update avalontools version to incorporate bug fixes #6513
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…e is out of bounds - removed 0-padding ahead of parsing bond line as it is unnecessary and potentially harmful - forked Avalon so it can be patched more conveniently
ptosco
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ptosco
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greglandrum
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greglandrum
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Jul 14, 2023
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@greglandrum absolutely. I did not want to do that without asking while you were on holiday, but since you are now proposing this I will go ahead and move it under https://github.com/rdkit. |
added 2 commits
July 14, 2023 10:19
…of-bounds-atom-idx
updated checksum and release
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@greglandrum Done. |
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Aug 17, 2023
* - fixed a crash in Avalon occurring when an atom idx in the bond table is out of bounds - removed 0-padding ahead of parsing bond line as it is unnecessary and potentially harmful - forked Avalon so it can be patched more conveniently * updated the Avalon pre-relase number and updated the checksum * updated pre-release number and checksum * moved the Avalon fork under RDKit organization updated checksum and release --------- Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
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This PR fixes a crash in Avalon occurring when an atom idx in the bond table is out of bounds.
I also decided to fork Avalon as previously discussed with @greglandrum. This allows to patch it more conveniently and avoid using horrible regular expressions in CMake files.
Finally, I added a couple of unit tests RDKit-side to test the fixes.