workshop 8: Keeping track of your files with version control

[ctb]

Tuesday August 24 from 9 am - 11:30 PDT

Instructors: Nick Ulle & Saranya Canchi Moderator: Marisa Helpers:

Zoom link:

Description:

This two hour workshop will show attendees how to use the git version control system to track changes to your files on the remote system, as well as backup your project files to github and transfer them to your laptop or desktop. We will demonstrate file sharing via github, and discuss ways to collaborate with a team.

draft lesson: ggg 298, git https://github.com/ngs-docs/2021-GGG298/tree/latest/Week7-Git_and_GitHub_for_file_tracking_and_sharing

owner: ???

[s-canchi]

Can't assign myself yet, but would love to teach/co-teach this workshop.

[nick-ulle]

I'd be happy to co-teach this.

[s-canchi]

@nick-ulle - Did you want to use the draft lesson or did you have a lesson in mind ? Happy to meet over zoom to discuss lesson plan and instructor hand offs.

[nick-ulle]

@s-canchi I'm okay with using the draft lesson. DataLab also has this reader and this reader from similar workshops we've done before.

[ctb]

note to self: fix forward link from workshop 2 materials to this lesson, when up on site

[s-canchi]

@nick-ulle - The datalab versions are also very nice! If using the draft lesson, I would like to teach the first half of setup until the Working with multiple files section. What do you think ?

[ctb]

let me know if you need any help sticking this into our ngs-docs site. If you've settled on a lesson, I can do an initial extraction into that. (It's not clear it's really needed since it's already in the right format, but 🤷 might as well be consistent, I guess, and it's nice to have it all in one place!)

should also brainstorm together three assessment questions. post here or in slack as you think of them!

[nick-ulle]

Found more of my notes: https://github.com/2019-winter-ucdavis-sta141b/notes/blob/master/lecture/01.15/notes.ipynb

[nick-ulle]

Link to planning HackMD: https://hackmd.io/cLZuRkaPQKu783AZDFPKbw

[ctb]

skimming through the lesson now. Any specific requests for review?

I think we should ask people to create github accounts before showing up tomorrow, seem reasonable?

do we want to be using snakemake as an example? We're not introducing it 'til the following day ;(

Do you have any assessment questions in mind?

[s-canchi]

The changes to the second half are due to be merged by @nick-ulle. First half is done pending an awesome diagram that @nick-ulle created talking about the three stages of git workflow. We were going to allocate some time to create the accounts on GitHub but is certainly reasonable if they can create one prior. It might be useful to link to create an account section of the lesson in the email.

For the examples, we were not going to use snakemake but work with text files instead.

For assessment, how about:

• I know what is version control and can use git and GitHub
• I know how to track changes across multiple files using git
• I can restore a file after changes have been made using version control

[jeremywalter]

Pre-Survey: https://forms.gle/1y7Hb4yhwfCR6A2s5 Post-Survey: https://forms.gle/v52Fv2sZoCuEfNF87

[nick-ulle]

@ctb Everything is ready to merge on our end.

[ctb]

presumably referring to https://github.com/ngs-docs/2021-august-remote-computing/pull/28 ;)

[marisalim]

some ppl got the PAT error at the git clone step (earlier than the git push step in the lesson)

remote: Support for password authentication was removed on August 13, 2021. Please use a personal access token instead.
remote: Please see https://github.blog/2020-12-15-token-authentication-requirements-for-git-operations/ for more information.
fatal: Authentication failed for 'https://github.com/USERNAME/2021-my-first-repo/'

maybe for a future github workshop, we could create an organization, and ask them to make repos within it - would be a little easier to troubleshoot/check progress

[marisalim]

the default editor that git opens on Farm is emacs, this is how you exit!

To exist out of emacs (the default editor for git message) hit the keys Ctrl + x, followed by Ctrl + c. And then type y

could add a git config step to configure the editor to i.e., nano

[s-canchi]

2021-remote-computing-8.pptx

[ctb]

the default editor that git opens on Farm is emacs, this is how you exit!

To exist out of emacs (the default editor for git message) hit the keys Ctrl + x, followed by Ctrl + c. And then type y

could add a git config step to configure the editor to i.e., nano

NOTE: this could be fixed by setting VISUAL (and maybe other environment variables). Or adding it to the git config step.