A Quick Introduction to Version Control with Git and GitHub
Publication Date
January 19, 2016
Journal
PLOS Computational Biology
Authors
John D. Blischak, Emily R. Davenport & Greg Wilson
Volume
12
Issue
1
Pages
e1004668
DOI
https://dx.plos.org/10.1371/journal.pcbi.1004668
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004668
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26785377
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718703
Europe PMC
http://europepmc.org/abstract/MED/26785377
Web of Science
000369366100015
Scopus
84956756030
Mendeley
http://www.mendeley.com/research/quick-introduction-version-control-git-github
Events
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CiteULike | Further Information

Mendeley | Further Information

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However, a few key problems can arise when iteratively developing code that make it difficult to document and track which code version was used to create each result. First, you often need to experiment with new ideas, such as adding new features to a script or increasing the speed of a slow step, but you do not want to risk breaking the currently working code. One often-utilized solution is to make a copy of the script before making new edits. However, this can quickly become a problem because it clutters your file system with uninformative filenames, e.g., analisys.sh, analysis_02.sh, analysis_03.sh, etc. It is difficult to remember the differences between the verions of the files and, more importantly, which version you used to produce specific results, especially if you return to the code months later. Second, you will likely share your code with multiple lab mates or collaborators, and they may have suggestions on how to improve it. If you email the code to multiple people, you will have to manually incorporate all the changes of them sends. Fortunately, software engineers have already developed software to manage these issues: version control. A version control system (VCS) allows you to track the iterative changes you make to your code, Thus, you can experiment with new ideas but always have the option to revert to a specific past version of the code you used to generate particular results. Furthermore, you can record messages as you save each successive version so that you (or anyone else) reviewing the development history of the code is able to understand the rationale for the given edits. It also facilitates collaboration. Using a VCS, your collaborators can make and save changes to the code, and you can automatically incorporate these changes to the main code base. 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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2628875"], "description"=>"<p>To store a snapshot of changes in your repository, first git add any files to the staging area you wish to commit (for example, you’ve updated the process.sh file). Second, type git commit with a message. Only files added to the staging area will be committed. All past commits are located in the hidden .git directory in your repository.</p>", "links"=>[], "tags"=>["Quick Introduction", "github", "version control"], "article_id"=>1638568, "categories"=>["Biological Sciences"], "users"=>["John D. Blischak", "Emily R. Davenport", "Greg Wilson"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004668.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_git_add_commit_process_/1638568", "title"=>"The git add/commit process.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:37:22"}
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  • {"files"=>["https://ndownloader.figshare.com/files/2628878"], "description"=>"<p>We would like you to add an empty file that is named after your GitHub username to the repo used to write this manuscript. (A) Using your internet browser, navigate to <a href=\"https://github.com/jdblischak/git-for-science\" target=\"_blank\">https://github.com/jdblischak/git-for-science</a>. (B) Click on the “Fork” button to create a copy of this repo on GitHub under your username. (C) On your computer, type git clone<a href=\"https://github.com/username/git-for-science.git\" target=\"_blank\">https://github.com/username/git-for-science.git</a>, which will create a copy of git-for-science on your local machine. (D) Navigate to the readers directory by typing cd git-for-science/readers/. Create an empty file that is titled with your GitHub username by typing touch username.txt. Commit that new file by adding it to the staging area (git add username.txt) and committing with a message (git commit -m \"Add username to directory of readers.\"). Note that your commit identifier will be different than what is shown here. (E) You have committed your new file locally, and the next step is to push that new commit up to the git-for-science repo under your username on GitHub. To do so, type git push origin master. (F) To request to add your commits to the original git-for-science repo, issue a pull request from the git-for-science repo under your username on GitHub. Once your Pull Request is reviewed and accepted, you will be able to see the file you committed with your username in the original git-for-science repository.</p>", "links"=>[], "tags"=>["Quick Introduction", "github", "version control"], "article_id"=>1638571, "categories"=>["Biological Sciences"], "users"=>["John D. Blischak", "Emily R. Davenport", "Greg Wilson"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004668.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contributing_to_open_source_projects_/1638571", "title"=>"Contributing to open source projects.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-28 12:37:22"}
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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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