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This PR closes #557 by fixing two bugs in
BSS.Align.generateNetwork, in both the main package and the Sandpit:work_dir: theinputsandoutputssub-directories are now replaced on each call. Previously, files left over from an earlier run with a different ligand set were also loaded by LOMAP. This gave duplicate edges, self-loops, and spurious scores. It only affects a user-specifiedwork_dir, since the default is a fresh temporary directory.links_file: the rewritten links file is now actually populated. Previously it was always empty, so user-specified links were silently ignored.Regression tests have been added for both. They fail on
develand pass on this branch.It also closes #556. NAGL is now always installed via
gufe, so the tests passuse_nagl=Falseto OpenFF parameterisation to keep the reference AM1-BCC charges.develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]