yaml update for mergeBack iin bfModel

notebooks/bfModel/bfModel.ipynb

@@ -503,6 +503,8 @@
     "mesh = pv.read('step15.vtk')\n",
     "elev = mesh.get_array(name='elev')\n",
     "\n",
+    "mesh.set_active_scalars(name='erodep')\n",
+    "\n",
     "earthRadius = 6.371e6\n",
     "scale = 20.\n",
     "factor = 1.+ (elev/earthRadius)*scale\n",
@@ -513,7 +515,7 @@
     "\n",
     "contour = mesh.contour([0])\n",
     "\n",
-    "plot = pv.PlotterITK()\n",
+    "plot = pv.Plotter()\n",
     "plot.add_mesh(mesh, scalars=\"elev\")\n",
     "plot.add_mesh(contour, color=\"black\", opacity=1.)\n",
     "plot.show()"
@@ -582,14 +584,16 @@
     "\n",
     "# Plot the tectonic vertical forcing by loading the created VTK file \n",
     "mesh = pv.read(checkvtk)\n",
+    "mesh.set_active_scalars(name='vTec')\n",
+    "\n",
     "elev = mesh.get_array(name='Z')\n",
     "scale = 20.\n",
     "factor = 1.+ (elev/radius)*scale\n",
     "mesh.points[:, 0] *= factor\n",
     "mesh.points[:, 1] *= factor\n",
     "mesh.points[:, 2] *= factor\n",
     "contour = mesh.contour([0])\n",
-    "plot = pv.PlotterITK()\n",
+    "plot = pv.Plotter()\n",
     "plot.add_mesh(mesh, scalars=\"vTec\")\n",
     "plot.add_mesh(contour, color=\"black\", opacity=1.)\n",
     "plot.show()"

notebooks/bfModel/scripts/getTecto.py

@@ -1,7 +1,7 @@
 import glob
 import h5py
 import numpy as np
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 from scipy import spatial
 
 
@@ -18,7 +18,8 @@ def __init__(self, filename=None):
 
         # Open YAML file
         with open(filename, "r") as finput:
-            self.input = yaml.load(finput, Loader=yaml.Loader)
+            yaml = YAML()
+            self.input = yaml.load(finput)
 
         self.radius = 6378137.0
         self._inputParser()

notebooks/bfModel/scripts/mergeBack.py

@@ -2,7 +2,7 @@
 import os
 import glob
 import shutil
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 
 
 def createOutputDir(output=None, makedir=False):
@@ -39,8 +39,8 @@ def readOutputs(filename=None):
         raise IOError("The input file is not found...")
 
     # Open YAML file
-    with open(filename, "r") as finput:
-        input = yaml.load(finput, Loader=yaml.Loader)
+    yaml = YAML()
+    input = yaml.load(finput)
 
     tStart, tEnd, tOut, outputDir = inputParser(input)
 

notebooks/bfModel/scripts/readOutput.py

@@ -4,7 +4,7 @@
 import meshio
 import numpy as np
 from scipy import spatial
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 
 
 class readOutput:
@@ -20,7 +20,8 @@ def __init__(self, filename=None, step=None):
 
         # Open YAML file
         with open(filename, "r") as finput:
-            self.input = yaml.load(finput, Loader=yaml.Loader)
+            yaml = YAML()
+            self.input = yaml.load(finput)
 
         self.radius = 6378137.0
         self._inputParser()

notebooks/dualLith/dualLithology.ipynb

@@ -7,7 +7,7 @@
     "# Dual-lithology example\n",
     "\n",
     "\n",
-    "To run the notebook several post and pre-processing librairies are required:\n",
+    "To run the notebook several post and pre-processing libraries are required:\n",
     "\n",
     "- `panel` \n",
     "- `pyvista` \n",
@@ -84,7 +84,7 @@
     "This function takes 3 arguments:\n",
     "\n",
     "* `t` the time interval in Ma of the starting simulation time (here 0 Ma as we start at present day),\n",
-    "* `d` the folder containing the input conditions. The code assumes that the paleo-elevations are located in the folder **data** under **paleomap** and are `netCDF` files of the form `XXMa.nc` with `XX` the specified time. It also assumes that the displacement maps are located in **velocity** and are off the form `velocity_ XXMa.xy`. Lastly for the paleo-precipitation, the assumed file is under **precipitation** and are `netCDF` files of the form `XXMa.nc` as well.\n",
+    "* `d` the folder containing the input conditions. The code assumes that the paleo-elevations are located in the folder **data** under **paleomap** and are `netCDF` files of the form `XXMa.nc` with `XX` the specified time. It also assumes that the displacement maps are located in **velocity** and are of the form `velocity_ XXMa.xy`. Lastly for the paleo-precipitation, the assumed file is under **precipitation** and are `netCDF` files of the form `XXMa.nc` as well.\n",
     "* `s` is the space conditions for the `jigsaw` algorithm and consists of 3 values: the spacing in km for the mesh in the deep ocean (<=-1000 m), the spacing in km across shelf margin (>=-1000 m and < 0m) and the spacing in km in the continental domain. Here, the resolution will vary from 5000 km to 1000 km and 100 km respectively. This is set at pretty low resolution to ensure a quicker runtime. We often use the following values `-s=100,30,15` in our run."
    ]
   },
@@ -149,7 +149,7 @@
     "\n",
     "In addition, to the layer thicknesses and compositions, `gospl` requires the porosity of each sediment type present in a given layer to be specified.\n",
     "\n",
-    "Here we follow the approach presented in the [technical guide](https://gospl.readthedocs.io/en/latest/tech_guide/strat.html#porosity-and-compaction) of the documentation, and the porosity is considered to varies with depth z.\n",
+    "Here we follow the approach presented in the [technical guide](https://gospl.readthedocs.io/en/latest/tech_guide/strat.html#porosity-and-compaction) of the documentation, and the porosity is considered to vary with depth z.\n",
     "\n",
     "$$\\phi(z) = \\phi_0 e^{−z/z_0}$$"
    ]