Switch Testing to PyTest and CI to GitHub Actions

.github/workflows/testing.yml

@@ -1,7 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python application
+name: Test GeoClaw
 
 on:
   push:
@@ -12,43 +9,47 @@ on:
 permissions:
   contents: read
 
+env:
+  CLAW: ${{ github.workspace }}
+
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
     steps:
     - name: Set up Python 3.10
       uses: actions/setup-python@v5
       with:
         python-version: "3.10"
-    - name: Checkout clawpack
-      uses: actions/[email protected]
-      with:
-        repository: clawpack/clawpack
     - name: Install dependencies
       run: |
         sudo apt-get update
         sudo apt-get install gfortran liblapack-pic liblapack-dev libnetcdf-dev libnetcdff-dev
         python -m pip install --upgrade pip
-        pip install flake8 pytest
-    - name: Setup clawpack super repository
-      run: |
-        git submodule init
-        git submodule update
-        pip install --user -e .
-    - name: Setup geoclaw
+        pip install flake8 meson-python ninja pytest numpy pandas xarray netCDF4
+        # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Checkout Clawpack
+      uses: actions/[email protected]
+      with:
+        repository: clawpack/clawpack
+        submodules: true
+    - name: Checkout GeoClaw branch
+      uses: actions/[email protected]
+      with:
+        path: geoclaw    
+
+    - name: Install clawpack
       run: |
-        cd geoclaw
-        git checkout ${{ github.ref }}
+        pip install --no-build-isolation --editable .
+
     - name: Lint with flake8
       run: |
-        cd geoclaw
+        cd ${CLAW}/geoclaw
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude old_dtopotools.py
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        cd geoclaw
+        cd ${CLAW}/geoclaw
         pytest

README.md

@@ -0,0 +1,6 @@
+# GeoClaw - Geophysical Shallow Flow Package
+
+[![Test GeoClaw](https://github.com/clawpack/geoclaw/actions/workflows/testing.yml/badge.svg)](https://github.com/clawpack/geoclaw/actions/workflows/testing.yml)
+
+This repository hosts the source code for GeoClaw.
+

examples/multi-layer/bowl-radial/setplot.py

@@ -74,15 +74,15 @@ def pcolor_afteraxes(current_data):
         # bathy_ref_lines(current_data)
         gauge_locations(current_data)
 
-    def contour_afteraxes(current_data):
-        # gauge_locations(current_data)
-        # m_to_km_labels()
-        plt.hold(True)
-        pos = -80.0 * (23e3 / 180) + 500e3 - 5e3
-        plt.plot([pos,pos],[-300e3,300e3],'b',[pos-5e3,pos-5e3],[-300e3,300e3],'y')
-        plt.hold(False)
-        wind_contours(current_data)
-        bathy_ref_lines(current_data)
+    # def contour_afteraxes(current_data):
+    #     # gauge_locations(current_data)
+    #     # m_to_km_labels()
+    #     plt.hold(True)
+    #     pos = -80.0 * (23e3 / 180) + 500e3 - 5e3
+    #     plt.plot([pos,pos],[-300e3,300e3],'b',[pos-5e3,pos-5e3],[-300e3,300e3],'y')
+    #     plt.hold(False)
+    #     wind_contours(current_data)
+    #     bathy_ref_lines(current_data)
 
     def profile_afteraxes(current_data):
         pass
@@ -259,23 +259,6 @@ def gaugetopo(current_data):
     plotitem.plot_var = gaugetopo
     plotitem.plotstyle = 'g-'
 
-    def add_zeroline(current_data):
-        from pylab import plot, legend, xticks, floor, axis, xlabel
-        t = current_data.t 
-        gaugeno = current_data.gaugeno
-
-        if gaugeno == 32412:
-            try:
-                plot(TG32412[:,0], TG32412[:,1], 'r')
-                legend(['GeoClaw','Obs'],loc='lower right')
-            except: pass
-            axis((0,t.max(),-0.3,0.3))
-
-        plot(t, 0*t, 'k')
-        n = int(floor(t.max()/3600.) + 2)
-        xticks([3600*i for i in range(n)], ['%i' % i for i in range(n)])
-        xlabel('time (hours)')
-
 
     #-----------------------------------------
 

examples/multi-layer/plane_wave/setplot.py

@@ -76,7 +76,7 @@ def transform_p2c(x, y, x0, y0, theta):
 
     plotdata.clearfigures()
     plotdata.save_frames = False
-    plotdata.format = 'ascii'
+    # plotdata.format = 'ascii'
 
     # ========================================================================
     #  Generic helper functions
@@ -88,7 +88,6 @@ def contour_afteraxes(current_data):
         pos = -80.0 * (23e3 / 180) + 500e3 - 5e3
         axes.plot([pos, pos], [-300e3, 300e3], 'b',
                   [pos-5e3, pos-5e3], [-300e3, 300e3], 'y')
-        wind_contours(current_data)
         bathy_ref_lines(current_data)
 
     def profile_afteraxes(current_data):
@@ -105,7 +104,6 @@ def bathy_ref_lines(current_data):
 
     # ========================================================================
     # Axis limits
-
     xlimits = [-0.5, 0.5]
     ylimits = [-0.5, 0.5]
     eta = [multilayer_data.eta[0], multilayer_data.eta[1]]
@@ -129,8 +127,6 @@ def bathy_ref_lines(current_data):
     plotaxes.ylimits = ylimits
     plotaxes.afteraxes = pcolor_afteraxes
     ml_plot.add_surface_elevation(plotaxes,1,bounds=top_surface_limits)
-    # ml_plot.add_surface_elevation(plotaxes,1,bounds=[-0.06,0.06])
-    # ml_plot.add_surface_elevation(plotaxes,1)
     ml_plot.add_land(plotaxes, 1)
 
     # Bottom surface
@@ -141,9 +137,7 @@ def bathy_ref_lines(current_data):
     plotaxes.xlimits = xlimits
     plotaxes.ylimits = ylimits
     plotaxes.afteraxes = pcolor_afteraxes
-    # ml_plot.add_surface_elevation(plotaxes,2,bounds=[-300-0.5,-300+0.5])
     ml_plot.add_surface_elevation(plotaxes,2,bounds=internal_surface_limits)
-    # ml_plot.add_surface_elevation(plotaxes,2)
     ml_plot.add_land(plotaxes, 2)
 
     # ========================================================================
@@ -177,6 +171,7 @@ def bathy_ref_lines(current_data):
 
     # ========================================================================
     #  Water Speed
+    # ========================================================================
     plotfigure = plotdata.new_plotfigure(name='speed')
     plotfigure.show = True
     plotfigure.kwargs = {'figsize': (14, 4)}
@@ -200,9 +195,7 @@ def bathy_ref_lines(current_data):
     plotaxes.ylimits = ylimits
     plotaxes.axescmd = 'subplot(1,2,2)'
     plotaxes.afteraxes = pcolor_afteraxes
-    # add_speed(plotaxes,2,bounds=[0.0,1e-10])
     ml_plot.add_speed(plotaxes,2,bounds=internal_speed_limits)
-    # add_speed(plotaxes,2)
     ml_plot.add_land(plotaxes, 2)
 
     # Individual components
@@ -218,7 +211,6 @@ def bathy_ref_lines(current_data):
     plotaxes.ylimits = ylimits
     plotaxes.axescmd = 'subplot(2,2,1)'
     plotaxes.afteraxes = pcolor_afteraxes
-    # add_x_velocity(plotaxes,1,bounds=[-1e-10,1e-10])
     ml_plot.add_x_velocity(plotaxes,1)
     ml_plot.add_land(plotaxes, 1)
 
@@ -229,7 +221,6 @@ def bathy_ref_lines(current_data):
     plotaxes.ylimits = ylimits
     plotaxes.axescmd = 'subplot(2,2,2)'
     plotaxes.afteraxes = pcolor_afteraxes
-    # add_y_velocity(plotaxes,1,bounds=[-0.000125,0.000125])
     ml_plot.add_y_velocity(plotaxes,1)
     ml_plot.add_land(plotaxes, 1)
 
@@ -241,7 +232,6 @@ def bathy_ref_lines(current_data):
     plotaxes.ylimits = ylimits
     plotaxes.axescmd = 'subplot(2,2,3)'
     plotaxes.afteraxes = pcolor_afteraxes
-    # add_x_velocity(plotaxes,2,bounds=[-1e-10,1e-10])
     ml_plot.add_x_velocity(plotaxes,2)
     ml_plot.add_land(plotaxes, 2)
 
@@ -252,10 +242,9 @@ def bathy_ref_lines(current_data):
     plotaxes.ylimits = ylimits
     plotaxes.axescmd = 'subplot(2,2,4)'
     plotaxes.afteraxes = pcolor_afteraxes
-    # add_y_velocity(plotaxes,2,bounds=[-0.8e-6,.8e-6])
     ml_plot.add_y_velocity(plotaxes,2)
-
     ml_plot.add_land(plotaxes, 2)
+
     # ========================================================================
     #  Profile Plots
     #  Note that these are not currently plotted by default - set
@@ -274,39 +263,40 @@ def bathy_ref_lines(current_data):
 
     # Internal surface
     def bathy_profile(current_data):
-        return current_data.x[:, slice_index], b(current_data)[:, slice_index]
+        return current_data.x[:, slice_index], \
+                    ml_plot.b(current_data)[:, slice_index]
 
     def lower_surface(current_data):
         if multilayer_data.init_type == 2:
             return current_data.x[:, slice_index],    \
-                    eta2(current_data)[:, slice_index]
+                    ml_plot.eta2(current_data)[:, slice_index]
         elif multilayer_data.init_type == 6:
             return current_data.y[slice_index, :],    \
-                    eta2(current_data)[slice_index, :]
+                    ml_plot.eta2(current_data)[slice_index, :]
 
     def upper_surface(current_data):
         if multilayer_data.init_type == 2:
             return current_data.x[:, slice_index],    \
-                    eta1(current_data)[:, slice_index]
+                    ml_plot.eta1(current_data)[:, slice_index]
         elif multilayer_data.init_type == 6:
             return current_data.y[slice_index, :],    \
-                    eta1(current_data)[slice_index, :]
+                    ml_plot.eta1(current_data)[slice_index, :]
 
     def top_speed(current_data):
         if multilayer_data.init_type == 2:
             return current_data.x[:, slice_index],    \
-                    water_u1(current_data)[:, slice_index]
+                    ml_plot.water_u1(current_data)[:, slice_index]
         elif multilayer_data.init_type == 6:
             return current_data.y[slice_index, :],    \
-                    water_u1(current_data)[slice_index, :]
+                    ml_plot.water_u1(current_data)[slice_index, :]
 
     def bottom_speed(current_data):
         if multilayer_data.init_type == 2:
             return current_data.x[:, slice_index],    \
-                    water_u2(current_data)[:, slice_index]
+                    ml_plot.water_u2(current_data)[:, slice_index]
         elif multilayer_data.init_type == 6:
             return current_data.y[slice_index, :],    \
-                    water_u2(current_data)[slice_index, :]
+                    ml_plot.water_u2(current_data)[slice_index, :]
 
     # Bathy
     plotitem = plotaxes.new_plotitem(plot_type='1d_from_2d_data')

examples/multi-layer/plane_wave/setrun.py

@@ -4,22 +4,22 @@
 that will be read in by the Fortran code.
 """
 
-from __future__ import absolute_import
-from __future__ import print_function
-import numpy
+import os
+
+import numpy as np
 
 import clawpack.geoclaw.data
 import clawpack.geoclaw.topotools as tt
 
 
 # Rotation transformations
 def transform_c2p(x,y,x0,y0,theta):
-    return ((x+x0)*numpy.cos(theta) - (y+y0)*numpy.sin(theta),
-            (x+x0)*numpy.sin(theta) + (y+y0)*numpy.cos(theta))
+    return ((x+x0)*np.cos(theta) - (y+y0)*np.sin(theta),
+            (x+x0)*np.sin(theta) + (y+y0)*np.cos(theta))
 
 def transform_p2c(x,y,x0,y0,theta):
-    return ( x*numpy.cos(theta) + y*numpy.sin(theta) - x0,
-            -x*numpy.sin(theta) + y*numpy.cos(theta) - y0)
+    return ( x*np.cos(theta) + y*np.sin(theta) - x0,
+            -x*np.sin(theta) + y*np.cos(theta) - y0)
 
 
 # Class containing some setup for the qinit especially for multilayer tests 
@@ -300,15 +300,15 @@ def setrun(claw_pkg='geoclaw'):
         # Do not checkpoint at all
         pass
 
-    elif numpy.abs(clawdata.checkpt_style) == 1:
+    elif np.abs(clawdata.checkpt_style) == 1:
         # Checkpoint only at tfinal.
         pass
 
-    elif numpy.abs(clawdata.checkpt_style) == 2:
+    elif np.abs(clawdata.checkpt_style) == 2:
         # Specify a list of checkpoint times.  
         clawdata.checkpt_times = [0.1,0.15]
 
-    elif numpy.abs(clawdata.checkpt_style) == 3:
+    elif np.abs(clawdata.checkpt_style) == 3:
         # Checkpoint every checkpt_interval timesteps (on Level 1)
         # and at the final time.
         clawdata.checkpt_interval = 5
@@ -384,8 +384,8 @@ def setrun(claw_pkg='geoclaw'):
     for (i,x_c) in enumerate(gauge_locations):
         # y0 = (self.run_data.clawdata.yupper - self.run_data.clawdata.ylower) / 2.0
         # x_p,y_p = transform_c2p(x_c,0.0,location[0],location[1],angle)
-        x_p = x_c * numpy.cos(0.0)
-        y_p = x_c * numpy.sin(0.0)
+        x_p = x_c * np.cos(0.0)
+        y_p = x_c * np.sin(0.0)
         # print "+=====+"
         # print x_c,0.0
         # print x_p,y_p
@@ -487,10 +487,10 @@ def write_topo_file(run_data, out_file, **kwargs):
     # Make topography
     topo_func = lambda x, y: bathy_step(x, y, **kwargs)
     topo = tt.Topography(topo_func=topo_func)
-    topo.x = numpy.linspace(run_data.clawdata.lower[0],
+    topo.x = np.linspace(run_data.clawdata.lower[0],
                             run_data.clawdata.upper[0],
                             run_data.clawdata.num_cells[0] + 8)
-    topo.y = numpy.linspace(run_data.clawdata.lower[1],
+    topo.y = np.linspace(run_data.clawdata.lower[1],
                             run_data.clawdata.upper[1],
                             run_data.clawdata.num_cells[1] + 8)
     topo.write(out_file)