# RSH HackMD

Link to this document: https://hackmd.io/@researchsoftwarehour/questions

You can use this file to write questions and comments. **To edit click edit button** (either top left or top right)
- Always write at the very bottom, this is easier for us to watch.
- We will note here URLs that we mention during the session.
- You may comment on, clean up, or answer other people's questions.
- **Be respectful** and form a good community.

- Jarno, you are a little quieter as the others ;)
- better ;) thanks!
-
- answer

- what is git?
- ou
- we will see in a moment

## Progression of use cases and topics

GitHub is used for:
- things for yourself (central location, backup, sharing, organizing, easy moving to later levels)
- things for small groups (organizations, shared repos with or without PRs, etc)
- things for community (outside collaborators, discussion, PRs, etc)

Where are you? Where do you want to be?

- questions

## Quick survey

I have used git before:
- yes: IoooooOooooIoooo
- no: Ooooooo0oooo

In the past I have already opened an issue on GitHub:
- yes: oIIoooIII
- no: OoOoooooooooooooo0ooo

In the past I have already creaded a pull request on GitHub (or merge request on GitLab):
- yes: ooooIooIo
- no: oOooooooooooooooo

---

## What is git?

- **Version control**
- Track changes
- Inspect history
- Work together
- Basically a requirement for any kind of serious programming work
- But also useful for others.
- *This talk is not about git: we assume you use it already*
- tracks code, manuscripts, theses, etc.

Example: https://github.com/bast/pr-exercise
- Demo:
- vim README.md
- git diff
- git add
- git commit -m "Adding a line during the stream"

- Is gitlab the same as github?
- GitLab does the same things as GitHub, but it is a separate program.
- The biggest difference is that you can run your own GitLab on a server
- We'll get to this in a bit.

## What is GitHub?

* Commercial company
* ... hosting a **web repository, Github**
* Very good free services for open-source projects.
* vs Gitlab
* Gitlab is open-source equivalent
* Many universities have their own (e.g. version.aalto.fi, source.coderefinery.org)
* For the most part, usage is the same.
* Interfaces: take your pick
* Git command line
* Github desktop and apps
* Github web interface
* Cost
* Github ownership

Question: Are there command line interfaces for Github that work on Windows?
- For git itself, Git for Windows. / gitbash https://gitforwindows.org/
- https://cli.github.com/
- This has some nice extra features (not just for Windows btw)

I don't know if it's changed, but last time I checked, the Github Desktop was pretty unstable in Windows.

## Basic features: pushing and pulling

Let's demo the basics of Github.

- You connect to other servers via **git remotes**, controlled with `git remote`.
- Once a remote is set, you `git push`, `git fetch`, and `git pull`
- It isn't our goal to go in detail about the technical implementation: you can read this later. (we'll talk about why instead)

Quick demo:
- New repository
- Create repository on Github
- Add remote
- Push to Github

demo commands:
- git log
- git remote -v
- git push origin master
-

## Git for small groups

- The next level is using Github among a research group, or something similarly small.
- To be a group, you need to work together. To work together, you need a place to do so.
- **Organizations**
- **User management**: share among a group
- **Issues**: Track things to do
- **Pull requests**: Code review

Question: I work with Jupyter Nitebooks. Is there an easy way to integrate those into github? thanks
- great question! I use this locally (nice tool to visually diff and merge notebooks): https://nbdime.readthedocs.io/ but I don't know of a good way to see nice diffs directly on GitHub. I anticipate that GitHub is working on that. Anybody knows some solution?
- Yeah, diffs not so good right now. I haven't heard of much beyond that, but many people do use git for notebooks, just realize that diffing and merging isn't so easy.
- the nbdime is great locally for this but would be nice to see it directly in pull requests +1

## Community projects: the next level

- So you have your own group working well. What comes next? The community
- There is little cost to accepting contributions from others.
- Minimizing information overload in big community projects.

## Important considerations

- Importance of a license file
- Don't accept contributions until you get this clarified
- How to contribute
- Issue templates, pull request templates, etc.
- Code of conduct

Comment:
- It's actually important that issues are not generally viewed as "problems" but more as improvement ideas, etc. cause otherwise some people tend to try to avoid having issues listed.

## Long term: archiving and Zenodo

- Github is the de-facto source for open research software (for better or for worse)
- Can you cite it in a paper?
- Can you expect Github to be around in 20 years?
- More likely than your university's Gitlab or personal webpage. (But does your user still exist?)
- For permanent storage, connect to Zenodo and publish releases.
- Zenodo is a EU-funded repository of science.

Video demo of Zenodo link: https://www.youtube.com/watch?v=Atp-GmhS7gY

## Actions

- Github Actions are continuous integration: they can run tests on every commit.
- Automatic testing on changes: great for making sure things work!
- Automatic deployment, for example push to git and a website gets updated.

## What's next?
- CodeRefinery courses: https://coderefinery.org/lessons/
- git-intro (by yourself)
- git-collaborative (Github + pull requsets)
- Automated testing: Github Actions
-
- Research Software Hour: https://researchsoftwarehour.github.io/
- Aalto Research Software Engineers: https://scicomp.aalto.fi/rse/
- Coderefinery chat: https://coderefinery.zulipchat.com/

## Feedback

One good thing about today:

- The demos were helpful! Thank you!
- Great introduction! Thank you!
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One thing to be improved:
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