davidfstein commented 1 year ago

Reference Issues/PRs

What does this implement/fix? Explain your changes

Fixes #238 Adds verbosity control to the protein graph construction. The drawback is that this solution still involves the creation of a Progress context even if no progress is shown. However, this overhead is minimal and obviates the need for try/catch/finally if using Progress non-contextually or shallow wrappers in construct_graph.

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

Passes the included tests.

Pull Request Checklist

[x] 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 .

davidfstein commented 1 year ago

@a-r-j Seems the docker build is failing. I didn't edit the build at all, is it working on master?

a-r-j commented 1 year ago

It can be a little unstable. I'm quite confident a rebuild will resolve the problem.

codecov-commenter commented 1 year ago

Codecov Report

Base: 40.27% // Head: 47.93% // Increases project coverage by +7.66% :tada:

Coverage data is based on head (f98ecf3) compared to base (8123f42). Patch coverage: 52.14% of modified lines in pull request are covered.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #242 +/- ## ========================================== + Coverage 40.27% 47.93% +7.66% ========================================== Files 48 92 +44 Lines 2811 5526 +2715 ========================================== + Hits 1132 2649 +1517 - Misses 1679 2877 +1198 ``` | [Impacted Files](https://codecov.io/gh/a-r-j/graphein/pull/242?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/242/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/242/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/242/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/242/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/242/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/242/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/rna/subgraphs.py](https://codecov.io/gh/a-r-j/graphein/pull/242/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcm5hL3N1YmdyYXBocy5weQ==) | `83.87% <ø> (ø)` | | | [graphein/rna/utils.py](https://codecov.io/gh/a-r-j/graphein/pull/242/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcm5hL3V0aWxzLnB5) | `38.46% <ø> (ø)` | | | [graphein/rna/visualisation.py](https://codecov.io/gh/a-r-j/graphein/pull/242/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcm5hL3Zpc3VhbGlzYXRpb24ucHk=) | `28.57% <ø> (+28.57%)` | :arrow_up: | | [graphein/testing/\_\_init\_\_.py](https://codecov.io/gh/a-r-j/graphein/pull/242/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vdGVzdGluZy9fX2luaXRfXy5weQ==) | `100.00% <ø> (ø)` | | | ... and [85 more](https://codecov.io/gh/a-r-j/graphein/pull/242/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)

:umbrella: View full report at Codecov.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.