From bb3388e26da92039075a736e3777043033992d99 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Tue, 26 Aug 2025 08:54:32 -0400
Subject: [PATCH 01/29] Add initial testing matrix

---
 .github/workflows/testing.yml | 96 +++++++++++++++++++++++++++++++----
 1 file changed, 87 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 5f6dfe7e..0bfda23b 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -15,18 +15,50 @@ 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]
+        python-version: [3.10, 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 matplotlib #Some imports require matplotlib
@@ -44,12 +76,49 @@ jobs:
       uses: actions/checkout@v4.1.5
       with:
         path: pyclaw
-    
+
     - name: Install clawpack
       run: |
+        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 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
+        else
+          echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
+          exit 1
+        fi
+        echo "Using `$FC --version`"
+        echo "FFLAGS: $FFLAGS"
+        echo "CFLAGS: $CFLAGS"
         cd ${CLAW}
         pip install --no-build-isolation --editable .
 
+    - name: Lint with flake8
+      if: ${{ matrix.build == 'debug' }}
+      run: |
+        cd ${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 dev
+        # 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
@@ -64,3 +133,12 @@ jobs:
       env:
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Upload test results
+      if: failure()
+      uses: actions/upload-artifact@v4
+      with:
+        name: test_results
+        # Currently this does not save anything
+        path: ${{ env.CLAW }}/pyclaw/*_output
+        if-no-files-found: ignore

From 38ef2aec77d8ff9056e9f76fed0861bedfd1f55b Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Tue, 26 Aug 2025 09:01:35 -0400
Subject: [PATCH 02/29] Fix bugs in testing script

---
 .github/workflows/testing.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0bfda23b..df93964b 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.10, 3.12]
+        python-version: ["3.10", "3.12"]
         build: [debug, opt]
         toolchain:
           - {compiler: gcc, version: 14}
@@ -100,6 +100,7 @@ jobs:
           else
             echo "Unknown build type: ${{ matrix.build }}"
             exit 1
+          fi
         else
           echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
           exit 1

From d9ce97a733044e05de9355611527544c2361c588 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Tue, 26 Aug 2025 09:11:05 -0400
Subject: [PATCH 03/29] Add macos to testing

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index df93964b..26d80562 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, macos-latest]
         python-version: ["3.10", "3.12"]
         build: [debug, opt]
         toolchain:

From 3f7766c146d2079c0da17009c3570c47bfcfbddd Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Tue, 26 Aug 2025 09:20:20 -0400
Subject: [PATCH 04/29] Cleanup some source that was failing via pyflake

---
 cleanup_examples.py                   | 18 ++++++++---------
 examples/compare_solvers.py           |  6 +++---
 fvmbook/chap22/inclusion/inclusion.py | 29 +++++++++++++--------------
 3 files changed, 26 insertions(+), 27 deletions(-)

diff --git a/cleanup_examples.py b/cleanup_examples.py
index 483a592f..d9627d89 100755
--- a/cleanup_examples.py
+++ b/cleanup_examples.py
@@ -4,16 +4,17 @@
 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)
@@ -21,15 +22,14 @@
     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)
diff --git a/examples/compare_solvers.py b/examples/compare_solvers.py
index de0902b1..1d40d761 100755
--- a/examples/compare_solvers.py
+++ b/examples/compare_solvers.py
@@ -160,12 +160,12 @@ 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:
@@ -173,7 +173,7 @@ def compare_2D(nx=(250,250)):
 
     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
 
diff --git a/fvmbook/chap22/inclusion/inclusion.py b/fvmbook/chap22/inclusion/inclusion.py
index bb3489be..0777bd1b 100644
--- a/fvmbook/chap22/inclusion/inclusion.py
+++ b/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
 
@@ -13,7 +13,7 @@ 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
@@ -21,12 +21,12 @@ def moving_wall_bc(state,dim,t,qbc,auxbc,num_ghost):
         # 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()
-

From ebce14678bd2fecca70869ec8a597d93b1b51ae9 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Tue, 26 Aug 2025 09:31:55 -0400
Subject: [PATCH 05/29] Tweak flake8 call

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 26d80562..b59a973e 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.10", "3.12"]
+        python-version: ["3.8", "3.12"]
         build: [debug, opt]
         toolchain:
           - {compiler: gcc, version: 14}
@@ -116,7 +116,7 @@ jobs:
       run: |
         cd ${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 dev
+        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
 

From 6dbc5c4b2fc46f72f74477f67edf7a3f7fb2890a Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Tue, 26 Aug 2025 09:41:39 -0400
Subject: [PATCH 06/29] Limit build options and python versions to see if the
 testing can pass again

---
 .github/workflows/testing.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index b59a973e..eca9bc7e 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.12"]
+        python-version: ["3.12"]
         build: [debug, opt]
         toolchain:
           - {compiler: gcc, version: 14}
@@ -84,7 +84,8 @@ jobs:
             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="-O1 -funroll-loops -finline-functions -ftree-vectorize -fstack-protector-strong -flto -march=native"
+            export FFLAGS=""
             export CFLAGS=""
           else
             echo "Unknown build type: ${{ matrix.build }}"

From 449197ead520ca0abc6ff79a83ceb27c468bf820 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Tue, 26 Aug 2025 09:48:27 -0400
Subject: [PATCH 07/29] Try using current numpy

---
 .github/workflows/testing.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index eca9bc7e..280be50c 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -60,7 +60,8 @@ jobs:
     - 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

From de9baa170b0a21d03244ef254ef4934c1635249d Mon Sep 17 00:00:00 2001
From: David Ketcheson <dketch@gmail.com>
Date: Wed, 3 Sep 2025 07:03:58 +0300
Subject: [PATCH 08/29] Verbose pytest output.

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 280be50c..c1351d99 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -125,7 +125,7 @@ jobs:
     - name: Test with pytest
       run: |
         cd ${CLAW}/pyclaw
-        coverage run --source=src -m pytest --ignore=development -k "not test_shallow_sphere"
+        coverage run --source=src -m pytest -vv --showlocals --ignore=development -k "not test_shallow_sphere"
 
     - name: Upload to Coveralls
       if: always()

From 9bcbb123eaa94c5c3839a2ac5f2c4a4039d35c99 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:05:39 -0400
Subject: [PATCH 09/29] Add test summary action

---
 .github/workflows/testing.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index c1351d99..e8665494 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -125,7 +125,15 @@ jobs:
     - name: Test with pytest
       run: |
         cd ${CLAW}/pyclaw
-        coverage run --source=src -m pytest -vv --showlocals --ignore=development -k "not test_shallow_sphere"
+        coverage run --source=src -m pytest -vv --showlocals --ignore=development -k "not test_shallow_sphere" --junitxml=test-results.xml
+
+    - name: Process test results
+      uses: test-summary/action@v2.4
+      if: always()
+      with:
+        paths: .test_report.xml
+        output: test-summary.md
+        show: all
 
     - name: Upload to Coveralls
       if: always()

From 8788601d84366472281f356e1cc9ea03d76eb843 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:12:33 -0400
Subject: [PATCH 10/29] Restrict coverage uploading to one config

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index e8665494..442e2507 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -136,7 +136,7 @@ jobs:
         show: all
 
     - name: Upload to Coveralls
-      if: always()
+      if: ${ matrix.os == 'ubuntu-latest' matrix.toolchain.compiler == 'gcc' && matrix.build == 'opt' && python-version == '3.12' }
       run: |
         cd ${CLAW}/pyclaw
         ls -l .coverage

From 9912138f2b5985cbb82de55b7c5680e58a382342 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:12:55 -0400
Subject: [PATCH 11/29] Fix errant .

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 442e2507..39e73ff3 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -131,7 +131,7 @@ jobs:
       uses: test-summary/action@v2.4
       if: always()
       with:
-        paths: .test_report.xml
+        paths: test_report.xml
         output: test-summary.md
         show: all
 

From b91bce4d563d02d91dcd10240f8e58dc6d4c30a4 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:16:30 -0400
Subject: [PATCH 12/29] Correct some github action syntax bugs

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 39e73ff3..8298b08b 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -136,7 +136,7 @@ jobs:
         show: all
 
     - name: Upload to Coveralls
-      if: ${ matrix.os == 'ubuntu-latest' matrix.toolchain.compiler == 'gcc' && matrix.build == 'opt' && python-version == '3.12' }
+      if: ${{ matrix.os == 'ubuntu-latest' && matrix.toolchain.compiler == 'gcc' && matrix.build == 'opt' && matrix.python-version == '3.12' }}
       run: |
         cd ${CLAW}/pyclaw
         ls -l .coverage

From 306968340cf0ccde173d5e1f68d5be9223555a1e Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:23:56 -0400
Subject: [PATCH 13/29] Correct missing path info

---
 .github/workflows/testing.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 8298b08b..25d9a939 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -110,13 +110,13 @@ jobs:
         echo "Using `$FC --version`"
         echo "FFLAGS: $FFLAGS"
         echo "CFLAGS: $CFLAGS"
-        cd ${CLAW}
+        cd ${{ env.CLAW }}
         pip install --no-build-isolation --editable .
 
     - name: Lint with flake8
       if: ${{ matrix.build == 'debug' }}
       run: |
-        cd ${CLAW}/pyclaw
+        cd ${{ env.CLAW }}
         # 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
@@ -124,21 +124,21 @@ jobs:
 
     - name: Test with pytest
       run: |
-        cd ${CLAW}/pyclaw
+        cd ${{ env.CLAW }}
         coverage run --source=src -m pytest -vv --showlocals --ignore=development -k "not test_shallow_sphere" --junitxml=test-results.xml
 
     - name: Process test results
       uses: test-summary/action@v2.4
       if: always()
       with:
-        paths: test_report.xml
+        paths: ${{ env.CLAW }}/pyclaw/test_report.xml
         output: test-summary.md
         show: all
 
     - 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:
@@ -146,10 +146,10 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Upload test results
-      if: failure()
+      # if: failure()
+      if: always()
       uses: actions/upload-artifact@v4
       with:
         name: test_results
-        # Currently this does not save anything
-        path: ${{ env.CLAW }}/pyclaw/*_output
+        path: ${{ env.CLAW }}/pyclaw/test-summary.md
         if-no-files-found: ignore

From 33307b4df0dbd7f2411a3eecbd6ee7ed902bba4c Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:30:14 -0400
Subject: [PATCH 14/29] Fix bad path/naming again

---
 .github/workflows/testing.yml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 25d9a939..cedce054 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -20,7 +20,7 @@ jobs:
       ${{ 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
+      fail-fast: true # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: ["3.12"]
@@ -125,7 +125,7 @@ jobs:
     - name: Test with pytest
       run: |
         cd ${{ env.CLAW }}
-        coverage run --source=src -m pytest -vv --showlocals --ignore=development -k "not test_shallow_sphere" --junitxml=test-results.xml
+        coverage run --source=src -m pytest -vv --showlocals --ignore=development -k "not test_shallow_sphere" --junitxml=test-report.xml
 
     - name: Process test results
       uses: test-summary/action@v2.4
@@ -135,6 +135,15 @@ jobs:
         output: test-summary.md
         show: all
 
+    - name: Upload test results
+      # if: failure()
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: test_results
+        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: |
@@ -144,12 +153,3 @@ jobs:
       env:
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-    - name: Upload test results
-      # if: failure()
-      if: always()
-      uses: actions/upload-artifact@v4
-      with:
-        name: test_results
-        path: ${{ env.CLAW }}/pyclaw/test-summary.md
-        if-no-files-found: ignore

From 9650824a526c98e27d7554726b30d1d84bdb11a8 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:37:30 -0400
Subject: [PATCH 15/29] Fix another path problem

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index cedce054..0b54c9c7 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -124,7 +124,7 @@ jobs:
 
     - name: Test with pytest
       run: |
-        cd ${{ env.CLAW }}
+        cd ${{ env.CLAW }}/pyclaw
         coverage run --source=src -m pytest -vv --showlocals --ignore=development -k "not test_shallow_sphere" --junitxml=test-report.xml
 
     - name: Process test results

From 6506f858658c8273c7fa94ca829c0992647e3a2e Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:45:15 -0400
Subject: [PATCH 16/29] Try confusing pathing fix

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0b54c9c7..29e0e1c5 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -131,7 +131,7 @@ jobs:
       uses: test-summary/action@v2.4
       if: always()
       with:
-        paths: ${{ env.CLAW }}/pyclaw/test_report.xml
+        paths: ${{ env.CLAW }}/test_report.xml
         output: test-summary.md
         show: all
 
@@ -141,7 +141,7 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: test_results
-        path: ${{ env.CLAW }}/pyclaw/test-summary.md
+        path: ${{ env.CLAW }}/test-summary.md
         if-no-files-found: ignore
 
     - name: Upload to Coveralls

From f6c82efa067ba2877910e30cf5b82f5dc4f87b33 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 10:58:52 -0400
Subject: [PATCH 17/29] Fix linting path

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 29e0e1c5..8fdfac14 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -116,7 +116,7 @@ jobs:
     - name: Lint with flake8
       if: ${{ matrix.build == 'debug' }}
       run: |
-        cd ${{ env.CLAW }}
+        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

From bf6b195b1384d2522757e8f8a99da420f8fb17d9 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 11:35:49 -0400
Subject: [PATCH 18/29] One more try at getting pathing right

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 8fdfac14..9a0ee2c3 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -131,7 +131,7 @@ jobs:
       uses: test-summary/action@v2.4
       if: always()
       with:
-        paths: ${{ env.CLAW }}/test_report.xml
+        paths: ${{ env.CLAW }}/pyclaw/test_report.xml
         output: test-summary.md
         show: all
 
@@ -141,7 +141,7 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: test_results
-        path: ${{ env.CLAW }}/test-summary.md
+        path: ${{ env.CLAW }}/pyclaw/test-summary.md
         if-no-files-found: ignore
 
     - name: Upload to Coveralls

From 1d3feaec918abb2c2fa2b5c92d0d7b5eb5b54037 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 11:43:53 -0400
Subject: [PATCH 19/29] This is on me, clearly I cannot deal with paths

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 9a0ee2c3..b4fa4a2c 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -131,7 +131,7 @@ jobs:
       uses: test-summary/action@v2.4
       if: always()
       with:
-        paths: ${{ env.CLAW }}/pyclaw/test_report.xml
+        paths: ${{ env.CLAW }}/pyclaw/test-report.xml
         output: test-summary.md
         show: all
 

From 42a61ca3c6b6f31e1d072c686fac22209a19145f Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 12:09:05 -0400
Subject: [PATCH 20/29] Turn off fast fail

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index b4fa4a2c..ce5c6612 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -20,7 +20,7 @@ jobs:
       ${{ matrix.os }} - py ${{ matrix.python-version }} - ${{ matrix.toolchain.compiler }} ${{ matrix.build }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: true # Probably want to turn this off for a large matrix
+      fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: ["3.12"]
@@ -133,7 +133,7 @@ jobs:
       with:
         paths: ${{ env.CLAW }}/pyclaw/test-report.xml
         output: test-summary.md
-        show: all
+        show: "all"
 
     - name: Upload test results
       # if: failure()

From dbc8e26beda7d6505763c72033928a33ca21a7f6 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 12:55:05 -0400
Subject: [PATCH 21/29] Adjust archive source file path

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index ce5c6612..df53cd47 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -132,7 +132,7 @@ jobs:
       if: always()
       with:
         paths: ${{ env.CLAW }}/pyclaw/test-report.xml
-        output: test-summary.md
+        output: ${{ env.CLAW }}/pyclaw/test-summary.md
         show: "all"
 
     - name: Upload test results

From a16fcb8f34ac98248b220bee3db16ebbbeec030b Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 13:04:25 -0400
Subject: [PATCH 22/29] Uniquely identify test results

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index df53cd47..0f817480 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -140,7 +140,7 @@ jobs:
       if: always()
       uses: actions/upload-artifact@v4
       with:
-        name: test_results
+        name: ${{ matrix.os }}-py${{ matrix.python-version }}-{{ matrix.toolchain.compiler }}-{{ matrix.build }}
         path: ${{ env.CLAW }}/pyclaw/test-summary.md
         if-no-files-found: ignore
 

From a60230c2075adfe867547273e36d576690078109 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 4 Sep 2025 15:09:50 -0400
Subject: [PATCH 23/29] Fix missing variable declarations in archiving step

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0f817480..3ec07532 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -140,7 +140,7 @@ jobs:
       if: always()
       uses: actions/upload-artifact@v4
       with:
-        name: ${{ matrix.os }}-py${{ matrix.python-version }}-{{ matrix.toolchain.compiler }}-{{ matrix.build }}
+        name: ${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.toolchain.compiler }}-${{ matrix.build }}
         path: ${{ env.CLAW }}/pyclaw/test-summary.md
         if-no-files-found: ignore
 

From d30fdcb2e489a4e7fbd0c54840d58c06ad0da8ba Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 5 Sep 2025 10:09:19 -0400
Subject: [PATCH 24/29] Do not capture output in pytest

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 3ec07532..b33b4ae2 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -125,7 +125,7 @@ jobs:
     - name: Test with pytest
       run: |
         cd ${{ env.CLAW }}/pyclaw
-        coverage run --source=src -m pytest -vv --showlocals --ignore=development -k "not test_shallow_sphere" --junitxml=test-report.xml
+        coverage run --source=src -m pytest -vv -s --showlocals --ignore=development -k "not test_shallow_sphere" --junitxml=test-report.xml
 
     - name: Process test results
       uses: test-summary/action@v2.4

From ffc2ece1aa53eddaf3a948ceb8c0111cdaad35c3 Mon Sep 17 00:00:00 2001
From: David Ketcheson <dketch@gmail.com>
Date: Mon, 6 Oct 2025 12:25:45 -0700
Subject: [PATCH 25/29] Update the expected dimension of limiters array.

For sharpclaw, this is sometimes num_eqn and sometimes num_waves depending on options.
---
 src/pyclaw/sharpclaw/solver.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/pyclaw/sharpclaw/solver.py b/src/pyclaw/sharpclaw/solver.py
index 77865ccb..f0553572 100644
--- a/src/pyclaw/sharpclaw/solver.py
+++ b/src/pyclaw/sharpclaw/solver.py
@@ -518,10 +518,16 @@ 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 not isinstance(self.limiters,list): self._mthlim=[self._mthlim]
+            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 not isinstance(self.limiters,list): self._mthlim=[self._mthlim]
+            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):

From ed97c6d483e5aa03bbfcc4733be5aea91dcf6234 Mon Sep 17 00:00:00 2001
From: David Ketcheson <dketch@gmail.com>
Date: Mon, 6 Oct 2025 12:38:05 -0700
Subject: [PATCH 26/29] Make sure limiters is a list.

---
 src/pyclaw/sharpclaw/solver.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/pyclaw/sharpclaw/solver.py b/src/pyclaw/sharpclaw/solver.py
index f0553572..2961f807 100644
--- a/src/pyclaw/sharpclaw/solver.py
+++ b/src/pyclaw/sharpclaw/solver.py
@@ -518,6 +518,7 @@ 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 self.char_decomp == 0:  # entry-wise limiting
             if len(self._mthlim)==1: self._mthlim = self._mthlim * self.num_eqn
             if not isinstance(self.limiters,list): self._mthlim=[self._mthlim]

From 92b956ce9a49ad274c25d72874f5997d4d6cbf98 Mon Sep 17 00:00:00 2001
From: David Ketcheson <dketch@gmail.com>
Date: Mon, 6 Oct 2025 12:50:52 -0700
Subject: [PATCH 27/29] Fix stupid bug I just introduced.

---
 src/pyclaw/sharpclaw/solver.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pyclaw/sharpclaw/solver.py b/src/pyclaw/sharpclaw/solver.py
index 2961f807..644c141e 100644
--- a/src/pyclaw/sharpclaw/solver.py
+++ b/src/pyclaw/sharpclaw/solver.py
@@ -519,14 +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]
+        print(len(self._mthlim), self._mthlim)
         if self.char_decomp == 0:  # entry-wise limiting
             if len(self._mthlim)==1: self._mthlim = self._mthlim * self.num_eqn
-            if not isinstance(self.limiters,list): self._mthlim=[self._mthlim]
+            print(len(self._mthlim), self._mthlim)
             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 not isinstance(self.limiters,list): self._mthlim=[self._mthlim]
             if len(self._mthlim)!=self.num_waves:
                 raise Exception('Length of solver.limiters is not equal to 1 or to solver.num_waves')
 

From 0fefb498cfb9337eb44832f9d17d0dcd4a036124 Mon Sep 17 00:00:00 2001
From: David Ketcheson <dketch@gmail.com>
Date: Mon, 6 Oct 2025 12:59:54 -0700
Subject: [PATCH 28/29] Avoid explicitly indexing into empty aux array.

---
 src/pyclaw/classic/flux3.f90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pyclaw/classic/flux3.f90 b/src/pyclaw/classic/flux3.f90
index ac3f316f..545dea34 100644
--- a/src/pyclaw/classic/flux3.f90
+++ b/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)

From 86c212b9a69e23135a2139319e24d3dff7634b4c Mon Sep 17 00:00:00 2001
From: David Ketcheson <dketch@gmail.com>
Date: Mon, 6 Oct 2025 16:49:31 -0700
Subject: [PATCH 29/29] Remove debugging print statements.

---
 src/pyclaw/sharpclaw/solver.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/pyclaw/sharpclaw/solver.py b/src/pyclaw/sharpclaw/solver.py
index 644c141e..7f991e6d 100644
--- a/src/pyclaw/sharpclaw/solver.py
+++ b/src/pyclaw/sharpclaw/solver.py
@@ -519,10 +519,8 @@ 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]
-        print(len(self._mthlim), self._mthlim)
         if self.char_decomp == 0:  # entry-wise limiting
             if len(self._mthlim)==1: self._mthlim = self._mthlim * self.num_eqn
-            print(len(self._mthlim), self._mthlim)
             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