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Merged
merged 26 commits into from
Nov 13, 2025
Merged

Major refactor 2.0.0b2 #359

merged 26 commits into from
Nov 13, 2025

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@pbashyal-nmdp
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@pbashyal-nmdp pbashyal-nmdp commented Oct 22, 2025 •
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Major refactor 2.0

  • Specialized Handler Classes for allele, glstring, mac etc in handlers/ directory
  • Each reduction mode is a strategy in reducers/ directory
  • Loading of each IPD/IMGT file in loaders/ directory
  • Add pytest for all new code
  • Add documentation and comments for code
  • Extract config to standardized ARDConfig class
  • Bump version: 2.0.0b1 → 2.0.0b2

pbashyal-nmdp and others added 19 commits October 6, 2025 14:00
@pbashyal-nmdp
create Specialized Handler Classes for allele, glstring, mac etc.
de49ecf
@pbashyal-nmdp
Strategies
21ccae1 
 - Refactored so that each reduction mode is a strategy.
@pbashyal-nmdp
Setup handlers first before building database
ce1ef2b
@pbashyal-nmdp
Rename Strategy to Reducer
367710b
@pbashyal-nmdp
Update python-tests action for unit test path
f6990ce
@pbashyal-nmdp
Bump version: 1.5.5 → 2.0.0b1
2593218
@pbashyal-nmdp
Make some private methods to public
52ff655
@pbashyal-nmdp
Cleanup
c5a1ada 
- Make `is_valid_allele` public
- misc cleanup
@pbashyal-nmdp
Consolidate HLA- prefix handling
a063e4b 
Clean up imports
@pbashyal-nmdp
extract _redux_non_glstring method from redux
85066e0
@pbashyal-nmdp
Bump version: 2.0.0b1 → 2.0.0b2
3236056
@pbashyal-nmdp
Update changelog for 2.0.0b1
681760b 
    This commit was created by changelog-from-release in 'Post release' CI workflow
@pbashyal-nmdp
Merge branch 'master' into major_refactor_2.0
a1e374f
@pbashyal-nmdp
@OverRide is only available for Python >= 3.12
b310ee6
@pbashyal-nmdp
@OverRide is only available for Python >= 3.12
ada59b0
@pbashyal-nmdp
Merge remote-tracking branch 'origin/major_refactor_2.0' into major_r…
8429ac2 
…efactor_2.0
@pbashyal-nmdp
Remove @OverRide
bfb286e
@pbashyal-nmdp
added check for TYPE_CHECKING
f8df7ad
@pbashyal-nmdp
Update setup.py
c0021c2 
 - Use `find_packages` to get all subpackages
@pbashyal-nmdp pbashyal-nmdp self-assigned this Oct 29, 2025
@pbashyal-nmdp pbashyal-nmdp added this to the py-ard version 2.0 milestone Oct 29, 2025
@pbashyal-nmdp
Tests for reducers
6b41868
@pbashyal-nmdp
Document modules
26a7dd0 
- Document all the modules in loader/reducers and handlers packages
@pbashyal-nmdp
Document pyard.* modules
e5ba343
@pbashyal-nmdp
Handler Tests
2437d68 
 - Add tests for all handlers
@pbashyal-nmdp
Make refactored ARD the default.
7515e69
@pbashyal-nmdp
Extract config
9c27981 
 - Instead of dictionary, create ARDConfig that encapsulates the configuration properties
@pbashyal-nmdp pbashyal-nmdp added enhancement New feature or request documentation labels Nov 5, 2025
@pbashyal-nmdp pbashyal-nmdp changed the title WIP: Major refactor 2.0 Major refactor 2.0 Nov 5, 2025
@pbashyal-nmdp pbashyal-nmdp changed the title Major refactor 2.0 Major refactor 2.0.0b1 Nov 5, 2025
@pbashyal-nmdp pbashyal-nmdp changed the title Major refactor 2.0.0b1 Major refactor 2.0.0b2 Nov 5, 2025
mmaiers-nmdp
mmaiers-nmdp approved these changes Nov 13, 2025
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LGTM

@mmaiers-nmdp mmaiers-nmdp merged commit 38102dc into nmdp-bioinformatics:master Nov 13, 2025
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