1.5.0 patch3 #189
Merged
1.5.0 patch3 #189
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Cam <73625486 [email protected]>
|
SonarCloud Quality Gate failed.
|
a-r-j
added a commit
that referenced
this pull request
Jul 14, 2022
* update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> * 1.5.0 patch3 (#189) * refactor PDB download to support parallelisation * add tests for PDB download * refactor PDB download function call in getcontacts * add salt bridges and vdw interactions * use multiprocess downloading in torch datasets * add additional edge funcs * add residue_id to dfs and additional constants * update tests to account for residue id column * update dl func to check for obsolete PDBs * fix type error on paths * fix obsolete test * add bad pdb attr * add return to PDB download util * Merge master -> Patch (#190) * update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Cam <73625486 [email protected]> * patch torch geometric dataset and update changelog * black, isort * isort Co-authored-by: Cam <73625486 [email protected]> * 1.5.0 patch3 (#191) * refactor PDB download to support parallelisation * add tests for PDB download * refactor PDB download function call in getcontacts * add salt bridges and vdw interactions * use multiprocess downloading in torch datasets * add additional edge funcs * add residue_id to dfs and additional constants * update tests to account for residue id column * update dl func to check for obsolete PDBs * fix type error on paths * fix obsolete test * add bad pdb attr * add return to PDB download util * Merge master -> Patch (#190) * update bioservices to account for new UniProt API (#187) * update bioservices to account for new UniProt API * update changelog * Update PULL_REQUEST_TEMPLATE.md * Graph plots (#186) * Fix param name typo in function docstring * add scaling node size by "rsa" feature as well as degree * add option for scaling node size by meiler embedding dimensions. Takes negative values to be zero. * remove walrus operator := for compatability * Add type hints * Update changelog Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Cam <73625486 [email protected]> * patch torch geometric dataset and update changelog * black, isort * isort * add edge tests * remove unused workflow action * bump for 1.5.0 * add vdw clashes to constants Co-authored-by: Cam <73625486 [email protected]> Co-authored-by: Cam <73625486 [email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Reference Issues/PRs
What does this implement/fix? Explain your changes
What testing did you do to verify the changes in this PR?
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 .