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mosdef-hub / mbuild

A hierarchical, component based molecule builder
https://mbuild.mosdef.org
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Add warnings for deprecated file formats (protobuf, hoomdxml, Hoomd-Blue and LAMMPS simulation writers) #1187

Closed chrisjonesBSU closed 3 months ago

chrisjonesBSU commented 3 months ago

PR Summary:

Per the last few dev meetings, we've been discussing what needs to be done before releasing 1.0. We decided to clean up and consolidate conversion.py which involves moving the backend to GMSO wherever possible, and removing .hoomdxml and .pb2 readers and writers. Also, we decided to remove any mbuild.format writers that are now duplicated by GMSO such as create_hoomd_simulation and create_hoomd_forcefield, and write_lammpsdata.

We decided that the first step was including the necessary deprecation warnings in a minor release, which this PR gets started. I think this covers everything that will be removed from mBuild, and any other changes to readers and writers will just involve changing the backend and won't require a deprecation warning. Let me know if I'm missing anything.

I can start making the changes needed in a separate PR.

chrisjonesBSU commented 3 months ago

oops..I guess this includes a bunch of old commits. I'm not sure how that happened, as I started a new branch from main. Regardless, it looks like the only actual changs are ones I made for this PR specifically.

chrisjonesBSU commented 3 months ago

Ok, I didn't look closely enough at the deprecated decorator in utils, I thought it just threw a warning message, but it actually deprecates the function its used on, which we don't want yet. I'll make a new PR.

chrisjonesBSU commented 3 months ago

I found the issue..

The deprecated decorator in utils was missing a return statement, so it was just returning None. I'll clean up my fork and branch and re-open this.