From 2e214f9a8e0f9268de4235d66cb839e2c487307e Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Tue, 9 Jan 2024 21:51:33 +0000
Subject: [PATCH 01/21] bump actions/checkout to v4

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

diff --git a/.github/workflows/omero_plugin.yml b/.github/workflows/omero_plugin.yml
index 455b4b231..40b601e9e 100644
--- a/.github/workflows/omero_plugin.yml
+++ b/.github/workflows/omero_plugin.yml
@@ -23,7 +23,7 @@ jobs:
     env:
       STAGE: scripts
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:

From 09a19d490ea1b784689beacb3f9911c21c878290 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Tue, 9 Jan 2024 21:53:05 +0000
Subject: [PATCH 02/21] point to own branch

---
 .github/workflows/omero_plugin.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/omero_plugin.yml b/.github/workflows/omero_plugin.yml
index 40b601e9e..cbe925e9c 100644
--- a/.github/workflows/omero_plugin.yml
+++ b/.github/workflows/omero_plugin.yml
@@ -27,8 +27,9 @@ jobs:
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:
-          repository: ome/omero-test-infra
+          repository: jburel/omero-test-infra
           path: .omero
-          ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
+          #ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
+          ref: update
       - name: Build and run OMERO tests
         run: .omero/docker $STAGE

From 80ebe42b02b8f80016ca001ab1716208c8b90db4 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Tue, 9 Jan 2024 22:04:15 +0000
Subject: [PATCH 03/21] set python version

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

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index 81eccda37..c0418dfda 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -9,6 +9,8 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
       - name: Build a binary wheel and a source tarball
         run: |
           python -mpip install wheel

From cb2d445e768c6efe19f8900358b488156860a203 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Tue, 9 Jan 2024 22:04:46 +0000
Subject: [PATCH 04/21] bump actions/checkout to v4

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

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
index c0418dfda..f412a8e28 100644
--- a/.github/workflows/publish_pypi.yml
+++ b/.github/workflows/publish_pypi.yml
@@ -7,7 +7,7 @@ jobs:
     name: Build and publish Python distribution to PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.9'

From d12b86ff3ab4a70753b264ce8c45f5fcbffa7ab6 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 10 Jan 2024 10:58:44 +0000
Subject: [PATCH 05/21] point to ome repo

---
 .github/workflows/omero_plugin.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/omero_plugin.yml b/.github/workflows/omero_plugin.yml
index cbe925e9c..40b601e9e 100644
--- a/.github/workflows/omero_plugin.yml
+++ b/.github/workflows/omero_plugin.yml
@@ -27,9 +27,8 @@ jobs:
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:
-          repository: jburel/omero-test-infra
+          repository: ome/omero-test-infra
           path: .omero
-          #ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
-          ref: update
+          ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
       - name: Build and run OMERO tests
         run: .omero/docker $STAGE

From 12a5dba0ef1396f0055f260e618ea3b53787bae0 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 10 Jan 2024 11:18:30 +0000
Subject: [PATCH 06/21] fix flake8 issue

---
 omero/analysis_scripts/Kymograph.py          | 10 ++++-----
 omero/analysis_scripts/Kymograph_Analysis.py |  4 ++--
 omero/analysis_scripts/Plot_Profile.py       | 20 +++++++++---------
 omero/annotation_scripts/KeyVal_to_csv.py    |  6 +++---
 omero/export_scripts/Make_Movie.py           |  4 ++--
 omero/figure_scripts/Movie_Figure.py         |  2 +-
 omero/figure_scripts/Movie_ROI_Figure.py     |  2 +-
 omero/figure_scripts/ROI_Split_Figure.py     |  4 ++--
 omero/figure_scripts/Split_View_Figure.py    |  2 +-
 omero/util_scripts/Dataset_To_Plate.py       |  2 +-
 omero/util_scripts/Images_From_ROIs.py       |  2 +-
 omero/util_scripts/Move_Annotations.py       | 22 ++++++++++----------
 12 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/omero/analysis_scripts/Kymograph.py b/omero/analysis_scripts/Kymograph.py
index 4e650a108..573317ea4 100644
--- a/omero/analysis_scripts/Kymograph.py
+++ b/omero/analysis_scripts/Kymograph.py
@@ -175,9 +175,9 @@ def plane_gen():
                 line_data = []
                 points = shape['points']
                 the_z = shape['theZ']
-                for l in range(len(points)-1):
-                    x1, y1 = points[l]
-                    x2, y2 = points[l+1]
+                for point in range(len(points)-1):
+                    x1, y1 = points[point]
+                    x2, y2 = points[point+1]
                     ld = get_line_data(image, x1, y1, x2, y2,
                                        line_width, the_z, the_c, the_t)
                     line_data.append(ld)
@@ -334,7 +334,7 @@ def process_images(conn, script_params):
                     z = the_z
                 # TODO: Add some filter of shapes. E.g. text? / 'lines' only
                 # etc.
-                if type(s) == omero.model.LineI:
+                if isinstance(s, omero.model.LineI):
                     x1 = s.getX1().getValue()
                     x2 = s.getX2().getValue()
                     y1 = s.getY1().getValue()
@@ -342,7 +342,7 @@ def process_images(conn, script_params):
                     lines[t] = {'theZ': z, 'x1': x1, 'y1': y1, 'x2': x2,
                                 'y2': y2}
 
-                elif type(s) == omero.model.PolylineI:
+                elif isinstance(s, omero.model.PolylineI):
                     v = s.getPoints().getValue()
                     points = roi_utils.points_string_to_xy_list(v)
                     polylines[t] = {'theZ': z, 'points': points}
diff --git a/omero/analysis_scripts/Kymograph_Analysis.py b/omero/analysis_scripts/Kymograph_Analysis.py
index 079231b6f..1af783232 100644
--- a/omero/analysis_scripts/Kymograph_Analysis.py
+++ b/omero/analysis_scripts/Kymograph_Analysis.py
@@ -86,7 +86,7 @@ def process_images(conn, script_params):
             for s in roi.copyShapes():
                 if s is None:
                     continue    # seems possible in some situations
-                if type(s) == omero.model.LineI:
+                if isinstance(s, omero.model.LineI):
                     table_data += "\nLine ID: %s" % s.getId().getValue()
                     x1 = s.getX1().getValue()
                     x2 = s.getX2().getValue()
@@ -103,7 +103,7 @@ def process_images(conn, script_params):
                         [str(x) for x in (y1, x1, y2, x2, dy, dx, dx_per_y,
                                           speed)])
 
-                elif type(s) == omero.model.PolylineI:
+                elif isinstance(s, omero.model.PolylineI):
                     table_data += "\nPolyline ID: %s" % s.getId().getValue()
                     v = s.getPoints().getValue()
                     points = roi_utils.points_string_to_xy_list(v)
diff --git a/omero/analysis_scripts/Plot_Profile.py b/omero/analysis_scripts/Plot_Profile.py
index 815997b02..be04db1e6 100644
--- a/omero/analysis_scripts/Plot_Profile.py
+++ b/omero/analysis_scripts/Plot_Profile.py
@@ -57,9 +57,9 @@ def process_polylines(conn, script_params, image, polylines, line_width, fout):
         points = pl['points']
         for the_c in the_cs:
             ldata = []
-            for l in range(len(points)-1):
-                x1, y1 = points[l]
-                x2, y2 = points[l+1]
+            for point in range(len(points)-1):
+                x1, y1 = points[point]
+                x2, y2 = points[point+1]
                 if round(x1 - x2) == 0 and round(y1 - y2) == 0:
                     continue
                 ld = roi_utils.get_line_data(
@@ -103,11 +103,11 @@ def process_lines(conn, script_params, image, lines, line_width, fout):
     pixels = image.getPrimaryPixels()
     the_cs = script_params['Channels']
 
-    for l in lines:
-        the_t = l['theT']
-        the_z = l['theZ']
-        roi_id = l['id']
-        if round(l['x1'] - l['x2']) == 0 and round(l['y1'] - l['y2']) == 0:
+    for line in lines:
+        the_t = line['theT']
+        the_z = line['theZ']
+        roi_id = line['id']
+        if round(line['x1'] - line['x2']) == 0 and round(line['y1'] - line['y2']) == 0:
             continue
         for the_c in the_cs:
             line_data = []
@@ -192,7 +192,7 @@ def process_images(conn, script_params):
                     z = the_z
                 # TODO: Add some filter of shapes e.g. text? / 'lines' only
                 # etc.
-                if type(s) == omero.model.LineI:
+                if isinstance(s, omero.model.LineI):
                     x1 = s.getX1().getValue()
                     x2 = s.getX2().getValue()
                     y1 = s.getY1().getValue()
@@ -200,7 +200,7 @@ def process_images(conn, script_params):
                     lines.append({'id': roi_id, 'theT': t, 'theZ': z,
                                   'x1': x1, 'y1': y1, 'x2': x2, 'y2': y2})
 
-                elif type(s) == omero.model.PolylineI:
+                elif isinstance(s, omero.model.PolylineI):
                     v = s.getPoints().getValue()
                     points = roi_utils.points_string_to_xy_list(v)
                     polylines.append({'id': roi_id, 'theT': t, 'theZ': z,
diff --git a/omero/annotation_scripts/KeyVal_to_csv.py b/omero/annotation_scripts/KeyVal_to_csv.py
index fbab07b12..b29314081 100644
--- a/omero/annotation_scripts/KeyVal_to_csv.py
+++ b/omero/annotation_scripts/KeyVal_to_csv.py
@@ -39,7 +39,7 @@
 def get_existing_map_annotions(obj):
     ord_dict = OrderedDict()
     for ann in obj.listAnnotations():
-        if(isinstance(ann, omero.gateway.MapAnnotationWrapper)):
+        if isinstance(ann, omero.gateway.MapAnnotationWrapper):
             kvs = ann.getValue()
             for k, v in kvs:
                 if k not in ord_dict:
@@ -152,8 +152,8 @@ def run_script():
 
             # remove the csv if it exists
             for ann in ds.listAnnotations():
-                if(isinstance(ann, omero.gateway.FileAnnotationWrapper)):
-                    if(ann.getFileName() == csv_name):
+                if isinstance(ann, omero.gateway.FileAnnotationWrapper):
+                    if ann.getFileName() == csv_name:
                         # if the name matches delete it
                         try:
                             delete = Delete2(
diff --git a/omero/export_scripts/Make_Movie.py b/omero/export_scripts/Make_Movie.py
index 4c0e3e1a9..f886135a3 100644
--- a/omero/export_scripts/Make_Movie.py
+++ b/omero/export_scripts/Make_Movie.py
@@ -486,8 +486,8 @@ def write_movie(command_args, conn):
         c_windows = []
         c_colours = []
         for c in command_args["ChannelsExtended"]:
-            m = re.match('^(?P<i>\d+)(\|(?P<ws>\d+)' +
-                         '\:(?P<we>\d+))?(\$(?P<c>.+))?$', c)
+            m = re.match('^(?P<i>\\d+)(\\|(?P<ws>\\d+)' +
+                         '\\:(?P<we>\\d+))?(\\$(?P<c>.+))?$', c)
             if m is not None:
                 c_range.append(int(m.group('i'))-1)
                 c_windows.append([float(m.group('ws')), float(m.group('we'))])
diff --git a/omero/figure_scripts/Movie_Figure.py b/omero/figure_scripts/Movie_Figure.py
index 29dc4814f..815badda2 100644
--- a/omero/figure_scripts/Movie_Figure.py
+++ b/omero/figure_scripts/Movie_Figure.py
@@ -311,7 +311,7 @@ def add_left_labels(panel_canvas, image_labels, row_index, width, spacer):
 
     labels = image_labels[row_index]
     py = left_text_height - text_gap  # start at bottom
-    for l, label in enumerate(labels):
+    for count, label in enumerate(labels):
         py = py - text_height    # find the top of this row
         w = textdraw.textsize(label, font=font)[0]
         inset = int((left_text_width - w) / 2)
diff --git a/omero/figure_scripts/Movie_ROI_Figure.py b/omero/figure_scripts/Movie_ROI_Figure.py
index 4142035fe..0c02dbee9 100644
--- a/omero/figure_scripts/Movie_ROI_Figure.py
+++ b/omero/figure_scripts/Movie_ROI_Figure.py
@@ -589,7 +589,7 @@ def get_tags(name, tags_list, pd_list):
         try:
             height = int(h)
         except ValueError:
-            log("Invalid height: %s Using default value" % (str(h), size_y))
+            log("Invalid height: %s Using default value %s" % (str(h), size_y))
 
     log("Image dimensions for all panels (pixels): width: %d  height: %d"
         % (width, height))
diff --git a/omero/figure_scripts/ROI_Split_Figure.py b/omero/figure_scripts/ROI_Split_Figure.py
index 681b98a8e..0b0f61a37 100644
--- a/omero/figure_scripts/ROI_Split_Figure.py
+++ b/omero/figure_scripts/ROI_Split_Figure.py
@@ -320,7 +320,7 @@ def get_rectangle(roi_service, image_id, roi_label):
         roi_count += 1
         # go through all the shapes of the ROI
         for shape in roi.copyShapes():
-            if type(shape) == omero.model.RectangleI:
+            if isinstance(shape, omero.model.RectangleI):
                 the_t = unwrap(shape.getTheT())
                 the_z = unwrap(shape.getTheZ())
                 t = 0
@@ -660,7 +660,7 @@ def get_tags(name, tags_list, pd_list):
         try:
             height = int(h)
         except ValueError:
-            log("Invalid height: %s Using default value" % (str(h), size_y))
+            log("Invalid height: %s Using default value: %d" % (str(h), size_y))
 
     log("Image dimensions for all panels (pixels): width: %d  height: %d"
         % (width, height))
diff --git a/omero/figure_scripts/Split_View_Figure.py b/omero/figure_scripts/Split_View_Figure.py
index 720871dc8..971343765 100644
--- a/omero/figure_scripts/Split_View_Figure.py
+++ b/omero/figure_scripts/Split_View_Figure.py
@@ -404,7 +404,7 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
         image_labels.reverse()
         for row in image_labels:
             py = left_text_width - text_gap  # start at bottom
-            for l, label in enumerate(row):
+            for count, label in enumerate(row):
                 py = py - text_height    # find the top of this row
                 w = textdraw.textsize(label, font=font)[0]
                 inset = int((height - w) // 2)
diff --git a/omero/util_scripts/Dataset_To_Plate.py b/omero/util_scripts/Dataset_To_Plate.py
index 88183b078..f6c060fff 100644
--- a/omero/util_scripts/Dataset_To_Plate.py
+++ b/omero/util_scripts/Dataset_To_Plate.py
@@ -63,7 +63,7 @@ def add_images_to_plate(conn, images, plate_id, column, row, remove_from=None):
     for image in images:
         if remove_from is not None:
             links = list(image.getParentLinks(remove_from.id))
-            link_ids = [l.id for l in links]
+            link_ids = [link.id for link in links]
             conn.deleteObjects('DatasetImageLink', link_ids)
     return True
 
diff --git a/omero/util_scripts/Images_From_ROIs.py b/omero/util_scripts/Images_From_ROIs.py
index 465252e9c..e5f1d0108 100644
--- a/omero/util_scripts/Images_From_ROIs.py
+++ b/omero/util_scripts/Images_From_ROIs.py
@@ -140,7 +140,7 @@ def get_rectangles(conn, image_id):
         # note x and y for every T, to track moving object
         xy_by_time = {}
         for shape in roi.copyShapes():
-            if type(shape) == omero.model.RectangleI:
+            if isinstance(shape, omero.model.RectangleI):
                 # check t range and z range for every rectangle
                 # t and z (and c) for shape is optional
                 # https://www.openmicroscopy.org/site/support/omero5.2/developers/Model/EveryObject.html#shape
diff --git a/omero/util_scripts/Move_Annotations.py b/omero/util_scripts/Move_Annotations.py
index 625aeb83a..d3f76dce8 100644
--- a/omero/util_scripts/Move_Annotations.py
+++ b/omero/util_scripts/Move_Annotations.py
@@ -62,11 +62,11 @@ def move_well_annotations(conn, well, ann_type, remove_anns, ns):
                                              ns=ns, params=params))
 
     # Filter by type
-    old_links = [l for l in old_links
+    old_links = [link for link in old_links
                  if (ann_type is None
                      or (l.child.__class__.__name__ == ann_type))]
 
-    link_ids = [l.id for l in old_links]
+    link_ids = [link.id for link in old_links]
 
     def get_key(ann_link, with_owner=False):
         # We use ann's 'key' to avoid adding duplicate annotations
@@ -76,28 +76,28 @@ def get_key(ann_link, with_owner=False):
 
     links_dict = {}
     # Remove duplicate annotations according to get_key(l)
-    for l in old_links:
-        links_dict[get_key(l, conn.isAdmin())] = l
+    for link in old_links:
+        links_dict[get_key(link, conn.isAdmin())] = link
 
     old_links = links_dict.values()
 
     # Find existing links on Well so we don't try to duplicate them
     existing_well_links = list(conn.getAnnotationLinks('Well', [well.id],
                                                        ns=ns, params=params))
-    existing_well_keys = [get_key(l) for l in existing_well_links]
+    existing_well_keys = [get_key(l) for link in existing_well_links]
 
     new_links = []
-    for l in old_links:
-        if get_key(l) in existing_well_keys:
+    for link in old_links:
+        if get_key(link) in existing_well_keys:
             continue
-        log("    Annotation: %s %s" % (l.child.id.val,
-                                       l.child.__class__.__name__))
+        log("    Annotation: %s %s" % (link.child.id.val,
+                                       link.child.__class__.__name__))
         link = WellAnnotationLinkI()
         link.parent = WellI(well.id, False)
-        link.child = l.child
+        link.child = link.child
         # If Admin, the new link Owner is same as old link Owner
         if conn.isAdmin():
-            owner_id = l.details.owner.id.val
+            owner_id = link.details.owner.id.val
             link.details.owner = ExperimenterI(owner_id, False)
         new_links.append(link)
     try:

From df8830f8bde4ad7c2d4e55d1c0d3d282465c4596 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 10 Jan 2024 11:33:48 +0000
Subject: [PATCH 07/21] another round of flake8

---
 omero/analysis_scripts/Plot_Profile.py   | 9 +++++----
 omero/export_scripts/Make_Movie.py       | 2 +-
 omero/figure_scripts/ROI_Split_Figure.py | 2 +-
 omero/util_scripts/Move_Annotations.py   | 4 ++--
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/omero/analysis_scripts/Plot_Profile.py b/omero/analysis_scripts/Plot_Profile.py
index be04db1e6..4d2cabaab 100644
--- a/omero/analysis_scripts/Plot_Profile.py
+++ b/omero/analysis_scripts/Plot_Profile.py
@@ -107,13 +107,14 @@ def process_lines(conn, script_params, image, lines, line_width, fout):
         the_t = line['theT']
         the_z = line['theZ']
         roi_id = line['id']
-        if round(line['x1'] - line['x2']) == 0 and round(line['y1'] - line['y2']) == 0:
+        if round(line['x1'] - line['x2']) == 0 and round(line['y1'] - line['y2']) == 0:  # noqa
             continue
         for the_c in the_cs:
             line_data = []
-            line_data = roi_utils.get_line_data(pixels, l['x1'], l['y1'],
-                                                l['x2'], l['y2'], line_width,
-                                                the_z, the_c, the_t)
+            line_data = roi_utils.get_line_data(pixels, line['x1'], line['y1'],
+                                                line['x2'], line['y2'],
+                                                line_width, the_z, the_c,
+                                                the_t)
 
             if script_params['Sum_or_Average'] == 'Sum':
                 output_data = line_data.sum(axis=0)
diff --git a/omero/export_scripts/Make_Movie.py b/omero/export_scripts/Make_Movie.py
index f886135a3..b4dec6bd5 100644
--- a/omero/export_scripts/Make_Movie.py
+++ b/omero/export_scripts/Make_Movie.py
@@ -594,7 +594,7 @@ def write_movie(command_args, conn):
         movie_name = "%s.%s" % (movie_name, ext)
 
     # spaces etc in file name cause problems
-    movie_name = re.sub("[$&\;|\(\)<>' ]", "", movie_name)
+    movie_name = re.sub("[$&\\;|\\(\\)<>' ]", "", movie_name)
     frames_per_sec = 2
     if "FPS" in command_args:
         frames_per_sec = command_args["FPS"]
diff --git a/omero/figure_scripts/ROI_Split_Figure.py b/omero/figure_scripts/ROI_Split_Figure.py
index 0b0f61a37..c2cff9aee 100644
--- a/omero/figure_scripts/ROI_Split_Figure.py
+++ b/omero/figure_scripts/ROI_Split_Figure.py
@@ -660,7 +660,7 @@ def get_tags(name, tags_list, pd_list):
         try:
             height = int(h)
         except ValueError:
-            log("Invalid height: %s Using default value: %d" % (str(h), size_y))
+            log("Invalid height: %s Using default value: %d" % (str(h), size_y))  # noqa
 
     log("Image dimensions for all panels (pixels): width: %d  height: %d"
         % (width, height))
diff --git a/omero/util_scripts/Move_Annotations.py b/omero/util_scripts/Move_Annotations.py
index d3f76dce8..e2d2258ae 100644
--- a/omero/util_scripts/Move_Annotations.py
+++ b/omero/util_scripts/Move_Annotations.py
@@ -64,7 +64,7 @@ def move_well_annotations(conn, well, ann_type, remove_anns, ns):
     # Filter by type
     old_links = [link for link in old_links
                  if (ann_type is None
-                     or (l.child.__class__.__name__ == ann_type))]
+                     or (link.child.__class__.__name__ == ann_type))]
 
     link_ids = [link.id for link in old_links]
 
@@ -84,7 +84,7 @@ def get_key(ann_link, with_owner=False):
     # Find existing links on Well so we don't try to duplicate them
     existing_well_links = list(conn.getAnnotationLinks('Well', [well.id],
                                                        ns=ns, params=params))
-    existing_well_keys = [get_key(l) for link in existing_well_links]
+    existing_well_keys = [get_key(link) for link in existing_well_links]
 
     new_links = []
     for link in old_links:

From ab5df602e36e2a838edcb9427999e023cf7020dc Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 10 Jan 2024 12:28:48 +0000
Subject: [PATCH 08/21] replace getsize by getbbox

---
 omero/figure_scripts/Movie_Figure.py      |  6 +++---
 omero/figure_scripts/Movie_ROI_Figure.py  |  6 +++---
 omero/figure_scripts/ROI_Split_Figure.py  | 10 +++++-----
 omero/figure_scripts/Split_View_Figure.py |  8 ++++----
 omero/figure_scripts/Thumbnail_Figure.py  | 14 +++++++-------
 5 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/omero/figure_scripts/Movie_Figure.py b/omero/figure_scripts/Movie_Figure.py
index 815badda2..b8a4438a3 100644
--- a/omero/figure_scripts/Movie_Figure.py
+++ b/omero/figure_scripts/Movie_Figure.py
@@ -192,7 +192,7 @@ def createmovie_figure(conn, pixel_ids, t_indexes, z_start, z_end, width,
         col_count = min(max_col_count, len(rendered_images))
         row_count = int(math.ceil(len(rendered_images) / col_count))
         font = image_utils.get_font(width // 12)
-        font_height = font.getsize("Textq")[1]
+        font_height = font.getbbox("Textq")[3]
         canvas_width = ((width + spacer) * col_count) + spacer
         canvas_height = row_count * (spacer // 2 + font_height +
                                      spacer + height)
@@ -211,7 +211,7 @@ def createmovie_figure(conn, pixel_ids, t_indexes, z_start, z_end, width,
             if t_index >= size_t:
                 continue
             time = time_labels[t]
-            text_w = font.getsize(time)[0]
+            text_w = font.getbbox(time)[2]
             inset = (width - text_w) // 2
             textdraw = ImageDraw.Draw(canvas)
             textdraw.text((text_x+inset, text_y), time, font=font,
@@ -295,7 +295,7 @@ def add_left_labels(panel_canvas, image_labels, row_index, width, spacer):
     mode = "RGB"
     white = (255, 255, 255)
     font = image_utils.get_font(width/12)
-    text_height = font.getsize("Sampleq")[1]
+    text_height = font.getbbox("Sampleq")[3]
     text_gap = spacer / 2
 
     # find max number of labels
diff --git a/omero/figure_scripts/Movie_ROI_Figure.py b/omero/figure_scripts/Movie_ROI_Figure.py
index 0c02dbee9..69c51596d 100644
--- a/omero/figure_scripts/Movie_ROI_Figure.py
+++ b/omero/figure_scripts/Movie_ROI_Figure.py
@@ -203,7 +203,7 @@ def get_roi_movie_view(re, query_service, pixels, time_shape_map,
             row_count += 1
         col_count = max_columns
     font = image_utils.get_font(font_size)
-    text_height = font.getsize("Textq")[1]
+    text_height = font.getbbox("Textq")[3]
     # no spaces around panels
     canvas_width = ((panel_width + spacer) * col_count) - spacer
     row_height = rendered_images[0].size[1] + spacer + text_height
@@ -221,7 +221,7 @@ def get_roi_movie_view(re, query_service, pixels, time_shape_map,
     col = 0
     for i, img in enumerate(rendered_images):
         label = time_labels[i]
-        indent = (panel_width - (font.getsize(label)[0])) // 2
+        indent = (panel_width - (font.getbbox(label)[2])) // 2
         draw.text((px+indent, text_y), label, font=font, fill=(0, 0, 0))
         image_utils.paste_image(img, canvas, px, panel_y)
         if col == (col_count - 1):
@@ -381,7 +381,7 @@ def get_split_view(conn, image_ids, pixel_ids, merged_indexes, merged_colours,
     elif width > 200:
         font_size = 16
     font = image_utils.get_font(font_size)
-    text_height = font.getsize("Textq")[1]
+    text_height = font.getbbox("Textq")[3]
     max_count = 0
     for row in image_labels:
         max_count = max(max_count, len(row))
diff --git a/omero/figure_scripts/ROI_Split_Figure.py b/omero/figure_scripts/ROI_Split_Figure.py
index c2cff9aee..3e56dd85c 100644
--- a/omero/figure_scripts/ROI_Split_Figure.py
+++ b/omero/figure_scripts/ROI_Split_Figure.py
@@ -224,7 +224,7 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
 
     # now assemble the roi split-view canvas
     font = image_utils.get_font(fontsize)
-    text_height = font.getsize("Textq")[1]
+    text_height = font.getbbox("Textq")[3]
     top_spacer = 0
     if show_top_labels:
         if merged_names:
@@ -247,7 +247,7 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
     draw = ImageDraw.Draw(canvas)
     for i, index in enumerate(split_indexes):
         label = channel_names.get(index, index)
-        indent = (panel_width - (font.getsize(label)[0])) // 2
+        indent = (panel_width - (font.getbbox(label)[2])) // 2
         # text is coloured if channel is not coloured AND in the merged image
         rgb = (0, 0, 0)
         if index in merged_colours:
@@ -275,12 +275,12 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
                     name = channel_names[index]
                 else:
                     name = str(index)
-                comb_text_width = font.getsize(name)[0]
+                comb_text_width = font.getbbox(name)[2]
                 inset = int((panel_width - comb_text_width) / 2)
                 draw.text((px + inset, text_y), name, font=font, fill=rgb)
                 text_y = text_y - text_height
         else:
-            comb_text_width = font.getsize("Merged")[0]
+            comb_text_width = font.getbbox("Merged")[2]
             inset = int((panel_width - comb_text_width) / 2)
             draw.text((px + inset, text_y), "Merged", font=font,
                       fill=(0, 0, 0))
@@ -431,7 +431,7 @@ def get_split_view(conn, image_ids, pixel_ids, split_indexes, channel_names,
     elif width > 200:
         fontsize = 16
     font = image_utils.get_font(fontsize)
-    text_height = font.getsize("Textq")[1]
+    text_height = font.getbbox("Textq")[3]
     max_count = 0
     for row in image_labels:
         max_count = max(max_count, len(row))
diff --git a/omero/figure_scripts/Split_View_Figure.py b/omero/figure_scripts/Split_View_Figure.py
index 971343765..afa612673 100644
--- a/omero/figure_scripts/Split_View_Figure.py
+++ b/omero/figure_scripts/Split_View_Figure.py
@@ -386,7 +386,7 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
     font = image_utils.get_font(fontsize)
     mode = "RGB"
     white = (255, 255, 255)
-    text_height = font.getsize("Textq")[1]
+    text_height = font.getbbox("Textq")[3]
 
     # if adding text to the left, write the text on horizontal canvas, then
     # rotate to vertical (below)
@@ -442,7 +442,7 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
     py = top_text_height + spacer - (text_height + text_gap)
     for index in split_indexes:
         # calculate the position of the text, centered above the image
-        w = font.getsize(channel_names[index])[0]
+        w = font.getbbox(channel_names[index])[2]
         inset = int((width - w) // 2)
         # text is coloured if channel is grey AND in the merged image
         rgba = (0, 0, 0, 255)
@@ -465,12 +465,12 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
                 if rgba == (255, 255, 255, 255):  # if white (unreadable)
                     rgba = (0, 0, 0, 255)  # needs to be black!
             name = channel_names[index]
-            comb_text_width = font.getsize(name)[0]
+            comb_text_width = font.getbbox(name)[2]
             inset = int((width - comb_text_width) // 2)
             draw.text((px + inset, py), name, font=font, fill=rgba)
             py = py - text_height
     else:
-        comb_text_width = font.getsize("Merged")[0]
+        comb_text_width = font.getbbox("Merged")[2]
         inset = int((width - comb_text_width) // 2)
         px = px + inset
         draw.text((px, py), "Merged", font=font, fill=(0, 0, 0))
diff --git a/omero/figure_scripts/Thumbnail_Figure.py b/omero/figure_scripts/Thumbnail_Figure.py
index d303dcdf3..1dbbe1f18 100644
--- a/omero/figure_scripts/Thumbnail_Figure.py
+++ b/omero/figure_scripts/Thumbnail_Figure.py
@@ -144,10 +144,10 @@ def paint_thumbnail_grid(thumbnail_store, length, spacing, pixel_ids,
             fontsize = (length // 10) + 5
         font = get_font(fontsize)
         if left_label:
-            text_width, text_height = font.getsize(left_label)
+            text_width, text_height = font.getbbox(left_label)[2:]
             left_space = spacing + text_height + spacing
         if top_label:
-            text_width, text_height = font.getsize(top_label)
+            text_width, text_height = font.getbbox(top_label)[2:]
             top_space = spacing + text_height + spacing
             min_width = left_space + text_width + spacing
 
@@ -168,7 +168,7 @@ def paint_thumbnail_grid(thumbnail_store, length, spacing, pixel_ids,
         label_size = (label_canvas_width, label_canvas_height)
         text_canvas = Image.new(mode, label_size, bg)
         draw = ImageDraw.Draw(text_canvas)
-        text_width = font.getsize(left_label)[0]
+        text_width = font.getbbox(left_label)[2]
         text_x = (label_canvas_width - text_width) // 2
         draw.text((text_x, spacing), left_label, font=font, fill=text_color)
         vertical_canvas = text_canvas.rotate(90)
@@ -297,7 +297,7 @@ def paint_dataset_canvas(conn, images, title, tag_ids=None,
     # set-up fonts
     fontsize = length/7 + 5
     font = get_font(fontsize)
-    text_height = font.getsize("Textq")[1]
+    text_height = font.getbbox("Textq")[3]
     top_spacer = spacing + text_height
     left_spacer = spacing + text_height
 
@@ -372,11 +372,11 @@ def paint_dataset_canvas(conn, images, title, tag_ids=None,
             'showSubsetLabels': show_subset_labels})
 
         # Find the indent we need
-        max_tag_name_width = max([font.getsize(ts['tagText'])[0]
+        max_tag_name_width = max([font.getbbox(ts['tagText'])[2]
                                  for ts in toptag_sets])
         if show_untagged:
             max_tag_name_width = max(max_tag_name_width,
-                                     font.getsize("Not Tagged")[0])
+                                     font.getbbox("Not Tagged")[2])
 
         tag_sub_panes = []
 
@@ -435,7 +435,7 @@ def make_tagset_canvas(tag_string, tagset_pix_ids, show_subset_labels):
                 p_y += pane.size[1]
             if tag_text is not None:
                 draw = ImageDraw.Draw(tag_canvas)
-                tt_w, tt_h = font.getsize(tag_text)
+                tt_w, tt_h = font.getbbox(tag_text)[2:]
                 h_offset = (total_height - tt_h)/2
                 draw.text((spacing, h_offset), tag_text, font=font,
                           fill=(50, 50, 50))

From 46081bba7fa28cd62f6b58314c1bf80accffa232 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 10 Jan 2024 13:20:33 +0000
Subject: [PATCH 09/21] replace textsize by textbbox

---
 omero/figure_scripts/Movie_Figure.py      | 2 +-
 omero/figure_scripts/Split_View_Figure.py | 2 +-
 omero/figure_scripts/Thumbnail_Figure.py  | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/omero/figure_scripts/Movie_Figure.py b/omero/figure_scripts/Movie_Figure.py
index b8a4438a3..d84f8b7a9 100644
--- a/omero/figure_scripts/Movie_Figure.py
+++ b/omero/figure_scripts/Movie_Figure.py
@@ -313,7 +313,7 @@ def add_left_labels(panel_canvas, image_labels, row_index, width, spacer):
     py = left_text_height - text_gap  # start at bottom
     for count, label in enumerate(labels):
         py = py - text_height    # find the top of this row
-        w = textdraw.textsize(label, font=font)[0]
+        w = textdraw.textbbox(label, font=font)[2]
         inset = int((left_text_width - w) / 2)
         textdraw.text((inset, py), label, font=font, fill=(0, 0, 0))
         py = py - text_gap    # add space between rows
diff --git a/omero/figure_scripts/Split_View_Figure.py b/omero/figure_scripts/Split_View_Figure.py
index afa612673..2998760df 100644
--- a/omero/figure_scripts/Split_View_Figure.py
+++ b/omero/figure_scripts/Split_View_Figure.py
@@ -406,7 +406,7 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
             py = left_text_width - text_gap  # start at bottom
             for count, label in enumerate(row):
                 py = py - text_height    # find the top of this row
-                w = textdraw.textsize(label, font=font)[0]
+                w = textdraw.textbbox(label, font=font)[2]
                 inset = int((height - w) // 2)
                 textdraw.text((px+inset, py), label, font=font,
                               fill=(0, 0, 0))
diff --git a/omero/figure_scripts/Thumbnail_Figure.py b/omero/figure_scripts/Thumbnail_Figure.py
index 1dbbe1f18..7fdd6e93d 100644
--- a/omero/figure_scripts/Thumbnail_Figure.py
+++ b/omero/figure_scripts/Thumbnail_Figure.py
@@ -476,8 +476,8 @@ def make_tagset_canvas(tag_string, tagset_pix_ids, show_subset_labels):
     #     figureDate = "%s - %s" % (firstdate, lastdate)
 
     draw = ImageDraw.Draw(full_canvas)
-    # dateWidth = draw.textsize(figureDate, font=font)[0]
-    # titleWidth = draw.textsize(title, font=font)[0]
+    # dateWidth = draw.textbbox(figureDate, font=font)[2]
+    # titleWidth = draw.textbbox(title, font=font)[2]
     # dateX = fullCanvas.size[0] - spacing - dateWidth
     # title
     draw.text((left_spacer, spacing), title, font=font, fill=(0, 0, 0))

From 10ba321cf39dec06a2a0fe0a22cd78aef7bc5be9 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 10 Jan 2024 13:23:22 +0000
Subject: [PATCH 10/21] replace ANTIALIAS by LANCZOS

---
 omero/export_scripts/Batch_Image_Export.py | 4 ++--
 omero/export_scripts/Make_Movie.py         | 2 +-
 omero/figure_scripts/ROI_Split_Figure.py   | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/omero/export_scripts/Batch_Image_Export.py b/omero/export_scripts/Batch_Image_Export.py
index 6f1ec1d28..f4fdd4747 100644
--- a/omero/export_scripts/Batch_Image_Export.py
+++ b/omero/export_scripts/Batch_Image_Export.py
@@ -123,7 +123,7 @@ def save_plane(image, format, c_name, z_range, project_z, t=0, channel=None,
         w, h = plane.size
         fraction = (float(zoom_percent) / 100)
         plane = plane.resize((int(w * fraction), int(h * fraction)),
-                             Image.ANTIALIAS)
+                             Image.LANCZOS)
 
     if format == "PNG":
         img_name = make_image_name(
@@ -572,7 +572,7 @@ def run_script():
         scripts.String(
             "Zoom", grouping="7", values=zoom_percents,
             description="Zoom (jpeg, png or tiff) before saving with"
-            " ANTIALIAS interpolation", default="100%"),
+            " LANCZOS interpolation", default="100%"),
 
         scripts.String(
             "Format", grouping="8",
diff --git a/omero/export_scripts/Make_Movie.py b/omero/export_scripts/Make_Movie.py
index b4dec6bd5..bd3c096eb 100644
--- a/omero/export_scripts/Make_Movie.py
+++ b/omero/export_scripts/Make_Movie.py
@@ -355,7 +355,7 @@ def reshape_to_fit(image, size_x, size_y, bg=(0, 0, 0)):
     # scale
     ratio = min(float(size_x) / image_w, float(size_y) / image_h)
     image = image.resize(map(lambda x: int(x*ratio), image.size),
-                         Image.ANTIALIAS)
+                         Image.LANCZOS)
     # paste
     bg = Image.new("RGBA", (size_x, size_y), (0, 0, 0))     # black bg
     ovlpos = (size_x-image.size[0]) / 2, (size_y-image.size[1]) / 2
diff --git a/omero/figure_scripts/ROI_Split_Figure.py b/omero/figure_scripts/ROI_Split_Figure.py
index 3e56dd85c..db84e30bf 100644
--- a/omero/figure_scripts/ROI_Split_Figure.py
+++ b/omero/figure_scripts/ROI_Split_Figure.py
@@ -180,7 +180,7 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
                 # hoping that when we zoom, don't zoom fullImage
             if roi_zoom != 1:
                 new_size = (int(roi_width*roi_zoom), int(roi_height*roi_zoom))
-                roi_image = roi_image.resize(new_size, Image.ANTIALIAS)
+                roi_image = roi_image.resize(new_size, Image.LANCZOS)
             rendered_images.append(roi_image)
             panel_width = roi_image.size[0]
             re.setActive(index, False)  # turn the channel off again!
@@ -213,7 +213,7 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
 
     if roi_zoom != 1:
         new_size = (int(roi_width*roi_zoom), int(roi_height*roi_zoom))
-        roi_merged_image = roi_merged_image.resize(new_size, Image.ANTIALIAS)
+        roi_merged_image = roi_merged_image.resize(new_size, Image.LANCZOS)
 
     if channel_mismatch:
         log(" WARNING channel mismatch: The current image has fewer channels"

From 030a841623272e78613d6e59447232bb69ad5257 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 10 Jan 2024 15:25:15 +0000
Subject: [PATCH 11/21] use textlength

---
 omero/figure_scripts/Movie_Figure.py      | 2 +-
 omero/figure_scripts/Split_View_Figure.py | 2 +-
 omero/figure_scripts/Thumbnail_Figure.py  | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/omero/figure_scripts/Movie_Figure.py b/omero/figure_scripts/Movie_Figure.py
index d84f8b7a9..9dfd21f82 100644
--- a/omero/figure_scripts/Movie_Figure.py
+++ b/omero/figure_scripts/Movie_Figure.py
@@ -313,7 +313,7 @@ def add_left_labels(panel_canvas, image_labels, row_index, width, spacer):
     py = left_text_height - text_gap  # start at bottom
     for count, label in enumerate(labels):
         py = py - text_height    # find the top of this row
-        w = textdraw.textbbox(label, font=font)[2]
+        w = textdraw.textlength(label, font=font)
         inset = int((left_text_width - w) / 2)
         textdraw.text((inset, py), label, font=font, fill=(0, 0, 0))
         py = py - text_gap    # add space between rows
diff --git a/omero/figure_scripts/Split_View_Figure.py b/omero/figure_scripts/Split_View_Figure.py
index 2998760df..eb06da484 100644
--- a/omero/figure_scripts/Split_View_Figure.py
+++ b/omero/figure_scripts/Split_View_Figure.py
@@ -406,7 +406,7 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
             py = left_text_width - text_gap  # start at bottom
             for count, label in enumerate(row):
                 py = py - text_height    # find the top of this row
-                w = textdraw.textbbox(label, font=font)[2]
+                w = textdraw.textlength(label, font=font)
                 inset = int((height - w) // 2)
                 textdraw.text((px+inset, py), label, font=font,
                               fill=(0, 0, 0))
diff --git a/omero/figure_scripts/Thumbnail_Figure.py b/omero/figure_scripts/Thumbnail_Figure.py
index 7fdd6e93d..025d67087 100644
--- a/omero/figure_scripts/Thumbnail_Figure.py
+++ b/omero/figure_scripts/Thumbnail_Figure.py
@@ -476,8 +476,8 @@ def make_tagset_canvas(tag_string, tagset_pix_ids, show_subset_labels):
     #     figureDate = "%s - %s" % (firstdate, lastdate)
 
     draw = ImageDraw.Draw(full_canvas)
-    # dateWidth = draw.textbbox(figureDate, font=font)[2]
-    # titleWidth = draw.textbbox(title, font=font)[2]
+    # dateWidth = draw.textlength(figureDate, font=font)
+    # titleWidth = draw.textlength(title, font=font)
     # dateX = fullCanvas.size[0] - spacing - dateWidth
     # title
     draw.text((left_spacer, spacing), title, font=font, fill=(0, 0, 0))

From cd7f4a3e86cce35280cdef36d941034066c35123 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 11 Jan 2024 07:55:30 +0000
Subject: [PATCH 12/21] use branch

---
 .github/workflows/omero_plugin.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/omero_plugin.yml b/.github/workflows/omero_plugin.yml
index 40b601e9e..e70759e87 100644
--- a/.github/workflows/omero_plugin.yml
+++ b/.github/workflows/omero_plugin.yml
@@ -27,8 +27,9 @@ jobs:
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:
-          repository: ome/omero-test-infra
+          repository: jburel/omero-test-infra
           path: .omero
-          ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
+          ref: test_omero-py
+          # ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
       - name: Build and run OMERO tests
         run: .omero/docker $STAGE

From f9a6048ea7423f349864c393b4d43fef2c78f29f Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 11 Jan 2024 11:42:00 +0000
Subject: [PATCH 13/21] use getbbox to determine size

---
 omero/figure_scripts/Movie_Figure.py      |  9 +++++---
 omero/figure_scripts/Movie_ROI_Figure.py  |  9 +++++---
 omero/figure_scripts/ROI_Split_Figure.py  | 15 ++++++++-----
 omero/figure_scripts/Split_View_Figure.py | 12 ++++++----
 omero/figure_scripts/Thumbnail_Figure.py  | 27 +++++++++++++++--------
 5 files changed, 48 insertions(+), 24 deletions(-)

diff --git a/omero/figure_scripts/Movie_Figure.py b/omero/figure_scripts/Movie_Figure.py
index 9dfd21f82..8593e1979 100644
--- a/omero/figure_scripts/Movie_Figure.py
+++ b/omero/figure_scripts/Movie_Figure.py
@@ -192,7 +192,8 @@ def createmovie_figure(conn, pixel_ids, t_indexes, z_start, z_end, width,
         col_count = min(max_col_count, len(rendered_images))
         row_count = int(math.ceil(len(rendered_images) / col_count))
         font = image_utils.get_font(width // 12)
-        font_height = font.getbbox("Textq")[3]
+        box = font.getbbox("Textq")
+        font_height = box[3] - box[1]
         canvas_width = ((width + spacer) * col_count) + spacer
         canvas_height = row_count * (spacer // 2 + font_height +
                                      spacer + height)
@@ -211,7 +212,8 @@ def createmovie_figure(conn, pixel_ids, t_indexes, z_start, z_end, width,
             if t_index >= size_t:
                 continue
             time = time_labels[t]
-            text_w = font.getbbox(time)[2]
+            box = font.getbbox(time)
+            text_w = box[2] - box[0]
             inset = (width - text_w) // 2
             textdraw = ImageDraw.Draw(canvas)
             textdraw.text((text_x+inset, text_y), time, font=font,
@@ -295,7 +297,8 @@ def add_left_labels(panel_canvas, image_labels, row_index, width, spacer):
     mode = "RGB"
     white = (255, 255, 255)
     font = image_utils.get_font(width/12)
-    text_height = font.getbbox("Sampleq")[3]
+    box = font.getbbox("Sampleq")
+    text_height = box[3] - box[1]
     text_gap = spacer / 2
 
     # find max number of labels
diff --git a/omero/figure_scripts/Movie_ROI_Figure.py b/omero/figure_scripts/Movie_ROI_Figure.py
index 69c51596d..dc2e97597 100644
--- a/omero/figure_scripts/Movie_ROI_Figure.py
+++ b/omero/figure_scripts/Movie_ROI_Figure.py
@@ -203,7 +203,8 @@ def get_roi_movie_view(re, query_service, pixels, time_shape_map,
             row_count += 1
         col_count = max_columns
     font = image_utils.get_font(font_size)
-    text_height = font.getbbox("Textq")[3]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     # no spaces around panels
     canvas_width = ((panel_width + spacer) * col_count) - spacer
     row_height = rendered_images[0].size[1] + spacer + text_height
@@ -221,7 +222,8 @@ def get_roi_movie_view(re, query_service, pixels, time_shape_map,
     col = 0
     for i, img in enumerate(rendered_images):
         label = time_labels[i]
-        indent = (panel_width - (font.getbbox(label)[2])) // 2
+        box = font.getbbox(label)
+        indent = (panel_width - (box[2] - box[0])) // 2
         draw.text((px+indent, text_y), label, font=font, fill=(0, 0, 0))
         image_utils.paste_image(img, canvas, px, panel_y)
         if col == (col_count - 1):
@@ -381,7 +383,8 @@ def get_split_view(conn, image_ids, pixel_ids, merged_indexes, merged_colours,
     elif width > 200:
         font_size = 16
     font = image_utils.get_font(font_size)
-    text_height = font.getbbox("Textq")[3]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     max_count = 0
     for row in image_labels:
         max_count = max(max_count, len(row))
diff --git a/omero/figure_scripts/ROI_Split_Figure.py b/omero/figure_scripts/ROI_Split_Figure.py
index db84e30bf..5c534719a 100644
--- a/omero/figure_scripts/ROI_Split_Figure.py
+++ b/omero/figure_scripts/ROI_Split_Figure.py
@@ -224,7 +224,8 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
 
     # now assemble the roi split-view canvas
     font = image_utils.get_font(fontsize)
-    text_height = font.getbbox("Textq")[3]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     top_spacer = 0
     if show_top_labels:
         if merged_names:
@@ -247,7 +248,8 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
     draw = ImageDraw.Draw(canvas)
     for i, index in enumerate(split_indexes):
         label = channel_names.get(index, index)
-        indent = (panel_width - (font.getbbox(label)[2])) // 2
+        box = font.getbbox(label)
+        indent = (panel_width - (box[2] - box[0])) // 2
         # text is coloured if channel is not coloured AND in the merged image
         rgb = (0, 0, 0)
         if index in merged_colours:
@@ -275,12 +277,14 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
                     name = channel_names[index]
                 else:
                     name = str(index)
-                comb_text_width = font.getbbox(name)[2]
+                box = font.getbbox(name)
+                comb_text_width = box[2] - box[0]
                 inset = int((panel_width - comb_text_width) / 2)
                 draw.text((px + inset, text_y), name, font=font, fill=rgb)
                 text_y = text_y - text_height
         else:
-            comb_text_width = font.getbbox("Merged")[2]
+            box = font.getbbox("Merged")
+            comb_text_width = box[2] - box[0]
             inset = int((panel_width - comb_text_width) / 2)
             draw.text((px + inset, text_y), "Merged", font=font,
                       fill=(0, 0, 0))
@@ -431,7 +435,8 @@ def get_split_view(conn, image_ids, pixel_ids, split_indexes, channel_names,
     elif width > 200:
         fontsize = 16
     font = image_utils.get_font(fontsize)
-    text_height = font.getbbox("Textq")[3]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     max_count = 0
     for row in image_labels:
         max_count = max(max_count, len(row))
diff --git a/omero/figure_scripts/Split_View_Figure.py b/omero/figure_scripts/Split_View_Figure.py
index eb06da484..293a6dcaa 100644
--- a/omero/figure_scripts/Split_View_Figure.py
+++ b/omero/figure_scripts/Split_View_Figure.py
@@ -386,7 +386,8 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
     font = image_utils.get_font(fontsize)
     mode = "RGB"
     white = (255, 255, 255)
-    text_height = font.getbbox("Textq")[3]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
 
     # if adding text to the left, write the text on horizontal canvas, then
     # rotate to vertical (below)
@@ -442,7 +443,8 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
     py = top_text_height + spacer - (text_height + text_gap)
     for index in split_indexes:
         # calculate the position of the text, centered above the image
-        w = font.getbbox(channel_names[index])[2]
+        box = font.getbbox(channel_names[index])
+        w = box[2] - box[0]
         inset = int((width - w) // 2)
         # text is coloured if channel is grey AND in the merged image
         rgba = (0, 0, 0, 255)
@@ -465,12 +467,14 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
                 if rgba == (255, 255, 255, 255):  # if white (unreadable)
                     rgba = (0, 0, 0, 255)  # needs to be black!
             name = channel_names[index]
-            comb_text_width = font.getbbox(name)[2]
+            box = font.getbbox(name)
+            comb_text_width = box[2] - box[0]
             inset = int((width - comb_text_width) // 2)
             draw.text((px + inset, py), name, font=font, fill=rgba)
             py = py - text_height
     else:
-        comb_text_width = font.getbbox("Merged")[2]
+        box = font.getbbox("Merged")
+        comb_text_width = box[2] - box[0]
         inset = int((width - comb_text_width) // 2)
         px = px + inset
         draw.text((px, py), "Merged", font=font, fill=(0, 0, 0))
diff --git a/omero/figure_scripts/Thumbnail_Figure.py b/omero/figure_scripts/Thumbnail_Figure.py
index 025d67087..95fc6e978 100644
--- a/omero/figure_scripts/Thumbnail_Figure.py
+++ b/omero/figure_scripts/Thumbnail_Figure.py
@@ -144,10 +144,14 @@ def paint_thumbnail_grid(thumbnail_store, length, spacing, pixel_ids,
             fontsize = (length // 10) + 5
         font = get_font(fontsize)
         if left_label:
-            text_width, text_height = font.getbbox(left_label)[2:]
+            box = font.getbbox(left_label)
+            text_width = box[2] - box[0]
+            text_height = box[3] - box[1]
             left_space = spacing + text_height + spacing
         if top_label:
-            text_width, text_height = font.getbbox(top_label)[2:]
+            box = font.getbbox(top_label)
+            text_width = box[2] - box[0]
+            text_height = box[3] - box[1]
             top_space = spacing + text_height + spacing
             min_width = left_space + text_width + spacing
 
@@ -168,7 +172,8 @@ def paint_thumbnail_grid(thumbnail_store, length, spacing, pixel_ids,
         label_size = (label_canvas_width, label_canvas_height)
         text_canvas = Image.new(mode, label_size, bg)
         draw = ImageDraw.Draw(text_canvas)
-        text_width = font.getbbox(left_label)[2]
+        box = font.getbbox(left_label)
+        text_width = box[2] - box[0]
         text_x = (label_canvas_width - text_width) // 2
         draw.text((text_x, spacing), left_label, font=font, fill=text_color)
         vertical_canvas = text_canvas.rotate(90)
@@ -297,7 +302,8 @@ def paint_dataset_canvas(conn, images, title, tag_ids=None,
     # set-up fonts
     fontsize = length/7 + 5
     font = get_font(fontsize)
-    text_height = font.getbbox("Textq")[3]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     top_spacer = spacing + text_height
     left_spacer = spacing + text_height
 
@@ -372,11 +378,12 @@ def paint_dataset_canvas(conn, images, title, tag_ids=None,
             'showSubsetLabels': show_subset_labels})
 
         # Find the indent we need
-        max_tag_name_width = max([font.getbbox(ts['tagText'])[2]
-                                 for ts in toptag_sets])
+        for ts in toptag_sets:
+            box = font.getbbox(ts['tagText'])
+            max_tag_name_width = max(box[2] - box[0])
         if show_untagged:
-            max_tag_name_width = max(max_tag_name_width,
-                                     font.getbbox("Not Tagged")[2])
+            box = font.getbbox("Not Tagged")
+            max_tag_name_width = max(max_tag_name_width, (box[2] - box[0]))
 
         tag_sub_panes = []
 
@@ -435,7 +442,9 @@ def make_tagset_canvas(tag_string, tagset_pix_ids, show_subset_labels):
                 p_y += pane.size[1]
             if tag_text is not None:
                 draw = ImageDraw.Draw(tag_canvas)
-                tt_w, tt_h = font.getbbox(tag_text)[2:]
+                box = font.getbbox(tag_text)
+                tt_w = box[2] - box[0]
+                tt_h = box[3] - box[1]
                 h_offset = (total_height - tt_h)/2
                 draw.text((spacing, h_offset), tag_text, font=font,
                           fill=(50, 50, 50))

From b26d67a20908f754fca2467b42da04d2b5035edf Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Wed, 17 Jan 2024 11:16:41 +0000
Subject: [PATCH 14/21] use branch

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

diff --git a/.github/workflows/omero_plugin.yml b/.github/workflows/omero_plugin.yml
index e70759e87..72635a09c 100644
--- a/.github/workflows/omero_plugin.yml
+++ b/.github/workflows/omero_plugin.yml
@@ -29,7 +29,7 @@ jobs:
         with:
           repository: jburel/omero-test-infra
           path: .omero
-          ref: test_omero-py
+          ref: use_latest_omero_py
           # ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
       - name: Build and run OMERO tests
         run: .omero/docker $STAGE

From c651c496000386bbb23f6bd449a935d62dd25e16 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 1 Feb 2024 15:30:45 +0000
Subject: [PATCH 15/21] use the main branch

---
 .github/workflows/omero_plugin.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/omero_plugin.yml b/.github/workflows/omero_plugin.yml
index 72635a09c..40b601e9e 100644
--- a/.github/workflows/omero_plugin.yml
+++ b/.github/workflows/omero_plugin.yml
@@ -27,9 +27,8 @@ jobs:
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:
-          repository: jburel/omero-test-infra
+          repository: ome/omero-test-infra
           path: .omero
-          ref: use_latest_omero_py
-          # ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
+          ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
       - name: Build and run OMERO tests
         run: .omero/docker $STAGE

From 85c3c0c9534e081bbf8c5679be3d1336edec5c71 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 1 Feb 2024 15:35:02 +0000
Subject: [PATCH 16/21] remove unused variable

---
 omero/figure_scripts/Thumbnail_Figure.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/omero/figure_scripts/Thumbnail_Figure.py b/omero/figure_scripts/Thumbnail_Figure.py
index 95fc6e978..b06f76b50 100644
--- a/omero/figure_scripts/Thumbnail_Figure.py
+++ b/omero/figure_scripts/Thumbnail_Figure.py
@@ -443,7 +443,6 @@ def make_tagset_canvas(tag_string, tagset_pix_ids, show_subset_labels):
             if tag_text is not None:
                 draw = ImageDraw.Draw(tag_canvas)
                 box = font.getbbox(tag_text)
-                tt_w = box[2] - box[0]
                 tt_h = box[3] - box[1]
                 h_offset = (total_height - tt_h)/2
                 draw.text((spacing, h_offset), tag_text, font=font,

From e1407cce7658d69ab7f6f00517ae6f579c841c04 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 1 Feb 2024 15:58:05 +0000
Subject: [PATCH 17/21] add missing value

---
 omero/figure_scripts/Thumbnail_Figure.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/omero/figure_scripts/Thumbnail_Figure.py b/omero/figure_scripts/Thumbnail_Figure.py
index b06f76b50..9abd2c504 100644
--- a/omero/figure_scripts/Thumbnail_Figure.py
+++ b/omero/figure_scripts/Thumbnail_Figure.py
@@ -380,7 +380,7 @@ def paint_dataset_canvas(conn, images, title, tag_ids=None,
         # Find the indent we need
         for ts in toptag_sets:
             box = font.getbbox(ts['tagText'])
-            max_tag_name_width = max(box[2] - box[0])
+            max_tag_name_width = max(max_tag_name_width, box[2] - box[0])
         if show_untagged:
             box = font.getbbox("Not Tagged")
             max_tag_name_width = max(max_tag_name_width, (box[2] - box[0]))

From 06984bf63d28cd975e9022916f6bcc401ac28fd8 Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 1 Feb 2024 16:04:38 +0000
Subject: [PATCH 18/21] set default

---
 omero/figure_scripts/Thumbnail_Figure.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/omero/figure_scripts/Thumbnail_Figure.py b/omero/figure_scripts/Thumbnail_Figure.py
index 9abd2c504..0f905b1c5 100644
--- a/omero/figure_scripts/Thumbnail_Figure.py
+++ b/omero/figure_scripts/Thumbnail_Figure.py
@@ -378,6 +378,7 @@ def paint_dataset_canvas(conn, images, title, tag_ids=None,
             'showSubsetLabels': show_subset_labels})
 
         # Find the indent we need
+        max_tag_name_width = 0
         for ts in toptag_sets:
             box = font.getbbox(ts['tagText'])
             max_tag_name_width = max(max_tag_name_width, box[2] - box[0])

From f7f368d8223fd8080cb20cd352b782f841b3ee8d Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 1 Feb 2024 16:59:53 +0000
Subject: [PATCH 19/21] exclude script for now

---
 test/integration/test_util_scripts.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/integration/test_util_scripts.py b/test/integration/test_util_scripts.py
index 63a716ddd..42b7cb53d 100644
--- a/test/integration/test_util_scripts.py
+++ b/test/integration/test_util_scripts.py
@@ -198,6 +198,7 @@ def test_dataset_to_plate(self, image_names):
         images_in_plate.sort()
         assert images_in_plate == image_ids
 
+    @pytest.mark.skip(reason="Issue with moving annotation on well")
     @pytest.mark.parametrize("remove", [True, False])
     @pytest.mark.parametrize("script_runner", ['user', 'admin'])
     def test_move_annotations(self, remove, script_runner):

From e5853229d30cf262ddfb0386f799a3f8133d3b1f Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 1 Feb 2024 20:11:47 +0000
Subject: [PATCH 20/21] fix parameter

---
 omero/util_scripts/Move_Annotations.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/omero/util_scripts/Move_Annotations.py b/omero/util_scripts/Move_Annotations.py
index e2d2258ae..a57583905 100644
--- a/omero/util_scripts/Move_Annotations.py
+++ b/omero/util_scripts/Move_Annotations.py
@@ -87,17 +87,17 @@ def get_key(ann_link, with_owner=False):
     existing_well_keys = [get_key(link) for link in existing_well_links]
 
     new_links = []
-    for link in old_links:
-        if get_key(link) in existing_well_keys:
+    for old_link in old_links:
+        if get_key(old_link) in existing_well_keys:
             continue
-        log("    Annotation: %s %s" % (link.child.id.val,
-                                       link.child.__class__.__name__))
+        log("    Annotation: %s %s" % (old_link.child.id.val,
+                                       old_link.child.__class__.__name__))
         link = WellAnnotationLinkI()
         link.parent = WellI(well.id, False)
-        link.child = link.child
+        link.child = old_link.child
         # If Admin, the new link Owner is same as old link Owner
         if conn.isAdmin():
-            owner_id = link.details.owner.id.val
+            owner_id = old_link.details.owner.id.val
             link.details.owner = ExperimenterI(owner_id, False)
         new_links.append(link)
     try:

From 92d3bd19e713dd4fe70b53d9697ab192bc5254cd Mon Sep 17 00:00:00 2001
From: Jean-Marie Burel <j.burel@dundee.ac.uk>
Date: Thu, 1 Feb 2024 20:12:15 +0000
Subject: [PATCH 21/21] enable test

---
 test/integration/test_util_scripts.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/integration/test_util_scripts.py b/test/integration/test_util_scripts.py
index 42b7cb53d..63a716ddd 100644
--- a/test/integration/test_util_scripts.py
+++ b/test/integration/test_util_scripts.py
@@ -198,7 +198,6 @@ def test_dataset_to_plate(self, image_names):
         images_in_plate.sort()
         assert images_in_plate == image_ids
 
-    @pytest.mark.skip(reason="Issue with moving annotation on well")
     @pytest.mark.parametrize("remove", [True, False])
     @pytest.mark.parametrize("script_runner", ['user', 'admin'])
     def test_move_annotations(self, remove, script_runner):