fixes #2659 once fully implemented (#2570)

* fixes #2659 once fully implemented

* in theory everything should work, but unable to test locally

* added caching and a longer sleep cycle

* building on push only

* exposing cache and putting in another sleep after launching apollo

* fixed bad directory defintion

* installing arrow correctly hopefully

* fixed linting error

* fixed bad call

* setting arrow commands

* getting a timer

* need to copy in newer apollo-config.groovy

* pushing final version

.github/workflows/python-apollo.yml

@@ -0,0 +1,88 @@
+name: Python-Apollo
+
+on: ["push", "pull_request"]
+
+jobs:
+  test-python-apollo:
+    name: test-python-apollo
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8.7]
+    steps:
+      - name: Checkout Apollo
+        uses: actions/checkout@v2
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v1
+        with:
+          java-version: 1.8
+      - name: Run Apollo
+        run: |
+          cp test/config/python-apollo.travis apollo-config.groovy
+          date
+          ./grailsw run-app &
+          echo "Sleeping here while Apollo builds"
+          sleep 240
+          echo "Done sleeping, I hope it is working"
+          curl -i 'http://localhost:8080/apollo/annotator/system'
+      - name: Setup python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Checkout Pypi
+        uses: actions/checkout@v2
+        with:
+          repository: galaxy-genome-annotation/python-apollo
+          path: python-apollo
+          ref: master
+      - name: Python install
+        run: |
+          pwd
+          cd python-apollo
+          pip install -U pip setuptools nose apollo
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Bootstrap
+        run: |
+          pwd
+          echo "Testing if awake"
+          curl -i 'http://localhost:8080/apollo/annotator/system'
+          cd python-apollo
+          pwd
+          export ARROW_GLOBAL_CONFIG_PATH=`pwd`/test-data/local-apollo2-arrow.yml
+          echo "Testing arrow command"
+          arrow users get_users
+          echo $ARROW_GLOBAL_CONFIG_PATH
+          ls $ARROW_GLOBAL_CONFIG_PATH
+          cat $ARROW_GLOBAL_CONFIG_PATH
+          ./bootstrap_apollo.sh --nodocker
+      - name: Run tests
+        run: |
+          pwd
+          cd python-apollo
+          pwd
+          export ARROW_GLOBAL_CONFIG_PATH=`pwd`/test-data/local-apollo2-arrow.yml
+          python setup.py nosetests
+
+      - uses: actions/cache@v2
+        with:
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
+          restore-keys: |
+            ${{ runner.os }}-gradle-
+      - name: Cache local Maven repository
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+
+

.github/workflows/gradle.yml → .github/workflows/test.yml

@@ -3,14 +3,10 @@
 
 name: Java CI with Gradle
 
-on:
-  push:
-    branches: [ develop , master ]
-  pull_request:
-    branches: [ develop ]
+on: ["push", "pull_request"]
 
 jobs:
-  build:
+  test-grails:
 
     runs-on: ubuntu-latest
 
@@ -22,5 +18,6 @@ jobs:
         java-version: 1.8
     - name: Grant execute permission for gradlew
       run: chmod +x gradlew
-    - name: Build with Gradle
-      run: ./gradlew installJBrowseWebOnly gwtc installJBrowseTools && ./grailsw refresh-dependencies --stacktrace && ./grailsw test-app --stacktrace 
+    - name: Build and test with Gradle
+      run: ./gradlew installJBrowseWebOnly gwtc installJBrowseTools && ./grailsw refresh-dependencies --stacktrace && ./grailsw test-app --stacktrace
+