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Better failure detection.
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mcquin committed Sep 8, 2017
1 parent 1417066 commit d0ae004
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1 change: 1 addition & 0 deletions .travis.yml
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apt: true
directories: $HOME/.cache/pip
dist: trusty
after_script: make clean
env:
- LC_ALL="en_US.UTF-8" CP_MYSQL_TEST_HOST="127.0.0.1" CP_MYSQL_TEST_USER="root" CP_MYSQL_TEST_PASSWORD=""
install:
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185 changes: 112 additions & 73 deletions Makefile
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.PHONY: test

test:
# ExampleCometAssay
cellprofiler -c -r -p ExampleCometAssay/ExampleCometAssay.cppipe -i ExampleCometAssay/images -o ExampleCometAssay/output
.PHONY: clean test

clean:
rm -rf ExampleCometAssay/output

# ExampleFly
cellprofiler -c -r -p ExampleFly/ExampleFly.cppipe -i ExampleFly/images -o ExampleFly/output

rm -rf ExampleFly/output

# ExampleHuman
cellprofiler -c -r -p ExampleHuman/ExampleHuman.cppipe -i ExampleHuman/images -o ExampleHuman/output

rm -rf ExampleHuman/output

# ExamplePercentPositive
cellprofiler -c -r -p ExamplePercentPositive/ExamplePercentPositive.cppipe -i ExamplePercentPositive/images -o ExamplePercentPositive/output

rm -rf ExamplePercentPositive/output

# ExampleTumor
cellprofiler -c -r -p ExampleTumor/ExampleTumor.cppipe -i ExampleTumor/images -o ExampleTumor/output

rm -rf ExampleTumor/output

# ExampleYeastColonies
cellprofiler -c -r -p ExampleYeastColonies/ExampleYeastColonies.cppipe -i ExampleYeastColonies/images -o ExampleYeastColonies/output

rm -rf ExampleYeastColonies/output

# ExampleYeastPatches
cellprofiler -c -r -p ExampleYeastPatches/ExampleYeastPatches.cppipe -i ExampleYeastPatches/images -o ExampleYeastPatches/output

rm -rf ExampleYeastPatches/output

# ExampleColocalization
cellprofiler -c -r -p ExampleColocalization/ExampleColocalization.cppipe -i ExampleColocalization/images -o ExampleColocalization/output

rm -rf ExampleColocalization/output

# ExampleIlluminationCorrection_Example1_AllMethod
cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example1_AllMethod.cppipe -i ExampleIlluminationCorrection/images -o ExampleIlluminationCorrection/output

rm -rf ExampleIlluminationCorrection/output

# ExampleIlluminationCorrection_Example1_EachMethod
cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example1_EachMethod.cppipe -i ExampleIlluminationCorrection/images -o ExampleIlluminationCorrection/output

rm -rf ExampleIlluminationCorrection/output

# ExampleIlluminationCorrection_Example2
cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example2.cppipe -i ExampleIlluminationCorrection/images -o ExampleIlluminationCorrection/output

rm -rf ExampleIlluminationCorrection/output

# ExampleIlluminationCorrection_Example3
cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example3.cppipe -i ExampleIlluminationCorrection/images -o ExampleIlluminationCorrection/output

rm -rf ExampleIlluminationCorrection/output

# ExampleNeighbors
cellprofiler -c -r -p ExampleNeighbors/ExampleNeighbors.cppipe -i ExampleNeighbors/images -o ExampleNeighbors/output

rm -rf ExampleIlluminationCorrection/output_all
rm -rf ExampleIlluminationCorrection/output_each
rm -rf ExampleIlluminationCorrection/output2
rm -rf ExampleIlluminationCorrection/output3
rm -rf ExampleNeighbors/output

# ExampleSpeckles
cellprofiler -c -r -p ExampleSpeckles/ExampleSpeckles.cppipe -i ExampleSpeckles/images -o ExampleSpeckles/output

rm -rf ExampleSpeckles/output

# ExampleTrackObjects
cellprofiler -c -r -p ExampleTrackObjects/ExampleTrackObjects.cppipe -i ExampleTrackObjects/images -o ExampleTrackObjects/output

rm -rf ExampleTrackObjects/output

# ExampleWoundHealing
cellprofiler -c -r -p ExampleWoundHealing/ExampleWoundHealing.cppipe -i ExampleWoundHealing/images -o ExampleWoundHealing/output

rm -rf ExampleWoundHealing/output

# ExampleImagingFlowCytometryObjectsInGrid
cellprofiler -c -r -p ExampleImagingFlowCytometryObjectsInGrid/ExampleImagingFlowCytometryObjectsInGrid.cppipe -i ExampleImagingFlowCytometryObjectsInGrid/images -o ExampleImagingFlowCytometryObjectsInGrid/output

rm -rf ExampleImagingFlowCytometryObjectsInGrid/output

test:
cellprofiler -c -r -p ExampleCometAssay/ExampleCometAssay.cppipe \
-i ExampleCometAssay/images \
-o ExampleCometAssay/output \
-d ExampleCometAssay/output/done

cellprofiler -c -r -p ExampleFly/ExampleFly.cppipe \
-i ExampleFly/images \
-o ExampleFly/output \
-d ExampleFly/output/done

cellprofiler -c -r -p ExampleHuman/ExampleHuman.cppipe \
-i ExampleHuman/images \
-o ExampleHuman/output \
-d ExampleHuman/output/done

cellprofiler -c -r -p ExamplePercentPositive/ExamplePercentPositive.cppipe \
-i ExamplePercentPositive/images \
-o ExamplePercentPositive/output \
-d ExamplePercentPositive/output/done

cellprofiler -c -r -p ExampleTumor/ExampleTumor.cppipe \
-i ExampleTumor/images \
-o ExampleTumor/output \
-d ExampleTumor/output/done

cellprofiler -c -r -p ExampleYeastColonies/ExampleYeastColonies.cppipe \
-i ExampleYeastColonies/images \
-o ExampleYeastColonies/output \
-d ExampleYeastColonies/output/done

cellprofiler -c -r -p ExampleYeastPatches/ExampleYeastPatches.cppipe \
-i ExampleYeastPatches/images \
-o ExampleYeastPatches/output \
-d ExampleYeastPatches/output/done

cellprofiler -c -r -p ExampleColocalization/ExampleColocalization.cppipe \
-i ExampleColocalization/images \
-o ExampleColocalization/output \
-d ExampleColocalization/output/done

cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example1_AllMethod.cppipe \
-i ExampleIlluminationCorrection/images \
-o ExampleIlluminationCorrection/output_all \
-d ExampleIlluminationCorrection/output_all/done

cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example1_EachMethod.cppipe \
-i ExampleIlluminationCorrection/images \
-o ExampleIlluminationCorrection/output_each \
-d ExampleIlluminationCorrection/output_each/done

cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example2.cppipe \
-i ExampleIlluminationCorrection/images \
-o ExampleIlluminationCorrection/output2 \
-d ExampleIlluminationCorrection/output2/done

cellprofiler -c -r -p ExampleIlluminationCorrection/ExampleIlluminationCorrection_Example3.cppipe \
-i ExampleIlluminationCorrection/images \
-o ExampleIlluminationCorrection/output3 \
-d ExampleIlluminationCorrection/output3/done

cellprofiler -c -r -p ExampleNeighbors/ExampleNeighbors.cppipe \
-i ExampleNeighbors/images \
-o ExampleNeighbors/output \
-d ExampleNeighbors/output/done

cellprofiler -c -r -p ExampleSpeckles/ExampleSpeckles.cppipe \
-i ExampleSpeckles/images \
-o ExampleSpeckles/output \
-d ExampleSpeckles/output/done

cellprofiler -c -r -p ExampleTrackObjects/ExampleTrackObjects.cppipe \
-i ExampleTrackObjects/images \
-o ExampleTrackObjects/output \
-d ExampleTrackObjects/output/done

cellprofiler -c -r -p ExampleWoundHealing/ExampleWoundHealing.cppipe \
-i ExampleWoundHealing/images \
-o ExampleWoundHealing/output \
-d ExampleWoundHealing/output/done

cellprofiler -c -r -p ExampleImagingFlowCytometryObjectsInGrid/ExampleImagingFlowCytometryObjectsInGrid.cppipe \
-i ExampleImagingFlowCytometryObjectsInGrid/images \
-o ExampleImagingFlowCytometryObjectsInGrid/output \
-d ExampleImagingFlowCytometryObjectsInGrid/output/done

@if [ $$(cat ExampleCometAssay/output/done) = Failure ] || \
[ $$(cat ExampleFly/output/done) = Failure ] || \
[ $$(cat ExampleHuman/output/done) = Failure ] || \
[ $$(cat ExamplePercentPositive/output/done) = Failure ] || \
[ $$(cat ExampleTumor/output/done) = Failure ] || \
[ $$(cat ExampleYeastColonies/output/done) = Failure ] || \
[ $$(cat ExampleYeastPatches/output/done) = Failure ] || \
[ $$(cat ExampleColocalization/output/done) = Failure ] || \
[ $$(cat ExampleIlluminationCorrection/output_all/done) = Failure ] || \
[ $$(cat ExampleIlluminationCorrection/output_each/done) = Failure ] || \
[ $$(cat ExampleIlluminationCorrection/output2/done) = Failure ] || \
[ $$(cat ExampleIlluminationCorrection/output3/done) = Failure ] || \
[ $$(cat ExampleNeighbors/output/done) = Failure ] || \
[ $$(cat ExampleSpeckles/output/done) = Failure ] || \
[ $$(cat ExampleTrackObjects/output/done) = Failure ] || \
[ $$(cat ExampleWoundHealing/output/done) = Failure ] || \
[ $$(cat ExampleImagingFlowCytometryObjectsInGrid/output/done) = Failure ]; then \
false; \
else true; fi

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