MAINT: calculations.py function and dirpar_ deprecations

[nawtrey]

Description

• Deprecates the parameter dirpar_edges in the following functions:

  • calculations.calc_sigma
  • calculations.calc_state_probs_from_diags
  • calculations.calc_net_cycle_flux_from_diags

• Re-introduces (with deprecated status) the calculations.calc_net_cycle_flux to allow
  for KDA paper code to continue working

• Updates docstrings for aforementioned functions so it is clear under which circumstances the
  deprecation warnings will be produced

• Updates Test_Diagram_Generation.test_diagram_counts and Test_Diagram_Generation.test_max_connected_diagram_counts to remove mentions of dirpars

• Updates to test_function_inputs:

  • Adds 3 test cases to confirm DeprecationWarnings are triggered when dirpar_edges is used in calc_sigma, calc_state_probs_from_diags, etc.
  • Adds 2 test cases to confirm a TypeError is raised when no directional diagram edges/diagrams are input
  • Adds 2 test cases to confirm multiple DeprecationWarnings are raised when calling calc_state_probs_from_diags or calc_net_cycle_flux_from_diags with the deprecated parameter dirpar_edges

Status

• Ready to go

[nawtrey]

One of the new test cases failed --

        with pytest.warns(DeprecationWarning) as record:
            # call using deprecated parameter, `dirpar_edges`
            calculations.calc_net_cycle_flux_from_diags(
                G, cycle=cycle, dirpar_edges=dir_edges, order=order,
                key="val", output_strings=False,
            )
            # check that both DeprecationWarnings are raised
            dep_msg_1 = record[0].message.args[0]
            dep_msg_2 = record[1].message.args[0]
>           assert len(record) == 2
E           assert 4 == 2
E            +  where 4 = len(WarningsChecker(record=True))

I looked into it locally, and it turns out this is related to pandas somehow. If I uninstall pandas and print all 4 warnings, this is what I get:

kda\tests\test_kda.py record 1 The `dirpar_edges` parameter is deprecated and will be removed in a future release. Please use `dir_edges` instead.
record 2 `kda.calculations.calc_net_cycle_flux_from_diags` is deprecatedand will be removed in a future release. Use `kda.calculations.calc_cycle_flux` with parameter `dir_edges`.
record 3 pandas not found, skipping conversion test.
record 4 pandas not found, skipping conversion test.

If I install pandas, warnings 3 and 4 go away.

On further inspection it looks like its coming from networkx (see here). The assertion regarding the number of records is not important, so I think I'll just drop it.

[nawtrey]

Alright, all tests are passing, docs look good, and the KDA paper code still works on this branch (primarily due to the re-introduction of calc_net_cycle_flux). The code coverage looks good. Merging.