Dolfyn updates + turbulence analysis

[jmcvey3]

A slew of bugfixes and inconsistency cleanup, as well as including ADCP turbulence functionality for #227

Changelog:

• Bugfixes

  • Added check to ensure n_bin is shorter than the total data length when calling dolfyn.TimeBinner.reshape
  • Added checks to ensure n_fft and n_fft_coh can't be greater than n_bin
  • Fixed bug where dolfyn.adp.nan_beyond_surface overtrimmed TRDI instrument data
  • Fixed bug where dolfyn.ADVBinner.cross_spectral_density would fail if n_fft != n_fft_coh
  • Improved robustness of Nortek Signature reader for deployments not measuring water velocity
  • log file extension changed from ".log" to ".dolfyn.log"

• API/Useability

  • Calculation of depth from pressure sensor updated to use linear approximation of the equation of state, rather than EOS-80
  • Added warnings for ADV motion and turbulence functions
  • Updated dataset.velds.U_dir shortcut to automatically convert "degrees CCW from X/East/streamwise" to "degrees CW from X/North/streamwise"
  • dolfyn.ADVBinner.cross_spectral_density now returns frequency coordinate coh_freq instead of freq
  • Added ADCP turbulence functions
  • Added function to calculate Doppler noise to ADV turbulence functions
  • Added "beam_angle" attribute to Nortek Signature datasets
  • Saved full Nortek Signature "config" dictionary as json string in attributes
  • Added warning if "rotate_vars" attribute not found
  • Standardized variable metadata based on CF conventions

[ssolson]

James pulling the latest develop branch should fix your test failures

[jmcvey3]

@browniea I've finished my updates for this PR, though I need to update documentation and add an example notebook. Was there something else you wanted to add to it?

[jmcvey3]

Currently working on adding turbulence functions to ADCP example notebook

[ssolson]

@jmcvey3 in #236 you said:

@ssolson I just remembered there are some changes in the dolfyn PR (namely to the function/shortcut dolfyn.velocity.U_dir) that will affect this one. I'll try to wrap the dolfyn PR soon here so we can merge these back to back.

So we need to complete this PR first then #236? I am only confused because it seems #236 has passed all tests.

[jmcvey3]

@ssolson Just pushed some updates to the jupyter notebooks to incorporate the ADCP turbulence analysis.

@jmcvey3 in #236 you said:

@ssolson I just remembered there are some changes in the dolfyn PR (namely to the function/shortcut dolfyn.velocity.U_dir) that will affect this one. I'll try to wrap the dolfyn PR soon here so we can merge these back to back.

So we need to complete this PR first then #236? I am only confused because it seems #236 has passed all tests.

Just to have this on paper, it's a change relevant to the tidal performance jupyter notebook

[jmcvey3]

@ssolson Just pushed some updates to the jupyter notebooks to incorporate the ADCP turbulence analysis. This PR should be good to go for final review

[ssolson]

@jmcvey3 please ping me when you are ready for me to take a look. On this PR I have https://github.com/jmcvey3/MHKiT-Python/pull/4 open agains your branch for my suggestions for the ipython notebook.

[jmcvey3]

@ssolson Ready to go! I cleaned up the rest of the docstrings (I think I got everything) and added more checks for function inputs.

[ssolson]

James thank you making all those changes.

Currently the CI/CD has passed all but the hindcast which this PR does not modify. As such I am going to proceed with the merge.