Version release 0.12.0

Merge dev into main for v0.12.0

Author: clemekay

.github/workflows/docs_test.yml

@@ -0,0 +1,30 @@
+name: Test Build the Docs
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-22.04"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.11"
+    - name: debug
+      run: |
+        pwd
+        ls
+    - uses: mpi4py/setup-mpi@v1
+    - name: Install dependencies
+      run: |
+        pip install --user . mcdc[docs]
+        pip list 
+    - name: Build the Docs
+      run: |
+        cd docs
+        make html

.github/workflows/manual_publish.yml

@@ -36,9 +36,6 @@ jobs:
         python -m pip install --upgrade pip
         pip install .
         pip install build
-    - name: Patch Numba
-      run : |
-        bash .github/workflows/patch.sh
     - name: Build package
       run: python -m build
     - name: Publish package distributions to PyPI

.github/workflows/patch.sh

@@ -19,7 +19,7 @@ permissions:
 
 jobs:
   deploy:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     permissions:
         id-token: write
     steps: 
@@ -35,9 +35,6 @@ jobs:
         python -m pip install --upgrade pip
         pip install .
         pip install build
-    - name: Patch Numba
-      run : |
-        bash .github/workflows/patch.sh
     - name: Build package
       run: python -m build
     - name: Publish package distributions to PyPI

.github/workflows/python-publish.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-            os: ["ubuntu-latest"]
+            os: ["ubuntu-22.04"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up python 3.11
@@ -24,9 +24,6 @@ jobs:
       run: |
         pip install -e .
         pip list 
-    - name: Patch Numba
-      run : |
-        bash .github/workflows/patch.sh
     - name: Regression Test - Numba
       run: |
           cd test/regression

.github/workflows/regression_test-numba_cpu.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-            os: ["ubuntu-latest"]
+            os: ["ubuntu-22.04"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up python 3.11
@@ -24,10 +24,8 @@ jobs:
       run: |
         pip install -e .
         pip list 
-    - name: Patch Numba
-      run : |
-        bash .github/workflows/patch.sh
     - name: Regression Test - Numba and MPI
       run: |
-          cd test/regression
-          python run.py --mode=numba --mpiexec=4
+        cd test/regression
+        python run.py --mode=numba --mpiexec=4
+        python run.py --mode=numba --mpiexec=16 --name=slab_reed_dd_3d

.github/workflows/regression_test-numba_cpu_mpi.yml

@@ -1,35 +1,36 @@
-name: Regression test on slef hosted
-
-runs-on: self-hosted
+name: GPU regression test
 
 on: [push, pull_request]
 
 jobs:
   build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-        fail-fast: false
-        matrix:
-            os: ["ubuntu-latest"]
+    runs-on: self-hosted
     steps:
     - uses: actions/checkout@v3
-    - name: Set up python 3.11
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.11"
-    - name: debug
+    - name: Load modules and build python venv
       run: |
         pwd
-        ls
-    - uses: mpi4py/setup-mpi@v1
-    - name: Install dependencies
+        cd ..
+        pwd
+        module load cuda/11.8 gcc/10.3 mpich/4.0h_gcc-10 python/3.11
+        rm -rf ci_testing
+        python -m venv ci_testing
+        module unload python/3.11
+        source ci_testing/bin/activate
+        pip install --upgrade pip
+        pwd
+    - name: Install MC/DC and Harmonize
       run: |
+        source ../ci_testing/bin/activate
+        pwd
+        pip install -e .
+        git clone https://github.com/CEMeNT-PSAAP/harmonize.git
+        cd harmonize
         pip install -e .
-        pip list 
-    - name: Patch Numba
-      run : |
-        bash .github/workflows/patch.sh
-    - name: Regression Test - Numba
+        cd ..
+    - name: Regression Test - GPU
       run: |
+          pwd
+          source ../ci_testing/bin/activate
           cd test/regression
           python run.py --mode=numba --target=gpu

.github/workflows/regression_test-numba_gpu.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-            os: ["ubuntu-latest"]
+            os: ["ubuntu-22.04"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up python 3.11
@@ -24,9 +24,6 @@ jobs:
       run: |
         pip install -e .
         pip list 
-    - name: Patch Numba
-      run : |
-        bash .github/workflows/patch.sh
     - name: Regression Test - Python
       run: |
           cd test/regression

.github/workflows/regression_test-python.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-            os: ["ubuntu-latest"] #, "macos-latest"
+            os: ["ubuntu-22.04"] #, "macos-latest"
     steps:
     - uses: actions/checkout@v3
     - name: Set up python 3.11
@@ -24,10 +24,8 @@ jobs:
       run: |
         pip install -e .
         pip list 
-    - name: Patch Numba
-      run : |
-        bash .github/workflows/patch.sh
     - name: Regression Test - MPI
       run: |
         cd test/regression
         python run.py --mpiexec=4
+        python run.py --mpiexec=16 --name=slab_reed_dd_3d

.github/workflows/regression_test-python_mpi.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-            os: ["ubuntu-latest"]
+            os: ["ubuntu-22.04"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up python 3.11
@@ -26,9 +26,6 @@ jobs:
         pip install numpy numba h5py matplotlib scipy pytest colorama mpi4py ngsolve distinctipy
         pip list 
         pip install -e .
-    - name: Patch Numba
-      run : |
-        bash .github/workflows/patch.sh
     - name: Unit Test
       run : |
-          pytest
+          pytest