Long workshop status

[kevinrue]

This issue tracks the status of long workshops.

A passing badge is expected to reflect that the workshop:

• can be built as an R package
• can deploy pkgdown documentation to the gh-pages branch of the repository
• can push a Docker container to Docker Hub.

---

Dimension Reduction for Beginners

Epidemiology for Bioinformaticians

Reproducing a single-cell proteomics data analysis using QFeatures and scp

Introduction to the Terra/AnVIL Cloud-based Genomics Platform

Building Carpentries-based Bioconductor Lessons

Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment

Effectively using the DelayedArray framework to support the analysis of large datasets

Introduction to Bioconductor annotation resources

Trajectory inference across conditions: differential expression and differential progression

systemPipe: Workflow and Visualization Toolkit

Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment

[jdrnevich]

Hi @kevinrue . I see our Building Carpentries-based Bioconductor Lessons is failing. Is there any information on what is failing?

[kevinrue]

Latest CI run report here: https://github.com/jdrnevich/BuildACarpentriesWorkshop/runs/2124169713?check_suite_focus=true

Issue is about Docker Hub credentials it seems

denied: requested access to the resource is denied

I suggest we open an issue on the workshop repository instead. Otherwise this one would rapidly get overcrowded.

[kevinrue]

@jdrnevich

Uh oh. It seems that cloning Sean's repo has undesirable side effects, as in it is not possible to open issues on the repository. We need to update the instructions to say that people should use the "Use as template" button instead.

[jdrnevich]

Yeah, I figured that out the hard way. I'm not seeing certain other things either. I wonder if I should scrap it and start again?

[kevinrue]

To me, it would feel cleaner to restart it using as template, yes. Changing settings on the current setup may not guarantee that the result is the same as using as template, which worked when I tested.

[lwaldron]

Yes, I think you have to start again by deleting your forked repository and re-creating a new one under the same name, or creating the new one under a different name then re-naming it to the name of your former forked repo. You could start by creating from template but you don't have to, if you want to keep your commit history you could import your local local git project to github: https://docs.github.com/en/github/importing-your-projects-to-github/importing-source-code-to-github/importing-a-git-repository-using-the-command-line

[jdrnevich]

I don't care that much about the commit history. I did clone the template properly to https://github.com/jdrnevich/testWorkshop doing the minimal changes necessary, although it's still failing at the Docker step (hoping I just input my DOCKER_PASSWORD wrong). Once I get that to work, I'll copy over the few pages I had customized from the previous one, then delete the old one and re-name the new one.

[mdozmorov]

@kevinrue, what do you think about creating a workshop page on the website, like we had last year https://bioc2020.bioconductor.org/workshops, and moving those status badges there?

[kevinrue]

Sure! About to have dinner now, but I can look at that later.

[mdozmorov]

Last year, Marcel @LiNk-NY created a nice code that compiles the workshop page in markdown, https://github.com/Bioconductor/BioC2020/blob/master/docs/workshops.Rmd. Should be straightforward to adapt for this year.

[kevinrue]

Would you mind giving me write access to the repository? Otherwise I can make a fork, if you prefer. @mdozmorov

[mdozmorov]

Should be done. Please, let me know if I can help.

[kevinrue]

For some reason it still doesn't work

git push -u origin workshops

No problem. I'll make a fork.

Also it's still a work in progress. We can have some rounds of feedback about the layout. I'm not sure you'd want the CI badges on the conference website, which is why I created this issue in the first place.

[mdozmorov]

It still shows "Awaiting response." Did you receive an e-mail to click through the invite?

And yes, badges on the website, an additional column. It may take creating shortcodes.

[kevinrue]

Ah right - I didn't see the invitation email. Those tend to fly under the radar, unlike github action build reports.

[kevinrue]

I guess we can close this issue, now that the badges are on the main website. (Even closed, this issue will keep showing the badges anyway, actually)

[mdozmorov]

Yes, the status page https://bioc2021.bioconductor.org/workshops-status/ looks great. Thanks so much, @kevinrue!