Add pair_coalescence_counts method

[nspope]

Reprise of #2915

[mergify]

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

[codecov]

Codecov Report

❌ Patch coverage is 0.72464% with 137 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.60%. Comparing base (045b419) to head (77bbe72).
⚠️ Report is 409 commits behind head on main.

Files with missing lines	Patch %	Lines
python/tskit/trees.py	0.72%	137 Missing ⚠️

❌ Your project status has failed because the head coverage (80.78%) is below the target coverage (85.00%). You can increase the head coverage or adjust the target coverage.

Additional details and impacted files

@@            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	Coverage Δ
c-tests	86.21% <ø> (ø)
lwt-tests	80.78% <ø> (ø)
python-c-tests	68.45% <0.72%> (+0.74%)	⬆️
python-tests	98.97% <ø> (+0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
python/tskit/stats.py	35.13% <ø> (+24.79%)	⬆️
python/tskit/trees.py	43.88% <0.72%> (-2.75%)	⬇️

... and 2 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[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:

tskit/.github/workflows/tests.yml

Line 159 in 9e1bf0d

uses: codecov/codecov-action@v3

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:

tskit/.github/workflows/tests.yml

Line 159 in 9e1bf0d

uses: codecov/codecov-action@v3

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