mmore500 / hstrat

hstrat enables phylogenetic inference on distributed digital evolution populations
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Fixup calc provided uncertainty #115

Closed mmore500 closed 1 year ago

mmore500 commented 1 year ago

Based on readthrough Friday with @rodsan0

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 76.92% and project coverage change: -22.24 :warning:

Comparison is base (1bfac67) 97.51% compared to head (e4681c9) 75.27%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #115 +/- ## =========================================== - Coverage 97.51% 75.27% -22.24% =========================================== Files 576 584 +8 Lines 7761 7807 +46 =========================================== - Hits 7568 5877 -1691 - Misses 193 1930 +1737 ``` | Flag | Coverage Δ | | |---|---|---| | tests | `75.27% <76.92%> (-22.24%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno) | Coverage Δ | | |---|---|---| | [hstrat/\_auxiliary\_lib/\_bit\_ceil.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L19hdXhpbGlhcnlfbGliL19iaXRfY2VpbC5weQ==) | `14.28% <0.00%> (-85.72%)` | :arrow_down: | | [...tapered\_algo/\_scry/\_CalcMrcaUncertaintyRelExact.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L3N0cmF0dW1fcmV0ZW50aW9uX3N0cmF0ZWd5L3N0cmF0dW1fcmV0ZW50aW9uX2FsZ29yaXRobXMvZ2VvbV9zZXFfbnRoX3Jvb3RfdGFwZXJlZF9hbGdvL19zY3J5L19DYWxjTXJjYVVuY2VydGFpbnR5UmVsRXhhY3QucHk=) | `100.00% <ø> (ø)` | | | [...c\_algo/\_invar/\_CalcMrcaUncertaintyRelUpperBound.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L3N0cmF0dW1fcmV0ZW50aW9uX3N0cmF0ZWd5L3N0cmF0dW1fcmV0ZW50aW9uX2FsZ29yaXRobXMvcHNldWRvc3RvY2hhc3RpY19hbGdvL19pbnZhci9fQ2FsY01yY2FVbmNlcnRhaW50eVJlbFVwcGVyQm91bmQucHk=) | `100.00% <ø> (ø)` | | | [...ic\_algo/\_invar/\_CalcNumStrataRetainedUpperBound.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L3N0cmF0dW1fcmV0ZW50aW9uX3N0cmF0ZWd5L3N0cmF0dW1fcmV0ZW50aW9uX2FsZ29yaXRobXMvcHNldWRvc3RvY2hhc3RpY19hbGdvL19pbnZhci9fQ2FsY051bVN0cmF0YVJldGFpbmVkVXBwZXJCb3VuZC5weQ==) | `100.00% <ø> (ø)` | | | [...olution\_algo/\_scry/\_CalcMrcaUncertaintyRelExact.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L3N0cmF0dW1fcmV0ZW50aW9uX3N0cmF0ZWd5L3N0cmF0dW1fcmV0ZW50aW9uX2FsZ29yaXRobXMvcmVjZW5jeV9wcm9wb3J0aW9uYWxfcmVzb2x1dGlvbl9hbGdvL19zY3J5L19DYWxjTXJjYVVuY2VydGFpbnR5UmVsRXhhY3QucHk=) | `100.00% <ø> (ø)` | | | [...\_IterRetainedRanks\_/\_IterRetainedRanksReference.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L3N0cmF0dW1fcmV0ZW50aW9uX3N0cmF0ZWd5L3N0cmF0dW1fcmV0ZW50aW9uX2FsZ29yaXRobXMvcmVjZW5jeV9wcm9wb3J0aW9uYWxfcmVzb2x1dGlvbl9hbGdvL19zY3J5L19JdGVyUmV0YWluZWRSYW5rc18vX0l0ZXJSZXRhaW5lZFJhbmtzUmVmZXJlbmNlLnB5) | `47.05% <47.05%> (ø)` | | | [...IterRetainedRanks\_/\_IterRetainedRanksProduction.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L3N0cmF0dW1fcmV0ZW50aW9uX3N0cmF0ZWd5L3N0cmF0dW1fcmV0ZW50aW9uX2FsZ29yaXRobXMvcmVjZW5jeV9wcm9wb3J0aW9uYWxfcmVzb2x1dGlvbl9hbGdvL19zY3J5L19JdGVyUmV0YWluZWRSYW5rc18vX0l0ZXJSZXRhaW5lZFJhbmtzUHJvZHVjdGlvbi5weQ==) | `94.44% <94.44%> (ø)` | | | [hstrat/\_auxiliary\_lib/\_bit\_floor.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L19hdXhpbGlhcnlfbGliL19iaXRfZmxvb3IucHk=) | `100.00% <100.00%> (ø)` | | | [...esolution\_algo/\_impl/\_calc\_provided\_uncertainty.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L3N0cmF0dW1fcmV0ZW50aW9uX3N0cmF0ZWd5L3N0cmF0dW1fcmV0ZW50aW9uX2FsZ29yaXRobXMvZGVwdGhfcHJvcG9ydGlvbmFsX3Jlc29sdXRpb25fYWxnby9faW1wbC9fY2FsY19wcm92aWRlZF91bmNlcnRhaW50eS5weQ==) | `100.00% <100.00%> (ø)` | | | [...n\_tapered\_algo/\_impl/\_calc\_provided\_uncertainty.py](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno#diff-aHN0cmF0L3N0cmF0dW1fcmV0ZW50aW9uX3N0cmF0ZWd5L3N0cmF0dW1fcmV0ZW50aW9uX2FsZ29yaXRobXMvZGVwdGhfcHJvcG9ydGlvbmFsX3Jlc29sdXRpb25fdGFwZXJlZF9hbGdvL19pbXBsL19jYWxjX3Byb3ZpZGVkX3VuY2VydGFpbnR5LnB5) | `100.00% <100.00%> (ø)` | | | ... and [3 more](https://app.codecov.io/gh/mmore500/hstrat/pull/115?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno) | | ... and [237 files with indirect coverage changes](https://app.codecov.io/gh/mmore500/hstrat/pull/115/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Matthew+Andres+Moreno)

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