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@mptino mptino commented Oct 26, 2025

This PR brings several simplifications to the names of key functions or submodules, as well as restoring the original import scheme from the JOSS paper. We also added deprecated function handling, so that importing function names from the paper will work but will warn the user to use the new function name, e.g.

python3 -c "from shapelets.self_assembly import rdistance"
<string>:1: DeprecationWarning: rdistance() is deprecated, please use response_distance() instead.

@mptino mptino changed the title Modify function/module names and importing conventions Deprecated fn handling and restored module importing scheme Oct 26, 2025
@mptino mptino changed the title Deprecated fn handling and restored module importing scheme Deprecated fn handling & restored module importing scheme Oct 26, 2025
@mptino mptino merged commit df41084 into uw-comphys:main Oct 26, 2025
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