NEq cycling rebase using openfe utils

.github/workflows/ci.yaml

@@ -0,0 +1,84 @@
+name: "CI"
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  schedule:
+    # At 07:00 UTC on Monday and Thursday.
+    - cron: "0 7 * * *"
+  release:
+    types:
+      - published
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}-latest
+    name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu"]
+        python-version:
+          - "3.9"
+          - "3.10"
+          - "3.11"
+        include:
+          - os: "macos"
+            python-version: "3.11"
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: devtools/conda-envs/test_env.yaml
+          environment-name: feflow-env
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+          init-shell: bash
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import feflow; print(feflow.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: "Run tests"
+        env:
+          # Set the OFE_SLOW_TESTS to True if running a Cron job
+          OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
+        run: |
+          pytest -n auto -v --cov=feflow --cov-report=xml --durations=10
+
+      - name: codecov
+        if: ${{ github.repository == 'choderalab/feflow'
+                && github.event_name == 'pull_request' }}
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml
+          fail_ci_if_error: False
+          verbose: True

devtools/conda-envs/test_env.yaml

@@ -2,26 +2,18 @@ name: feflow-test
 channels:
   - conda-forge
   - defaults
-  - openeye  # TODO: Remove once we don't depend on openeye
 dependencies:
     # Base depends
+  - gufe
   - openfe  # TODO: Remove once we don't depend on openfe
   - python
   - pip
 
-  # Perses depends (TODO: Remove once we don't depend on perses)
-  - openmoltools
-  - cloudpathlib
-  - dask
-  - openeye-toolkits
-
     # Testing
   - pytest
   - pytest-cov
+  - pytest-xdist
   - codecov
 
-    # Pip-only installs
-  - pip:
-      - git+https://github.com/choderalab/perses.git@protocol-neqcyc  # TODO: Remove once it only depends on openmmtools/openfe
   #  - codecov
 

feflow/__init__.py

@@ -1,6 +1,5 @@
-"""Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits"""
-
-# Add imports here
-from .feflow import *
+"""Recipes and protocols for molecular free energy calculations using the
+openmmtools/perses and Open Free Energy toolkits"""
 
 from importlib.metadata import version
+__version__ = version("openfe")