Add GHA CI

.github/workflows/CI.yaml

@@ -0,0 +1,119 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - "master"
+  schedule:
+    # nightly tests
+    - cron: "0 0 * * *"
+  push:
+    branches:
+      - master
+
+jobs:
+  test:
+    name: Test on ${{ matrix.cfg.os }}, Python ${{ matrix.cfg.python-version }}, OpenMM ${{ matrix.cfg.openmm }}
+    runs-on: ${{ matrix.cfg.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        cfg:
+          - { os: ubuntu-latest, python-version: 3.7, docs: true,  openmm: latest }
+          - { os: macos-latest,  python-version: 3.7, docs: true,  openmm: latest }
+          - { os: ubuntu-latest, python-version: 3.8, docs: false, openmm: latest }
+          - { os: ubuntu-latest, python-version: 3.7, docs: false, openmm: nightly }
+          - { os: ubuntu-latest, python-version: 3.8, docs: false, openmm: nightly }
+          - { os: ubuntu-latest, python-version: 3.7, docs: false, openmm: conda-forge }
+          - { os: ubuntu-latest, python-version: 3.8, docs: false, openmm: conda-forge }
+
+    env:
+      OPENMM: ${{ matrix.cfg.openmm }}
+      OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+      PACKAGENAME: yank
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - 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
+        with:
+          python-version: ${{ matrix.cfg.python-version }}
+          environment-file: devtools/conda-envs/test_env.yaml
+          activate-environment: test
+          auto-update-conda: true
+          auto-activate-base: false
+          show-channel-urls: true
+
+      - name: Refine test environment
+        shell: bash -l {0}
+        run: |
+          case ${{ matrix.cfg.openmm }} in
+            latest)
+              echo "Using latest release OpenMM."
+              conda install --quiet -c omnia openmm;;
+            rc)
+              echo "Using OpenMM rc"
+              conda install --quiet -c omnia/label/rc openmm;;
+            beta)
+              echo "Using OpenMM beta"
+              conda install --quiet -c omnia/label/beta openmm;;
+            nightly)
+              echo "Using OpenMM nightly dev build."
+              conda install --quiet -c omnia-dev openmm;;
+            conda-forge)
+              echo "Using OpenMM conda-forge testing build."
+              conda install --quiet -c conda-forge/label/test openmm;;
+          esac
+
+      - name: Install package
+        shell: bash -l {0}
+        run: |
+          python -m pip install --no-deps -v .
+
+      - name: Environment Information
+        shell: bash -l {0}
+        run: |
+          conda info -a
+          conda list
+
+      - name: Decrypt licenses
+        # TODO: MODELLER
+        shell: bash -l {0}
+        env:
+          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+        run: |
+          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+          python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
+
+      - name: Test the package
+        shell: bash -l {0}
+        run: |
+          export OE_LICENSE="$HOME/oe_license.txt"
+          export TRAVIS=true
+          pushd .
+          nosetests ${PACKAGENAME} --nocapture --with-coverage --verbosity=3 --with-timer -a '!slow' --cover-xml --cover-xml-file=./coverage.xml
+          popd
+
+      - name: Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+
+      - name: Build docs
+        shell: bash -l {0}
+        if: matrix.cfg.docs
+        run: |
+          cd docs && make html; cd ..
+          # Move the docs into a versioned subdirectory
+          python devtools/travis-ci/set_doc_version.py
+          # Prepare versions.json
+          python devtools/travis-ci/update_versions_json.py

README.md

@@ -1,3 +1,4 @@
+[![GH Actions Status](https://github.com/choderalab/perses/workflows/CI/badge.svg)](https://github.com/choderalab/perses/actions?query=branch%3Amaster)
 [![Travis Build Status](https://travis-ci.org/choderalab/yank.png)](https://travis-ci.org/choderalab/yank)
 [![Anaconda Cloud Badge](https://anaconda.org/omnia/yank/badges/version.svg)](https://anaconda.org/omnia/yank)
 [![Anaconda Cloud Downloads](https://anaconda.org/omnia/yank/badges/downloads.svg)](https://anaconda.org/omnia/yank)

Yank/__init__.py

@@ -6,13 +6,24 @@
 """
 
 # Define global version.
-from . import version  # Needed for yank 3.X.
+try:
+    from . import version  # Needed for yank 3.X.
+except:
+    # Fill in information manually.
+    class _Version:
+        short_version = "dev"
+        version = "dev"
+        full_version = "dev"
+        git_revision = "dev"
+        release = False
+
+    version = _Version()
+
+__version__ = version.version
 
 # Self module imports
 from . import utils
 from . import restraints
 from . import pipeline
 from . import experiment
 from .yank import Topography, AlchemicalPhase
-
-__version__ = version.version

devtools/conda-envs/test_env.yaml

@@ -0,0 +1,42 @@
+name: test
+channels:
+  - conda-forge
+  - defaults
+  - omnia
+  - openeye
+  - salilab
+dependencies:
+  - compilers
+  - python
+  - pip
+  - pandas
+  - numpy >=1.14
+  - scipy
+  - openmm >=7.3
+  - mdtraj >=1.7.2
+  - openmmtools >=0.18.3
+  - pymbar
+  - ambermini >=16.16.0
+  - docopt
+  - openmoltools >=0.7.5
+  - mpiplus
+  - pyyaml
+  - clusterutils
+  - sphinxcontrib-bibtex
+  - cerberus ==1.1 # yank uses buggy cerberus 1.1 behavior as a feature ¯\_(ツ)_/¯
+  - matplotlib
+  - jupyter
+  - pdbfixer
+  - openeye-toolkits
+  - modeller
+  # test
+  - nose
+  - nose-timer
+  - coverage
+  # docs
+  - sphinx
+  - sphinx_rtd_theme
+  - jinja2
+  - runipy
+  - pip:
+      - msmb_theme