Add CI github actions workflow

.github/workflows/ci.yml

@@ -1,5 +1,8 @@
 name: CI
-on: [push, pull_request]
+on:
+  push:
+    branches: [develop]
+  pull_request:
 
 env:
   CXXFLAGS: "-fprofile-arcs -ftest-coverage"
@@ -9,31 +12,38 @@ jobs:
     name: "Python ${{ matrix.python-version }} / ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         python-version: ["2.7", "3.6"]
         os: [ubuntu-18.04]
         compiler: [gcc]
     env:
       CC: ${{ matrix.compiler }}
       PY2: ${{ startsWith(matrix.python-version, 2) && 'on' || 'off' }}
+      BUILD: "-j 2 IMP.kernel IMP.test IMP.core IMP.algebra IMP.container"
+      PERCPP: "kernel"
     steps:
       - uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
       - name: Install dependencies
         run: |
           sudo apt-get update -qq
           sudo apt-get install -qq libboost-all-dev swig libhdf5-serial-dev libeigen3-dev \
-            cmake libcgal-dev libcgal-qt5-dev \
-            libfftw3-dev libopencv-dev libgsl0-dev libann-dev \
-            libprotobuf-dev protobuf-compiler \
-            libopenmpi-dev
+            cmake libcgal-dev libcgal-qt5-dev libfftw3-dev libopencv-dev libgsl0-dev \
+            libann-dev libprotobuf-dev protobuf-compiler libopenmpi-dev
           if [ "${{ env.PY2 }}" == "on" ]
           then
             sudo apt-get install -qq python-dev python-numpy python-protobuf \
-                                     python-nose python-pip python-biopython
+                                     python-coverage python-pip \
+                                     python-biopython python-pytest-xdist \
+                                     python-pytest-cov
             export PIP=pip2
           else
             sudo apt-get install -qq python3-dev python3-numpy python3-protobuf \
-                                     python3-nose python3-pip python3-biopython
+                                     python3-coverage python3-pip \
+                                     python3-biopython python3-pytest-xdist \
+                                     python3-pytest-cov
             export PIP=pip3
           fi
           $PIP install codecov
@@ -43,5 +53,21 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake .. -DUSE_PYTHON2=${{ env.PY2 }} -DCMAKE_CXX_FLAGS="${{ env.CXXFLAGS }}" -DCGAL_DIR=/usr/lib/x86_64-linux-gnu/cmake/CGAL/
-          make -k -j 2
+          cmake .. -DUSE_PYTHON2=${{ env.PY2 }} -DCMAKE_CXX_FLAGS="${{ env.CXXFLAGS }}" \
+                   -DCGAL_DIR=/usr/lib/x86_64-linux-gnu/cmake/CGAL/ \
+                   -DIMP_PER_CPP_COMPILATION=${{ env.PERCPP }}
+          make -k ${{ env.BUILD }}
+      - name: Run tests
+        run: |
+          if [ "${{ env.PY2 }}" == "on" ]; then
+            export PYTEST=pytest
+          else
+            export PYTEST=pytest-3
+          fi
+          cd build
+          ./setup_environment.sh $PYTEST --cov=.. --cov-report=xml --cov-branch --forked ../modules/kernel/test/test_*.py
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          fail_ci_if_error: false
+          directory: build

modules/kernel/test/test_progress.py

@@ -1,14 +1,21 @@
 import IMP
+import IMP.test
 import sys
 
-IMP.set_deprecation_exceptions(True)
 
-IMP.setup_from_argv(sys.argv, "Test progress bar")
-IMP.set_log_level(IMP.PROGRESS)
-IMP.set_progress_display("Test progress", 110)
-for i in range(0, 110, 5):
-    IMP.add_to_progress_display(5)
+class Tests(IMP.test.TestCase):
 
-IMP.set_progress_display("Test progress round 2", 130)
-for i in range(0, 130, 5):
-    IMP.add_to_progress_display(5)
+    def test_progress(self):
+        """Test progress bar"""
+        IMP.set_log_level(IMP.PROGRESS)
+        IMP.set_progress_display("Test progress", 110)
+        for i in range(0, 110, 5):
+            IMP.add_to_progress_display(5)
+
+        IMP.set_progress_display("Test progress round 2", 130)
+        for i in range(0, 130, 5):
+            IMP.add_to_progress_display(5)
+
+
+if __name__ == '__main__':
+    IMP.test.main()