Merge pull request #5 from fusion-energy/develop

Develop

.circleci/config.yml

@@ -13,17 +13,7 @@ jobs:
       - run:
           name: install
           command: |
-            python setup.py install  # this dosen't support the optional packages like pip install .[neutronics] does
-
-      - run:
-          name: run neutronics_utils tests
-          command: 
-            pytest tests/test_neutronics_utils.py -v --cov=paramak --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
-
-      - run:
-          name: run neutronics_example tests
-          command: 
-            pytest tests/test_example_neutronics_simulations.py -v --cov=paramak --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+            python setup.py install
 
       - run:
           name: run utils tests
@@ -55,11 +45,6 @@ jobs:
           command: 
             pytest tests/test_parametric_reactors/ -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
 
-      - run:
-          name: run neutronics tests
-          command: 
-            pytest tests/test_parametric_neutronics/ -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
-
       - run:
           name: run example shape tests
           command: 
@@ -73,7 +58,7 @@ jobs:
       - run:
           name: run example reactor tests
           command: 
-            pytest tests/test_example_reactors.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+            pytest --capture=tee-sys tests/test_example_reactors.py -v --cov=paramak --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
 
       - store_test_results:
           path: test-reports

.github/pull_request_template.md

@@ -22,7 +22,3 @@ _Put an `x` in the boxes that apply. You can also fill these out after creating
 - [ ] Unit tests pass locally with my changes
 - [ ] I have added tests that prove my fix is effective or that my feature works
 - [ ] I have added necessary documentation (if appropriate)
-
-## Further comments
-
-If this is a relatively large or complex change, kick off the discussion by explaining why you chose the solution you did and what alternatives you considered, etc...

.github/workflows/docker_ci_develop.yml

@@ -0,0 +1,21 @@
+
+name: CI - Develop
+on:  
+  pull_request:    
+    branches:
+    - develop  
+jobs:  
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        cadquery-version: [2.1]
+        include-neutronics: [true]
+
+    steps:    
+    - uses: actions/checkout@v1
+    - name: Build and test with Docker
+      run: |
+        docker build -t paramak --build-arg include_neutronics=${{ matrix.include-neutronics }} --build-arg cq_version=${{ matrix.cadquery-version}} --build-arg compile_cores=2 .
+        docker run --rm paramak  /bin/bash -c "bash run_tests.sh include_neutronics=${{ matrix.include-neutronics }} && curl -s https://codecov.io/bash | bash"

.github/workflows/docker_ci_main.yml

@@ -0,0 +1,21 @@
+
+name: CI - Main
+on:
+  pull_request:
+    branches:
+    - main
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        cadquery-version: [2.1, master]
+        include-neutronics: [true]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Build and test with Docker
+      run: |
+        docker build -t paramak --build-arg include_neutronics=${{ matrix.include-neutronics }} --build-arg cq_version=${{ matrix.cadquery-version}} --build-arg compile_cores=2 .
+        docker run --rm paramak  /bin/bash -c "bash run_tests.sh include_neutronics=${{ matrix.include-neutronics }} && curl -s https://codecov.io/bash | bash"

.github/workflows/dockerhub-publish-dependencies.yml

@@ -31,11 +31,11 @@ jobs:
         id: docker_build
         uses: docker/build-push-action@v2
         with:
-          file: DockerfileDependencies
           push: true
           tags: ukaea/paramak:dependencies
+          target: dependencies
           build-args: |
-            cq_version=master
+            cq_version=2.1
             compile_cores=2
             include_neutronics=true
       -

.github/workflows/dockerhub-publish-dev.yml

@@ -0,0 +1,40 @@
+# This yml file will trigger a Github Action on pushes to the main branch.
+# This Action will build and upload a Docker image to Dockerhub
+# https://github.com/marketplace/actions/publish-docker
+
+name: dockerhub-publish-dev
+
+on:
+  push:
+    branches: develop
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: ukaea/paramak:dev
+          build-args: |
+            cq_version=2.1
+            compile_cores=2
+            include_neutronics=true
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/dockerhub-publish-geometry-dependencies.yml

@@ -2,11 +2,13 @@
 # This Action will build and upload a Docker image to Dockerhub
 # https://github.com/marketplace/actions/publish-docker
 
-name: dockerhub-publish-dev
+name: dockerhub-publish-geometry-dependencies
 
 on:
   push:
-    branches: develop
+    branches:
+      - develop
+      - main
 
 jobs:
   main:
@@ -32,7 +34,7 @@ jobs:
           push: true
           tags: ukaea/paramak:geometry-dependencies
           build-args: |
-            cq_version=master
+            cq_version=2.1
             compile_cores=2
             include_neutronics=false
       -

.github/workflows/dockerhub-publish-stable.yml

@@ -30,9 +30,9 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           push: true
-          tags: ukaea/paramak:latest
+          tags: ukaea/paramak:stable
           build-args: |
-            cq_version=master
+            cq_version=2.1
             compile_cores=2
             include_neutronics=true
       -

.github/workflows/python-publish.yml

@@ -6,9 +6,8 @@
 name: Upload Python Package
 
 on:
-  push:
-    branches:
-      - main
+  release:
+    types: [created]
 
 jobs:
   deploy:
@@ -27,7 +26,7 @@ jobs:
         pip install setuptools wheel twine
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}  # TODO change to token
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel

.gitignore

@@ -24,9 +24,11 @@ paramak.egg-info/
 coverage.xml
 .coverage
 
-# trelis journal files
+# trelis output files
 *.jou
 *.log
+*.trelis
+*.cub
 
 # neutronics geometry files
 *.h5m
@@ -59,3 +61,7 @@ test-reports/
 
 # ppp output directory
 manifest_processed/
+
+# conda buid and dist dir
+build/
+dist/

Dockerfile

@@ -20,7 +20,7 @@
 #   Options: [1, 2, 3, 4, 5, 6...]
 #
 # Example builds:
-# Building using the defaults (cq_version 2, no neutronics and 1 core compile)
+# Building using the defaults (cq_version 2.1, no neutronics and 1 core compile)
 # docker build -t ukaea/paramak .
 #
 # Building to include cadquery master, neutronics dependencies and use 8 cores.
@@ -40,10 +40,10 @@
 # docker run --rm ukaea/paramak pytest /tests
 # docker run --rm ukaea/paramak  /bin/bash -c "cd .. && bash run_tests.sh"
 
-FROM continuumio/miniconda3:4.9.2
+FROM continuumio/miniconda3:4.9.2 as dependencies
 
 # By default this Dockerfile builds with the latest release of CadQuery 2
-ARG cq_version=2
+ARG cq_version=2.1
 ARG include_neutronics=false
 ARG compile_cores=1
 
@@ -62,12 +62,13 @@ RUN apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev \
                        apt-get clean
 
 # Installing CadQuery
-# jupyter is installed before cadquery to avoid a conflict
 RUN echo installing CadQuery version $cq_version && \
-    conda install jupyter -y --quiet && \
-    conda install -c cadquery -c conda-forge cadquery="$cq_version" && \
+    conda install -c conda-forge -c python python=3.8 && \
+    conda install -c conda-forge -c cadquery cadquery="$cq_version" && \
+    pip install jupyter-cadquery==2.1.0 && \
     conda clean -afy
 
+
 # Install neutronics dependencies from Debian package manager
 RUN if [ "$include_neutronics" = "true" ] ; \
     then echo installing with include_neutronics=true ; \
@@ -88,20 +89,9 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     apt-get --yes install libglfw3-dev ; \
     fi
 
-# Clone and install NJOY2016
-RUN if [ "$include_neutronics" = "true" ] ; \
-    then git clone --single-branch --branch master https://github.com/njoy/NJOY2016.git /opt/NJOY2016 ; \
-    cd /opt/NJOY2016 ; \
-    mkdir build ; \
-    cd build ; \
-    cmake -Dstatic=on .. ; \
-    make 2>/dev/null ; \
-    make install ; \
-    fi
-
 # Clone and install Embree
 RUN if [ "$include_neutronics" = "true" ] ; \
-    then git clone --single-branch --branch master https://github.com/embree/embree.git ; \
+    then git clone --single-branch --branch v3.12.2 --depth 1 https://github.com/embree/embree.git ; \
     cd embree ; \
     mkdir build ; \
     cd build ; \
@@ -117,7 +107,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     mkdir MOAB ; \
     cd MOAB ; \
     mkdir build ; \
-    git clone  --single-branch --branch develop https://bitbucket.org/fathomteam/moab.git ; \
+    git clone  --single-branch --branch 5.2.1 --depth 1 https://bitbucket.org/fathomteam/moab.git ; \
     cd build ; \
     cmake ../moab -DENABLE_HDF5=ON \
                   -DENABLE_NETCDF=ON \
@@ -141,7 +131,6 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     python setup.py install ; \
     fi
 
-
 # Clone and install Double-Down
 RUN if [ "$include_neutronics" = "true" ] ; \
     then git clone --single-branch --branch main https://github.com/pshriwise/double-down.git ; \
@@ -159,7 +148,7 @@ RUN if [ "$include_neutronics" = "true" ] ; \
 RUN if [ "$include_neutronics" = "true" ] ; \
     then mkdir DAGMC ; \
     cd DAGMC ; \
-    git clone --single-branch --branch develop https://github.com/svalinn/DAGMC.git ; \
+    git clone --single-branch --branch 3.2.0 --depth 1 https://github.com/svalinn/DAGMC.git ; \
     mkdir build ; \
     cd build ; \
     cmake ../DAGMC -DBUILD_TALLY=ON \
@@ -187,23 +176,30 @@ RUN if [ "$include_neutronics" = "true" ] ; \
     make -j"$compile_cores" install ; \
     cd ..  ; \
     pip install -e .[test] ; \
-    /opt/openmc/tools/ci/download-xs.sh ; \
     fi
 
-ENV OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml
-
 RUN if [ "$include_neutronics" = "true" ] ; \
     then pip install vtk ; \
     pip install parametric_plasma_source ; \
-    pip install neutronics_material_maker ; \
+    pip install neutronics_material_maker==0.3.2 ; \
+    pip install openmc_data_downloader ; \
+    openmc_data_downloader -e all -i H3 -l ENDFB-7.1-NNDC TENDL-2019 -p neutron photon ; \
     fi
 
 COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt
 
-# @pullrequest reviewer, we would like to make the copy optional but don't know
-# how. Then we can build a dependency image for use in circle ci.
-# Copy over the source code, examples and tests
+ENV OPENMC_CROSS_SECTIONS=/cross_sections.xml
+ENV PATH="/MOAB/build/bin:${PATH}"
+ENV PATH="/DAGMC/bin:${PATH}"
+
+RUN mkdir /home/paramak
+EXPOSE 8888
+WORKDIR /home/paramak
+
+
+FROM dependencies as final
+
 COPY run_tests.sh run_tests.sh
 COPY paramak paramak/
 COPY examples examples/
@@ -213,3 +209,7 @@ COPY README.md README.md
 
 # using setup.py instead of pip due to https://github.com/pypa/pip/issues/5816
 RUN python setup.py install
+
+# this helps prevent the kernal failing
+RUN echo "#!/bin/bash\n\njupyter lab --notebook-dir=/home/paramak --port=8888 --no-browser --ip=0.0.0.0 --allow-root" >> /home/paramak/docker-cmd.sh
+CMD bash /home/paramak/docker-cmd.sh