Add `pair_coalescence_counts` method

[nspope]

Reprise of #2915

[mergify[bot]]

⚠️ The sha of the head commit of this PR conflicts with #2915. Mergify cannot evaluate rules on this PR. ⚠️

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 0.72464% with 137 lines in your changes are missing coverage. Please review.

Project coverage is 81.60%. Comparing base (045b419) to head (77bbe72).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #2920 +/- ## ========================================== + Coverage 81.31% 81.60% +0.29% ========================================== Files 48 48 Lines 37856 37426 -430 Branches 7295 7232 -63 ========================================== - Hits 30782 30542 -240 + Misses 5653 5466 -187 + Partials 1421 1418 -3 ``` | [Flag](https://app.codecov.io/gh/tskit-dev/tskit/pull/2920/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-tests](https://app.codecov.io/gh/tskit-dev/tskit/pull/2920/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `86.21% <ø> (ø)` | | | [lwt-tests](https://app.codecov.io/gh/tskit-dev/tskit/pull/2920/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `80.78% <ø> (ø)` | | | [python-c-tests](https://app.codecov.io/gh/tskit-dev/tskit/pull/2920/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `68.45% <0.72%> (+0.74%)` | :arrow_up: | | [python-tests](https://app.codecov.io/gh/tskit-dev/tskit/pull/2920/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `98.97% <ø> (+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/tskit/pull/2920?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 | | |---|---|---| | [python/tskit/stats.py](https://app.codecov.io/gh/tskit-dev/tskit/pull/2920?src=pr&el=tree&filepath=python%2Ftskit%2Fstats.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev#diff-cHl0aG9uL3Rza2l0L3N0YXRzLnB5) | `35.13% <ø> (+24.79%)` | :arrow_up: | | [python/tskit/trees.py](https://app.codecov.io/gh/tskit-dev/tskit/pull/2920?src=pr&el=tree&filepath=python%2Ftskit%2Ftrees.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev#diff-cHl0aG9uL3Rza2l0L3RyZWVzLnB5) | `43.88% <0.72%> (-2.75%)` | :arrow_down: | ... and [2 files with indirect coverage changes](https://app.codecov.io/gh/tskit-dev/tskit/pull/2920/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev)

[jeromekelleher]

@benjeffery any idea what's going on with codecov here?

[jeromekelleher]

Would it help to merge a small PR which doesn't do much to try and reset codecov's view of HEAD?

[nspope]

The Codecov uploads are failing with:

[2024-04-10T04:25:12.526Z] ['verbose'] The error stack is: Error: Error uploading to https://codecov.io: Error: There was an error fetching the storage URL during POST: 404 - {'detail': ErrorDetail(string='Unable to locate build via Github Actions API. Please upload with the Codecov repository upload token to resolve issue.', code='not_found')}

Looks like this has been cropping up elsewhere? In particular, with PRs coming from forked repos.

[nspope]

FWIW it sounds like bumping the codecov-action version from 3 to 4 may fix the issue:

https://github.com/tskit-dev/tskit/blob/9e1bf0d99746093d66f1e435301ac901d2795d13/.github/workflows/tests.yml#L159

there's a blurb in the v4 notes here,

v3 versions and below will not have access to CLI features (e.g. global upload token, ATS).

[benjeffery]

FWIW it sounds like bumping the codecov-action version from 3 to 4 may fix the issue:

https://github.com/tskit-dev/tskit/blob/9e1bf0d99746093d66f1e435301ac901d2795d13/.github/workflows/tests.yml#L159

there's a blurb in the v4 notes here,

v3 versions and below will not have access to CLI features (e.g. global upload token, ATS).

Will try that - thanks for the pointer.

[nspope]

Closing in favor of #2915