pyBadlands has been deprecated, the new version is now called badlands

Update Dockerfile, Use pip to install badlands, this should also ix issues on magnus as badlands is not installed in /opt anymore

Update links to Badlands

Author: Romain Beucher

Dockerfile

@@ -6,6 +6,7 @@ ENV NB_WORK /home/$NB_USER
 
 WORKDIR /opt
 
+# UWGeodynamics
 RUN git clone -b master https://github.com/underworldcode/UWGeodynamics.git UWGeodynamics&& \
     pip3 install --no-cache-dir UWGeodynamics/ && \
     rm -rf $NB_WORK/UWGeodynamics && \
@@ -17,26 +18,10 @@ RUN git clone -b master https://github.com/underworldcode/UWGeodynamics.git UWGe
     rm -rf UWGeodynamics && \
     chown -R $NB_USER:users $NB_WORK/UWGeodynamics
 
-# Badlands dependency
-RUN pip3 install --no-cache-dir pandas \
-                ez_setup \ 
-                tribad \
-                git+https://github.com/awickert/gFlex.git \
-                git+https://github.com/matplotlib/legacycontour.git \
-                git+https://github.com/matplotlib/cmocean.git \
-                colorlover matplotlib
-
-# Compile and install pyBadlands
-RUN git clone https://github.com/rbeucher/pyBadlands_serial.git pyBadlands &&\
-    cd pyBadlands/pyBadlands/libUtils && \
-    make && \
-    cd /opt && \
-    pip3 install --no-cache-dir -e pyBadlands && \
-    rm -rf pyBadlands/Examples
+#Badlands
+RUN pip3 install badlands
 
 USER jovyan
-ENV PATH $PATH:/opt/pyBadlands/pyBadlands/libUtils
-ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/opt/pyBadlands/pyBadlands/libUtils
 
 WORKDIR $NB_WORK
 CMD ["jupyter", "notebook", "--ip='0.0.0.0'", "--no-browser"]

UWGeodynamics/surfaceProcesses.py

@@ -53,10 +53,10 @@ def __init__(self, airIndex,
                  restartFolder=None, restartStep=None, timeField=None,
                  minCoord=None, maxCoord=None, aspectRatio2d=1.):
         try:
-            import pyBadlands
+            import badlands
 
         except ImportError:
-            raise ImportError("""pyBadlands import as failed. Please check your
+            raise ImportError("""badlands import as failed. Please check your
                               installation, PYTHONPATH and PATH environment
                               variables""")
 
@@ -95,7 +95,7 @@ def _init_model(self):
             self.maxCoord = (self.maxCoord[0], self.aspectRatio2d*self.maxCoord[0])
 
         if rank == 0:
-            from pyBadlands.model import Model as BadlandsModel
+            from badlands.model import Model as BadlandsModel
             self.badlands_model = BadlandsModel()
             self.badlands_model.load_xml(self.XML)
 

docs/source/User Guide.rst

@@ -1780,7 +1780,7 @@ model than in the thermo-mechanical model.
     If the thermomechanical model is 3D the coupling is done in 3D.
 
 
-.. _documentation: https://github.com/badlands-model/pyBadlands
+.. _documentation: https://github.com/badlands-model/badlands
 .. _XML example: ressources/badlands.xml
 
 Deforming Mesh
@@ -1933,4 +1933,4 @@ See below for a sample.
 .. _Lavavu: https://github.com/OKaluza/LavaVu
 .. _HDF5: http://portal.hdfgroup.org/display/support
 .. _Paraview: https://www.paraview.org/
-.. _Badlands: https://github.com/badlands-model/pyBadlands
+.. _Badlands: https://github.com/badlands-model/badlands