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Merged
jbousquin merged 50 commits into from
Dec 18, 2025
Merged

657 bot updates for maintenance tasks #661

jbousquin merged 50 commits into from
Dec 18, 2025

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@jbousquin jbousquin commented Sep 29, 2025 •
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Added maintain.yml and all other file changes are done by bot commits. See issue #657 for links to specific workflow runs and options.

Note: By design this may have merge conflicts because the branch was before a merge that updated reference files to ensure these workflows would bot-update those files.

jbousquin and others added 12 commits September 25, 2025 15:29
@jbousquin
Create maintain.yaml
413056c 
Init commit - anticipate it breaking...
@jbousquin
Update maintain.yaml
d24be95 
Run on push not pull
@jbousquin
Update maintain.yaml
e30826a 
Install via remotes (note this wouldn't be current branch)
@jbousquin
Update maintain.yaml
b2103fc 
Give it token
@github-actions
Update Notebook
edcbc45
@jbousquin
Update maintain.yaml
40d92af 
Edit commit message
@jbousquin
Add example data refresh as additional steps in existing workflow (sh…
353b3b2 
…ould update 5 rda files)
@github-actions
Update reference files
f89f778
@jbousquin
Try adding to namespace using library() again? Otherwise, and/or may …
792e231 
…be better, to specify the lib for each function (e.g., EPATADA::TADA_DataRetrieval).
@jbousquin
Merge branch '657-bot-updates-for-maintenance-tasks' of https://githu…
3d748a1 
…b.com/USEPA/EPATADA into 657-bot-updates-for-maintenance-tasks
@github-actions
Update example data
292db32
@jbousquin
Update maintain.yaml
1c8c265 
Prep for PR
@jbousquin jbousquin linked an issue Sep 29, 2025 that may be closed by this pull request
Bot updates for maintenance tasks #657
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github-actions bot commented Sep 29, 2025 •
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coverage-report

File Coverage Missing
All files 32% ✅
R/ATTAINSCrosswalks.R 24% ✅ 63-873 1081-1096 1100-1104 1109-1114 1119 1125-1145 1151-1154 1159-1183 1194-1209 1262-1265 1444-1502 1509-1767 1953-1965 1969-1972 1977-1979 2007-2010 2025-2028 2036-2040 2056-2060 2076-2082 2090-2105 2110 2116-2129 2149-2152 2310-2319 2324-2334 2497-2775 2961-3506 3646-3665 3669-3672 3681-3694 3701-3721 3729-3733 3746-3750 3781-3891 3943-4089 4094-4097 4104-4253
R/ATTAINSRefTables.R 0% ❌ 24-637
R/autoClean.R 89% ✅ 152-153 247-253 415-416 426-430
R/autoFilter.R 0% ❌ 31-493
R/CensoredDataSuite.R 86% ✅ 52-53 142 182-183 255-261 380-388 501-502 507-509 512-514 522 569-576 579-580 586-591 608-610
R/CriteriaComparison.R 87% ✅ 175-179 184 194-196 243-268
R/CriteriaMethods.R 17% ✅ 161-234 238-240 257-259 264-266 271-273 283-296 333-360 527-531 547-551 729-924 930-1037 1071-1678 1696-2011
R/CriteriaRefTables.R 0% ❌ 22-198
R/DataDiscoveryRetrieval.R 33% ✅ 199 210-215 232-237 250-255 261 265 282-752 766-768 776 778 783-790 798 804 806 810 812 818 822 824 834 836 840 846 848 852 854 859 861 865 872-879 887 899-913 926-932 963-977 991-1005 1026 1129-1163 1268-1275 1377-1417 1510-1513 1582-1760
R/DepthProfile.R 0% ❌ 102-2052
R/Figures.R 0% ❌ 64-1559
R/GeospatialFunctions.R 15% ✅ 114-118 193-195 223-225 287-291 317 352-583 603-605 731-1278 1464-1470 1477-2413 2504 2606 2633-3177 3351-4604
R/MaintenanceScheduled.R 0% ❌ 42-448
R/Maps.R 0% ❌ 26-495
R/RequiredCols.R 20% ✅ 391-638
R/ResultFlagsDependent.R 56% ✅ 60-62 67 112-121 146-153 256 297-301 323-329 336-339 355-371 436 459-461 467-468 474 522-533 539-546 609-612 624 640-651 676-678 691-697 768-895 964-967 1012 1079-1091 1115-1117 1121-1123 1129-1138
R/ResultFlagsIndependent.R 63% ✅ 70-72 78 127-161 269-271 276 280 284 294 393-396 408-440 530-532 537-539 548 669-687 702-727 816-818 823-825 834 955-973 988-1175 1220 1242-1261 1274-1279 1382 1386 1444-1459 1464 1468-1475 1539-1540 1635-1722 1850-1864
R/Tables.R 84% ✅ 19-30 92-94
R/TADAGeospatialRefLayers.R 0% ❌ 8-13
R/TADARefTables.R 85% ✅ 86-88 105-111
R/Transformations.R 86% ✅ 76-77 82-84 220-231 397-398 447-450 542 815 845-860 947-948 965 996-1007 1010-1027 1031-1039
R/UnitConversions.R 82% ✅ 148 426 433 440 447-449 456 463-465 474-477 487-488 645-728 751-800 823 871 884-898 1131-1135 1215 1292-1295 1337
R/Utilities.R 54% ✅ 12-16 478 596-597 601 606-608 703 832-843 904-905 912 997-998 1029-1033 1138-1139 1143-1144 1154-1158 1163-1168 1210-1545 1571-1572 1585-1588 1659-2082 2283-2352
R/WQPWQXRefTables.R 67% ✅ 21-95 119 131 137-143 154-158 180 192 198-206 286-290 312 324 330-336 431-435 456 468 474-480 626-630 652 664 670-676 696-700 723 735 741-747 1067-1297

Minimum allowed coverage is 10%

Generated by 🐒 cobertura-action against 32a4184

cristinamullin
cristinamullin reviewed Sep 29, 2025
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@jbousquin
Resolve reviewer comment
79bdc52 
Should install EPATADA depends not shiny
@jbousquin
Update maintain.yaml
df1286f 
This may or may not address issue of commit not being on a branch
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jbousquin commented Sep 30, 2025

actions/checkout@v4 should be checking out the 'develop' branch, not sure why it is finding itself in a detached head state. Possible because merging is blocked? I'll try being more direct with what to checkout.

jbousquin and others added 3 commits September 30, 2025 09:24
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jbousquin commented Sep 30, 2025 •
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Running this on a PR works, hoping once this is merged scheduled runs do most of the work. FYI on timing and current sticking point:

  • On initiation of the PR and subsequent commits it'll run the updates at the same time as tests.
  • If no changes it'll run checks just like normal.
  • If it finds changes to make it'll bot-commit those to the PR.
    The current sticking point is for it to re-run checks after the bot-commit. github recognizes the default github_token the workflow is set up with and ignores the new commit for CI runs. It does that to avoid circular CI (where a check would commit, cause itself to run again, etc.). Ideally we want it to run checks only after the workflow completes and not re-run itself. If we have to use a token I'd rather it be at the repo level not associated with a specific admin user.

jbousquin and others added 7 commits September 30, 2025 10:53
@jbousquin
Add checks as part of commit
a86a255
@github-actions
Update example data
5a30497 
request-checks: true
@jbousquin
revert maintain.yaml
e166253
@jbousquin
Update maintain.yaml
53c8523 
Try granting read permissions instead of using token
@jbousquin
Update maintain.yaml
b83cd35 
Try adding token at a lower level instead of adding it to env
@jbousquin
Update maintain.yaml
df7bf5a 
Not sure how to get token for step not using action. Moved token up to checkout but suspect that will either not make it available to other steps or still skip CI.
@jbousquin
Update maintain.yaml
cd75520 
quick fix
cristinamullin
cristinamullin reviewed Oct 3, 2025
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@jbousquin jbousquin marked this pull request as draft October 3, 2025 17:53
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jbousquin commented Oct 10, 2025

On a PR in another repo (harmonize-wq) I was able to confirm even if the token is not specified as part of checkout it still just commits changes without re-running checks after (specific commit).

What to try next:

  1. Figure out as pre-commit for format/lint (new issue Pre-commit formatting/linting #674), and then see if that approach is a viable solution here
  2. Add action to hold checks until after commit
  3. Set up a bot token to get it to still run the checks

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cristinamullin commented Dec 17, 2025

@jbousquin what are your thoughts on next steps for this PR? I wonder if might be best to set it up similar to format-batch-update.yaml for now? Then it could be run on a branch as needed. I think that alone might save us a lot of time.

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jbousquin commented Dec 17, 2025

You can manually trigger maintenance-scheduled.yaml on your branch/PR to accomplish similar but I think that would commit the change to the maintenance-branch instead. Will play around with/put some thought into that. Also OK with closing this PR if we're happy with just the maintenance bot.

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jbousquin commented Dec 18, 2025 •
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Updating this to run manually on branch before PR (like format-update).

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jbousquin commented Dec 18, 2025

Updating scheduled to no longer run manually (help keep it clear what to run when)

@jbousquin
Update maintenance-scheduled.yaml
1fa4933 
Run on schedule only (differentiate from Component File Update)
@jbousquin jbousquin marked this pull request as ready for review December 18, 2025 17:18
@jbousquin jbousquin mentioned this pull request Dec 18, 2025
Merged
@jbousquin jbousquin merged commit b63261a into develop Dec 18, 2025
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@jbousquin jbousquin deleted the 657-bot-updates-for-maintenance-tasks branch December 18, 2025 21:23
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Bot updates for maintenance tasks

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