From 3f6b21b575c94399cdd44ee990b036ca83e1e94d Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 22:16:45 +0100
Subject: [PATCH 01/14] try workflow structure that defaults to latest release
 but takes manual input

---
 .github/workflows/NewUpdate.yml  | 322 +++++++++++++++++--------------
 .github/workflows/PythonTest.yml | 230 ++++++++++++----------
 .github/workflows/RTest.yml      | 291 +++++++++++++++-------------
 .github/workflows/RunTests.yml   |  21 +-
 4 files changed, 480 insertions(+), 384 deletions(-)

diff --git a/.github/workflows/NewUpdate.yml b/.github/workflows/NewUpdate.yml
index 2a082fc8..a3502ff6 100644
--- a/.github/workflows/NewUpdate.yml
+++ b/.github/workflows/NewUpdate.yml
@@ -6,163 +6,187 @@ on:
       target_branch:
         type: string
         required: true
-  
+      sirius_version:
+        description: "Optional SIRIUS version to download (e.g. 6.3.3). Leave blank for latest."
+        type: string
+        required: false
+
 jobs:
   UpdateClients:
-    # The type of runner that the job will run on
     runs-on: ubuntu-latest
     timeout-minutes: 90
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-    # Runs using the runners shell
-    - name: checkout repo
-      uses: actions/checkout@v3.1.0
-    - name: Download latest generators
-      run: |
-        cd .updater/openapi_generator
-        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:
-        max_attempts: 5
-        timeout_minutes: 5
-        command: |
+      - name: checkout repo
+        uses: actions/checkout@v3.1.0
+      - name: Download latest generators
+        run: |
+          cd .updater/openapi_generator
+          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 SIRIUS Release
+        uses: nick-fields/retry@v2
+        with:
+          max_attempts: 5
+          timeout_minutes: 5
+          command: |
             cd .updater/api
-            curl -s https://api.github.com/repositories/94561614/releases > ./releases.json
-            packageVersion=$(cat ./releases.json  | grep 'name.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d - -f 2)
-            echo "Writing Version files: $packageVersion"
-            echo $packageVersion > ./packageVersion.txt
-            echo "Downloading Version: $packageVersion"
-            cat ./releases.json | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i -
-            echo "Download Complete"
-            unzip *.zip
-            echo "Api Ready"
-    - name: Run Rest Api with strings
-      run: |
-        bash .updater/api/sirius/bin/sirius REST --headless --api-mode=STABLE -p 8080 -s &
-    - name: Update api-docs-strings.json
-      run: |
-        while ! nc -z localhost 8080; do sleep 0.1; done
-        cd .updater/api
-        wget -nv http://localhost:8080/v3/api-docs -O api-docs-strings.json
-    - name: Shutdown SIRIUS
-      run: curl -X POST http://localhost:8080/actuator/shutdown
-    - name: Run Rest Api with enums
-      run: |
-        bash .updater/api/sirius/bin/sirius REST --headless --api-mode=STABLE --enums-as-ref -p 8080 -s &
-    - name: Update api-docs-enums.json
-      run: |
-        while ! nc -z localhost 8080; do sleep 0.1; done
-        cd .updater/api
-        wget -nv http://localhost:8080/v3/api-docs -O api-docs-enums.json
-    - name: Shutdown SIRIUS
-      run: curl -X POST http://localhost:8080/actuator/shutdown
-    - name: Update Clients
-      run: |
-        # load package version from file
-        packageVersion=$(cat .updater/api/packageVersion.txt)
-        
-        echo "generating Python Code with packageVersion=$packageVersion"
-        rm -rf client-api_python/generated/docs
-        rm -rf client-api_python/generated/PySirius
-       
-        java -jar .updater/openapi_generator/openapi-generator-cli-7.16.jar generate -i .updater/api/api-docs-enums.json -c .updater/config/Python/config.json -g python -o client-api_python/generated -t client-api_python/templates/python --additional-properties=packageVersion=$packageVersion
-        
-        echo "temporarily move R manual folder"
-        mv client-api_r/generated/man/ client-api_r/
-        
-        echo "generating R Code with packageVersion=$packageVersion"
-        rm -rf client-api_r/generated/docs
-        rm -rf client-api_r/generated/R
-
-        java -jar .updater/openapi_generator/openapi-generator-cli-7.10.jar generate -i .updater/api/api-docs-strings.json -c .updater/config/R/config.json -g r -o client-api_r/generated -t client-api_r/templates/r --additional-properties=packageVersion=$packageVersion
-        
-        echo "recover R manual folder"
-        mv client-api_r/man/ client-api_r/generated/
-        
-        echo "generating Finished!"
-    - name: Format Python Package
-      run: |
-        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/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
-        
-        chmod +x ./client-api_r/patches/insert_wait_for_job_completion_in_rsirius_api.sh
-        ./client-api_r/patches/insert_wait_for_job_completion_in_rsirius_api.sh
-    - name: Remove Sirius Rest Api
-      run: |
-        cd .updater/api
-        rm -rf *sirius*
-        rm -rf releases.json
-        echo "Done"
-    - name: Remove Openapi Generator Files
-      run: |
-        rm .updater/openapi_generator/*.jar
-        ls ./.github/workflows
-        echo "Done"
-    - name: update file and push to remote
-      uses: stefanzweifel/git-auto-commit-action@v4.15.2
-      with:
-        commit_message: Auto-Updated OpenAPI Clients
-    - name: Run RManualGeneration
-      run: |
-        gh workflow run RManualGeneration.yml --ref ${GITHUB_REF##*/}
-        echo "dispatched workflow"
-        echo "sleeping for 30s to make sure it started"
-        sleep 30
-        list=$(gh run list --workflow RManualGeneration --branch ${GITHUB_REF##*/})
-        id=$(echo $list | grep -oP 'in_progress RManualGeneration RManualGeneration [^ ]* workflow_dispatch \K\d+')
-        echo "run ID of RManualGeneration is: $id"
-        gh run watch $id --exit-status --interval 3
-        echo "generation done!"
-      env:
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-    - name: update file and create pull request
-      id: open-pr
-      uses: repo-sync/pull-request@v2
-      with:
+            
+            if [ -n "${{ github.event.inputs.sirius_version }}" ]; then
+              # Manual version provided
+              version="${{ github.event.inputs.sirius_version }}"
+              echo "Using manually provided SIRIUS version: $version"
+              echo "$version" > ./packageVersion.txt
+            
+              url="https://github.com/sirius-ms/sirius/releases/download/v${version}/sirius-${version}-linux-x64.zip"
+              echo "Downloading from: $url"
+              wget -nv "$url" -O sirius-${version}-linux-x64.zip
+            else
+              # Fallback to automatic latest detection
+              echo "No version provided — fetching latest release..."
+              curl -s https://api.github.com/repos/sirius-ms/sirius/releases/latest > ./release.json
+              version=$(jq -r '.tag_name' ./release.json | sed 's/^v//')
+              echo "Latest version: $version"
+              echo "$version" > ./packageVersion.txt
+            
+              url=$(jq -r '.assets[] | select(.name | test("linux-x64.zip$")) | .browser_download_url' ./release.json)
+              echo "Downloading from: $url"
+              wget -nv "$url" -O sirius-${version}-linux-x64.zip
+            fi
+            
+            echo "Unzipping..."
+            unzip -q sirius-*-linux-x64.zip
+            echo "API Ready"
+      - name: Run Rest Api with strings
+        run: |
+          bash .updater/api/sirius/bin/sirius REST --headless --api-mode=STABLE -p 8080 -s &
+      - name: Update api-docs-strings.json
+        run: |
+          while ! nc -z localhost 8080; do sleep 0.1; done
+          cd .updater/api
+          wget -nv http://localhost:8080/v3/api-docs -O api-docs-strings.json
+      - name: Shutdown SIRIUS
+        run: curl -X POST http://localhost:8080/actuator/shutdown
+      - name: Run Rest Api with enums
+        run: |
+          bash .updater/api/sirius/bin/sirius REST --headless --api-mode=STABLE --enums-as-ref -p 8080 -s &
+      - name: Update api-docs-enums.json
+        run: |
+          while ! nc -z localhost 8080; do sleep 0.1; done
+          cd .updater/api
+          wget -nv http://localhost:8080/v3/api-docs -O api-docs-enums.json
+      - name: Shutdown SIRIUS
+        run: curl -X POST http://localhost:8080/actuator/shutdown
+      - name: Update Clients
+        run: |
+          # load package version from file
+          packageVersion=$(cat .updater/api/packageVersion.txt)
+          
+          echo "generating Python Code with packageVersion=$packageVersion"
+          rm -rf client-api_python/generated/docs
+          rm -rf client-api_python/generated/PySirius
+          
+          java -jar .updater/openapi_generator/openapi-generator-cli-7.16.jar generate -i .updater/api/api-docs-enums.json -c .updater/config/Python/config.json -g python -o client-api_python/generated -t client-api_python/templates/python --additional-properties=packageVersion=$packageVersion
+          
+          echo "temporarily move R manual folder"
+          mv client-api_r/generated/man/ client-api_r/
+          
+          echo "generating R Code with packageVersion=$packageVersion"
+          rm -rf client-api_r/generated/docs
+          rm -rf client-api_r/generated/R
+          
+          java -jar .updater/openapi_generator/openapi-generator-cli-7.10.jar generate -i .updater/api/api-docs-strings.json -c .updater/config/R/config.json -g r -o client-api_r/generated -t client-api_r/templates/r --additional-properties=packageVersion=$packageVersion
+          
+          echo "recover R manual folder"
+          mv client-api_r/man/ client-api_r/generated/
+          
+          echo "generating Finished!"
+      - name: Format Python Package
+        run: |
+          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/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
+          
+          chmod +x ./client-api_r/patches/insert_wait_for_job_completion_in_rsirius_api.sh
+          ./client-api_r/patches/insert_wait_for_job_completion_in_rsirius_api.sh
+      - name: Remove Sirius Rest Api
+        run: |
+          cd .updater/api
+          rm -rf *sirius*
+          rm -rf releases.json
+          echo "Done"
+      - name: Remove Openapi Generator Files
+        run: |
+          rm .updater/openapi_generator/*.jar
+          ls ./.github/workflows
+          echo "Done"
+      - name: update file and push to remote
+        uses: stefanzweifel/git-auto-commit-action@v4.15.2
+        with:
+          commit_message: Auto-Updated OpenAPI Clients
+      - name: Run RManualGeneration
+        run: |
+          gh workflow run RManualGeneration.yml --ref ${GITHUB_REF##*/}
+          echo "dispatched workflow"
+          echo "sleeping for 30s to make sure it started"
+          sleep 30
+          list=$(gh run list --workflow RManualGeneration --branch ${GITHUB_REF##*/})
+          id=$(echo $list | grep -oP 'in_progress RManualGeneration RManualGeneration [^ ]* workflow_dispatch \K\d+')
+          echo "run ID of RManualGeneration is: $id"
+          gh run watch $id --exit-status --interval 3
+          echo "generation done!"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: update file and create pull request
+        id: open-pr
+        uses: repo-sync/pull-request@v2
+        with:
           destination_branch: ${{ inputs.target_branch }}
           github_token: ${{ secrets.GITHUB_TOKEN }}
           pr_label: "Feature"
           pr_title: "AutoUpdated"
           pr_allow_empty: true
-    - name: check if request has been created
-      run: echo ${{steps.open-pr.outputs.pr_created}}
-    - name: lock pull request
-      continue-on-error: true
-      id: lockpull
-      uses: sudo-bot/action-pull-request-lock@v1.1.0
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        number: ${{steps.open-pr.outputs.pr_number}}
-        lock-reason: resolved
-    - name: Run tests if no changes occure
-      env:
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-#      if: steps.lockpull.outcome == 'failure'
-      run: |
-        gh workflow run RunTests.yml --ref ${GITHUB_REF##*/}
-        echo "sleeping for 30min before temp branch removal"
-        sleep 1800
-    - name: Delete temp branches if no changes occure
-      if: steps.lockpull.outcome == 'failure'
-      uses: dawidd6/action-delete-branch@v3
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        prefix: temp_
-        soft_fail: true
+      - name: check if request has been created
+        run: echo ${{steps.open-pr.outputs.pr_created}}
+      - name: lock pull request
+        continue-on-error: true
+        id: lockpull
+        uses: sudo-bot/action-pull-request-lock@v1.1.0
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{steps.open-pr.outputs.pr_number}}
+          lock-reason: resolved
+      - name: Run tests if no changes occure
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          version=$(cat .updater/api/packageVersion.txt)
+          echo "Running RunTests workflow with SIRIUS version: $version"
+          gh workflow run RunTests.yml --ref ${GITHUB_REF##*/} -f sirius_version="$version"
+          echo "sleeping for 30min before temp branch removal"
+          sleep 1800
+        #      if: steps.lockpull.outcome == 'failure'
+        run: |
+          gh workflow run RunTests.yml --ref ${GITHUB_REF##*/}
+          echo "sleeping for 30min before temp branch removal"
+          sleep 1800
+      - name: Delete temp branches if no changes occure
+        if: steps.lockpull.outcome == 'failure'
+        uses: dawidd6/action-delete-branch@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          prefix: temp_
+          soft_fail: true
diff --git a/.github/workflows/PythonTest.yml b/.github/workflows/PythonTest.yml
index d37b5e2d..185eb03a 100644
--- a/.github/workflows/PythonTest.yml
+++ b/.github/workflows/PythonTest.yml
@@ -4,11 +4,20 @@
 name: PythonTest
 
 
-on: 
+on:
   workflow_dispatch:
+    inputs:
+      sirius_version:
+        description: "SIRIUS version to use for testing"
+        required: false
+        type: string
   workflow_call:
+    inputs:
+      sirius_version:
+        required: false
+        type: string
   pull_request:
-    
+
 
 
 jobs:
@@ -18,107 +27,124 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
     env:
       SIRIUS_USER: ${{ secrets.SIRIUS_USER }}
       SIRIUS_PW: ${{ secrets.SIRIUS_PW }}
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      id: pysirius_install
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8
-        pip install ./client-api_python/generated
-        echo "Finished Installing"
-    - name: Cache Sirius Release
-      id: cache-sirius
-      uses: actions/cache@v3
-      with:
-        path: .updater/api/sirius
-        key: sirius
-        fail-on-cache-miss: true
-    - 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
-        flake8 ./client-api_python --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 ./client-api_python --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Unset DISPLAY
-      run: echo "JAVA_TOOL_OPTIONS=-Djava.awt.headless=true" >> $GITHUB_ENV
-    - name: Check SIRIUS download
-      run: |
-        echo "Show content of cache download (.updater/api/)"
-        ls -lah .updater/api/
-        echo "Show content of cache download (.updater/api/sirius)"
-        ls -lah .updater/api/sirius
-        echo "Show content of cache download (.updater/api/sirius/bin)"
-        ls -lah .updater/api/sirius/bin
-    - name: Run Rest Api
-      run: bash .updater/api/sirius/bin/sirius REST -p 8080 -s &
-    - name: Wait for Api to start
-      id: api_start
-      run: while ! nc -z localhost 8080; do sleep 0.1; done
-    - name: Login to SIRIUS
-      id: login
-      run: |
-        import os
-        import PySirius
-        accept_terms = True
-        account_credentials = PySirius.AccountCredentials(username=os.environ['SIRIUS_USER'], password=os.environ['SIRIUS_PW'])
-        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...')
-          exit(1)
-      shell: python
-    - name: Test actuator API
-      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 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 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
-      working-directory: client-api_python/generated/test
-    - name: Test projects API
-      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
\ No newline at end of file
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        id: pysirius_install
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8
+          pip install ./client-api_python/generated
+          echo "Finished Installing"
+      - name: Determine SIRIUS version
+        id: sirius_version
+        run: |
+          if [ -n "${{ inputs.sirius_version }}" ]; then
+            echo "Using version from workflow input: ${{ inputs.sirius_version }}"
+            echo "version=${{ inputs.sirius_version }}" >> $GITHUB_OUTPUT
+          elif [ -f ".updater/api/packageVersion.txt" ]; then
+            version=$(cat .updater/api/packageVersion.txt)
+            echo "Using version from packageVersion.txt: $version"
+            echo "version=$version" >> $GITHUB_OUTPUT
+          else
+            echo "No version found — defaulting to latest."
+            version=$(curl -s https://api.github.com/repos/sirius-ms/sirius/releases/latest | jq -r '.tag_name' | sed 's/^v//')
+            echo "version=$version" >> $GITHUB_OUTPUT
+          fi
+      - name: Download SIRIUS
+        run: |
+          version="${{ steps.sirius_version.outputs.version }}"
+          mkdir -p .updater/api
+          cd .updater/api
+          url="https://github.com/sirius-ms/sirius/releases/download/v${version}/sirius-${version}-linux-x64.zip"
+          echo "Downloading $url"
+          wget -nv "$url" -O sirius-${version}-linux-x64.zip
+          unzip -q sirius-${version}-linux-x64.zip
+      - 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
+          flake8 ./client-api_python --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 ./client-api_python --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Unset DISPLAY
+        run: echo "JAVA_TOOL_OPTIONS=-Djava.awt.headless=true" >> $GITHUB_ENV
+      - name: Check SIRIUS download
+        run: |
+          echo "Show content of cache download (.updater/api/)"
+          ls -lah .updater/api/
+          echo "Show content of cache download (.updater/api/sirius)"
+          ls -lah .updater/api/sirius
+          echo "Show content of cache download (.updater/api/sirius/bin)"
+          ls -lah .updater/api/sirius/bin
+      - name: Run Rest Api
+        run: bash .updater/api/sirius/bin/sirius REST -p 8080 -s &
+      - name: Wait for Api to start
+        id: api_start
+        run: while ! nc -z localhost 8080; do sleep 0.1; done
+      - name: Login to SIRIUS
+        id: login
+        run: |
+          import os
+          import PySirius
+          accept_terms = True
+          account_credentials = PySirius.AccountCredentials(username=os.environ['SIRIUS_USER'], password=os.environ['SIRIUS_PW'])
+          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...')
+            exit(1)
+        shell: python
+      - name: Test actuator API
+        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 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 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
+        working-directory: client-api_python/generated/test
+      - name: Test projects API
+        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
\ No newline at end of file
diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml
index 4383b2ff..2f5c0d1e 100644
--- a/.github/workflows/RTest.yml
+++ b/.github/workflows/RTest.yml
@@ -4,7 +4,20 @@
 name: RTest
 
 
-on: [workflow_dispatch, workflow_call, pull_request]
+on:
+  workflow_dispatch:
+    inputs:
+      sirius_version:
+        description: "SIRIUS version to use for testing"
+        required: false
+        type: string
+  workflow_call:
+    inputs:
+      sirius_version:
+        required: false
+        type: string
+  pull_request:
+
 
 
 jobs:
@@ -14,136 +27,154 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        r-version: ["4.1", "4.2", "4.3", "4.4", "4.5"]
+        r-version: [ "4.1", "4.2", "4.3", "4.4", "4.5" ]
     env:
       SIRIUS_USER: ${{ secrets.SIRIUS_USER }}
       SIRIUS_PW: ${{ secrets.SIRIUS_PW }}
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up R ${{ matrix.r-version }}
-      uses: r-lib/actions/setup-r@v2
-      with:
-        r-version: ${{ matrix.r-version }}
-    - name: Install RSirius dependencies
-      uses: r-lib/actions/setup-r-dependencies@v2
-      with:
-        cache: false
-        working-directory: ./client-api_r/generated
-    - name: Install RSirius
-      id: rsirius_install
-      run: |
-        install.packages("/home/runner/work/sirius-client-openAPI/sirius-client-openAPI/client-api_r/generated", repos = NULL, type = "source")
-      shell: Rscript {0}
-    - name: Cache Sirius Release
-      uses: actions/cache@v3
-      with:
-        path: .updater/api/sirius
-        key: sirius
-        fail-on-cache-miss: true
-    - 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 $HOME/tomato_small.sirius
-    - name: Check SIRIUS download
-      run: |
-        echo "Show content of cache download (.updater/api/)"
-        ls -lah .updater/api/
-        echo "Show content of cache download (.updater/api/sirius)"
-        ls -lah .updater/api/sirius
-        echo "Show content of cache download (.updater/api/sirius/bin)"
-        ls -lah .updater/api/sirius/bin
-    - name: Run Rest Api
-      run: bash .updater/api/sirius/bin/sirius REST -p 8080 -s &
-    - name: Wait for Api to start
-      id: api_start
-      run: while ! nc -z localhost 8080; do sleep 0.1; done
-    - name: Login to SIRIUS
-      id: login
-      run: |
-        library(RSirius)
-        var_accept_terms <- TRUE
-        var_account_credentials <- AccountCredentials$new(Sys.getenv('SIRIUS_USER'), Sys.getenv('SIRIUS_PW'))
-        api_instance <- rsirius_api$new()
-        api_response <- api_instance$login_and_account_api$Login(var_accept_terms, var_account_credentials)
-        if (inherits(api_response, "AccountInfo")) {
-          print('Login successful!')
-          quit(status=0)
-        } else {
-          print('Login failed, aborting...')
-          quit(status=1)
-        }
-      shell: Rscript {0}
-    - name: Test Actuator API
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_actuator_api.R", reporter=multi_reporter)
-      shell: Rscript {0}
-    - name: Test Info API
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_info_api.R", reporter=multi_reporter)
-      shell: Rscript {0}
-    - name: Test Login and Account API
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_login_and_account_api.R", reporter=multi_reporter)
-      shell: Rscript {0}
-    - name: Test Projects API
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_projects_api.R", reporter=multi_reporter)
-      shell: Rscript {0}
-    - name: Test Compounds API
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_compounds_api.R", reporter=multi_reporter)
-      shell: Rscript {0}
-    - name: Test Databases API
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_searchable_databases_api.R", reporter=multi_reporter)
-      shell: Rscript {0}
-    - name: Test Features API
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_features_api.R", reporter=multi_reporter)
-      shell: Rscript {0}
-    - name: Test Jobs API
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_jobs_api.R", reporter=multi_reporter)
-      shell: Rscript {0}
-    - name: Test acceptance
-      if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
-      run: |
-        library(RSirius)
-        library(testthat)
-        multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
-        test_file("client-api_r/generated/tests/testthat/test_acceptance.R", reporter=multi_reporter)
-      shell: Rscript {0}
\ No newline at end of file
+      - uses: actions/checkout@v3
+      - name: Set up R ${{ matrix.r-version }}
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.r-version }}
+      - name: Install RSirius dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: false
+          working-directory: ./client-api_r/generated
+      - name: Install RSirius
+        id: rsirius_install
+        run: |
+          install.packages("/home/runner/work/sirius-client-openAPI/sirius-client-openAPI/client-api_r/generated", repos = NULL, type = "source")
+        shell: Rscript {0}
+      - name: Determine SIRIUS version
+        id: sirius_version
+        run: |
+          if [ -n "${{ inputs.sirius_version }}" ]; then
+            echo "Using version from workflow input: ${{ inputs.sirius_version }}"
+            echo "version=${{ inputs.sirius_version }}" >> $GITHUB_OUTPUT
+          elif [ -f ".updater/api/packageVersion.txt" ]; then
+            version=$(cat .updater/api/packageVersion.txt)
+            echo "Using version from packageVersion.txt: $version"
+            echo "version=$version" >> $GITHUB_OUTPUT
+          else
+            echo "No version found — defaulting to latest."
+            version=$(curl -s https://api.github.com/repos/sirius-ms/sirius/releases/latest | jq -r '.tag_name' | sed 's/^v//')
+            echo "version=$version" >> $GITHUB_OUTPUT
+          fi
+      - name: Download SIRIUS
+        run: |
+          version="${{ steps.sirius_version.outputs.version }}"
+          mkdir -p .updater/api
+          cd .updater/api
+          url="https://github.com/sirius-ms/sirius/releases/download/v${version}/sirius-${version}-linux-x64.zip"
+          echo "Downloading $url"
+          wget -nv "$url" -O sirius-${version}-linux-x64.zip
+          unzip -q sirius-${version}-linux-x64.zip
+      - 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 $HOME/tomato_small.sirius
+      - name: Check SIRIUS download
+        run: |
+          echo "Show content of cache download (.updater/api/)"
+          ls -lah .updater/api/
+          echo "Show content of cache download (.updater/api/sirius)"
+          ls -lah .updater/api/sirius
+          echo "Show content of cache download (.updater/api/sirius/bin)"
+          ls -lah .updater/api/sirius/bin
+      - name: Run Rest Api
+        run: bash .updater/api/sirius/bin/sirius REST -p 8080 -s &
+      - name: Wait for Api to start
+        id: api_start
+        run: while ! nc -z localhost 8080; do sleep 0.1; done
+      - name: Login to SIRIUS
+        id: login
+        run: |
+          library(RSirius)
+          var_accept_terms <- TRUE
+          var_account_credentials <- AccountCredentials$new(Sys.getenv('SIRIUS_USER'), Sys.getenv('SIRIUS_PW'))
+          api_instance <- rsirius_api$new()
+          api_response <- api_instance$login_and_account_api$Login(var_accept_terms, var_account_credentials)
+          if (inherits(api_response, "AccountInfo")) {
+            print('Login successful!')
+            quit(status=0)
+          } else {
+            print('Login failed, aborting...')
+            quit(status=1)
+          }
+        shell: Rscript {0}
+      - name: Test Actuator API
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_actuator_api.R", reporter=multi_reporter)
+        shell: Rscript {0}
+      - name: Test Info API
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_info_api.R", reporter=multi_reporter)
+        shell: Rscript {0}
+      - name: Test Login and Account API
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_login_and_account_api.R", reporter=multi_reporter)
+        shell: Rscript {0}
+      - name: Test Projects API
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_projects_api.R", reporter=multi_reporter)
+        shell: Rscript {0}
+      - name: Test Compounds API
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_compounds_api.R", reporter=multi_reporter)
+        shell: Rscript {0}
+      - name: Test Databases API
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_searchable_databases_api.R", reporter=multi_reporter)
+        shell: Rscript {0}
+      - name: Test Features API
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_features_api.R", reporter=multi_reporter)
+        shell: Rscript {0}
+      - name: Test Jobs API
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_jobs_api.R", reporter=multi_reporter)
+        shell: Rscript {0}
+      - name: Test acceptance
+        if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success'
+        run: |
+          library(RSirius)
+          library(testthat)
+          multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new()))
+          test_file("client-api_r/generated/tests/testthat/test_acceptance.R", reporter=multi_reporter)
+        shell: Rscript {0}
\ No newline at end of file
diff --git a/.github/workflows/RunTests.yml b/.github/workflows/RunTests.yml
index 44d801da..0f378d31 100644
--- a/.github/workflows/RunTests.yml
+++ b/.github/workflows/RunTests.yml
@@ -1,13 +1,28 @@
-# This workflow will start all individual Tests
-
 name: RunTests
 
-on: [workflow_dispatch, workflow_call, pull_request]
+on:
+  workflow_dispatch:
+    inputs:
+      sirius_version:
+        description: "SIRIUS version to test (passed from NewUpdate)"
+        required: false
+        type: string
+  workflow_call:
+    inputs:
+      sirius_version:
+        required: false
+        type: string
+  pull_request:
 
 jobs:
   RTest:
     uses: ./.github/workflows/RTest.yml
     secrets: inherit
+    with:
+      sirius_version: ${{ inputs.sirius_version }}
+
   PythonTest:
     uses: ./.github/workflows/PythonTest.yml
     secrets: inherit
+    with:
+      sirius_version: ${{ inputs.sirius_version }}

From 6de5e7155b7aeffc74a161cffbeebac2474965da Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 22:28:48 +0100
Subject: [PATCH 02/14] forgot ClientUpdater and SetupBranch

---
 .github/workflows/SetupBranch.yml | 34 +++++++++++++++++-------------
 .github/workflows/updater.yml     | 35 ++++++++++++++-----------------
 2 files changed, 36 insertions(+), 33 deletions(-)

diff --git a/.github/workflows/SetupBranch.yml b/.github/workflows/SetupBranch.yml
index 4c6cf3f5..66a2e105 100644
--- a/.github/workflows/SetupBranch.yml
+++ b/.github/workflows/SetupBranch.yml
@@ -1,33 +1,39 @@
-
 name: SetupBranch
 
-# Controls when the action will run. Workflow runs when manually triggered using the UI
-# or API.
 on:
   workflow_dispatch:
     inputs:
       target_branch:
         type: string
         required: true
-  
-  
+      sirius_version:
+        description: "Optional: specify SIRIUS version to use (e.g. 6.3.3)"
+        required: false
+        type: string
+
 jobs:
   CreateTempBranch:
     runs-on: ubuntu-latest
     steps:
-    - name: Create Branch
-      uses: peterjgrainger/action-create-branch@v2.2.0
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      with:
-        branch: ${{ inputs.target_branch }}
+      - name: Create Branch
+        uses: peterjgrainger/action-create-branch@v2.2.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          branch: ${{ inputs.target_branch }}
+
   UpdateOnNewBranch:
     needs: CreateTempBranch
     runs-on: ubuntu-latest
     steps:
       - name: checkout repo
-        uses: actions/checkout@v3.1.0
-      - name: Call Workflow
-        run: gh workflow run NewUpdate.yml --ref ${{ inputs.target_branch }} -f target_branch=${GITHUB_REF##*/}
+        uses: actions/checkout@v3
+      - name: Call NewUpdate
+        run: |
+          version_input=""
+          if [ -n "${{ inputs.sirius_version }}" ]; then
+            version_input="-f sirius_version=${{ inputs.sirius_version }}"
+          fi
+          gh workflow run NewUpdate.yml --ref ${{ inputs.target_branch }} -f target_branch=${GITHUB_REF##*/} $version_input
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/updater.yml b/.github/workflows/updater.yml
index e70438eb..c2445206 100644
--- a/.github/workflows/updater.yml
+++ b/.github/workflows/updater.yml
@@ -1,32 +1,29 @@
-# This is a basic workflow that is manually triggered
-
 name: Client_Updater
 
-# Controls when the action will run. Workflow runs when manually triggered using the UI
-# or API.
 on:
-  [workflow_dispatch, repository_dispatch]
-    # Inputs the workflow accepts.
-#    inputs:
- #     name:
-  #      # Friendly description to be shown in the UI instead of 'name'
-   #     description: 'Person to greet'
-    #    # Default value if no value is explicitly provided
-     ##   default: 'World'
-       # # Input has to be provided for the workflow to run
-        #required: true
+  workflow_dispatch:
+    inputs:
+      sirius_version:
+        description: "Optional: specify SIRIUS version to use (e.g. 6.3.3)"
+        required: false
+        type: string
+  repository_dispatch:
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # does not run on the temp branch itself
   UpdateCache:
     uses: ./.github/workflows/update-api.yml
+
   UpdateOnNewBranch:
     runs-on: ubuntu-latest
     steps:
       - name: checkout repo
-        uses: actions/checkout@v3.1.0
-      - name: Call Workflow
-        run: gh workflow run SetupBranch.yml --ref ${GITHUB_REF##*/} -f target_branch=$(echo -en temp_;date +"%Y%m%d%H%M%S%N")
+        uses: actions/checkout@v3
+      - name: Call SetupBranch
+        run: |
+          version_input=""
+          if [ -n "${{ inputs.sirius_version }}" ]; then
+            version_input="-f sirius_version=${{ inputs.sirius_version }}"
+          fi
+          gh workflow run SetupBranch.yml --ref ${GITHUB_REF##*/} -f target_branch=$(echo -en temp_;date +"%Y%m%d%H%M%S%N") $version_input
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

From 1c837cb1090625931517b3faf17b470446cf373b Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 22:31:28 +0100
Subject: [PATCH 03/14] remove cache update

---
 .github/workflows/updater.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/updater.yml b/.github/workflows/updater.yml
index c2445206..82d7df05 100644
--- a/.github/workflows/updater.yml
+++ b/.github/workflows/updater.yml
@@ -10,9 +10,6 @@ on:
   repository_dispatch:
 
 jobs:
-  UpdateCache:
-    uses: ./.github/workflows/update-api.yml
-
   UpdateOnNewBranch:
     runs-on: ubuntu-latest
     steps:

From 0043c50e23b6e05bc7ff9c223a656b8cd1248ec0 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 22:45:26 +0100
Subject: [PATCH 04/14] add descriptions

---
 .github/workflows/NewUpdate.yml   | 1 +
 .github/workflows/SetupBranch.yml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.github/workflows/NewUpdate.yml b/.github/workflows/NewUpdate.yml
index a3502ff6..bab79561 100644
--- a/.github/workflows/NewUpdate.yml
+++ b/.github/workflows/NewUpdate.yml
@@ -6,6 +6,7 @@ on:
       target_branch:
         type: string
         required: true
+        description: "Target branch to put update commits on."
       sirius_version:
         description: "Optional SIRIUS version to download (e.g. 6.3.3). Leave blank for latest."
         type: string
diff --git a/.github/workflows/SetupBranch.yml b/.github/workflows/SetupBranch.yml
index 66a2e105..1d55432b 100644
--- a/.github/workflows/SetupBranch.yml
+++ b/.github/workflows/SetupBranch.yml
@@ -6,6 +6,7 @@ on:
       target_branch:
         type: string
         required: true
+        description: "Temporary branch to create (NewUpdate will commit to that branch)."
       sirius_version:
         description: "Optional: specify SIRIUS version to use (e.g. 6.3.3)"
         required: false

From 7204341218f7551370539e5540a679511c8b56d8 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 22:47:32 +0100
Subject: [PATCH 05/14] remove duplicate run

---
 .github/workflows/NewUpdate.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/NewUpdate.yml b/.github/workflows/NewUpdate.yml
index bab79561..d1550ea1 100644
--- a/.github/workflows/NewUpdate.yml
+++ b/.github/workflows/NewUpdate.yml
@@ -180,10 +180,6 @@ jobs:
           echo "sleeping for 30min before temp branch removal"
           sleep 1800
         #      if: steps.lockpull.outcome == 'failure'
-        run: |
-          gh workflow run RunTests.yml --ref ${GITHUB_REF##*/}
-          echo "sleeping for 30min before temp branch removal"
-          sleep 1800
       - name: Delete temp branches if no changes occure
         if: steps.lockpull.outcome == 'failure'
         uses: dawidd6/action-delete-branch@v3

From 51153d425bf65a8250786e3b50672ccc9cdda015 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 22:54:13 +0100
Subject: [PATCH 06/14] openapi_generator directory handling

---
 .github/workflows/NewUpdate.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/NewUpdate.yml b/.github/workflows/NewUpdate.yml
index d1550ea1..af309ccd 100644
--- a/.github/workflows/NewUpdate.yml
+++ b/.github/workflows/NewUpdate.yml
@@ -21,6 +21,7 @@ jobs:
         uses: actions/checkout@v3.1.0
       - name: Download latest generators
         run: |
+          mkdir .updater/openapi_generator
           cd .updater/openapi_generator
           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
@@ -131,7 +132,7 @@ jobs:
           echo "Done"
       - name: Remove Openapi Generator Files
         run: |
-          rm .updater/openapi_generator/*.jar
+          rm -rf .updater/openapi_generator
           ls ./.github/workflows
           echo "Done"
       - name: update file and push to remote

From b313437bfa4113df142a680fd31a8a6d872c6ae5 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 23:38:04 +0100
Subject: [PATCH 07/14] delete release json in workflow

---
 .github/workflows/NewUpdate.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/NewUpdate.yml b/.github/workflows/NewUpdate.yml
index af309ccd..747cb47c 100644
--- a/.github/workflows/NewUpdate.yml
+++ b/.github/workflows/NewUpdate.yml
@@ -47,6 +47,7 @@ jobs:
               echo "No version provided — fetching latest release..."
               curl -s https://api.github.com/repos/sirius-ms/sirius/releases/latest > ./release.json
               version=$(jq -r '.tag_name' ./release.json | sed 's/^v//')
+              rm ./release.json
               echo "Latest version: $version"
               echo "$version" > ./packageVersion.txt
             

From ceea0b8b23d9c0fec432c3bd79b372e2f9b73f1d Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 23:41:48 +0100
Subject: [PATCH 08/14] clean up version fetch

---
 .github/workflows/NewUpdate.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/NewUpdate.yml b/.github/workflows/NewUpdate.yml
index 747cb47c..2399525d 100644
--- a/.github/workflows/NewUpdate.yml
+++ b/.github/workflows/NewUpdate.yml
@@ -45,9 +45,7 @@ jobs:
             else
               # Fallback to automatic latest detection
               echo "No version provided — fetching latest release..."
-              curl -s https://api.github.com/repos/sirius-ms/sirius/releases/latest > ./release.json
-              version=$(jq -r '.tag_name' ./release.json | sed 's/^v//')
-              rm ./release.json
+              version=$(curl -s https://api.github.com/repos/sirius-ms/sirius/releases/latest | jq -r '.tag_name' | sed 's/^v//')
               echo "Latest version: $version"
               echo "$version" > ./packageVersion.txt
             

From 5eae02917dc64719da2852c40cfa288c0568cc1b Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 23:47:31 +0100
Subject: [PATCH 09/14] fix url for latest version fetch

---
 .github/workflows/NewUpdate.yml | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/NewUpdate.yml b/.github/workflows/NewUpdate.yml
index 2399525d..ed6eb63b 100644
--- a/.github/workflows/NewUpdate.yml
+++ b/.github/workflows/NewUpdate.yml
@@ -36,24 +36,19 @@ jobs:
             if [ -n "${{ github.event.inputs.sirius_version }}" ]; then
               # Manual version provided
               version="${{ github.event.inputs.sirius_version }}"
-              echo "Using manually provided SIRIUS version: $version"
-              echo "$version" > ./packageVersion.txt
-            
-              url="https://github.com/sirius-ms/sirius/releases/download/v${version}/sirius-${version}-linux-x64.zip"
-              echo "Downloading from: $url"
-              wget -nv "$url" -O sirius-${version}-linux-x64.zip
+              echo "Using manually provided SIRIUS version: $version"          
             else
               # Fallback to automatic latest detection
               echo "No version provided — fetching latest release..."
               version=$(curl -s https://api.github.com/repos/sirius-ms/sirius/releases/latest | jq -r '.tag_name' | sed 's/^v//')
               echo "Latest version: $version"
-              echo "$version" > ./packageVersion.txt
-            
-              url=$(jq -r '.assets[] | select(.name | test("linux-x64.zip$")) | .browser_download_url' ./release.json)
-              echo "Downloading from: $url"
-              wget -nv "$url" -O sirius-${version}-linux-x64.zip
             fi
             
+            echo "$version" > ./packageVersion.txt
+            url="https://github.com/sirius-ms/sirius/releases/download/v${version}/sirius-${version}-linux-x64.zip"
+            echo "Downloading from: $url"
+            wget -nv "$url" -O sirius-${version}-linux-x64.zip
+            
             echo "Unzipping..."
             unzip -q sirius-*-linux-x64.zip
             echo "API Ready"

From 8d19ae36fb5ead9c544589ec5e201cb62b6af6b9 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 23:49:49 +0100
Subject: [PATCH 10/14] use $GITHUB_OUTPUT

---
 .github/workflows/SetupBranch.yml | 14 ++++++++++----
 .github/workflows/updater.yml     | 14 ++++++++++----
 2 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/SetupBranch.yml b/.github/workflows/SetupBranch.yml
index 1d55432b..49c852a3 100644
--- a/.github/workflows/SetupBranch.yml
+++ b/.github/workflows/SetupBranch.yml
@@ -15,6 +15,8 @@ on:
 jobs:
   CreateTempBranch:
     runs-on: ubuntu-latest
+    outputs:
+      target_branch: ${{ steps.output.outputs.target_branch }}
     steps:
       - name: Create Branch
         uses: peterjgrainger/action-create-branch@v2.2.0
@@ -22,6 +24,10 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           branch: ${{ inputs.target_branch }}
+      - name: Set output
+        id: output
+        run: |
+          echo "target_branch=${{ inputs.target_branch }}" >> $GITHUB_OUTPUT
 
   UpdateOnNewBranch:
     needs: CreateTempBranch
@@ -31,10 +37,10 @@ jobs:
         uses: actions/checkout@v3
       - name: Call NewUpdate
         run: |
-          version_input=""
           if [ -n "${{ inputs.sirius_version }}" ]; then
-            version_input="-f sirius_version=${{ inputs.sirius_version }}"
+            gh workflow run NewUpdate.yml --ref ${{ inputs.target_branch }} -f target_branch=${GITHUB_REF##*/} -f sirius_version=${{ inputs.sirius_version }}
+          else
+            gh workflow run NewUpdate.yml --ref ${{ inputs.target_branch }} -f target_branch=${GITHUB_REF##*/}
           fi
-          gh workflow run NewUpdate.yml --ref ${{ inputs.target_branch }} -f target_branch=${GITHUB_REF##*/} $version_input
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file
diff --git a/.github/workflows/updater.yml b/.github/workflows/updater.yml
index 82d7df05..9fc58c45 100644
--- a/.github/workflows/updater.yml
+++ b/.github/workflows/updater.yml
@@ -12,15 +12,21 @@ on:
 jobs:
   UpdateOnNewBranch:
     runs-on: ubuntu-latest
+    outputs:
+      target_branch: ${{ steps.setup.outputs.target_branch }}
     steps:
       - name: checkout repo
         uses: actions/checkout@v3
       - name: Call SetupBranch
+        id: setup
         run: |
-          version_input=""
+          target_branch=$(echo -en temp_;date +"%Y%m%d%H%M%S%N")
+          echo "target_branch=$target_branch" >> $GITHUB_OUTPUT
+          
           if [ -n "${{ inputs.sirius_version }}" ]; then
-            version_input="-f sirius_version=${{ inputs.sirius_version }}"
+            gh workflow run SetupBranch.yml --ref ${GITHUB_REF##*/} -f target_branch=$target_branch -f sirius_version=${{ inputs.sirius_version }}
+          else
+            gh workflow run SetupBranch.yml --ref ${GITHUB_REF##*/} -f target_branch=$target_branch
           fi
-          gh workflow run SetupBranch.yml --ref ${GITHUB_REF##*/} -f target_branch=$(echo -en temp_;date +"%Y%m%d%H%M%S%N") $version_input
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file

From 5474d35db6f7708558ba96c86198618739d53b6e Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Thu, 13 Nov 2025 23:58:27 +0100
Subject: [PATCH 11/14] small cleanup

---
 .github/workflows/SetupBranch.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/SetupBranch.yml b/.github/workflows/SetupBranch.yml
index 49c852a3..1967270a 100644
--- a/.github/workflows/SetupBranch.yml
+++ b/.github/workflows/SetupBranch.yml
@@ -15,8 +15,6 @@ on:
 jobs:
   CreateTempBranch:
     runs-on: ubuntu-latest
-    outputs:
-      target_branch: ${{ steps.output.outputs.target_branch }}
     steps:
       - name: Create Branch
         uses: peterjgrainger/action-create-branch@v2.2.0
@@ -24,10 +22,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           branch: ${{ inputs.target_branch }}
-      - name: Set output
-        id: output
-        run: |
-          echo "target_branch=${{ inputs.target_branch }}" >> $GITHUB_OUTPUT
 
   UpdateOnNewBranch:
     needs: CreateTempBranch

From 4706d9d073dd880392d603c9bd528216681cec79 Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Fri, 14 Nov 2025 00:05:21 +0100
Subject: [PATCH 12/14] update action version

---
 .github/workflows/SetupBranch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/SetupBranch.yml b/.github/workflows/SetupBranch.yml
index 1967270a..cc05ccc8 100644
--- a/.github/workflows/SetupBranch.yml
+++ b/.github/workflows/SetupBranch.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Create Branch
-        uses: peterjgrainger/action-create-branch@v2.2.0
+        uses: peterjgrainger/action-create-branch@v3.0.0
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:

From cca514bcf82cfd5372e42d298ed1cdb4541f93ed Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Fri, 14 Nov 2025 10:11:03 +0100
Subject: [PATCH 13/14] remove obsolete caching workflow

---
 .github/workflows/update-api.yml | 41 --------------------------------
 1 file changed, 41 deletions(-)
 delete mode 100644 .github/workflows/update-api.yml

diff --git a/.github/workflows/update-api.yml b/.github/workflows/update-api.yml
deleted file mode 100644
index 37293bb0..00000000
--- a/.github/workflows/update-api.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-name: UpdateApi
-on: [workflow_call, workflow_dispatch]
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    timeout-minutes: 10
-    steps:
-    - uses: actions/checkout@v3
-    - name: Cache Sirius Release
-      id: cache-sirius
-      uses: actions/cache@v3
-      with:
-        path: .updater/api/sirius
-        key: sirius
-    - name: Check if cache is Empty
-      if: steps.cache-sirius.outputs.cache-hit != 'true'
-      uses: nick-fields/retry@v2
-      with:
-        max_attempts: 5
-        timeout_minutes: 2
-        command: |
-            cd .updater/api
-            curl -s  https://api.github.com/repositories/94561614/releases | 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 -o *.zip
-            echo "Api Ready"
-    - name: Check cached version
-      uses: nick-fields/retry@v2
-      with:
-        max_attempts: 5
-        timeout_minutes: 2
-        command: |
-            cd .updater/api
-            currVersion=$(cat ./sirius/HashCode)
-            curl -s  https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i -            newVersion=$(cat *.sha256 | cut -d " " -f 1)
-            echo New Version is $newVersion
-            if [ "$currVersion" != "$newVersion" ]; then
-            sleep 1
-            curl -s  https://api.github.com/repositories/94561614/releases | grep 'browser_download_url.*linux-x64.zip\"' | sort | tac | head -n 1 | cut -d : -f 2,3 | tr -d \" | wget -nv -i -
-            unzip -o *.zip
-            echo $newVersion > ./sirius/HashCode
-            fi
\ No newline at end of file

From 1d9bdedfc8e4e82915ec0f650eaadfe9dd0b547b Mon Sep 17 00:00:00 2001
From: joXemMx <jonas.em@t-online.de>
Date: Fri, 14 Nov 2025 13:06:10 +0100
Subject: [PATCH 14/14] link tests in package readme

---
 client-api_python/README.md | 5 +++--
 client-api_r/README.md      | 5 +++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/client-api_python/README.md b/client-api_python/README.md
index 1ed09fb1..15404336 100644
--- a/client-api_python/README.md
+++ b/client-api_python/README.md
@@ -1,8 +1,9 @@
 # PySirius
 REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as entry-point for scripting languages and software integration SDKs.
 
-- to [fine-grained documentation](#documentation-for-api-endpoints)
-- to our [example workflow](#example-usage-of-pysirius)
+- To our [example workflow](#example-usage-of-pysirius)
+- To the [fine-grained documentation](#documentation-for-api-endpoints)
+- To the [tests](generated/test/)
 
 ## Installation & Usage
 
diff --git a/client-api_r/README.md b/client-api_r/README.md
index 89ed5c22..b285b222 100644
--- a/client-api_r/README.md
+++ b/client-api_r/README.md
@@ -7,8 +7,9 @@
 REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as
 entry-point for scripting languages and software integration SDKs.
 
-- to [fine-grained documentation](#documentation-for-api-endpoints)
-- to our [example workflow](#example-usage-of-rsirius)
+- To our [example workflow](#example-usage-of-rsirius)
+- To the [fine-grained documentation](#documentation-for-api-endpoints)
+- To the [tests](generated/tests/testthat/)
 
 ## Installation & Usage