Serialized XML objects in small molecule pipeline have the wrong extension

[Iván Pulido]

When we serialize objects in

perses/perses/app/setup_relative_calculation.py

Lines 733 to 735 in 4e36a6b

 data.serialize(htf[phase].hybrid_system, trajectory_directory / "xml" /f"{phase}-hybrid-system.gz") 
 data.serialize(htf[phase]._old_system, trajectory_directory / "xml" / f"{phase}-old-system.gz") 
 data.serialize(htf[phase]._new_system, trajectory_directory / "xml" /f"{phase}-new-system.gz") 

They are supposed to be gzipped files, but while inspecting these files one can easily tell they are directly the XML files. As in:

❯ file *
complex-hybrid-system.gz: XML 1.0 document, ASCII text
complex-new-system.gz:    XML 1.0 document, ASCII text
complex-old-system.gz:    XML 1.0 document, ASCII text
solvent-hybrid-system.gz: XML 1.0 document, ASCII text
solvent-new-system.gz:    XML 1.0 document, ASCII text
solvent-old-system.gz:    XML 1.0 document, ASCII text

Instead of the expected "gzip compressed data".

[Mike Henry]

Do we want to have them zipped, or do we want to keep them uncompressed?

[Iván Pulido]

We do want to compress them.

[Mike Henry]

Okay this was a fun one: https://github.com/choderalab/perses/blob/main/perses/utils/data.py#L114-L127

We do save the xml with gzip, but then since there is an if instead of elif when checking for bz2, we overwrite the file with an uncompressed version when we hit the else block. I've got a PR incoming with some extra debug that will help troubleshoot issues like this.