From fbff777e41ceb79a264dbe92297cd3a07c0eb426 Mon Sep 17 00:00:00 2001
From: shachafl <66333410+shachafl@users.noreply.github.com>
Date: Tue, 4 Nov 2025 16:01:37 +0200
Subject: [PATCH 1/4] Add dartfish pipeline data processing example CI job

---
 .github/workflows/starfish-prod-ci.yml | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/.github/workflows/starfish-prod-ci.yml b/.github/workflows/starfish-prod-ci.yml
index a9e78d33..c01049a3 100644
--- a/.github/workflows/starfish-prod-ci.yml
+++ b/.github/workflows/starfish-prod-ci.yml
@@ -458,3 +458,28 @@ jobs:
       - name: Run Data Processing Example Test
         run: |
           make TESTING=1 iss_pipeline.py
+
+dartfish-pipeline-data-processing-example:
+    name: dartfish_pipeline.py Data Processing Example
+    needs: starfish-slow
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.9'
+
+      - uses: actions/cache@v4
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
+
+      - name: Install Dependencies
+        run: |
+          make install-dev
+
+      - name: Run Data Processing Example Test
+        run: |
+          make dartfish_pipeline.py

From 8444dd5dbf6e694f171230893a9d78f51e9a6480 Mon Sep 17 00:00:00 2001
From: shachafl <66333410+shachafl@users.noreply.github.com>
Date: Tue, 4 Nov 2025 16:07:06 +0200
Subject: [PATCH 2/4] Update IPython magic commands for matplotlib

---
 examples/pipelines/dartfish_pipeline.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/examples/pipelines/dartfish_pipeline.py b/examples/pipelines/dartfish_pipeline.py
index 935a8220..0cdfe5df 100644
--- a/examples/pipelines/dartfish_pipeline.py
+++ b/examples/pipelines/dartfish_pipeline.py
@@ -16,11 +16,15 @@
 from IPython import get_ipython
 import matplotlib
 import matplotlib.pyplot as plt
+import sys
 
-# equivalent to %gui qt and %matplotlib inline
+# equivalent to using in a notebook cell: %matplotlib inline
 ipython = get_ipython()
-ipython.run_line_magic("gui", "qt5")
-ipython.run_line_magic("matplotlib", "inline")
+if ipython is not None:
+    if 'ipykernel' in sys.modules: # running in Jupyter
+        ipython.run_line_magic('matplotlib', 'inline')
+    else: # terminal IPython
+        ipython.run_line_magic('matplotlib', 'qt5')
 
 matplotlib.rcParams["figure.dpi"] = 150
 

From 09f523d0de41389996ed6b732a91b2836ae5bea2 Mon Sep 17 00:00:00 2001
From: shachafl <66333410+shachafl@users.noreply.github.com>
Date: Tue, 4 Nov 2025 16:08:35 +0200
Subject: [PATCH 3/4] Fix indentation for dartfish pipeline job

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

diff --git a/.github/workflows/starfish-prod-ci.yml b/.github/workflows/starfish-prod-ci.yml
index c01049a3..a50f88e5 100644
--- a/.github/workflows/starfish-prod-ci.yml
+++ b/.github/workflows/starfish-prod-ci.yml
@@ -459,7 +459,7 @@ jobs:
         run: |
           make TESTING=1 iss_pipeline.py
 
-dartfish-pipeline-data-processing-example:
+  dartfish-pipeline-data-processing-example:
     name: dartfish_pipeline.py Data Processing Example
     needs: starfish-slow
     runs-on: ubuntu-latest

From 2bb202df68fad220a3f3dcaa71ddebec3604089f Mon Sep 17 00:00:00 2001
From: shachafl <66333410+shachafl@users.noreply.github.com>
Date: Tue, 4 Nov 2025 17:04:06 +0200
Subject: [PATCH 4/4] Add Napari to job dependencies in CI workflow

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

diff --git a/.github/workflows/starfish-prod-ci.yml b/.github/workflows/starfish-prod-ci.yml
index a50f88e5..591b7cb3 100644
--- a/.github/workflows/starfish-prod-ci.yml
+++ b/.github/workflows/starfish-prod-ci.yml
@@ -461,7 +461,7 @@ jobs:
 
   dartfish-pipeline-data-processing-example:
     name: dartfish_pipeline.py Data Processing Example
-    needs: starfish-slow
+    needs: lint
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
@@ -479,6 +479,7 @@ jobs:
       - name: Install Dependencies
         run: |
           make install-dev
+          pip install -r requirements/REQUIREMENTS-NAPARI-CI.txt
 
       - name: Run Data Processing Example Test
         run: |