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Add cpdb support to speed up parsing #323

Merged
merged 37 commits into from
Aug 4, 2024
Merged

Add cpdb support to speed up parsing #323

merged 37 commits into from
Aug 4, 2024

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a-r-j
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@a-r-j a-r-j commented Jun 26, 2023 •
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What does this implement/fix? Explain your changes

Uses cpdb to parse PDB files for improved performance

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

Added + modified tests.

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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sonarcloud bot commented Jul 6, 2023

SonarCloud Quality Gate failed.    Quality Gate failed

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
64.1% 64.1% Duplication

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sonarcloud bot commented Aug 31, 2023

SonarCloud Quality Gate failed.    Quality Gate failed

Bug E 1 Bug
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
28.0% 28.0% Duplication

idea Catch issues before they fail your Quality Gate with our IDE extension sonarlint SonarLint

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sonarcloud bot commented Oct 28, 2023

SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 1 Code Smell

No Coverage information No Coverage information
25.5% 25.5% Duplication

idea Catch issues before they fail your Quality Gate with our IDE extension sonarlint SonarLint

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sonarcloud bot commented Oct 28, 2023

SonarCloud Quality Gate failed.    Quality Gate failed

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
21.5% 21.5% Duplication

idea Catch issues before they fail your Quality Gate with our IDE extension sonarlint SonarLint

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sonarcloud bot commented Feb 7, 2024

Quality Gate Failed Quality Gate failed

Failed conditions

1 Security Hotspot
13.7% Duplication on New Code (required ≤ 5%)

See analysis details on SonarCloud

@a-r-j a-r-j requested a review from kierandidi August 3, 2024 17:22
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sonarcloud bot commented Aug 3, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

@a-r-j a-r-j merged commit 4d8dc64 into master Aug 4, 2024
23 of 54 checks passed
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@kierandidi kierandidi Awaiting requested review from kierandidi

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