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ENH, API: Remove "key" and "name" parameters #84

Merged
merged 2 commits into from
Jun 6, 2024
Merged

ENH, API: Remove "key" and "name" parameters #84

merged 2 commits into from
Jun 6, 2024

Commits on Jun 6, 2024

  1. ENH, API: Remove "key" and "name" parameters 

    * Remove the "key" and "name" parameters from
all functions in `calculations.py`. Edge
weights are now stored under a standard
attribute name `weight`. For functions
requiring the variable names (i.e. "k12") the
strings are simply created on the fly using
the available edge data.

* Update `graph_utils.retrieve_rate_matrix`
to use `NetworkX.to_numpy_array`.

* Update function calls in `test_kda.py` to
reflect parameter changes

* Fix `diagrams.enumerate_partial_diagrams`
to build the adjacency matrix without
retrieving the edge weights from the diagram

* Fix issue #56
    @nawtrey
    nawtrey committed Jun 6, 2024
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  2. Remove unused function 

    * Remove `graph_utils.generate_K_string_matrix`
since it is no longer necessary for generating
kinetic diagrams
    @nawtrey
    nawtrey committed Jun 6, 2024
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