update bioservices to account for new UniProt API #187
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Codecov Report
@@ Coverage Diff @@
## master #187 +/- ##
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+ Coverage 40.27% 48.33% +8.06%
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Files 48 92 +44
Lines 2811 5313 +2502
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+ Hits 1132 2568 +1436
- Misses 1679 2745 +1066
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a-r-j
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Jul 11, 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 <arjamasb@gmail.com> Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com>
a-r-j
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Jul 11, 2022
* 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 <arjamasb@gmail.com> Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com> * patch torch geometric dataset and update changelog * black, isort * isort Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com>
a-r-j
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Jul 12, 2022
* 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 <arjamasb@gmail.com> Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com> * 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+cimranm@users.noreply.github.com>
a-r-j
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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 <arjamasb@gmail.com> * 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 <arjamasb@gmail.com> Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com> * patch torch geometric dataset and update changelog * black, isort * isort Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com> * 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 <arjamasb@gmail.com> Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com> * 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+cimranm@users.noreply.github.com> Co-authored-by: Cam <73625486+cimranm@users.noreply.github.com>
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Reference Issues/PRs
New UniProt API (and bioservices update) introduces breaking changes into sequence retrieval.