Dolfyn general updates (#186)

* Initial push

* Latest bugfixes

* Remove phase-in text

* Update docstrings

* Readability, imports

* Make functions public

* Docstring updates

* Fix test oversight

* Fix docstring

* Missing timestamp fix for classic Nortek

* Docstring updates

* Renaming functions per mhkit standards

* Single array vs binned array functions

* Reorganizing analysis code

* Update invalid orientation matrix warning

* Add config details to dataset attributes

* dolfyn bugfixes

* ADV updates
:

* Update compression option for netcdf4

* Remove compression options

* Fix clean function

* Set functions as private

* Move stress functions to ADV dir

* Add bottleneck to reqs

* Minor changes

* Remove old functions

* Code simplification

* Update examples

* Make functions public

* Add bottleneck to dependencies

* Fix notebook

* Bugfix for beam vars

Co-authored-by: jmcvey3 <[email protected]>

Author: jmcvey3

examples/adcp_example.ipynb

@@ -34,7 +34,7 @@
             },
             "outputs": [],
             "source": [
-                "from mhkit import dolfyn as dlfn\n",
+                "from mhkit import dolfyn\n",
                 "from mhkit.dolfyn.adp import api"
             ]
         },
@@ -77,7 +77,7 @@
                 }
             ],
             "source": [
-                "ds = dlfn.read('data/dolfyn/Sig1000_tidal.ad2cp')"
+                "ds = dolfyn.read('data/dolfyn/Sig1000_tidal.ad2cp')"
             ]
         },
         {
@@ -1464,8 +1464,8 @@
                 }
             ],
             "source": [
-                "dlfn.set_declination(ds, 15.8, inplace=True) # 15.8 deg East\n",
-                "dlfn.rotate2(ds, 'earth', inplace=True)"
+                "dolfyn.set_declination(ds, 15.8, inplace=True) # 15.8 deg East\n",
+                "dolfyn.rotate2(ds, 'earth', inplace=True)"
             ]
         },
         {
@@ -1481,8 +1481,8 @@
             "metadata": {},
             "outputs": [],
             "source": [
-                "ds.attrs['principal_heading'] = dlfn.calc_principal_heading(ds['vel'].mean('range'))\n",
-                "ds_streamwise = dlfn.rotate2(ds, 'principal', inplace=False)"
+                "ds.attrs['principal_heading'] = dolfyn.calc_principal_heading(ds['vel'].mean('range'))\n",
+                "ds_streamwise = dolfyn.rotate2(ds, 'principal', inplace=False)"
             ]
         },
         {
@@ -3295,7 +3295,7 @@
                 "ds_avg['U_mag'] = ds_avg.velds.U_mag\n",
                 "\n",
                 "ds_avg['U_dir'] = ds_avg.velds.U_dir\n",
-                "ds_avg['U_dir'].values = dlfn.tools.misc.convert_degrees(ds_avg['U_dir'].values, tidal_mode=True)"
+                "ds_avg['U_dir'].values = dolfyn.tools.misc.convert_degrees(ds_avg['U_dir'].values, tidal_mode=True)"
             ]
         },
         {
@@ -3347,7 +3347,7 @@
                 "\n",
                 "ax = plt.figure(figsize=(12,8)).add_axes([.14, .14, .8, .74])\n",
                 "# Plot flow speed\n",
-                "t =  dlfn.time.dt642date(ds_avg['time'])\n",
+                "t =  dolfyn.time.dt642date(ds_avg['time'])\n",
                 "plt.pcolormesh(t, ds_avg['range'], ds_avg['U_mag'], cmap='Blues', shading='nearest')\n",
                 "# Plot the water surface\n",
                 "ax.plot(t, ds_avg['depth'])\n",
@@ -3414,8 +3414,8 @@
             "outputs": [],
             "source": [
                 "# Uncomment these lines to save and load to your current working directory\n",
-                "#dlfn.save(ds, 'your_data.nc')\n",
-                "#ds_saved = dlfn.load('your_data.nc')"
+                "#dolfyn.save(ds, 'your_data.nc')\n",
+                "#ds_saved = dolfyn.load('your_data.nc')"
             ]
         }
     ],