Set up GitHub Actions CI (#367)

* MAINT: Bump Python versions in CI

* Set up GitHub Actions CI

* Fix test env name

* Drop coverage in tests and Python 3.8

* Add travis back, update miniconda URL

* curl -> wget

* Fix URL

* Fix env name

* Fix typo

* Fix typo

* Update script to cookiecutter

* Fix brew

Author: mattwthompson

.github/workflows/ci.yaml

@@ -0,0 +1,53 @@
+name: ci
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, ubuntu-latest]
+        python-version: [3.6, 3.7]
+    env:
+      CI_OS: ${{ matrix.os }}
+      PYVER: ${{ matrix.python-version }}
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - uses: goanpeca/setup-miniconda@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+        activate-environment: intermol-test-env
+        mamba-version: "*"
+        channels: conda-forge,omnia,bioconda,defaults
+        channel-priority: true
+        environment-file: devtools/conda-envs/test_env.yaml
+        auto-activate-base: false
+
+    - name: Additional info about the build
+      shell: bash
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+
+    - name: Environment Information
+      shell: bash -l {0}
+      run: |
+        conda info
+        conda list
+
+    - name: Install package
+      shell: bash -l {0}
+      run: |
+        python -m pip install --no-deps .
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        pytest --pyargs intermol -v

.travis.yml

@@ -3,20 +3,17 @@ sudo: false
 
 matrix:
   include:
-    - { os: linux, env: PYTHON_VERSION=2.7 }
-    - { os: linux, env: PYTHON_VERSION=3.4 }
-    - { os: linux, env: PYTHON_VERSION=3.5 }
-    - { os: osx, env: PYTHON_VERSION=2.7 }
-    - { os: osx, env: PYTHON_VERSION=3.4 }
-    - { os: osx, env: PYTHON_VERSION=3.5 }
+    - { os: linux, env: PYTHON_VERSION=3.6 }
+    - { os: linux, env: PYTHON_VERSION=3.7 }
+    - { os: osx, env: PYTHON_VERSION=3.6 }
+    - { os: osx, env: PYTHON_VERSION=3.7 }
 
 install:
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi
   - source devtools/travis-ci/install_conda.sh
 
   - conda config --set always_yes yes --set changeps1 no
-  - conda env create -q -n test-environment python=$PYTHON_VERSION -f environment.yml
-  - source activate test-environment
+  - conda env create -q python=$PYTHON_VERSION -f devtools/conda-envs/test_env.yaml
+  - source activate intermol-test-env
   - pip install -e .
 
 script:

devtools/conda-envs/test_env.yaml

@@ -0,0 +1,20 @@
+name: intermol-test-env
+channels:
+  - conda-forge
+  - omnia
+  - bioconda
+  - defaults
+dependencies:
+    # Core
+  - numpy
+  - parmed
+  - openmm
+  - six
+
+    # Engines
+  - ambertools
+  - gromacs
+  - lammps
+
+    # Testing
+  - pytest

devtools/travis-ci/install_conda.sh

@@ -1,10 +1,17 @@
 #!/bin/bash
 
-if [[ "$TRAVIS_OS_NAME" == "osx" ]];   then MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh; fi
-if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then MINICONDA=Miniconda3-latest-Linux-x86_64.sh;  fi
+if [ "$TRAVIS_OS_NAME" == "osx" ]; then
+    # Make OSX md5 mimic md5sum from linux, alias does not work
+    md5sum () {
+        command md5 -r "$@"
+    }
+    MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh
+else
+    MINICONDA=Miniconda3-latest-Linux-x86_64.sh
+fi
 
-MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
-wget https://repo.continuum.io/miniconda/$MINICONDA
+MINICONDA_MD5=$(wget -qO- https://repo.anaconda.com/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+wget -q https://repo.anaconda.com/miniconda/$MINICONDA
 if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
     echo "Miniconda MD5 mismatch"
     exit 1