Merge pull request #469 from kbase/develop

Release 0.2.5: SAM-119, SAM-209, SAM-236

Author: dakotablair

.github/workflows/non_sdk_test.yml

@@ -24,80 +24,20 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Set up test environment
-        if: "!contains(github.event.head_commit.message, 'skip ci')"
-        shell: bash
-        env:
-          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
-          MONGODB_VER: mongodb-linux-x86_64-3.6.16
-          ARANGODB_VER: 3.5.1
-          ARANGODB_V: 35
-          KAFKA_VER: 2.8.1
-          SCALA_VER: 2.12
-        run: |
-          # upgrade and update
-          apt update && apt upgrade
-          # Download necessary components for testing
-          # mongo is only a test dependency, no point in matrixing it
-          cd ..
-          wget http://fastdl.mongodb.org/linux/$MONGODB_VER.tgz
-          # file may be gzipped over transfer
-          gzip -d $MONGODB_VER.tgz
-          tar xf $MONGODB_VER.tar
-          export MONGOD=`pwd`/$MONGODB_VER/bin/mongod
-          cd -
-          echo "Done with Mongo"
-
-          # arango
-          cd ..
-          curl -O https://download.arangodb.com/arangodb$ARANGODB_V/Community/Linux/arangodb3-linux-$ARANGODB_VER.tar.gz
-          tar -xf arangodb3-linux-$ARANGODB_VER.tar.gz
-          export ARANGO_EXE=$(pwd)/arangodb3-$ARANGODB_VER/usr/sbin/arangod
-          export ARANGO_JS=$(pwd)/arangodb3-$ARANGODB_VER/usr/share/arangodb3/js/
-          cd -
-          echo "Done with Arango"
-
-          # kafka
-          cd ..
-          curl -O http://mirror.metrocast.net/apache/kafka/$KAFKA_VER/kafka_$SCALA_VER-$KAFKA_VER.tgz
-          tar -xzf kafka_$SCALA_VER-$KAFKA_VER.tgz
-          export KAFKA_BIN_DIR=$(pwd)/kafka_$SCALA_VER-$KAFKA_VER/bin
-          cd -
-          echo "Done with Kafka"
+      - name: Install pipenv
+        run: pip install -r requirements.txt
 
-          # jars
-          cd ..
-          git clone https://github.com/kbase/jars
-          export JARS=$(pwd)/jars/lib/jars
-          cd -
-          echo "Done with Jars"
-
-          # copy to test.cfg file
-          cd test
-          cp test.cfg.example test.cfg
-          sed -i "s#^test.jars.dir=.*#test.jars.dir=$JARS#" test.cfg
-          sed -i "s#^test.temp.dir=.*#test.temp.dir=temp_test_dir#" test.cfg
-          sed -i "s#^test.arango.exe.*#test.arango.exe=$ARANGO_EXE#" test.cfg
-          sed -i "s#^test.arango.js.*#test.arango.js=$ARANGO_JS#" test.cfg
-          sed -i "s#^test.mongo.exe.*#test.mongo.exe=$MONGOD#" test.cfg
-          sed -i "s#^test.kafka.bin.dir.*#test.kafka.bin.dir=$KAFKA_BIN_DIR#" test.cfg
-          sed -i "s#^test.mongo.wired_tiger.*#test.mongo.wired_tiger=true#" test.cfg
-          cat test.cfg
-          cd -
-
-      - name: Install Python dependencies
+      - name: Set up for tests
+        if: "!contains(github.event.head_commit.message, 'skip ci')"
         shell: bash
         run: |
-          pip install --upgrade pip
-          pip install -r requirements.txt
+          make test-setup
 
       - name: Run tests
         shell: bash
         run: |
-          echo "Create fake deployment config"
-          echo "[SampleService]" > service.cfg
-          echo "srv_wiz_url = https://ci.kbase.us/services/service_wizard" >> service.cfg
-          export KB_DEPLOYMENT_CONFIG=`pwd`/service.cfg
-          pipenv install --dev
-          pipenv run make test-sdkless
+          make test
 
+      - name: Coverage Summary
+        run: |
+          make coverage-summary

.gitignore

@@ -1,10 +1,31 @@
-.DS_Store
-.idea
-test/test.cfg
-test_local
+# Development
 __pycache__
 .vscode
 deploy.cfg
+lib/SampleService/SampleServiceImpl.py.bak*
+test/test.cfg.bak
+/_temp
+.mypy_cache
+.pytest_cache
+
+# Testing
+test/test.cfg
+test_local
 .coverage
 test/test_temp/
-lib/SampleService/SampleServiceImpl.py.bak*
+test/bin/jars
+test/bin/mongo
+test/bin/arangodb
+test/bin/kafka
+test/bin/temp
+htmlcov/
+cov_profile.lcov
+temp_test_dir
+mongo.log
+
+# IDE
+.vscode
+.idea
+
+# OS
+.DS_Store

Makefile

@@ -38,15 +38,14 @@ compile:
 		--out . \
 		--html \
 
-test:
-	echo Use test-sdkless
+test: test-sdkless coverage-reports
 
 test-sdkless:
-# TODO flake8 and bandit
-# TODO check tests run with kb-sdk test - will need to install mongo and update config
-	MYPYPATH=$(MAKEFILE_DIR)/$(LIB_DIR) mypy --namespace-packages $(LIB_DIR)/$(SERVICE_CAPS)/core $(TEST_DIR)
-	PYTHONPATH=$(PYPATH) SAMPLESERV_TEST_FILE=$(TSTFL) pytest --verbose --cov $(LIB_DIR)/$(SERVICE_CAPS) --cov-config=$(TEST_DIR)/coveragerc $(TEST_SPEC)
-# to print test output immediately: --capture=tee-sys
+	# TODO flake8 and bandit
+	# TODO check tests run with kb-sdk test - will need to install mongo and update config
+	MYPYPATH=$(MAKEFILE_DIR)/$(LIB_DIR) pipenv run mypy --namespace-packages $(LIB_DIR)/$(SERVICE_CAPS)/core $(TEST_DIR)
+	PYTHONPATH=$(PYPATH) SAMPLESERV_TEST_FILE=$(TSTFL) pipenv run pytest --verbose --cov $(LIB_DIR)/$(SERVICE_CAPS) --cov-config=$(TEST_DIR)/coveragerc $(TEST_SPEC)
+	# to print test output immediately: --capture=tee-sys
 
 clean:
 	rm -rfv $(LBIN_DIR)
@@ -58,3 +57,18 @@ host-start-dev-server:
 
 host-stop-dev-server:
 	source scripts/dev-server-env.sh && sh scripts/stop-dev-server.sh
+
+# Test support
+
+test-setup:
+	bash test/scripts/test-setup.sh
+
+coverage-reports:
+	@echo "Creating html coverage report"
+	pipenv run coverage html
+	@echo "Converting coverage to lcov"
+	pipenv run coverage lcov --data-file .coverage -o cov_profile.lcov
+
+coverage-summary:
+	@echo "Coverage summary:"
+	pipenv run coverage report

Pipfile

@@ -4,38 +4,37 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
-pytest = "*"
-pytest-cov = "*"
-mypy = "*"
-coveralls = "*"
-flake8 = "*"
-pymongo = "*"
-semver = "*"
-ipython = "*"
-black = "*"
+pytest = "==7.1.2"
+pytest-cov = "==3.0.0"
+mypy = "==0.942"
+coveralls = "==3.3.1"
+flake8 = "==4.0.1"
+semver = "==2.13.0"
+coverage = "==6.3.2"
+pymongo = "==4.1.1"
 
 [packages]
 python-arango = "==5.0.0"
 jsonrpcbase = "==0.2.0"
-apscheduler = "==3.6.3"
+apscheduler = "==3.9.1"
 maps = "==5.1.1"
-requests = "==2.22.0"
-cacheout = "==0.11.2"
-pyyaml = "==5.4"
+requests = "==2.27.1"
+cacheout = "==0.13.1"
+pyyaml = "==6.0"
 jsonschema = "==3.2.0"
-pint = "==0.10.1"
-python-ranges = "==0.1.3"
-pygtrie = "==2.3.2"
-jinja2 = "==2.11.3"
-gevent = "==20.5.0"
-gunicorn = "==20.0.4"
-kafka-python = "==2.0.1"
-greenlet = "==0.4.16"
-typing-extensions = "*"
-types-pyyaml = "*"
-types-requests = "*"
-pipenv = "*"
-shell = "*"
+# hold pint back to 0.17 - requires code changes at 0.18
+pint = "==0.17"
+python-ranges = "==0.2.0"
+pygtrie = "==2.4.2"
+jinja2 = "==3.1.1"
+gevent = "==21.12.0"
+gunicorn = "==20.1.0"
+kafka-python = "==2.0.2"
+greenlet = "==1.1.2"
+typing-extensions = "==4.2.0"
+types-pyyaml = "==6.0.7"
+types-requests = "==2.27.20"
+shell = "==1.0.1"
 
 [requires]
 python_version = "3.7"