pymmcore-plus/pymmcore-plus - CodSpeed

pymmcore-plus

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chore: changelog v0.16.0

main

2 days ago

fix: reset core configuration to handle non-programmatic changes (#504)

main

2 days ago

fix: reset core configuration to handle non-programmatic changes (#504)

main

2 days ago

fix: reset core configuration to handle non-programmatic changes

tlambert03:fix-stale-config

2 days ago

feat: add utilities for converting Summary/FrameMetadata to ome_types.OME object (#500) * feat: Implement enhanced OME metadata generation and add tests * wip * wip * wip * wip * wip * wip * wip * Refactor OME metadata handling and update test for enhanced OME generation * wip * store meta to disk * fix * grid * Refactor OME metadata handling: improve error handling, enhance parsing, and streamline dimension info extraction * plate * plate * Enhance OME metadata generation: add plate plan handling and improve image ID mapping * update * Refactor OME metadata handling: remove unused attributes and simplify metadata creation * Enhance OME TIFF writer: implement position-specific metadata updates and add new test script for multi-position acquisition * Refactor OME metadata creation: streamline functions and enhance image handling for multi-position data * Refactor OME metadata handling: create OME metadata directory and remove obsolete test script * undo some changes, update tests * remove ome-old * ci(pre-commit.ci): autoupdate (#497) updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.7...v0.12.11) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fix: Don't emit propertyChanged for empty shutter (#496) We found a case where a widget (preset table) was assuming the device label to be valid (non-mepty) and failing. I think it's reasonable to suppress the signal entirely when there is no current shutter. * refactor: improve device discovery structure (#494) * improve device discovery structure * undo change * fix test * add test adapters * add better err * update pymmcore dependency version and streamline version retrieval in CI workflow * fix suffix * fix ci * feat: Restore initial state after MDA sequence with intelligent defaults (#491) * Initial plan * Implement state restoration feature for MDA sequences Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> * style(pre-commit.ci): auto fixes [...] * update code * refactor: update state dictionary and streamline position restoration logic * fix tests * fix test * cleaner test * fix test * remove psygnal testing * add cov skip * add autoshutter state capture and restoration in MDAEngine * add safety * update MDAEngine to allow None for restore_initial_state and adjust focus direction handling in tests --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> Co-authored-by: federico gasparoli <70725613+fdrgsp@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Talley Lambert <talley.lambert@gmail.com> * test: add reference cleanup tests (#485) * test: add cleanup tests * dev accum * update tests * remove del method * fix mock * update runner matrix * break loop * weakref * fix ipython * skip * undo change * try latest * try timeout * increase timeout * bump timeout again * relax timeout * bump again * remove timeout * coverage * add prints * remove prints * skip test waiting * feat: Restore initial state after MDA sequence with intelligent defaults (#491) * Initial plan * Implement state restoration feature for MDA sequences Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> * style(pre-commit.ci): auto fixes [...] * update code * refactor: update state dictionary and streamline position restoration logic * fix tests * fix test * cleaner test * fix test * remove psygnal testing * add cov skip * add autoshutter state capture and restoration in MDAEngine * add safety * update MDAEngine to allow None for restore_initial_state and adjust focus direction handling in tests --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> Co-authored-by: federico gasparoli <70725613+fdrgsp@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Talley Lambert <talley.lambert@gmail.com> * unicore first * don't use global * fix hang * fix windows test * remove perma-executor * less weakref resolution --------- Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> Co-authored-by: federico gasparoli <70725613+fdrgsp@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * ci(dependabot): bump CodSpeedHQ/action from 3 to 4 (#499) * ci(dependabot): bump CodSpeedHQ/action from 3 to 4 Bumps [CodSpeedHQ/action](https://github.com/codspeedhq/action) from 3 to 4. - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/v3...v4) --- updated-dependencies: - dependency-name: CodSpeedHQ/action dependency-version: '4' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * add mode --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Talley Lambert <talley.lambert@gmail.com> * refactor: streamline OME metadata creation and improve test coverage * remove file * fix test * fix pin * min pin lxml as well * refactor * remove second grid from pos key * remove build instrument comment --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Talley Lambert <talley.lambert@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mark Tsuchida <matsuchida@wisc.edu> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

main

2 days ago

Update src/pymmcore_plus/mda/_runner.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

tlambert03:store-meta

6 days ago

Merge branch 'main' into use-ome-writers

tlambert03:use-ome-writers

6 days ago

feat: add utilities for converting Summary/FrameMetadata to ome_types.OME object (#500) * feat: Implement enhanced OME metadata generation and add tests * wip * wip * wip * wip * wip * wip * wip * Refactor OME metadata handling and update test for enhanced OME generation * wip * store meta to disk * fix * grid * Refactor OME metadata handling: improve error handling, enhance parsing, and streamline dimension info extraction * plate * plate * Enhance OME metadata generation: add plate plan handling and improve image ID mapping * update * Refactor OME metadata handling: remove unused attributes and simplify metadata creation * Enhance OME TIFF writer: implement position-specific metadata updates and add new test script for multi-position acquisition * Refactor OME metadata creation: streamline functions and enhance image handling for multi-position data * Refactor OME metadata handling: create OME metadata directory and remove obsolete test script * undo some changes, update tests * remove ome-old * ci(pre-commit.ci): autoupdate (#497) updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.7...v0.12.11) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fix: Don't emit propertyChanged for empty shutter (#496) We found a case where a widget (preset table) was assuming the device label to be valid (non-mepty) and failing. I think it's reasonable to suppress the signal entirely when there is no current shutter. * refactor: improve device discovery structure (#494) * improve device discovery structure * undo change * fix test * add test adapters * add better err * update pymmcore dependency version and streamline version retrieval in CI workflow * fix suffix * fix ci * feat: Restore initial state after MDA sequence with intelligent defaults (#491) * Initial plan * Implement state restoration feature for MDA sequences Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> * style(pre-commit.ci): auto fixes [...] * update code * refactor: update state dictionary and streamline position restoration logic * fix tests * fix test * cleaner test * fix test * remove psygnal testing * add cov skip * add autoshutter state capture and restoration in MDAEngine * add safety * update MDAEngine to allow None for restore_initial_state and adjust focus direction handling in tests --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> Co-authored-by: federico gasparoli <70725613+fdrgsp@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Talley Lambert <talley.lambert@gmail.com> * test: add reference cleanup tests (#485) * test: add cleanup tests * dev accum * update tests * remove del method * fix mock * update runner matrix * break loop * weakref * fix ipython * skip * undo change * try latest * try timeout * increase timeout * bump timeout again * relax timeout * bump again * remove timeout * coverage * add prints * remove prints * skip test waiting * feat: Restore initial state after MDA sequence with intelligent defaults (#491) * Initial plan * Implement state restoration feature for MDA sequences Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> * style(pre-commit.ci): auto fixes [...] * update code * refactor: update state dictionary and streamline position restoration logic * fix tests * fix test * cleaner test * fix test * remove psygnal testing * add cov skip * add autoshutter state capture and restoration in MDAEngine * add safety * update MDAEngine to allow None for restore_initial_state and adjust focus direction handling in tests --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> Co-authored-by: federico gasparoli <70725613+fdrgsp@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Talley Lambert <talley.lambert@gmail.com> * unicore first * don't use global * fix hang * fix windows test * remove perma-executor * less weakref resolution --------- Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> Co-authored-by: federico gasparoli <70725613+fdrgsp@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * ci(dependabot): bump CodSpeedHQ/action from 3 to 4 (#499) * ci(dependabot): bump CodSpeedHQ/action from 3 to 4 Bumps [CodSpeedHQ/action](https://github.com/codspeedhq/action) from 3 to 4. - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/v3...v4) --- updated-dependencies: - dependency-name: CodSpeedHQ/action dependency-version: '4' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * add mode --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Talley Lambert <talley.lambert@gmail.com> * refactor: streamline OME metadata creation and improve test coverage * remove file * fix test * fix pin * min pin lxml as well * refactor * remove second grid from pos key * remove build instrument comment --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Talley Lambert <talley.lambert@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mark Tsuchida <matsuchida@wisc.edu> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: tlambert03 <1609449+tlambert03@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

main

6 days ago

Active Branches

feat: store metadata in runner, update sequenceFinished

last run

6 days ago

0%

feat: add ome-writers backed handlers [WIP]

last run

6 days ago

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feat: add pixel calibration routine

last run

7 months ago

0%

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