Merge pull request svalinn#105 from svalinn/oo_version

Object-oriented upgrade

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: Regular CI testing for parastell
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  pull_request:
+    paths-ignore:
+      - 'Dockerfile'
+      - '.github/workflows/docker_publish.yml'
+      - 'environment.yml'
+
+jobs:
+  test-dependency-img:
+    runs-on: ubuntu-latest
+    container: ghcr.io/svalinn/parastell-ci
+
+    name: Perform CI Tests
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Populate environment and run tests
+        run: |
+          . /opt/etc/bashrc
+          sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic
+          export PYTHONPATH=${PYTHONPATH}:`pwd`
+          cd tests
+          pytest -v .
+        env:
+          rlmSERVER: ${{ secrets.RLMSERVER }}
+          rlmPASSWD: ${{ secrets.RLMPASSWORD }}

.github/workflows/docker_publish.yml

@@ -0,0 +1,61 @@
+name: Build & publish Docker image for ParaStell CI
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  push:
+    paths:
+      - 'Dockerfile'
+      - '.github/workflows/docker_publish.yml'
+      - 'environment.yml'
+
+jobs:
+  build-dependency-img:
+    runs-on: ubuntu-latest
+
+    name: Install Dependencies
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log into GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push ParaStell Docker image
+        id: build-parastell
+        uses: docker/build-push-action@v5
+        with:
+          cache-from: type=registry,ref=ghcr.io/svalinn/parastell:ci-layer-cache
+          cache-to: type=registry,ref=ghcr.io/svalinn/parastell:ci-layer-cache,mode=max
+          file: Dockerfile
+          push: true
+          target: parastell-deps
+          tags: ghcr.io/svalinn/parastell-ci
+
+  test-dependency-img:
+    needs: build-dependency-img
+    runs-on: ubuntu-latest
+    container: ghcr.io/svalinn/parastell-ci
+
+    name: Test CI Image
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Populate environment and run tests
+        run: |
+          . /opt/etc/bashrc
+          sed -e "s/@SERVER@/${rlmSERVER}/" -e "s/@PASSWORD@/${rlmPASSWD}/" /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in > /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.lic
+          export PYTHONPATH=${PYTHONPATH}:`pwd`
+          cd tests
+          pytest -v .
+        env:
+          rlmSERVER: ${{ secrets.RLMSERVER }}
+          rlmPASSWD: ${{ secrets.RLMPASSWORD }}

.gitignore

@@ -1,3 +1,23 @@
+
+# PRoject specific
+*.csv
+*.step
+*.h5m
+*.txt
+*.nc
+*.jou
+*.ods
+*.vtk
+*.cub
+*.cub5
+*.h5
+*.exo
+!wout_vmec.nc
+.vscode
+*.yaml
+!config.yaml
+*.lic
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -128,14 +148,3 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-*.csv
-*.step
-*.h5m
-*.txt
-*.nc
-*.jou
-*.ods
-*.vtk
-*.cub
-*.cub5
-*.h5

Dockerfile

@@ -0,0 +1,55 @@
+FROM continuumio/miniconda3 as parastell-deps
+
+ENV TZ=America/Chicago
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+RUN apt-get update -y
+RUN apt-get upgrade -y
+
+# Install dependencies
+RUN apt-get install -y libgl1-mesa-glx \
+                        libgl1-mesa-dev \
+                        libglu1-mesa-dev \
+                        freeglut3-dev \
+                        libosmesa6 \
+                        libosmesa6-dev \
+                        libgles2-mesa-dev \
+                        curl \
+                        wget \
+                        libx11-6 \
+                        libxt6 \
+                        libgl1 \
+                        libxcb-icccm4 \
+                        libxcb-image0 \
+                        libxcb-keysyms1 \
+                        libxcb-render-util0 \
+                        libxkbcommon-x11-0 \
+                        libxcb-randr0 \
+                        libxcb-xinerama0 \
+                        libxm4 \
+                        libtiff5 \
+                        libxcursor1 \
+                        libxinerama1
+
+# Download Coreform Cubit
+RUN wget -O /cubit.deb https://f002.backblazeb2.com/file/cubit-downloads/Coreform-Cubit/Releases/Linux/Coreform-Cubit-2023.11%2B43088-Lin64.deb
+
+# Install Cubit
+RUN dpkg -i cubit.deb
+ENV PYTHONPATH=/opt/Coreform-Cubit-2023.11/bin/
+COPY ./rlmcloud.in /opt/Coreform-Cubit-2023.11/bin/licenses/rlmcloud.in
+
+RUN mkdir -p /opt/etc
+RUN cp /root/.bashrc /opt/etc/bashrc
+
+# Install Python dependencies in parastell env conda environment
+COPY ./environment.yml /environment.yml
+RUN conda env create -f environment.yml
+RUN echo "conda activate parastell_env" >> /opt/etc/bashrc
+
+WORKDIR /opt
+
+# Install PyStell-UW
+RUN git clone https://github.com/aaroncbader/pystell_uw.git
+ENV PYTHONPATH=$PYTHONPATH:/opt/pystell_uw
+
+WORKDIR /