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refactor logging control #243

Merged
merged 13 commits into from
May 21, 2024
Merged

refactor logging control #243

merged 13 commits into from
May 21, 2024

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CunliangGeng
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@CunliangGeng CunliangGeng commented May 10, 2024

To improve the use of logging in nplinker.

Major changes:

  1. add dependency rich to colourise log message and to replace tdqm library
  2. add function setup_logging to easily setup the logging for nplinker
  3. remove the complex class LogConfig
  4. use the standard module logging to replace LogConfig
  5. update nplinker config template (nplinker.toml) for logging section

Note:

  • Since lots of code files are changed on logging, please ignore the failed checks on format and static typing.
  • Ignore the failed unit tests on podp_download_and_extract_antismash_data, caused by external reason.

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@CunliangGeng CunliangGeng requested a review from gcroci2 May 10, 2024 14:22
@CunliangGeng CunliangGeng marked this pull request as ready for review May 10, 2024 14:22
@CunliangGeng CunliangGeng self-assigned this May 10, 2024
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CunliangGeng commented May 21, 2024

Merge activity

@CunliangGeng CunliangGeng merged commit e5e4ecb into dev May 21, 2024
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@CunliangGeng CunliangGeng deleted the refactor_logging branch May 21, 2024 07:59
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2 participants