release before adding channel config files management (for different objectives)

What's Changed

• feat: improve laser autofocus with robust spot detection and error handling by @hongquanli in #101
• feat: improve piezo stage control by @hongquanli in #106
• pull from master by @hongquanli in #107
• bug fix by @hongquanli in #108
• bug fix for updated laser autofocus by @hongquanli in #109
• fix: for both config editors, catch and alert on file permission errors by @ianohara in #105
• fixes(tests): move tests to existing location, fix (or ignore) broken tests by @ianohara in #110
• laser af init bug fix by @hongquanli in #113

Full Changelog: v0.5...v0.5.1

v0.5 - release before updating laser af

What's Changed

• logging: add logging mechanism, hooks to log uncaught crashes, and an example use of the logging tools by @ianohara in #1
• software/main_: Delete unused imports, convert the main and gui to use loggers. by @ianohara in #4
• control/microcontroller: convert to using Logger and remove some unused/commented code by @ianohara in #5
• logging: add a helper for registering a rotating file log that captures all output regardless of stdout log level by @ianohara in #6
• control/camera_toupcam: use loggers by @ianohara in #7
• logging: add missing close quote in logging message by @ianohara in #8
• gitignore: add .idea/ directories. by @ianohara in #9
• Merge hongquanli/octopi-research/master and fix conflicts by @ianohara in #16
• microcontroller: fix reset cmd_id bug by @ianohara in #10
• microcontroller: combine the move commands via a helper by @ianohara in #11
• microcontroller: for simulation, use a stub serial device instead of copy/pasted implementation by @ianohara in #12
• microcontroller: add the notion of aborted commands, and throw TimeoutError on failed waits by @ianohara in #13
• gui_hcs: if the microcontroller times out during initialization, reset it before failing by @ianohara in #14
• firmware: fix bug where hardware trigger interrupt was able to access partially written data by @ianohara in #15
• Merge octopi-research/master (click to move update and sample format bug fix) by @hongquanli in #17
• sample format bug fix (glass slide) by @hongquanli in #18
• restore x,y,z position update in simulated microcontroller by @hongquanli in #21
• click-to-move in navigationViewer by @sohamazing in #19
• click-to-move navigation viewer offset by @sohamazing in #23
• manually merge commits from Soham (mostly sample format related bug fix) by @hongquanli in #25
• setup and cleanup: fix setup scripts for new repo, delete outdate and move tools. Add action for install + tests. by @ianohara in #31
• microscope: fix simulated mode in microscope by @ianohara in #32
• Flexible scan grid by @sohamazing in #27
• Hamamatsu hardware trigger bug fix by @Alpaca233 in #26
• add support for celesta by @hongquanli in #41
• microcontroller: remove is_simulated at Microcontroller level, and instead implement simulated firmware at Serial level by @ianohara in #33
• tracking: remove unused and incomplete tracking implementations. Those in core.py and widgets.py stay. by @ianohara in #43
• update live scan grid: delay live scan grid generation when xy-stage moving, init live scan grid to 1mm by @sohamazing in #36
• signal cleanup: remove redundant signals, streamline acquisition signal and slot logic by @sohamazing in #37
• bug fix: edits to manual region shape should not update scan coordinates while on flexible widget by @sohamazing in #38
• cleanup: remove tileddisplaywidget and multipointwidget and cleanup spaces by @sohamazing in #39
• Pr filterspin by @veerwang in #46
• pulled out region_coordinates from MultiPointWidgets into ScanCoordinates by @sohamazing in #47
• interface: start pulling out the stage concept by @ianohara in #34
• stage: integrate into the system (replace NavigationController) by @ianohara in #48
• IlluminationController class initial commit by @Alpaca233 in #42
• interface: start pulling out illumination control by @hongquanli in #54
• add support for celesta by @hongquanli in #40
• add manual focus map function by @hongquanli in #56
• add manual focus map by @hongquanli in #57
• focus-map: (manual focus point grid) - specify z level at points, fit to 3d surface, interpolate for acquisition scan fovs by @sohamazing in #50
• fix bug comes from merging code by @veerwang in #55
• fix: celesta should be off by default by @ianohara in #58
• fix: send pos from movement updater, and start movement updater by @ianohara in #59
• formatting: format entire repo with black by @ianohara in #49
• fix: scan coordinate preview by @hongquanli in #62
• improvement: prevent constant update of scan coordinate preview by @hongquanli in #63
• Prior stage with abstract stage class by @Alpaca233 in #65
• fix a bug of axis move direct by @veerwang in #66
• Prior stage bug fix by @Alpaca233 in #67
• fix(microcontroller): microcontroller test rel moves are correct now by @ianohara in #70
• Focus map refactoring by @Alpaca233 in #69
• fix(core): remove duplicate initializations by @ianohara in #72
• fix(lint action): Fail linting action if formatting would have happened by @ianohara in #73
• fix(formatting): Run black on whole repo again to get to clean lint state by @ianohara in #74
• debug(laser af): only catch Exception, print exec_info, indicate failure for caller in autofocus method by @ianohara in #75
• fix(acquisition abort): Aborting acquisitions midway left the ui in an invalid state by @ianohara in #76
• fix(MultiPointWorker): logging in update_use_piezo had a missing format in string by @ianohara in #77
• acquisitions: catch TimeoutErrors in acquisitions, and abort acquisition cleanly by @ianohara in #81
• utils: add a directory creation helper, and use it instad of os.mkdirs by @ianohara in #82
• feature: add Jupyter console by @hongquanli in #71
• 2 position objective changer by @Alpaca233 in #83
• New scan shape: Rectangle by @Alpaca233 in #85
• add auto offset adjustment for objective switching by @hongquanli in #87
• Fix LDI laser engine errors caused by IlluminationController by @Alpaca233 in #86
• fix(stage): pass in PriorStage config when using Prior by @ianohara in #88
• stage: prior: add a position polling timer by @ianohara in #91
• manual roi: fix incorrect index by @ianohara in #92
• prior: use a thread instead of timers by @ianohara in #93
• manual regions: add corner check for inclusion criteria by @ianohara in #95
• feat(microcontroller): Add a mechanism for automatic serial reconnect, and use it by @ianohara in #78
• make the downsampling in mosaic view scale with objectice mag by @hongquanli in #94
• acquistions: when we abort, do not let another start until previous is finished by @ianohara in #96
• fix: move lighting tools to their own module to avoid circular import by @ianohara in #89
• objective switcher init bug fix by @hongquanli in #99
• manual focus map improvements by @Alpaca233 in #98
• fix: napari init attrib bug, and add unit tests by @ianohara in #102
• logging&utils: add helper for getting squid repo state, log state on startup by @ianohara in #103
• simulated micro: fix to be thread safe by @ianohara in #104

New Contributors

• @sohamazing made their first contribution in #19
• @Alpaca233 made their first contribution in #26
• @veerwang made their first contribution in https://github.com/Cephla-Lab...