles/ -[NumFOCUS]: https://www.numfocus.org -[simple majority]: https://en.wikipedia.org/wiki/Majority#Majority_vote -[orgrepo]: https://github.com/MDAnalysis -[Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ diff --git a/pages/blog/index.html b/pages/blog/index.html deleted file mode 100644 index 91142459..00000000 --- a/pages/blog/index.html +++ /dev/null @@ -1,38 +0,0 @@ ---- -layout: page -title: Blog -order: 12 ---- - -
- {% for post in paginator.posts %} -
-

- - {{ post.title }} - -

- - {{ post.date | date_to_string }} - - {{ post.content }} -
- {% endfor %} -
- - diff --git a/pages/team.md b/pages/team.md index cd07f8fe..12be7e2f 100644 --- a/pages/team.md +++ b/pages/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 contributing 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 pages/about.md %}#mdanalysis-emeriti-core-developers). +In this section we list major contributors who are currently contributing 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). Names are listed in *alphabetical* order. From 6a4ae608dae50eca83909cb7a061f0878d409755 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 14 Mar 2025 10:31:13 +0100 Subject: [PATCH 3/4] address PR review comments --- _config.yml | 8 ++------ _includes/sidebar.html | 18 +++++++++--------- 2 files changed, 11 insertions(+), 15 deletions(-) diff --git a/_config.yml b/_config.yml index 637d7c67..8f8b860f 100644 --- a/_config.yml +++ b/_config.yml @@ -41,7 +41,7 @@ plugins: # Blog pagination paginate_path: "/blog/page:num/" -paginate: 12 +paginate: 3 # jekyll-feed # - our previous feed was called atom.xml so we use it instead @@ -123,8 +123,4 @@ numfocus: sponsored_project: https://numfocus.org/project/mdanalysis donate_button: Donate Now -social: - linkedin: "https://www.linkedin.com/company/mdanalysis/" - bsky: "https://bsky.app/profile/mdanalysis.bsky.social" - discord: "https://discord.com/invite/fXTSfDJyxE" - github: "https://github.com/MDAnalysis/mdanalysis" + diff --git a/_includes/sidebar.html b/_includes/sidebar.html index a3804fc8..53b06d20 100644 --- a/_includes/sidebar.html +++ b/_includes/sidebar.html @@ -11,16 +11,16 @@

- + - + Bluesky - + - +
@@ -40,14 +40,14 @@

The code below dynamically generates a sidebar nav of pages with `layout: page` in the front-matter. See readme for usage. {% endcomment %} - + {% assign blogpagedir = site.paginate_path | split: ":" | first %} {% assign blogpagedir_len = blogpagedir | size %} {% assign pages_list = site.pages | sort: "order" %} {% for node in pages_list %} - {% if node.title != null%} - {% if node.layout == "page"%} - {% assign prefix = node.url | truncate: blogpagedir_len, '' %} + {% if node.title != null %} + {% if node.layout == "page" %} + {% assign prefix = node.url | truncate: blogpagedir_len, '' %} {% if prefix != blogpagedir %} {{ node.title }} {% endif %} @@ -55,7 +55,7 @@

{% endif %} {% endfor %} - +

© {{ site.time | date: '%Y' }}. All rights reserved.

From 6235184b5081b4a0755cf955cbd27149a7db6a04 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 21 Mar 2025 17:40:52 +0000 Subject: [PATCH 4/4] address PR review comment --- pages/team.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/team.md b/pages/team.md index 12be7e2f..46a3ac53 100644 --- a/pages/team.md +++ b/pages/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 contributing 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.url }}{% link about.md %}#mdanalysis-emeriti-core-developers). Names are listed in *alphabetical* order.