Merge branch 'MDAnalysis:master' into gsoc-intro

Author: jennaswa

Gemfile

@@ -1,7 +1,18 @@
 source 'https://rubygems.org'
-ruby "~> 2.6"
+ruby ">= 2.7", "< 4"
 
-gem 'ffi', '=1.16.3'
 gem 'github-pages'
 gem 'rouge'
 gem "webrick", "~> 1.7"
+
+# rdiscount is a dependency of github-pages but earlier
+# version may trigger issue https://github.com/davidfstr/rdiscount/issues/145
+# (at least on macOS) so we explicitly pin here
+gem "rdiscount", ">= 2.2.0.2"
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library; see https://jekyllrb.com/docs/installation/windows/
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end

INSTALL.md

@@ -0,0 +1,139 @@
+# Running Jekyll locally
+
+Follow the [GitHub: Testing your GitHub Pages site locally with
+Jekyll](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/testing-your-github-pages-site-locally-with-jekyll) instructions
+
+Two possible approaches: Either install `ruby` (>= 2.7) and
+[jekyll](https://jekyllrb.com/) locally or use a Docker image with a
+jekyll installation. The local ruby/jekyll is more flexible if you can
+get it to work.
+
+## Local jekyll installation
+
+Basically follow [GitHub: Testing your GitHub Pages site locally with
+Jekyll](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/testing-your-github-pages-site-locally-with-jekyll)
+and in particular [Jekyll's  installation
+instructions](https://jekyllrb.com/docs/installation/).
+
+
+### macOS
+
+Do not use the system ruby (i.e., not `/usr/bin/ruby`) but install
+your own version. The [Jekyll macOS
+instructions](https://jekyllrb.com/docs/installation/macos/) use
+[homebrew](https://brew.sh/) but this works equally well with
+[macports](https://www.macports.org/). 
+
+#### Overview
+
+1. Use `chruby` and `ruby-install` to manage different ruby versions.
+2. Build ruby 3.4.1 (this was the recommended version in the Jekyll
+   instructions at the time)
+3. Install all necessary gems from [Gemfile][] with `bundle`.
+
+
+#### ruby installation with macports
+
+Install `chruby` and `ruby-install`: On macos with macports
+
+    sudo port install chruby ruby-install
+
+Update `~/.bash_profile` (or your `~/.zshrc`) with
+
+    # chruby (macports)
+    source /opt/local/share/chruby/chruby.sh
+
+    # To enable auto-switching of Rubies specified by .ruby-version files, add the
+    # following to ~/.bash_profile or ~/.zshrc:
+    source /opt/local/share/chruby/auto.sh
+
+Install ruby (compile from source, this requires Xcode and development
+tools on macOS and will take a while):
+
+    ruby-install ruby 3.4.1
+
+Switch to using it (can also be added to `~/.bash_profile`)
+
+    chruby ruby-3.4.1
+
+To always activate this version, add a `.ruby-version` file in the
+directory with the `Gemfile` (see [How to install different versions
+of ruby and automatically switch between them](https://www.moncefbelyamani.com/how-to-install-xcode-homebrew-git-rvm-ruby-on-mac/#how-to-install-different-versions-of-ruby-and-switch-between-them)
+-- also needs chruby to be active):
+
+    echo "3.4.1" > .ruby-version
+
+(May need to open a new terminal to let `.bash_profile` changes to take effect).
+
+
+### All OS: install gems (including jekyll)
+
+Ensure that the correct version of ruby is use (`ruby --version`) and
+then 
+
+    bundle install
+	
+should download and build the appropriate gems.
+
+The `Gemfile.lock` should show something like
+```ruby
+GEM
+  remote: https://rubygems.org/
+  specs:
+    ...
+    github-pages (232)
+      github-pages-health-check (= 1.18.2)
+      jekyll (= 3.10.0)
+      ...
+```
+
+### Run jekyll locally
+
+Start jekyll and have it serve the site at http://127.0.0.1:4000
+```bash
+rm -r _site
+bundle exec jekyll serve --watch --livereload --future --incremental
+```
+
+(See the [serve commandline
+options](https://jekyllrb.com/docs/configuration/options/#serve-command-options)
+for more details.)
+
+
+
+## Docker image
+
+### macOS docker installation
+
+- install Docker Desktop https://docs.docker.com/desktop/install/mac-install/
+- start docker
+- follow the solution from  https://stackoverflow.com/a/58850151/ as
+  described next
+
+
+### Build the site
+
+To build the static site, run `jekyll build` inside docker:
+```bash
+export JEKYLL_VERSION=4.0
+docker run --rm \
+  --volume="$PWD:/srv/jekyll" \
+  -it jekyll/jekyll:$JEKYLL_VERSION \
+  jekyll build
+```
+The static site files are stored in the `_site` directory.
+
+### Serve the static site
+
+Then you must *serve* the site:
+```bash
+cd _site
+python -m http.serve
+```
+
+Point your browser to http://localhost:8000
+
+When you make changes, you need to re-build the site.
+
+
+

README.md

@@ -201,7 +201,7 @@ described next:
 
 To **build the static site**, run `jekyll build` inside docker:
 ```bash
-export JEKYLL_VERSION=3.8
+export JEKYLL_VERSION=4.0
 docker run --rm \
   --volume="$PWD:/srv/jekyll" \
   -it jekyll/jekyll:$JEKYLL_VERSION \
@@ -227,27 +227,28 @@ will appear on the web.*
 #### Build site locally ####
 
 To run Jekyll in a way that matches the GitHub Pages build server, run `Jekyll`
-with `Bundler`. Use the command
+with `Bundler`. See [INSTALL](INSTALL.md) for notes on how to install Jekyll
+locally.
 
-    bundle exec jekyll serve
+Use the command
+
+    bundle exec jekyll serve --watch --livereload --future --incremental
 
 in the root of your repository (after switching to the gh-pages branch for
 project repositories), and your site should be available at
 <http://localhost:4000>. 
 
-For a full list of Jekyll commands, see the [Jekyll
-documentation](https://jekyllrb.com/docs/).
+Running Jekyll locally has the advantage that you can have it update
+the site continuously while you're editing files.
 
+(See the [serve commandline
+options](https://jekyllrb.com/docs/configuration/options/#serve-command-options)
+for more details.)
 
-##### Advanced Jekyll usage #####
+For a full list of Jekyll commands, see the [Jekyll
+documentation](https://jekyllrb.com/docs/).
 
-Running Jekyll locally has the advantage that you can have it update
-the site continuously while you're editing files:
 
-    bundle exec jekyll serve --livereload
-	
-In this way, the site is immediately rebuilt when you save changes to
-a file. 
 
 
 ##### Updating the github-pages plugin #####
@@ -261,6 +262,12 @@ with
 
 ##### Problems with jekyll and required packages? #####
 
+* See [INSTALL](INSTALL.md) and if in doubt, follow the latest instructions from
+  [GitHub: Testing your GitHub Pages site locally with
+  Jekyll](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/testing-your-github-pages-site-locally-with-jekyll)
+  and in particular [Jekyll's installation
+  instructions](https://jekyllrb.com/docs/installation/)
+
 * **Problems with installing jekyll/github-pages?** If the standard
   installation for jekyll does not work for you (many people complain,
   for instance, *commonmarker* does not install

_config.yml

@@ -24,7 +24,7 @@ url:              https://www.mdanalysis.org
 baseurl:          
 author:
   name:           The MDAnalysis Team
-  url:            https://twitter.com/mdanalysis
+  url:            https://www.mdanalysis.org/pages/team/
   email:          [email protected]
 
 images:           /public/images
@@ -49,6 +49,11 @@ paginate:        3
 feed:
   path: atom.xml
 
+# do not build these files/dirs:
+# see https://jekyllrb.com/docs/configuration/options/#global-configuration
+# (explicitly include the defaults for jekyll 3.x)
+exclude: [".sass-cache/", "gemfiles/", ".jekyll-cache/", "Gemfile", "Gemfile.lock", "README.md", "**/README.md", "INSTALL.md"]
+
 # Custom vars
 version:          2.0.0
 
@@ -63,6 +68,10 @@ pypi:
   package:        https://pypi.org/project/MDAnalysis
   tests:          https://pypi.org/project/MDAnalysisTests
   docs:           https://docs.mdanalysis.org
+mdakits:
+  registry:       https://mdakits.mdanalysis.org/mdakits.html
+  guide:          https://mdakits.mdanalysis.org/makingakit.html 
+  issues:         https://github.com/MDAnalysis/MDAKits/issues
 mailinglists:
   discussion:
     name:         GitHub Discussions
@@ -76,6 +85,12 @@ mailinglists:
 twitter:
   name:           mdanalysis
   url:            https://twitter.com/mdanalysis
+linkedin:
+  name:           mdanalysis
+  url:            https://linkedin.com/company/mdanalysis
+bluesky:
+  name:           mdanalysis.bsky.social
+  url:            https://bsky.app/profile/mdanalysis.bsky.social
 discord:
   name:           MDAnalysis
   url:            https://discord.com/channels/807348386012987462/
@@ -90,6 +105,8 @@ docs:
   userguide:
     name:         User Guide
     url:          https://userguide.mdanalysis.org
+    repo:         https://github.com/MDAnalysis/UserGuide
+    issues:       https://github.com/MDAnalysis/UserGuide/issues
   quickstart:
     name:         Quick Start Guide
     url:          https://userguide.mdanalysis.org/stable/examples/quickstart.html
@@ -106,3 +123,4 @@ numfocus:
   sponsored_project: https://numfocus.org/project/mdanalysis
   donate_button:     <a href="https://numfocus.org/donate-to-mdanalysis" target="_blank" style="background:#FF9200;padding:10px;margin:10px 0px;text-align:center;text-decoration:none;font-size:12pt;color:#000000;display:inline-block;border-radius:3px">Donate Now</a>
 
+

_data/team/roles/community_engagement.yml

@@ -1,7 +1,10 @@
 role: Community engagement
 tasks: 
-  - Responding to questions on Discord and GitHub Discussions
-  - Managing and triaging conversations on Discord and GitHub Discussions
+  - Responding to questions on [Discord]({{ site.discord.url }}) and [GitHub Discussions]({{ site.mailinglists.discussion.url }})
+  - Managing and triaging conversations on [Discord]({{ site.discord.url }}) and [GitHub Discussions]({{ site.mailinglists.discussion.url }})
+  - General management and administration of social accounts (i.e., [LinkedIn]({{ site.linkedin.url}}), [Bluesky]({{ site.bluesky.url }})), [website]({{ site.url }}), and [blog]({{ site.blog }}), including...
+    - *Posting announcements of new developments*
+    - *Moderating content*
 
 current_members:
   - "[Brady Johnston](https://github.com/bradyajohnston)"

_data/team/roles/core_library_maintenance.yml

@@ -33,8 +33,9 @@ subroles:
 
   - subrole: General maintenance
     tasks:
-      - Monitoring and acting on maintenance needs across the MDAnalysis ecosystem
-      - Standards compliance (e.g. managing metadata such as the author list)
+      - Monitoring maintenance needs across the MDAnalysis ecosystem
+      - Acting on maintenance needs, or delegating to appropriate managers of sub-projects, as necessary
+      - Standards compliance (e.g., managing metadata such as the author list)
       - Tracking new dependencies
       - Emergency fixes
       - Other general maintenance tasks

_data/team/roles/documentation.yml

@@ -11,6 +11,8 @@ current_members:
   - "[Egor Marin](https://github.com/marinegor)"
   - "[Irfan Alibay](https://github.com/IAlibay)"
   - "[Lily Wang](https://github.com/lilyminium)"
+  - "[Micaela Matta](https://github.com/micaela-matta)"
+  - "[Namir Oues](https://github.com/namiroues) (technical writer)"
+  - "[Oliver Beckstein](https://github.com/orbeckst)"
   - "[Rocco Meli](https://github.com/RMeli)"
-
-
+  

_data/team/roles/external_liaison.yml

@@ -6,5 +6,7 @@ tasks:
 
 current_members:
   - "[Irfan Alibay](https://github.com/IAlibay)"
-  - "[Oliver Beckstein](https://github.com/orbeckst)"
   - "[Jenna Swarthout Goddard](https://github.com/jennaswa)"
+  - "[Micaela Matta](https://github.com/micaela-matta)"
+  - "[Oliver Beckstein](https://github.com/orbeckst)"
+  - "[Yuxuan Zhuang](https://github.com/yuxuanzhuang)"

_data/team/roles/mdakit_registry.yml

@@ -3,7 +3,7 @@ tasks:
   - Managing submissions to MDAKits registry
   - Managing manual review process of new MDAKits
   - Managing automated test and badge infrastructure of all MDAKits
-  - Manage helping with MDAKits who need assistance
+  - Offer input on failures due to the MDAKit registry
 current_members:
   - "[Irfan Alibay](https://github.com/IAlibay)"
   - "[Fiona Naughton](https://github.com/fiona-naughton)"

_data/team/roles/outreach.yml

@@ -2,14 +2,18 @@ role: Outreach
 subroles:
   - subrole: Workshops and meetings
     tasks:
-    - Identifying workshop and event opportunities
+    - Identifying workshop and event opportunities and sponsors
     - Organising workshops and events
     - Gathering and coordinating volunteers
     - Managing content, presentations and teaching at workshops
+    - Managing teaching materials on GitHub for workshops and events
+    - Maintaining and fixing materials
     current_members:
       - "[Brady Johnston](https://github.com/bradyajohnston)"
       - "[Jenna Swarthout Goddard](https://github.com/jennaswa)"
       - "[Micaela Matta](https://github.com/micaela-matta)"
+      - "[Rocco Meli](https://github.com/RMeli)"
+      - "[Yuxuan Zhuang](https://github.com/yuxuanzhuang)"
 
   - subrole: Mentoring programs
     tasks:
@@ -21,12 +25,3 @@ subroles:
       - "[Egor Marin](https://github.com/marinegor)"
       - "[Jenna Swarthout Goddard](https://github.com/jennaswa)"
       - "[Google Summer of Code (GSoC) mentors](https://github.com/MDAnalysis/mdanalysis/wiki/Google-Summer-Of-Code#available-mentors)"
-    
-  - subrole: Teaching materials
-    tasks:
-      - Managing teaching materials on GitHub for workshops and events
-      - Maintaining and fixing materials
-    current_members:
-      - "[Rocco Meli](https://github.com/RMeli)"
-      - "[Micaela Matta](https://github.com/micaela-matta)"
-      - "[Jenna Swarthout Goddard](https://github.com/jennaswa)"