copilot enabling #9306
copilot enabling #9306
Conversation
cmungall
commented
Jul 11, 2025
cmungall
commented
- removed
- symlink
- set up copilot, fixes Set up github copilot for this repo #9305
cmungall
requested review from
nicolevasilevsky,
sabrinatoro and
twhetzel
as code owners
cmungall
requested review from
Copilot and
matentzn
and removed request for
nicolevasilevsky,
sabrinatoro and
twhetzel
There was a problem hiding this comment.
Pull Request Overview
This PR enables Copilot by adding a dedicated setup workflow and streamlining the Copilot instructions.
- Introduces
.github/workflows/copilot-setup-steps.ymlto install ROBOT, OBO scripts, Python tools, and configure the environment for Copilot. - Replaces the detailed
.github/copilot-instructions.mdwith a single-line symlink to../CLAUDE.md. - Adds a
robot-versioninput but continues to hard-code version references in cache keys and download URLs.
Reviewed Changes
Copilot reviewed 2 out of 3 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| .github/workflows/copilot-setup-steps.yml | New CI job to set up required tools (ROBOT, obo-scripts, uv, Python) |
| .github/copilot-instructions.md | Replaced full instruction content with a symlink to external file |
Comments suppressed due to low confidence (2)
.github/workflows/copilot-setup-steps.yml:45
- The
robot-versioninput is not used here; the cache key—and similarly the download URLs—are hard-coded to v1.9.7. Parameterize these values using${{ inputs.robot-version }}to respect the input.
key: ${{ runner.os }}-robot-v1.9.7
.github/copilot-instructions.md:1
- This file now only contains a symlink reference and all previous Mondo ontology guidelines were removed. Ensure those guidelines remain accessible—either by migrating them or updating references—so developers aren’t left without critical documentation.
../CLAUDE.md
There was a problem hiding this comment.
I see this is symlinked to CLAUDE.md, however a lot of what was in this file is not in the CLAUDE.md file and these examples look useful. Should more content from the copilot instructions file be moved into the CLAUDE.md file?
There was a problem hiding this comment.
I definitely encourage trying adding more examples!
|
|
||
| - name: Add obo-scripts to PATH | ||
| run: | | ||
| git clone https://github.com/cmungall/obo-scripts.git ${{ github.workspace }}/tools/obo-scripts |
There was a problem hiding this comment.
do the obo-scripts exist in any other project directory vs. a personal repo? for initial testing these seems ok
There was a problem hiding this comment.
not sure I follow the Q....
There was a problem hiding this comment.
This is cloning a repo in your personal GitHub space, which is ok for now. I was asking if this repo with obo-scripts existed anywhere else within an existing project.
| run: | | ||
| mkdir -p ~/.jar-cache | ||
| if [ ! -f ~/.jar-cache/robot.jar ]; then | ||
| curl -L https://github.com/ontodev/robot/releases/download/v1.9.7/robot.jar -o ~/.jar-cache/robot.jar |
There was a problem hiding this comment.
ODK version 1.5.4 uses ROBOT version 1.9.8. is something incompatible with this ROBOT version?
There was a problem hiding this comment.
Or to ask it another way - why not just use ODK instead of downloading the JAR file?
There was a problem hiding this comment.
If you can figure out how to do that!
|
Would it be enough to include this under container: obolibrary/odkfull:latest |
| jobs: | ||
| # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot. | ||
| copilot-setup-steps: | ||
| runs-on: ubuntu-latest |
There was a problem hiding this comment.
| runs-on: ubuntu-latest | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:1.6 |
Lets just try this?
|
I think the instructions will need to include an introduction to the ODK toolset and some examples. |
