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Merged
p-zubieta merged 1 commit into from
Apr 30, 2025
Merged

Bring CI up to date #348

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28 changes: 16 additions & 12 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,19 +20,22 @@ jobs:
strategy:
fail-fast: false
matrix:
os: [ubuntu-20.04, macos-latest]
python-version: [3.8, 3.9, 3.11]
os: [ubuntu-latest, macos-latest]
python-version: [3.9, 3.13]
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- name: Install python dependecies
- name: Install python dependencies
env:
JAX_MD_PKG: jax-md-v0.2.${{ matrix.python-version == '3.9' && 24 || 25 }}.zip
run: |
python -m pip install --upgrade pip
pip install ase dill "dm-haiku<0.0.11" "e3nn-jax!=0.20.4" "jax<=0.4.15" "jaxlib<=0.4.15" "jax-md>=0.2.7" jaxopt pytest matplotlib "scipy<1.13"
pip install https://github.com/jax-md/jax-md/archive/refs/tags/${{ env.JAX_MD_PKG }}
pip install ase dill pytest matplotlib

- name: Install pysages
run: pip install .
Expand All @@ -44,23 +47,24 @@ jobs:
mv *.pdf /tmp/test_plots

- name: Upload artifact
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: test_plots
name: test_plots-${{ matrix.os }}-py${{ matrix.python-version }}
path: /tmp/test_plots

doc-test:
runs-on: ubuntu-20.04
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: 3.9
- name: Install python dependecies
run: |
python -m pip install --upgrade pip
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
pip install https://github.com/jax-md/jax-md/archive/refs/tags/jax-md-v0.2.24.zip
pip install dill pytest pylint flake8
pip install -r docs/requirements.txt
- name: Install pysages
run: pip install .
Expand Down
8 changes: 4 additions & 4 deletions .github/workflows/docker-base.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,21 +9,21 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check Out Repo
uses: actions/checkout@v3
uses: actions/checkout@v4

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

- name: Set up Docker Buildx
id: buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3

- name: Build and push
id: docker_build
uses: docker/build-push-action@v3
uses: docker/build-push-action@v6
with:
context: ./
file: ./Dockerfile-base
Expand Down
92 changes: 46 additions & 46 deletions .github/workflows/docker-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,17 +22,17 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
uses: actions/checkout@v4
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Build and export
uses: docker/build-push-action@v3
uses: docker/build-push-action@v6
with:
context: .
tags: pysages:latest
outputs: type=docker,dest=/tmp/pysages.tar
- name: Upload artifact
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: pysages
path: /tmp/pysages.tar
Expand All @@ -43,9 +43,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -62,9 +62,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -78,9 +78,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -96,9 +96,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -112,9 +112,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -128,9 +128,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -148,9 +148,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -164,9 +164,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -180,9 +180,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -196,9 +196,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -216,9 +216,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -234,9 +234,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -250,9 +250,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -268,9 +268,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -286,9 +286,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -297,7 +297,7 @@ jobs:
docker load --input /tmp/pysages.tar
docker run -v/tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/harmonic_bias/ && ./run.sh && mv hist.pdf /tmp/"
- name: Upload artifact
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: harmonic-hist.pdf
path: /tmp/hist.pdf
Expand All @@ -308,9 +308,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -324,9 +324,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -335,7 +335,7 @@ jobs:
docker load --input /tmp/pysages.tar
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/"
- name: Upload artifacts
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: umbrella-integration-plots
path: /tmp/plots
Expand All @@ -346,9 +346,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -357,7 +357,7 @@ jobs:
docker load --input /tmp/pysages.tar
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/"
- name: Upload artifacts
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: spline-string-plots
path: /tmp/plots
Expand All @@ -368,9 +368,9 @@ jobs:
needs: build
steps:
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
uses: actions/download-artifact@v4
with:
name: pysages
path: /tmp
Expand All @@ -385,7 +385,7 @@ jobs:
docker load --input /tmp/pysages.tar
docker run -v /tmp:/tmp -t pysages bash -c "${SCRIPT}"
- name: Upload artifacts
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: umbrella-integration-mpi-plots
path: /tmp/plots
Expand Down
8 changes: 4 additions & 4 deletions .github/workflows/docker.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,21 +15,21 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check Out Repo
uses: actions/checkout@v3
uses: actions/checkout@v4

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

- name: Set up Docker Buildx
id: buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3

- name: Build and push
id: docker_build
uses: docker/build-push-action@v3
uses: docker/build-push-action@v6
with:
context: ./
file: ./Dockerfile
Expand Down
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