Merge pull request #159 from Becksteinlab/gh-ci

switch to GitHub actions

.github/workflows/ci.yaml

@@ -0,0 +1,101 @@
+name: CI
+
+on:
+  # run once a day at 5:55 UTC
+  schedule:
+    - cron: "55 5 * * *"
+  push:
+    branches:
+      - "develop"
+      - "master"
+  pull_request:
+    branches:
+      - "develop"
+
+concurrency:
+  group: "${{ github.ref }}-${{ github.head_ref }}"
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macOS-latest]
+        python-version: [2.7] 
+        #python-version: [2.7, 3.8] 
+        #python-version: [2.7, 3.6, 3.7, 3.8, 3.9]
+        gromacs-version: ["4.6.5", "2018.6", "2019.1", "2021.1"]
+        # only test one GROMACS version on macOS to keep the testing
+        # matrix manageable
+        exclude:
+          - os: macOS-latest
+            gromacs-version: "4.6.5"
+          - os: macOS-latest
+            gromacs-version: "2018.6"
+          - os: macOS-latest
+            gromacs-version: "2019.1"
+
+    env:
+      MPLBACKEND: agg
+
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{ matrix.python-version }}      
+        auto-update-conda: true
+        mamba-version: "*"
+        channels: conda-forge,bioconda,defaults
+        channel-priority: true
+        show-channel-urls: true
+
+    - name: Conda info
+      shell: bash -l {0}
+      run: |
+         conda info
+         conda list
+         conda config --show-sources
+         conda config --show
+
+    - name: Python version
+      shell: bash -l {0}
+      run: |
+         python -c "import sys; print(sys.version)"                
+
+    - name: Install package dependencies
+      shell: bash -l {0}
+      run: |
+         mamba install six numpy scipy matplotlib pandas scikit-learn pyyaml mdanalysis numexpr
+         python -m pip install --no-deps numkit gromacswrapper
+         python -m pip install alchemlyb
+
+    - name: Install pytest+plugins and pybol
+      shell: bash -l {0}
+      run: |
+         mamba install pytest pytest-pep8 pytest-cov codecov
+         python -m pip install pybol
+
+    - name: Install GROMACS (${{ matrix.gromacs-version }})
+      shell: bash -l {0}
+      run: |
+         mamba install 'gromacs==${{ matrix.gromacs-version }}' pocl
+
+    - name: Install package
+      shell: bash -l {0}
+      run: |
+        python -m pip install --no-deps .
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        pytest -v --durations=20 --cov=mdpow --cov-report=xml ./mdpow/tests
+
+    - name: Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+        fail_ci_if_error: true

README.rst

@@ -81,9 +81,9 @@ Footnotes
 .. [#GromacsWrapperNote] The package is built on top of the GromacsWrapper_
                          framework (which is automatically installed).
 
-.. |build| image:: https://travis-ci.org/Becksteinlab/MDPOW.svg?branch=develop
+.. |build| image:: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml/badge.svg?branch=develop
    :alt: Build Status
-   :target: https://travis-ci.org/Becksteinlab/MDPOW
+   :target: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml
 
 .. |cov| image:: https://codecov.io/github/Becksteinlab/MDPOW/coverage.svg?branch=develop
    :alt: Coverage Status

mdpow/forcefields.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # POW package __init__.py
 # Copyright (c) 2012 Oliver Beckstein <[email protected]>
 # Released under the GNU Public License 3 (or higher, your choice)
@@ -146,7 +147,7 @@ def get_water_model(watermodel=DEFAULT_WATER_MODEL):
 
 #: Other solvents (not water, see :data:`GROMACS_WATER_MODELS` for those).
 new_octanol = '''Zangi R (2018) Refinement of the OPLSAA force-field
-                for liquid alcohols.; ACS Omega 3(12):18089–18099.
+                for liquid alcohols.; ACS Omega 3(12):18089-18099.
                 doi: 10.1021/acsomega.8b03132'''
 
 OPLS_SOLVENT_MODELS = {

mdpow/tests/test_runinput.py

@@ -79,7 +79,7 @@ class TestAlteredConfig(object):
             'stepout': 12000,
             'verbose': False,
             'nice': 12,
-            'maxthreads': 3
+            'maxthreads': 1
             }
     }
 

mdpow/tests/test_solvation.py

@@ -52,7 +52,11 @@ def test_solvation_octanol(setup, ff):
 def test_solvation_cyclohexane(setup):
     solvation(setup, "cyclohexane")
 
-@pytest.mark.xfail("gromacs.release().startswith('2019')")
+@pytest.mark.xfail(gromacs.release.startswith('4')
+                   or gromacs.release.startswith('5')
+                   or gromacs.release.startswith('2016'),
+                   reason="GROMACS < 2018 cannot easily work with mixed solvents "
+                   "(see issue #111)")
 @pytest.mark.parametrize("ff", ['OPLS-AA', 'CHARMM', 'AMBER'])
 def test_solvation_wetoctanol(setup, ff):
     solvation(setup, "wetoctanol", ff)

mdpow/tests/testing_resources/states/base/runinput.yml

@@ -119,8 +119,6 @@ mdrun:
          # report progress verbosely (True is -v)
     nice: 19
          # nicel level
-    maxthreads: 3
+    maxthreads: None
          # maximum number of threads (-nt), 0 or None lets mdrun
          # automatically choose
-         # For testing on travis, needs to be either 3 or 1.
-         # See https://github.com/Becksteinlab/MDPOW/pull/77

mdpow/tests/testing_resources/states/md_npt/runinput.yml

@@ -119,8 +119,7 @@ mdrun:
          # report progress verbosely (True is -v)
     nice: 19
          # nicel level
-    maxthreads: 3
+    maxthreads: None
          # maximum number of threads (-nt), 0 or None lets mdrun
          # automatically choose
-         # For testing on travis, needs to be either 3 or 1.
-         # See https://github.com/Becksteinlab/MDPOW/pull/77
+

mdpow/tests/testing_resources/test_configurations/altered_runinput.yml

@@ -119,5 +119,5 @@ mdrun:
          # report progress verbosely (True is -v)
     nice: 12
          # nicel level
-    maxthreads: 3
+    maxthreads: 1
          # maximum number of threads (-nt), 0 or None lets mdrun automatically choose