The major change in this PR is that all matchmaps utilities now support phenix 1.21 as well as previous versions. Along the way, various other changes were made:
refactoring phenix-calling methods out of _utils.py into the new file _phenix_utils.py
Various other refactorings for efficiency and clarity
Output script includes the phenix version that was used. This is notable because the analogous matchmaps calls with phenix 1.20 or 1.21 seem to produce slightly different results.
The parameter --phenix-version allows the user to override the automatically detected phenix version from the environment. I don't know why one would need to do this, but it was easy to support.
The major change in this PR is that all matchmaps utilities now support
phenix 1.21as well as previous versions. Along the way, various other changes were made:_utils.pyinto the new file_phenix_utils.py--phenix-versionallows the user to override the automatically detected phenix version from the environment. I don't know why one would need to do this, but it was easy to support.