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Bring CI up to date (#348)
2 parents 6f67266 + 941fd60 commit 1195618

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‎.github/workflows/ci.yml‎

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@@ -20,19 +20,22 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-20.04, macos-latest]
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python-version: [3.8, 3.9, 3.11]
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os: [ubuntu-latest, macos-latest]
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python-version: [3.9, 3.13]
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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: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install python dependecies
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- name: Install python dependencies
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env:
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JAX_MD_PKG: jax-md-v0.2.${{ matrix.python-version == '3.9' && 24 || 25 }}.zip
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run: |
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python -m pip install --upgrade pip
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pip install ase dill "dm-haiku<0.0.11" "e3nn-jax!=0.20.4" "jax<=0.4.15" "jaxlib<=0.4.15" "jax-md>=0.2.7" jaxopt pytest matplotlib "scipy<1.13"
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pip install https://github.com/jax-md/jax-md/archive/refs/tags/${{ env.JAX_MD_PKG }}
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pip install ase dill pytest matplotlib
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- name: Install pysages
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run: pip install .
@@ -44,23 +47,24 @@ jobs:
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mv *.pdf /tmp/test_plots
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- name: Upload artifact
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: test_plots
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name: test_plots-${{ matrix.os }}-py${{ matrix.python-version }}
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path: /tmp/test_plots
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doc-test:
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runs-on: ubuntu-20.04
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runs-on: ubuntu-latest
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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: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: 3.9
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- name: Install python dependecies
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run: |
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python -m pip install --upgrade pip
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pip install dill "dm-haiku<0.0.11" "e3nn-jax!=0.20.4" "jax<=0.4.15" "jaxlib<=0.4.15" "jax-md>=0.2.7" jaxopt pytest pylint flake8
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pip install https://github.com/jax-md/jax-md/archive/refs/tags/jax-md-v0.2.24.zip
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pip install dill pytest pylint flake8
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pip install -r docs/requirements.txt
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- name: Install pysages
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run: pip install .

‎.github/workflows/docker-base.yml‎

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@@ -9,21 +9,21 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: Check Out Repo
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Login to Docker Hub
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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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username: ${{ secrets.DOCKER_HUB_USERNAME }}
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password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
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- name: Set up Docker Buildx
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id: 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: Build and push
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id: docker_build
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uses: docker/build-push-action@v3
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uses: docker/build-push-action@v6
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with:
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context: ./
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file: ./Dockerfile-base

‎.github/workflows/docker-ci.yml‎

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@@ -22,17 +22,17 @@ jobs:
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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@v3
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uses: actions/checkout@v4
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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: Build and export
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uses: docker/build-push-action@v3
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uses: docker/build-push-action@v6
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with:
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context: .
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tags: pysages:latest
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outputs: type=docker,dest=/tmp/pysages.tar
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- name: Upload artifact
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: pysages
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path: /tmp/pysages.tar
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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docker load --input /tmp/pysages.tar
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docker run -v/tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/harmonic_bias/ && ./run.sh && mv hist.pdf /tmp/"
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- name: Upload artifact
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: harmonic-hist.pdf
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path: /tmp/hist.pdf
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
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docker load --input /tmp/pysages.tar
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docker run -v /tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/umbrella_integration && python3 ./gen_gsd.py && python3 integration.py --replicas=5 --time-steps=1000 && mkdir /tmp/plots && mv *.pdf /tmp/plots/"
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- name: Upload artifacts
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: umbrella-integration-plots
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path: /tmp/plots
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
@@ -357,7 +357,7 @@ jobs:
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docker load --input /tmp/pysages.tar
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docker run -v /tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/string && python3 ./gen_gsd.py && python3 spline_string.py --replicas=5 --time-steps=1000 --log-delay=0 --string-steps=2 && mkdir /tmp/plots && mv *.pdf /tmp/plots/"
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- name: Upload artifacts
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: spline-string-plots
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path: /tmp/plots
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needs: build
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steps:
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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: Download artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: pysages
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path: /tmp
@@ -385,7 +385,7 @@ jobs:
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docker load --input /tmp/pysages.tar
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docker run -v /tmp:/tmp -t pysages bash -c "${SCRIPT}"
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- name: Upload artifacts
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: umbrella-integration-mpi-plots
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path: /tmp/plots

‎.github/workflows/docker.yml‎

Lines changed: 4 additions & 4 deletions
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@@ -15,21 +15,21 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: Check Out Repo
18-
uses: actions/checkout@v3
18+
uses: actions/checkout@v4
1919

2020
- name: Login to Docker Hub
21-
uses: docker/login-action@v2
21+
uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKER_HUB_USERNAME }}
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password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
2525

2626
- name: Set up Docker Buildx
2727
id: buildx
28-
uses: docker/setup-buildx-action@v2
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uses: docker/setup-buildx-action@v3
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3030
- name: Build and push
3131
id: docker_build
32-
uses: docker/build-push-action@v3
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uses: docker/build-push-action@v6
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with:
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context: ./
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file: ./Dockerfile

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