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Merge pull request #3 from scientificcomputing/finsberg/updates
Restructure repo and add workflow for reproducing results
2 parents eb9eaff + 2327f4f commit 363f6c0

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‎.dockerignore‎

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data/*
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code/results/*
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code/figures/*
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_build
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### Python ###

‎.flake8‎

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‎.github/workflows/build_docs.yml‎

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name: Github Pages
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# Simple workflow for deploying static content to GitHub Pages
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name: Deploy static content to Pages
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on:
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push:
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branches: ["main"]
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pull_request:
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branches: ["main"]
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PUBLISH_DIR: ./_build/html
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- name: Cache
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id: cache
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uses: actions/cache@v3
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with:
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path: |
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~/.cache/pip
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~/_build
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key: cache_v1
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restore-keys: |
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cache_v1
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- name: Install dependencies
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run: python3 -m pip install -r requirements-docs.txt
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- name: Build docs
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run: jupyter book build .
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- name: Upload documentation as artifact
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uses: actions/upload-artifact@v3
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v2
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with:
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name: documentation
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path: ${{ env.PUBLISH_DIR }}
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if-no-files-found: error
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# Single deploy job since we're just deploying
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deploy:
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if: github.ref == 'refs/heads/main'
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needs: build
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup Pages
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uses: actions/configure-pages@v3
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v2

‎.github/workflows/deploy.yml‎

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‎.github/workflows/docker-image.yml‎

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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v2
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uses: docker/setup-qemu-action@v3
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2
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uses: docker/setup-buildx-action@v3
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- name: Log in to the Container registry
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v4
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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- name: Build and push Docker image
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uses: docker/build-push-action@v4
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uses: docker/build-push-action@v5
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with:
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context: .
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push: true

‎.github/workflows/pre-commit.yml‎

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name: Pre-commit
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on:
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push:
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branches: ["main"]
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pull_request:
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branches: ["main"]
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jobs:
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check-code:
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runs-on: ubuntu-22.04
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steps:
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# This action sets the current path to the root of your github repo
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- uses: actions/checkout@v4
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- name: Install pre-commit
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run: python3 -m pip install pre-commit
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- name: Run hooks
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run: pre-commit run --all

‎.github/workflows/reproduce_results.yml‎

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# Simple workflow for deploying static content to GitHub Pages
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name: Reproduce results
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on:
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push:
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branches: ["main"]
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pull_request:
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branches: ["main"]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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workflow_call:
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jobs:
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run:
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runs-on: ubuntu-22.04
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env:
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# Directory that will be published on github pages
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DATAPATH: ./artifacts/data/data.json
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FIGDIR: ./artifacts/figures
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RESULTDIR: ./artifacts/results
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steps:
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- uses: actions/checkout@v4
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- name: Cache
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id: cache
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uses: actions/cache@v3
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with:
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path: |
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~/.cache/pip
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key: cache_v1
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restore-keys: |
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cache_v1
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- name: Install dependencies
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run: python3 -m pip install -r requirements.txt
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- name: Run pre-processing
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run: python3 code/pre_processing.py --datapath=${{ env.DATAPATH }}
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- name: Run simulation
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run: python3 code/run_all.py --resultdir=${{ env.RESULTDIR }}
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- name: Postprocess
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run: python3 code/postprocess.py --resultdir=${{ env.RESULTDIR }} --datapath=${{ env.DATAPATH }} --figdir=${{ env.FIGDIR }}
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- name: Upload artifact
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if: always()
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uses: actions/upload-artifact@v3
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with:
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path: ./artifacts
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if-no-files-found: error

‎.gitignore‎

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_build
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code/results
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data/data.txt
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data/data.json
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code/figures
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.DS_Store
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# Created by https://www.toptal.com/developers/gitignore/api/python,visualstudiocode
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# Edit at https://www.toptal.com/developers/gitignore?templates=python,visualstudiocode
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‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.3.0
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rev: v4.5.0
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hooks:
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- id: check-yaml
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- id: end-of-file-fixer
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- id: trailing-whitespace
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- id: check-docstring-first
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- id: debug-statements
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- id: requirements-txt-fixer
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- id: check-added-large-files
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- id: check-toml
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- repo: https://github.com/asottile/reorder_python_imports
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rev: v3.8.3
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- repo: https://github.com/asottile/add-trailing-comma
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rev: v3.1.0
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hooks:
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- id: reorder-python-imports
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- id: add-trailing-comma
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- repo: https://github.com/psf/black
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rev: 22.10.0
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rev: 23.10.1
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hooks:
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- id: black
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.0.0
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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# Ruff version.
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rev: 'v0.1.4'
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hooks:
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- id: flake8
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- id: ruff
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- repo: https://github.com/asottile/add-trailing-comma
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rev: v2.3.0
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hooks:
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- id: add-trailing-comma
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v0.982
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rev: v1.6.1
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hooks:
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- id: mypy
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.1.0
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- repo: https://github.com/streetsidesoftware/cspell-cli
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rev: v7.3.2
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hooks:
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- id: pyupgrade
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args: [--py38-plus]
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- id: cspell
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files: docs/(.+).md|README.md

‎README.md‎

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This repository contains supplementary code for the paper
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> Finsberg, H., Dokken, J. 2022.
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> Title of paper, Journal of blabla, volume, page, url
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> Title of paper, Journal of ..., volume, page, url
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## Abstract
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Provide the abstract of the paper
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## Getting started
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We provide a pre-build Docker image which can be used to run the the code in this repository. First thing you need to do is in ensure that you have [docker installed](https://docs.docker.com/get-docker/).
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We provide a pre-build Docker image which can be used to run the the code in this repository. First thing you need to do is to ensure that you have [docker installed](https://docs.docker.com/get-docker/).
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To start an interactive docker container you can execute the following command
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