fix mypy and ruff errors

NPLinker / nplinker

A python framework for data mining microbial natural products by integrating genomics and metabolomics data

https://nplinker.github.io/nplinker

Apache License 2.0

17 stars 13 forks source link

fix mypy and ruff errors #257

Closed CunliangGeng closed 4 months ago

CunliangGeng commented 4 months ago

This PR tries to solve all type hints errors (mypy), formatting errors (ruff) and typos for refactored code. As for non-refactored code, we keep it as it is.

As for type hints, the changes follow the rules below:

use @overload for different data types of the same argument
use broader type hints Sequence and Mapping to replace list and dict, respectively, as much as possible
Use TYPE_CHECKING to only avoid circular imports

CunliangGeng commented 4 months ago

#260
#259
#258
#257 👈
#256
#255
#254
#253
#252
#250
#249
#248
#247
#246
#245
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CunliangGeng commented 4 months ago

It's ready for review.

CunliangGeng commented 4 months ago

Merge activity

Jun 14, 7:27 AM EDT: @CunliangGeng started a stack merge that includes this pull request via Graphite.
Jun 14, 7:36 AM EDT: Graphite rebased this pull request as part of a merge.
Jun 14, 7:38 AM EDT: @CunliangGeng merged this pull request with Graphite.

sonarcloud[bot] commented 4 months ago

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
82.4% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud