False positive — CodeQL failing due to lack of Python files when they only exist on the `main` branch

[andrzej-pomirski-yohana]

Description of the false positive

Hi, I encountered a weird issue with CodeQL. My pull request is based on a slightly older version of the codebase, which did not have any Python files. However, there is now a single Python file in main. CodeQL runs, but fails due to lack of Python files, which blocks a perfectly valid PR.

Unfortunately, the code is private, so I am not able to share the repository, but the main branch contains a Python script in scripts/, while the PR version of the codebase doesn't.

The exact error is

 /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/codeql database finalize --finalize-dataset --threads=2 --ram=6920 /home/runner/work/_temp/codeql_databases/python
  CodeQL detected code written in C/C++, Swift, GitHub Actions and Java/Kotlin, but not any written in Python. Confirm that there is some source code for Python in the project. For more information, review our troubleshooting guide at https://gh.io/troubleshooting-code-scanning/no-source-code-seen-during-build .
  Error: Encountered a fatal error while running "/opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/codeql database finalize --finalize-dataset --threads=2 --ram=6920 /home/runner/work/_temp/codeql_databases/python". Exit code was 32 and last log line was: CodeQL detected code written in C/C++, Swift, GitHub Actions and Java/Kotlin, but not any written in Python. Confirm that there is some source code for Python in the project. For more information, review our troubleshooting guide at https://gh.io/troubleshooting-code-scanning/no-source-code-seen-during-build . See the logs for more details.

I don't believe that CodeQL should be configured to run on file types that do not exist on a given branch. This can be fixed in a pretty simple way — rebasing the branch on top of HEAD, but still, I don't believe this should be a cause for failure in the first place.

[d10c]

Hi @andrzej-pomirski-yohana 👋🏻 Thanks for creating the issue. This looks like a bug. Would you be able to share the full log up to that error?

[andrzej-pomirski-yohana]

Hi, here's the log (AI-anonymised) from the Python action. Do you want the root-level log as well?

github_actions_log_anonymized.txt

[d10c]

Thanks. After looking into it, it looks like this is the standard behaviour at the moment. The set of languages is configured for each repository as a whole.

If we're not detecting the right set of languages from the default branch, the recommendation is to configure the right languages - either in Advanced Setup (by modifying the workflow file with a matrix of single-language jobs), or in Default Setup (by selecting the right languages in the UI.)

I realize it's not ideal for repos that differ widely in languages per branch, so it may change if we see more reports like this.