These changes are motivated by the desire to completely remove the calc_state_probs_from_diags and calc_net_cycle_flux_from_diags functions since they are completely unnecessary. They are not in use in the KDA paper code at all, so they could probably be removed at any time. I chose to leave them in (with DeprecationWarnings) in case they are in use in other locations (like in the kda-examples repo) so I don't have to fix a bunch of code elsewhere.
Changes
Move main code for calculating state probabilities into calc_state_probs, add dir_edges parameter, and add DeprecationWarning to calc_state_probs_from_diags.
Impliment the same changes as above for calc_net_cycle_flux and calc_net_cycle_flux_from_diags
Update tests to use the updated versions of calc_state_probs and calc_net_cycle_flux
Add checks for DeprecationWarnings
to test_function_inputs for
calc_state_probs_from_diags and
calc_net_cycle_flux_from_diags
Update docstrings for all functions using directional edges
Description
These changes are motivated by the desire to completely remove the
calc_state_probs_from_diagsandcalc_net_cycle_flux_from_diagsfunctions since they are completely unnecessary. They are not in use in the KDA paper code at all, so they could probably be removed at any time. I chose to leave them in (withDeprecationWarnings) in case they are in use in other locations (like in thekda-examplesrepo) so I don't have to fix a bunch of code elsewhere.Changes
Move main code for calculating state probabilities into
calc_state_probs, adddir_edgesparameter, and addDeprecationWarningtocalc_state_probs_from_diags.Impliment the same changes as above for
calc_net_cycle_fluxandcalc_net_cycle_flux_from_diagsUpdate tests to use the updated versions of
calc_state_probsandcalc_net_cycle_fluxAdd checks for
DeprecationWarnings totest_function_inputsforcalc_state_probs_from_diagsandcalc_net_cycle_flux_from_diagsUpdate docstrings for all functions using directional edges