Repository navigation
Coverage: upload with codecov-action (org tokens work); opt-in covr report without Codecov - #37
Merged
Merged
Conversation
covr::codecov() uses Codecov's legacy endpoint, which rejects global upload tokens, so an organization-level CODECOV_TOKEN silently uploaded nothing. Write a Cobertura report with covr and upload it with codecov/codecov-action, installing gpg (missing from the Bioconductor container) for the uploader's signature check. Coverage steps never fail the check, and the uploader's telemetry is off. ADR 0011 (Proposed). Co-authored-by: Claude Code <noreply@anthropic.com>
Opt-in input that computes coverage with covr, saves the covr::report() HTML as the coverage-report artifact, and writes per-file percentages to the run summary. Needs no token, so it also works on fork pull requests. Coverage is computed once when both this and the Codecov upload are on. ADR 0012 (Proposed). Co-authored-by: Claude Code <noreply@anthropic.com>
lwaldron
force-pushed
the
codecov-action-upload
branch
from
October 31, 2026 05:20
7cfa4ea to
f543f29
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Two changes to test coverage in
bioccheck.yml, one commit each so either can be reverted alone.1. Upload coverage with
codecov/codecov-actionso organization tokens work (ADR 0011, Proposed)covr::codecov()uploads to Codecov's legacy endpoint, which rejects an organization's global upload token ("Could not find a repository associated with upload token"). An organization that storesCODECOV_TOKENonce as an organization secret therefore gets no coverage, and because upload errors don't fail the step, runs still look green.covr::to_cobertura()writescoverage.xml, andcodecov/codecov-action@v7uploads it. Repository tokens keep working.continue-on-error, so coverage never fails the package check (as before), and the uploader's telemetry is off.2. New opt-in input
enable_coverage_report(ADR 0012, Proposed)Computes coverage with covr without Codecov: the
covr::report()HTML is saved as thecoverage-reportartifact, and total and per-file percentages go to the run summary. No account or token, so it also works on fork PRs. Coverage is computed once when both options are on. The default path is unchanged: no coverage steps, no coverage packages installed.Docs: Test Coverage section in
bioccheck_usage.md, inputs table, and a generator checkbox.Testing
Run locally with
actinbioconductor/bioconductor_docker:devel(linux/amd64) on a minimal package:covr::codecov()was also re-tested with the same global token and still fails with the 404, which is why the upload method changes. Not testable withact:actions/upload-artifact@v7(its artifact server doesn't support v7); I'll confirm the artifact on GitHub runners before merging. Reviewed by a Gemini review agent; its fixes are included.Drafted with Claude Code.