diff --git a/.github/workflows/rhiza_deptry.yml b/.github/workflows/rhiza_deptry.yml
index 30220daa..a81dff67 100644
--- a/.github/workflows/rhiza_deptry.yml
+++ b/.github/workflows/rhiza_deptry.yml
@@ -37,9 +37,45 @@ jobs:
         with:
           token: ${{ secrets.GH_PAT }}
 
-      - name: Run deptry
-        run: make deptry
-        # NOTE: make deptry is good style because it encapsulates the folders to check
-        # (e.g. src and book/marimo) and keeps CI in sync with local development.
-        # Since we use a 'uv' container, the Makefile is optimised to use the
-        # pre-installed 'uv' and 'uvx' from the system PATH.
+      - name: Extract folder variables
+        id: folders
+        run: |
+          # Extract SOURCE_FOLDER from the project configuration (via Makefile)
+          # shellcheck disable=SC2016 # Single quotes intentional - Make syntax, not shell expansion
+          SOURCE_FOLDER=$(make -s -f Makefile -f - <<< 'print: ; @echo $(or $(SOURCE_FOLDER),src)' print)
+          echo "source=$SOURCE_FOLDER" >> "$GITHUB_OUTPUT"
+          
+          # Extract MARIMO_FOLDER from the project configuration (via Makefile)
+          # shellcheck disable=SC2016 # Single quotes intentional - Make syntax, not shell expansion
+          MARIMO_FOLDER=$(make -s -f Makefile -f - <<< 'print: ; @echo $(or $(MARIMO_FOLDER),marimo)' print)
+          echo "marimo=$MARIMO_FOLDER" >> "$GITHUB_OUTPUT"
+          
+          # Extract Python version
+          PYTHON_VERSION=$(cat .python-version 2>/dev/null || echo "3.13")
+          echo "python_version=$PYTHON_VERSION" >> "$GITHUB_OUTPUT"
+          
+          echo "Detected SOURCE_FOLDER: $SOURCE_FOLDER"
+          echo "Detected MARIMO_FOLDER: $MARIMO_FOLDER"
+          echo "Using Python version: $PYTHON_VERSION"
+
+      - name: Run deptry on source folder
+        if: steps.folders.outputs.source != ''
+        run: |
+          if [ -d "${{ steps.folders.outputs.source }}" ]; then
+            uvx -p "${{ steps.folders.outputs.python_version }}" deptry "${{ steps.folders.outputs.source }}"
+          else
+            echo "Source folder ${{ steps.folders.outputs.source }} does not exist, skipping"
+          fi
+
+      - name: Run deptry on marimo folder
+        if: steps.folders.outputs.marimo != ''
+        run: |
+          if [ -d "${{ steps.folders.outputs.marimo }}" ]; then
+            if [ -d "${{ steps.folders.outputs.source }}" ]; then
+              uvx -p "${{ steps.folders.outputs.python_version }}" deptry "${{ steps.folders.outputs.marimo }}" "${{ steps.folders.outputs.source }}" --ignore DEP004
+            else
+              uvx -p "${{ steps.folders.outputs.python_version }}" deptry "${{ steps.folders.outputs.marimo }}" --ignore DEP004
+            fi
+          else
+            echo "Marimo folder ${{ steps.folders.outputs.marimo }} does not exist, skipping"
+          fi
diff --git a/.gitlab/README.md b/.gitlab/README.md
index b0523a79..47d3d008 100644
--- a/.gitlab/README.md
+++ b/.gitlab/README.md
@@ -63,7 +63,8 @@ This directory contains GitLab CI/CD workflow configurations that mirror the fun
 - On merge requests to main/master
 
 **Key Features:**
-- Automatic source folder detection
+- Extracts SOURCE_FOLDER and MARIMO_FOLDER from Makefile configuration
+- Automatically detects and checks all configured source folders
 - Identifies unused dependencies
 
 **Equivalent GitHub Action:** `.github/workflows/rhiza_deptry.yml`
diff --git a/.gitlab/TESTING.md b/.gitlab/TESTING.md
index 8bbcd93e..32deb7c3 100644
--- a/.gitlab/TESTING.md
+++ b/.gitlab/TESTING.md
@@ -98,12 +98,16 @@ This workflow is designed for repositories that use rhiza as a template, not for
 
 **Expected behavior:**
 - Checks for missing/obsolete dependencies
-- Automatically detects source folder (`src/` or `.`)
+- Automatically extracts SOURCE_FOLDER and MARIMO_FOLDER from Makefile configuration
+- Runs deptry on detected folders if they exist
 - Reports unused dependencies
 
 **Manual test:**
 ```bash
-# Run deptry locally
+# Run deptry locally using make (recommended)
+make deptry
+
+# Or run deptry directly
 uvx deptry src/
 ```
 
diff --git a/.gitlab/workflows/rhiza_deptry.yml b/.gitlab/workflows/rhiza_deptry.yml
index e2f15f18..b0c3456b 100644
--- a/.gitlab/workflows/rhiza_deptry.yml
+++ b/.gitlab/workflows/rhiza_deptry.yml
@@ -15,7 +15,34 @@ deptry:check:
   needs: []
   image: ghcr.io/astral-sh/uv:0.9.30-bookworm
   script:
-    - make deptry
+    # Extract SOURCE_FOLDER and MARIMO_FOLDER from the project configuration
+    # and run deptry on detected folders
+    - |
+      SOURCE_FOLDER=$(make -s -f Makefile -f - <<< 'print: ; @echo $(or $(SOURCE_FOLDER),src)' print)
+      MARIMO_FOLDER=$(make -s -f Makefile -f - <<< 'print: ; @echo $(or $(MARIMO_FOLDER),marimo)' print)
+      PYTHON_VERSION=$(cat .python-version 2>/dev/null || echo "3.13")
+      
+      echo "Detected SOURCE_FOLDER: $SOURCE_FOLDER"
+      echo "Detected MARIMO_FOLDER: $MARIMO_FOLDER"
+      echo "Using Python version: $PYTHON_VERSION"
+      
+      # Run deptry on source folder if it exists
+      if [ -n "$SOURCE_FOLDER" ] && [ -d "$SOURCE_FOLDER" ]; then
+        uvx -p "$PYTHON_VERSION" deptry "$SOURCE_FOLDER"
+      else
+        echo "Source folder $SOURCE_FOLDER does not exist, skipping"
+      fi
+      
+      # Run deptry on marimo folder if it exists
+      if [ -n "$MARIMO_FOLDER" ] && [ -d "$MARIMO_FOLDER" ]; then
+        if [ -d "$SOURCE_FOLDER" ]; then
+          uvx -p "$PYTHON_VERSION" deptry "$MARIMO_FOLDER" "$SOURCE_FOLDER" --ignore DEP004
+        else
+          uvx -p "$PYTHON_VERSION" deptry "$MARIMO_FOLDER" --ignore DEP004
+        fi
+      else
+        echo "Marimo folder $MARIMO_FOLDER does not exist, skipping"
+      fi
   rules:
     - if: $CI_PIPELINE_SOURCE == "merge_request_event"
     - if: $CI_COMMIT_BRANCH