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Merged
cristinamullin merged 10 commits into from
Sep 25, 2025
Merged

632 leverage coverage in pr review #656

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ca9d68e
Update test-coverage.yaml
jbousquin Aug 15, 2025
19fb73b
Update test-coverage.yaml
jbousquin Aug 15, 2025
8485aca
Update test-coverage.yaml
jbousquin Aug 15, 2025
35326b8
Update test-coverage.yaml
jbousquin Aug 15, 2025
b0e440e
Update test-coverage.yaml
jbousquin Aug 26, 2025
4b43e11
Merge pull request #650 from USEPA/develop
jbousquin Aug 26, 2025
7f0319b
Update test-coverage.yaml
jbousquin Sep 23, 2025
52316ec
Merge remote-tracking branch 'origin/develop' into 632-leverage-cover…
jbousquin Sep 24, 2025
f273029
update WQX refs
cristinamullin Sep 25, 2025
705e47b
Update test-coverage.yaml
jbousquin Sep 25, 2025
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26 changes: 24 additions & 2 deletions .github/workflows/test-coverage.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,11 @@ on:

name: test-coverage

permissions:
contents: write
checks: write
pull-requests: write

jobs:
test-coverage:
runs-on: ubuntu-latest
Expand All @@ -23,16 +28,18 @@ jobs:

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::covr
extra-packages: any::covr, any::xml2
needs: coverage

- name: Test coverage
run: |
covr::codecov(
cov <- covr::package_coverage(
quiet = FALSE,
clean = FALSE,
install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
)
print(cov)
covr::to_cobertura(cov)
shell: Rscript {0}

- name: Show testthat output
Expand All @@ -49,3 +56,18 @@ jobs:
name: coverage-test-failures
path: ${{ runner.temp }}/package
if-no-files-found: ignore # Suppress warnings if no files are found

- name: Upload coverage report
uses: actions/upload-artifact@v4
with:
name: coverage-report
path: ./cobertura.xml

- name: Comment coverage
uses: 5monkeys/cobertura-action@master
with:
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Collaborator Author

@jbousquin jbousquin Sep 25, 2025 •
edited
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Add/update with inputs to this part of workflow if you want to change what is included in coverage comment (e.g., only_changed_files if you only want coverage for files changed by the PR)

report_name: coverage-report
path: ./cobertura.xml
minimum_coverage: 10
show_missing: true
link_missing_lines: true
2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -44,7 +44,7 @@ Copyright: This software is in the public domain because it contains materials
that originally came from the U.S. Environmental Protection Agency.
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
RoxygenNote: 7.3.3
Imports:
plyr,
data.table,
Expand Down
32 changes: 20 additions & 12 deletions inst/extdata/WQXCharacteristicRef.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -522,7 +522,6 @@
"(Z)-Octadec-9-enyl (5-(((2-(((perfluorooctyl)sulphonyl)methylamino)ethoxy)carbonyl)amino)-o-tolyl)carbamate","Accepted",""
"(Z,Z)-11,13-Hexadecadienal","Accepted",""
"({4-[(1,2,3,3,4,4,5,5,6,6,6-Undecafluorohex-1-en-1-yl)oxy]phenyl}methyl)phosphonic acid","Accepted",""
"****renamed","Accepted",""
".alpha.,.alpha.-Dimethylphenethylamine","Accepted",""
".alpha.,2,6-Trichlorotoluene","Accepted",""
".alpha.-1,2,3,4,5,6-Hexachlorocyclohexane-D6 or alpha-HCH D6","Accepted",""
Expand Down Expand Up @@ -1784,7 +1783,7 @@
"1,2-Dichloro-4-(trifluoromethyl)benzene","Accepted",""
"1,2-Dichloro-4-iodoperfluorobutane","Accepted",""
"1,2-Dichlorobenzene-d4","Accepted",""
"1,2-Dichlorobenzene/1,4-dichlorobenzene","Accepted",""
"1,2-Dichlorobenzene/1,4-dichlorobenzene***retired***use Benzene, 1,2(or 1,4)-dichloro-","Deprecated",""
"1,2-Dichlorobutane","Accepted",""
"1,2-Dichlorodecafluorocyclohexane","Accepted",""
"1,2-Dichloroethane","Accepted",""
Expand Down Expand Up @@ -5172,6 +5171,7 @@
"2-(4-Bromophenoxy)-1,1,2,2-tetrafluoroethane-1-sulfonyl fluoride","Accepted",""
"2-(4-Octylphenoxy)ethanol","Accepted",""
"2-(4-Trimethylammoniophenyl)perfluoro(4-methyl-3-(propan-2-yl)pent-2-ene) iodide","Accepted",""
"2-(4-morpholinyl)-benzothiazole","Accepted",""
"2-(4H-Perfluorobutyl)-2-propanol","Accepted",""
"2-(5,5,7,7,8,8,10,10,11,11,13,13,14,14,15,15,16,16,16-Nonadecafluoro-2-oxo-3,6,9,12-tetraoxa-1-azahexadecan-1-yl)ethyl 2-methylprop-2-enoate","Accepted",""
"2-(5,5,7,7,8,8,10,10,11,11,13,13,14,14,16,16,17,17,18,18,19,19,19-Tricosafluoro-2-oxo-3,6,9,12,15-pentaoxa-1-azanonadecan-1-yl)ethyl 2-methylprop-2-enoate","Accepted",""
Expand Down Expand Up @@ -7978,7 +7978,7 @@
"4,6-Dinitro-o-cresol","Accepted",""
"4,7-Dimethylindan","Accepted",""
"4,7-Dimethylundecane","Accepted",""
"4,7-Methanoisobenzofuran, 4,5,6,7,8,8-hexachloro-1,3,3a,4,7,7a-hexahydro-","Accepted",""
"4,7-Methanoisobenzofuran, 4,5,6,7,8,8-hexachloro-1,3,3a,4,7,7a-hexahydro-****retired***use Endosulfan ether","Deprecated",""
"4,7-Methanoisobenzofuran-1,3-dione, 3a,4,7,7a-tetrahydro-5-methyl-, reaction products with hexahydro-1,3-isobenzofurandi","Accepted",""
"4,7-Methanoisobenzofuran-1,3-dione, 3a,4,7,7a-tetrahydro-5-methyl-, reaction products with hexahydro-1,3-isobenzofurandione and 2,2,3,3-tetrafluoro-1-propanol","Accepted",""
"4,7-Methanoisobenzofuran-1,3-dione, hexahydro-, 5-[(.gamma.-.omega.-perfluoro-C8-20-alkyl)thio] derivs.","Accepted",""
Expand Down Expand Up @@ -8279,7 +8279,6 @@
"4-Hydroxy molinate","Accepted",""
"4-Hydroxy-3-(hydroxyimino)-4-(nonafluorobutyl)-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one","Accepted",""
"4-Hydroxy-4-methyl-2-pentanone","Accepted",""
"4-Hydroxy-chlorothalonil","Accepted",""
"4-Hydroxy-tert-fluometuron","Accepted",""
"4-Hydroxybenzophenone","Accepted",""
"4-Hydroxybenzotriazole","Accepted",""
Expand Down Expand Up @@ -8345,7 +8344,7 @@
"4-Nonylphenol hexadecaethoxylates","Accepted",""
"4-Nonylphenol hexaethoxylate","Accepted",""
"4-Nonylphenol hexaethoxylates","Accepted",""
"4-Nonylphenol monoethoxylates","Accepted",""
"4-Nonylphenol monoethoxylates***retired***use Ethanol, 2-(4-nonylphenoxy)-","Deprecated",""
"4-Nonylphenol nonaethoxylate","Accepted",""
"4-Nonylphenol nonaethoxylates","Accepted",""
"4-Nonylphenol octadecaethoxylate","Accepted",""
Expand Down Expand Up @@ -8777,6 +8776,7 @@
"5-alpha-Dihydrotestosterone","Accepted",""
"5-bromo-4,4,5,5-tetrafluoropentan-1-ol","Accepted",""
"5-fluoro-2-methyl-6-(pentafluoroethyl)pyrimidin-4(1h)-one","Accepted",""
"5-methyl-1-H-benzotriazole","Accepted",""
"5-methylbenzotriazole***retired***use 5-Tolyltriazole","Deprecated","5-TOLYLTRIAZOLE"
"5-tert-Butyl-7-(heptafluoropropyl)-2-phenylpyrazolo[1,5-a]pyrimidine","Accepted",""
"5-{[(3,3,4,4,5,5,6,6,7,7,8,8,8-Tridecafluorooctyl)oxy]methyl}-1H-1,2,3-triazole","Accepted",""
Expand Down Expand Up @@ -12550,6 +12550,8 @@
"Depth of pond or reservoir in feet","Accepted",""
"Depth of water column","Accepted",""
"Depth to Ground from Casing Rim","Accepted",""
"Depth to Water (from bottom of meter box)","Accepted",""
"Depth to Water (from shutoff valve)","Accepted",""
"Depth to bottom of sample interval","Accepted",""
"Depth to top of sample interval","Accepted",""
"Depth to water from rim of well casing","Accepted",""
Expand Down Expand Up @@ -13736,6 +13738,7 @@
"Extract volume","Accepted",""
"Extractable fuel hydrocarbons (C13-C22 DRO)","Accepted",""
"Extractable hydrocarbons","Accepted",""
"Extractable hydrocarbons, C8 and up","Accepted",""
"Extractable organic matter (EOM)","Accepted","Organic matter"
"Ezetimibe","Accepted",""
"Ezetimibe-d4","Accepted",""
Expand Down Expand Up @@ -14801,7 +14804,6 @@
"Imidacloprid desnitro","Accepted",""
"Imidacloprid desnitro-olefin","Accepted",""
"Imidacloprid desnitro-olefin hydrochloride","Accepted",""
"Imidacloprid urea","Accepted",""
"Imidacloprid-d4","Accepted",""
"Imidacloprid-olefin","Accepted",""
"Imidacloprid-urea","Accepted",""
Expand Down Expand Up @@ -14856,6 +14858,7 @@
"Initial Void Ratio","Accepted",""
"Initial sample volume","Accepted",""
"Inorganic antimony(III)","Accepted",""
"Inorganic arsenic (arsenate and arsenite)","Accepted",""
"Inorganic carbon","Accepted",""
"Inorganic fraction","Accepted",""
"Inorganic monomeric aluminum","Accepted",""
Expand Down Expand Up @@ -15035,7 +15038,7 @@
"Isoxaben","Accepted",""
"Isoxadifen-ethyl","Accepted",""
"Isoxaflutole","Accepted",""
"Isoxaflutole acid RPA 203328","Accepted",""
"Isoxaflutole acid RPA 203328***retired***use 2-(Methylsulfonyl)-4-(trifluoromethyl)benzoic acid","Deprecated",""
"Isoxaflutole acid metabolite","Accepted",""
"Isoxaflutole methylbenzoate","Accepted",""
"Ivermectin","Accepted",""
Expand Down Expand Up @@ -15599,6 +15602,7 @@
"Methane, (difluoromethoxy)trifluoro-","Accepted",""
"Methane, 1,1'-oxybis[1,1,1-trifluoro-","Accepted",""
"Methane, bis(difluoromethoxy)difluoro-","Accepted",""
"Methane, bis[(trifluoromethyl)sulfonyl]-","Accepted",""
"Methane, bromodichloronitro-","Accepted",""
"Methane, bromodiiodo-","Accepted",""
"Methane, chloro(difluoromethoxy)difluoro-","Accepted",""
Expand Down Expand Up @@ -15911,6 +15915,7 @@
"Methylperfluoro-2,5,8-trimethyl-3,6,9-trioxadodecanoic acid","Accepted",""
"Methylphenanthrene","Accepted",""
"Methylphenidate","Accepted",""
"Methylphosphinicopropionic acid","Accepted",""
"Methylprednisolone***retired***use Pregna-1,4-diene-3,20-dione, 11,17,21-trihydroxy-6-methyl-, (6.alpha.,11.beta.)-","Deprecated","PREGNA-1,4-DIENE-3,20-DIONE, 11,17,21-TRIHYDROXY-6-METHYL-, (6.ALPHA.,11.BETA.)-"
"Methylprednisolone-d3","Accepted",""
"Methylpyridine","Accepted",""
Expand Down Expand Up @@ -16730,6 +16735,7 @@
"N-[8-(Heptafluoropropyl)-9H-purin-6-yl]acetamide","Accepted",""
"N-[[3-[[(Perfluorooctyl)sulfonyl](propyl)amino]propyl]sulfonyl]-2-hydroxy-N,N-dimethylethanaminium chloride","Accepted",""
"N-[[4-[(Heptadecafluorononenyl)oxy]phenyl]sulfonyl]-N-methylglycine sodium salt","Accepted",""
"N-cyclohexyl-1.3-benzothiazole-2-amine","Accepted",""
"N-ethyl Perfluorooctane sulfonamide****retired***use Sulfluramid","Deprecated",""
"N-ethyl Perfluorooctane sulfonamide***retired***use Sulfluramid","Deprecated",""
"N-ethyl perfluoro-1-octanesulfonamide","Accepted",""
Expand Down Expand Up @@ -17012,7 +17018,7 @@
"Nonylphenol, diethoxy- (total, NPEO2)","Accepted",""
"Nonylphenol, diethoxylate- (total, NPEO2)","Accepted",""
"Nonylphenol, monoethoxy- (total NPEO1)","Accepted",""
"Nonylphenoxyacetic acid","Accepted",""
"Nonylphenoxyacetic acid***retired***use Acetic acid, 2-(4-nonylphenoxy)-","Accepted",""
"Norbuprenorphine","Accepted",""
"Norcarfentanil","Accepted",""
"Norcarfentanil (hydrochloride)","Accepted",""
Expand Down Expand Up @@ -17091,7 +17097,6 @@
"O-Ethyl S-methyl S-propyl phosphorodithioate","Accepted",""
"O-Ethyl S-propyl phosphorothioate","Accepted",""
"O-Ethyl-S-methyl-S-propyl phosphorodithioate","Accepted",""
"O-Ethyl-S-propyl phosphorothioate","Accepted",""
"O-xylene & N-nonane","Accepted",""
"Observed Recreational Use - Boating (Y/N) (choice list)","Accepted",""
"Observed Recreational Use - Fishing (Y/N) (choice list)","Accepted",""
Expand Down Expand Up @@ -18205,6 +18210,7 @@
"Perfluoro-4-(2-sulfoethoxy)pentanoic acid","Accepted",""
"Perfluoro-4-(pentafluoro-omega6-sulfanyl)butanoic acid","Accepted",""
"Perfluoro-4-butylcyclopentane-1-carboxylic acid","Accepted",""
"Perfluoro-4-ethenyloxybutane-1-sulfonic acid","Accepted",""
"Perfluoro-4-ethylcyclopentane-1-carboxylic acid","Accepted",""
"Perfluoro-4-ethylhexanoic acid","Accepted",""
"Perfluoro-4-hexene-1-sulfonic acid","Accepted",""
Expand Down Expand Up @@ -19831,6 +19837,7 @@
"Protactinium-234m","Accepted",""
"Protanypus","Accepted",""
"Prothioconazole","Accepted",""
"Prothioconazole-desthio","Accepted",""
"Prothiofos","Accepted",""
"Protoaricia","Accepted",""
"Protohydra","Accepted",""
Expand Down Expand Up @@ -21333,16 +21340,16 @@
"Tebuconazole tert-Butylhydroxy","Accepted",""
"Tebuconazole-d6","Accepted",""
"Tebufenozide","Accepted",""
"Tebupirimfos","Accepted",""
"Tebupirimfos oxon","Accepted",""
"Tebupirimfos***retired***use Phostebupirim","Deprecated",""
"Tebupirimphos oxon","Accepted",""
"Tebuthiuron","Accepted",""
"Tebuthiuron TP 104","Accepted",""
"Tebuthiuron TP 106","Accepted",""
"Tebuthiuron TP 108","Accepted",""
"Tebuthiuron TP 109 (OH)","Accepted",""
"Tebuthiuron Transformation Product 108","Accepted",""
"Tebuthiuron Transformation Product 109","Accepted",""
"Tebuthiuron Transformation Product 109***retired***use Hydroxytebuthiuron","Deprecated",""
"Technetium","Accepted",""
"Technetium-99","Accepted",""
"Technitium-99","Accepted",""
Expand Down Expand Up @@ -22105,6 +22112,7 @@
"Tripropyltin chloride","Accepted",""
"Tripylidae","Accepted",""
"Tris((perfluorohexyl)ethyl)stannane","Accepted",""
"Tris((trifluoromethyl)sulfonyl)methane","Accepted",""
"Tris(1,1,1,2,3,3-hexafluoropropan-2-yl) borate","Accepted",""
"Tris(1,1,2,2,2-pentafluoroethyl) phosphate","Accepted",""
"Tris(1,3-dichloro-2-propyl) Phosphate-d15","Accepted",""
Expand Down Expand Up @@ -22883,7 +22891,7 @@
"o,p-DDD","Accepted",""
"o,p-DDE","Accepted",""
"o,p-DDT","Accepted",""
"o,p-xylene","Accepted",""
"o,p-xylene***retired***use ortho & para Xylene mix","Accepted",""
"o-Anisidine","Accepted",""
"o-Chloroaniline","Accepted",""
"o-Chloronitrobenzene","Accepted",""
Expand Down
2 changes: 2 additions & 0 deletions inst/extdata/WQXMeasureQualifierCodeRef.csv
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Expand Up @@ -147,6 +147,8 @@
"Result Measure Qualifier(MeasureQualifierCode)",162,"JCW","Sample Container Damaged, sample lost","3/16/2016 1:04:25 PM","Suspect"
"Result Measure Qualifier(MeasureQualifierCode)",66,"K","Value below the detection Limit. For BOD: depletion is less than 1.0","8/22/2013 1:44:00 PM","Non-Detect"
"Result Measure Qualifier(MeasureQualifierCode)",608,"K10","Initial Dissolved Oxygen (DO) or temperature conditions of BOD, or Biochemical Oxygen Demand sample unacceptable","7/10/2025 2:35:46 PM","Not Reviewed"
"Result Measure Qualifier(MeasureQualifierCode)",609,"K11","All dilutions result in residual D.O. <1 mg/L","9/15/2025 11:26:05 AM","Not Reviewed"
"Result Measure Qualifier(MeasureQualifierCode)",610,"K12","Test replicates show >30% difference between high and low values","9/15/2025 11:26:05 AM","Not Reviewed"
"Result Measure Qualifier(MeasureQualifierCode)",1198,"K5","The dilution water D.O. depletion was > 0.2 mg/L","8/1/2024 7:33:52 PM","Not Reviewed"
"Result Measure Qualifier(MeasureQualifierCode)",1197,"K6","Glucose/glutamic acid BOD was below method acceptance criteria","8/1/2024 7:33:52 PM","Not Reviewed"
"Result Measure Qualifier(MeasureQualifierCode)",604,"K7","GGA Average not within 198 +/- 30.5 (167.5-228.5 mg/L)","7/10/2025 2:35:46 PM","Not Reviewed"
Expand Down
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