tskit-dev / tsinfer

Infer a tree sequence from genetic variation data.
GNU General Public License v3.0
56 stars 13 forks source link

Allow VariantData to take either a vcz path or the zarr store itself #966

Closed hyanwong closed 2 months ago

hyanwong commented 2 months ago

Starts to address https://github.com/tskit-dev/tsinfer/issues/924

Changes are very minor: most of this is just in testing

codecov[bot] commented 2 months ago

Codecov Report

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

Project coverage is 93.17%. Comparing base (6c02f9d) to head (fe0b969). Report is 1 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #966 +/- ## ======================================= Coverage 93.16% 93.17% ======================================= Files 18 18 Lines 6337 6343 +6 Branches 1133 1134 +1 ======================================= + Hits 5904 5910 +6 Misses 294 294 Partials 139 139 ``` | [Flag](https://app.codecov.io/gh/tskit-dev/tsinfer/pull/966/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/tsinfer/pull/966/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `93.17% <100.00%> (+<0.01%)` | :arrow_up: | | [python](https://app.codecov.io/gh/tskit-dev/tsinfer/pull/966/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `95.54% <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.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

benjeffery commented 2 months ago

@mergifyio rebase

mergify[bot] commented 2 months ago

rebase

☑️ Nothing to do

- [ ] `-conflict` [📌 rebase requirement] - [X] `-closed` [📌 rebase requirement] - [X] `queue-position=-1` [📌 rebase requirement] - [X] any of: - [X] `#commits-behind>0` [📌 rebase requirement] - [X] `#commits>1` [📌 rebase requirement] - [ ] `-linear-history` [📌 rebase requirement]