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Version 3.0.0 changes#351

Merged
nevrome merged 80 commits intomasterfrom
Schema_300_dev
Mar 22, 2026
Merged

Version 3.0.0 changes#351
nevrome merged 80 commits intomasterfrom
Schema_300_dev

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@stschiff
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@stschiff stschiff commented Jun 24, 2025

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nevrome commented Aug 21, 2025

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.

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nevrome commented Aug 21, 2025

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

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stschiff commented Aug 21, 2025

Rough division of labour:

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

nevrome and others added 17 commits August 24, 2025 21:42
@nevrome
added .janno column Species
73731f9
@nevrome
turned Collection_ID into a list column
9fcbbf1
@nevrome
added a Custodian_Institution column
7ae46fc
@nevrome
added .janno columns for cultural and archaeological group attribution
f2c2fec
@nevrome
added the new Chromosomal_Anomalies .janno column
ff70a71
@nevrome
soft-retiring of the Capture_Type ReferenceGenome
014e154
@nevrome
turned Damage into a list-column
45ab988
@nevrome
mechanism to apply adjustments to .janno columns Endogenous and Damag…
1823987 
…e for packages in old Poseidon versions
@nevrome
added the new submitted_md5 column to the .ssf implementation and als…
6858403 
…o added row-wise consistency checks accordingly
@nevrome
replaced Source_Tissue with Source_Material + Source_Material_Note
566ef0b
@nevrome
note fields should not be list columns
6afce07
@nevrome
stylish-haskell
7f9b8b2
@nevrome
reworking the tests after the preceding changes
acc47e6
@nevrome
moved the Species column after the mandatory ones
ca6174e
@nevrome
testing two new possible error states
f3576be
@nevrome
update of golden test data
5f31750
@nevrome
stylish-haskell
6c6400c
@nevrome nevrome mentioned this pull request Aug 28, 2025
Merged
nevrome and others added 15 commits January 18, 2026 12:57
@nevrome
switch to Poseidon v3.0.0.
f6ca17a
@nevrome
added a warning about the outdated Source_Tissue column
7132fd9
@nevrome
made some cross-column consistency checks dependent on the Poseidon v…
c699e45 
…ersion
@nevrome
changelog
fa035f8
@nevrome
Merge pull request #364 from poseidon-framework/versionedcsvparsing
aa4e4db 
.janno & .ssf field parsing depending on a package's Poseidon version
@nevrome @stschiff
Update src/Poseidon/ColumnTypesJanno.hs
d79014a 
Co-authored-by: Stephan Schiffels <stephan_schiffels@mac.com>
@nevrome
moved helper funtion
cbead18
@nevrome
github code suggestion system did not work
3b7fc1b
@nevrome
added cli option to select poseidon version for validate --janno and …
f179256 
…--ssf
@nevrome
poseidon version setting also for jannocoalesce
4f049e0
@nevrome
improved error message
589c474
@stschiff
downgraded illegale characters to suspicous
8c00316
@nevrome
made outFile mandatory to make the writing versioning semantics clearer
72b2f5b
@stschiff
removed InstanceSig
323f546
@stschiff
Merge pull request #362 from poseidon-framework/poseidon_id_restr_ascii
d5767dd 
implemented new ByteString for PoseidonID and GroupNames, with character warning
@nevrome
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nevrome commented Mar 16, 2026 •
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Could you please add a line to the changelog and fix the merge conflicts to complete #362, @stschiff?

Edit: Nevermind - I got you 👍

@nevrome nevrome marked this pull request as ready for review March 16, 2026 07:53
@stschiff stschiff mentioned this pull request Mar 17, 2026
Merged
stschiff
stschiff commented Mar 19, 2026
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looks good, thanks a lot for the release text!

@nevrome nevrome merged commit 7495418 into master Mar 22, 2026
2 of 4 checks passed
@nevrome nevrome deleted the Schema_300_dev branch March 22, 2026 11:28
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@stschiff @nevrome