Version 3.0.0 changes

[stschiff]

No description provided.

[nevrome]

Decisions for .janno column changes:

1. ReferenceGenome in Capture_Type: Read into legacy constructor with make, warn about it with inspect, return NA with show.
2. Endogenous+Damage: No change in parser, manual post-processing in readJannoFileRow: rescale by factor 100 in case of version < 3.0.0.

[nevrome]

For unix line endings: Packages should be checked for that and a warning thrown (one per package). They should be read anyway, though.

[stschiff]

Rough division of labour:

• Stephan: Changes in YAML and Poseidon_ID + Xerxes mono repo merge
• Clemens. Changes in Janno and SSF

[nevrome]

Meeting 2025/12/01: Clemens will revert 05a23a1 and merge #357 when reviewed.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 56.83%. Comparing base (78cc88b) to head (8865d3d).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #351   +/-   ##
=======================================
  Coverage   56.83%   56.83%           
=======================================
  Files          33       33           
  Lines        4993     4993           
  Branches      546      546           
=======================================
  Hits         2838     2838           
  Misses       1609     1609           
  Partials      546      546           

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[nevrome]

I finally went ahead and reverted 05a23a1 to turn this PR to a clean slate for all Poseidon v3.0.0-related changes. I also redirected #357 to be merged into this branch. So I think the next steps should be as follows:

1. Stephan finishes Server retired packages #356 and Clemens finishes Changes to .janno and .ssf columns for Poseidon v3.0.0 #357 with reciprocal review.
2. Changes to .janno and .ssf columns for Poseidon v3.0.0 #357 gets merged into Version 3.0.0 changes #351 here.
3. Stephan branches of from here and implements the changes documented above as Changes in YAML and Poseidon_ID + Xerxes mono repo merge. He delegates tasks as he deems useful.

[stschiff]

OK, I finished #356 and will now start with the YAML and Poseidon_ID changes.