chore(release): Bump version to 0.9.2 (#553)

* chore(release): Bump version to 0.9.2

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* style: fix ruff format trailing-comma violations in codecs/README.md

Unrelated pre-existing formatting drift surfaced by CI's Lint job on this
PR (first PR since #549 to touch code paths and trigger ruff format --check).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

chore(release): Bump version to 0.9.1 (#544)

Claude-Session: https://claude.ai/code/session_011DiaqkmRcp1L9yD8dx4jLj

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

chore(release): Bump version to 0.9.0 (#541)

Claude-Session: https://claude.ai/code/session_011DiaqkmRcp1L9yD8dx4jLj

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

fix(io): preserve isolated-node order in standalone skeleton JSON (L3) (

#512)

The jsonpickle skeleton decoder built the final node list only from py/id
back-references in the nodes section, so isolated (edge-less) nodes — emitted
inline as full py/object entries — were missed, tripping the "natural order"
fallback that appends them at the tail (e.g. [iso, a, b] decoded to [a, b, iso]).
Resolve both py/id refs and inline py/object nodes (by name, to the canonical
decoded object) so the declared nodes-section order is preserved. The .slp path
was already unaffected; #438 had already stopped the prior node-dropping.


Claude-Session: https://claude.ai/code/session_01A6ZBs7Yww49sCmFF6XSSHs

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

chore(release): Bump version to 0.7.1 (#437)

Includes small follow-ups surfaced by the v0.7.1 release review:

- docs(cli): Document --trails / --trail-* flags under `sio render`
  (Quick Reference + Motion Trail Options subtable). Closes the only
  CLI doc gap from #434.
- docs(model/labels): Cross-reference Labels.match_video and the
  widened lookup signatures introduced in #436 from the Querying
  section.
- docs(matching): Refresh ConflictResolution.conflict_type docstring
  to cite the actually-emitted values ("instance_conflict",
  "negative_flag_conflict" from #432) instead of the stale
  "duplicate_instance" / "skeleton_mismatch" examples.
- docs(codecs): Note that to_analysis_arrays is an internal building
  block behind save_analysis_h5 (it is intentionally omitted from
  sleap_io.codecs.__all__).

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

fix(io/tiff): suppress ambiguous-pages warning when content rules out…

… class-stack (#422)

Multi-page TIFFs with no axis metadata previously always warned "Assuming
pages are time... pass pages_as='classes'", even when pages had multiple
distinct positive label IDs per page. That layout cannot be a stack of
binary class masks, so the suggested alternative would destructively
collapse instance IDs via from_binary_masks.

Gate the warning on _pages_could_be_class_stack(): inspect each loaded
page and suppress the warning if any page has >1 unique positive value.
Purely binary multi-page TIFFs remain genuinely ambiguous and still warn.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

fix: Preserve ROIs/masks in lazy copy and fix COCO empty segmentation…

… fallback (#361)

- Fix lazy Labels.copy() to include rois and masks (previously omitted, causing
  data loss when copying lazy-loaded labels with ROI/mask annotations)
- Fix COCO reader to fall back to bbox ROI when segmentation is an empty list
  (previously only checked for None, missing the [] case)
- Add tests for both edge cases

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

chore: Bump version to 0.6.4 (#349)

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

chore: Bump version to 0.6.3 (#342)

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

chore: Bump version to 0.6.2 (#339)

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>