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updating shaclgen.py to accept custom shape_uris via annotations and use linkml native names to fix issue #2084

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This PR is intended as a fix for issue https://github.com/linkml/linkml/issues/2084, in that it allows to have freely defined shacl_shape_uri's cia annotations['shacl_uri'] and by switching from the previously implemented shacl shape...

HendrikBorgelt

For example, suppose I have field in my data named body_mass. I learn from the investigators that the unit is always in kilograms. I can do apply some of the...

sierra-moxon

CSV/TSV loader does not split brackets-free, multivalued primitive slots (with pipe delimiter)

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## Summary When loading CSV/TSV files, multivalued primitive slots (e.g., `slot_name: string*` or `multivalued: true` with a primitive range) are not properly handled. Values like `a|b|c` are not split into...

turbomam

[docs]: Update docs & FAQ for dynamic enums

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This PR addresses #2653 In addition, it makes 2 small related docs changes that I thought were generally useful: - adding `PHONY` tag to `make docs` task, as the make...

clevinson

## Summary When a LinkML slot has an example with `object` (instead of `value`), gen-rdf and gen-owl serialize it differently: ### gen-rdf (via JSON-LD) Uses LinkML blank node structure: ```turtle...

turbomam

Update get-involved section of the documentation on linkml.io/linkml

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- Update the get-involved index.rst to now include information about mailing lists, slack, linkedin, mastodon. - Create a new workshops-and-presenations.md under the get-involved section of the documentation where we can...

sagehrke

`gen-owl` doesn't retain examples (although `gen-rdf` does)

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The RDF generator preserves examples via one blank node ```turtle a linkml:SlotDefinition ; linkml:examples [ a linkml:Example ; skos:example "xyz" ] ; ``` If we preserved the examples in OWL,...

turbomam

pydanticgen: make the default for optional list configurable

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Historical behaviour for optional lists in pydantic was to initialise them with None. However, https://github.com/linkml/linkml/pull/2877 changed this behaviour to empty list. This caused regressions for us (see example below). This...

kervel

LinkML JSON Schema Generator - Incorrect Type Conversion

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**Describe the bug** The LinkML JSON Schema generator translates `custom data types` such as `rdf:langString` and specific URI-related types (`uri, uriorcurie`) always to `"type": "string"` types in the generated JSON...

mahdanoura

Bump astral-sh/setup-uv from 5 to 7

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Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 5 to 7. Release notes Sourced from astral-sh/setup-uv's releases. v7.0.0 🌈 node24 and a lot of bugfixes Changes This release comes with a load of bug fixes...

dependabot[bot]