Merge pull request #146 from griffithlab/kcotto-patch-1

Setup github action testing

Author: kcotto

.github/workflows/cmake.yml

@@ -0,0 +1,51 @@
+name: CMake
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: coverage
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally
+    # well on Windows or Mac.  You can convert this to a matrix build if you need
+    # cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+
+    - name: Build
+      # Build your program with the given configuration
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+    - name: Test
+      working-directory: ${{github.workspace}}/build
+      # Execute tests defined by the CMake configuration.  
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: ctest -V
+
+    - name: Install dependencies
+      shell: bash
+      run: sudo apt-get update ; sudo apt-get install lcov
+
+    - name: Coverage
+      run: cd build && lcov -c -d . -o cov.txt && lcov -e cov.txt "*/regtools/src/*" -o coverage.run.filtered.1 && lcov -r coverage.run.filtered.1 "*src/utils/*" "*/tests/*" -o coverage.run.filtered
+      
+    - name: Coveralls
+      uses: coverallsapp/github-action@master
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        path-to-lcov: build/coverage.run.filtered
+      

build-common/python/integrationtest.py

@@ -34,7 +34,7 @@ def inputFiles(self, *names):
         return rv
 
     def execute(self, args):
-        print "args ", args
+        print("args ", args)
         cmdline = "%s %s" %(self.exe_path, " ".join(args))
         vglog_file = self.tempFile("valgrind.log")
         return ValgrindWrapper(shlex.split(cmdline), vglog_file).run()
@@ -69,7 +69,7 @@ def assertMultiLineEqual(self, first, second, msg=None):
 
 def main():
     if len(sys.argv) < 2:
-        print "Error: required argument (path to test executable) missing"
+        print('Error: required argument (path to test executable) missing')
         sys.exit(1)
     IntegrationTest.exe_path = sys.argv.pop()
     unittest.main()

tests/integration-test/test_cis_splice_effects_identify.py

@@ -241,7 +241,7 @@ def test_anchor_stranded(self):
         output_annotatedjunctions = self.tempFile("observed-cse-identify.out")
         output_annotatedvariants = self.tempFile("observed-cse-identify-variants.out")
         output_junctions = self.tempFile("observed-cse-identify-junctions.out")
-        print "BAM1 is ", bam1
+        print("BAM1 is ", bam1)
         for anchor in ["", "30"]:
             if anchor != "":
                 anchor = "-a " + anchor
@@ -267,7 +267,7 @@ def test_anchor(self):
         output_annotatedjunctions = self.tempFile("observed-cse-identify.out")
         output_annotatedvariants = self.tempFile("observed-cse-identify-variants.out")
         output_junctions = self.tempFile("observed-cse-identify-junctions.out")
-        print "BAM1 is ", bam1
+        print("BAM1 is ", bam1)
         for anchor in ["", "30"]:
             if anchor != "":
                 anchor = "-a " + anchor

tests/integration-test/test_junctions_extract.py

@@ -33,7 +33,7 @@ class TestExtract(IntegrationTest, unittest.TestCase):
     def test_junctions_extract_anchor_stranded(self):
         bam1 = self.inputFiles("bam/test_hcc1395.bam")[0]
         output_file = self.tempFile("extract.out")
-        print "BAM1 is ", bam1
+        print("BAM1 is ", bam1)
         for anchor in ["", "30"]:
             expected_file = self.inputFiles("junctions-extract/expected-stranded-a" +
                                             anchor + ".out")[0]
@@ -47,7 +47,7 @@ def test_junctions_extract_anchor_stranded(self):
     def test_junctions_extract_anchor(self):
         bam1 = self.inputFiles("bam/test_hcc1395.bam")[0]
         output_file = self.tempFile("extract.out")
-        print "BAM1 is ", bam1
+        print("BAM1 is ", bam1)
         for anchor in ["", "30"]:
             expected_file = self.inputFiles("junctions-extract/expected-a" +
                                             anchor + ".out")[0]