Automatically apply air formatting by cristinamullin · Pull Request #873 · USEPA/EPATADA

cristinamullin · 2026-03-04T16:42:30Z

Implements using a pre-commit hook to commit format changes before a PR goes to other checks as suggested here:

cristinamullin · 2026-03-04T16:42:52Z

I tested this on my fork and it is running successfully: cristinamullin#4

remove concurrency

cristinamullin · 2026-03-04T17:02:22Z

@jbousquin After closer look, all the workflows are stuck in queued status after the formatting commit is applied. It seems like there is no trigger to start running them on the new commit. Looking into that now.

github-actions · 2026-03-04T17:05:53Z

coverage-report

File	Coverage		Missing
All files	`48%`	✅
R/ATTAINSCrosswalks.R	`24%`	✅	`32-868` `1074-1089` `1093-1097` `1102-1107` `1112` `1118-1131` `1137-1140` `1145-1166` `1177-1192` `1413-1469` `1476-1739` `1923-1935` `1939-1942` `1947` `1975-1978` `1990-1993` `2001-2005` `2021-2025` `2041-2047` `2055-2070` `2075` `2081-2094` `2262-2271` `2276-2286` `2446-2719` `2915-3443` `3597-3616` `3620-3623` `3631-3636` `3642-3662` `3670-3674` `3687-3691` `3722-3832` `3884-4040` `4045-4048` `4055-4198`
R/autoClean.R	`89%`	✅	`152-153` `248-254` `397-398` `403` `413-417`
R/autoFilter.R	`57%`	✅	`31-228` `403-406` `412` `414` `429` `439` `491-504` `532` `623-626`
R/CensoredDataSuite.R	`97%`	✅	`126-127` `143` `311` `642-643` `648` `651`
R/CriteriaComparison.R	`87%`	✅	`173-177` `182` `191-193` `240-265`
R/CriteriaMethods.R	`15%`	✅	`227-238` `242-244` `261-263` `268-270` `275` `287-300` `308-335` `509-513` `529-533` `639-965` `983-1162` `1167-1168` `1196-1245` `1279-1839` `1857-2173`
R/DataDiscoveryRetrieval.R	`32%`	✅	`199` `210-213` `230-233` `246-249` `255` `259` `276-751` `765-767` `775` `777` `782-789` `797` `803` `805` `809` `811` `817` `821` `823` `833` `835` `839` `845` `847` `851` `853` `858` `860` `864` `871-878` `886` `898-916` `927-933` `962-980` `994-1012` `1033` `1130-1161` `1266-1273` `1371-1407` `1500-1503` `1572-1750`
R/DepthProfile.R	`0%`	❌	`102-2033`
R/Figures.R	`0%`	❌	`64-1524`
R/GeospatialFunctions.R	`50%`	✅	`66-70` `198-202` `278-280` `308-310` `334-336` `488` `567-572` `576` `634-636` `642-645` `712-716` `727-732` `738-743` `749-754` `761-765` `812-813` `820-825` `829` `837-1007` `1149-1155` `1162-1444` `1548-1551` `1556-1579` `1624-1627` `1694-1702` `1826-1829` `1874-1878` `1931-1962` `2177-2187` `2234-2244` `2279-2281` `2347` `2351` `2380-2382` `2386` `2390-2415` `2507-2595` `2743-2772` `2899` `2920-3504`
R/GeospatialUtilities.R	`74%`	✅	`108` `132` `189` `194` `290-299` `304-352` `357-381` `470` `499-510` `517-528` `567-577` `658-687` `692` `701-703` `710-724` `747-750` `801` `872-878` `885` `913-928` `1042-1048` `1106` `1276` `1310-1319` `1331-1334` `1446-1448` `1453-1460` `1498-1500` `1545-1547` `1597-1599` `1651-1656` `1739-1748` `1808-1810` `1846`
R/MaintenanceScheduled.R	`0%`	❌	`42-474`
R/Maps.R	`80%`	✅	`128-129` `131` `138` `182-189` `298-302` `382-395` `416-418` `472-592` `752`
R/RequiredCols.R	`30%`	✅	`405-648`
R/ResultFlagsDependent.R	`55%`	✅	`60-62` `67` `110-119` `125-129` `144-151` `254` `291-295` `317-320` `327-330` `346-362` `423` `446-448` `454-455` `461` `509-520` `526-533` `596-599` `611` `623-634` `656-658` `671-677` `748-875` `972-975` `994` `1012-1018` `1027` `1047-1061` `1149-1157` `1164-1171` `1181-1183`
R/ResultFlagsIndependent.R	`70%`	✅	`70-72` `78` `115-119` `129-157` `265-267` `272` `276` `280` `290` `388-391` `403-435` `525-527` `532-534` `543` `671-681` `696-721` `810-812` `817-819` `828` `956-966` `981-1168` `1213` `1235-1254` `1267-1272` `1412` `1416` `1474-1489` `1498-1505` `1569-1570` `1665-1681` `1753-1758` `1879-1893`
R/Tables.R	`86%`	✅	`18-29` `110-117` `125-127`
R/TADAGeospatialRefLayers.R	`0%`	❌	`8-13`
R/TADARefTables.R	`91%`	✅	`75-78` `207-214` `322-324` `386-399` `410` `882-894` `955` `965-967` `972-974` `997-1013` `1027` `1157-1161` `1373-1381`
R/Transformations.R	`60%`	✅	`71-72` `77-79` `110` `139` `153` `176-178` `196-198` `271-280` `302` `307` `449-450` `458-461` `466-469` `474-477` `482-485` `499-502` `569` `683-873` `984-985` `1007-1009` `1040-1051` `1056-1080` `1084-1092`
R/UnitConversions.R	`82%`	✅	`147` `421` `428` `435` `442-444` `451` `458-460` `469-472` `482-484` `634-716` `738-784` `807` `855` `868-882` `1115-1119` `1199` `1276-1279` `1321`
R/Utilities.R	`64%`	✅	`511` `629-630` `634` `639-641` `736` `748-777` `865-876` `1020-1022` `1090-1091` `1145-1149` `1259-1260` `1264-1265` `1275-1279` `1284-1289` `1331-1456` `1597` `1664` `1670-1690` `1716-1717` `1730-1733` `1829-1832` `1859-2174` `2201-2205` `2214-2218` `2435` `2488` `2494-2497` `2501` `2512` `2531-2532` `2534-2549` `2551` `2553` `2555-2556` `2558-2559` `2561-2564` `2566` `2568` `2571` `2586` `2592` `2600` `2605` `2613-2618` `2623-2628` `2647` `2657-2658`
R/WQPWQXATTAINSCSTRefs.R	`67%`	✅	`33` `43` `102` `118` `124` `166` `168-172` `174` `176-178` `180` `192` `201-202` `204` `207-208` `210` `213` `219-257` `270-275` `289-295` `297` `317-391` `417-420` `425` `431` `436` `443` `452-454` `505-516` `539` `554` `556` `559-563` `580` `587-590` `617-621` `696-700` `746` `769-789` `1175-1178` `1189` `1208-1210` `1230` `1260-1302` `1325-1329` `1352-1361` `1374` `1437` `1448` `1477-1490` `1517` `1540-1549` `1574` `1601-1610` `1632-1639` `1660-1669` `1688` `1691-1695` `1714` `1729-1738` `2066-2070` `2093-2102` `2149` `2178-2181` `2183-2219` `2223` `2232` `2238` `2252` `2254` `2265` `2270-2271` `2273` `2292` `2295` `2313` `2318-2331` `2344-2353` `2397-2403` `2408-2424` `2437-2660` `2692` `2706` `2743` `2748` `2764-2831` `2842` `2850-2853` `2874` `2888-2914` `2930` `2966` `2970` `2974` `2980-2990` `2995-3000` `3028` `3031` `3039` `3046` `3059` `3064` `3090` `3149` `3200` `3233` `3251`

Minimum allowed coverage is 10%

Generated by 🐒 cobertura-action against 44839b7

cristinamullin · 2026-03-04T17:44:27Z

This appears to be working correctly now: cristinamullin#8

jbousquin · 2026-03-05T18:49:56Z

If all you are trying to do is use a pre-commit hook to commit format changes before a PR goes to other checks I think you can do that in a much simpler way. See this example PR on my fork:
https://github.com/jbousquin/EPATADA-1/pull/3
Note how my commit just has the pre-commit run on it, and then the pre-commit's commit has all the other checks.
All I changed on fork-develop for that was to add the yml:
develop...jbousquin:EPATADA-1:develop
With this approach I'd recommend getting rid of both format workflows like you did on this PR (unless you want to keep batch air update on manual trigger only so it can be run on a branch outside a PR - but that seems superfluous to me).

As an alternative approach there is the pre-commit/action@v3.0.1.

Update test-coverage.yaml

cristinamullin · 2026-03-12T13:51:43Z

It looks like the current workflows in this PR are working: cristinamullin#20

cristinamullin · 2026-03-13T16:00:48Z

The [pre-commit.ci] auto fixes from pre-commit.com hooks works, but checks are still running on the initial commit and follow up auto-format commit. In this PR, make sure they only run on the follow up auto-format commit (not both commits).

jbousquin · 2026-03-13T16:30:11Z

checks are still running on the initial commit

Is this being observed on a commit to a new PR or only new commits to an existing PR?

cristinamullin · 2026-03-19T14:29:33Z

  pull_request:
-    branches: develop
+    branches: [develop]
+    types: [opened, reopened, synchronize, ready_for_review]


This can always run - it's fast!

cristinamullin · 2026-03-19T14:34:28Z

@@ -1,20 +1,26 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:


Coverage report:

consider full coverage report only on pushes to develop branch?

consider additional coverage report only for scope of PR?

jbousquin · 2026-03-31T14:15:58Z

    steps:
      - uses: actions/checkout@v6
-
+      


added whitespace?

jbousquin · 2026-03-31T14:21:02Z

seems out of scope for this PR - make sure its not reverting a merge conflict

This is a correct updates - but it should have been included in the previous PR merge (needed to run devtools::document() once more there).

cristinamullin added 4 commits March 4, 2026 09:10

Create .pre-commit-config.yaml

f331563

Move to correct location

969a3fd

auto format

543a810

Delete format-auto.yaml

7b5beb2

cristinamullin requested a review from jbousquin March 4, 2026 16:43

Delete format-batch-update.yaml

ed4df03

cristinamullin mentioned this pull request Mar 4, 2026

Make github automated workflows more efficient #846

Closed

Update pkgdown.yaml

2f80d60

remove concurrency

cristinamullin marked this pull request as draft March 4, 2026 17:01

Run on pre-commit.ci autofix commits in PRs; otherwise run on push

15f294b

cristinamullin added 6 commits March 4, 2026 13:01

cancel in process runs

4fc68f0

wait until “pre-commit.ci - pr” check succeeds

9b2662e

Wait for pre-commit workflow

f5803d0

lightweight, cross‑platform wait step using actions/github-script

92c3c5b

do not run on draft PRs

1e46b8d

wait for formatter to succeed

6642761

cristinamullin added 3 commits March 12, 2026 09:43

Update test-coverage.yaml

f5b7abc

Merge pull request #880 from cristinamullin/air-formatting

a82ae27

Update test-coverage.yaml

Merge branch 'develop' into air-formatting

290bb6a

cristinamullin marked this pull request as ready for review March 12, 2026 13:52

Merge branch 'develop' into air-formatting

fee628e

cristinamullin marked this pull request as draft March 12, 2026 18:28

cristinamullin added 2 commits March 12, 2026 15:38

Update pkgdown.yaml

6b8b99d

Update spellcheck-package.yaml

9da0d22

cristinamullin added 3 commits March 12, 2026 15:39

Update test-coverage.yaml

dac6551

Update R-CMD-check.yaml

da6661f

Update spellcheck-package.yaml

a1c6ae9

cristinamullin commented Mar 19, 2026

View reviewed changes

Merge branch 'develop' into air-formatting

99cdefb

cristinamullin marked this pull request as ready for review March 25, 2026 17:58

cristinamullin added 5 commits March 30, 2026 15:03

Merge branch 'develop' into air-formatting

1821210

do not restrict spelling check

5e7e054

Update spellcheck-package.yaml

2fa94bd

Update spellcheck-package.yaml

3e9c13f

Update spellcheck-package.yaml

44839b7

cristinamullin merged commit 8021c69 into develop Mar 31, 2026
8 of 9 checks passed

cristinamullin deleted the air-formatting branch March 31, 2026 13:29

jbousquin reviewed Mar 31, 2026

View reviewed changes

Comment thread .github/workflows/pkgdown.yaml

steps:

- uses: actions/checkout@v6

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added whitespace?

jbousquin reviewed Mar 31, 2026

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