02 Call Digest [ 2022-noaa-swfsc-pifsc-fall ]

[stefaniebutland]

Hi @nmfs-openscapes/2022-noaa-swfsc-pifsc-fall-cohort

Now that you’ve learned about GitHub Issues, we’ll be posting Cohort Call Digests here and not emailing them 😁. You can try clicking on the digest issue label; it will show only issues that have that label.

On top of practicing following so many windows - Zoom video and chat, Slides when we’re not screensharing, Google doc - there was a lot of content to absorb. Feel like you missed something in the live demos? The video of our Call is in our Google Cohort Folder.

It was wonderful to see folks going from “What if I want to …” to creating their first repo or from creating their GitHub account to making their first commit. Thank you for being willing to screenshare to allow others to learn along with you. Thank you to those who share their thoughts, clarifications, and questions to our collaborative Google doc during the Call. Finally, it makes us really happy to see people asking and responding to questions in Google Spaces and Slack! Vulnerability? Yes! Shame? No!

Wishing you a growth mindset 😉,

Stef, Julie, Kevin, Amanda, Juliette

Digest: Cohort Call 02 [ 2022-noaa-swfsc-pifsc-fall ]

Cohort Google Drive folder - contains agendas, video recordings, slides, pathways folder
openscapes.github.io/2022-noaa-swfsc-pifsc-fall - cohort webpage

Goals: We practiced GitHub hands-on for collaborative research through publication and project management, from the browser.

Task: Have a Seaside Chat about GitHub. Please see the Agenda doc (under Closing) for more details.

Slide Deck: GitHub Clinic: Contributing from the browser (slides)

Coworking and learning opportunities (optional)

This week, Wed Oct 26, we have SWFSC-PIFSC coworking 1:00 - 2:00 pm PT, and during Themed Cross-Cohort Coworking Tues Oct 25, 1:00 - 2:30 pm PT Eli Holmes will lead a guided session to work on your Pathways “Next steps”--where you want to get to and what you can do to get you there. Eli will give a brief intro to the ideas around using short sets of tasks (can be accomplished in 2-3 weeks) to make headway on amorphous or overwhelming goals (aka agile methodologies). Changing individual or team workflows and learning new skills definitely falls into this category! You can review Eli's talks on Agile workflows from the summer if you like, but you don’t need to be familiar with the concepts. It’s pretty straight-forward and on Tuesday, we’ll be learning by working on our Pathways.

• Intro to Agile and Kanban with GitHub project boards
• Intro to Agile Part 2: Scrum with GitHub issues and project boards

There’s going to be a chunk of time (~40mins) for you to work on next steps for your Pathway. It’s totally ok to use this as your Seaside Chat time.

A few lines from shared notes in the Agenda doc, excerpted from all 4 NMFS Cohorts:

• Our group talked about labels vs. milestones, and assignees (to add folks to the issue) vs. the @ tool within a specific comment to flag the comment to a particular person within the issue subgroup.
• What if I want to do work outside of nmfs-openscapes?
  • Create a new repository in your personal or NOAA account
• Thoughts on collaborating on writing projects on GitHub vs Google docs or Word
  • Google doc is great for fast progress - lots of people working nearly simultaneously
  • Depends on how complicated your manuscript is. Get to a point where [you’re] happy with it, then move to Google doc to get input from folks who don’t use GitHub.
  • Reports = R Markdown or Quarto; Live writing together (coworking) = Google doc
• Is there a file size limit for GitHub?
  • See About large files on GitHub
  • ~50 mb will generate a warning, 100 mb hard stop, adding files via the browser are limited to 25 mb; But, there are options for sharing large files via releases or Git LFS
  • For general best practices, Megsie Siple recommends avoiding putting bulky data files etc on GitHub (store on Google Drive and link to GitHub)
• Using Branches on GitHub
  • https://rverse-tutorials.github.io/RWorkflow-NWFSC-2022/week2-github.html
  • https://rverse-tutorials.github.io/WSDS-StLouis/WSDS_2022.pdf
  • GitHub documentation on branches
• Can Rmarkdown be linked to Endnote for inserting citations into a document?
  • You can’t directly add a citation from Endnote to an Rmarkdown document. You need to export your endnote library as a bibtex file first. You can add citations with Rmarkdown using the {bookdown} package, and others. Quarto allows you to directly add citations from a Zotero library.

Bonus post-Call resource!

Eli Holmes (NWFSC) shared 3 GitHub template repositories!

How templates work: Click the green "Use This Template" button to make a copy of the repo with all the files. Then follow the instructions in the readme.

Try it without any set-up! There is a RStudio Cloud project set up for the Quarto and Distill templates. Click the button and it is all set-up for you to add content and try building the website.

• A blank repo with the NOAA disclaimer, license and Readme template files https://github.com/nmfs-opensci/NOAA-blank
• A basic (and kind of ugly) RStudio+R Markdown website with NOAA palette and fonts https://github.com/nmfs-opensci/NOAA-branded-simple
• A pretty R Markdown + distill + postcards website with NOAA palette and fonts https://github.com/nmfs-opensci/NOAA-distill-website
• A Quarto website that looks a bit like a online book (on purpose) https://github.com/nmfs-opensci/NOAA-quarto-simple