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0x00b1 fix tests (#3802)
* 2to3-3.7 --write tests/

* test_align

* fixes

* fixes for test to pass (#3807)

* test_createbatchfiles (#3808)

* had to modify pipeline.load() again to match tests

tested on ubuntu and windows for cppipe versions 3, 4, and 5

* fixes for test_loadsingleImage

* test_loadimages fix depends on pipeline.load() change

* test_loadimages (#3813)

* test_loadimages

* python 3.7+ no longer has os.stat_float_times()

* stripping out all whitespace around the text

* deleted since dict cannot be sorted in this fashion

groupings variable appear to be sorted already; only issue for test_loadimages is "HTTP Error 301: Moved Permanently" for some link

* Test_exporttodatabase (#3812)

* changing fd to open in text mode instead of binary

also changed how to read exception messages, need to decode() the other MySqldb.escape_string()s, also need to test with internet connection

* updated how to retrieve exception message

* complained that 'cursor' was not initialized for finally block

* MySQLdb.escape_string() returns bytes, so decode() to str

* use legacy equals for simplicity

sometimes value variable will be bytes, sometimes str

* no longer need ord() since digest[] will return correct int

* got test_08_02_image_thumbnails_sqlite to pass

* Set module num via setter (#3811)

* removed the MATLAB test, cppipe v1 from test_align

* test_calculatestatistics

* test_colortogray

* fix was to use the setter

* test_crop

* test_displaydataonimage

* test_expandorshrinkobjects

* test_flagimages

* removed v1 matlab test from test_flagimages

* test_flipandrotate module num

* removed v1 matlab test from test_flipandrotate

* test_graytocolor

* test_groups; not sure if can remove sorted() to fix completely

* test_identifydeadworms

* test_identifyobjectsingrid

* fixed most but not all in test_identifyprimaryobjects

* test_identifysecondaryobjects

* test_identifytertiaryobjects

* test_imagemath

* test_images

* removed matlab v1 test from test_invertforprinting

* test_invertforprinting

* test_labelimages

* test_loaddata

* removed matlab v1 test for test_makeprojection

* test_makeprojection

* test_maskimage

* test_maskobjects

* module.module_num = (\d)

* scipy.stats.pearsonr

* // and removed fixture annotation (#3825)

helper function instead

* // and set_module_num() (#3824)

* .value and removed matlab v1 test (#3823)

>           dict[key] = im
E           TypeError: unhashable type: 'ImageNameSubscriber'

* Matplotlib requires fd in bytes for tests (#3810)

* removed matlab v1 test and also fixed matplotlib error using BytesIO

although matplotlib 3.1.0 documentation mentions it taking a str, it is actually bytes

* removed commented v1 test

* needed to reassign sorted()

mistake made in test_exporttodatabase PR

* JAVA_HOME (#3822)

javabridge setup was unable to find JAVA_HOME so setting to /usr/lib/jvm/default-java

* unittest2pytest

* unittest2pytest

* renamed tests to remove numeric prefixes

* optimized imports

* removed class

* removed classes

* removed classes

* removed self

* removed file docstring

* removed set_headless

* fix errors

* remove aliases

* fixtures

* fixtures

* fixtures

* fixtures

* fixtures

* fixtures

* fixtures

* formatting

* fixes

* fixes

* fixes

* fixes

* fixed resize and smooth

* removed matlab tests

* fix measureobjectintensitydistribution

* fix measureobjectintensitydistribution tests

* fix measureobjectintensitydistribution tests

* fix measureobjectneighbors tests

* fix measureobjectoverlap tests

* fix measureobjectskeleton tests

* fix rescaleintensity tests

* fixtures

* fix imagemath tests

* test graytocolor tests

* fix flipandrotate tests

* fix identifyprimaryobjects tests

* straightenworms fixes
Latest commit 4a9d014 Sep 5, 2019
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plugins Python 3 (#3761) Aug 12, 2019
UntangleWorms.xsd reformatted Mar 21, 2016
__init__.py Python 3 (#3761) Aug 12, 2019
_help.py wxPython 4 migration (WIP) (#3599) May 31, 2019
align.py wxPython 4 migration (WIP) (#3599) May 31, 2019
calculatemath.py black integration (#3801) Aug 12, 2019
calculatestatistics.py Python 3 (#3761) Aug 12, 2019
classifyobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
closing.py wxPython 4 migration (WIP) (#3599) May 31, 2019
colortogray.py Python 3 (#3761) Aug 12, 2019
convertimagetoobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
convertobjectstoimage.py wxPython 4 migration (WIP) (#3599) May 31, 2019
correctilluminationapply.py Python 3 (#3761) Aug 12, 2019
correctilluminationcalculate.py wxPython 4 migration (WIP) (#3599) May 31, 2019
createbatchfiles.py Python 3 (#3761) Aug 12, 2019
crop.py wxPython 4 migration (WIP) (#3599) May 31, 2019
definegrid.py wxPython 4 migration (WIP) (#3599) May 31, 2019
dilateimage.py wxPython 4 migration (WIP) (#3599) May 31, 2019
dilateobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
displaydataonimage.py black integration (#3801) Aug 12, 2019
displaydensityplot.py Python 3 (#3761) Aug 12, 2019
displayhistogram.py wxPython 4 migration (WIP) (#3599) May 31, 2019
displayplatemap.py black integration (#3801) Aug 12, 2019
displayscatterplot.py wxPython 4 migration (WIP) (#3599) May 31, 2019
editobjectsmanually.py wxPython 4 migration (WIP) (#3599) May 31, 2019
enhanceedges.py wxPython 4 migration (WIP) (#3599) May 31, 2019
enhanceorsuppressfeatures.py wxPython 4 migration (WIP) (#3599) May 31, 2019
erosion.py wxPython 4 migration (WIP) (#3599) May 31, 2019
expandorshrinkobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
exporttodatabase.py fix tests (#3802) Sep 5, 2019
exporttospreadsheet.py fix tests (#3802) Sep 5, 2019
fillobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
filterobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
flagimage.py wxPython 4 migration (WIP) (#3599) May 31, 2019
flipandrotate.py wxPython 4 migration (WIP) (#3599) May 31, 2019
gaussianfilter.py wxPython 4 migration (WIP) (#3599) May 31, 2019
graytocolor.py wxPython 4 migration (WIP) (#3599) May 31, 2019
groups.py fix tests (#3802) Sep 5, 2019
identify.py Python 3 (#3761) Aug 12, 2019
identifydeadworms.py wxPython 4 migration (WIP) (#3599) May 31, 2019
identifyobjectsingrid.py wxPython 4 migration (WIP) (#3599) May 31, 2019
identifyobjectsmanually.py wxPython 4 migration (WIP) (#3599) May 31, 2019
identifyprimaryobjects.py black integration (#3801) Aug 12, 2019
identifysecondaryobjects.py Update identifysecondaryobjects.py (#3821) Aug 21, 2019
identifytertiaryobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
imagemath.py wxPython 4 migration (WIP) (#3599) May 31, 2019
images.py black integration (#3801) Aug 12, 2019
injectimage.py wxPython 4 migration (WIP) (#3599) May 31, 2019
invertforprinting.py wxPython 4 migration (WIP) (#3599) May 31, 2019
labelimages.py wxPython 4 migration (WIP) (#3599) May 31, 2019
loaddata.py black integration (#3801) Aug 12, 2019
loadimages.py fix tests (#3802) Sep 5, 2019
loadsingleimage.py fix tests (#3802) Sep 5, 2019
makeprojection.py wxPython 4 migration (WIP) (#3599) May 31, 2019
maskimage.py wxPython 4 migration (WIP) (#3599) May 31, 2019
maskobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
matchtemplate.py wxPython 4 migration (WIP) (#3599) May 31, 2019
measurecolocalization.py fix tests (#3802) Sep 5, 2019
measuregranularity.py wxPython 4 migration (WIP) (#3599) May 31, 2019
measureimageareaoccupied.py Python 3 (#3761) Aug 12, 2019
measureimageintensity.py fix tests (#3802) Sep 5, 2019
measureimageoverlap.py wxPython 4 migration (WIP) (#3599) May 31, 2019
measureimagequality.py fix tests (#3802) Sep 5, 2019
measureimageskeleton.py wxPython 4 migration (WIP) (#3599) May 31, 2019
measureobjectintensity.py wxPython 4 migration (WIP) (#3599) May 31, 2019
measureobjectintensitydistribution.py fix tests (#3802) Sep 5, 2019
measureobjectneighbors.py fix tests (#3802) Sep 5, 2019
measureobjectoverlap.py fix tests (#3802) Sep 5, 2019
measureobjectsizeshape.py wxPython 4 migration (WIP) (#3599) May 31, 2019
measureobjectskeleton.py wxPython 4 migration (WIP) (#3599) May 31, 2019
measuretexture.py Python 3 (#3761) Aug 12, 2019
medialaxis.py wxPython 4 migration (WIP) (#3599) May 31, 2019
medianfilter.py wxPython 4 migration (WIP) (#3599) May 31, 2019
mergeoutputfiles.py Python 3 (#3761) Aug 12, 2019
metadata.py black integration (#3801) Aug 12, 2019
morph.py Python 3 (#3761) Aug 12, 2019
morphologicalskeleton.py wxPython 4 migration (WIP) (#3599) May 31, 2019
namesandtypes.py black integration (#3801) Aug 12, 2019
opening.py wxPython 4 migration (WIP) (#3599) May 31, 2019
overlayobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
overlayoutlines.py black integration (#3801) Aug 12, 2019
reducenoise.py wxPython 4 migration (WIP) (#3599) May 31, 2019
relateobjects.py reformatted Aug 13, 2019
removeholes.py wxPython 4 migration (WIP) (#3599) May 31, 2019
removeobjectsbysize.py wxPython 4 migration (WIP) (#3599) May 31, 2019
rescaleintensity.py wxPython 4 migration (WIP) (#3599) May 31, 2019
resize.py Python 3 (#3761) Aug 12, 2019
resizeobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
savecroppedobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
saveimages.py wxPython 4 migration (WIP) (#3599) May 31, 2019
shrinktoobjectcenters.py wxPython 4 migration (WIP) (#3599) May 31, 2019
smooth.py wxPython 4 migration (WIP) (#3599) May 31, 2019
splitormergeobjects.py wxPython 4 migration (WIP) (#3599) May 31, 2019
straightenworms.py fix tests (#3802) Sep 5, 2019
threshold.py Python 3 (#3761) Aug 12, 2019
tile.py wxPython 4 migration (WIP) (#3599) May 31, 2019
trackobjects.py Python 3 (#3761) Aug 12, 2019
unmixcolors.py wxPython 4 migration (WIP) (#3599) May 31, 2019
untangleworms.py black integration (#3801) Aug 12, 2019
watershed.py wxPython 4 migration (WIP) (#3599) May 31, 2019
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