INCATools / INCATools/ontology-access-kit
Create a generic Jupyter notebook parameterizable by ontology selector
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
Create a generic notebook that demonstrates all core functionality
- CLI and Python side by side
- show timings for each command
Create a workflow that will execute this using papermill for core backends
- sqlite
- ubergraph
- obo/pronto
- rdf
This will serve multiple purposes
- integration tests (should be run outside github actions, these may involve large sqlite files, network connections, ...)
- documentation of which methods are implemented where
This will give us something like the robot docs system (e.g http://robot.obolibrary.org/reason), in which documentation is tested over.
Contributor guide
Research direction
Start by locating the project's notebook and workflow conventions, then review how the CLI and Python interfaces expose core functionality. Build a generic parameterizable notebook and a papermill workflow covering sqlite, ubergraph, obo/pronto, and rdf backends. Done means the notebook shows side-by-side commands and timings, and the workflow documents and tests backend method coverage outside GitHub Actions.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python, sqlite
- Domain
- database, documentation, testing
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100