Merge pull request #751 from kbase/dev-update_ci_test

Update test.yml and fix failed tests

Author: Xiangs18

.github/workflows/test.yml

@@ -19,12 +19,12 @@ on:
 jobs:
 
   workspace_container_tests:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python 3.10
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
@@ -40,7 +40,7 @@ jobs:
           sh test/run_tests.sh
 
   workspace_deluxe_tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     strategy:
       fail-fast: false
       matrix:
@@ -57,18 +57,18 @@ jobs:
             wired_tiger: 'false'
             gradle_test: 'testQuick'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: ${{matrix.java}}
 
-      - name: Set up Python 3.7  # sample service is on 3.7, handle service is on sdkbase2.latest
-        uses: actions/setup-python@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.7"
+          python-version: "3.9.19"
 
       - name: Install dependencies and set up test config
         shell: bash
@@ -92,23 +92,19 @@ jobs:
           export ARANGO_EXE=$(pwd)/arangodb3-linux-$ARANGODB_VER/bin/arangod
           export ARANGO_JS=$(pwd)/arangodb3-linux-$ARANGODB_VER/usr/share/arangodb3/js/
 
-           # set up handle service
-          export HS_COMMIT=08e18379817e16db920501b66ba62b66598f506c
-          export LOG_COMMIT=b549c557e3c519e0a55eadf7863a93db25cd6806
+          # set up handle service
+          # HS_COMMIT corresponds to Handle Service2 tag v1.0.7
+          export HS_COMMIT=335020d26f3663da456be5afee3cb4b8ed8622f4
           git clone https://github.com/kbase/handle_service2.git
           cd handle_service2/
           git checkout $HS_COMMIT
-          sudo chmod -R 777 .
           cd lib/
-          mkdir biokbase
-          cd biokbase/
-          wget https://raw.githubusercontent.com/kbase/sdkbase2/$LOG_COMMIT/log.py
-          cd ..
           export HSDIR=`pwd`
           cd ../..
 
           # set up sample service
-          export SAMPLE_COMMIT=6813fb148e95db2b11db6eea04f4d1d45cbb7119
+          # SAMPLE_COMMIT corresponds to Sample Service tag v0.2.1
+          export SAMPLE_COMMIT=aa0303c4d5d4aa1e3cf0c9ecb36366fb1127f93e
           git clone https://github.com/kbase/sample_service.git
           cd sample_service
           git checkout $SAMPLE_COMMIT
@@ -151,7 +147,7 @@ jobs:
           ./gradlew ${{matrix.gradle_test}}
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

python_dependencies/Pipfile

@@ -11,27 +11,35 @@ jsonrpcbase = "==0.2.0"
 requests = "==2.22.0"
 
 # handle service dependencies
-cachetools = "*"
-configparser = "*"
-pymongo = "==3.11.0"
-uwsgi = "==2.0.18"
+cachetools = "==4.2.2"
+pymongo = "==4.7.2"
+uwsgi = "==2.0.22"
 
 # sample service dependencies
 python-arango = "==5.0.0"
-apscheduler = "==3.6.3"
+# Upgraded to fix timezone TypeError; supports zoneinfo in Python 3.9+
+apscheduler = "==3.9.1"
 maps = "==5.1.1"
 cacheout = "==0.11.2"
+# Downgraded from 5.4 to resolve Pipfile.lock generation issues
 pyyaml = "==5.3"
 jsonschema = "==3.2.0"
-pint = "==0.10.1"
+# Fixed import error with pkg_resources.extern on Python 3.9
+pint = "==0.17"
 python-ranges = "==0.1.3"
 pygtrie = "==2.3.2"
-jinja2 = "==2.11.2"
-gevent = "==20.5.0"
+jinja2 = "==2.11.3"
+# Updated to support Python 3.9.19
+gevent = "==24.11.1"
 gunicorn = "==20.0.4"
 kafka-python = "==2.0.1"
-greenlet = "==0.4.16"
+# Compatible with gevent and Python 3.9
+greenlet = "==3.1.1"
 typing-extensions = "*"
+types-pyyaml = "*"
+types-requests = "*"
+pipenv = "*"
+shell = "*"
 
 [requires]
-python_version = "3.7"
+python_version = "3.9.19"