a-r-j commented 1 year ago

Reference Issues/PRs

N/A

What does this implement/fix? Explain your changes

Refactors logging to use loguru consistently. Also provides global enable/disable.

What testing did you do to verify the changes in this PR?

WIP

Pull Request Checklist

[ ] Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
[x] Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
[x] Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
[x] Ran python -m py.test tests/ and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., python -m py.test tests/protein/test_graphs.py)
[x] Checked for style issues by running black . and isort .

codecov-commenter commented 1 year ago

Codecov Report

Base: 40.27% // Head: 47.51% // Increases project coverage by +7.23% :tada:

Coverage data is based on head (7e583c4) compared to base (8123f42). Patch coverage: 51.15% of modified lines in pull request are covered.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #221 +/- ## ========================================== + Coverage 40.27% 47.51% +7.23% ========================================== Files 48 85 +37 Lines 2811 5382 +2571 ========================================== + Hits 1132 2557 +1425 - Misses 1679 2825 +1146 ``` | [Impacted Files](https://codecov.io/gh/a-r-j/graphein/pull/221?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | Coverage Δ | | |---|---|---| | [graphein/ml/diffusion.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvZGlmZnVzaW9uLnB5) | `0.00% <0.00%> (ø)` | | | [graphein/ppi/graph\_metadata.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL2dyYXBoX21ldGFkYXRhLnB5) | `0.00% <0.00%> (ø)` | | | [graphein/ppi/visualisation.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL3Zpc3VhbGlzYXRpb24ucHk=) | `0.00% <0.00%> (ø)` | | | [graphein/protein/analysis.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9hbmFseXNpcy5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/protein/features/sequence/utils.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9mZWF0dXJlcy9zZXF1ZW5jZS91dGlscy5weQ==) | `28.00% <0.00%> (+3.00%)` | :arrow_up: | | [graphein/protein/features/utils.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9mZWF0dXJlcy91dGlscy5weQ==) | `27.77% <0.00%> (ø)` | | | [graphein/utils/config.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vdXRpbHMvY29uZmlnLnB5) | `100.00% <ø> (+100.00%)` | :arrow_up: | | [graphein/utils/config\_parser.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vdXRpbHMvY29uZmlnX3BhcnNlci5weQ==) | `100.00% <ø> (ø)` | | | [graphein/utils/utils.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vdXRpbHMvdXRpbHMucHk=) | `52.22% <ø> (+17.70%)` | :arrow_up: | | [graphein/ml/clustering.py](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvY2x1c3RlcmluZy5weQ==) | `7.42% <7.42%> (ø)` | | | ... and [81 more](https://codecov.io/gh/a-r-j/graphein/pull/221/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb)

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