So you want to know something about Git - Maria Lehtivaara (CSC -IT Center for Science) - Eduuni-wiki
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So you want to know something about Git Maria Lehtivaara (CSC –IT Center for Science) 16.6.2021 CSC – Finnish expertise in ICT for research, education, culture and public administration
Aim of this presentation
• Give a brief idea of how Git can be used in producing re-producable science
Hopefully you will:
o recognise the tools & some terms, can map these to some context
othink of possible use cases
o know how to learn more
Disclaimers
• You are not a Git guru after this 20 mins L
oI’m not a Git guru -just a humble user
• Git usage or git tools are not specifically maintained
or supported by CSC. Except…
oour manuals and training material
oNEIC CodeRefinery collaboration
oWe are quite friendly thou J servicedesk@csc.fi
2 10.6.2021
Hey, can you check which parameters were
Reproducability: used to get these results? Could we try this
Bad vs small modification?
better situation
• Typing commands directly on the command • Typing commands and comments to version controlled
prompt files, using automated workflows
• Storing files in personal computer in random • Storing files in (public/joined) repositories in cloud
hierarchy • Having the softwares installed as documented
• Having the softwares installed (only) in your own containers
(…but
computer
PLEASE
Sure! Let me
don’t ask
just check my
Ummm… I HAD some me again
repository, and
results here on my after 5
we can re-run
laptop… and I THINK this years…)
the needed
was the laptop where I sections in these
had the softwares containers!
installed…
3 7.6.2021
Git -what & why?
• Version control system
• Used by developers / coders, but useful to anyone who
writes (code) or needs to track changes to files =>
:
that’s basically everyone, right! Example
oTracks the changes you make to files
oAllows to revert to specific versions (= recovery from “oopsies”)
oMakes collaboration easier (allow changes by multiple people
P.S: Git was
to all be merged into one source) developed by
Linus “Linux”
Torvalds 200
5, and
it’s free J
Source: https://www.nobledesktop.com/blog/what-is-git-and-why-should-you-use-it
4 8.6.2021 Bread example: https://github.com/hendricius/the-bread-code
Git -what & why?
• The life of a document:
Video: https://youtu.be/CvbLVVRzJF8
5 7.6.2021
Git, GitHub, GitLab –what’s the difference?
• Git = version control • GitHub = web-based Git • GitLab = like GitHub, but:
system repository hosting service oSome terminology & workflow
oIn cloud, for sharing difference
oOn your own computer
oFree when using public repos -> oPrivate repos free?
oFree
good for open source o“Open core” source code
o“the base” development o => many organisations host
o private repos for 3 members their own GitLab
only! o Data stays more locally
oGraphical web user interface & o Authentication
extra tools oFor example:
oVery popular https://coderefinery.org/repository/
Sources: https://blog.devmountain.com/git-vs-github-whats-the-difference/
6 10.6.2021 https://blogs.helsinki.fi/thinkopen/versionhallinta-on-valttamaton-tyokalu-tutkimukselle/
So… what is where?
Normal folder Git repository Remote repository
archive &
reference
repositories
Files + revision history Files + revision history
Files for everyone*
for you
(= team, company, everyone…)
Your computer Your computer Cloud Check these:
https://guides.github.com/activities/citable-code/
https://www.softwareheritage.org/save-and-reference-research-software/
7 16.6.2021 Source: https://www.nobledesktop.com/blog/what-is-git-and-why-should-you-use-it
Do I have… options?
• Yep, there are other Version Control • Yep, there are other repository hosting
Systems (VCSs): services:
oOr “revision control”, “source code
management”…
9 7.6.2021
Some Git-terminology
• Some terms you might run into ( over-simplified! )
Repository: branch
pull from push to
master master
merge
branches
one commit
(several changed files)
conflict
(overlapping changes, solve!)
10 7.6.2021 Source: https://www.nobledesktop.com/blog/what-is-git-and-why-should-you-use-it
Tools for Git
• Command line (=terminal)
• GitHub
• Handy graphical GUIs to your
own computer
oGitHub Desktop, Visual Studio
Code, Sourcetree, Fork…
• Directly from RStudio…
• Lot’s of great easy-to-approach
material online!
ohttps://coderefinery.org/lessons/
11 7.6.2021Some use cases –have you considered these?
• Code development
oDeveloping analysis pipeline or tool
• Data analysis
o”What did I do again? Did I test that already? Can you continue this phD students work?”
oPublications link to Git repos containing everything needed to repeat the analysis
• Writing
oAnything in plain text* format: article, blog post, notes… (* Markdown, LaTeX…)
• Guides, learning materials…
Fee
l free to use
oCSC’s user guides: docs.csc.fi and develop
!
oCSCs course materials: https://github.com/csc-training
12 8.6.2021Workflow sneak peak: editing our user guide
At docs.csc.fi:
15 7.6.2021In GitHub:
type type type
16 7.6.2021Commit -> branch + pull request -> review -> accept pull request + merge 17 7.6.2021
More info –where?
• CSC services: servicedesk@csc.fi
• Your organisations own IT support
oThey might have some system in use, like GitLab
o in HY for example, version.helsinki.fi
• NEIC CodeRefinery (NEICSome learning curve in the beginning -patience J 20 8.6.2021 https://xkcd.com/1597/
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