Git Tips and Tricks for Code Management

Code and data management with Git
Git Tips and Tricks
Wibowo Arindrarto
Department of Human Genetics

Center for Human and Clinical Genetics
Introduction
We have only been playing with some of what git offers. In reality,
you can do much more with it. It also allows for a wide array of
customizations.
We will look into some of these customizations now.
1/20 Code and data management with Git 14-06-2019

Custom Prompt
Checking which branch you are working on and its status is routine.

Custom Prompt
“git status” is useful, but quickly feels repetitive.

1 $ git branch
2 * master
3 $ git status
4 nothing to commit , working directory clean
Listing 1: Routine git checking

Custom Prompt
“git status” is useful, but quickly feels repetitive.

1 $ git branch
2 * master
3 $ git status
Listing 1: Routine git checking
Solution: use a custom shell prompt that displays git status.

1 ( master ) $ git st
Listing 2: Git checking with custom prompt

Custom Prompt
The git-approved way to do this is to use the “\_\_git\_ps1” shell

function defined in the “git-prompt.sh” file.

Custom Prompt

The location of this file depends on your OS and git version. For
now, you can download a copy of this file from our GitLab.

Custom Prompt

The location of this file depends on your OS and git version. For
now, you can download a copy of this file from our GitLab.
Then, in your “.bashrc” file, add “\_\_git\_ps1” to the “PS1” vari-

able, and source your “.bashrc” again.

Useful git commands
git blame
Git tracks each line of each file in its repository.

Useful git commands
git blame
You can view who committed the line change, the commit hash, and
the commit time using “git blame”.
1 $ git blame README
2 a4394d28 ( bow 2014 -06 ...) Second version .
Listing 3: git blame command

Useful git commands
git blame
You can view who committed the line change, the commit hash, and
the commit time using “git blame”.
1 $ git blame README
2 a4394d28 ( bow 2014 -06 ...) Second version .
Listing 3: git blame command
Similar functionality is also available in GitLab by clicking on the

blame button when viewing a file.

Useful git commands
git tag
Sometimes, it is practical to refer to a commit with a name instead
of a hash.

Useful git commands
git tag
of a hash.
Official releases, for example, are better referred to as v1.0 than

a76a0fx.

Useful git commands
git tag
of a hash.
Official releases, for example, are better referred to as v1.0 than

a76a0fx.
This can be done using “git tag”.

Useful git commands
git tag
1 $ git tag " v0 .0.1"

2 $ git show v0 .0.1
3 commit a 4 3 9 4 d 2 8 e 6 b a 3 0 b e 1 9 3 1 8 e e 7 4 f 7 3 2 a 1 0 3 b 8 f f d f 2
4 Author : bow < bow@bow . web . id >
5 Date : Sat Jun 21 13:47:03 2014 +0200
6
7 Second commit
8
9 diff -- git a / README b / README
10 index efe6f7c ..4 fe6328 100644
11 --- a / README
12 +++ b / README
13 @@ -1 +1 @@
14 - First version .
15 + Second version .
Listing 4: Adding a tag

Useful git commands
git tag
What we did previously is to add what is called a lightweight tag.
Lightweight tags are essentially commit aliases.

Useful git commands
git tag
There is another type of tag, called the annotated tag.

Useful git commands
git tag
There is another type of tag, called the annotated tag.
Annotated tags contain more information: tagger identity, tagging

message, tagging date, and can be verified with GPG.

Useful git commands
git tag
1 $ git tag -a " v0 .0.1" -m " Alpha version "
2 tag v0 .1.0
3 Tagger : bow < bow@bow . web . id >
4 Date : Sat Jun 21 15:11:53 2014 +0200
5
6 Alpha version
7
8 commit a 4 3 9 4 d 2 8 e 6 b a 3 0 b e 1 9 3 1 8 e e 7 4 f 7 3 2 a 1 0 3 b 8 f f d f 2
9 Author : bow < bow@bow . web . id >
10 Date : Sat Jun 21 13:47:03 2014 +0200
11
12 Second commit
13
14 diff -- git a / README b / README
15 index efe6f7c ..4 fe6328 100644
16 --- a / README
17 +++ b / README
18 @@ -1 +1 @@
19 - First version .
20 + Second version .
Listing 5: Adding an annotated tag

Useful git options
git diff -w
Sometimes, you want to hide whitespace differences when using
“git diff”.

Useful git options
git diff -w
“git diff”.
This can be done via “git diff -w”.

1 $ git diff -w
Listing 6: git diff without whitespace

Useful git options
git diff -w
“git diff”.
This can be done via “git diff -w”.

1 $ git diff -w
Listing 6: git diff without whitespace
Note that while this aids visualization of the diff, git will still commit
the whitespace change.

Useful git options
git commit –amend

Git gives you total control over your history, which means you can
also change them.

Useful git options
git commit –amend

also change them.
This practice is potentially dangerous and should not be part of your

regular workflow. This is especially true for public commits.

Useful git options
git commit –amend

also change them.

Still, there are times when changing that one last commit makes
more sense than doing a “git revert”

Useful git options
git commit –amend

also change them.

Still, there are times when changing that one last commit makes
more sense than doing a “git revert”
“git commit --amend” allows you to do that: changing your last com-
mit.

Useful git options
git commit –amend

When run on a clean branch (no uncommitted changes),
“git commit --amend” allows you to change your last commit mes-
sage.

Useful git options
git commit –amend

When run on a clean branch (no uncommitted changes),
“git commit --amend” allows you to change your last commit mes-
sage.
You can also use the command to meld current staged changes to
your last committed change.
1 $ git status
2 Changes to be committed :
3 modified : README
4 $ git commit -- amend -m " Update README "
5 [ master b60437d ] Second update
6 1 file changed , 1 insertion (+) , 1 deletion ( -)
Listing 7: git commit –amend

Useful git options
git add –patch

Often, uncommited change overextends. You start with the inten-
tion of fixing bug A, but in the middle found that you can implement
feature B and feature C while also squashing bug D.

Useful git options
git add –patch

At the end of the day, only “git commit -am "Updates"” is done and
the whole change is saved in a single comit.

Useful git options
git add –patch

At the end of the day, only “git commit -am "Updates"” is done and
the whole change is saved in a single comit.
This defeats the purpose of tracking your changes in commits. Com-

mits ideally represents a single, functional update, which you can
understand later on.

Useful git options
git add –patch

You can, infact, commit the line changes selectively. This helps split
a mesh of changes into separate commits.
1 $ git add -- patch
Listing 8: git add –patch

Main Configuration File
Viewing
In Linux, git uses the “~/.gitconfig” file as its main configuration
file.

Viewing
In Linux, git uses the “~/.gitconfig” file as its main configuration
file.
To see the current configuration values, use “git config --list”.

1 $ git config -- list
2 user . name = bow
3 user . email = bow@bow . web . id
4 color . ui = auto
Listing 9: Git config values

Modifying
To edit the file directly, open “~/.gitconfig” in a text editor and
save your changes.
1 $ vim ~/. gitconfig
Listing 10: Modifying the config file

Modifying
To edit the file directly, open “~/.gitconfig” in a text editor and
save your changes.
1 $ vim ~/. gitconfig
Listing 10: Modifying the config file
You can also use the “git config --global” to set the values via the
shell.
1 $ git config -- global user . name " Linus Torvalds "
Listing 11: Modifying via the shell

Modifying: global ignore

We will look at two examples now: setting a global ignore file and
setting aliases.


setting aliases.
In addition to setting a directory-specific “.gitignore” file, you can

also set a global ignore file.


setting aliases.
In addition to setting a directory-specific “.gitignore” file, you can

also set a global ignore file.
You can name this file anything. The convention is to use

“.gitignore\_global” and place the file in your home directory.


The global ignore file has the same format as the per-directory
“.gitignore” file, only visible to all git repositories.


1 $ echo "*. out " > ~/. gitignore_g l ob a l

2 $ echo " testing . txt " >> ~/. gitignore_g lo ba l
3 $ git config -- global core . excludesfile \
4 "~/. gitignore_g l ob a l "
Listing 12: Setting the global ignore file


1 $ echo "*. out " > ~/. gitignore_g l ob a l

2 $ echo " testing . txt " >> ~/. gitignore_g lo ba l
3 $ git config -- global core . excludesfile \
4 "~/. gitignore_g l ob a l "
Listing 12: Setting the global ignore file
1 $ echo " Is this the real life ?" > this . out
2 $ touch testing . txt
3 $ git status
Listing 13: Ignoring via the global file

Aliases
You can alias simple commands.
1 $ git config -- global alias . st status
2 $ git st
Listing 14: Simple alias

Aliases
You can alias simple commands.
1 $ git config -- global alias . st status
2 $ git st
Listing 14: Simple alias
Or more complex commands.

1 $ git config -- global alias . qlog \
2 " log -- pretty = oneline "
3 $ git qlog
4 a4394d28e ... Second commit
5 80 eafd7e6 ... First commit
Listing 15: Complex alias

GitLab and GitHub
Demo time!

Acknowledgements
Martijn Vermaat
Wibowo Arindrarto
Szymon Kielbasa
Jeroen Laros
http://git-scm.com/book

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Code and data management with Git

Git Tips and Tricks

Department of Human Genetics

We will look into some of these customizations now.

1/20 Code and data management with Git 14-06-2019

2/20 Code and data management with Git 14-06-2019

“git status” is useful, but quickly feels repetitive.

Listing 1: Routine git checking

2/20 Code and data management with Git 14-06-2019

“git status” is useful, but quickly feels repetitive.

Listing 1: Routine git checking

Solution: use a custom shell prompt that displays git status.

Listing 2: Git checking with custom prompt

The git-approved way to do this is to use the “\_\_git\_ps1” shell

3/20 Code and data management with Git 14-06-2019

The git-approved way to do this is to use the “\_\_git\_ps1” shell

3/20 Code and data management with Git 14-06-2019

The git-approved way to do this is to use the “\_\_git\_ps1” shell

Then, in your “.bashrc” ﬁle, add “\_\_git\_ps1” to the “PS1” vari-

3/20 Code and data management with Git 14-06-2019

4/20 Code and data management with Git 14-06-2019

Listing 3: git blame command

4/20 Code and data management with Git 14-06-2019

Listing 3: git blame command

Similar functionality is also available in GitLab by clicking on the

4/20 Code and data management with Git 14-06-2019

5/20 Code and data management with Git 14-06-2019

Oﬃcial releases, for example, are better referred to as v1.0 than

5/20 Code and data management with Git 14-06-2019

Oﬃcial releases, for example, are better referred to as v1.0 than

This can be done using “git tag”.

5/20 Code and data management with Git 14-06-2019

1 $ git tag " v0 .0.1"

Listing 4: Adding a tag

6/20 Code and data management with Git 14-06-2019

7/20 Code and data management with Git 14-06-2019

There is another type of tag, called the annotated tag.

7/20 Code and data management with Git 14-06-2019

There is another type of tag, called the annotated tag.

Annotated tags contain more information: tagger identity, tagging

7/20 Code and data management with Git 14-06-2019

Listing 5: Adding an annotated tag

9/20 Code and data management with Git 14-06-2019

This can be done via “git diff -w”.

Listing 6: git diff without whitespace

9/20 Code and data management with Git 14-06-2019

This can be done via “git diff -w”.

Listing 6: git diff without whitespace

9/20 Code and data management with Git 14-06-2019

git commit –amend

10/20 Code and data management with Git 14-06-2019

git commit –amend

This practice is potentially dangerous and should not be part of your

10/20 Code and data management with Git 14-06-2019

git commit –amend

This practice is potentially dangerous and should not be part of your

10/20 Code and data management with Git 14-06-2019

git commit –amend

This practice is potentially dangerous and should not be part of your

10/20 Code and data management with Git 14-06-2019

git commit –amend

11/20 Code and data management with Git 14-06-2019

git commit –amend