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Catch AF2 download error #225 #226

Merged
merged 8 commits into from
Nov 10, 2022
Merged

Catch AF2 download error #225 #226

merged 8 commits into from
Nov 10, 2022

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a-r-j
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@a-r-j a-r-j commented Oct 31, 2022

Reference Issues/PRs

#225

What does this implement/fix? Explain your changes

Adds a try/except to catch failed AF2 downloads.

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

None

Pull Request Checklist

  • Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
  • Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
  • Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
  • 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)
  • Checked for style issues by running black . and isort .

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codecov-commenter commented Oct 31, 2022

Codecov Report

Base: 40.27% // Head: 47.49% // Increases project coverage by +7.22% 🎉

Coverage data is based on head (5cb8d6d) compared to base (8123f42).
Patch coverage: 51.13% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #226      +/-   ##
==========================================
+ Coverage   40.27%   47.49%   +7.22%     
==========================================
  Files          48       85      +37     
  Lines        2811     5386    +2575     
==========================================
+ Hits         1132     2558    +1426     
- Misses       1679     2828    +1149     
Impacted Files Coverage Δ
graphein/ml/diffusion.py 0.00% <0.00%> (ø)
graphein/ppi/graph_metadata.py 0.00% <0.00%> (ø)
graphein/ppi/visualisation.py 0.00% <0.00%> (ø)
graphein/protein/analysis.py 0.00% <0.00%> (ø)
graphein/protein/features/sequence/utils.py 28.00% <0.00%> (+3.00%) ⬆️
graphein/protein/features/utils.py 27.77% <0.00%> (ø)
graphein/utils/config.py 100.00% <ø> (+100.00%) ⬆️
graphein/utils/config_parser.py 100.00% <ø> (ø)
graphein/utils/utils.py 52.22% <ø> (+17.70%) ⬆️
graphein/ml/clustering.py 7.42% <7.42%> (ø)
... and 81 more

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@a-r-j a-r-j added enhancement New feature or request 1 - Priority P1 High Priority labels Nov 2, 2022
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sonarcloud bot commented Nov 9, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@a-r-j a-r-j merged commit 3a27130 into master Nov 10, 2022
@a-r-j a-r-j deleted the alphafold_download_fix branch November 10, 2022 12:45
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2 participants