poseidon-framework / poseidon-hs

A toolset to work with modular genotype databases in the Poseidon format
https://poseidon-framework.github.io/#/trident
MIT License
7 stars 2 forks source link

Changes for Poseidon v2.7.1 #245

Closed nevrome closed 1 year ago

nevrome commented 1 year ago

Working though the validation of real world .ssf files provided by @93Boy in https://github.com/poseidon-framework/published_data/pull/114/ exposed various flaws in trident and the Poseidon schema (e.g. https://github.com/poseidon-framework/poseidon2-schema/issues/61). In this PR I will collect the changes necessary to trident in anticipation of changes to the schema.

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 57.89% and project coverage change: -0.64 :warning:

Comparison is base (5ccae44) 69.86% compared to head (419910f) 69.23%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #245 +/- ## ========================================== - Coverage 69.86% 69.23% -0.64% ========================================== Files 19 19 Lines 2522 2587 +65 Branches 274 282 +8 ========================================== + Hits 1762 1791 +29 - Misses 486 514 +28 - Partials 274 282 +8 ``` | [Impacted Files](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework) | Coverage Δ | | |---|---|---| | [src/Poseidon/Package.hs](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL1BhY2thZ2UuaHM=) | `72.37% <0.00%> (ø)` | | | [src/Poseidon/Janno.hs](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0phbm5vLmhz) | `81.96% <25.00%> (-0.11%)` | :arrow_down: | | [src/Poseidon/SequencingSource.hs](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL1NlcXVlbmNpbmdTb3VyY2UuaHM=) | `72.17% <59.61%> (-9.45%)` | :arrow_down: | | [src/Poseidon/CLI/Forge.hs](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0NMSS9Gb3JnZS5ocw==) | `68.05% <100.00%> (ø)` | | | [src/Poseidon/PoseidonVersion.hs](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL1Bvc2VpZG9uVmVyc2lvbi5ocw==) | `80.00% <100.00%> (ø)` | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/245/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework)

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nevrome commented 1 year ago

I didn't test any of the potential error states. For the janno code we have some tests for these, but also no fully comprehensive system. I think it's OK to leave it like that for now, but my arguments are weak:

Maybe we do a test-hackathon one day to get to 90+%