Upload tools search for files even when the files is provided

[kojiromike]

I've been trying to get high quality code coverage reporting on the open source OpenEMR project. The testing workflows for that project are pretty complicated. (Note that OpenEMR only collects coverage on the PHP 8.4 - apache - mariadb 11.4 test configuration to limit the performance hit.)

Before we were using codecov.io, I ran all the different test suites, and used a manual step to collect and combine the coverage reports in a single report, uploading those artifacts to GH. Then I added codecov.io. Since I understand it combines different reports into a comprehensive view, I added individual upload steps for each testsuite, like:

    - name: Upload api test coverage to Codecov
      if: ${{ env.ENABLE_COVERAGE == 'true' && !cancelled() && hashFiles('coverage.api.clover.xml') != '' }}
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: coverage.api.clover.xml
        flags: api,php${{ steps.parse.outputs.php }},${{ steps.parse.outputs.webserver }},${{ steps.parse.outputs.database }}${{ steps.parse.outputs.db }}

This does create a report, but there are a few problems with it. The codecov tool finds all the coverage files from all the previous testsuites in the workflow, even though the files option is there. Consider these logs

==> CLI integrity verified

 -> Token length: 36
==> Running upload-coverage
      ./codecov  upload-coverage -t <redacted> --git-service github --file coverage.controllers.clover.xml --flag controllers --flag php8.4 --flag apache --flag mariadb11.4 --gcov-executable gcov
info - 2025-10-25 21:35:14,209 -- ci service found: github-actions
warning - 2025-10-25 21:35:14,252 -- xcrun is not installed or can't be found.
warning - 2025-10-25 21:35:15,171 -- No gcov data found.
warning - 2025-10-25 21:35:15,172 -- coverage.py is not installed or can't be found.
info - 2025-10-25 21:35:16,259 -- Found 12 coverage files to report
info - 2025-10-25 21:35:16,259 -- > /home/runner/work/openemr/openemr/coverage.fixtures.clover.xml
info - 2025-10-25 21:35:16,259 -- > /home/runner/work/openemr/openemr/coverage.unit.clover.xml
info - 2025-10-25 21:35:16,259 -- > /home/runner/work/openemr/openemr/coverage.services.clover.xml
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage/coverage.controllers.cov
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage/coverage.unit.cov
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage.api.clover.xml
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage/coverage.validators.cov
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage/coverage.fixtures.cov
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage.controllers.clover.xml
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage.validators.clover.xml
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage/coverage.api.cov
info - 2025-10-25 21:35:16,260 -- > /home/runner/work/openemr/openemr/coverage/coverage.services.cov
warning - 2025-10-25 21:35:16,959 -- There was an issue decoding: library/classes/smtp/sasl.php, file fixes were not applied to this file.
info - 2025-10-25 21:35:20,431 -- Your upload is now processing. When finished, results will be available at: https://app.codecov.io/github/openemr/openemr/commit/f8f46908eae992beffad823571b6756562dbc341
info - 2025-10-25 21:35:21,233 -- Process Upload complete

I'm not sure that codecov actually knows how to parse the .cov files, or what it does with duplicates. However, the reports in codecov.io looked mostly OK, but had "Multiple flags detected. Please ensure one flag per upload.".

I thought maybe the issue with that was due to the multiple files, so I attempted to fix that with disable_search: true. When I added that, I kept getting the flags error, but also started getting "Unusable report due to issues such as source code unavailability, path mismatch, empty report, or incorrect data format."

I thought maybe that error was caused by disable_search preventing access to the source code, so I removed disable_search: true and added a complicated process by which each coverage file is renamed to something that codecov.io won't find after reporting it.

Unfortunately, I'm still getting all these errors now, and don't really know which direction to try next. Any guidance will be appreciated.