BMI Bug Fixes

[madMatchstick]

Addresses assortment of bmi implementation concerns; many previously posted under GitHub's Issues. See listing below

Additions

1. Reintroduces fractional update calls.

   def update_frac(self, time_frac):
       """Update model by a fraction of a time step.
       Parameters
       ----------
       time_frac : float
           Fraction fo a time step.
       """
       if self.verbose > 0:
           print("Warning: This version of the LSTM is designed to make predictions on one hour timesteps.")
       time_step = self.get_time_step()
       self._time_step_size = time_frac * self._time_step_size
       self.update()
       self._time_step_size = time_step

   Know this function is called in bmi.update_until() only.

2. Include a python script, lstm_serialization_test.py, for testing serialization, similar to existing jupyter notebook. Fixes #15

Changes

1. Use python's built-in getattr() or set_attr() approach vs self._values[var_name]. Fixes #5. For example,

   def get_value_ptr(self, var_name):
       """Reference to values.
       Parameters
       ----------
       var_name : str
           Name of variable as CSDMS Standard Name.
       Returns
       -------
       array_like
           Value array.
       """      
       return getattr(self, var_name)  # IN USE
   #       return self._values[var_name]   # NO LONGER IN USE

   This effects the following functions

   • create_scaled_input_tensor()
   • bmi.get_value_ptr()
   • bmi.initialize()
   • scale_output()
   • set_static_attributes()
   • set_value()

2. Directory structure:

   • jupyter notebooks in /notebooks
   • python scripts in /src
   • all links and refs adjusted for pathing change

3. Updates to readme & markdown docs

4. Bound runoff to zero; fixes #17 self.surface_runoff_mm = max(self.surface_runoff_mm,0.0)

5. Remove any - and replace with _ in py scripts

Testing

1. Executables in /notebooks and /src

[SnowHydrology]

@madMatchstick can you resolve the merge conflicts?

[SnowHydrology]

https://www.youtube.com/watch?v=roRQ2mNwMMQ