Merge pull request #7 from fusion-energy/develop

adding CI to the repo

.github/workflows/ci_with_docker_build.yml

@@ -0,0 +1,22 @@
+# Builds a dockerimage and then runs tests from within the docker enviroment
+
+name: CI with docker build
+on:
+  pull_request:
+    branches:
+    - develop
+    - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Build and test with Docker
+        run: |
+        
+          docker build -t paramak-neutronics --build-arg cq_version=2.1 --build-arg compile_cores=2 .
+          docker run --rm paramak-neutronics  /bin/bash -c "bash run_tests.sh"

.github/workflows/ci_with_install.yml

@@ -0,0 +1,29 @@
+
+# This CI will lauch a Docker image that contains all the dependencies required
+# within that image the pytest test suite is run 
+
+
+name: CI with install
+
+on:
+  pull_request:    
+    branches:
+    - develop
+    - main
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/fusion-energy/paramak-neutronics:dependencies
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: install package
+        run: |
+          python setup.py install
+      - name: run tests
+        run: |
+          bash run_tests.sh
+          curl -s https://codecov.io/bash

.github/workflows/docker_publish.yml

@@ -0,0 +1,70 @@
+# This yml file will trigger a Github Action on release creation.
+# This Action will build and upload a Docker image to GHCR
+# https://github.com/marketplace/actions/publish-docker
+
+name: docker-publish-release
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build_and_push_dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v2
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      -
+        name: Build and push Docker image
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          target: dependencies
+          tags: ghcr.io/fusion-energy/paramak-neutronics:dependencies
+          build-args: |
+            cq_version=2.1
+            compile_cores=2
+
+  build_and_push_release:
+    runs-on: ubuntu-latest
+    needs: build_and_push_dependencies
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v2
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      -
+        name: Build and push Docker image
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: ghcr.io/fusion-energy/paramak-neutronics
+          build-args: |
+            cq_version=2.1
+            compile_cores=2

Dockerfile

@@ -0,0 +1,176 @@
+# This Dockerfile creates an enviroment / dependancies needed to run the 
+# paramank_neutronics package.
+
+# This dockerfile provides an API endpoint that accepts arguments to drive
+# the neutronics model production and subsequent simulation
+
+# To build this Dockerfile into a docker image:
+# docker build -t paramank_neutronics .
+
+# To build this Dockerfile and use multiple cores to compile:
+# docker build -t paramank_neutronics --build-arg compile_cores=7 .
+
+# To run the resulting Docker image:
+# docker run -it paramank_neutronics
+
+# Run with the following command for a jupyter notebook interface
+# docker run -p 8888:8888 ukaea/paramak /bin/bash -c "jupyter notebook --notebook-dir=/examples --ip='*' --port=8888 --no-browser --allow-root"
+
+
+# TODO save build time by basing this on FROM ghcr.io/fusion-energy/paramak:latest
+# This can't be done currently as the base images uses conda installs for moab / dagmc which don't compile with OpenMC
+FROM continuumio/miniconda3:4.9.2 as dependencies
+
+ARG compile_cores=1
+
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 \
+    PATH=/opt/openmc/bin:$PATH \
+    LD_LIBRARY_PATH=/opt/openmc/lib:$LD_LIBRARY_PATH \
+    CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx \
+    DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update -y && \
+    apt-get upgrade -y
+
+RUN apt-get install -y libgl1-mesa-glx \
+                       libgl1-mesa-dev \
+                       libglu1-mesa-dev \
+                       freeglut3-dev \
+                       libosmesa6 \
+                       libosmesa6-dev \
+                       libgles2-mesa-dev \
+                       curl && \
+                       apt-get clean
+
+# Installing CadQuery
+RUN conda install -c conda-forge -c python python=3.8 && \
+    conda install -c conda-forge -c cadquery cadquery=2.1 && \
+    pip install jupyter-cadquery==2.1.0 && \
+    conda clean -afy
+
+
+# Install neutronics dependencies from Debian package manager
+RUN apt-get install -y \
+    wget \
+    git \
+    gfortran g++ cmake \
+    mpich \
+    libmpich-dev \
+    libhdf5-serial-dev \
+    libhdf5-mpich-dev \
+    imagemagick
+
+
+# install addition packages required for MOAB
+RUN apt-get --yes install libeigen3-dev && \
+    apt-get --yes install libblas-dev && \
+    apt-get --yes install liblapack-dev && \
+    apt-get --yes install libnetcdf-dev && \
+    apt-get --yes install libtbb-dev && \
+    apt-get --yes install libglfw3-dev
+
+
+# Clone and install Embree
+RUN git clone --single-branch --branch v3.12.2 --depth 1 https://github.com/embree/embree.git && \
+    cd embree && \
+    mkdir build && \
+    cd build && \
+    cmake .. -DCMAKE_INSTALL_PREFIX=.. \
+             -DEMBREE_ISPC_SUPPORT=OFF && \
+    make -j"$compile_cores" && \
+    make -j"$compile_cores" install
+
+
+# Clone and install MOAB
+RUN pip install --upgrade numpy cython && \
+    mkdir MOAB && \
+    cd MOAB && \
+    mkdir build && \
+    git clone  --single-branch --branch 5.2.1 --depth 1 https://bitbucket.org/fathomteam/moab.git && \
+    cd build && \
+    cmake ../moab -DENABLE_HDF5=ON \
+                  -DENABLE_NETCDF=ON \
+                  -DENABLE_FORTRAN=OFF \
+                  -DENABLE_BLASLAPACK=OFF \
+                  -DBUILD_SHARED_LIBS=OFF \
+                  -DCMAKE_INSTALL_PREFIX=/MOAB && \
+    make -j"$compile_cores" && \
+    make -j"$compile_cores" install && \
+    rm -rf * && \
+    cmake ../moab -DENABLE_HDF5=ON \
+                  -DENABLE_PYMOAB=ON \
+                  -DENABLE_FORTRAN=OFF \
+                  -DBUILD_SHARED_LIBS=ON \
+                  -DENABLE_BLASLAPACK=OFF \
+                  -DCMAKE_INSTALL_PREFIX=/MOAB && \
+    make -j"$compile_cores" && \
+    make -j"$compile_cores" install && \
+    cd pymoab && \
+    bash install.sh && \
+    python setup.py install
+
+
+# Clone and install Double-Down
+RUN git clone --single-branch --branch main https://github.com/pshriwise/double-down.git && \
+    cd double-down && \
+    mkdir build && \
+    cd build && \
+    cmake .. -DMOAB_DIR=/MOAB \
+             -DCMAKE_INSTALL_PREFIX=.. \
+             -DEMBREE_DIR=/embree && \
+    make -j"$compile_cores" && \
+    make -j"$compile_cores" install
+
+
+# Clone and install DAGMC
+RUN mkdir DAGMC && \
+    cd DAGMC && \
+    # git clone --single-branch --branch 3.2.0 --depth 1 https://github.com/svalinn/DAGMC.git && \
+    git clone --single-branch --branch 9b59a53311e94b8a49c8405d730aeef84f4ca3e2 --depth 1 https://github.com/svalinn/DAGMC.git && \
+    mkdir build && \
+    cd build && \
+    cmake ../DAGMC -DBUILD_TALLY=ON \
+                   -DMOAB_DIR=/MOAB \
+                   -DDOUBLE_DOWN=ON \
+                   -DBUILD_STATIC_EXE=OFF \
+                   -DBUILD_STATIC_LIBS=OFF \
+                   -DCMAKE_INSTALL_PREFIX=/DAGMC/ \
+                   -DDOUBLE_DOWN_DIR=/double-down  && \
+    make -j"$compile_cores" install && \
+    rm -rf /DAGMC/DAGMC /DAGMC/build
+
+# Clone and install OpenMC with DAGMC
+RUN git clone --recurse-submodules https://github.com/openmc-dev/openmc.git /opt/openmc && \
+    cd /opt/openmc && \
+    mkdir build && \
+    cd build && \
+    cmake -Doptimize=on \
+          -Ddagmc=ON \
+          -DDAGMC_DIR=/DAGMC/ \
+          -DHDF5_PREFER_PARALLEL=on ..  && \
+    make -j"$compile_cores" && \
+    make -j"$compile_cores" install && \
+    cd ..  && \
+    pip install -e .[test]
+
+# installs python packages and nuclear data
+RUN pip install vtk && \
+    pip install neutronics_material_maker && \
+    pip install openmc_data_downloader && \
+    openmc_data_downloader -e all -i H3 -l ENDFB-7.1-NNDC TENDL-2019 -p neutron photon
+
+# setting enviromental varibles
+ENV OPENMC_CROSS_SECTIONS=/cross_sections.xml
+ENV PATH="/MOAB/build/bin:${PATH}"
+ENV PATH="/DAGMC/bin:${PATH}"
+
+RUN pip install paramak
+
+FROM dependencies as final
+
+COPY run_tests.sh run_tests.sh
+COPY paramak_neutronics paramak_neutronics/
+COPY examples examples/
+COPY setup.py setup.py
+COPY tests tests/
+COPY README.md README.md

docs/source/conf.py

@@ -21,7 +21,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "Paramak"
+project = "Paramak-neutronics"
 copyright = "Paramak-neutronics contributors"
 author = "Paramak contributors"
 

environment.yml

@@ -0,0 +1,25 @@
+name: docs-environment
+
+channels:
+  - conda-forge
+  - cadquery
+
+dependencies:
+  - pytest
+  - plotly
+  - scipy
+  - numpy
+  - matplotlib
+  - Pillow
+  - cadquery=2.1
+  - openmc
+  - moab
+  - pip:
+    - neutronics-material-maker
+    - remove_dagmc_tags
+    - sympy
+    - plasmaboundaries
+    - sphinx-autodoc-typehints
+    - sphinxcadquery
+    - defusedxml
+

readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optional additional build formats
+# formats:
+#   - pdf
+
+# this is not needed if using conda environment
+# python:
+#   version: 3.7
+#   install:
+#     - requirements: requirements.txt
+
+# specify conda environment needed for build
+conda:
+  environment: environment.yml

run_tests.sh

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+
+pytest tests/notebook_testing.py -v --cov=paramak_neutronics --cov-append -- --cov-report term --cov-report xml
+pytest tests/test_NeutronicModel.py -v --cov=paramak_neutronics --cov-append -- --cov-report term --cov-report xml
+pytest tests/test_Reactor_neutronics.py -v --cov=paramak_neutronics --cov-append -- --cov-report term --cov-report xml
+pytest tests/test_Shape_neutronics.py -v --cov=paramak_neutronics --cov-append -- --cov-report term --cov-report xml
+pytest tests/test_example_neutronics_simulations.py -v --cov=paramak_neutronics --cov-append -- --cov-report term --cov-report xml
+pytest tests/test_neutronics_utils.py -v --cov=paramak_neutronics --cov-append -- --cov-report term --cov-report xml