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Allow latest linkml/linkml-runtime and require dandi>=0.76.5#2217

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Allow latest linkml/linkml-runtime and require dandi>=0.76.5#2217
rly wants to merge 2 commits into
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allow-latest-linkml-dandi

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@rly

@rly rly commented Jul 3, 2026

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Motivation

dandi/dandi-cli#1883 has been merged and released in dandi 0.76.5, lifting dandi's click<8.2 bound. That bound previously conflicted with the click>=8.2 requirement of linkml 1.11 when the termset and docs stacks were installed together in the gallery environment, which is why the linkml/linkml-runtime extras were capped at <1.11.

Changes

  • pyproject.toml: remove the <1.11 cap on the linkml (>=1.5.0) and linkml-runtime (>=1.5.5) termset extras and drop the obsolete explanatory comment.
  • pyproject.toml: bump the dandi docs dependency from >=0.46.6 to >=0.76.5.
  • environment-ros3.yml: pin dandi to 0.76.5.
  • CHANGELOG.md: add an entry under 4.0.1 (Unreleased).

Testing

Verified the previously conflicting resolution in a fresh conda env (python=3.13) by running the documented docs install, pip install --group docs ".[zarr,termset]":

  • Resolves with dandi 0.76.5, linkml 1.11.1, linkml-runtime 1.11.1, and click 8.4.2 (satisfies linkml 1.11's click>=8.2).
  • pynwb wheel builds and installs; pynwb, linkml, linkml_runtime, dandi, click import.
  • pip check reports no broken requirements.

🤖 Generated with Claude Code

rly and others added 2 commits July 2, 2026 17:31
dandi 0.76.5 lifts its click<8.2 bound (dandi/dandi-cli#1883), which had
conflicted with the click>=8.2 requirement of linkml 1.11. Remove the
<1.11 caps on the linkml and linkml-runtime termset extras, bump the
dandi docs dependency to >=0.76.5, and pin the ros3 env to dandi 0.76.5.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@codecov

codecov Bot commented Jul 3, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.99%. Comparing base (e3127b2) to head (4455931).

Additional details and impacted files
@@           Coverage Diff           @@
##              dev    #2217   +/-   ##
=======================================
  Coverage   95.99%   95.99%           
=======================================
  Files          30       30           
  Lines        2970     2970           
  Branches      431      431           
=======================================
  Hits         2851     2851           
  Misses         67       67           
  Partials       52       52           
Flag Coverage Δ
integration 74.27% <ø> (ø)
unit 86.70% <ø> (ø)

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@rly rly marked this pull request as ready for review July 3, 2026 00:43
@rly rly enabled auto-merge (squash) July 3, 2026 00:43
@rly rly requested a review from oruebel July 3, 2026 00:43
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