Merge pull request #4695 from galaxyproject/manx-puffin

Add inline contributor badges from `@gtn:username`

_includes/contributor-badge-inline.html

@@ -0,0 +1,9 @@
+{%- assign contributor_badge_entity = site | fetch_contributor: include.id -%}
+{%- assign name = contributor_badge_entity.short_name | default: contributor_badge_entity.name | default: include.id -%}
+<a href="{{ site.baseurl }}/hall-of-fame/{{ include.id }}/" class="contributor-badge-inline contributor-{{ include.id }}">
+  {{ contributor_badge_entity | fetch_entity_avatar:include.id, 36 }}
+  {{ name }}
+{%- if include.activity -%}
+{%- include _includes/contributor-human-icons.html activity=include.activity -%}
+{%- endif -%}
+</a>

_plugins/gtn.rb

@@ -508,6 +508,35 @@ def group_icons(icons)
   post.data['image'] = post.data['cover']
 end
 
+# We're going to do some find and replace, to replace `@gtn:contributorName` with a link to their profile.
+Jekyll::Hooks.register :site, :pre_render do |site|
+  site.posts.docs.each do |post|
+    if post.content
+      post.content = post.content.gsub(/@gtn:([a-zA-Z0-9_-]+)/) do |match|
+        # Get first capture
+        name = match.gsub('@gtn:', '')
+        if site.data['contributors'].key?(name)
+          "{% include _includes/contributor-badge-inline.html id=\"#{name}\" %}"
+        else
+          match
+        end
+      end
+    end
+  end
+  site.pages.each do |page|
+    if page.content
+      page.content = page.content.gsub(/@gtn:([a-zA-Z0-9_-]+)/) do |match|
+        name = match.gsub('@gtn:', '')
+        if site.data['contributors'].key?(name)
+          "{% include _includes/contributor-badge-inline.html id=\"#{name}\" %}"
+        else
+          match
+        end
+      end
+    end
+  end
+end
+
 # Create back-refs for affiliations
 Jekyll::Hooks.register :site, :post_read do |site|
   # Users list affiliations on their profile in site.data['contributors']

assets/css/main.scss

@@ -1175,6 +1175,17 @@ nav[data-toggle='toc'] {
     }
 }
 
+.contributor-badge-inline {
+    /* prevent breaking across lines */
+    white-space: nowrap;
+    img {
+	height: 1em !important;
+	width: 1em !important;
+        border-radius: 50%;
+        margin: 0 0.25em 0 0;
+    }
+}
+
 table.contributions{
     tr td:nth-child(1) {
         display: flex;

news/_posts/2021-03-16-slides_to_videos.md

@@ -10,7 +10,7 @@ This past year has been a struggle for all of us, but one task has become appare
 
 We have found ourselves spending countless hours recording video lectures, producing videos of us giving slide decks, and videos of us giving trainings on how to run tools in Galaxy. Worse, whenever changes were made we would have to re-record lessons!
 
-Inspired by the efforts of {% include _includes/contributor-badge.html id="delphine-l" %} in her [video-lectures](https://github.com/galaxyproject/video-lectures/) series, {% include _includes/contributor-badge.html id="hexylena" %} has implemented a similar feature of automatic Text-to-Speech (TTS) in the [Galaxy Training Network]({% link topics/contributing/tutorials/slides-with-video/tutorial.md %}).
+Inspired by the efforts of @gtn:delphine-l in her [video-lectures](https://github.com/galaxyproject/video-lectures/) series, @gtn:hexylena has implemented a similar feature of automatic Text-to-Speech (TTS) in the [Galaxy Training Network]({% link topics/contributing/tutorials/slides-with-video/tutorial.md %}).
 
 The GTN had existing infrastructure for producing slide decks from easy-to-maintain markdown documents, and, key to the success, existing syntax for writing "Speaker Notes" on slides. These were intended to be little reminders to instructors giving slide decks about what they should say on each slide.
 

news/_posts/2021-04-06-new-video-player.md

@@ -8,6 +8,6 @@ coveralt: Example of video player mimicking youtube's interface with a video at
 layout: news
 ---
 
-One of our contributors ({% include _includes/contributor-badge.html id="mtekman" %}) found himself wanting to link to a specific time point in a video. We said "Wow, what a fantastic idea!" and then we implemented it. To support that we developed a very simple standalone video player page where you can view the GTN videos and browse through our catalog. It features the full transcript on the left, some suggested videos on the right, and a very standard `<video>` player.
+One of our contributors (@gtn:mtekman) found himself wanting to link to a specific time point in a video. We said "Wow, what a fantastic idea!" and then we implemented it. To support that we developed a very simple standalone video player page where you can view the GTN videos and browse through our catalog. It features the full transcript on the left, some suggested videos on the right, and a very standard `<video>` player.
 
 Check out the [new GTN Video home now]({{site.baseurl}}/videos/) now.

news/_posts/2021-05-20-spanish_project_begins.md

@@ -9,6 +9,6 @@ tutorial: "topics/introduction/tutorials/galaxy-intro-short/tutorial_ES.html"
 layout: news
 ---
 
-¡El primer tutorial en español ya está disponible! Galaxy siempre ha tenido tutoriales traducidos automáticamente mediante Google-Translate, ahora nos estamos embarcando en un nuevo proyecto para estudiar la experiencia de aprendizaje con tutoriales en bioinformática traducidos por humanos. Nuestro objetivo es crear un paquete de tutoriales para el análisis de datos single-cell (célula única) en primera instancia, con el fin de estudiar su uso y utilidad en un taller para hablantes nativos de español. Agradecemos enormemente a las nuevas participantes {% include _includes/contributor-badge.html id="pclo" %} y {% include _includes/contributor-badge.html id="ales-ibt" %} (EMBL-EBI) así como a las miembros existentes de GTN {% include _includes/contributor-badge.html id="beatrizserrano" %} (University of Freiburg), {% include _includes/contributor-badge.html id="shiltemann" %} & {% include _includes/contributor-badge.html id="hexylena" %} (Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a {% include _includes/contributor-badge.html id="nomadscientist" %} (The Open University/EBI) como líder de proyecto.
+¡El primer tutorial en español ya está disponible! Galaxy siempre ha tenido tutoriales traducidos automáticamente mediante Google-Translate, ahora nos estamos embarcando en un nuevo proyecto para estudiar la experiencia de aprendizaje con tutoriales en bioinformática traducidos por humanos. Nuestro objetivo es crear un paquete de tutoriales para el análisis de datos single-cell (célula única) en primera instancia, con el fin de estudiar su uso y utilidad en un taller para hablantes nativos de español. Agradecemos enormemente a las nuevas participantes @gtn:pclo y @gtn:ales-ibt (EMBL-EBI) así como a las miembros existentes de GTN @gtn:beatrizserrano (University of Freiburg), @gtn:shiltemann & @gtn:hexylena (Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a @gtn:nomadscientist (The Open University/EBI) como líder de proyecto.
 
-The first Spanish tutorial is live! Galaxy has always had google-translated tutorials, but we are now embarking on a project to assess the learning experience with human-translated, vs google-translated, bioinformatics tutorials. We are aiming to create a package of tutorials for single-cell analysis, in the first instance, and survey usage and utility in a workshop for native Spanish speakers. A big thanks to new contributors {% include _includes/contributor-badge.html id="pclo" %} and {% include _includes/contributor-badge.html id="ales-ibt" %} (EMBL-EBI), as well as GTN overlords {% include _includes/contributor-badge.html id="beatrizserrano" %} (University of Freiburg), {% include _includes/contributor-badge.html id="shiltemann" %} & {% include _includes/contributor-badge.html id="hexylena" %} (Erasmus-MC), for their hard work on this project from translation to sustainability, and, of course, {% include _includes/contributor-badge.html id="nomadscientist" %} (The Open University/EBI) for leading the project!
+The first Spanish tutorial is live! Galaxy has always had google-translated tutorials, but we are now embarking on a project to assess the learning experience with human-translated, vs google-translated, bioinformatics tutorials. We are aiming to create a package of tutorials for single-cell analysis, in the first instance, and survey usage and utility in a workshop for native Spanish speakers. A big thanks to new contributors @gtn:pclo and @gtn:ales-ibt (EMBL-EBI), as well as GTN overlords @gtn:beatrizserrano (University of Freiburg), @gtn:shiltemann & @gtn:hexylena (Erasmus-MC), for their hard work on this project from translation to sustainability, and, of course, @gtn:nomadscientist (The Open University/EBI) for leading the project!

news/_posts/2021-05-25-abbreviations-tag.md

@@ -7,7 +7,7 @@ tutorial: "topics/dev/tutorials/bioblend-dev/tutorial.html"
 layout: news
 ---
 
-Thanks to the great tutorial developed by first time contributor {% include _includes/contributor-badge.html id="rikeshi" %} and edited by {% include _includes/contributor-badge.html id="simonbray" %}, we noticed that they defined a number of abbreviations and re-used those throughout their tutorial.
+Thanks to the great tutorial developed by first time contributor @gtn:rikeshi and edited by @gtn:simonbray, we noticed that they defined a number of abbreviations and re-used those throughout their tutorial.
 
 As the GTN is intended to be easy for contributors and easy for learners, we wanted to make use of the [`<abbr>`](https://developer.mozilla.org/en-US/docs/Web/HTML/Element/abbr) tag which allows you to define commonly re-used terms in your HTML. However this is a bit clumsy to write every time, so we've implemented a tag and some metadata which permits easily defining and referencing abbreviations throughout your text.
 

news/_posts/2021-05-25-new-dev-tutorial.md

@@ -7,5 +7,5 @@ tutorial: "topics/dev/tutorials/bioblend-dev/tutorial.html"
 layout: news
 ---
 
-The first of the developer tutorials for GCC2021 is live, first time contributor {% include _includes/contributor-badge.html id="rikeshi" %} has produced a fantastic tutorial covering how to develop new functions in BioBlend for new APIs in Galaxy. Many thanks to {% include _includes/contributor-badge.html id="simonbray" %} for editing!
+The first of the developer tutorials for GCC2021 is live, first time contributor @gtn:rikeshi has produced a fantastic tutorial covering how to develop new functions in BioBlend for new APIs in Galaxy. Many thanks to @gtn:simonbray for editing!
 

news/_posts/2021-07-27-a11y.md

@@ -17,4 +17,4 @@ Additionally we've made a number of other minor accessibility improvements:
 - Remove repetitive image labels on author badges.
 - etc.
 
-Some of these were done after ({% include _includes/contributor-badge.html id="hexylena" %}) learned to use Android's TalkBack and noticed the site could be unpleasant to go through. While absolutely not a replacement for someone who deeply understands the needs of visually impaired users or experiences such needs themselves, hopefully this makes the GTN a little bit more pleasant for everyone.
+Some of these were done after (@gtn:hexylena) learned to use Android's TalkBack and noticed the site could be unpleasant to go through. While absolutely not a replacement for someone who deeply understands the needs of visually impaired users or experiences such needs themselves, hopefully this makes the GTN a little bit more pleasant for everyone.

topics/admin/tutorials/gxadmin/tutorial.md

@@ -27,7 +27,7 @@ We will just briefly cover the features available in `gxadmin`, there are lots o
 
 It started life as a small shell script that Helena wrote because she couldn't remember what [Gravity](https://github.com/galaxyproject/gravity) was called or where it could be found. Some of the functions needed for things like swapping zerglings are still included in gxadmin but are highly specific to UseGalaxy.eu and not generally useful.
 
-Since then it became the home for "all of the SQL queries we [galaxy admins] run regularly." @hexylena and @natefoo often shared SQL queries with each other in private chats, but this wasn't helpful to the admin community at large, so they decided to put them all in `gxadmin` and make it as easy to install as possible. We are continually trying to make this tool more generic and generally useful, if you notice something that's missing or broken, or have a new query you want to run, just [let us know](https://github.com/usegalaxy-eu/gxadmin/issues/new).
+Since then it became the home for "all of the SQL queries we [galaxy admins] run regularly." @gtn:hexylena and @gtn:natefoo often shared SQL queries with each other in private chats, but this wasn't helpful to the admin community at large, so they decided to put them all in `gxadmin` and make it as easy to install as possible. We are continually trying to make this tool more generic and generally useful, if you notice something that's missing or broken, or have a new query you want to run, just [let us know](https://github.com/usegalaxy-eu/gxadmin/issues/new).
 
 > <agenda-title></agenda-title>
 >
@@ -148,7 +148,7 @@ Meta          | `meta`              | More miscellaneous commands, and a built-i
 
 ## Admin Favourite Queries
 
-**@slugger70's favourite**: `gxadmin query old-histories`. He contributed this function to find old histories, as their instance has a 90 day limit on histories, anything older than that might be automatically removed. This helps their group identify any histories that can be purged in order to save space. Running this on UseGalaxy.eu, we have some truly ancient histories, and maybe could benefit from a similar policy.
+**@gtn:slugger70's favourite**: `gxadmin query old-histories`. He contributed this function to find old histories, as their instance has a 90 day limit on histories, anything older than that might be automatically removed. This helps their group identify any histories that can be purged in order to save space. Running this on UseGalaxy.eu, we have some truly ancient histories, and maybe could benefit from a similar policy.
 
 > <code-in-title></code-in-title>
 > ```
@@ -169,7 +169,7 @@ Meta          | `meta`              | More miscellaneous commands, and a built-i
 >
 {: .code-out}
 
-**@natefoo's favourite**: `gxadmin query job-inputs`. He contributed this function which helps him debug jobs which are not running and should be.
+**@gtn:natefoo's favourite**: `gxadmin query job-inputs`. He contributed this function which helps him debug jobs which are not running and should be.
 
 > <code-in-title></code-in-title>
 > ```
@@ -183,7 +183,7 @@ hda-id   | hda-state | hda-deleted | hda-purged |  d-id   | d-state | d-deleted
 8638195  |           | f           | f          | 8246852 | running | f         | f        | files9
 8638195  |           | f           | f          | 8246852 | running | f         | f        | files9
 
-**@bgruening's favourite**: `gxadmin query latest-users` let's us see who has recently joined our server. We sometimes notice that people are running a training on our infrastructure and they haven't registered for [training infrastructure as a service](https://galaxyproject.eu/tiaas) which helps us coordinate infrastructure for them so they don't have bad experiences.
+**@gtn:bgruening's favourite**: `gxadmin query latest-users` let's us see who has recently joined our server. We sometimes notice that people are running a training on our infrastructure and they haven't registered for [training infrastructure as a service](https://galaxyproject.eu/tiaas) which helps us coordinate infrastructure for them so they don't have bad experiences.
 
 > <code-in-title></code-in-title>
 > ```
@@ -199,7 +199,7 @@ id    |        create_time         | disk_usage | username | email | groups | ac
 3934  | 2019-01-27 10:06:40.973938 | 0 bytes    | xxxx     | xxxx  |        | f
 3933  | 2019-01-27 10:01:22.562782 |            | xxxx     | xxxx  |        | f
 
-**@hexylena's favourite** `gxadmin report job-info`. This command gives more information than you probably need on the execution of a specific job, formatted as markdown for easy sharing with fellow administrators.
+**@gtn:hexylena's favourite** `gxadmin report job-info`. This command gives more information than you probably need on the execution of a specific job, formatted as markdown for easy sharing with fellow administrators.
 
 > <code-in-title></code-in-title>
 > ```
@@ -273,7 +273,7 @@ id    |        create_time         | disk_usage | username | email | groups | ac
 > ```
 {: .code-out}
 
-**@cat-bro** contributed the 'jobs' query: `gxadmin query jobs` lets you list jobs that have been run on your Galaxy. It's a **lot** more flexible than `queue-overview` and we suggest using it instead, in most places. E.g. to find `circos` jobs that were recently run:
+**@gtn:cat-bro contributed** the 'jobs' query: `gxadmin query jobs` lets you list jobs that have been run on your Galaxy. It's a *lot* more flexible than `queue-overview` and we suggest using it instead, in most places. E.g. to find `circos` jobs that were recently run:
 
 
 > <code-in-title></code-in-title>

topics/assembly/tutorials/debruijn-graph-assembly/tutorial.md

@@ -27,7 +27,7 @@ contributors:
 
 In this activity, we will perform *de novo* assemblies of a short read set using the Velvet Optimiser and the SPAdes assemblers. We are using the Velvet Optimiser for illustrative purposes. For real assembly work, a more suitable assembler should be chosen - such as SPAdes.
 
-The Velvet Optimiser is a script written by {% include _includes/contributor-badge.html id="slugger70" %} to optimise the k-mer size and coverage cutoff parameters for Velvet. More information can be found [in its repository](https://github.com/slugger70/VelvetOptimiser).
+The Velvet Optimiser is a script written by @gtn:slugger70 to optimise the k-mer size and coverage cutoff parameters for Velvet. More information can be found [in its repository](https://github.com/slugger70/VelvetOptimiser).
 
 SPAdes is a de novo genome assembler written by Pavel Pevzner's group in St. Petersburg. More details on it can be found [on Spades' website](http://cab.spbu.ru/software/spades/)>
 

topics/dev/tutorials/tool-generators-advanced/tutorial.md

@@ -1044,8 +1044,8 @@ Thanks all! It has been a lot of fun.
 
 Special thanks to:
 
-- {% include _includes/contributor-badge.html id="hexylena" %} for
+- @gtn:hexylena for
     - review and contribution to the tutorial and associated code.
     - the vision of instant installation of generated tools for developer feedback.
     - elegantly generated lint-free XML provided by [galaxyml code](https://github.com/hexylena/galaxyxml)
-- {% include _includes/contributor-badge.html id="mvdbeek" %} for thoughtful comments on the role of the ToolFactory that helped motivate the tutorial.
+- @gtn:mvdbeek for thoughtful comments on the role of the ToolFactory that helped motivate the tutorial.

topics/dev/tutorials/tool-generators/tutorial.md

@@ -627,8 +627,8 @@ Thanks all! It has been a lot of fun.
 
 Special thanks to:
 
-- {% include _includes/contributor-badge.html id="hexylena" %} for
+- @gtn:hexylena for
     - review and contribution to the tutorial and associated code.
     - the vision of instant installation of generated tools for developer feedback.
     - elegantly generated lint-free XML provided by [galaxyml code](https://github.com/hexylena/galaxyxml)
-- {% include _includes/contributor-badge.html id="mvdbeek" %} for thoughtful comments on the role of the ToolFactory that helped motivate the tutorial.
+- @gtn:mvdbeek for thoughtful comments on the role of the ToolFactory that helped motivate the tutorial.