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add ProteinsX dataset classes #204

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add ProteinsX dataset classes #204

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a-r-j
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@a-r-j a-r-j commented Aug 2, 2022

Reference Issues/PRs

Adds dataloaders for the following built in datasets: #13

  • PROTEINS_METAL
  • PROTEINS_NUCLEIC
  • PROTEINS_LIGANDS
  • PROTEINS_NUCLEOTIDES

What does this implement/fix? Explain your changes

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

  • Local testing.

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 .

@codecov-commenter
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Codecov Report

Merging #204 (2db8ce2) into master (8123f42) will increase coverage by 6.56%.
The diff coverage is 41.53%.

@@            Coverage Diff             @@
##           master     #204      +/-   ##
==========================================
+ Coverage   40.27%   46.83%   +6.56%     
==========================================
  Files          48       93      +45     
  Lines        2811     5647    +2836     
==========================================
+ Hits         1132     2645    +1513     
- Misses       1679     3002    +1323     
Impacted Files Coverage Δ
graphein/grn/parse_trrust.py 37.77% <ø> (ø)
graphein/ml/datasets/proteins_x.py 0.00% <0.00%> (ø)
graphein/ml/diffusion.py 0.00% <0.00%> (ø)
graphein/ppi/edges.py 100.00% <ø> (ø)
graphein/ppi/graph_metadata.py 0.00% <ø> (ø)
graphein/ppi/graphs.py 54.34% <ø> (ø)
graphein/ppi/parse_biogrid.py 75.00% <ø> (ø)
graphein/ppi/visualisation.py 0.00% <0.00%> (ø)
graphein/protein/analysis.py 0.00% <0.00%> (ø)
graphein/protein/edges/intramolecular.py 22.68% <0.00%> (ø)
... and 87 more

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@sonarqubecloud
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sonarqubecloud bot commented Aug 8, 2022

SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 2 Security Hotspots
Code Smell A 6 Code Smells

No Coverage information No Coverage information
3.5% 3.5% Duplication

@sonarqubecloud
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SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot E 13 Security Hotspots
Code Smell A 6 Code Smells

No Coverage information No Coverage information
3.5% 3.5% Duplication

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2 participants