panic macro prefix

[pflanze]

Summary

gtest has an ASSERT_EQ macro just like panic.h, and maybe there are more clashes. They weren't a problem at first, but with the command line parsing changes some tests now include panic.h and fail. Solve it once and for all by prefixing all the macro names.

PR Checklist

• All necessary documentation has been adapted or there is an issue to do so.
• The implemented feature is covered by an appropriate test. (Existing tests.)

[Taepper]

Note that the linter error is a false positive caused by the downgrade of clang-tidy

[fengelniederhammer]

The tests don't build yet:
/src/src/silo/common/panic.test.cpp:113:4: error: ‘DEBUG_ASSERT_GE’ was not declared in this scope; did you mean ‘SILO_DEBUG_ASSERT_GE’?

Is this intentionally a draft PR? Or is it actually ready for review?

[pflanze]

The tests don't build yet: /src/src/silo/common/panic.test.cpp:113:4: error: ‘DEBUG_ASSERT_GE’ was not declared in this scope; did you mean ‘SILO_DEBUG_ASSERT_GE’?

Is this intentionally a draft PR? Or is it actually ready for review?

As mentioned in the standup, that's an oversight (and then I was side tracked by the second unrelated issue first). I'll submit a fixed PR later, Alex will first submit a PR to fix the linter update issues.

[pflanze]

Now should be fixed, except it's not based on a fixed main yet so the linter will still trigger.

BTW I forgot to mention the first of the two commits, which introduces TODO (now SILO_TODO), which is the panic macro I actually most in Rust. Meant to be used temporarily while working on a feature.

[github-actions]

This is a preview of the changelog of the next release. If this branch is not up-to-date with the current main branch, the changelog may not be accurate. Rebase your branch on the main branch to get the most accurate changelog.

Note that this might contain changes that are on main, but not yet released.

Changelog:

0.4.0 (2024-11-14)

⚠ BREAKING CHANGES

• metadataInputFile key in preprocessing config file has been removed. Instead, ndjson files should be used and specified with the ndjsonInputFilename option

Features

• remove tsv/fasta/sam input format (#562) (fd7dc6f)

Bug Fixes

• preprocessing: correct error message when field is in config but not in metadata file (828182a)
• remove shared_ptr in lambda captures which might lead to memory leaks (a26d8b8)

[pflanze]

Ah and yes, draft was accidental, because Github reused the mode from the last PR.