NatLabRockies · malihass · Jul 31, 2026 · Jul 31, 2026 · Jul 31, 2026 · Jul 31, 2026
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -33,7 +33,7 @@ jobs:
         os: ['ubuntu-latest']
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
         working-directory: ${{github.workspace}}
     steps:
       - uses: actions/checkout@v4
@@ -67,7 +67,7 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest']
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
         working-directory: ${{github.workspace}}
 
     steps:
@@ -106,7 +106,7 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest']
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
         working-directory: ${{github.workspace}}
 
     steps:
@@ -119,7 +119,7 @@ jobs:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
 
-      - name: Formatting and sorting import
+      - name: Test
         run: |
           pixi run test
 
@@ -133,7 +133,7 @@ jobs:
         os: ['ubuntu-latest']
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
         working-directory: ${{github.workspace}}
     steps:
       - uses: actions/checkout@v4
@@ -172,7 +172,7 @@ jobs:
         os: ['ubuntu-22.04']
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
         working-directory: ${{github.workspace}}
     steps:
       - uses: actions/checkout@v4
@@ -205,58 +205,47 @@ jobs:
           cd OFsolvers/OF9/birdmultiphaseEulerFoam
           export WM_COMPILE_OPTION=Debug
           ./Allwmake
-          cd ../../../
       - name: Run deckwer17 PBE
         run: |
           cd experimental_cases/OF9/deckwer17
           bash run.sh 
-          cd ../../../
       - name: Run deckwer17 constantD
         run: |
           cd experimental_cases/OF9/deckwer17
           cp constant/phaseProperties_constantd constant/phaseProperties
           bash run.sh 
-          cd ../../../
       - name: Run deckwer19 PBE
         run: |
           cd experimental_cases/OF9/deckwer19
           bash run.sh 
-          cd ../../../
       - name: Run side sparger tutorial
         run: |
           cd tutorial_cases/OF9/side_sparger
           bash run.sh 
-          cd ../../../
       - name: Run bubble column tutorial
         run: |
           cd tutorial_cases/OF9/bubble_column_20L
           bash run.sh 
-          cd ../../../
       - name: Run stirred-tank tutorial
         run: |
           cd tutorial_cases/OF9/stirred_tank
           bash run.sh 
-          cd ../../../
       - name: Run reactive loop reactor tutorial
         run: |
           cd tutorial_cases/OF9/loop_reactor_reacting
           bash run.sh 
-          cd ../../../
       - name: Run mixing loop reactor tutorial
         run: |
           cd tutorial_cases/OF9/loop_reactor_mixing
           bash run.sh 
-          cd ../../../
       - name: Run airlift reactor tutorial
         run: |
           cd tutorial_cases/OF9/airlift_40m
           bash run.sh
-          cd ../../../
       - name: Run flat panel reactor tutorial
         run: |
           cd tutorial_cases/OF9/FlatPanel_250L_ASU
           bash run.sh
-          cd ../../../
 
   Regression-Test-OF13:
     name: Regression-Test-OF13 (${{ matrix.python-version }}, ${{ matrix.os }})
@@ -268,7 +257,7 @@ jobs:
         os: ['ubuntu-22.04']
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
         working-directory: ${{github.workspace}}
     steps:
       - uses: actions/checkout@v4
@@ -301,33 +290,29 @@ jobs:
           cd OFsolvers/OF13/birdmultiphaseEuler
           export WM_COMPILE_OPTION=Debug
           ./Allwmake
-          cd ../../../
       - name: Run bubble column
         run: |
           cd tutorial_cases/OF13/bubble_column
           ./Allrun --test 
-          cd ../../../
       - name: STR MRF
         run: |
           cd tutorial_cases/OF13/STR_MRF
           ./Allrun --test 
-          cd ../../../
       - name: STR rotating mesh
         run: |
           cd tutorial_cases/OF13/STR_rotatingMesh
           ./Allrun --test 
-          cd ../../../
 
-  Regression-Test-OF-pixi:
-    name: Regression-Test-OF-pixi (${{ matrix.os }})
+  Regression-Test-OF9-pixi:
+    name: Regression-Test-OF9-pixi (${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: ['ubuntu-22.04']
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -leo pipefail {0}
         working-directory: ${{github.workspace}}
     steps:
       - uses: actions/checkout@v4
@@ -345,10 +330,8 @@ jobs:
           cd OFsolvers/OF9/birdmultiphaseEulerFoam
           export WM_COMPILE_OPTION=Debug
           ./Allwmake
-          cd ../../../
       - name: Run bubble column tutorial
         run: |
           cd tutorial_cases/OF9/bubble_column_20L
           bash run_pixi.sh 
-          cd ../../../
 
diff --git a/bird/meshing/stirred_tank_mesh.py b/bird/meshing/stirred_tank_mesh.py
@@ -11,7 +11,7 @@ def get_reactor_geom(yamlfile):
 
 def write_ofoam_preamble(outfile, react):
     outfile.write(
-        r"/*--------------------------------*- C++ -*----------------------------------*\\\n"
+        "/*--------------------------------*- C++ -*----------------------------------*\\\n"
     )
     outfile.write(
         "| =========                 |                                                 |\n"
@@ -29,7 +29,7 @@ def write_ofoam_preamble(outfile, react):
         "|    \\/     M anipulation  |                                                 |\n"
     )
     outfile.write(
-        r"\*---------------------------------------------------------------------------*/\n"
+        "/*---------------------------------------------------------------------------*/\n"
     )
     outfile.write("FoamFile\n")
     outfile.write("{\n")
@@ -39,18 +39,18 @@ def write_ofoam_preamble(outfile, react):
     outfile.write("\tobject      blockMeshDict;\n")
     outfile.write("}\n\n")
     outfile.write(
-        r"// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n\n"
+        "// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n\n"
     )
     outfile.write("convertToMeters 1.0;\n\n")
     outfile.write(
-        r"// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n\n"
+        "// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n\n"
     )
 
 
 def write_vertices(outfile, react):
     outfile.write(
         "\n"
-        + r"// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //"
+        + "// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //"
         + "\n"
     )
     outfile.write("vertices\n(\n")
@@ -166,7 +166,7 @@ def write_edges(outfile, react):
     reacthts = react.reacthts
 
     outfile.write(
-        r"\n// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n"
+        "\n// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n"
     )
     outfile.write("edges\n(\n")
 
@@ -204,7 +204,7 @@ def write_edges(outfile, react):
 
 def write_blocks(outfile, react):
     outfile.write(
-        r"\n// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n"
+        "\n// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //\n"
     )
     outfile.write("blocks\n(\n")
 
@@ -326,7 +326,7 @@ def write_patches(outfile, react):
 
     outfile.write(
         "\n"
-        + r"// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //"
+        + "// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //"
         + "\n"
     )
     outfile.write("patches\n(\n")

diff --git a/experimental_cases/OF9/deckwer17/run.sh b/experimental_cases/OF9/deckwer17/run.sh
@@ -7,20 +7,21 @@ else
     ./Allclean
 fi
 
-set -e  # Exit on any error
-# Define what to do on error
-trap 'echo "ERROR: Something failed! Running cleanup..."; ./Allclean' ERR
-
+set -Eeuo pipefail   # -E: trap also fires inside functions/subshells
+trap 'exit_code=$?
+      echo "ERROR: Something failed! Running cleanup..."
+      ./Allclean || true
+      exit $exit_code' ERR
 
 if ! type "python" &> /dev/null; then
     echo "<python> could not be found"
     echo "Skipping Mesh generation"
 else
     # Generate blockmeshDict
-    python ../../applications/write_block_cyl_mesh.py -i ../../bird/meshing/block_cyl_mesh_templates/coflowing/input.json  -t ../../bird/meshing/block_cyl_mesh_templates/coflowing/topology.json -o system
+    python ../../../applications/write_block_cyl_mesh.py -i ../../../bird/meshing/block_cyl_mesh_templates/coflowing/input.json  -t ../../../bird/meshing/block_cyl_mesh_templates/coflowing/topology.json -o system
 
     # Generate species thermo properties
-    python ../../applications/write_species_thermo_prop.py -cf .
+    python ../../../applications/write_species_thermo_prop.py -cf .
 
 fi
 

diff --git a/experimental_cases/OF9/deckwer19/run.sh b/experimental_cases/OF9/deckwer19/run.sh
@@ -1,7 +1,10 @@
 #!/bin/bash
-set -e  # Exit on any error
-# Define what to do on error
-trap 'echo "ERROR: Something failed! Running cleanup..."; ./Allclean' ERR
+
+set -Eeuo pipefail   # -E: trap also fires inside functions/subshells
+trap 'exit_code=$?
+      echo "ERROR: Something failed! Running cleanup..."
+      ./Allclean || true
+      exit $exit_code' ERR
 
 if ! type "blockMesh" &> /dev/null; then
     echo "<blockMesh> could not be found"
@@ -16,10 +19,10 @@ if ! type "python" &> /dev/null; then
     echo "Skipping Mesh generation"
 else
     # Generate blockmeshDict
-    python ../../applications/write_block_cyl_mesh.py -i ../../bird/meshing/block_cyl_mesh_templates/coflowing/input.json  -t ../../bird/meshing/block_cyl_mesh_templates/coflowing/topology.json -o system
+    python ../../../applications/write_block_cyl_mesh.py -i ../../../bird/meshing/block_cyl_mesh_templates/coflowing/input.json  -t ../../../bird/meshing/block_cyl_mesh_templates/coflowing/topology.json -o system
 
     # Generate species thermo properties
-    python ../../applications/write_species_thermo_prop.py -cf .
+    python ../../../applications/write_species_thermo_prop.py -cf .
 
 fi
 

diff --git a/tutorial_cases/OF9/FlatPanel_250L_ASU/presteps.sh b/tutorial_cases/OF9/FlatPanel_250L_ASU/presteps.sh
@@ -1,7 +1,9 @@
 #!/bin/bash
-set -e  # Exit on any error
-# Define what to do on error
-trap 'echo "ERROR: Something failed! Running cleanup..."; ./Allclean' ERR
+set -Eeuo pipefail   # -E: trap also fires inside functions/subshells
+trap 'exit_code=$?
+      echo "ERROR: Something failed! Running cleanup..."
+      ./Allclean || true
+      exit $exit_code' ERR
 
 cp -r 0.orig 0
 m4 ./system/panel.m4 > ./system/blockMeshDict

diff --git a/tutorial_cases/OF9/airlift_40m/presteps.sh b/tutorial_cases/OF9/airlift_40m/presteps.sh
@@ -1,7 +1,9 @@
 #!/bin/bash
-set -e  # Exit on any error
-# Define what to do on error
-trap 'echo "ERROR: Something failed! Running cleanup..."; ./Allclean' ERR
+set -Eeuo pipefail   # -E: trap also fires inside functions/subshells
+trap 'exit_code=$?
+      echo "ERROR: Something failed! Running cleanup..."
+      ./Allclean || true
+      exit $exit_code' ERR
 
 m4 system/conc_cylinder_mesh.m4 > system/blockMeshDict
 rm -rf 0

diff --git a/tutorial_cases/OF9/bubble_column_20L/run.sh b/tutorial_cases/OF9/bubble_column_20L/run.sh
@@ -3,20 +3,22 @@
 # Clean case
 ./Allclean
 
-set -e  # Exit on any error
-# Define what to do on error
-trap 'echo "ERROR: Something failed! Running cleanup..."; ./Allclean' ERR
+set -Eeuo pipefail   # -E: trap also fires inside functions/subshells
+trap 'exit_code=$?
+      echo "ERROR: Something failed! Running cleanup..."
+      ./Allclean || true
+      exit $exit_code' ERR
 
 
 echo PRESTEP 1
 # Generate blockmeshDict
-python ../../applications/write_block_cyl_mesh.py -i system/mesh.json -t system/topology.json -o system
+python ../../../applications/write_block_cyl_mesh.py -i system/mesh.json -t system/topology.json -o system
 
 # Generate boundary stl
-python ../../applications/write_stl_patch.py -i system/inlets_outlets.json
+python ../../../applications/write_stl_patch.py -i system/inlets_outlets.json
 
 # Generate species thermo properties
-python ../../applications/write_species_thermo_prop.py -cf .
+python ../../../applications/write_species_thermo_prop.py -cf .
 
 
 echo PRESTEP 2
@@ -27,7 +29,8 @@ transformPoints "scale=(0.001 0.001 0.001)"
 
 # Inlet BC
 surfaceToPatch -tol 1e-3 inlets.stl
-export newmeshdir=$(foamListTimes -latestTime)
+newmeshdir=$(foamListTimes -latestTime)
+export newmeshdir
 rm -rf constant/polyMesh/
 cp -r $newmeshdir/polyMesh ./constant
 rm -rf $newmeshdir

diff --git a/tutorial_cases/OF9/bubble_column_20L/run_pixi.sh b/tutorial_cases/OF9/bubble_column_20L/run_pixi.sh
@@ -10,13 +10,13 @@ trap 'echo "ERROR: Something failed! Running cleanup..."; ./Allclean' ERR
 
 echo PRESTEP 1
 # Generate blockmeshDict
-pixi run python ../../applications/write_block_cyl_mesh.py -i system/mesh.json -t system/topology.json -o system
+pixi run python ../../../applications/write_block_cyl_mesh.py -i system/mesh.json -t system/topology.json -o system
 
 # Generate boundary stl
-pixi run python ../../applications/write_stl_patch.py -i system/inlets_outlets.json
+pixi run python ../../../applications/write_stl_patch.py -i system/inlets_outlets.json
 
 # Generate species thermo properties
-pixi run python ../../applications/write_species_thermo_prop.py -cf .
+pixi run python ../../../applications/write_species_thermo_prop.py -cf .
 
 
 echo PRESTEP 2