[Jakub Wlodek (jwlodek)]

• Loosen pins for ophyd-async and bluesky. Update lockfile
• Simplify tomography plans, add additional metadata to nd tomo scans
• Add comprehensive test suite for tomography flyscan plans

[Copilot]

🟡 Changes recommended

Unresolved dependency compatibility, silent acquisition skips for negative retry counts, and unused imports need correction.

3 open issues

• Remove unused Flyable and MsgGenerator imports · New
• Ensure Bluesky installations provide the required fly_stub API · New
• Reject non-positive retry counts before hardware actions · New

What changed in this PR

This PR consolidates tomography scan orchestration, adds metadata linking grid-point runs, and expands automated coverage for acquisition and data storage.

Changes:

• Reuses the ND step-scan plan for repeated flyscans and adopts Bluesky’s built-in flyscan helper.
• Adds grid-position metadata and tests for sequencing, retries, pauses, cleanup, and Tiled integration.
• Switches ophyd-async to upstream development sources and refreshes dependency pins.

File	Description
tests/​tomography/​test_flyscans.py	Adds mock-based plan tests and Tiled integration coverage.
src/​hextools/​tomography/​flyscans.py	Consolidates orchestration and adds repetition, checkpoints, and run metadata.
src/​hextools/​specs.py	Documents optional grid metadata fields.
pixi.toml	Switches ophyd-async to upstream main.
pixi.lock	Updates Bluesky and ophyd-async revisions and package metadata.

_{Review effort: Balanced}

[Copilot]

🔵 Needs a closer look

The previously reported Bluesky dependency compatibility issue remains an approval blocker for installations outside Pixi.

3 open issues

• Ensure Bluesky installations provide the required fly_stub API
• Remove unused Flyable and MsgGenerator imports
• Reject non-positive retry counts before hardware actions

_{Review effort: Balanced}

[Anthony Sligar (sligara7)]

#107 merged into main and also adds tests/tomography/test_flyscans.py, so this branch now conflicts (add/add on that file; flyscans.py merges cleanly and keeps the VELO restore).

I've pushed a merge of main into this branch: sligara7:pr108-merge-main (8397121). It keeps your test suite and adds #107's check as one test, test_tomo_flyscan_restores_rotation_speed (success and failure paths, on FlyRig). With this branch's locked dev env: test_flyscans.py 62 passed, 1 xfailed; non-GUI suite 388 passed.

To take it:

git pull https://github.com/sligara7/hextools.git pr108-merge-main

Lint is failing on this branch independently:

• src/hextools/specs.py:149 line too long (89 > 88)
• src/hextools/tomography/flyscans.py: unused imports Flyable, MsgGenerator; blank line after the tomo_nd_step_scan docstring

[Anthony Sligar (sligara7)]

A few tiny things (#108 (comment)), but looks good to simplifying the tomography plans.

[Copilot]

🔵 Needs a closer look

Unresolved hardware-cleanup failure paths and coordinated dependency upgrades require fixes and final human validation.

3 open issues

• Avoid restoring rotation position when shutter check aborts scan · New
• Ensure Bluesky installations provide the required fly_stub API
• Restore velocity even when return-to-start move fails · New

2 resolved since last review

• Remove unused Flyable and MsgGenerator imports
• Reject non-positive retry counts before hardware actions

_{Review effort: Balanced}

[Copilot]

🟡 Changes recommended

An unused import in the alignment tests violates the configured Ruff rules and causes the CI lint job to fail.

1 open issue

• Remove unused get_mock_put import causing Ruff F401 failure · New

3 resolved since last review

• Avoid restoring rotation position when shutter check aborts scan
• Ensure Bluesky installations provide the required fly_stub API
• Restore velocity even when return-to-start move fails

_{Review effort: Balanced}

[Copilot]

🔵 Needs a closer look

Hardware cleanup changes include an unresolved recovery issue, and core dependency upgrades warrant human validation beyond mocked coverage.

1 open issue

• Restore motor position and velocity before restarting camera preview · New

1 resolved since last review

• Remove unused get_mock_put import causing Ruff F401 failure

_{Review effort: Balanced}

[Anthony Sligar (sligara7)]

Looks good