🐛 fix: resolve cleanup jq parsing and cellprofiler build issues

- Fix jq error with paginated API responses using jq -s 'add'
- Pin numpy<2 and pre-install scikit-learn for cellprofiler

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: FloWuenne

.github/workflows/cleanup-pr-images.yml

@@ -22,17 +22,17 @@ jobs:
 
           echo "Cleaning up images for PR #${PR_NUMBER}..."
 
-          # Get all versions of the package
+          # Get all versions of the package (merge paginated arrays)
           VERSIONS=$(gh api \
             -H "Accept: application/vnd.github+json" \
             -H "X-GitHub-Api-Version: 2022-11-28" \
             "/orgs/seqeralabs/packages/container/${PACKAGE_NAME}/versions" \
-            --paginate 2>/dev/null || echo "[]")
+            --paginate 2>/dev/null | jq -s 'add // []')
 
           # Find all versions with tags ending in -pr<PR_NUMBER>
           echo "$VERSIONS" | jq -r --arg pr "pr${PR_NUMBER}" '
             .[] |
-            select(.metadata.container.tags[] | endswith("-" + $pr)) |
+            select(.metadata.container.tags[]? | endswith("-" + $pr)) |
             .id
           ' | while read -r VERSION_ID; do
             if [[ -n "$VERSION_ID" ]]; then

kasmVNC/cellprofiler/Dockerfile

@@ -42,8 +42,9 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 # Set JAVA_HOME for CellProfiler
 ENV JAVA_HOME=/usr/lib/jvm/default-java
 
-# Install CellProfiler (requires numpy first)
-RUN pip3 install --no-cache-dir numpy && \
+# Install CellProfiler with compatible dependencies
+# Pin numpy<2 to avoid scikit-learn build issues with numpy 2.x
+RUN pip3 install --no-cache-dir "numpy<2" scikit-learn && \
     pip3 install --no-cache-dir cellprofiler
 
 # Single-app mode: application launches directly, no desktop