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Add non-strict mode #273

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Merged
merged 7 commits into from
Oct 4, 2023
Merged

Add non-strict mode #273

merged 7 commits into from
Oct 4, 2023

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@pbashyal-nmdp pbashyal-nmdp commented Oct 3, 2023 •
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  • Use non strict mode in config to reduce alleles that may be valid with expression characters.
>>> my_configs = {'strict': False, 'verbose_log': True}
>>> import pyard
>>> ard = pyard.init(config=my_configs, load_mac=False)

>>> ard.redux('A*24:329', 'lgx')
A*24:329 is not valid. Using A*24:329Q
'A*24:329Q'

>>> ard.redux('DQB1*03:276', 'lgx')
DQB1*03:276 is not valid. Using DQB1*03:276N
'DQB1*03:01'
  • Add non_strict and verbose modes to pyard CLI.
❯ pyard --gl "DQB1*03:276" -r lgx
Typing Error: DQB1*03:276 is not valid GL String.
 DQB1*03:276 is not a valid Allele

❯ pyard --non-strict --gl "DQB1*03:276" -r lgx
DQB1*03:01

❯ pyard --non-strict --verbose --gl "DQB1*03:276" -r lgx
DQB1*03:276 is not valid. Using DQB1*03:276N
DQB1*03:01

Closes #272
Fixes #266

Bump version: 1.0.4 → 1.0.5

pbashyal-nmdp and others added 3 commits October 3, 2023 12:12
@pbashyal-nmdp
non-strict mode makes valid alleles by adding expression characters t…
1487e44 
…o invalid alleles
@pbashyal-nmdp
Fix username on docker (nmdp-bioinformatics#271)
4f6f76e 
* When running without a login, `os.getlogin()` fails. Switch to using `getuser()` from `getpass` module.

* Bump version: 1.0.3 → 1.0.4
@pbashyal-nmdp
Update changelog for "1.0.4"
dffdaaf 
    This commit was created by changelog-from-release in 'Post release' CI workflow
@pbashyal-nmdp pbashyal-nmdp added the enhancement New feature or request label Oct 3, 2023
@pbashyal-nmdp pbashyal-nmdp self-assigned this Oct 3, 2023
@pbashyal-nmdp pbashyal-nmdp changed the title Add strict flag Add non-strict mode Oct 3, 2023
@pbashyal-nmdp
Bump version: 1.0.4 → 1.0.5
f4d2638
@pbashyal-nmdp
Merge branch 'master' into add_strict_flag
3cd6e48
@pbashyal-nmdp
Add non_strict and verbose modes to pyard CLI.
898ca56 
```python
❯ scripts/pyard --gl "DQB1*03:276" -r lgx
Typing Error: DQB1*03:276 is not valid GL String.
 DQB1*03:276 is not a valid Allele
❯ scripts/pyard --non-strict --gl "DQB1*03:276" -r lgx
DQB1*03:01
❯ scripts/pyard --non-strict --verbose --gl "DQB1*03:276" -r lgx
DQB1*03:276 is not valid. Using DQB1*03:276N
DQB1*03:01
```
@pbashyal-nmdp
Fix issue when validating gl argument
b6c9408
mmaiers-nmdp
mmaiers-nmdp approved these changes Oct 4, 2023
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yes

@mmaiers-nmdp mmaiers-nmdp merged commit b26c187 into nmdp-bioinformatics:master Oct 4, 2023
@pbashyal-nmdp pbashyal-nmdp deleted the add_strict_flag branch October 17, 2023 18:41
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Version 1.x - Bug fixes + Enhancements

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Allow non strict mode pyard --validate fails for non-cwd options

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