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Poseidon version cli for validate and jannocoalesce#367

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nevrome wants to merge 3 commits intoposeidon300colsfrom
versionInput
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Poseidon version cli for validate and jannocoalesce#367
nevrome wants to merge 3 commits intoposeidon300colsfrom
versionInput

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@nevrome nevrome commented Feb 10, 2026

In your review of #357 you remarked that validate and jannocoalesce should not be limited to the latest Poseidon version, @stschiff. This PR adds command line options to set the versions manually.

@nevrome nevrome requested a review from stschiff February 10, 2026 12:52
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codecov bot commented Feb 10, 2026

Codecov Report

❌ Patch coverage is 20.00000% with 24 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.56%. Comparing base (3b7fc1b) to head (589c474).

Files with missing lines Patch % Lines
src/Poseidon/CLI/OptparseApplicativeParsers.hs 0.00% 21 Missing ⚠️
src/Poseidon/CLI/Jannocoalesce.hs 60.00% 1 Missing and 1 partial ⚠️
src/Poseidon/CLI/Validate.hs 75.00% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@                 Coverage Diff                 @@
##           poseidon300cols     #367      +/-   ##
===================================================
- Coverage            55.70%   55.56%   -0.14%     
===================================================
  Files                   33       33              
  Lines                 5235     5248      +13     
  Branches               631      631              
===================================================
  Hits                  2916     2916              
- Misses                1688     1701      +13     
  Partials               631      631              

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Hmm, I'm still a bit confused. So you now have VersionedFiles as Input and Output. So for input this makes sense, as upon reading, the parser has to know which version, so that it can for example scale the damage and endogenous values. But for writing, how does this exactly work? Say I request things to be written as 2.7.1. Then this line here:

JannoRows targetRows <- readJannoFile targetPV [] targetPath

will work just fine. But that doesn't mean that the writing will properly respect the version?

I think the writing will always write in Version 3.0.0 format, won't it?

Perhaps we should make this simple, and forbid any choice of the target version to be selected? Maybe this needs to be discussed.

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