[WIP] Convert to LinkML #9
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Created with
cruft create https://github.com/linkml/linkml-project-cookiecutter
make setup
- Temporarily remove tomoacquisition & shunt tomography slots into acquisition - Remove aliases (error: alias not permitted in slot_usage) - Distinguish temperature_range (class) from [Tt]emperature slots - Replace `number` range with `float`
- rename problematic identifiers (name, class)
`make all`
Reorganize and add CI/CD
The following now pass (with warnings):
make all
make lint
Some tests still fail.
Summary of changes:
- Updated dependencies
- Use distinct `id` for each schema
- Remove `default_prefix: ex` that was causing collisions
- (Breaking) Move some utility types to `types` (Range, Series, etc).
These should be replaced with versions from existing ontologies.
- (Breaking) Fix name collisions between schemas:
- type -> instrument_type | molecular_type (with alias: type)
- temperature -> temperature_range (alias: temperature)
- Generate the project (`make all`)
- Fix EMDataset-001.yaml so it validates - (Breaking) Replace `type` with `instrument_type` or `molecular_type`. Otherwise it breaks python tests. - (Breaking) Remove multivalued from institution - Fix datetime range Running `rm -r examples/output; make test-examples` still fails
Closed
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Convert schemas to linkml (#5).
This is WIP to test the github actions.