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a-r-j / graphein

Protein Graph Library
https://graphein.ai/
MIT License
1.03k stars 131 forks source link

Patch 1 #154

Closed amorehead closed 2 years ago

amorehead commented 2 years ago

Reference Issues/PRs

I noticed a TODO statement that I could readily address.

What does this implement/fix? Explain your changes

I added a way of checking that DSSP is executable before trying to use it.

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

I made sure the code runs locally.

a-r-j commented 2 years ago

Thanks @amorehead ! Appreciate the PR :) Commented on a few nits.

Would you also mind updating the changelog and add yourself to the contributors if you wish?

amorehead commented 2 years ago

@a-r-j,

No problem! Happy to contribute where I can. I've updated the CHANGELOG.md and CONTRIBUTORS.md files as you mentioned (https://github.com/a-r-j/graphein/pull/154/commits/847187626edb7552de0256d88901ab683e2776e6 and https://github.com/a-r-j/graphein/pull/154/commits/441f94e91f2df95e6634973e0fb3514bde457759), however, I cannot see your latest comments on my proposed changes. Any ideas why that may be?

a-r-j commented 2 years ago

@a-r-j,

No problem! Happy to contribute where I can. I've updated the CHANGELOG.md and CONTRIBUTORS.md files as you mentioned (8471876 and 441f94e), however, I cannot see your latest comments on my proposed changes. Any ideas why that may be?

Apologies, forgot to submit the review :)

sonarcloud[bot] commented 2 years ago

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
5.8% 5.8% Duplication

codecov-commenter commented 2 years ago

Codecov Report

Merging #154 (4088b3f) into master (8123f42) will increase coverage by 7.63%. The diff coverage is 56.23%.

@@            Coverage Diff             @@
##           master     #154      +/-   ##
==========================================
+ Coverage   40.27%   47.90%   +7.63%     
==========================================
  Files          48       58      +10     
  Lines        2811     3822    +1011     
==========================================
+ Hits         1132     1831     +699     
- Misses       1679     1991     +312
Impacted Files Coverage Δ
graphein/grn/parse_trrust.py 37.77% <ø> (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/features/sequence/sequence.py 71.42% <0.00%> (+2.67%) :arrow_up:
graphein/protein/features/sequence/utils.py 28.00% <0.00%> (+3.00%) :arrow_up:
... and 44 more

Continue to review full report at Codecov.

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