Build with 6.3.3

.github/workflows/NewUpdate.yml

@@ -20,8 +20,8 @@ jobs:
     - name: Download latest generators
       run: |
         cd .updater/openapi_generator
-        wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.10.0/openapi-generator-cli-7.10.0.jar -O openapi-generator-cli.jar
-        java -jar openapi-generator-cli.jar version > version
+        wget -nv https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.10.0/openapi-generator-cli-7.10.0.jar -O openapi-generator-cli-7.10.jar
+        wget -nv https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.16.0/openapi-generator-cli-7.16.0.jar -O openapi-generator-cli-7.16.jar
     - name: Download latest Sirius Release
       uses: nick-fields/retry@v2
       with:
@@ -34,7 +34,7 @@ jobs:
             echo "Writing Version files: $packageVersion"
             echo $packageVersion > ./packageVersion.txt
             echo "Downloading Version: $packageVersion"
-            cat ./releases.json | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -i -
+            cat ./releases.json | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i -
             echo "Download Complete"
             unzip *.zip
             echo "Api Ready"
@@ -45,7 +45,7 @@ jobs:
       run: |
         while ! nc -z localhost 8080; do sleep 0.1; done
         cd .updater/api
-        wget http://localhost:8080/v3/api-docs -O api-docs-strings.json
+        wget -nv http://localhost:8080/v3/api-docs -O api-docs-strings.json
     - name: Shutdown SIRIUS
       run: curl -X POST http://localhost:8080/actuator/shutdown
     - name: Run Rest Api with enums
@@ -55,7 +55,7 @@ jobs:
       run: |
         while ! nc -z localhost 8080; do sleep 0.1; done
         cd .updater/api
-        wget http://localhost:8080/v3/api-docs -O api-docs-enums.json
+        wget -nv http://localhost:8080/v3/api-docs -O api-docs-enums.json
     - name: Shutdown SIRIUS
       run: curl -X POST http://localhost:8080/actuator/shutdown
     - name: Update Clients
@@ -67,7 +67,7 @@ jobs:
         rm -rf client-api_python/generated/docs
         rm -rf client-api_python/generated/PySirius
 
-        java -jar .updater/openapi_generator/openapi-generator-cli.jar generate -i .updater/api/api-docs-enums.json -c .updater/config/Python/config.json -g python -o client-api_python/generated -t client-api_python/templates/python --additional-properties=packageVersion=$packageVersion
+        java -jar .updater/openapi_generator/openapi-generator-cli-7.16.jar generate -i .updater/api/api-docs-enums.json -c .updater/config/Python/config.json -g python -o client-api_python/generated -t client-api_python/templates/python --additional-properties=packageVersion=$packageVersion
 
         echo "temporarily move R manual folder"
         mv client-api_r/generated/man/ client-api_r/
@@ -76,28 +76,28 @@ jobs:
         rm -rf client-api_r/generated/docs
         rm -rf client-api_r/generated/R
 
-        java -jar .updater/openapi_generator/openapi-generator-cli.jar generate -i .updater/api/api-docs-strings.json -c .updater/config/R/config.json -g r -o client-api_r/generated -t client-api_r/templates/r --additional-properties=packageVersion=$packageVersion
+        java -jar .updater/openapi_generator/openapi-generator-cli-7.10.jar generate -i .updater/api/api-docs-strings.json -c .updater/config/R/config.json -g r -o client-api_r/generated -t client-api_r/templates/r --additional-properties=packageVersion=$packageVersion
 
         echo "recover R manual folder"
         mv client-api_r/man/ client-api_r/generated/
 
-        # echo "generating Ruby Code"
-        # rm -rf client-api_ruby/generated/*
-        # java -jar .updater/openapi_generator/openapi-generator-cli.jar generate -i .updater/api/api-docs.json -c .updater/config/Ruby/config.json -g ruby -o client-api_ruby/generated
         echo "generating Finished!"
     - name: Format Python Package
       run: |
-         cp client-api_python/sirius_api.py client-api_python/generated/PySirius
-         cp client-api_python/sirius.py client-api_python/generated/PySirius
-
-         echo "from PySirius.sirius_api import PySiriusAPI" >> client-api_python/generated/PySirius/__init__.py
-         echo "from PySirius.sirius import SiriusSDK" >> client-api_python/generated/PySirius/__init__.py
+        cp client-api_python/pysirius_api.py client-api_python/generated/PySirius
+        cp client-api_python/pysirius_sdk.py client-api_python/generated/PySirius
+        cp client-api_python/pysirius_helper.py client-api_python/generated/PySirius
+
+        chmod +x ./client-api_python/formatting/format_init.sh
+        ./client-api_python/formatting/format_init.sh
     - name: Format R package
       run: |
-        cp client-api_r/SiriusSDK.R  client-api_r/generated/R/SiriusSDK.R
+        cp client-api_r/rsirius_sdk.R  client-api_r/generated/R/rsirius_sdk.R
+        cp client-api_r/rsirius_helper.R  client-api_r/generated/R/rsirius_helper.R
         echo >> client-api_r/generated/NAMESPACE
         echo "# SDK" >> client-api_r/generated/NAMESPACE
         echo "export(SiriusSDK)" >> client-api_r/generated/NAMESPACE
+        echo "export(Helper)" >> client-api_r/generated/NAMESPACE
 
         chmod +x ./client-api_r/patches/list_syntax_fix.sh
         ./client-api_r/patches/list_syntax_fix.sh
@@ -109,7 +109,7 @@ jobs:
         echo "Done"
     - name: Remove Openapi Generator Files
       run: |
-        rm .updater/openapi_generator/openapi-generator-cli.jar
+        rm .updater/openapi_generator/*.jar
         ls ./.github/workflows
         echo "Done"
     - name: update file and push to remote

.github/workflows/PythonTest.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     env:
       SIRIUS_USER: ${{ secrets.SIRIUS_USER }}
       SIRIUS_PW: ${{ secrets.SIRIUS_PW }}
@@ -42,10 +42,12 @@ jobs:
         path: .updater/api/sirius
         key: sirius
         fail-on-cache-miss: true
-    - name: Download tomato_small project space
-      run: wget ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O tomato_small.sirius
     - name: Change HOME to working directory of runner
       run: echo "HOME=/home/runner/work/sirius-client-openAPI" >> $GITHUB_ENV
+    - name: Download tomato_small project space
+      run: | 
+        wget -nv ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O $HOME/tomato_small.sirius
+        chmod 666 $HOME/tomato_small.sirius
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -74,10 +76,11 @@ jobs:
         import PySirius
         accept_terms = True
         account_credentials = PySirius.AccountCredentials(username=os.environ['SIRIUS_USER'], password=os.environ['SIRIUS_PW'])
-        sdk = SiriusSDK().attach_or_start_sirius()
-        api_instance = PySirius.LoginAndAccountApi(sdk.get_client())
+        api = PySirius.SiriusSDK().attach_to_sirius(sirius_port=8080)
+        api_instance = api.account()
         api_response = api_instance.login(accept_terms, account_credentials)
         if isinstance(api_response, PySirius.AccountInfo):
+          print('Login successful!')
           exit(0)
         else:
           print('Login failed, aborting...')
@@ -87,22 +90,10 @@ jobs:
       if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: python test_actuator_api.py
       working-directory: client-api_python/generated/test
-    - name: Test compounds API
-      if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: python test_compounds_api.py
-      working-directory: client-api_python/generated/test
-    - name: Test features API
-      if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: python test_features_api.py
-      working-directory: client-api_python/generated/test
     - name: Test info API
       if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: python test_info_api.py
       working-directory: client-api_python/generated/test
-    - name: Test jobs API
-      if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: python test_jobs_api.py
-      working-directory: client-api_python/generated/test
     - name: Test login_and_account API
       if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: python test_login_and_account_api.py
@@ -111,7 +102,23 @@ jobs:
       if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: python test_projects_api.py
       working-directory: client-api_python/generated/test
+    - name: Test compounds API
+      if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
+      run: python test_compounds_api.py
+      working-directory: client-api_python/generated/test
     - name: Test searchable_databases API
       if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
       run: python test_searchable_databases_api.py
+      working-directory: client-api_python/generated/test
+    - name: Test features API
+      if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
+      run: python test_features_api.py
+      working-directory: client-api_python/generated/test
+    - name: Test jobs API
+      if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
+      run: python test_jobs_api.py
+      working-directory: client-api_python/generated/test
+    - name: Test acceptance
+      if: always() && steps.api_start.outcome == 'success' && steps.pysirius_install.outcome == 'success' && steps.login.outcome == 'success'
+      run: python test_acceptance.py
       working-directory: client-api_python/generated/test

.github/workflows/RManualGeneration.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        r-version: ["4.4.0"]
+        r-version: ["4.5"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up R ${{ matrix.r-version }}