SLEDO v0.1.1

.github/workflows/build-ci.yml

@@ -0,0 +1,60 @@
+name: CI
+
+# This section controls when the workflow will run
+on:
+  # Run the workflow on push to "main" branch
+  push:
+    branches: [ "main" ]
+  # Run the workflow on pull request to "main" branch
+  pull_request:
+    branches: [ "main"]
+  # Run the workflow manually
+  workflow_dispatch:
+
+# This section controls which jobs the workflow will run
+jobs:
+  run-linter:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Create venv and install requirements
+        run: |
+          python3 -m venv venv
+          . venv/bin/activate
+          pip3 install build --upgrade
+          python3 -m build
+          pip3 install ./dist/*.whl
+
+      - name: Run linter
+        run: |
+          . venv/bin/activate
+          pip3 install flake8
+          flake8 . --exclude=venv* --count --max-complexity=10 --max-line-length=79 --statistics
+
+  build-and-test:
+    runs-on: ubuntu-latest
+
+    env:
+      PRCOMMITSHA : ${{ github.event.pull_request.head.sha }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Print github context
+        run: echo $PRCOMMITSHA
+
+      - name: Docker build (pull request)
+        if:  ${{ github.event.pull_request.head.sha != '' }}
+        run: docker build -t ci-sledo-ubuntu --build-arg build_git_sha=$PRCOMMITSHA docker/sledo-ubuntu/
+
+      - name:  Docker build (push)
+        if:  ${{ github.event.pull_request.head.sha == '' }}
+        run: docker build -t ci-sledo-ubuntu --build-arg build_git_sha=$GITHUB_SHA docker/sledo-ubuntu/
+
+      - name: Run tests
+        run: |
+          pip3 install pytest
+          pytest tests
+

.gitignore

@@ -158,3 +158,12 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# Ignore vscode files
+.vscode
+
+# Ignore any results folders
+results
+
+# Ignore config file
+config.yaml

README.md

@@ -1,2 +1,81 @@
 # sledo
-Sequential learning engineering design optimiser.
+
+SLEDO (Sequential Learning Engineering Design Optimiser) is a tool for optimising parametric component designs, developed for fusion engineering.
+
+Sledo uses Bayesian Optimisation to intelligently select candidate designs from a parametric search space and MOOSE to evaluate the design performance via scalable multiphysics simulation.
+
+# Installation
+
+## Linux
+
+We recommend creating a virtual environment before running `sledo`.
+Skip this step if you intend to install `sledo` into an existing python environment.
+```
+python3 -m venv venv
+source venv/bin/activate
+```
+
+### Standard install
+To install `sledo`, run the following:
+```
+# Ensure `build` package is installed.
+pip3 install build --upgrade
+
+# Build the distribution package.
+python3 -m build
+
+# Install the built distribution.
+pip3 install ./dist/*.whl
+```
+
+If you intend to use the jupyter notebook tutorials, also run the following line:
+```
+# Enable virtual environment in the tutorial notebooks.
+python3 -m ipykernel install --user --name=venv
+```
+
+Sledo can now be imported into python as:
+```
+import sledo
+```
+
+To test the installation, run `python3 -c "import sledo"`. If the installation was unsuccessful, an error will be raised.
+
+In order to run simulations, make sure to add the path to your MOOSE app of choice to `config.yaml`.
+
+### Editable install (developer mode)
+Developers may wish to create an editable installation. This allows changes to the source code to immediately take effect without the need to re-package and re-install sledo. This can be useful when running tests and other scripts.
+
+To install `sledo` this way, run the following:
+```
+# Install as an editable installation.
+pip3 install --editable .
+```
+
+# Getting started
+
+To start using sledo, please refer to the `tutorials` and `examples` folders for example usage.
+
+# Contributors
+
+Luke Humphrey, UK Atomic Energy Authority
+
+Aleksander Dubas, UK Atomic Energy Authority
+
+Andrew Davis, UK Atomic Energy Authority
+
+Lloyd Fletcher, UK Atomic Energy Authority
+
+# Citing Sledo
+
+If using Sledo in your research, please cite the following:
+
+> Citation TBC
+
+Please also cite Sledo's dependencies as indicated on their individual websites:
+
+- MOOSE (https://mooseframework.inl.gov/citing.html)
+- BoTorch (https://botorch.org/docs/papers)
+- NumPy (https://numpy.org/citing-numpy/)
+- SciPy (https://scipy.org/citing-scipy/)
+- Matplotlib (https://matplotlib.org/stable/users/project/citing.html)

config.yaml

@@ -0,0 +1,2 @@
+# Path to default moose app for running simulations.
+MOOSE_PATH: None

docker/sledo-ubuntu/Dockerfile

@@ -0,0 +1,23 @@
+# Get base image
+FROM idaholab/moose:latest
+
+ARG WORKDIR="opt"
+
+# By default, checkout the main branch
+ARG build_git_sha="main"
+
+# Build Sledo
+RUN cd /$WORKDIR && \
+    git clone https://github.com/aurora-multiphysics/sledo.git && \
+    cd sledo && \
+    git checkout "$build_git_sha" && \
+    sudo apt update -y && \
+    sudo apt install python3 -y && \
+    sudo apt install python3.9-venv -y && \
+    python3 -m pip install --upgrade pip && \
+    chmod +x install.sh && \
+    ./install.sh
+
+# Add MOOSE python packages to python path
+RUN export PYTHONPATH=${PYTHONPATH}:/${WORKDIR}/moose/python/pyhit && \
+    export PYTHONPATH=${PYTHONPATH}:/${WORKDIR}/moose/python/moosetree

examples/example_1_simple_monoblock.py

@@ -0,0 +1,37 @@
+from sledo.optimiser import Optimiser
+from sledo.simulation import ThermoMechSimulation
+
+DATA_DIR = "./results/example_1"
+
+search_space = (
+    {
+        "name": "Armour height",
+        "type": "range",
+        "hit_name": "monoBArmHeight",
+        "hit_block": "",
+        "bounds": [1e-3, 20e-3],
+    },
+    {
+        "name": "Block width",
+        "type": "range",
+        "hit_name": "monoBWidth",
+        "hit_block": "",
+        "bounds": [17e-3, 34e-3],
+    },
+)
+
+opt = Optimiser(
+    name="simple_monoblock",
+    search_space=search_space,
+    simulation_class=ThermoMechSimulation,
+    data_dir=DATA_DIR,
+)
+
+opt.load_input_file("./input_files/simple_monoblock.i")
+opt.run_optimisation_loop(
+    objective_name="stress",
+    max_iter=20,
+    minimise=True,
+)
+
+opt.pickle()

examples/example_2_monoblock.py

@@ -0,0 +1,51 @@
+from sledo.optimiser import Optimiser
+from sledo.simulation import ThermoMechSimulation
+
+DATA_DIR = "./results/example_2"
+
+search_space = (
+    {
+        "name": "Pipe thickness",
+        "type": "range",
+        "hit_name": "pipeThick",
+        "hit_block": "",
+        "bounds": [1e-3, 6e-3],
+    },
+    {
+        "name": "Interlayer thickness",
+        "type": "range",
+        "hit_name": "intLayerThick",
+        "hit_block": "",
+        "bounds": [1e-3, 6e-3],
+    },
+    {
+        "name": "Block thickness",
+        "type": "range",
+        "hit_name": "monoBThick",
+        "hit_block": "",
+        "bounds": [1e-3, 6e-3],
+    },
+    {
+        "name": "Armour height",
+        "type": "range",
+        "hit_name": "monoBArmHeight",
+        "hit_block": "",
+        "bounds": [1e-3, 16e-3],
+    },
+)
+
+opt = Optimiser(
+    name="monoblock",
+    search_space=search_space,
+    simulation_class=ThermoMechSimulation,
+    data_dir=DATA_DIR,
+)
+
+opt.load_input_file("./input_files/monoblock.i")
+opt.run_optimisation_loop(
+    objective_name="stress",
+    max_iter=20,
+    minimise=True,
+)
+
+opt.pickle()