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Beta diversity tweaks#114

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Bribak merged 9 commits intoBojarLab:devfrom
Glycocalex:dev
Apr 10, 2026
Merged

Beta diversity tweaks#114
Bribak merged 9 commits intoBojarLab:devfrom
Glycocalex:dev

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@Glycocalex
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⚠️ IMPORTANT: Branch Strategy

This repository follows a strict branch strategy:

  • master branch is ONLY for PyPI release mirroring
  • All development PRs MUST target the dev branch
  • If your PR targets master, it will be flagged and you'll be asked to retarget to dev

Description of Changes

beta diversity output changed to include distance matrix
...

Changelog

  • I have added my changes to CHANGELOG.md under the appropriate module/submodule section

@Glycocalex Glycocalex requested a review from Bribak April 7, 2026 15:00
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codacy-production bot commented Apr 7, 2026

Up to standards ✅

🟢 Issues 1 high · 1 medium

Results:
2 new issues

Category Results
UnusedCode 1 medium
ErrorProne 1 high

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🟢 Metrics 0 complexity · 0 duplication

Metric Results
Complexity 0 (≤ 20 complexity)
Duplication 0 (≤ 15 duplication)

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TIP This summary will be updated as you push new changes. Give us feedback

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Bribak commented Apr 8, 2026

Thank you! Will be a nice improvement

Just a few to-dos here:

  • no need to import DataFrame, since we typically just use pd.DataFrame
  • no need to import List, since we use the nice typing introduced by Python 3.10
  • you don't need to wrap the outputs into a list, just having both outputs in the same return line will output a tuple, which is better
  • You'll need to update the test_get_biodiversity unit tests in test_core_functions to deal with this changed output format, so that the tests will run through successfully before I merge:-)

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Bribak commented Apr 9, 2026

Pythonic tuple construction works like (pd.DataFrame, pd.DataFrame) (in theory you can do tuple((pd.DataFrame, pd.DataFrame)) but it's a bit cumbersome:-)
I'd recommend running the tests locally until they run through (or at least try to run the biodiversity unit test in isolation until it passes). But we should be almost there I think

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codecov bot commented Apr 10, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.69%. Comparing base (7ca4484) to head (34c1666).
⚠️ Report is 10 commits behind head on dev.

Additional details and impacted files
@@           Coverage Diff           @@
##              dev     #114   +/-   ##
=======================================
  Coverage   96.69%   96.69%           
=======================================
  Files          18       18           
  Lines        7264     7266    +2     
=======================================
+ Hits         7024     7026    +2     
  Misses        240      240           

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@Bribak Bribak merged commit dca7820 into BojarLab:dev Apr 10, 2026
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2 participants