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increase package-wide unit test coverage #143

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brownag opened this issue Jun 24, 2020 · 3 comments
Open

increase package-wide unit test coverage #143

brownag opened this issue Jun 24, 2020 · 3 comments
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@brownag
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enhancement
Milestone
aqp 2.0

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@brownag
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brownag commented Jun 24, 2020

We can use the {covr} package to see which parts of the codebase need unit tests developed.

I am not sure that this is picking up everything... investigate further perhaps at finer level of detail (i.e. individual exported functions)

By this estimate, we are just below 50% coverage right now.

library(covr)
package_coverage(type="tests")

aqp Coverage: 49.38%
R/AAAA.R: 0.00%
R/accuracy_uncertainty.R: 0.00%
R/addBracket.R: 0.00%
R/aggregateSoilDepth.R: 0.00%
R/checkSPC.R: 0.00%
R/colorContrastPlot.R: 0.00%
R/colorQuantiles.R: 0.00%
R/contrastChart.R: 0.00%
R/depthOf.R: 0.00%
R/depthWeights.R: 0.00%
R/evalGenHz.R: 0.00%
R/f.noise.R: 0.00%
R/factor-level-setters.R: 0.00%
R/get.ml.hz.R: 0.00%
R/getCambicBounds.R: 0.00%
R/glomApply.R: 0.00%
R/group_by.R: 0.00%
R/groupedProfilePlot.R: 0.00%
R/guessGenHzLevels.R: 0.00%
R/hzTransitionProbabilities.R: 0.00%
R/make.segments.R: 0.00%
R/missingDataGrid.R: 0.00%
R/mollicEpipedon.R: 0.00%
R/mostLikelyHzSequence.R: 0.00%
R/mutate.R: 0.00%
R/mutate_profile.R: 0.00%
R/panel.depth_function.R: 0.00%
R/permute_profile.R: 0.00%
R/plot_distance_graph.R: 0.00%
R/plotMultipleSPC.R: 0.00%
R/prepanel.depth_function.R: 0.00%
R/previewColors.R: 0.00%
R/resample.twotheta.R: 0.00%
R/soilPalette.R: 0.00%
R/summarize.R: 0.00%
R/tauW.R: 0.00%
R/test_hz_logic.R: 0.00%
R/texture-low-rv-high.R: 0.00%
R/texture.R: 0.00%

## >0%

R/soilColorSignature.R: 37.50%
R/generalize.hz.R: 44.44%
R/genSlabLabels.R: 52.94%
R/glom.R: 55.24%
R/plotSPC.R: 55.79%
R/estimatePSCS.R: 57.14%
R/SoilProfileCollection-methods.R: 62.73%
R/aggregateColor.R: 65.67%
R/Class-SoilProfileCollection.R: 67.67%
R/slab.R: 68.04%
R/getArgillicBounds.R: 71.08%
R/profile_compare.R: 71.43%
R/SoilProfileCollection-coercion.R: 71.43%
R/unroll.R: 72.73%

## >75%

R/SoilProfileCollection-operators.R: 75.17%
R/guessColumnNames.R: 75.93%
R/rebuildSPC.R: 78.57%
R/SoilProfileCollection-slice-methods.R: 79.49%
R/SoilProfileCollection-iterators.R: 79.63%
R/SoilProfileCollection-setters.R: 81.35%
R/sketch-utils.R: 84.21%
R/random_profile.R: 84.29%
R/denormalize.R: 85.71%
R/split.R: 85.71%
R/getSurfaceHorizonDepth.R: 86.21%
R/get.increase.matrix.R: 86.36%
R/union.R: 86.75%
R/SoilProfileCollection-integrity.R: 88.10%
R/munsell2rgb.R: 88.89%
R/huePosition.R: 91.67%
R/estimateSoilDepth.R: 92.00%
R/SoilProfileCollection-spatial.R: 92.86%
R/soilColorIndices.R: 94.44%
R/addVolumeFraction.R: 94.83%
R/colorContrast.R: 95.83%
R/contrastClass.R: 95.83%
R/evalMissingData.R: 95.83%
R/lunique.R: 96.55%
R/checkHzDepthLogic.R: 96.88%
R/compositeSPC.R: 100.00%
R/explainPlotSPC.R: 100.00%
R/getSoilDepthClass.R: 100.00%
R/sim.R: 100.00%
R/zzz.R: 100.00%
@brownag brownag self-assigned this Jun 24, 2020
@brownag brownag added this to the aqp 2.0 milestone Jun 24, 2020
brownag added a commit that referenced this issue Aug 2, 2020
@brownag
adjust for hzdesgn+texcl @metadata; add tests for guessX functions #143
7be0b0b
brownag added a commit that referenced this issue Aug 2, 2020
@brownag
improve unit test coverage #143
c78c408
@brownag
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brownag commented Aug 2, 2020 

aqp Coverage: 64.47%
R/aggregateSoilDepth.R: 0.00%
R/colorContrastPlot.R: 0.00%
R/colorQuantiles.R: 0.00%
R/contrastChart.R: 0.00%
R/f.noise.R: 0.00%
R/factor-level-setters.R: 0.00%
R/groupedProfilePlot.R: 0.00%
R/hzBoundary.R: 0.00%
R/invertLabelColor.R: 0.00%
R/make.segments.R: 0.00%
R/missingDataGrid.R: 0.00%
R/mostLikelyHzSequence.R: 0.00%
R/panel.depth_function.R: 0.00%
R/plot_distance_graph.R: 0.00%
R/plotMultipleSPC.R: 0.00%
R/prepanel.depth_function.R: 0.00%
R/previewColors.R: 0.00%
R/resample.twotheta.R: 0.00%
R/segment.R: 0.00%
R/soilPalette.R: 0.00%
R/tauW.R: 0.00%
R/test_hz_logic.R: 0.00%
R/texture-low-rv-high.R: 0.00%
R/texture.R: 0.00%
R/soilColorSignature.R: 37.50%
R/plotSPC.R: 44.16%
R/generalize.hz.R: 44.44%
R/SoilProfileCollection-methods.R: 61.94%
R/group_by.R: 70.00%
R/SoilProfileCollection-coercion.R: 71.43%
R/profile_compare.R: 71.62%
R/unroll.R: 72.73%
R/enforce_df_class.R: 78.57%
R/SoilProfileCollection-slice-methods.R: 79.49%
R/union.R: 79.84%
R/sketch-utils.R: 80.43%
R/SoilProfileCollection-operators.R: 81.93%
R/mollicEpipedon.R: 82.02%
R/getArgillicBounds.R: 82.22%
R/SoilProfileCollection-setters.R: 84.65%
R/summarize.R: 84.85%
R/glomApply.R: 85.71%
R/random_profile.R: 85.71%
R/slab.R: 86.60%
R/glom.R: 86.72%
R/addBracket.R: 87.50%
R/aggregateColor.R: 88.06%
R/munsell2rgb.R: 88.89%
R/rebuildSPC.R: 88.89%
R/Class-SoilProfileCollection.R: 88.95%
R/getSurfaceHorizonDepth.R: 89.66%
R/mutate.R: 90.00%
R/permute_profile.R: 90.14%
R/evalGenHz.R: 90.70%
R/get.increase.matrix.R: 90.91%
R/huePosition.R: 91.67%
R/estimateSoilDepth.R: 92.00%
R/hzTransitionProbabilities.R: 92.50%
R/guessColumnNames.R: 92.86%
R/SoilProfileCollection-spatial.R: 92.86%
R/genSlabLabels.R: 94.12%
R/mutate_profile.R: 94.12%
R/estimatePSCS.R: 95.24%
R/split.R: 95.24%
R/colorContrast.R: 95.83%
R/evalMissingData.R: 95.83%
R/lunique.R: 96.55%
R/get.ml.hz.R: 97.14%
R/getCambicBounds.R: 97.96%
R/AAAA.R: 100.00%
R/accuracy_uncertainty.R: 100.00%
R/addVolumeFraction.R: 100.00%
R/checkHzDepthLogic.R: 100.00%
R/checkSPC.R: 100.00%
R/compositeSPC.R: 100.00%
R/contrastClass.R: 100.00%
R/denormalize.R: 100.00%
R/depthOf.R: 100.00%
R/depthWeights.R: 100.00%
R/explainPlotSPC.R: 100.00%
R/getSoilDepthClass.R: 100.00%
R/guessGenHzLevels.R: 100.00%
R/sim.R: 100.00%
R/soilColorIndices.R: 100.00%
R/SoilProfileCollection-integrity.R: 100.00%
R/SoilProfileCollection-iterators.R: 100.00%
R/zzz.R: 100.00%

@dylanbeaudette
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dylanbeaudette commented Jan 3, 2022 •
edited
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Update:

aqp Coverage: 68.21%
R/allocate.R: 0.00%
R/colorChart.R: 0.00%
R/colorContrastPlot.R: 0.00%
R/contrastChart.R: 0.00%
R/factor-level-setters.R: 0.00%
R/groupedProfilePlot.R: 0.00%
R/hzBoundary.R: 0.00%
R/mostLikelyHzSequence.R: 0.00%
R/panel.depth_function.R: 0.00%
R/plot_distance_graph.R: 0.00%
R/plotColorMixture.R: 0.00%
R/plotMultipleSPC.R: 0.00%
R/previewColors.R: 0.00%
R/slicedHSD.R: 0.00%
R/soilPalette.R: 0.00%
R/tauW.R: 0.00%
R/generalize.hz.R: 44.44%
R/texture.R: 48.59%
R/similarMunsellChips.R: 55.56%
R/depthOf.R: 59.14%
R/HzDepthLogicSubset.R: 62.50%
R/SoilProfileCollection-coercion.R: 64.29%
R/prepanel.depth_function.R: 64.71%
R/soilColorSignature.R: 65.42%
R/glom.R: 66.46%
R/plotSPC.R: 67.54%
R/SoilProfileCollection-methods.R: 67.69%
R/combine.R: 68.48%
R/profile_compare.R: 71.62%
R/unroll.R: 73.68%
R/getArgillicBounds.R: 74.55%
R/findOverlap-fixOverlap.R: 74.58%
R/bootstrapSoilTexture.R: 76.74%
R/group_by.R: 77.78%
R/enforce_df_class.R: 78.57%
R/SoilProfileCollection-slice-methods.R: 80.49%
R/mutate_profile.R: 80.56%
R/mollicEpipedon.R: 80.65%
R/missingDataGrid.R: 80.85%
R/alignTransect.R: 81.25%
R/L1_profiles.R: 82.35%
R/Class-SoilProfileCollection.R: 83.05%
R/split.R: 83.33%
R/mixMunsell.R: 84.03%
R/SoilProfileCollection-operators.R: 84.80%
R/perturb.R: 84.82%
R/glomApply.R: 85.71%
R/random_profile.R: 85.71%
R/colorQuantiles.R: 86.32%
R/parseMunsell.R: 86.44%
R/accumulateDepths.R: 86.59%
R/SoilProfileCollection-setters.R: 87.40%
R/harmonize.R: 87.88%
R/addBracket.R: 87.93%
R/rebuildSPC.R: 88.00%
R/SoilProfileCollection-spatial.R: 88.00%
R/munsell2rgb.R: 88.06%
R/slab.R: 88.29%
R/PMS2Munsell.R: 88.89%
R/repairMissingHzDepths.R: 89.47%
R/huePosition.R: 90.00%
R/aggregateColor.R: 90.36%
R/dice.R: 90.48%
R/guessColumnNames.R: 90.62%
R/summarize.R: 90.62%
R/get.increase.matrix.R: 90.91%
R/transform.R: 90.91%
R/estimateSoilDepth.R: 91.67%
R/estimateAWC.R: 92.00%
R/evalGenHz.R: 92.00%
R/hzTransitionProbabilities.R: 92.50%
R/aggregateSoilDepth.R: 92.59%
R/spc2mpspline.R: 92.73%
R/estimatePSCS.R: 93.55%
R/SoilProfileCollection-metadata.R: 93.98%
R/genSlabLabels.R: 94.12%
R/sketch-utils.R: 94.52%
R/simulateColor.R: 94.55%
R/getClosestMunsellChip.R: 94.74%
R/textureTriangleSummary.R: 94.87%
R/segment.R: 94.92%
R/splitLogicErrors.R: 95.45%
R/profileInformationIndex.R: 95.65%
R/evalMissingData.R: 95.83%
R/colorContrast.R: 96.30%
R/getSoilDepthClass.R: 96.43%
R/soilColorIndices.R: 96.43%
R/lunique.R: 96.55%
R/SoilProfileCollection-iterators.R: 96.88%
R/SoilProfileCollection-integrity.R: 97.30%
R/get.ml.hz.R: 97.73%
R/getCambicBounds.R: 97.96%
R/checkHzDepthLogic.R: 98.36%
R/getSurfaceHorizonDepth.R: 98.36%
R/AAAA.R: 100.00%
R/accuracy_uncertainty.R: 100.00%
R/addVolumeFraction.R: 100.00%
R/checkSPC.R: 100.00%
R/compositeSPC.R: 100.00%
R/contrastClass.R: 100.00%
R/datadots.R: 100.00%
R/denormalize.R: 100.00%
R/depthWeights.R: 100.00%
R/duplicate.R: 100.00%
R/explainPlotSPC.R: 100.00%
R/fillHzGaps.R: 100.00%
R/getLastHorizonID.R: 100.00%
R/guessGenHzLevels.R: 100.00%
R/huePositionCircle.R: 100.00%
R/invertLabelColor.R: 100.00%
R/sim.R: 100.00%
R/spec2Munsell.R: 100.00%
R/zzz.R: 100.00%

@dylanbeaudette
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Just those without 100% coverage.

aqp Coverage: 69.80%
R/allocate.R: 0.00%
R/colorChart.R: 0.00%
R/colorContrastPlot.R: 0.00%
R/compareSites.R: 0.00%
R/contrastChart.R: 0.00%
R/groupedProfilePlot.R: 0.00%
R/mostLikelyHzSequence.R: 0.00%
R/panel.depth_function.R: 0.00%
R/plot_distance_graph.R: 0.00%
R/plotColorMixture.R: 0.00%
R/plotMultipleSPC.R: 0.00%
R/previewColors.R: 0.00%
R/slicedHSD.R: 0.00%
R/soilPalette.R: 0.00%
R/tauW.R: 0.00%
R/similarMunsellChips.R: 51.72%
R/SoilProfileCollection-spatial.R: 52.38%
R/texture.R: 55.78%
R/segment.R: 59.22%
R/plotSPC.R: 59.89%
R/addBracket.R: 60.34%
R/factor-level-setters.R: 63.64%
R/soilColorSignature.R: 64.04%
R/prepanel.depth_function.R: 64.71%
R/SoilProfileCollection-coercion.R: 65.12%
R/SoilProfileCollection-methods.R: 65.93%
R/rebuildSPC.R: 68.57%
R/glom.R: 68.75%
R/huePositionCircle.R: 68.97%
R/generalize.hz.R: 69.77%
R/combine.R: 70.06%
R/profile_compare.R: 71.71%
R/unroll.R: 73.68%
R/findOverlap-fixOverlap.R: 74.58%
R/bootstrapSoilTexture.R: 76.74%
R/groupSPC.R: 77.78%
R/enforce_df_class.R: 78.57%
R/missingDataGrid.R: 80.85%
R/alignTransect.R: 81.25%
R/sketch-utils.R: 81.40%
R/L1_profiles.R: 82.61%
R/split.R: 83.33%
R/Class-SoilProfileCollection.R: 83.52%
R/slab-utils.R: 83.72%
R/depthOf.R: 84.16%
R/reduce.R: 84.62%
R/SoilProfileCollection-operators.R: 84.92%
R/mixMunsell.R: 85.11%
R/SoilProfileCollection-slice-methods.R: 85.33%
R/glomApply.R: 85.71%
R/random_profile.R: 85.71%
R/slab.R: 85.90%
R/hzOffset.R: 86.05%
R/colorQuantiles.R: 86.32%
R/get.increase.matrix.R: 86.36%
R/parseMunsell.R: 86.89%
R/SoilProfileCollection-setters.R: 87.40%
R/HzDepthLogicSubset.R: 87.50%
R/harmonize.R: 87.88%
R/munsell2rgb.R: 88.41%
R/NCSP.R: 89.13%
R/mutate_profile.R: 89.29%
R/accumulateDepths.R: 89.87%
R/huePosition.R: 90.00%
R/perturb.R: 90.00%
R/aggregateColor.R: 90.36%
R/guessColumnNames.R: 90.62%
R/summarize.R: 90.62%
R/reaction.R: 90.91%
R/transform.R: 90.91%
R/dice.R: 91.67%
R/evalGenHz.R: 92.00%
R/repairMissingHzDepths.R: 92.00%
R/hzTransitionProbabilities.R: 92.50%
R/aggregateSoilDepth.R: 92.59%
R/explainPlotSPC.R: 93.75%
R/estimateAWC.R: 94.23%
R/simulateColor.R: 94.55%
R/mollicEpipedon.R: 94.68%
R/textureTriangleSummary.R: 94.87%
R/estimatePSCS.R: 94.94%
R/accuracy_uncertainty.R: 95.24%
R/splitLogicErrors.R: 95.45%
R/profileInformationIndex.R: 95.65%
R/estimateSoilDepth.R: 95.83%
R/evalMissingData.R: 95.83%
R/get.ml.hz.R: 96.00%
R/SoilProfileCollection-metadata.R: 96.04%
R/colorContrast.R: 96.30%
R/getClosestMunsellChip.R: 96.43%
R/getSoilDepthClass.R: 96.43%
R/soilColorIndices.R: 96.43%
R/lunique.R: 96.55%
R/SoilProfileCollection-iterators.R: 96.97%
R/getCambicBounds.R: 97.01%
R/spec2Munsell.R: 97.14%
R/SoilProfileCollection-integrity.R: 97.30%
R/getArgillicBounds.R: 97.50%
R/spc2mpspline.R: 97.67%
R/fillHzGaps.R: 98.18%
R/getSurfaceHorizonDepth.R: 98.18%
R/checkHzDepthLogic.R: 98.36%

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@dylanbeaudette @brownag