The yoda surface#

The package is pydseams. The compiled extension inside it is yoda. That split is deliberate.

The 2020 name#

d-SEAMS shipped in 2020 as yodaStruct (Goswami, Goswami, Singh, J. Chem. Inf. Model. 2020, DOI 10.1021/acs.jcim.0c00031). The C++ library is still libyodaLib in seams-core. The Lua and Fennel front end still lives in yodaStruct (require("dseams")).

The nanobind module is yoda because that is the 2020 compiled surface name: NB_MODULE(yoda, ...) and Meson’s extension_module('yoda', ..., subdir: 'pydseams'). Importing pydseams.yoda is the same object the C++ engine always was.

The Python package is pydseams, not yoda. yoda is the extension, the way libyodaLib is the engine and dseams is the Lua module. import pydseamslib still works; that is the 2.0 / repository name, re-exported from pydseams.

Why helpers stay in Python#

yoda registers the engine: PointCloudDouble, the readers, neighbour lists, CHILL, rings, cages, Steinhardt, SOAP. It does not own suffix dispatch, ASE Atoms, or solvis.

Frame, read, from_ase, from_arrays, from_xyz, from_chemfiles, from_con, and to_solvis sit in Python on that surface. The compiled ABI does not grow a second I/O layer. A new reader extra or a viewer extra is a Python module plus an optional dependency (pydseams[ase], pydseams[solvis]), not a bump of the C++ module.

ds.read looks at the suffix and calls the matching constructor. yoda.readLammpsTrjreduced and friends stay available for callers that want the raw cloud.

The trade-off is a thin compiled surface and a small Python adapter layer. Application code imports pydseams and uses Frame. The seams CLI and Lua dseams stay in their own repositories and share libyodaLib.

Aliases of the same module#

import pydseams as ds

assert ds._core is ds.yoda
assert ds.cyoda is ds.yoda

name	role
`pydseams.yoda`	compiled module (canonical)
`pydseams._core`	same object; 2.1 helper-layer name
`pydseams.cyoda`	same object; older compiled-module name
`pydseamslib`	package alias of `pydseams`
`pydseams.Trajectory`	alias of `Frame`

_core is the private-looking name used when the helpers first sat on the compiled surface. cyoda is the older import kept so from pydseams import cyoda still resolves. New code imports yoda.