Update CI action

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/CI.yaml

@@ -1,75 +1,51 @@
 name: CI
 
 on:
-  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
-  # Existing codes likely still have "master" as the primary branch
-  # Both are tracked here to keep legacy and new codes working
   push:
     branches:
-      - "master"
       - "main"
   pull_request:
     branches:
-      - "master"
       - "main"
   schedule:
-    # Nightly tests run on master by default:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "0 0 * * *"
 
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
 jobs:
   test:
     name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v1
 
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
-
-
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
+    - name: Set up conda environment with micromamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-
-        channels: conda-forge,defaults
-
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
+        micromamba-binary-path: ~/.local/bin/micromamba
+        environment-file: devtools/conda-envs/proteinbenchmark.yaml
+        create-args: >-
+          python=${{ matrix.python-version }}
 
     - name: Install package
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
       run: |
         python -m pip install . --no-deps
-        conda list
-
+        micromamba list
 
     - name: Run tests
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
-
       run: |
-        pytest -v --cov=proteinbenchmark --cov-report=xml --color=yes proteinbenchmark/tests/
+        python -m pytest -v proteinbenchmark/tests/ \
+            --cov=proteinbenchmark --cov-report=xml --color=yes
 
     - name: CodeCov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: unittests

devtools/conda-envs/proteinbenchmark.yaml

@@ -2,11 +2,7 @@ name: openff-proteinbenchmark
 channels:
   - conda-forge
   - openeye
-  - defaults
 dependencies:
-  - black
-  - click
-  - isort
   - pip
   - python
 
@@ -17,8 +13,7 @@ dependencies:
 
   # MM calculations
   - ambertools
-  - cudatoolkit
-  - openeye-toolkits=2022.1.1
+  - openeye-toolkits
   - openff-forcefields
   - openff-toolkit>=0.13.0
   - openff-units
@@ -27,7 +22,7 @@ dependencies:
   - openmmtools
 
   # Analysis
-  - loos
+  - loos ==4.1
   - pandas
   - pymol-open-source
   - seaborn