Development workflow - webdev

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This page describes the development model used by the web development team at WormBase using git as our version control system. This includes our branching strategy and release management. We use git and GitHub to help us manage development.

Overview Diagram

Git Workflow - WormBase4.png

Editable version of the diagram


Whenever you begin work on a new issue you should create a new branch for it. Any new features should branch off staging. Once the feature is ready for testing, you can submit a pull request to staging for code review. Feature branches aren't necessarily branches in the main repository - they can in the main WormBase repository, or on a developer's fork. Read more on our branching strategy

git checkout -b myFeature staging

Now you can make your changes and commit some code. Read more on commit messages

git commit -m "Descriptive commit message"

When you're ready, you can push your branch to GitHub

git push origin myFeature

Continue making changes until your code is ready for a code review. Is my code ready for review?

When your code is ready, go to GitHub and create a Pull Request. More info on Pull Requests.

  1. Go to the repository where you pushed your changes
  2. Using the drop down, switch to your branch (e.g. myFeature)
  3. Click the green Compare & review button
  4. After reviewing all the changes, click on Create pull request in the header to send the pull request
  5. In the description, write a short summary of the issues (along with a link to the issue) and changes made along with some links for testing

Wait for another member of the web development team to review and merge your pull request. If more changes are requested, you can push more commits to the same branch and it will be added to the pull request.

Once your pull request is merged, locally bring in the changes and delete your issue branch

git checkout staging
git pull
git branch -d myFeature

Go to the original github issue:

  1. Add the Under testing label to your issue
  2. Comment on the issue to notify all involved that it is ready for testing. Add links for testing for the ease of testers.
  3. Another member of the WormBase group will close the issue once they have tested it

Note: You can view all merged pull requests using this link:

Is my code ready for review?

Before you send a Pull Request, please make sure you have completed the following:

  • Written tests (API tests or REST tests) demonstrating the problem in the issue. More info on testing
  • Fix the problem (ie pass the tests)
  • Complete the issue as much as possible without curators seeing an example
  • Code style meeting the WormBase coding standards (indentation, comments, no debug statements)

What info should I include in a Pull Request?

To help your reviewer understand your code, please try to include the following in the Pull Request description

  • A link to the issue being addressed
  • Short summary of the problem
  • Some links to use for testing
  • Any other information that may be needed to testing (ie wormbase_local.conf changes, extra files needed, etc)

Commit messages


Keep your commit message as descriptive as possible, reference any issues affected by the issue number (#YYY):

This is a summary of my commit.
* here is a breakdown of the different changes
* mention github users (@tharris) when appropriate
* related to #529
* #945

Here is a template originally written by Tim Pope at

Short (50 chars or less) summary of changes

More detailed explanatory text, if necessary.  Wrap it to about 72
characters or so.  In some contexts, the first line is treated as the
subject of an email and the rest of the text as the body.  The blank
line separating the summary from the body is critical (unless you omit
the body entirely); tools like rebase can get confused if you run the
two together.

Further paragraphs come after blank lines.

 - Bullet points are okay, too

 - Typically a hyphen or asterisk is used for the bullet, preceded by a
   single space, with blank lines in between, but conventions vary here

Code Review

All changes must go through a code review before being merged to the staging branch. At WormBase, this is done using Pull Requests. All members of the core development team are expected to keep an eye on the open Pull Requests and reviewing the ones they are assigned.

  • Test out the pull request (check out the branch)
  • Take a quick look at the code (are there comments? anything obvious missing)
  • Run the tests written for this issue
  • Leave a comment on the PR if you notice anything that needs to be fixed
  • Merge the PR if you think it looks good
    • Begin by merging staging into the feature branch.
    • If there are conflicts, ask the owner of the PR to help resolve them.


All issues need to be tested and closed by at least one person who is not the developer who made the change. Ideally, it would be the curator asking for the feature/fix.

If you would like to help test:

  • Look at the open issues 'under testing'.
  • All the changes for these issues are available for testing on
  • You can test out the changes and leave any feedback you have in the issue comments.
  • If you think this feature/fix is ready for production, please close the issue.

Branch Strategy

We use branches to help with our release management, testing strategy, and helping with parallel development among the team.

Main branches

Inside the WormBase/website repository, there are three main branches: master, staging and production.

  • master: current, stable code. All new changes brought into master have been tested on and approved by either the curator requesting the change, or the development lead.
  • staging: all changes get pushed to the staging branch after code review. This code gets pushed immediately to
  • production: the code currently in production. Branched off of master at each release.

Feature branches

Any new features should branch off staging. Read more on feature branches in our contribution guidelines


If a major bugfix is needed in production, create a hotfix branch from production. When finished, the branch needs to be merged (via PR/code review) back into production and staging

Begining a fix

git checkout -b hotfix-issXXX production

Fix the bug and commit the fix in one or more commits. Reference the github issue:

git commit -m "Severe production bug
* search redirecting to home page
* fix #XXX"

Closing the fix

To close the fix, send a Pull Request to both the production and staging for code review. The reviewer will merge the branch.

Development Timeline

See: WormBase Release Workflow

Release Management

When production is ready to updated for release WSXXX:

  1. Create a new pull request from staging to master.
  2. Review all changes going into new release. Merge in the pull request.
  3. Create a new pull request from master to production.
  4. Review all changes going into new release. Merge in the pull request.
  5. Tag production branch with appropriate release name.

git checkout production
git tag -a WSXXX