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Increase package test coverage #120

Merged
merged 4 commits into from Apr 24, 2024
Merged

Increase package test coverage #120

merged 4 commits into from Apr 24, 2024

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scheidec
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  • added unit tests for getSomaScanLiftCCC(), parseCheck() and release utilities which were previously untested
  • increased overall package test coverage from 70.87% to 82.98%
  • new covr::package_coverage() is:
SomaDataIO Coverage: 82.98%
===============================
R/parseCheck.R: 52.69%
R/utils-read-adat.R: 59.03%
R/groupGenerics.R: 63.04%
R/read-annotations.R: 64.29%
R/zzz.R: 71.74%
R/s3-print-soma-adat.R: 73.21%
======== 75% ===============
R/pivotExpressionSet.R: 76.47%
R/s3-transform.R: 77.78%
R/syncColMeta.R: 77.78%
R/prepHeaderMeta.R: 78.18%
R/utils-lift.R: 80.00%
R/adat2eSet.R: 83.72%
R/rownames.R: 83.87%
R/utils-release.R: 85.23%
R/is-intact-attr.R: 85.37%
R/utils.R: 87.50%
R/write-adat.R: 88.12%
======== 90% =========
R/diffAdats.R: 90.57%
R/getMeta.R: 90.91%
R/loadAdatsAsList.R: 91.67%
R/read-adat.R: 93.88%
R/getAnalytes.R: 94.12%
R/parseHeader.R: 96.15%
R/lift-adat.R: 97.06%
R/adat-helpers.R: 100.00%
R/addAttributes.R: 100.00%
R/addClass.R: 100.00%
R/cleanNames.R: 100.00%
R/convertColMeta.R: 100.00%
R/dplyr-verbs.R: 100.00%
R/genRowNames.R: 100.00%
R/getAnalyteInfo.R: 100.00%
R/getSomaScanLiftCCC.R: 100.00%
R/getTargetNames.R: 100.00%
R/is-seqFormat.R: 100.00%
R/matchSeqIds.R: 100.00%
R/merge-clin.R: 100.00%
R/s3-merge-soma-adat.R: 100.00%
R/s3-soma-adat.R: 100.00%
R/s3-summary-soma-adat.R: 100.00%
R/scaleAnalytes.R: 100.00%
R/SeqId.R: 100.00%
R/tidyr-verbs.R: 100.00%

@scheidec
Increase package test coverage
9496eea 
- added unit tests for getSomaScanLiftCCC(),
  parseCheck() and release utilities which
  were previously untested
- increased overall package test coverage
  from 70.87% to 82.98%
- closes SomaLogic#112
@scheidec scheidec requested a review from stufield April 18, 2024 16:45
@stufield
Update read_annotations() example
09ccf4f 
- docs now point to the most recent 11k Excel
  annotations file
@stufield
Add more corner case unit tests
ffe49f8 
- closes SomaLogic#112
@stufield
Fixed bug in Summary.soma_adat() operations
895f3ca 
- these operations: min(), max(), any(), range(), etc.
- would return the incorrect value due to
  an `as.matrix()` conversion under the hood
- now skips that conversion, trips a warning,
  and carries on
- triggers an error of non-numerics are passed
  as part of the '...' outside of a `soma_adat`,
  just like `Summary.data.frame()`
- fixes SomaLogic#121
@stufield
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Contributor

New total package coverage after this PR:

SomaDataIO Coverage: 90.14%
========================
R/parseCheck.R: 52.69%
======== 75% ============
R/syncColMeta.R: 77.78%
R/prepHeaderMeta.R: 78.18%
R/utils-lift.R: 80.00%
R/rownames.R: 83.87%
R/utils-release.R: 85.23%
R/is-intact-attr.R: 85.37%
R/utils.R: 87.50%
R/read-annotations.R: 88.10%
R/write-adat.R: 88.12%
======== 90% ============
R/diffAdats.R: 90.57%
R/getMeta.R: 90.91%
R/loadAdatsAsList.R: 91.67%
R/adat2eSet.R: 92.31%
R/read-adat.R: 93.88%
R/getAnalytes.R: 94.12%
R/parseHeader.R: 96.15%
R/lift-adat.R: 97.06%
R/adat-helpers.R: 100.00%
R/addAttributes.R: 100.00%
R/addClass.R: 100.00%
R/cleanNames.R: 100.00%
R/convertColMeta.R: 100.00%
R/dplyr-verbs.R: 100.00%
R/genRowNames.R: 100.00%
R/getAnalyteInfo.R: 100.00%
R/getSomaScanLiftCCC.R: 100.00%
R/getTargetNames.R: 100.00%
R/groupGenerics.R: 100.00%
R/is-seqFormat.R: 100.00%
R/matchSeqIds.R: 100.00%
R/merge-clin.R: 100.00%
R/pivotExpressionSet.R: 100.00%
R/s3-merge-soma-adat.R: 100.00%
R/s3-print-soma-adat.R: 100.00%
R/s3-soma-adat.R: 100.00%
R/s3-summary-soma-adat.R: 100.00%
R/s3-transform.R: 100.00%
R/scaleAnalytes.R: 100.00%
R/SeqId.R: 100.00%
R/tidyr-verbs.R: 100.00%
R/utils-read-adat.R: 100.00%
R/zzz.R: 100.00%

@stufield stufield merged commit bda55a1 into SomaLogic:main Apr 24, 2024
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@stufield stufield stufield approved these changes

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Increase package test coverage
2 participants
@scheidec @stufield