Major refactor

.github/workflows/black_lint.yml

@@ -1,7 +1,6 @@
 name: Black Style Check
 
 on:
-  push:
   pull_request:
 
 jobs:

.github/workflows/docs_test.yml

@@ -1,30 +1,36 @@
 name: Test Build the Docs
 
-on: [push, pull_request, workflow_dispatch]
+on:
+  pull_request:
+  workflow_dispatch:
 
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-        fail-fast: false
-        matrix:
-            os: ["ubuntu-22.04"]
+  build-docs:
+    runs-on: "ubuntu-22.04"
+    timeout-minutes: 60
+
     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
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: pip
+
+      - name: Set up MPI
+        uses: mpi4py/setup-mpi@v1
+
+      - name: Install docs dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # If you have extras for docs, use this:
+          python -m pip install ".[docs]"
+          # Otherwise, something like:
+          # python -m pip install . sphinx sphinx-autodoc-typehints ...
+          python -m pip list
+
+      - name: Build the docs
+        working-directory: docs
+        run: make html

.github/workflows/regression_test-numba_gpu.yml → .github/workflows/regression_test-gpu.yml

@@ -1,8 +1,7 @@
 name: GPU regression test
 
 on:
-  push:
-  pull_request:
+  workflow_dispatch:
 
 jobs:
   build:

.github/workflows/regression_test.yml

@@ -1,7 +1,6 @@
 name: Regression Tests
 
 on:
-  push:
   pull_request:
 
 jobs:
@@ -37,12 +36,14 @@ jobs:
 
       - name: Install MC/DC
         run: |
-          pip install -e .
+          pip install -e .[dev]
           pip list
 
       - name: Run Python regression tests (serial)
         working-directory: test/regression
-        run: python run.py
+        run: |
+          git clone https://github.com/CEMeNT-PSAAP/MCDC-regression_test_data.git
+          python run.py --include_native_physics
 
   python-regression-mpi:
     name: Python regression (MPI)
@@ -76,14 +77,15 @@ jobs:
 
       - name: Install MC/DC
         run: |
-          pip install -e .
+          pip install -e .[dev]
           pip list
 
       - name: Run Python regression tests (MPI)
         working-directory: test/regression
         run: |
-          python run.py --mpiexec=4
-          python run.py --mpiexec=16 --name=slab_reed_dd_3d
+          git clone https://github.com/CEMeNT-PSAAP/MCDC-regression_test_data.git
+          python run.py --include_native_physics --mpiexec=4
+          python run.py --include_native_physics --mpiexec=16 --name=slab_reed_dd_3d
 
   numba-regression-serial:
     name: Numba regression (serial)
@@ -117,12 +119,14 @@ jobs:
 
       - name: Install MC/DC
         run: |
-          pip install -e .
+          pip install -e .[dev]
           pip list
 
       - name: Run Numba regression tests (serial)
         working-directory: test/regression
-        run: python run.py --mode numba
+        run: |
+          git clone https://github.com/CEMeNT-PSAAP/MCDC-regression_test_data.git
+          python run.py --include_native_physics --mode numba
 
   numba-regression-mpi:
     name: Numba regression (MPI)
@@ -156,11 +160,12 @@ jobs:
 
       - name: Install MC/DC
         run: |
-          pip install -e .
+          pip install -e .[dev]
           pip list
 
       - name: Run Numba regression tests (MPI)
         working-directory: test/regression
         run: |
-          python run.py --mode numba --mpiexec=4
-          python run.py --mode numba --mpiexec=16 --name=slab_reed_dd_3d
+          git clone https://github.com/CEMeNT-PSAAP/MCDC-regression_test_data.git
+          python run.py --include_native_physics --mode numba --mpiexec=4
+          python run.py --include_native_physics --mode numba --mpiexec=16 --name=slab_reed_dd_3d

.github/workflows/unit_test.yml

@@ -1,7 +1,6 @@
 name: Unit Tests
 
 on:
-  push:
   pull_request:
 
 jobs:
@@ -37,7 +36,7 @@ jobs:
 
       - name: Install MC/DC
         run: |
-          pip install -e .
+          pip install -e .[dev]
           pip list
 
       - name: Run unit tests