Merge branch 'main' of https://github.com/shac170/MCDC

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: docs/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: docs/paper.pdf

.github/workflows/mpi_numba_reg.yml

@@ -0,0 +1,35 @@
+name: Regression Test - Numba and MPI (2 threads)
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"] #, "macos-latest"
+    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: |
+        #sudo apt-get install libopenmpi-dev
+        #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: Regression Test - Numba and MPI
+      run: |
+          cd test/regression
+          python run.py --mode=numba --mpiexec=2

.github/workflows/mpi_numba_regII.yml

@@ -0,0 +1,35 @@
+name: Regression Test - Numba and MPI (4 threads)
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"] #, "macos-latest"
+    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: |
+        #sudo apt-get install libopenmpi-dev
+        #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: Regression Test - Numba and MPI
+      run: |
+          cd test/regression
+          python run.py --mode=numba --mpiexec=2

.github/workflows/mpi_reg.yml

@@ -0,0 +1,36 @@
+name: Regression Test - MPI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"] #, "macos-latest"
+    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: |
+        #sudo apt-get install libopenmpi-dev
+        #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: Regression Test - MPI
+      run: |
+        cd test/regression
+        python run.py --mpiexec=4
+        python run.py --mpiexec=2

.github/workflows/numba_reg.yml

@@ -0,0 +1,35 @@
+name: Regression Test - Numba
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+    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: |
+        #sudo apt-get install libopenmpi-dev
+        #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: Regression Test - Numba
+      run: |
+          cd test/regression
+          python run.py --mode=numba

.github/workflows/python-publish.yml

@@ -0,0 +1,45 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+    release:
+      types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - uses: mpi4py/setup-mpi@v1
+    - name: Install dependencies
+      run: |
+        python --version
+        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
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/python_reg.yml

@@ -0,0 +1,35 @@
+name: Regression Test - Python
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+    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: |
+        #sudo apt-get install libopenmpi-dev
+        #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: Regression Test - Python
+      run: |
+          cd test/regression
+          python run.py

.github/workflows/unit_tests.yml

@@ -0,0 +1,34 @@
+name: Unit Test
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+    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: |
+        #sudo apt-get install libopenmpi-dev
+        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

.gitignore

@@ -3,6 +3,10 @@ build
 .eggs
 mcdc.egg-info
 
+# Material Data
+mcdc_xs
+MCDC-Xsec
+
 # Python cache
 __pycache__
 *.pyc
@@ -12,6 +16,7 @@ __pycache__
 # Editor
 .spyproject
 *.swp
+.vscode/
 
 # Output
 *output.h5