CHANGELOG.md

Changelog

v0.12.0 (2024-10-05)

Full Changelog

Implemented enhancements:

• feat: add support for MDAEvent.reset_event_timer #383 (tlambert03)

Fixed bugs:

• fix: serialization of GridPlan in ome-zarr writer when msgspec is not installed #378 (tlambert03)

Merged pull requests:

• chore: fix typing on Signal.disconnect protocol #381 (tlambert03)
• build: drop python 3.8 #377 (tlambert03)
• ci(pre-commit.ci): autoupdate #374 (pre-commit-ci[bot])

v0.11.1 (2024-08-28)

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Implemented enhancements:

• feat: enable hardware sequencing by default #373 (tlambert03)

Fixed bugs:

• docs: fix typos etc. #370 (marktsuchida)

Merged pull requests:

• ci(dependabot): bump CodSpeedHQ/action from 2 to 3 #371 (dependabot[bot])

v0.11.0 (2024-07-06)

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Implemented enhancements:

• feat: add mmcore use to set the active micro-manager installation #368 (tlambert03)
• feat: enable StrictInitializationChecks #367 (tlambert03)
• feat: create Microscope (model) from summary metadata #359 (tlambert03)
• feat: Formalize schema for metadata used by MDA (and elsewhere) #358 (tlambert03)

Fixed bugs:

• fix: fix failure to collect elapsed time during sequenced acquisition #361 (tlambert03)

Merged pull requests:

• docs: document cli #369 (tlambert03)
• refactor: use only pydantic2 syntax #366 (tlambert03)
• perf: benchmark metadata #363 (tlambert03)
• refactor: remove state and move metadata #362 (tlambert03)
• docs: deploy docs preview #360 (tlambert03)

v0.10.2 (2024-06-13)

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Implemented enhancements:

• feat: make CMMCoreSignaler and MDASignaler signal groups #357 (tlambert03)

v0.10.1 (2024-06-10)

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Fixed bugs:

• fix: fix setup sequence #356 (tlambert03)

v0.10.0 (2024-06-07)

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Implemented enhancements:

• feat: add tensorstore writer #348 (tlambert03)

Fixed bugs:

• fix: add stopPropertySequence before loadPropertySequence in setup_sequenced_event #353 (tlambert03)

Merged pull requests:

• ci: pre-commit update #347 (tlambert03)

v0.9.5 (2024-05-04)

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Implemented enhancements:

• feat: update 5d writer with isel method, make zarr output nicer to xarray, add a bit more metadata #344 (tlambert03)

Fixed bugs:

• fix: fixing tests and better auto-qt detection #345 (tlambert03)
• ci: use pyapp-kit workflows for dependency tests #338 (tlambert03)

Merged pull requests:

• ci(dependabot): bump softprops/action-gh-release from 1 to 2 #340 (dependabot[bot])

v0.9.4 (2024-03-06)

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Fixed bugs:

• fix: Fix pyside2 issue when disconnecting listeners_connected #337 (tlambert03)

v0.9.3 (2024-03-04)

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Implemented enhancements:

• feat: support linux on mmcore build-dev, test on linux, make device list editable #331 (tlambert03)

Merged pull requests:

• chore: use ruff format instead of black #335 (tlambert03)
• ci: cache built drivers for all platforms #333 (tlambert03)
• test: allow testing without Qt installed #332 (tlambert03)
• perf: add benchmarks #330 (tlambert03)
• chore: misc dependency updates #329 (tlambert03)

v0.9.2 (2024-02-27)

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Implemented enhancements:

• feat: add mmcore info command #328 (tlambert03)

v0.9.1 (2024-02-22)

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Fixed bugs:

• fix: remove zarr dependency #327 (tlambert03)

v0.9.0 (2024-02-15)

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Implemented enhancements:

• feat: support basic ImageJ hyperstack #323 (tlambert03)
• feat: control signal backend with MMCORE_PLUS_SIGNALS_BACKEND #321 (tlambert03)
• feat: add post_sequence_started #319 (tlambert03)
• feat: new runner signals awaitingEvent and eventStarted #316 (tlambert03)
• feat: Add file saving output argument to MDARunner.run #313 (tlambert03)
• feat: OMETiff writer #265 (tlambert03)

Fixed bugs:

• fix: re-engage hardware autofocus after performing autofocus action if it was engaged #326 (fdrgsp)
• fix: fix autofocus z_correction delta #317 (fdrgsp)
• fix: only allow 'AcquireImage' Actions (or None) to be sequenced #315 (fdrgsp)
• fix: fix excess reading of frame metadata in OMEZarrWriter #305 (wl-stepp)

Merged pull requests:

• ci(dependabot): bump codecov/codecov-action from 3 to 4 #325 (dependabot[bot])
• chore: remove deprecated stuff for next version bump #320 (tlambert03)
• refactor: move imageSnapped event #314 (tlambert03)
• refactor!: more minimal, and overridable MDA metadata #312 (tlambert03)

v0.8.7 (2024-01-25)

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Fixed bugs:

• fix: fix available peripherals for libraries with multiple hubs #309 (tlambert03)

v0.8.6 (2024-01-24)

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Implemented enhancements:

• feat: update OMEZarrWriter to position-specific sub-MDAsequences #299 (fdrgsp)

Fixed bugs:

• fix: fix available_peripherals for loaded hub devices #308 (tlambert03)
• fix: Zarr part mda #302 (wl-stepp)

Merged pull requests:

• fix: avoid hardware errors while running sequences with NIDAQ stages #307 (tlambert03)

v0.8.5 (2023-12-18)

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Implemented enhancements:

• feat: OMEZarr writer #263 (tlambert03)

Fixed bugs:

• fix: fix available version lookup on windows #301 (tlambert03)
• docs: minor update #297 (fdrgsp)

Merged pull requests:

• ci(dependabot): bump actions/setup-python from 4 to 5 #298 (dependabot[bot])

v0.8.4 (2023-12-06)

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Implemented enhancements:

• feat: Add basic msgpack decoding for images from SequenceTester #296 (tlambert03)

Fixed bugs:

• fix: subclass apply_to_core method for PixelSizeGroup in model #287 (fdrgsp)

Merged pull requests:

• fix: trying to fix windows tests #293 (tlambert03)
• fix: remove alpha on rgb images #292 (tlambert03)
• refactor: change exec_events to iterable #290 (tlambert03)
• fix: Remove unused fields from SystemInfoDict for mmcore11 compatibility #284 (tlambert03)
• chore: convert verysilent to silent #282 (tlambert03)

v0.8.3 (2023-10-24)

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Implemented enhancements:

• feat: support py312 #281 (tlambert03)
• feat: add systemConfigurationFile to retrieve last config path #277 (tlambert03)
• feat: ImageSequenceWriter #267 (tlambert03)

Tests & CI:

• test: skip flaky thread tests #279 (tlambert03)

Merged pull requests:

• feat: make pretty output optional when using mmcore install #280 (tlambert03)
• fix: some fixes to mmcore install on macos #278 (tlambert03)
• feat: support DeviceInitializationState, fix issue with microscope model #276 (tlambert03)
• chore: deprecate mmcore find in favor of mmcore list #275 (tlambert03)
• refactor: update state method on MMCorePlus #274 (tlambert03)
• fix: Fix propertyChanged value type for setShutterOpen #273 (tlambert03)
• feat: autofind autofocus offset devices #270 (tlambert03)
• docs: clarify get/setZPosition in docs and update call #269 (tlambert03)
• feat: emit metadata as second argument of sequenceStarted #268 (tlambert03)
• docs: fix Documentation of events might be out of date. #266 (tlambert03)
• feat: make first instance of CMMCorePlus the global instance #264 (tlambert03)
• feat: add mda thread relay #262 (tlambert03)
• feat: add name_map to listeners_connect #260 (tlambert03)

v0.8.2 (2023-09-05)

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Merged pull requests:

• fix: don't check is_busy when updating device in model #258 (tlambert03)
• ci(dependabot): bump actions/checkout from 3 to 4 #257 (dependabot[bot])

v0.8.1 (2023-08-30)

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Fixed bugs:

• fix: fix a bug in saveSystemConfiguration method #248 (fdrgsp)

Merged pull requests:

• feat: microscope model, for building configs and in-memory representations of core #255 (tlambert03)
• feat: add keyword, CFGCommand and other enums on global strings #254 (tlambert03)
• fix: fix find micromanager bug #253 (tlambert03)
• feat: add getMultiROI method, bump core dep #251 (tlambert03)
• refactor: remove AvailableDevice #250 (tlambert03)
• docs: mark deprecated functions #249 (tlambert03)
• feat: add listeners_connected utility #247 (tlambert03)
• feat: add metadata to frameready signal, add getTaggedImage #246 (tlambert03)
• docs: add pycro-manager API adapter as an educational example #245 (tlambert03)
• test: adding test and coverage #244 (tlambert03)
• docs: add migration info for pycro-manager users #243 (tlambert03)
• docs: adding acquisition engine docs #242 (tlambert03)
• build: make cli dependencies (typer and rich) optional #240 (tlambert03)
• refactor: remove loguru #239 (tlambert03)

v0.8.0 (2023-07-31)

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Tests & CI:

• test: don't test private attribute of useq #230 (tlambert03)

Merged pull requests:

• feat: implement keep shutter open for engine #237 (tlambert03)
• refactor: rename _events to _signals in Runner #236 (tlambert03)
• refactor: make hardware sequencing detection opt-in #235 (tlambert03)
• bug: add warnings if devices are not found #233 (fdrgsp)
• feat: use new fov on useq grid objects, support pydantic2 #231 (tlambert03)
• fix: fix payload for sequenced objects #228 (tlambert03)
• feat: add attribute to control hardware sequencing #227 (tlambert03)
• chore: miscellaneous build and linting updates #224 (tlambert03)

v0.7.1 (2023-07-28)

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Merged pull requests:

• fix: fix bug in sequencing #225 (tlambert03)
• perf: Pop images from circular buffer during sequence #223 (tlambert03)
• ci: test napari-micromanager #221 (tlambert03)

v0.7.0 (2023-07-27)

Full Changelog

Implemented enhancements:

• feat:update saveSystemConfiguration method #214 (fdrgsp)
• feat: update engine with autofocus using user Action #204 (fdrgsp)
• feat: set sequence fov size in engine setup_sequence + add test #198 (fdrgsp)

Merged pull requests:

• feat: add logging to file and cli command #219 (tlambert03)
• feat: add MMCorePlus.describe method #218 (tlambert03)
• docs: fix docs build #216 (tlambert03)
• feat: add Adapter object #213 (tlambert03)
• refactor: move loadDevice logic from Device to MMCorePlus #212 (tlambert03)
• fix: don't use invalid plans in test #211 (tlambert03)
• fix doc #209 (tlambert03)
• refactor: Remove remote feature #208 (tlambert03)
• feat: add general retry utility #207 (tlambert03)
• feat: Add support for hardware sequencing #206 (tlambert03)
• refactor: relax signature of MDARunner.run to Iterable[MDAEvent] #205 (tlambert03)
• test: use PyQt6 for testing #203 (fdrgsp)
• feat: add build-dev command to build dev dependencies on apple silicon #202 (tlambert03)
• fix: fix snap emission events #197 (tlambert03)
• test: fix scope of ignore warning on test #195 (tlambert03)

v0.6.7 (2023-04-10)

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Merged pull requests:

• fix: fix for loguru 0.7.0 #193 (tlambert03)
• docs: fix links #188 (tlambert03)
• fix: small fix in get state #185 (tlambert03)

v0.6.6 (2023-01-13)

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Implemented enhancements:

• feat: add propertyChanged to setFocusDevice method + test #182 (fdrgsp)
• feat: emit channelGroupChanged signal when calling setChannelGroup #180 (fdrgsp)

Fixed bugs:

• fix: update for newest micromanager demo cfg #183 (fdrgsp)

Merged pull requests:

• style: update pre-commit #184 (tlambert03)

v0.6.5 (2022-12-07)

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Merged pull requests:

• fix: fix logging import #179 (tlambert03)
• docs: add favicon #178 (ianhi)
• feat: add run (mda) command to cli #171 (tlambert03)

v0.6.4 (2022-12-05)

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Merged pull requests:

• style: update precommit #177 (tlambert03)
• fix: fix _PropertySignal cleanup #176 (tlambert03)
• ci: add test for pymmcore-widgets #174 (tlambert03)

v0.6.3 (2022-12-05)

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Merged pull requests:

• feat: enhanced iterProperties and iterDevices #173 (tlambert03)
• feat: add mmcore command line program #170 (tlambert03)
• feat: add config group object #169 (tlambert03)

v0.6.2 (2022-11-29)

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Merged pull requests:

• fix: vendor private psygnal func #168 (tlambert03)
• build: support python 3.11 #167 (tlambert03)

v0.6.1 (2022-11-24)

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Merged pull requests:

• refactor: enable strict typing #166 (tlambert03)
• docs: remove direct griffe from extra #165 (tlambert03)

v0.6.0 (2022-11-22)

Full Changelog

Implemented enhancements:

• feat: New engine protocol #140 (tlambert03)

Fixed bugs:

• fix: fix signal names #163 (fdrgsp)

Merged pull requests:

• docs: update readme #164 (tlambert03)
• fix: return getLastImageMD to original signature, add getLastImageAndMD #161 (tlambert03)
• docs: update documentation (using mkdocs) #160 (tlambert03)
• docs: fix api docs #159 (tlambert03)
• docs: fix docs after cleanup #158 (tlambert03)
• ci(dependabot): bump styfle/cancel-workflow-action from 0.9.1 to 0.11.0 #157 (dependabot[bot])
• ci(dependabot): bump actions/setup-python from 2 to 4 #156 (dependabot[bot])
• ci(dependabot): bump actions/checkout from 2 to 3 #155 (dependabot[bot])
• ci(dependabot): bump codecov/codecov-action from 2 to 3 #154 (dependabot[bot])
• refactor: big typing cleanup, move to using hatch and ruff #153 (tlambert03)
• test: fix tests and update pre-commit #152 (tlambert03)

v0.5.1 (2022-10-31)

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Merged pull requests:

• fix: fix missing typing import from psygnal #149 (tlambert03)

v0.5.0 (2022-10-17)

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Implemented enhancements:

• feat: use private loguru logger #146 (tlambert03)
• feat: new signals to handle pixel size configurations #143 (fdrgsp)
• feat: add a new signals and methods for groups and presets + test #139 (fdrgsp)

Merged pull requests:

• fix: fix test error after psygnal update #147 (tlambert03)
• test: skip test_lock_and_callbacks on windows CI #142 (tlambert03)
• feat: add a signal when the camera ROI changes + test #138 (fdrgsp)
• chore: update links to new organization #135 (tlambert03)
• fix: make mda engine exit gracefully after an exception #133 (ianhi)
• fix: Make sure to set xy in mda even if they are 0 #131 (ianhi)

v0.4.5 (2022-05-19)

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Merged pull requests:

• fix nightly link #128 (tlambert03)

v0.4.4 (2022-05-12)

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Merged pull requests:

• fix potential typererror if canceled while waiting #127 (ianhi)
• Fix waiting for mda events #126 (ianhi)

v0.4.3 (2022-05-02)

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Fixed bugs:

• update setShutterOpen() method #124 (fdrgsp)

v0.4.2 (2022-04-23)

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Merged pull requests:

• Ensure import of QtWidgets in check_qt_app #122 (ianhi)
• add setContext method #120 (ianhi)

v0.4.1 (2022-04-21)

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Merged pull requests:

• micromanager shutter and autoshutter signals #123 (fdrgsp)
• Add a new SequenceAcquisition event signals #115 (fdrgsp)
• fix flaky tests #114 (ianhi)

v0.4.0 (2022-03-08)

Full Changelog

Implemented enhancements:

• Adds DeviceProperty class - a view onto a core property with a nicer API #107 (tlambert03)

Fixed bugs:

• Switch to user swappable mda-engines #102 (ianhi)

Merged pull requests:

• add devicePropertyChanged and valueChanged signal on DeviceProperty object. #111 (tlambert03)
• reconfigure MDAEngine to make it easier to subclass #110 (ianhi)
• Adds Device class - a view onto a core device with a nicer API #109 (tlambert03)
• use better globals for State and Label #106 (tlambert03)

v0.3.1 (2022-03-04)

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Fixed bugs:

• Fix event emission when setting property on a state device #105 (tlambert03)
• fix remote typing #103 (ianhi)

v0.3.0 (2022-03-03)

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Merged pull requests:

• undo subclass of QCoreSignaler in remote #99 (tlambert03)
• Add events protocol, rename some internal classes, make CMMCoreSignaler public, and fix flaky thread test #98 (tlambert03)
• Ensure propertyChanged event occurs for setState and setStateLabel #97 (tlambert03)
• Doc follow ups #94 (ianhi)
• fix python version in RTD build #93 (tlambert03)
• Move remote stuff to subfolder, make pyro5 optional [remote] extra #91 (tlambert03)
• remove setup.py, add ian as author #90 (tlambert03)
• remove leftover debug statements #89 (ianhi)
• Fix flaky metadata test #88 (tlambert03)
• make find_micromanager public #86 (tlambert03)
• add quiet --yes install flag #85 (tlambert03)
• create docs #84 (ianhi)
• fix QSignal instance check in test_core #83 (tlambert03)

v0.2.1 (2022-02-21)

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Merged pull requests:

• restore setPosition overloading #82 (ianhi)

v0.2.0 (2022-02-19)

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Merged pull requests:

• remove caching #76 (ianhi)
• update install link #75 (ianhi)
• Add a snap method and signal #74 (ianhi)
• Start using threads #73 (ianhi)

v0.1.8 (2022-01-28)

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Merged pull requests:

• Allow more options when loading config #71 (ianhi)
• Download latest MM by default #69 (ianhi)
• getOrGuessChannelGroup -> list #67 (fdrgsp)
• Add getPixelSizeConfigData() to config overrides #61 (fdrgsp)

v0.1.7 (2021-11-30)

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Merged pull requests:

• Run test suite once weekly #65 (ianhi)
• Fix Aliased signals #64 (ianhi)

v0.1.6 (2021-10-25)

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Merged pull requests:

• catch communication error on atexit #60 (tlambert03)
• Remove special casing of ENV path in tests #59 (ianhi)
• [pre-commit.ci] pre-commit autoupdate #57 (pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #56 (pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #55 (pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #54 (pre-commit-ci[bot])
• Add robust guess/get methods for objectives and channel group #53 (ianhi)

v0.1.5 (2021-08-31)

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Merged pull requests:

• [pre-commit.ci] pre-commit autoupdate #50 (pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #49 (pre-commit-ci[bot])
• Set minimum pymmcore version #48 (ianhi)
• Always call unloadAllDevices #47 (ianhi)
• Fix serialization of Configuration and Metadata objects #46 (tlambert03)
• fix func name in docstring #45 (ianhi)

v0.1.4 (2021-08-14)

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Merged pull requests:

• [pre-commit.ci] pre-commit autoupdate #41 (pre-commit-ci[bot])
• Return better config objects #40 (tlambert03)
• Change order of channels in _fix_image to BGRA #39 (tlambert03)
• add setProperty override that emits propertyChanged #38 (tlambert03)
• slightly better deviceSchema implementation #37 (tlambert03)
• add fix_image for cameras with getNumberOfComponents != 1 #36 (tlambert03)
• add getDeviceSchema and getDeviceProperties methods #35 (tlambert03)
• fix shared mem #34 (tlambert03)
• [pre-commit.ci] pre-commit autoupdate #33 (pre-commit-ci[bot])
• ENH: Check for mda canceled while waiting #32 (ianhi)
• add new configSet signal to qcallback #28 (ianhi)
• Add new configSet signal. #26 (ianhi)
• Set exposure after setting channel in run_mda #24 (ianhi)
• misc fixes #22 (tlambert03)
• improve test coverage #20 (tlambert03)
• Add pythonic Enums, Metadata and Configuration objects #16 (tlambert03)

v0.1.3 (2021-07-15)

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Merged pull requests:

• bring back qcallback #19 (tlambert03)

v0.1.2 (2021-07-13)

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v0.1.1 (2021-07-08)

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Merged pull requests:

• Unify callback API and restructure package #14 (tlambert03)
• Add automatic micromanager discovery for linux #12 (ianhi)
• [pre-commit.ci] pre-commit autoupdate #11 (pre-commit-ci[bot])

v0.1.0 (2021-07-03)

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Merged pull requests:

• Rename to pymmcore-plus, update readme #8 (tlambert03)
• add typing_extensions to install requires #5 (ianhi)
• emit_signal("onMDAFinished", sequence) #4 (fdrgsp)
• fix find-micromanager, add CI tests #3 (tlambert03)
• fix mda event serialization #2 (tlambert03)
• onMDAFrameReady #1 (fdrgsp)

v0.0.1 (2021-05-17)

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* This Changelog was automatically generated by github_changelog_generator