Add Testing Matrix (#748)

* Add initial testing matrix

* Fix bugs in testing script

* Add macos to testing

* Cleanup some source that was failing via pyflake

* Tweak flake8 call

* Limit build options and python versions to see if the testing can pass again

* Try using current numpy

* Verbose pytest output.

* Add test summary action

* Restrict coverage uploading to one config

* Fix errant .

* Correct some github action syntax bugs

* Correct missing path info

* Fix bad path/naming again

* Fix another path problem

* Try confusing pathing fix

* Fix linting path

* One more try at getting pathing right

* This is on me, clearly I cannot deal with paths

* Turn off fast fail

* Adjust archive source file path

* Uniquely identify test results

* Fix missing variable declarations in archiving step

* Do not capture output in pytest

* Update the expected dimension of limiters array.

For sharpclaw, this is sometimes num_eqn and sometimes num_waves depending on options.

* Make sure limiters is a list.

* Fix stupid bug I just introduced.

* Avoid explicitly indexing into empty aux array.

* Remove debugging print statements.

* Add a space to re-trigger tests on Github.

* Expand grid for 3D acoustics test.

* Test if WENO limiting passes for 3D acoustics.

---------

Co-authored-by: David Ketcheson <dketch@gmail.com>

Author: mandli

.github/workflows/testing.yml

@@ -1,4 +1,4 @@
-name: Test PyClaw
+name: Test PyClaw 
 
 on:
   push:
@@ -15,20 +15,53 @@ env:
   CLAW: ${{ github.workspace }}
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  tests:
+    name: >
+      ${{ matrix.os }} - py ${{ matrix.python-version }} - ${{ matrix.toolchain.compiler }} ${{ matrix.build }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false # Probably want to turn this off for a large matrix
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.12"]
+        build: [debug, opt]
+        toolchain:
+          - {compiler: gcc, version: 14}
+          - {compiler: gcc, version: 15}
+          # - {compiler: intel, version: '2025.0'}
+          # - {compiler: intel-classic, version: '2021.10'}
+          # - {compiler: nvidia-hpc, version: '25.1'} # does not build python
+          # - {compiler: lfortran, version: '0.45.0'} # lfortran not yet supported
+          # - {compiler: flang, version: '20.1.0'} # flang not yet supported
+        # include:
+        #   - os: ubuntu-latest
+        #     python-version: 3.10
+        #     build: opt
+        #     toolchain: {compiler: gcc, version: 14}
+        exclude:
+          - os: ubuntu-latest
+            toolchain: {compiler: gcc, version: 15}
+          - os: macos-latest
+            toolchain: {compiler: gcc, version: 14}
+
     steps:
-    - name: Set up Python 3.10
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
-    - name: Install dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install gfortran
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set up compilers
+      uses: fortran-lang/setup-fortran@v1
+      id: setup-fortran
+      with:
+        compiler: ${{ matrix.toolchain.compiler }}
+        version: ${{ matrix.toolchain.version }}
 
+    - name: Install python dependencies
+      run: |
         python -m pip install --upgrade pip
-        pip install 'numpy<2.0'
+        # pip install 'numpy<2.0'
+        pip install numpy
         pip install matplotlib #Some imports require matplotlib
         pip install scipy #To not skip tests
         pip install flake8 meson-python ninja pytest coveralls
@@ -44,21 +77,77 @@ jobs:
       uses: actions/checkout@v4.1.5
       with:
         path: pyclaw
-    
+
     - name: Install clawpack
       run: |
-        cd ${CLAW}
+        if [ "${{ matrix.toolchain.compiler }}" = "gcc" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-O0 -g -fcheck=all -fbacktrace -fbounds-check -ffpe-trap=invalid,zero,overflow -finit-real=nan -finit-integer=nan -Wall -Wunderflow -Wextra -Wconversion -Wuninitialized -Warray-bounds -Wshadow -Wno-unused-function -Wno-unused-variable -Wno-unused-parameter -Wno-unused-label -Wno-unused-but-set-variable"
+            export CFLAGS=""
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            # export FFLAGS="-O1 -funroll-loops -finline-functions -ftree-vectorize -fstack-protector-strong -flto -march=native"
+            export FFLAGS=""
+            export CFLAGS=""
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "intel" ] || [ "${{ matrix.toolchain.compiler }}" = "intel-classic" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS=""
+            export CFLAGS=""
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            export FFLAGS=""
+            export CFLAGS=""
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        else
+          echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
+          exit 1
+        fi
+        echo "Using `$FC --version`"
+        echo "FFLAGS: $FFLAGS"
+        echo "CFLAGS: $CFLAGS"
+        cd ${{ env.CLAW }}
         pip install --no-build-isolation --editable .
 
+    - name: Lint with flake8
+      if: ${{ matrix.build == 'debug' }}
+      run: |
+        cd ${{ env.CLAW }}/pyclaw
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude "development","src/pyclaw/fileio/netcdf.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 ${CLAW}/pyclaw
-        coverage run --source=src -m pytest --ignore=development -k "not test_shallow_sphere"
+        cd ${{ env.CLAW }}/pyclaw
+        coverage run --source=src -m pytest -vv -s --showlocals --ignore=development -k "not test_shallow_sphere" --junitxml=test-report.xml
 
-    - name: Upload to Coveralls
+    - name: Process test results
+      uses: test-summary/action@v2.4
+      if: always()
+      with:
+        paths: ${{ env.CLAW }}/pyclaw/test-report.xml
+        output: ${{ env.CLAW }}/pyclaw/test-summary.md
+        show: "all"
+
+    - name: Upload test results
+      # if: failure()
       if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.toolchain.compiler }}-${{ matrix.build }}
+        path: ${{ env.CLAW }}/pyclaw/test-summary.md
+        if-no-files-found: ignore
+
+    - name: Upload to Coveralls
+      if: ${{ matrix.os == 'ubuntu-latest' && matrix.toolchain.compiler == 'gcc' && matrix.build == 'opt' && matrix.python-version == '3.12' }}
       run: |
-        cd ${CLAW}/pyclaw
+        cd ${{ env.CLAW }}/pyclaw
         ls -l .coverage
         coveralls
       env:

cleanup_examples.py

@@ -4,32 +4,32 @@
 Cleans up by deleting object files, executable, and _output directory.
 """
 
-import os,sys,glob
+import os
+import sys
 import shutil
 
 if __name__ == "__main__":
 
     examples_dir = os.path.abspath('./examples')
-    print "Will remove all _output, _plots, and build directories from ",examples_dir
-    ans = raw_input("Ok? ")
+    print(f"Will remove all _output, _plots, and build directories from {examples_dir}")
+    ans = input("Ok? ")
     if ans.lower() not in ['y','yes']:
-        print "Aborting."
+        print("Aborting.")
         sys.exit()
 
     os.chdir(examples_dir)
     exdirlist = []
     for (dirpath, subdirs, files) in os.walk('.'):
         currentdir = os.path.abspath(os.getcwd())
         os.chdir(os.path.abspath(dirpath))
-        
-        print 'In directory ',dirpath
-        
+
+        print(f'In directory {dirpath}')
+
         if os.path.isdir('_output'):
             shutil.rmtree('./_output')
         if os.path.isdir('_plots'):
             shutil.rmtree('./_plots')
         if os.path.isdir('build'):
             shutil.rmtree('./build')
-            
-        os.chdir(currentdir)
 
+        os.chdir(currentdir)

examples/acoustics_3d_variable/acoustics_3d_interface.py

@@ -64,7 +64,7 @@ def setup(use_petsc=False,outdir='./_output',solver_type='classic',
         if solver_type=='classic':
             solver.dimensional_split=True
         else:
-            solver.lim_type = 1
+            solver.lim_type = 2
 
         solver.limiters = [4]
 

examples/acoustics_3d_variable/test_3d_acoustics.py

@@ -6,7 +6,7 @@
 
 def check_error(**kwargs):
 
-    claw = acoustics_3d_interface.setup(problem='homogeneous',mx=128,my=4,mz=4,disable_output=True,**kwargs)
+    claw = acoustics_3d_interface.setup(problem='homogeneous',mx=128,my=8,mz=8,disable_output=True,**kwargs)
     claw.run()
 
     test_pressure = claw.frames[-1].q[0,:,:,:]

examples/compare_solvers.py

@@ -160,20 +160,20 @@ def compare_2D(nx=(250,250)):
     import sys
 
     vis = True
-    
+
     if vis:
         compare_solvers.outdir='./_output'
     else:
         compare_solvers.outdir = None
-        
+
     if len(sys.argv) > 1:
         nx_1D = int(sys.argv[1])
     else:
         nx_1D = 500
 
     if len(sys.argv) > 2:
         # '(2,2)' -> (2,2)
-        nx_2D = tuple(int(i) for i in argv.split(','))
+        nx_2D = tuple(int(i) for i in sys.argv.split(','))
     else:
         nx_2D = 100,100
 

fvmbook/chap22/inclusion/inclusion.py

@@ -4,7 +4,7 @@
 Variable-coefficient elasticity example.
 """
 import numpy as np
-from six.moves import range
+
 t0wall  = 0.025
 tperiod = 0.05
 
@@ -13,20 +13,20 @@ def moving_wall_bc(state,dim,t,qbc,auxbc,num_ghost):
     if t<t0wall:
         s = np.sin(np.pi*t/tperiod)
     else:
-        s = 0.
+        s = 0.0
 
     for i in range(num_ghost):
         # First reflect-extrapolate
         qbc[:,i,:] = qbc[:,2*num_ghost-i-1,:]
         # Now set velocity
         qbc[3,i,:] = 2.0*s - qbc[3,i,:]
         qbc[4,i,:] =       - qbc[4,i,:]
-    
+
 
 #def no_stress_bc(state,dim,t,qbc,num_ghost):
 #    """No-stress boundary condition: sigma_{12} = sigma_{11} = 0"""
 #    if state.grid.on_lower_boundary[idim]:
-#        jghost = 
+#        jghost =
 #    # First extrapolate
 #    tmp = qbc[:,:,self.num_ghost]
 #    tmp = np.tile(tmp,(1,1,num_ghost))
@@ -35,8 +35,8 @@ def moving_wall_bc(state,dim,t,qbc,auxbc,num_ghost):
 #    # Then negate the sig12 and sig11 components
 
 def integrate_displacement(solver,state):
-    aux[5,:,:] = aux[5,:,:] + dt*q[3,:,:]
-    aux[6,:,:] = aux[6,:,:] + dt*q[4,:,:]
+    state.aux[5,:,:] = state.aux[5,:,:] + solver.dt * state.q[3,:,:]
+    state.aux[6,:,:] = state.aux[6,:,:] + solver.dt * state.q[4,:,:]
 
 
 def inclusion():
@@ -116,19 +116,19 @@ def inclusion():
 #--------------------------
 def setplot(plotdata):
 #--------------------------
-    
-    """ 
+
+    """
     Specify what is to be plotted at each frame.
     Input:  plotdata, an instance of visclaw.data.ClawPlotData.
     Output: a modified version of plotdata.
-    
-    """ 
+
+    """
 
 
     from clawpack.visclaw import colormaps
 
     plotdata.clearfigures()  # clear any old figures,axes,items data
-    
+
 
     # Figure for pressure
     # -------------------
@@ -148,11 +148,11 @@ def setplot(plotdata):
     plotitem.pcolor_cmap = colormaps.yellow_red_blue
     plotitem.add_colorbar = True
     plotitem.show = True       # show on plot?
-    
+
 
     # Figure for x-velocity plot
     # -----------------------
-    
+
     plotfigure = plotdata.new_plotfigure(name='x-Velocity', figno=1)
 
     # Set up for axes in this figure:
@@ -166,7 +166,7 @@ def setplot(plotdata):
     plotitem.pcolor_cmap = colormaps.yellow_red_blue
     plotitem.add_colorbar = True
     plotitem.show = True       # show on plot?
-    
+
     # Parameters used only when creating html and/or latex hardcopy
     # e.g., via visclaw.frametools.printframes:
 
@@ -190,4 +190,3 @@ def setplot(plotdata):
 
     from clawpack.pyclaw import plot
     plot.interactive_plot()
-

src/pyclaw/classic/flux3.f90

@@ -199,7 +199,7 @@ subroutine flux3(ixyz,maxm,num_eqn,num_waves,num_ghost,mx, &
 
     ! aux2(1-num_ghost,1,2) is the start of a 1d array now used by rpn3
     call rpn3(ixyz,maxm,num_eqn,num_waves,num_aux,num_ghost,mx,q1d,q1d, &
-              aux2(1,1-num_ghost,2),aux2(1,1-num_ghost,2),wave,s,amdq,apdq)
+              aux2(:,1-num_ghost,2),aux2(:,1-num_ghost,2),wave,s,amdq,apdq)
 
     ! Set qadd for the donor-cell upwind method (Godunov)
     forall (m = 1:num_eqn, i = 1:mx+1)

src/pyclaw/sharpclaw/solver.py

@@ -519,9 +519,14 @@ def check_3rd_ord_cond(self,state,step_index,dtFE):
     def _set_mthlim(self):
         self._mthlim = self.limiters
         if not isinstance(self.limiters,list): self._mthlim=[self._mthlim]
-        if len(self._mthlim)==1: self._mthlim = self._mthlim * self.num_waves
-        if len(self._mthlim)!=self.num_waves:
-            raise Exception('Length of solver.limiters is not equal to 1 or to solver.num_waves')
+        if self.char_decomp == 0:  # entry-wise limiting
+            if len(self._mthlim)==1: self._mthlim = self._mthlim * self.num_eqn
+            if len(self._mthlim)!=self.num_eqn:
+                raise Exception('Length of solver.limiters is not equal to 1 or to solver.num_eqn')
+        else: # Wave-wise limiting
+            if len(self._mthlim)==1: self._mthlim = self._mthlim * self.num_waves
+            if len(self._mthlim)!=self.num_waves:
+                raise Exception('Length of solver.limiters is not equal to 1 or to solver.num_waves')
 
 
     def dq(self,state):