From c466fffd33904123b5da343fd6eb5a81abdfe59b Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 19 Dec 2023 16:24:35 +0100 Subject: [PATCH] Fix many new linting complaints with news checking --- faqs/misc.bib | 148 +++++++++--------- news/_posts/2021-03-01-gat.md | 3 +- .../_posts/2021-03-30-tutorial_scrna_plant.md | 2 +- news/_posts/2021-05-25-abbreviations-tag.md | 4 +- news/_posts/2021-07-27-a11y.md | 2 - news/_posts/2021-09-29-survey.md | 4 +- .../2022-06-02-workflow-reports-tutorial.md | 2 - news/_posts/2023-02-08-top-tools.md | 2 +- news/_posts/2023-04-19-shortlinks.md | 2 +- 9 files changed, 86 insertions(+), 83 deletions(-) diff --git a/faqs/misc.bib b/faqs/misc.bib index 47e90c357df80e..7c09200ef27c6b 100644 --- a/faqs/misc.bib +++ b/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}, } diff --git a/news/_posts/2021-03-01-gat.md b/news/_posts/2021-03-01-gat.md index 12ba9c447e792d..e319d5a112e9b5 100644 --- a/news/_posts/2021-03-01-gat.md +++ b/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. diff --git a/news/_posts/2021-03-30-tutorial_scrna_plant.md b/news/_posts/2021-03-30-tutorial_scrna_plant.md index 135a7c3ecd6342..2776ba101c2869 100644 --- a/news/_posts/2021-03-30-tutorial_scrna_plant.md +++ b/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. diff --git a/news/_posts/2021-05-25-abbreviations-tag.md b/news/_posts/2021-05-25-abbreviations-tag.md index 5f5295cc244a80..e1d5b853168e71 100644 --- a/news/_posts/2021-05-25-abbreviations-tag.md +++ b/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 +> > Markdown > > > > The `/jobs` {API} will return {JSON}. When we call the {API} we'll get back this result {JSON}. > > > {: .code-in} > -> > ### {% icon code-out %} Output +> > > > > > The `/jobs` Application Programming Interface (API) will return JavaScript Object Notation (JSON). When we call the API we'll get back this result JSON. > > diff --git a/news/_posts/2021-07-27-a11y.md b/news/_posts/2021-07-27-a11y.md index 2f44cf4fa9b974..8ed850b09e679f 100644 --- a/news/_posts/2021-07-27-a11y.md +++ b/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!* diff --git a/news/_posts/2021-09-29-survey.md b/news/_posts/2021-09-29-survey.md index fa7366ed6fb612..0d6c80341ddd31 100644 --- a/news/_posts/2021-09-29-survey.md +++ b/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 [galaxytrainingnetwork@gmail.com](mailto:galaxytrainingnetwork@gmail.com) diff --git a/news/_posts/2022-06-02-workflow-reports-tutorial.md b/news/_posts/2022-06-02-workflow-reports-tutorial.md index 630cf50485f222..ea8d084b868d8b 100644 --- a/news/_posts/2022-06-02-workflow-reports-tutorial.md +++ b/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! - -
diff --git a/news/_posts/2023-02-08-top-tools.md b/news/_posts/2023-02-08-top-tools.md index f3cd6369e319de..89e3c988eb7fac 100644 --- a/news/_posts/2023-02-08-top-tools.md +++ b/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) diff --git a/news/_posts/2023-04-19-shortlinks.md b/news/_posts/2023-04-19-shortlinks.md index cc440f70dfc668..a7ae099c7a96b5 100644 --- a/news/_posts/2023-04-19-shortlinks.md +++ b/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?