Some files in coverage report not appearing in Codecov

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[N/A] I have validated my codecov.yaml configuration file.
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Description

Most files in the coverage report are showing up on Codecov, but some aren’t. I can’t see anything to differentiate between the files which are included and those which are not.

CI/CD URL

https://github.com/DeepSenseCA/echofilter/actions/runs/3473069984/jobs/5804670915#step:12:39

Codecov Output


  _____          _
 / ____|        | |
| |     ___   __| | ___  ___ _____   __
| |    / _ \ / _` |/ _ \/ __/ _ \ \ / /
| |___| (_) | (_| |  __/ (_| (_) \ V /
 \_____\___/ \__,_|\___|\___\___/ \_/
                              Bash-1.0.3


==> git version 2.38.1 found
==> curl 7.68.0 (x86_64-pc-linux-gnu) libcurl/7.68.0 OpenSSL/1.1.1f zlib/1.2.11 brotli/1.0.7 libidn2/2.2.0 libpsl/0.21.0 (+libidn2/2.2.0) libssh/0.9.3/openssl/zlib nghttp2/1.40.0 librtmp/2.3
Release-Date: 2020-01-08
Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtmp rtsp scp sftp smb smbs smtp smtps telnet tftp 
Features: AsynchDNS brotli GSS-API HTTP2 HTTPS-proxy IDN IPv6 Kerberos Largefile libz NTLM NTLM_WB PSL SPNEGO SSL TLS-SRP UnixSockets
==> GitHub Actions detected.
    Env vars used:
      -> GITHUB_ACTIONS:    true
      -> GITHUB_HEAD_REF:   
      -> GITHUB_REF:        refs/heads/master
      -> GITHUB_REPOSITORY: DeepSenseCA/echofilter
      -> GITHUB_RUN_ID:     3473069984
      -> GITHUB_SHA:        b1500d1d68a2be962425cf58caafc6c65dbb6ef9
      -> GITHUB_WORKFLOW:   tests
    project root: .
    Yaml not found, that's ok! Learn more at http://docs.codecov.io/docs/codecov-yaml
==> Running gcov in . (disable via -X gcov)
==> Searching for coverage reports in:
    + .
    -> Found 1 reports
==> Detecting git/mercurial file structure
==> Appending build variables
    + OS
    + PYTHON
==> Reading reports
    + ./coverage.xml bytes=282646
==> Appending adjustments
    https://docs.codecov.io/docs/fixing-reports
    -> No adjustments found
==> Gzipping contents
        24K	/tmp/codecov.2U9FEv.gz
==> Uploading reports
    url: https://codecov.io
    query: branch=master&commit=b1500d1d68a2be962425cf58caafc6c65dbb6ef9&build=3473069984&build_url=http%3A%2F%2Fgithub.com%2FDeepSenseCA%2Fechofilter%2Factions%2Fruns%2F3473069984&name=Python%203.7%20on%20Linux&tag=&slug=DeepSenseCA%2Fechofilter&service=github-actions&flags=unittests&pr=&job=tests&cmd_args=n,F,Q,e
->  Pinging Codecov
https://codecov.io/upload/v4?package=github-action-v1.5.2-1.0.3&token=secret&branch=master&commit=b1500d1d68a2be962425cf58caafc6c65dbb6ef9&build=3473069984&build_url=http%3A%2F%2Fgithub.com%2FDeepSenseCA%2Fechofilter%2Factions%2Fruns%2F3473069984&name=Python%203.7%20on%20Linux&tag=&slug=DeepSenseCA%2Fechofilter&service=github-actions&flags=unittests&pr=&job=tests&cmd_args=n,F,Q,e
->  Uploading to
https://storage.googleapis.com/codecov/v4/raw/2022-11-15/7A881893E24344C22A76AD0D417DDD76/b1500d1d68a2be962425cf58caafc6c65dbb6ef9/fc090c95-e495-4850-ac33-54c0b71cbd30.txt?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=GOOG1EJOGFN2JQ4OCTGA2MU5AEIT7OT5Z7HTFOAN2SPG4NWSN2UJYOY5U6LZQ%2F20221115%2FUS%2Fs3%2Faws4_request&X-Amz-Date=20221115T182206Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=3dd5d36d91888072ee6470a91b16e2a0a4d2603f4686a9594bd05ac158b037eb
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 23463    0     0  100 23463      0   101k --:--:-- --:--:-- --:--:--  101k
    -> Reports have been successfully queued for processing at https://app.codecov.io/github/DeepSenseCA/echofilter/commit/b1500d1d68a2be962425cf58caafc6c65dbb6ef9

Expected Results

All files in coverage.xml to appear on Codecov in the file tree.

Actual Results

Only some of the files in coverage.xml appear in the file tree on Codecov.

In particular, you can see files:
echofilter/inference.py
echofilter/utils.py
Appear in the coverage report on GHA: https://github.com/DeepSenseCA/echofilter/actions/runs/3473069984/jobs/5804670915#step:12:39
But these aren’t in the file list on Codecov: Codecov

These files do exist, and aren’t any different from other files in the same directory which are reported on Codecov.
The same files have been consistently dropped from the coverage report on Codecov for every CI run.

Additional Information

The paths to the files in the source are the same as paths in the coverage.xml file. I don’t have a codecov.yaml file, or a setup.cfg file. I’m expecting everything to work out of the box like Codecov previously has for me, and don’t see a reason why it wouldn’t in this case.

2

I resolved the issue by upgrading the GitHub codecov action from v1 to v3, which was discontinued and apparently no longer works. I am surprised that there is no message in the codecov v1 action’s report to indicate it was discontinued.

There was an issue with codecov@v3 not automatically determining the repo identity despite it being a public github repo. (This wasn’t an issue with v1 initially, but started to be an issue when I re-installed the the Codecov GitHub app at the request of the support checklist for this issue. It was in googling that error that I discovered v1 was discontinued.)

To get everything working, I needed to upgrade the action from v1 to v3, and also add my repo’s codecov token to the repo’s secrets and use the token with the codecov action.

The changes were implemented in this PR. https://github.com/DeepSenseCA/echofilter/pull/304

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