v1.6.0

[a-r-j]

What's Changed

• Correct the coordinates computation for small residue graohs, and when granularity: centroids by @manonreau in Correct the coordinates computation for small residue graohs, and when granularity: centroids #220
• Logging by @a-r-j in Logging #221
• Fix bug in add_k_nn_edges and add minor extension by @anton-bushuiev in Fix bug in add_k_nn_edges and add minor extension #229
• Catch AF2 download error AlphaFold download function fails if nonexistent Uniprot ID entry / 404 error  #225 by @a-r-j in Catch AF2 download error #225 #226
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in [pre-commit.ci] pre-commit autoupdate #233
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in [pre-commit.ci] pre-commit autoupdate #240
• Add minimal install workflow by @a-r-j in Add minimal install workflow #230
• Modify graphs.py to handle insertions when {'insertions': True} by @manonreau in Modify graphs.py to handle insertions when {'insertions': True} #223
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in [pre-commit.ci] pre-commit autoupdate #246
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in [pre-commit.ci] pre-commit autoupdate #249
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in [pre-commit.ci] pre-commit autoupdate #250
• control protein graph construction verbosity by @davidfstein in control protein graph construction verbosity #242
• fix peptide bonds for all atom graphs by @a-r-j in fix peptide bonds for all atom graphs #254
• Add tensor parsing util by @a-r-j in Add tensor parsing util #244
• Fix typo in problematic_pdbs.rst by @eltociear in Fix typo in problematic_pdbs.rst #258
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in [pre-commit.ci] pre-commit autoupdate #257
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in [pre-commit.ci] pre-commit autoupdate #260
• Fix and improve the utilities for PyG by @anton-bushuiev in Fix and improve the utilities for PyG #234
• add graph construction from a dataframe by @a-r-j in add graph construction from a dataframe #264
• Fix graph sequence (atomistic graphs in initialise_graph_with_metadata had duplicated residues) by @kamurani in Fix graph sequence (atomistic graphs in initialise_graph_with_metadata had duplicated residues)  #268
• Add improved error message for non standard node funcs esm_residue_embedding not working #274 by @a-r-j in Add improved error message for non standard node funcs #274 #275
• clean up unused files and move docs from root by @a-r-j in clean up unused files and move docs from root #276
• prelim path support construct_graph in protein.graphs should accept a Path object or str  #269 by @a-r-j in prelim path support #269 #277
• Switch to miniconda for build by @a-r-j in Switch to miniconda for build #278
• Improve altloc handling by @anton-bushuiev in Improve altloc handling #263
• Df processing protein_df_processing_functions arg to ProteinGraphConfig does not process pdb dataframe #216 by @a-r-j in Df processing #216 #222
• Minor patch convert_nx_to_pyg KeyError: 'kind' for split edge index by edge kind when converting nx to pyg #280 by @rg314 in Minor patch convert_nx_to_pyg #280 #281
• changes for 1.6.0 by @a-r-j in changes for 1.6.0 #279

New Contributors

• @manonreau made their first contribution in Correct the coordinates computation for small residue graohs, and when granularity: centroids #220
• @anton-bushuiev made their first contribution in Fix bug in add_k_nn_edges and add minor extension #229
• @pre-commit-ci made their first contribution in [pre-commit.ci] pre-commit autoupdate #233
• @davidfstein made their first contribution in control protein graph construction verbosity #242
• @eltociear made their first contribution in Fix typo in problematic_pdbs.rst #258

Full Changelog: v1.5.2...v1.6.0

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This discussion was created from the release v1.6.0.