Git for physicists - Jagiellonian Universityusers.uj.edu.pl/~ufkapano/git/seminar.pdf · cloud...

Git for physi ists

Andrzej Kapanowski

Institute of Physi s, Jagiellonian University, Krakow, Poland

De ember 21, 2015

A. Kapanowski (JU) Git for physi ists De ember 21, 2015 1 / 28

Outline

Outline

1

Motivation

2

Git basi s

3

Lo al repositories

4

Remote repositories

5

Git bran hing

6

Con�i ts

7

Remote bran hes

8

Summary


Motivation

Motivation

S ientists need many tools for their work: software for analysing

or visualizing data, sharing �les, ollaborating, writing up papers,

publishing, sear hing the literature. Programming languages are

needed to write unique programs or to glue di�erent systems.

Parallel omputing, loud omputing (PLGrid), big data,

bioinformati s (genomi s data), ...

Software Carpentry Foundation - tea hing resear hers basi

software skills (from 1998).

Publishing sour e ode of s ienti� programs - Nature 467

(2010).

There are many tools to learn - start from the best ones.


Git basi s

Getting started

Git is a free and open sour e distributed version ontrol system

designed to handle everything from small to very large proje ts

with speed and e� ien y.

Git home page: http://git-s m. om/.

Version ontrol is a system that re ords hanges to a set of �les

over time so that you an re all spe i� versions later.

Lo al VCS: keeping pat h sets.

Centralized VCS: a single server ontains all the versioned �les.

Distributed VCS: lients fully mirror the repository.

Git is available for all major platforms.

Proto ols: HTTP, FTP, rsyn , Git proto ole.


http://git-scm.com/

Git basi s

A short history of Git

Linus Torvalds (born in 1969) - the

reator of the Linux kernel.

1991-2002, Linux kernel with

pat hes and ar hived �les.

2002-2005, Linux kernel with

BitKeeper.

2005, Git was born.

Git = "unpleasant person" (British

English slang).

Git thinks about its data like a

stream of snapshots.


Git basi s

What to keep in a Git repo?

Short answer: text-based �les.

Sour e ode of programs written in Shell, Python, C/C++, ...

Websites (HTML, XHTML, CSS).

Arti les, reports, books (*.txt, *.tex, *. vs).

Sour e ode of programs for omputer algebra systems

(Maxima, Maple, Mathemati a).

Sour e ode of �gures in gnuplot, Pyxplot, ...

Use Dropbox (2.5 GB) or Google Drive (15 GB) for binaries.


Git basi s

First-time Git setup

The ommand line interfa e provides all Git ommands.

$ git --version # he k if Git is installed

$ git onfig --global user.name "Andrzej Kapanowski"

$ git onfig --global user.email

"andrzej.kapanowski�uj.edu.pl"

$ git onfig --list # he king settings

$ git help onfig # getting help

$ git onfig --help

$ man git- onfig


Git basi s

Getting a Git repository

Initializing a repo in an existing dire tory (git init).

$ d myproje t

$ git init # .git subdire tory is reated

$ git add -A # add all files to the staging area

$ git ommit -m "First ommit."

Cloning an existing repo (git lone).

$ git lone https://github. om/sympy/sympy.git


Lo al repositories

Che king the status of the repo

$ git status

# On bran h master

nothing to ommit (working dire tory lean)

$ vim README # a new file is reated

$ git status

# On bran h master

# Untra ked files:

# (use "git add <file>..." to in lude in what

# will be ommitted)

#

# README

nothing added to ommit but untra ked files present

(use "git add" to tra k)


Lo al repositories

Viewing the ommit history

$ git log # note SHA-1 hashes

ommit 48ae450a329 92558038de3b721a029d8eea8 14

Author: Andrzej Kapanowski <andrzej.kapanowski�uj.edu.pl>

Date: Wed De 9 09:54:56 2015 +0100

UnionFind hanged.

ommit 64e 8f8edb9 a891b18d94d906d885f91e67e220

Author: Andrzej Kapanowski <andrzej.kapanowski�uj.edu.pl>

Date: Tue De 8 14:12:12 2015 +0100

Sudoku 6x6 added.

...


Lo al repositories


$ git log --pretty=oneline -4

48ae UnionFind hanged.

64e Sudoku 6x6 added.

6355 Ri h omparisons.

60a6 lek ja10 hanged.

# Repo history:

# ...--60a6--6355--64e --48ae <-- master <-- HEAD

$ git log --grep=lek ja # "lek ja" in omments

$ git log --author=Andrzej


Lo al repositories


$ git bran h # lo al bran hes

* master

$ git he kout 60a6

Note: he king out '60a6'.

You are in 'deta hed HEAD' state.

...

HEAD is now at 60a68aa... lek ja10 hanged.

$ git bran h

* (no bran h)

master

$ git he kout master

...

Swit hed to bran h 'master'


Remote repositories

Remote repositories

github. om - over 30.2 million repositories, issue tra king, ode

reviews, syntax highlighted ode, markdown for formatting text,

paid plans. [GitHub Enterprise℄

bitbu ket.org - Atlassian (JIRA, Con�uen e), pull request,

bran h permissions, free private repos for up to 5 users.

[Bitbu ket Server℄

gitlab. om - private repos, ode reviews, issue tra king, wikis.

[GitLab Community Edition and Enterprise Edition℄


Remote repositories

Working with remotes

# git remote add [shortname℄ [url℄

$ git remote add origin

https://ufkapano�github. om/ufkapano/myproje t.git

$ git push -u origin master # only first time

$ git remote # show shortnames of remotes

origin


Remote repositories

Simple work�ow

$ git pull

# Changing files ...

$ git add -A

$ git ommit -m "Comments."

$ git push


Git bran hing

Bran hes in Git

A bran h is a lightweight movable pointer to a ommit.

Creating, deleting, and modifying bran hes is qui k and easy.

The default bran h name is master. This bran h points to the

last ommit we made. It moves forward automati ally after

every ommit.

Swit hing bran hes hanges �les in the working dire tory.


Git bran hing

Lo al bran hes

# git bran h [bran h_name℄ [sha1℄

$ git bran h testing

# A--B--C <-- master <-- HEAD

# ^

# |

# testing

$ git he kout testing

Swit hed to bran h 'testing'

# A--B--C <-- master

# ^

# |

# testing <-- HEAD


Git bran hing

Fast forward


# \

# D--E <-- testing <-- HEAD

$ git he kout master # it hanges files!


$ git merge testing

Updating ..eeee

Fast-forward

...

# A--B--C--D--E <-- master <-- HEAD

# ^

# |

# testing


Git bran hing

Removing bran hes


# \

# D--E <-- testing <-- HEAD

$ git he kout master # it hanges files!


$ git bran h -d testing # removing 'testing'

# A--B--C <-- master <-- HEAD

# \

# D--E (dangling ommits)


Git bran hing

Merging

# A--B--D <-- testing

# \

# C <-- master <-- HEAD

$ git merge testing # edit omments

Merge made by the 're ursive' strategy.

...


# \ \

# C--E <-- master <-- HEAD

$ git log --pretty=oneline -1

eeee Merge bran h 'testing'


Con�i ts

Merging with on�i ts


# \

# C <-- master <-- HEAD

$ git merge testing

Auto-merging a1.txt

CONFLICT ( ontent): Merge onfli t in a1.txt

Automati merge failed;

fix onfli ts and then ommit the result.


Con�i ts


$ at a1.txt

file a1

<<<<<<< HEAD

a1 hanged in master

=======

a1 hanged in testing

>>>>>>> testing


Con�i ts


$ git mergetool

merge tool andidates: meld opendiff kdiff3 tkdiff

xxdiff tortoisemerge gvimdiff diffuse e merge

p4merge araxis b 3 emerge vimdiff

Merging:

a1.txt

Normal merge onfli t for 'a1.txt':

{lo al}: modified file

{remote}: modified file

Hit return to start merge resolution tool (gvimdiff):


Con�i ts


$ git status

# On bran h master

# Changes to be ommitted:

#

# modified: a1.txt

#

# Untra ked files:

# (use "git add <file>..."

# to in lude in what will be ommitted)

#

# a1.txt.orig


Con�i ts


$ rm a1.txt.orig

$ git add -A

$ git ommit -m "Merge bran h testing."


Remote bran hes

Remote bran hes

$ git bran h --all # list all bran hes

* master # lo al bran h

remotes/origin/master # remote bran h


Remote bran hes

git pull = git fet h + git merge

$ git push

...

! [reje ted℄ master -> master (non-fast-forward)

...

# git fet h [remote_name℄ [bran h_name℄

$ git fet h origin master

$ git merge origin/master # onfli ts are possible ...

$ git add -A

$ git ommit -m "Merge bran h origin/master."

$ git push


Summary

Summary

Use Git to handle small and large proje ts like reating software,

writing s ienti� arti les, books, websites.

Use remote repositories to ollaborate with other persons, to

publish your software or data, for ba kups.

Thank you for your attention


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