2.3 Branching and merging

Branching and merging are key concepts in collaborative data science. They allow teams to work on different parts of a project simultaneously, experiment with new ideas, and integrate changes smoothly. Understanding these techniques is crucial for effective version control and reproducible research.

Git provides powerful tools for creating, managing, and merging branches. Mastering these skills enables data scientists to collaborate efficiently, maintain clean codebases, and implement robust workflows for developing and deploying statistical models and data analysis pipelines.

Fundamentals of branching

• Branching serves as a cornerstone of collaborative data science projects by enabling parallel development and experimentation
• Facilitates version control in reproducible research allowing multiple analyses to be explored simultaneously
• Supports team-based statistical modeling by isolating changes and promoting code review processes

Definition and purpose

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• Divergent line of development within a version-controlled repository
• Allows multiple developers to work on different features concurrently without interfering with the main codebase
• Promotes experimentation and testing of new statistical methods or data processing techniques
• Enables isolation of changes for easier debugging and code review in collaborative data analysis projects

Types of branches

• Feature branches created for developing new functionalities or conducting specific analyses
• Release branches used for preparing and stabilizing code for production deployment of statistical models
• Hotfix branches employed for quick fixes to critical issues in live data pipelines
• Development branches serving as integration points for ongoing work before merging to main
• Main (or master) branch representing the stable, production-ready version of the codebase

Branch naming conventions

• Use descriptive, hyphenated names reflecting the purpose of the branch (feature-add-regression-analysis)
• Include issue tracker IDs for easy reference (bugfix-issue-123-data-cleaning)
• Employ prefixes to categorize branches (feature/, bugfix/, hotfix/, release/)
• Keep names concise yet informative to aid in branch management and collaboration
• Avoid using personal names or overly generic terms in branch names

Creating branches

Command line branching

• Use

  git branch <branch-name>

  to create a new branch without switching to it
• Employ

  git checkout -b <branch-name>

  to create and switch to a new branch in one command
• Utilize

  git push -u origin <branch-name>

  to push a local branch to the remote repository
• Implement

  git branch -d <branch-name>

  to delete a local branch after merging
• Execute

  git fetch origin

  followed by

  git checkout -b <branch-name> origin/<branch-name>

  to create a local branch tracking a remote branch

GUI branching tools

• GitHub Desktop offers intuitive branch creation and management through its graphical interface
• GitKraken provides visual representation of branch structures and easy branch manipulation
• SourceTree enables branch creation, switching, and merging with a few clicks
• Visual Studio Code's built-in Git functionality allows branch operations within the editor
• RStudio's Git integration facilitates branch management for R-based data science projects

Remote vs local branches

• Local branches exist only on the developer's machine and allow for offline work
• Remote branches reside on the shared repository and are accessible to all collaborators
• Use

  git push

  to synchronize local branches with remote counterparts
• Employ

  git fetch

  to update local references to remote branches without merging
• Utilize

  git branch -r

  to list remote branches and

  git branch -a

  to show both local and remote branches

Working with branches

Switching between branches

• Use

  git checkout <branch-name>

  to switch to a different branch
• Employ

  git switch <branch-name>

  (Git 2.23+) as a more intuitive alternative to checkout
• Stash or commit changes before switching to prevent conflicts
• Utilize

  git checkout -

  to quickly switch back to the previously checked out branch
• Implement

  git worktree

  for working on multiple branches simultaneously in separate directories

Tracking branch changes

• Use

  git log

  to view commit history of the current branch
• Employ

  git diff <branch1> <branch2>

  to compare changes between branches
• Utilize

  git branch -v

  to see the last commit on each branch
• Implement

  git show-branch

  for a more detailed view of branch history and relationships
• Use

  git reflog

  to track reference updates and branch movements

Branch management strategies

• Implement a trunk-based development approach for continuous integration in data science workflows
• Utilize feature flags to control the activation of new features or analyses in production
• Employ short-lived feature branches to minimize merge conflicts and promote frequent integration
• Implement branch protection rules to enforce code review and maintain data integrity
• Regularly prune obsolete branches to keep the repository clean and manageable

Merging basics

Merge types

• Fast-forward merges occur when the target branch is a direct descendant of the source branch
• Three-way merges combine changes from two divergent branches and create a new merge commit
• Squash merges condense all commits from a feature branch into a single commit on the target branch
• Rebase merges rewrite history by applying commits from one branch onto another
• Octopus merges combine changes from more than two branches simultaneously (less common)

Fast-forward vs three-way merges

• Fast-forward merges maintain a linear history and don't create additional merge commits
• Three-way merges preserve branch history and create explicit merge points in the commit graph
• Fast-forward merges occur automatically when possible unless forced otherwise
• Three-way merges are necessary when branches have diverged and require manual conflict resolution
• Use

  git merge --no-ff

  to force a three-way merge even when a fast-forward is possible

Merge conflicts

• Arise when changes in different branches affect the same lines of code or data
• Require manual intervention to resolve conflicting changes
• Git marks conflict areas in files with

  <<<<<<<

  ,

  =======

  , and

  >>>>>>>

  delimiters
• Use tools like

  git mergetool

  or IDE integrations to assist in conflict resolution
• Employ

  git merge --abort

  to cancel a merge and return to the pre-merge state

Advanced merging techniques

Rebasing vs merging

• Rebasing rewrites commit history by applying commits from one branch onto another
• Merging preserves the original branch structure and creates explicit merge commits
• Rebasing results in a linear project history, while merging shows the full branching structure
• Use rebasing for cleaning up local changes before sharing them with others
• Prefer merging for integrating shared branches to maintain an accurate project history

Cherry-picking commits

• Allows selective application of specific commits from one branch to another
• Use

  git cherry-pick <commit-hash>

  to apply a single commit to the current branch
• Employ

  git cherry-pick -x <commit-hash>

  to include the original commit message in the cherry-pick
• Utilize

  git cherry-pick --no-commit <commit-hash>

  to stage changes without creating a new commit
• Resolve conflicts that may arise during cherry-picking similarly to merge conflicts

Squashing commits

• Combines multiple commits into a single, cohesive commit
• Use

  git [rebase](https://www.fiveableKeyTerm:Rebase) -i HEAD~n

  to interactively rebase and squash the last n commits
• Employ

  git merge --squash <branch-name>

  to squash all commits from a branch into a single commit
• Improves readability of commit history by grouping related changes
• Useful for cleaning up feature branches before merging into the main development branch

Collaborative branching

Feature branch workflow

• Create a new branch for each feature or analysis task
• Develop and test changes in isolation from the main branch
• Submit pull requests for code review before merging
• Merge feature branches back into the main branch upon completion
• Delete feature branches after successful integration to keep the repository clean

Gitflow workflow

• Maintain two primary branches main (or master) and develop
• Create feature branches off develop for new work
• Use release branches to prepare for production deployments
• Employ hotfix branches for critical bug fixes in production
• Merge completed features into develop and eventually into main for releases

Forking workflow

• Fork the main repository to create a personal copy
• Clone the forked repository to work locally
• Create feature branches in the forked repository
• Submit pull requests from the fork to the original repository
• Sync the fork with the upstream repository to stay up-to-date

Best practices

Branch lifecycle management

• Create branches for specific purposes (features, bugfixes, experiments)
• Keep branches short-lived to minimize divergence from the main branch
• Regularly update feature branches with changes from the main branch
• Delete branches promptly after merging to maintain a clean repository
• Use branch naming conventions consistently across the team

Code review in branching

• Submit pull requests for all significant changes before merging
• Assign appropriate reviewers based on code ownership and expertise
• Use code review tools to facilitate discussions and track comments
• Address feedback and make necessary revisions before merging
• Automate checks (linting, tests) to run on pull requests

Documentation for branches

• Maintain a README file explaining the project structure and branching strategy
• Use descriptive commit messages to document changes within branches
• Create release notes for major version branches
• Document branch purposes and statuses in issue tracking systems
• Update documentation when branching strategies or workflows change

Branching in popular platforms

GitHub branching features

• Offers protected branches to enforce review policies and status checks
• Provides branch comparison and pull request interfaces
• Supports branch deployment features for continuous delivery
• Offers branch-specific permissions and access controls
• Integrates with GitHub Actions for automated workflows on branch events

GitLab branching tools

• Provides merge request approvals and code owner configurations
• Offers environment-specific branch deployments
• Supports auto-merge functionality for branches passing all checks
• Integrates with GitLab CI/CD for automated testing and deployment
• Provides branch-level security scanning and vulnerability reports

Bitbucket branch management

• Offers branch permissions and restrictions
• Provides pull request workflows with customizable approval rules
• Supports branch comparison and diffing tools
• Integrates with Jira for issue tracking and branch management
• Offers branch-specific pipeline configurations in Bitbucket Pipelines

Troubleshooting

Common branching issues

• Merge conflicts arising from concurrent changes to the same code areas
• Divergent branches becoming difficult to reconcile over time
• Accidental commits to the wrong branch
• Loss of work due to improper branch management
• Performance issues with large numbers of branches or large repositories

Merge conflict resolution

• Identify conflicting files using

  git status

  after a failed merge
• Open conflicting files and locate conflict markers (

  <<<<<<<

  ,

  =======

  ,

  >>>>>>>

  )
• Manually edit files to resolve conflicts, removing conflict markers
• Use

  git add

  to stage resolved files and

  git commit

  to complete the merge
• Employ visual merge tools or IDE integrations for complex conflicts

Undoing merges

• Use

  git reset --hard HEAD~1

  to undo the last merge commit (local only)
• Employ

  git revert -m 1 <merge-commit-hash>

  to create a new commit undoing a merge
• Utilize

  git reflog

  to find the commit hash before the merge for manual resetting
• Implement

  git checkout -b <new-branch-name> <commit-before-merge>

  to create a new branch from pre-merge state
• Use

  git push --force

  cautiously to update remote branches after undoing merges (team communication crucial)