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Eric Nawrocki edited this page Aug 7, 2017 · 2 revisions

initial checkout

To clone a generate_vecscreen_candidates repository for the first time:

   $ git clone https://github.com/aaschaffer/generate_vecscreen_candidates.git

You're set up on the stable master branch. To do any development, you need to work on the develop branch, generally by creating and merging feature branches.

To switch to develop branches:

   $ cd generate_vecscreen_candidates
   $ git checkout develop

You will also need access to a local 'blast' executable (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) and 'srcchk' executable, as well as access to a system that uses Sun Grid Engine (most importantly the 'qsub' program) to submit jobs to a compute farm, such as the compute farm used at NCBI at NIH.

For information about our git workflow, read on.

git workflow

generate_vecscreen_candidates uses the popular git workflow that's often just called "git flow". Go read the 2010 blog post by Vincent Driessen that describes it. But we use it with the difference that we don't mind having feature branches on origin.

In what follows, first we'll give concise-ish examples of the flow for normal development, making a release, and making a "hotfix". A summary of the principles and rationale follows the examples.

Normal development

Generally, for any changes you make to our code, you will make on a feature branch, off of develop. So first you create your branch:

   $ git checkout -b myfeature develop

Now you work, for however long it takes. You can make commits on your myfeature branch locally, and/or you can push your branch up to the origin and commit there too, as you see fit.

When you're done, and you've tested your new feature, you merge it to develop (using --no-ff, which makes sure a clean new commit object gets created), and delete your feature branch:

   $ git checkout develop                     
   $ git merge --no-ff -m "Merges myfeature branch into develop" myfeature
   $ git branch -d myfeature
   $ git push origin --delete myfeature
   $ git push origin develop

Small features: single commits can be made to develop

Alternatively, if you're sure your change is going to be a single commit, you can work directly on the develop branch.

   $ git checkout develop                  
     # make your changes
   $ git commit
   $ git push origin develop

Big features: keeping up to date with develop

If your work on a feature is taking a long time (days, weeks...), and if the develop trunk is accumulating changes you want, you might want to periodically merge them in:

   $ git checkout myfeature
   $ git merge --no-ff -m "Merges develop branch into myfeature branch" develop

Making a release

To make a release, you're going to make a release branch of the code. You assign appropriate version numbers to each, test and stabilize. When everything is ready, you merge to master and tag that commit with the version number; then you also merge back to develop, and delete the release branch.

For example, here's the git flow for a generate_vecscreen_candidates release. Suppose generate_vecscreen_candidates is currently at 0.03 and we decide this release will be generate_vecscreen_candidates 0.1. To proceed we make a new release from generate_vecscreen_candidates's develop branch:

   $ cd generate_vecscreen_candidates
   $ git checkout develop # only necessary if you're not already on develop
   $ git checkout -b release-0.1 develop
     # change version numbers to 0.1 in README and in all scripts.
     # Go through entire README and make sure that run_script_tests.pl works and 
     # any sample runs work.
   $ git commit -a -m "Version number bumped to 0.1"
     # do and commit any other work needed to test/stabilize generate_vecscreen_candidates release.

When you're finished merge the generate_vecscreen_candidates release branch as follows:

   $ git checkout master
   $ git merge --no-ff -m "Merges release-0.1 branch into master" release-0.1
   $ git tag -a -m "Tags 0.1 release" 0.1
   $ git push origin 0.1
      # Now merge release branch back to develop...
   $ git checkout develop
   $ git merge --no-ff -m "Merges release-0.1 branch into develop" release-0.1
   $ git push
   $ git branch -d release-0.1
   $ git push origin --delete release-0.1

Fixing bugs: "hotfix" branches

If you need to fix a critical bug and make a new release immediately, you create a hotfix release with an updated version number, and the hotfix release is named accordingly: for example, if we screwed up generate_vecscreen_candidates 0.03, hotfix-0.04 is the updated 0.04 release.

A hotfix branch comes off master, but otherwise is much like a release branch.

   $ cd generate_vecscreen_candidates
   $ git checkout -b hotfix-0.04 master                 
     # change version numbers to 0.04 in README
     # Go through entire README and update version in all scripts and make sure that run_script_tests.pl works and 
     # any sample runs work.
   $ git commit -a -m "Version number bumped to 0.04"

Now you fix the bug(s), in one or more commits. When you're done, the finishing procedure is just like a release:

    $ git checkout master              
    $ git merge --no-ff -m "Merges hotfix-0.04 branch into master" hotfix-0.04
    $ git push
    $ git tag -a -m "Tags 0.04 release" 0.04
    $ git push origin 0.04
    $ git checkout develop              
    $ git merge --no-ff -m "Merges hotfix-0.04 branch into develop" hotfix-0.04
    $ git push
    $ git branch -d hotfix-0.04

Summary of main principles

There are two long-lived generate_vecscreen_candidates branches: origin/master, and origin/develop. All other branches have limited lifetimes.

master is stable. Every commit object on master is a tagged release, and vice versa.

develop is for ongoing development destined to be in the next release. develop should be in a close-to-release state. Therefore, commit objects on develop are either small features in a single commit, or a merge of a finished feature branch.

We make a feature branch off develop for any nontrivial new work -- anything that you aren't sure will be a single commit on develop. A feature branch:

  • comes from develop
  • is named anything informative (except master, develop, hotfix-* or release-*)
  • is merged back to develop (and deleted) when you're done
  • is deleted once merged

We make a release branch off develop when we're making a release. A release branch:

  • comes from develop
  • is named release-<version>, such as release-1.2
  • first commit on the hotfix branch consists of bumping version/date/copyright
  • is merged to master when you're done, and that new commit gets tagged as a release
  • is then merged back to develop too
  • is deleted once merged

We make a hotfix branch off master for a critical immediate fix to the current release. A hotfix branch:

  • comes from master
  • is named hotfix-<version>, such as hotfix-1.2.1
  • first commit on the hotfix branch consists of bumping version/date/copyright
  • is merged back to master when you're done, and that new commit object gets tagged as a release.
  • is then merged back to develop too
  • is deleted once merged

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