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

Integrate xerxes #265

Closed stschiff closed 1 year ago

stschiff commented 1 year ago

Still a draft, but integration was fairly easy. I will work on some tests now.

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 1.09% and project coverage change: -8.70% :warning:

Comparison is base (0570251) 70.78% compared to head (ee288c0) 62.09%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #265 +/- ## ========================================== - Coverage 70.78% 62.09% -8.70% ========================================== Files 23 26 +3 Lines 3207 3664 +457 Branches 350 350 ========================================== + Hits 2270 2275 +5 - Misses 587 1039 +452 Partials 350 350 ``` | [Files Changed](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/265?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/Analysis/FStatsConfig.hs](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/265?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0FuYWx5c2lzL0ZTdGF0c0NvbmZpZy5ocw==) | `0.00% <0.00%> (ø)` | | | [src/Poseidon/Analysis/Utils.hs](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/265?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0FuYWx5c2lzL1V0aWxzLmhz) | `0.00% <0.00%> (ø)` | | | [src/Poseidon/Analysis/CLI/FStats.hs](https://app.codecov.io/gh/poseidon-framework/poseidon-hs/pull/265?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0FuYWx5c2lzL0NMSS9GU3RhdHMuaHM=) | `1.82% <1.82%> (ø)` | |

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stschiff commented 1 year ago

See also https://github.com/poseidon-framework/poseidon-analysis-hs/pull/24

nevrome commented 1 year ago

Looks good :+1:

The test infrastructure in poseidon-analysis-hs was different than here. Maybe we want to unify that at some point, but if it all runs through it's fine for me. The .Rhistory file in manual_tests_xerxes should probably be added to the .gitignore.

How do we version xerxes from now on? Is there just one trident/xerxes version then? Or shall we try to establish a separate versioning system for the library and the two executables? Cabal/stack are not particularly helpful here.

Independent of that I think this warrants a change in the major version number. Maybe even in the era number.

stschiff commented 1 year ago

I removed the .Rhistory file. It was in fact historic.

I think Xerxes will follow the same versioning now as trident. That is - in my view - the condition that comes with merging it into one repository. Otherwise we have to introduce a separate versioning from the one in the cabal-file, and I fear that will get quite obfuscating.

Regarding the major version number, I agree. I have no opinion on the era-number, though I am a little afraid it might cause all too large expectations 😅

stschiff commented 1 year ago

OK, I have increased the first version number now, let's be bold.

Regarding the tests, just wanted to say that for FStats we have to do some manual tests, since I want to make sure that the results are similar to what previous tools, including Nick's admix tools gives. Those runs are too long to automate.

Let me know if there is anything else.

stschiff commented 1 year ago

We'll close this for now. Was not a good idea for now.