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Specify Hatch-managed env for auto converting `dandischema.models` to LinkML schema and back to Pydantic models
Provide script to translate `dandischema.models` in to a LinkML schema and overly it with definition provided by an overlay file.
Provide script to translate `dandischema/models.yaml` back to Pydantic models and store them in `dandischema/models.py`
These prefixes are copied from https://github.com/dandi/schema/blob/master/releases/0.7.0/context.json
The previous BRE pattern used `\+` (GNU sed extension) which silently fails on macOS BSD sed. Switch to `-E` (extended regex) with POSIX character class `[^[:space:]]` instead of `\S` (also unsupported by BSD sed), making the normalization work on both macOS and Linux. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Expand comment for linkml-auto-converted hatch env with usage instructions Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
There is no prefix defined as `dandi_default`. The intended default prefix is `dandi`
…ed and some symbols from _orig for now we do it so it does not overlay models.py since then git is unable to track renames
…into linkml-auto-converted
we had to maintain original filename for models.py to apply patches easily
yarikoptic
commented
Mar 20, 2026
tools/linkml_conversion
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| # Poor man patch queue implementation | ||
| # Edit this list if you want to merge or drop PRs branches to be patched with. | ||
| # Order matters | ||
| branches_to_merge=( remove-discriminated-unions ) |
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that is where we define branches from PRs to merge!
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Additional details and impacted files@@ Coverage Diff @@
## master #387 +/- ##
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- Coverage 97.92% 97.83% -0.09%
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Files 18 19 +1
Lines 2405 2407 +2
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Hits 2355 2355
- Misses 50 52 +2
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Provide a partial schema to be merged with the generated schema
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This is an extract with amends from
which (branch
linkml-auto-converted) would keep merging this branch into itself while reflecting on changes in the branch which could be rebased or gain merges from the master, and also can accumulate or drop "patch branches" from within its script defining what to patch with.This way
linkml-auto-convertedwould represent reflection of current state of conversionTODO/PLAN
hatch ... TODOmodels.pyintodandischema/models.yamland overlaid with an [dandischema/models_overlay.yaml] overlay file.tools/linkml_conversionto convert into ‘linkml-auto-converted’model_instances.yaml(or alike) which would define pre-populated records such as standards (bids, nwb, ...). aim for potentially multiple classes there.