Create a Pull Request in GitHub¶
Committing, pushing and making pull requests¶
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Review: Changes made to the ontology can be viewed in GitHub Desktop.
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Before committing, check the diff. An example diff from the Cell Ontology (CL) is pasted below. Large diffs are a sign that something went wrong. In this case, do not commit the changes and consider asking the ontology editor team for help instead.
Example 1 (Cell Ontology):
Example 2 (Mondo):
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Commit message: Before Committing, you must add a commit message. In GitHub Desktop in the Commit field in the lower left, there is a subject line and a description.
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Give a very descriptive title: Add a descriptive title in the subject line. For example: add new class ONTOLOGY:ID [term name] (e.g. add new class MONDO:0000006 heart disease)
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Write a great summary of what the change is in the Description box, referring to the issue. The sentence should clearly state how the issue is addressed.
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To link the issue, you can use the word 'fixes' or 'closes' in the description of the commit message, followed by the corresponding ticket number (in the format #1234) - these are magic words in GitHub; when used in combination with the ticket number, it will automatically close the ticket. Learn more on this GitHub Help Documentation page about Closing issues via commit messages.
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Note: 'Fixes' and "Closes' are case-insensitive.
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If you don't want to close the ticket, just refer to the ticket # without the word 'Fixes' or use 'Addresses'. The commit will be associated with the correct ticket but the ticket will remain open. 7.NOTE: It is also possible to type a longer message than allowed when using the '-m' argument; to do this, skip the -m, and a vi window (on mac) will open in which an unlimited description may be typed.
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Click Commit to [branch]. This will save the changes to the ontology edit file.
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Push: To incorporate the changes into the remote repository, click Publish branch.
Make a Pull Request¶
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Click: Create Pull Request in GitHub Desktop
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This will automatically open GitHub Desktop
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Click the green button 'Create pull request'
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You may now add comments to your pull request.
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The CL editors team will review your PR and either ask for changes or merge it.
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The changes will be available in the next release.