- Git
- please make sure you changed your protégé settings to numerical identifiers and got a personal ID to add new classes.
Please read the OEO best practices carefully.
programs used
🔷 - git: used for synchronising the code on your PC and online
🍏 - github: used for discussion and review
📙 - protege: used to change the ontology
📗 - text editor: used to change the ontology and other files
The workflow for contributing to this project has been inspired by the workflow described by Vincent Driessen.
Discussion
-
🍏 Create an issue on the GitHub repository describing the problem and proposed solution.
Choose the right issue type from among the available choices:
A) Adding a new entity to the ontology. Ideally, each issue should correspond to only one new term (with only a few subclasses, if needed)
B) Restructuring existing parts of the ontology
C) Updating definitions of existing entities in the ontology
D) Other issue
Assign a project (default "Issues") to the issue
Discussion about the implementation should take place within the issue. Important: Please discuss the proposal within the issue thread before starting to work on a solution. For minor changes, which include small changes to improve clarity of definitions and the addition of clarifying annotations, at least one other person from the project team should agree to the proposed change before it is implemented. For major changes, which include adding new entities and restructuring the ontology, at least two other members of the project team need to agree to the change before it is implemented, which should include at least one domain expert and at least one ontology expert. Issues which are contentious, for which it is difficult to reach agreement, should be added to the agenda of the next ontology working group teleconference for discussion to reach agreement amongst the full working group. Subsequent to such discussion, the issue's first thread should be updated with a documented record of the conclusions reached.
Implementation
-
🔷 Once a solution has been agreed, create a branch from
dev
to work on your issue (see below, the "Conventions for git and GitHub" section)Checkout the latest stand of
dev
git checkout dev
git pull
Branch from
dev
(see also section "Conventions for git and GitHub" below)git checkout -b feature-issueNumber-myfeature
It is best to merge one's changes as fast as possible (i.e. do not wait for 2 weeks) to avoid merging conflicts
-
📙 or 📗 Open Protégé or a text editor and work on the ontology. If you haven't already, make sure you change your protégé settings to use numeric identifiers. Please choose the right module of the oeo to do your changes, oeo.omn is in most cases not the right file to change. Refer to this article for detailed explanations on working with protégé.
One can also edit the files in a text editor
-
📙 Before committing your changes, open the
oeo.omn
file with Protégé and save the file from Protégé. You should also check if you included inconsistencies by following this ontology test procedureSee the "Conventions" section below for commit messages format tips
-
🔷 Get your changes online
stage the files you changed
git add [file_name]
commit your changes
git commit [-m " <commit_message> "]
push your branch to the remote server
git push
If your branch does not exist on the remote server yet, git will provide you with instructions, simply follow them.
Hint: You can create a draft pull request directly after your first commit 🍏, see 7.). Then you get the pull request number and 📙 implement the term tracker items in Protégé. Only after finishing the implementations you can assign reviewers and thus change the state of the PR. Using that workflow, it is clear whether a PR is actually ready for review.
-
🍏 Make sure that all automated tests are successful. This will be indicated by a green or red icon next to your most recent commit. In case an error occured that you don't know how to solve, write a comment in the PR and ask for help from the ontology-expert-team.
Review
-
🍏 Submit a pull request (PR)
- Follow the steps of the github help to create the PR.
- Please note that your PR should be directed from your branch (for example
myfeature
) towards the branchdev
- To make reviewing easier, briefly describe the changes you have made in the pull request and summarise the discussion and conclusions in the associated issue.
- Write the corresponding issue number in the pull request so that they are linked. Write it with one of the special keywords so that the issue will be automatically closed when the PR is merged (example:
Closes #<your issue number>
) - Add appropriate labels. See wiki for more information.
-
📗 Describe briefly (i.e. in one or two lines) what you changed in the
CHANGELOG.md
file. End the description by the number in parenthesis(#<your PR number>)
-
📙 Add term tracker items to the main changed classes of the ontology
-
🔷 stage, commit and push the changes of steps 7 and 8
-
🍏 Ask for review of your PR.
As the issue will have been discussed and agreed on prior to implementation, the purpose of the review step post-implementation is to check that the implementation has been faithful to what was agreed. One or two reviewers may be needed depending on the nature of the change that has been made. If the change involves adding content (A), a domain expert should review the issue. If the change involves restructuring the ontology (B), an ontology expert should review. If the change involves both changes to content and restructuring (B and C), it is best to ask both an ontology expert and a domain expert to review. See the section "Teams tag" of the README for more information about the expertise of the different team members.
Merge
-
🍏 Check that, after this whole process, your branch does not have conflicts with
dev
(GitHub will prevent you from merging if there are conflicts). In case of conflicts you are responsible for fixing them on your branch before you merge (see below "Fixing merge conflicts" section). If you need help, write a comment in the PR and ask for help from the ontology-expert-team. -
🍏 Once approved, merge the PR into
dev
and delete the branch on which you were working. In the merge message on github, you can notify people who are currently working on other branches that you just merged intodev
, so they know they have to check for potential conflicts withdev
Avoid large merge conflicts by merging the updated dev
versions in your branch.
In case of conflicts between your branch and dev
you must solve them either online via the "resolve conflicts" button (🍏) or locally (🔷+📗).
-
🔷 Get the latest version of
dev
git checkout dev
git pull
-
Switch to your branch
git checkout <your branch>
-
Merge
dev
into your branchgit merge dev
-
📗 The conflicts have to be manually resolved
🔷 Naming convention for branches
Follow the best-practices for git branching naming convention.
The convention is type
-issue-nr
-short-description
type
- master / main / stable - includes the current stable version
- dev - includes all current developments
- feature - includes the feature that will be implemented
- release - includes the current version to be released
The majority of the ontology development will be done in feature
branches.
issue-nr
Add the issue number where you describe, discuss and document your development.
short-description
Describe shortly what the branch is about. Avoid long and short descriptive names for branches, 2-4 words are optimal.
Other hints:
- Separate words with
-
(minus) - Do not put your name to the branch name, it's a collaborative project
- Avoid using numbers only
- Branch names should be precise and informative
- Avoid using capital letters
Examples of branch names : feature-43-add-new-ontology-class
or feature-711-branch-naming-convention
🔷 Commit messages
Try to follow esxisting conventions for commit messages:
- How to Write a Git Commit Message
- Keep the subject line short (i.e. do not commit more than a few changes at the time)
- Use imperative for commit messages
- Do not end the commit message with a period
You can use the command
git commit --amend
to edit the commit message of your latest commit (provided it is not already pushed on the remote server).
With --amend
you can even add/modify changes to the commit.
Feel free to ask the community if you need help. We are happy to support you.