control protein graph construction verbosity #242
Conversation
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@a-r-j Seems the docker build is failing. I didn't edit the build at all, is it working on master? |
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It can be a little unstable. I'm quite confident a rebuild will resolve the problem. |
Codecov ReportBase: 40.27% // Head: 47.93% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #242 +/- ##
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+ Coverage 40.27% 47.93% +7.66%
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Files 48 92 +44
Lines 2811 5526 +2715
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+ Hits 1132 2649 +1517
- Misses 1679 2877 +1198
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graphein/protein/graphs.py
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| @@ -697,12 +701,13 @@ def construct_graph( | |||
| if config is None: | |||
| config = ProteinGraphConfig() | |||
| with Progress(transient=True) as progress: | |||
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Do you think it would be better to use a pattern like this:
from contextlib import nullcontext
cm = Progress(transient=True) if verbose else nullcontext():
with cm as progress:
...
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Oh yeah thats really nice, didn't know about nullcontext. I'll refactor
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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
./CHANGELOG.mdfile (if applicable)./graphein/tests/*directories (if applicable)./notebooks/(if applicable)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)black .andisort .