Update Github CI

.github/workflows/CI.yaml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10"]
         exclude:
           - os: windows-latest
             python-version: "3.9"
@@ -29,19 +29,19 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba (Linux)
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment-dev.yml
           extra-specs: |
             python=${{ matrix.python-version }}
         if: runner.os != 'Windows'
 
       - name: Install Mamba (Windows)
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment-dev-win.yml
           extra-specs: |
@@ -70,11 +70,11 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment-dev.yml
           extra-specs: |
@@ -96,42 +96,45 @@ jobs:
           pip install -e gmso
           pip install -e .
 
-      - name: Run Bleeding Edge Tests
+      - name: Bleeding Edge Tests
         run: |
           python -m pytest -v --color yes --pyargs foyer
 
   docker:
     runs-on: ubuntu-latest
     needs: test
     name: Build Docker Image
-    if: github.event_name != 'pull_request'
+    #if: github.event_name != 'pull_request'
 
     steps:
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
 
       - name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          username: mtest2023
+          password: mtest2023
 
       - name: Get Tagged Version
         run: |
-          echo "DOCKER_TAGS=mosdef/foyer:${GITHUB_REF_NAME}, mosdef/foyer:stable" >> $GITHUB_ENV
+          echo "DOCKER_TAGS=mosdef/foyer:TEST, mosdef/foyer:stable" >> $GITHUB_ENV
         if: github.ref_type == 'tag'
 
       - name: Get Push Version
         run: |
-          echo "DOCKER_TAGS=mosdef/foyer:${GITHUB_REF_NAME}, mosdef/foyer:latest" >> $GITHUB_ENV
+          echo "DOCKER_TAGS=mosdef/foyer:TEST, mosdef/foyer:latest" >> $GITHUB_ENV
         if: github.ref_type == 'branch'
 
       - name: Docker Image Info
         run: |
           echo Docker Image tags: ${DOCKER_TAGS}
 
       - name: Build and Push
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v4
         with:
           push: true
           tags: ${{ env.DOCKER_TAGS }}

Dockerfile

@@ -1,5 +1,4 @@
-ARG PY_VERSION=3.8
-FROM continuumio/miniconda3:4.10.3-alpine AS builder
+FROM mambaorg/micromamba:1.4.3
 
 EXPOSE 8888
 
@@ -14,32 +13,17 @@ ADD . /foyer
 
 WORKDIR /foyer
 
-# Create a group and user
-RUN addgroup -S anaconda && adduser -S anaconda -G anaconda
+RUN apt-get update && apt-get install -y git
 
-RUN /sbin/apk add --no-cache git && \
-  conda update conda -yq && conda install -c conda-forge mamba && \
-  conda config --set always_yes yes --set changeps1 no && \
-  . /opt/conda/etc/profile.d/conda.sh && \
-  sed -i -E "s/python.*$/python="$(PY_VERSION)"/" environment-dev.yml && \
-  mamba env create nomkl -f environment-dev.yml && \
-  conda activate foyer-dev  && \
-  mamba install -c conda-forge nomkl jupyter python="$PY_VERSION" && \
-  python setup.py install && \
-  echo "source activate foyer-dev" >> /home/anaconda/.profile && \
-  conda clean -afy && \
-  mkdir -p /home/anaconda/data && \
-  chown -R anaconda:anaconda /foyer && \
-  chown -R anaconda:anaconda /opt && \
-  chown -R anaconda:anaconda /home/anaconda
+RUN micromamba create --file environment-dev.yml
+ARG MAMBA_DOCKERFILE_ACTIVATE=1  # (otherwise python will not be found)
 
-WORKDIR /home/anaconda
+RUN  micromamba install -c conda-forge nomkl jupyter python="3.10"
+RUN  python setup.py install
+RUN  echo "source activate foyer-dev" >> /home/.bashrc
+RUN  micromamba clean -afy
+RUN  mkdir -p /home/data
 
-COPY devtools/docker-entrypoint.sh /entrypoint.sh
 
-RUN chmod a+x /entrypoint.sh
-
-USER anaconda
-
-ENTRYPOINT ["/entrypoint.sh"]
+ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
 CMD ["jupyter"]

foyer/element.py

@@ -1,4 +1,6 @@
 """Element support in foyer."""
+import os
+
 import openmm.app.element as elem