Fix many new linting complaints with news checking

faqs/misc.bib

@@ -1,89 +1,95 @@
 @article{Rahbari_2009,
-	doi = {10.2144/000113089},
-	url = {https://doi.org/10.2144%2F000113089},
-	year = 2009,
-	month = {apr},
-	publisher = {Future Science Ltd},
-	volume = {46},
-	number = {4},
-	pages = {277--284},
-	author = {Raheleh Rahbari and Tom Sheahan and Vasileios Modes and Pam Collier and Catriona Macfarlane and Richard M. Badge},
-	title = {A novel L1 retrotransposon marker for {HeLa} cell line identification},
-	journal = {BioTechniques}}
+	title        = {A novel L1 retrotransposon marker for {HeLa} cell line identification},
+	author       = {Raheleh Rahbari and Tom Sheahan and Vasileios Modes and Pam Collier and Catriona Macfarlane and Richard M. Badge},
+	year         = 2009,
+	month        = {apr},
+	journal      = {BioTechniques},
+	publisher    = {Future Science Ltd},
+	volume       = 46,
+	number       = 4,
+	pages        = {277--284},
+	doi          = {10.2144/000113089},
+	url          = {https://doi.org/10.2144%2F000113089},
+}
 }
-
 @article{Beskow_2016,
-	doi = {10.1146/annurev-genom-083115-022536},
-	url = {https://doi.org/10.1146%2Fannurev-genom-083115-022536},
-	year = 2016,
-	month = {aug},
-	publisher = {Annual Reviews},
-	volume = {17},
-	number = {1},
-	pages = {395--417},
-	author = {Laura M. Beskow},
-	title = {Lessons from {HeLa} Cells: The Ethics and Policy of Biospecimens},
-	journal = {Annual Review of Genomics and Human Genetics}
+	title        = {Lessons from {HeLa} Cells: The Ethics and Policy of Biospecimens},
+	author       = {Laura M. Beskow},
+	year         = 2016,
+	month        = {aug},
+	journal      = {Annual Review of Genomics and Human Genetics},
+	publisher    = {Annual Reviews},
+	volume       = 17,
+	number       = 1,
+	pages        = {395--417},
+	doi          = {10.1146/annurev-genom-083115-022536},
+	url          = {https://doi.org/10.1146%2Fannurev-genom-083115-022536},
 }
-
 @misc{lacks_family_2013,
-	title = {Family of Henrietta Lacks Will Have Say in How Her Genetic Material is Used},
-	url = {https://hub.jhu.edu/2013/08/08/henrietta-lacks-hela-cells-agreement/},
-	publisher = {Johns Hopkins University},
-	author = {Johns Hopkins University},
-	month = aug,
-	year = {2013}
+	title        = {Family of Henrietta Lacks Will Have Say in How Her Genetic Material is Used},
+	author       = {Johns Hopkins University},
+	year         = 2013,
+	month        = aug,
+	publisher    = {Johns Hopkins University},
+	url          = {https://hub.jhu.edu/2013/08/08/henrietta-lacks-hela-cells-agreement/},
 }
-
 @misc{jhu_construction_announcement,
-	title = {Johns Hopkins presents initial design of building named in honor of Henrietta Lacks},
-	url = {https://hub.jhu.edu/2022/11/13/henrietta-lacks-building-design-update/},
-	publisher = {Johns Hopkins University},
-	author = {Johns Hopkins University},
-	month = nov,
-	year = {2022}
+	title        = {Johns Hopkins presents initial design of building named in honor of Henrietta Lacks},
+	author       = {Johns Hopkins University},
+	year         = 2022,
+	month        = nov,
+	publisher    = {Johns Hopkins University},
+	url          = {https://hub.jhu.edu/2022/11/13/henrietta-lacks-building-design-update/},
 }
-
 # https://www.who.int/news-room/fact-sheets/detail/tuberculosis
 @misc{who_tuberculosis_2023,
-	title = {Tuberculosis},
-	url = {https://www.who.int/news-room/fact-sheets/detail/tuberculosis},
-	urldate = {2023-04-21},
-	author = {{WHO}},
-	month = apr,
-	year = {2023}
+	title        = {Tuberculosis},
+	author       = {{Who}},
+	year         = 2023,
+	month        = apr,
+	url          = {https://www.who.int/news-room/fact-sheets/detail/tuberculosis},
+	urldate      = {2023-04-21},
 }
-
-@misc{ enwiki:1153394091,
-	author = "{Wikipedia contributors}",
-	title = "Alan L. Hart --- {Wikipedia}{,} The Free Encyclopedia",
-	year = "2023",
-	url = "https://en.wikipedia.org/w/index.php?title=Alan_L._Hart&oldid=1153394091",
-	note = "[Online; accessed 2-June-2023]"
+@misc{enwiki:1153394091,
+	title        = {Alan L. Hart --- {Wikipedia}{,} The Free Encyclopedia},
+	author       = {{Wikipedia contributors}},
+	year         = 2023,
+	url          = {https://en.wikipedia.org/w/index.php?title=Alan_L._Hart&oldid=1153394091},
+	note         = {[Online; accessed 2-June-2023]},
 }
-
 # https://www.cdc.gov/globalhealth/newsroom/topics/tb/index.html
 @misc{cdc_tuberculosis_2020,
-	title = {Tuberculosis},
-	url = {https://www.cdc.gov/globalhealth/newsroom/topics/tb/index.html},
-	urldate = {2020-04-06},
-	author = {{CDC}},
-	month = apr,
-	year = {2020}
+	title        = {Tuberculosis},
+	author       = {{Cdc}},
+	year         = 2020,
+	month        = apr,
+	url          = {https://www.cdc.gov/globalhealth/newsroom/topics/tb/index.html},
+	urldate      = {2020-04-06},
 }
-
-
-
 # doi = {10.1001/jama.1943.02840440079032}, This one isn't in scihub.
 @article{hart1943,
-	doi = {10.1093/ptj/23.4.190},
-	url = {https://doi.org/10.1093%2Fptj%2F23.4.190},
-	year = 1943,
-	month = {jul},
-	publisher = {Oxford University Press ({OUP})},
-	volume = {23},
-	number = {4},
-	pages = {190--190},
-	title = {These Mysterious Rays: A Nontechnical Discussion of the Uses of X-Rays and Radium, Chiefly in Medicine},
-	journal = {Physical Therapy}
+	title        = {These Mysterious Rays: A Nontechnical Discussion of the Uses of X-Rays and Radium, Chiefly in Medicine},
+	year         = 1943,
+	month        = {jul},
+	journal      = {Physical Therapy},
+	publisher    = {Oxford University Press ({OUP})},
+	volume       = 23,
+	number       = 4,
+	pages        = {190--190},
+	doi          = {10.1093/ptj/23.4.190},
+	url          = {https://doi.org/10.1093%2Fptj%2F23.4.190},
+}
+@article{Denyer_2019,
+	title        = {Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing},
+	author       = {Denyer, Tom and Ma, Xiaoli and Klesen, Simon and Scacchi, Emanuele and Nieselt, Kay and Timmermans, Marja C.P.},
+	year         = 2019,
+	month        = mar,
+	journal      = {Developmental Cell},
+	publisher    = {Elsevier BV},
+	volume       = 48,
+	number       = 6,
+	pages        = {840--852.e5},
+	doi          = {10.1016/j.devcel.2019.02.022},
+	issn         = {1534-5807},
+	url          = {http://dx.doi.org/10.1016/j.devcel.2019.02.022},
 }

news/_posts/2021-03-01-gat.md

@@ -9,6 +9,7 @@ contributions:
 
 The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event.
 
-**5 days, 106 registrations, 29 countries, 12.5 hours of video and 100% awesomeness.**
+> 5 days, 106 registrations, 29 countries, 12.5 hours of video and 100% awesomeness
+{: .quote}
 
 Read the full report for all the numbers, details, conclusions and feedback.

news/_posts/2021-03-30-tutorial_scrna_plant.md

@@ -12,4 +12,4 @@ layout: news
 
 Single cell RNA-seq analysis is a cornerstone of developmental research and provides a great level of detail in understanding the underlying dynamic processes within tissues. In the context of plants, this highlights some of the key differentiation pathways that root cells undergo.
 
-This tutorial replicates the paper ["Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing" (Denyer et al., 2019)](https://doi.org/10.1016/j.devcel.2019.02.022), where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells.
+This tutorial replicates the paper {% cite Denyer_2019 %}, where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells.

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

@@ -25,13 +25,13 @@ abbreviations:
 
 And in your text you can use braces to refer to the term
 
-> > ### {% icon code-in %} Input: Markdown
+> > <code-in-title>Markdown</code-in-title>
 > > <code>
 > > The `/jobs` &lbrace;API&rbrace; will return &lbrace;JSON&rbrace;. When we call the &lbrace;API&rbrace; we'll get back this result &lbrace;JSON&rbrace;.
 > > </code>
 > {: .code-in}
 >
-> > ### {% icon code-out %} Output
+> > <code-out-title></code-out-title>
 > >
 > > The `/jobs` Application Programming Interface (API) will return JavaScript Object Notation (JSON). When we call the <abbr title="Application Programming Interface">API</abbr> we'll get back this result <abbr title="JavaScript Object Notation">JSON</abbr>.
 > >

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

@@ -6,8 +6,6 @@ tags: [new feature]
 layout: news
 ---
 
-**Accessibility Improvements**
-
 One of our community members suggested on twitter that we support alternative formats for accessing our JavaScript based slides, as this can be difficult for users using screen readers. We've now added support for "plain text slides", where we render the slide decks as a single long document.
 
 The rendering is imperfect, due to how our slide deck library handles custom classes within slides, but it should still be an improvement for anyone who wants to scroll through the slides in an alternative format. You can find them linked from the first slide of each slide deck, or from the slides dropdown in the topic pages, *check them out!*

news/_posts/2021-09-29-survey.md

@@ -8,13 +8,13 @@ coveralt: "Adversitement for the survey. Written: Got a minute? Did you use Gala
 layout: news
 ---
 
-**Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.**
+**Do you use Galaxy for Training? Have your say!** Please take a few minutes to let us know about your training experiences.
 
 We, the Galaxy Training Network, would like to get feedback from instructors on the use of Galaxy for training, the preparation needed but also on the [Galaxy Training Material](https://training.galaxyproject.org/).
 
 This survey should take less than 10 minutes and every questions are optional and can be skipped. It will help us prioritise improvements to the training materials. We're currently focused on making it easier to prepare and give trainings.
 
-[**Fill the survey now**](https://forms.gle/YJq5rTEcdowjBiuh6){:.btn .btn-primary style="color: white; width: 100%; background-color: #528faa;border-color: #528faa;"}
+[Fill the survey now](https://forms.gle/YJq5rTEcdowjBiuh6){:.btn .btn-primary style="color: white; width: 100%; background-color: #528faa;border-color: #528faa;"}
 
 If you have any questions regarding this survey, please send an email to [[email protected]](mailto:[email protected])
 

news/_posts/2022-06-02-workflow-reports-tutorial.md

@@ -11,5 +11,3 @@ layout: news
 ---
 
 Workflow reports are a great Galaxy feature that enable you to define summary reports for any workflow to display the most important results in a single view. This tutorial will guide you through the basics of viewing, customizing, and sharing such workflow reports!
-
-<iframe width="560" height="315" src="https://www.youtube.com/embed/TmZzfaKf1V0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> <br>

news/_posts/2023-02-08-top-tools.md

@@ -9,7 +9,7 @@ contributions:
 layout: news
 ---
 
-Did you ever wonder which was the number one most used tool in the GTN? There is a new page of [Top Tools]({% link top-tools.html %}) where we list all of the top tools in the GTN, and which tutorials use them. We guessed "upload1", but it seems like not every author annotates that step explicitly in their tutorial, and of course it doesn't appear in the workflows which we also scan to create this tool listing.
+Did you ever wonder which was the number one most used tool in the GTN? There is a new page of [Top Tools]({% link stats/top-tools.html %}) where we list all of the top tools in the GTN, and which tutorials use them. We guessed "upload1", but it seems like not every author annotates that step explicitly in their tutorial, and of course it doesn't appear in the workflows which we also scan to create this tool listing.
 
 This list is also [available as a JSON API]({{ site.baseurl }}/api/top-tools.json). And additionally we have exposed them as individual page listings as well, e.g. if you wanted to link to "All GTN Tutorials Using My Tool", you could do that with one of [these pages like Cat1]({{ site.baseurl }}/by-tool/cat1.html), or [iuc/multiqc]({{ site.baseurl }}/by-tool/iuc/multiqc.html)
 

news/_posts/2023-04-19-shortlinks.md

@@ -16,7 +16,7 @@ PURLs are persistent URLs, and can be used to link to a specific version of a tu
 
 ## How do I use them?
 
-The PURLs are in the form `gxy.io/GTN:[id]`, where `[id]` is the identifier of the tutorial, slide, or FAQ. For example, the identifier for the [Galaxy Installation with Ansible](https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible-galaxy/tutorial.html) tutorial is `GTN:T00001`. The PURL for this tutorial is thus [gxy.io/GTN:T00001](https://gxy.io/GTN:T00001). This will always point to the Ansible Galaxy tutorial, no matter what changes are made to the tutorial in the future.
+The PURLs are in the form `gxy.io/GTN:[id]`, where `[id]` is the identifier of the tutorial, slide, or FAQ. For example, the identifier for the [Galaxy Installation with Ansible]({% link topics/admin/tutorials/ansible-galaxy/tutorial.md %}) tutorial is `GTN:T00001`. The PURL for this tutorial is thus [gxy.io/GTN:T00001](https://gxy.io/GTN:T00001). This will always point to the Ansible Galaxy tutorial, no matter what changes are made to the tutorial in the future.
 
 ## How do I find the PURL for a tutorial?