me: dr james hetherington -- ucl research software development team -- @uclrcsoftdev --...

Me:

Dr James Hetherington

-- UCL Research Software Development Team

-- @uclrcsoftdev

-- blogs.ucl.ac.uk/research-software-development/

-- www.mailinglists.ucl.ac.uk/mailman/listinfo/research-programming

Version Control and Issue Tracking

• Managing code inventory– “When did I introduce this bug?”– Undoing mistakes

• Working with other programmers– How can I merge my work with Jim’s?

• What’s the most important bug to fix next?

What is version control? (Solo version)

• Do some programming• > my_vcs commit• Program some more

– Realise mistake

• > my_vcs rollback– Mistake is undone

Syntax here is example only!

What is version control? (team version)

• … wait …• … wait …• Join the team• > my_vcs checkout• do some programming• > my_vcs commit• Do some programming• … more programming…• > my_vcs commit• … more programming …• … more programming …• … more programming …• … more programming …• … more programming …• > my_vcs commit

• Error again…

• Create some code• > my_vcs commit• …wait…• …wait…• …wait…• …wait…• >my_vcs update• Do some programming• … program some more• > my_vcs commit

• Oh Noes! Error message!• > my_vcs update• > my_vcs merge• > my_vcs commit• More programming…

Sue Jim

Centralised VCS concepts

• There is one, linear history of changes on the server or repository• Each revision has a unique identifier

• You have a working copy• You update the working copy to match the state of the repository• You commit your changes to the repository• If you someone else has changed it you have to resolve conflicts

between your changes and the repository, and then commit

Centralised VCS

Server

With All Committed

Versions

Client

At v4

Client

At v4+

Client

At v3

Centralised VCS solo workflow

svn checkout http://mysvn.ucl.ac.uk/mycodevim myfile.py

svn commit

touch mynewfile.ymlsvn add mynewfile.ymlvim mynewfile.yml

svn commit

Commands for this in Subversion:

Time

Centralised VCS Team workflow: no conflicts

Jim’s commands:

svn checkout http://…ac.uk/ourcode

vim jimfile.py

svn commit

Sue’s commands:

svn co http://mysvn.ucl.ac.uk/ourcode

svn updatecat jimfile.py # Sue can see changesvim suefile.py

svn commit

Centralised VCS with conflicts

Jim’s commands:

svn update

vim sharedfile.py

svn commit

Sue’s commands:

svn up

vim sharedfile.py

svn commit svn: Out of date: ’sharedfile.py’

svn upvim sharedfile.py

svn ci

Resolving conflicts

On update, you get a prompt like:> svn update Conflict discovered in ’sharedfile.py'. Select: (p) postpone, (df) diff-full, (e) edit, (mc) mine-conflict, (tc) theirs-conflict, (s) show all options:

If you choose (e) or (p) the conflicted file will look something like:

> cat sharedfile.pyprevious content<<<<<<< .mineSue’s content======= Jim’s content>>>>>>> .r4Previous content

You edit to fix this, then save.

Revisiting history

• You can update to a particular revision– svn up -r 3

• You can see the differences between your working area and a revision– svn diff (to current repository most recent version)– svn diff –r 3

• You can see which files you’ve changed or added– svn status

• You can get rid of changes to a file– svn revert myfile.py

Distributed and Centralized Version Control

• Centralized: – Some server contains the remote version– Your computer has your copy– To switch back to an old copy you need the internet– E.g. cvs, subversion (svn)

• Distributed:– Every user has a version of the full history– Users can synchronize their history with each other– Having a central “master” copy is a policy option

• Most groups do this

– E.g. git, mercurial (hg), bazaar (bzr)

Distributed VCS

In principle:

Master copy

(with v0,1,2,4,5)

Sue’s copy

(with v0,1,2,3)

Phil’s copy

(with v0,1,2,4,5,6)

Jim’s copy

(with v0,1,2,4,5)

In practice:

Pragmatic distributed VCS

Subversion

svn checkout http://mysvn.ucl.ac.uk/mycode

svn commit

svn up

svn status

svn diff

Git

git clone git@github.com:ucl/mycode.git git commit -agit push

git pull

git status

git diff

Why go distributed?

• Easy to start a repository (no server needed)• Easy to start a server• Can work without an internet connection• Better merges• Easy branching• More widespread support

Why not go distributed?

• More complex commands• Easier to get confused!

Distributed VCS concepts (1)

• Each revision has a parent that it is based on• These revisions form a graph

• The most recent in each copy is the head or tip• Each revision has a globally unique hash-code

– E.g. in Sue’s copy revision 43 is ab3578d6– Jim thinks that is revision 38

• When you bring in information from a remote the histories might conflict– Histories from different copies are merged together

Distributed VCS concepts (2)

• You have a working copy• You pick a subset of the files in your working copy

to add to the next commit: these go into the staging area or index

• When you commit, you commit:– from the staging area– to the local repository

• You push to remote repositories to share or publish your changes

• You pull or fetch to bring in from a remote

Distributed VCS solo workflow

Create a file myfile1.py

git init

git add .git commit

create a new file myfile2.pyand edit myfile1.pygit add file2.pygit commitOnly changes to file2 get into commit

Edit both files

git commit -a

Commands for this in Git:

Distributed VCS solo with publishing

git clone git@github.com:ucl/mycode.git

Edit a few files

git add --updategit commitgit push

Edit a few files

git commit -agit push

Commands for this in Git:

Distributed VCS Team workflow: no conflicts

Jim’s commands:git initgit add mycodegit commitgit remote add --track master origin git@github.com:ucl/foo.gitgit push

git fetchgit merge

git commit –agit push

Sue’s commands:

git clone git@github.com:ucl.foo.git

git commit –agit push

git pull

Distributed team workflow with conflicts

Jim’s commands:

git commit -a

git pushError: ! [rejected]git pull

git commit –a

git push

Sue’s commands:

git commit –a

git push

git commit –agit push

git commit -a

git commit –a

git pull

Really distributed: more than one remotegit remote add sue ssh://sue.ucl.ac.uk/somerepo

add a second remote

git remotelist available remotes

git push suegit push origin

push to a specific remote

Working with branches

Working with branches in git

> git branch* master

> git branch experiment> git branch

* masterexperiment

> git checkout experiment> git branch

master* experiment

Sharing branches in git

git push origin experimentpublish the branch to remote

git push -u origin experimentpublish the branch to remote(first time)

git branch -rdiscover branches on remote(s)

git checkout origin/experimentget a new branch from a remote

Merging and deleting branches

git checkout masterswitch back to master branch

git merge experimenttake all the changes from experiment into master

exactly like merging someone else’s work

git branch -d experimentthe experiment is done, get rid of local branch

git push --delete experimentgit rid of the branch on the remote

Working with branches

• You should have a development branch and a stable branch

• You should create temporary branches for experimental changes

• If you release code to others, you should make a release branch– Then you can make fixes to bugs they find– And control which of your work goes in the release

Tagging

• You should tag working versions• You should produce real science only with specific

tagged versions, and note which one

Tagging

git tag –a v1.3add a tag, labelling last commit

git tag –a v1.3 ab48dctag an old commit

git push --tagspublish the tags to origin

Branching and tagging in subversion

• You can do branches and tags in subversion too– But it’s harder– svn doesn’t have real branches or tags, instead you

make copies of code inside the repo– and you can merge between the copies– It works, but it’s cleaner in git– see subversion references if you need this

More comparisonsSubversion

svn up –r54 myfile.pysvn revert myfile.pysvn revert –depth=infinity .

Git

git checkout –r ab39d myfile.pygit checkout myfile.pygit reset –hard

But git can do more, e.g.:

git reset HEAD^

will undo the last commit from your local repository (providing you haven’t pushed)

Both git and svn have many options – have a look on the web!

http://gitref.org http://git-scm.com/book http://svnbook.red-bean.com/

Other version control systems

• vcs– Really old!– Works by “locking” files instead of resolving conflicts

• cvs– Very like svn

• hg– “mercurial”– Very like git

Hosting a server

• In git, any repository can be a remote for pulls– Just use

• git pull ssh://theircomputer/theirrepo

– There are problems with pushing to someone else’s working repo: don’t!

– You can, however, create a git repo with• git init --bare

– This bare repo has no working directory, – use it as a remote for push and pull via ssh://

• In subversion, the procedure is more complicated– You have to configure a server ‘daemon’

Hosting a server in the cloud

• There are many services which allow you to create git, mercurial, and subversion repositories online– Typically free for open source– Typically a fee for private repositories

• I recommend GitHub– Create an account at https://github.com/– Students can get five free private repositories at

• https://github.com/edu

– Can interact with GitHub repositories as either svn or git

• Bitbucket is also good

Working with GitHub

Set up ssh keys

Create repository

Social coding

Browse changes

Browse changes

Comment on and discuss code

Issue tracking

• Your code has bugs (defects)• Your code has things you want to do

(enhancements)• The best way to keep track of all this is with an

issue tracker

Issue tracking

Anatomy of an issue

• Type– Defect, enhancement, task

• Severity– Critical, blocker, major, minor, trivial

• Owner• Status

– Open, fixed, duplicate, blocked, under review, won’t fix, invalid, new…

• Estimated time and time spent?• Tags

Timeline of an issue

Some questions

• Public or private issues• Organising issues into milestones• Estimate effort?• Who can close an issue?• Review processes• Integration with version control

Some issue trackers

• Trac• Redmine• Jira• GitHub’s issue tracker• Bitbucket’s issue tracker

Issues on GitHub

The Pull Request

The Pull Request

Conclusions

• Tools can make your development easier, safer, more reliable, more correct, and more collaborative

• They can be complicated and take time to learn• Learn by practicing

– Use the tools– Pick an open source project on github or bitbucket and

start contributing

http://git-scm.com/book/

http://svnbook.red-bean.com/