Acq4

API / behavior changes:
Disabled HDF5 compression by default--lzf is not readable by most HDF5 libraries, and gzip is too slow.
(see the 'defaultCompression' config option).
Tasks now have a default timeout to prevent endless tasks locking up the system. For tasks that
require tolerance to long, unpredictable wait times (such as while waiting for an external
trigger), it is necessary to set {'protocol': {'timeout': None}}. Note that the TaskRunner
disables the default timeout for exactly this reason.
New Features:
Timelapse + z-stack in camera module
Motorized focus control interface in camera module
Support for tracking and controlling micromanipulators from camera module
Support for Scientifica PatchStar manipulators
Spiral scanning for single-cell photostimulation
Panic button: ESC key global shortcut closes shutters, stops stage/manipulator, aborts all tasks, etc.
Overhaul of 2p Imager module:
Uses services provided by scanner to provide raster scanning, which makes the behavior more consistent
with task runner.
Shares image display code and user interface with cameras to make imaging consistent across device types
MultiClamp can be used with 64-bit Python (by remote connection to a separate 32-bit Python)
Support for Thorlabs MFC-1 focus controller using ROE-200 unused z-axis
Added export option to ImageView
Added new online analysis module for photostimulation (replaces old Uncaging module)
Added support for controlling bidirectional filtering by NiDAQ device
NoiseMonitor module for tracking long-term changes in electrical noise
Added motion support to MPC200 device
Objectives now have z-offset
Bugfixes:
Fixed issues with Scanner grid controls in TaskRunner
Fixed issues with MultiClamp starting with wrong state in TaskRunner
Cleaned up MultiClamp manager UI
Fixed NiDAQ reporting incorrect sample rate in task runner
Fixed problems with DockArea not restoring its state correctly
Maintenance:
Performance improvements for 2p imaging and stage input
util.database now uses built-in sqlite3 module instead of QtSql

API / behavior changes:
Performance improvements for Camera module, MP285
generator pulse train parameter "interpulse_length" renamed to "period"
Renamed "task" -> "taskRunner" for clarity in all TaskGui classes
Simplified device config format by removing extra config: key from each device
(old format is still accepted)
MultiClamp, Camera configs use 'defaults' instead of 'settings'
Slowed down Camera acquisition loop; it was eating too much CPU
New Features:
rudimentary "runner" bin/acq4, acq4.bat to start acq4
Added --profile flag
function generator now supports execution of multiple python statements rather than just eval()
TaskRunner interface plots use downsampling and clip-to-view by default.
Add ability to specify QCam device by unique ID
Bugfixes:
Fixed Camera module re-center on camera sensor area after objective switch
fixed setup.py detection of git status
Fixed inconsistencies in Laser.oputputPower()
now returns _only_ the power value
Fixed improper reload prefix
Fixed bug when adding task runner analysis modules
TaskRunner and Manager now stack new docks in tabs to avoid generating excessively large windows
pg.MultiPlotItem imports correct metaarray module
Removed calls to non-existent DAQ methods in mock DAQ
Fix divide by zero in ViewBox
InfiniteLine cache bounding rect for speedup
Maintenance:
Added .mailmap to correct the last 7 years of negligence.
Removed duplicate entries from util.debug that also exist in pg.debug
corrected column stretch in taskrunner sequence dock template, axopatch

API / behavior changes:
Patch module defaults to -65 mV holding.
Imager now uses config parameters to determine names of devices to use.
Moved acq4.py script to acq4/__main__.py; now we start with python -m acq4
Updated config search path
setup.py install now copies config inside package install location
Invert mock camera in example config--this makes stored images appear in
the same orientation as they were recorded
(just to avoid unnecessary confusion)
Slow down camera module until interactivity bug is handled
CParser now requires explicit instruction to trigger a header re-parese.

New Features:
Added innosetup script for building Windows setup.exe
Nicer demo message
Added sigRemoved signal to Parameter class
New grid system for scanner tasks
Bugfixes:
Minor fixes in pyqtgraph.
Removed extra Log button from Manager gui
Avoid unnecessary rebuild of Ni header cache
Fixed behavior when no base dir is set
Imager requests camera module load if it does not exist yet
Add header cache files, .dll files to dist
Fixed logging bugs:
- documentation links work
- fixed import error in util.debug that prevented errors being logged
- log window no longer tries to follow its own links (these
are handled externally)
Doc link for no-storage-dir error
Manager no longer creates index in baseDir; this is deferred until a file is added.
Fixed setup.py config install path on linux
Maintenance:
Split documentation into its own repository.
Many cleanups and additions to example config.
Reorganized:
- __init__ now handles most of what was previously in __main__
- Manager now handles searching for config files
- added CONFIGPATH global variable listing candidate search paths
rebuildUi script now accepts path arguments
cleaned up Manifest.in
removed the 'storeSVG' and 'storePNG' buttons from the Canvas gui since
they were both broken and redundant with ViewBox's export system
disabled ImageCorrection buttons in MosaicEditor
fixes/cleanup of mosaic editor and cortexROI code, mosaic editor documentation

* Initial release with standard python package structure.