Skip to content

Match methods row and columns#56

Open
gph82 wants to merge 18 commits intomasterfrom
match_methods_row_and_columns
Open

Match methods row and columns#56
gph82 wants to merge 18 commits intomasterfrom
match_methods_row_and_columns

Conversation

@gph82
Copy link
Copy Markdown
Owner

@gph82 gph82 commented Oct 19, 2025

API Break: changes the way in which the *_match methods of AlignerConsensus work:

  • The lower method _match_only gets updated to trim() (which is exposed and documented)
  • trim() extends the logic to handle more cases and tries to be less opinionated how to drop rows or columns
  • The default is still to drop rows first, but drops can be any/all and swapped in order (columns first, then rows)
  • The docstrings become heavy with different scenarios, maybe we can compact here more.

@codecov-commenter
Copy link
Copy Markdown

codecov-commenter commented Oct 19, 2025

⚠️ Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

❌ Patch coverage is 85.90604% with 21 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.21%. Comparing base (768a2cc) to head (a288e4f).

Files with missing lines Patch % Lines
mdciao/nomenclature/nomenclature.py 81.70% 15 Missing ⚠️
tests/test_nomenclature.py 90.90% 6 Missing ⚠️
❗ Your organization needs to install the Codecov GitHub app to enable full functionality.
Additional details and impacted files
@@            Coverage Diff             @@
##           master      #56      +/-   ##
==========================================
- Coverage   96.33%   96.21%   -0.12%     
==========================================
  Files          52       52              
  Lines       14506    14621     +115     
==========================================
+ Hits        13974    14068      +94     
- Misses        532      553      +21     
Flag Coverage Δ
unittests 96.21% <85.90%> (-0.12%) ⬇️

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

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@gph82 gph82 force-pushed the match_methods_row_and_columns branch from eefd1c8 to 02ab85b Compare October 19, 2025 20:58
gph82 added 15 commits January 16, 2026 18:38
Makes _only_matches more flexible, adding ability to drop rows instead of columns.

pytest -k Test_trim works, the rest will be broken

Needs to be ported to all other methods depending on the old _only_matches
…p around trim, updated docstrings, tests

Indv docstrings now use _kwargs_subs, class docstring corrected to match new parameters
…ock detection in docstring to survive dedentation (py313 failed)

This was the origin of fails in the original logic between py312 and py313
https://docs.python.org/3/whatsnew/3.13.html#other-language-changes
… when pulling dosctrings from aligntop, other minor docstring
…As on the fly, inform and refuse to init, tests pending
Makes _only_matches more flexible, adding ability to drop rows instead of columns.

pytest -k Test_trim works, the rest will be broken

Needs to be ported to all other methods depending on the old _only_matches
… when pulling dosctrings from aligntop, other minor docstring
@gph82 gph82 force-pushed the match_methods_row_and_columns branch from c5eb6d1 to ff1ccf0 Compare January 18, 2026 16:12
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants