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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

Added a newtype `JannoFile` for `[JannoRow]` #232

Closed nevrome closed 1 year ago

nevrome commented 1 year ago

Here's an implementation of the idea shared in #229

codecov-commenter commented 1 year ago

Codecov Report

Base: 70.96% // Head: 70.93% // Decreases project coverage by -0.03% :warning:

Coverage data is based on head (ecb03d7) compared to base (fda9e36). Patch coverage: 82.50% of modified lines in pull request are covered.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #232 +/- ## ========================================== - Coverage 70.96% 70.93% -0.03% ========================================== Files 18 18 Lines 2211 2216 +5 Branches 245 245 ========================================== + Hits 1569 1572 +3 - Misses 397 399 +2 Partials 245 245 ``` | [Impacted Files](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/232?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/CLI/Forge.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0NMSS9Gb3JnZS5ocw==) | `61.60% <66.66%> (ø)` | | | [src/Poseidon/Janno.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0phbm5vLmhz) | `82.09% <78.26%> (-0.23%)` | :arrow_down: | | [src/Poseidon/Package.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL1BhY2thZ2UuaHM=) | `74.67% <85.71%> (+0.06%)` | :arrow_up: | | [src/Poseidon/CLI/List.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0NMSS9MaXN0Lmhz) | `80.88% <100.00%> (ø)` | | | [src/Poseidon/CLI/Summarise.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0NMSS9TdW1tYXJpc2UuaHM=) | `67.74% <100.00%> (ø)` | | | [src/Poseidon/CLI/Survey.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0NMSS9TdXJ2ZXkuaHM=) | `90.21% <100.00%> (ø)` | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?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

Right - my biggest concern is that JannoFile doesn't really capture the meaning. It's just an arbitrary list of JannoRows. I considered naming it JannoSet, but a set has no order. JannoList is already in use. Do you have a suggestion?

I replaced all instances of [JannoRow] to make sure that it becomes harder to accidentally run into the issue I describe in #229. But I understand that it looks a bit weird at times, not least because of the type name.

stschiff commented 1 year ago

Yes, the name isn't perfect. You could have used JannoMonoid, but that's not a name you want everywhere. What about JannoRows?

nevrome commented 1 year ago

JannoRows is simple and clear. I love it. Will use that. Thanks!