re-enable original tests & steps

Author: hcannoodt

.github/workflows/sbt_test.yml

@@ -84,31 +84,30 @@ jobs:
       with:
         python-version: '3.x'
 
-    # - name: Set up Nextflow
-    #   if: ${{ runner.os == 'Linux' && matrix.java.run_nextflow }}
-    #   uses: nf-core/setup-nextflow@v2
-    #   with:
-    #     version: ${{ matrix.java.nxf_ver }}
+    - name: Set up Nextflow
+      if: ${{ runner.os == 'Linux' && matrix.java.run_nextflow }}
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: ${{ matrix.java.nxf_ver }}
 
     - name: Run tests
       env:
         NXF_SYNTAX_PARSER: v1
       run: |
-        # if [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_coverage }}" == "true" ]]; then
-        #   # only run coverage on main runner
-        #   sbt clean coverage test coverageReport
-        # elif [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_nextflow }}" == "false" ]]; then
-        #   sbt 'testOnly -- -l io.viash.NextflowTest'
-        # elif [[ "${{ matrix.config.os }}" =~ ^macos.*$ ]]; then
-        #   # macOS on github actions does not have Docker, so skip those
-        #   sbt 'testOnly -- -l io.viash.DockerTest -l io.viash.NextflowTest'
-        # else
-        #   sbt test
-        # fi
-        sbt "testOnly *JsonParserTest"
-
-    # - name: Upload coverage on success
-    #   run: bash <(curl -s https://codecov.io/bash)
+        if [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_coverage }}" == "true" ]]; then
+          # only run coverage on main runner
+          sbt clean coverage test coverageReport
+        elif [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_nextflow }}" == "false" ]]; then
+          sbt 'testOnly -- -l io.viash.NextflowTest'
+        elif [[ "${{ matrix.config.os }}" =~ ^macos.*$ ]]; then
+          # macOS on github actions does not have Docker, so skip those
+          sbt 'testOnly -- -l io.viash.DockerTest -l io.viash.NextflowTest'
+        else
+          sbt test
+        fi
+
+    - name: Upload coverage on success
+      run: bash <(curl -s https://codecov.io/bash)
 
     - name: Upload check results on fail
       if: failure()