Switch from Travis to GitHub Actions

.github/workflows/build.yml

@@ -0,0 +1,36 @@
+name: build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04]
+        python-version: [2.7, 3.7, 3.8, 3.9]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      env:
+        KEY_MODELLER: ${{ secrets.KEY_MODELLER }}
+      run: |
+        tools/travis/install_deps.sh ${{ matrix.python-version }}
+    - name: Test
+      run: |
+        export CMAKE_INCLUDE_PATH=`pwd`/hdf5-inc
+        export CMAKE_LIBRARY_PATH=`pwd`/hdf5-libs
+        mkdir build && cd build
+        ../tools/coverage/setup.py
+        PYTHONPATH=`pwd`/coverage cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_C_FLAGS="-fprofile-arcs -ftest-coverage"
+        rm ../src/mdt_config.h
+        make
+        ctest --output-on-failure
+    - uses: codecov/codecov-action@v1

README.md

@@ -1,5 +1,5 @@
 [![docs](https://readthedocs.org/projects/mdt/badge/)](https://salilab.org/mdt/doc/)
-[![Build Status](https://api.travis-ci.org/salilab/mdt.svg?branch=develop)](https://travis-ci.org/salilab/mdt)
+[![Build Status](https://github.com/salilab/mdt/workflows/build/badge.svg?branch=develop)](https://github.com/salilab/mdt/actions?query=workflow%3Abuild)
 [![codecov](https://codecov.io/gh/salilab/mdt/branch/develop/graph/badge.svg)](https://codecov.io/gh/salilab/mdt)
 [![Coverity scan](https://img.shields.io/coverity/scan/8502.svg)](https://scan.coverity.com/projects/salilab-mdt)
 

tools/travis/install_deps.sh

@@ -1,35 +1,35 @@
 #!/bin/bash -e
 
-# Install dependencies for Travis.
+# Install dependencies for Travis or GitHub Actions.
 
-if [ $# -ne 2 ]; then
-  echo "Usage: $0 python_version modeller_license_file"
+if [ $# -ne 1 ]; then
+  echo "Usage: $0 python_version"
   exit 1
 fi
 
 python_version=$1
-modeller_license_file=$2
-MODELLER_VERSION=9.24
+MODELLER_VERSION=9.25
 HDF5_VERSION=1.10.5
 HDF5_SOVER=103
 HDF5_HL_SOVER=100
 
 sudo apt-get -qq update
 sudo apt-get install -y swig bc
+pip install coverage
 
 # Install Modeller
 modeller_url=https://salilab.org/modeller/${MODELLER_VERSION}
 wget ${modeller_url}/modeller_${MODELLER_VERSION}-1_amd64.deb
-export KEY_MODELLER=`cat ${modeller_license_file}`
-sudo dpkg -i modeller_${MODELLER_VERSION}-1_amd64.deb
+sudo --preserve-env=KEY_MODELLER dpkg -i modeller_${MODELLER_VERSION}-1_amd64.deb
 
 # Modeller installs for system Python, so link its Python packages into the
 # virtualenv Python path
-virtualenv_dir=$(dirname $(which python))/..
-ln -sf /usr/lib/python${python_version}/dist-packages/_modeller.so \
-       ${virtualenv_dir}/lib/*/site-packages/
-ln -sf /usr/lib/python${python_version}/dist-packages/modeller \
-       ${virtualenv_dir}/lib/*/site-packages/
+export PYTHON=`pip show coverage |grep Location|cut -b11-`
+# Modeller 9.25 doesn't support Python 3.9 but the 3.8 extension
+# should work
+if [ "${python_version}" = "3.9" ]; then python_version=3.8; fi
+ln -sf /usr/lib/python${python_version}/dist-packages/_modeller.so ${PYTHON}
+ln -sf /usr/lib/python${python_version}/dist-packages/modeller ${PYTHON}
 
 # Need to build MDT against the same version of HDF5 as Modeller, but Modeller
 # only includes the HDF5 libraries, so we need to get the corresponding