tskit-dev / msprime

Simulate genealogical trees and genomic sequence data using population genetic models
GNU General Public License v3.0
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add record_provenance argument to sim_mutations; closes #2272 #2273

Open petrelharp opened 3 months ago

petrelharp commented 3 months ago

I just followed what's done in ancestry.py here.

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 91.52%. Comparing base (a2d0753) to head (20cc812).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273/graphs/tree.svg?width=650&height=150&src=pr&token=1uZQV1KMkU&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev)](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) ```diff @@ Coverage Diff @@ ## main #2273 +/- ## ======================================= Coverage 91.52% 91.52% ======================================= Files 20 20 Lines 11337 11340 +3 Branches 2304 2306 +2 ======================================= + Hits 10376 10379 +3 Misses 523 523 Partials 438 438 ``` | [Flag](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | Coverage Δ | | |---|---|---| | [C](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `91.52% <100.00%> (+<0.01%)` | :arrow_up: | | [python](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `98.70% <100.00%> (+<0.01%)` | :arrow_up: | 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=tskit-dev#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | Coverage Δ | | |---|---|---| | [msprime/mutations.py](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev#diff-bXNwcmltZS9tdXRhdGlvbnMucHk=) | `97.32% <100.00%> (+0.02%)` | :arrow_up: | ------ [Continue to review full report in Codecov by Sentry](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273?dropdown=coverage&src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev). > **Legend** - [Click here to learn more](https://docs.codecov.io/docs/codecov-delta?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) > `Δ = absolute (impact)`, `ø = not affected`, `? = missing data` > Powered by [Codecov](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273?dropdown=coverage&src=pr&el=footer&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev). Last update [a2d0753...20cc812](https://app.codecov.io/gh/tskit-dev/msprime/pull/2273?dropdown=coverage&src=pr&el=lastupdated&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev).