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

[nawtrey]

Description

• Remove the key and names 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.

• Remove checks in calculations.py functions
  for key/output_strings mismatches as well
  as the test, test_kda.test_function_inputs, which
  checked TypeErrors were raised at appropriate
  times

• Remove names, val_key, name_key parameters from
  graph_utils.generate_edges, as well as the associate test
  test_generate_edges_errors which checked the input
  parameters raised TypeErrors at appropriate times

• Remove graph_utils.generate_K_string_matrix
  since it is no longer necessary for generating
  kinetic diagrams

• Update documentation for all functions
  to reflect parameter changes

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

• Update graph_utils.retrieve_rate_matrix
  to use NetworkX.to_numpy_array

• Update function calls in test_kda.py
  to reflect parameter changes

• Fix issue ENH: Change graphs to store rates as edge weights instead of attributes #56

Status

• Ready to go

[nawtrey]

The codecov report failed to run. Looking at the logs it looks like it failed due to hitting the "rate limit":

{'detail': ErrorDetail(string='Rate limit reached. Please upload with the Codecov repository upload token to resolve issue. Expected time to availability: 723s.', code='throttled')}{'detail': ErrorDetail(string='Rate limit reached. Please upload with the Codecov repository upload token to resolve issue. Expected time to availability: 721s.', code='throttled')}{'detail': ErrorDetail(string='Rate limit reached. Please upload with the Codecov repository upload token to resolve issue. Expected time to availability: 719s.', code='throttled')}{'detail': ErrorDetail(string='Rate limit reached. Please upload with the Codecov repository upload token to resolve issue. Expected time to availability: 717s.', code='throttled')}{'detail': ErrorDetail(string='Rate limit reached. Please upload with the Codecov repository upload token to resolve issue. Expected time to availability: 715s.', code='throttled')}{'detail': ErrorDetail(string='Rate limit reached. Please upload with the Codecov repository upload token to resolve issue. Expected time to availability: 712s.', code='throttled')}

It looks like this can be fixed by adding the codecov token to the repo and updating the YAML to snag it (see this comment and the codecov documentation).

I've already added the secret so I'll go ahead and open a new PR to update the YAML.

[nawtrey]

Okay, now that codecov is back online I can confirm the function graph_utils.generate_K_string_matrix is completely uncovered. I think this can now be removed since we no longer need to worry about creating the kij's as strings.

[nawtrey]

The only thing left to do would be to update the root README, but that'll get completely rewritten in #83 so I'll leave that for now.