Merge pull request #310 from EpistasisLab/coveralls

Fix coveralls in GitHub Action

.coveragerc

@@ -1,5 +1,6 @@
 [run]
-; source = 
+relative_files = True
+; source =
 ; 	ai
 ; 	machine
 ; 	lab/pyutils
@@ -12,5 +13,5 @@ parallel = True
 ; the first path is the path on the local (travis) filesystem
 ; the second path is the path as it appears within the Docker container
 source =
-  $TRAVIS_BUILD_DIR
+  $GITHUB_WORKSPACE
   /appsrc/

.github/workflows/pennai_tests.yml

@@ -54,8 +54,6 @@ jobs:
 
       # Runs a set of commands using the runners shell
       - name: Run Unit Tests
-        env:
-          COVERALLS_REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           git lfs fetch --all
           docker run -v $(pwd):/appsrc -w /appsrc pennai_unit_tester mocha machine/test/test.js
@@ -68,6 +66,12 @@ jobs:
               ai/tests/lab_*.py \
               ai/tests/test_re*.py \
               ai/tests/test_k*utils.py
+          coverage combine
+      - name: Coveralls
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          parallel: true
+          flag-name: Unit Test for webapp
 
   build_pypkg:
     name: Unit Tests for scikit-learn API
@@ -80,18 +84,45 @@ jobs:
       - uses: actions/setup-python@v2
         with:
           python-version: '3.7'
-
       - name: Build Docker Images
         run: |
+          pip install coveralls
           docker-compose -f ./docker-compose-unit-test.yml build -m 8g
-
       # Runs a set of commands using the runners shell
       - name: Run Unit Tests
         run: |
           git lfs fetch --all
           git lfs pull
-          docker run -v $(pwd):/appsrc -w /appsrc pennai_unit_tester nosetests -s -v ai/tests/test_sklearn_api.py
-      # Run deployment steps if pervious steps are success
+          docker run -v $(pwd):/appsrc -w /appsrc pennai_unit_tester coverage run -m nose -s -v ai/tests/test_sklearn_api.py
+          coverage combine
+      - name: Coveralls
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          parallel: true
+          flag-name: Unit Test for scikit-learn api
+
+  coveralls_finish:
+    name: Coveralls Done
+    needs: [build_web_app, build_pypkg]
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel-finished: true
+
+  deploy_pypkg:
+    name: Deploy python package
+    needs: build_pypkg
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
       - name: Install dependencies
         if: ${{ github.event_name == 'release' && github.event.action == 'published' }}
         run: |
@@ -108,7 +139,7 @@ jobs:
 
   build_docs:
     name: Doc Builder
-    needs: [build_int_test, build_web_app] 
+    needs: [build_int_test, build_web_app, build_pypkg]
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
     # Steps represent a sequence of tasks that will be executed as part of the job

.travis.yml

@@ -37,9 +37,9 @@ jobs:
             ai/tests/lab_*.py
             ai/tests/test_re*.py
             ai/tests/test_k*utils.py"
-        - coverage combine
+        #- coverage combine
         #- docker cp pennai_unit_tester:/.coverage ./
-        - coveralls
+        #- coveralls
     - stage: Test
       name: "Unit Tests for scikit-learn API"
       install:

docker/lab/files/requirements.txt

@@ -2,6 +2,7 @@ scikit-learn==0.22.1
 tqdm==4.32.2
 pymongo==3.8.0
 pandas==1.0.3
+numpy==1.19.5
 cython==0.29.2
 xgboost==0.82
 simplejson==3.16.0

docker/machine/files/requirements.txt

@@ -2,6 +2,7 @@ scikit-learn==0.22.1
 tqdm==4.32.2
 pymongo==3.8.0
 pandas==1.0.3
+numpy==1.19.5
 matplotlib==3.1.0
 mlxtend==0.16.0
 pydot==1.4.1