From 743e0f4b4bcdfc6084fae8b37a8b327405c56e79 Mon Sep 17 00:00:00 2001
From: Beth Cimini <bethac07@users.noreply.github.com>
Date: Tue, 23 Jul 2024 19:00:34 +0100
Subject: [PATCH 01/35] Bump centrosome

---
 setup.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/setup.py b/setup.py
index ea2665d3de..bf2d8e4da4 100644
--- a/setup.py
+++ b/setup.py
@@ -62,9 +62,9 @@ def package_data():
         "test": ["pytest>=3.3.2,<4"],
     },
     install_requires=[
-        "boto3==1.14.23",
-        "cellprofiler-core",
-        "centrosome==1.2.2",
+        "boto3>=1.12.28",
+        "cellprofiler-core==4.2.6",
+        "centrosome==1.2.3",
         "docutils==0.15.2",
         "h5py==3.6.0",
         "imageio==2.34.0",

From 84e6ad7c0632181b17f4eeeed4fe5b4af43f4b43 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Tue, 23 Jul 2024 23:31:53 +0100
Subject: [PATCH 02/35] Bump core

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index bf2d8e4da4..d56a5f5edb 100644
--- a/setup.py
+++ b/setup.py
@@ -63,7 +63,7 @@ def package_data():
     },
     install_requires=[
         "boto3>=1.12.28",
-        "cellprofiler-core==4.2.6",
+        "cellprofiler-core==4.2.7",
         "centrosome==1.2.3",
         "docutils==0.15.2",
         "h5py==3.6.0",

From 8d6ad4701abf6993bd5c20603b882121c6bb8606 Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Tue, 23 Jul 2024 11:43:31 -0400
Subject: [PATCH 03/35] Fix 3D display in MeasureImageOverlap

---
 cellprofiler/modules/measureimageoverlap.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/cellprofiler/modules/measureimageoverlap.py b/cellprofiler/modules/measureimageoverlap.py
index 72e4c41e23..7cf48128af 100644
--- a/cellprofiler/modules/measureimageoverlap.py
+++ b/cellprofiler/modules/measureimageoverlap.py
@@ -310,6 +310,9 @@ def run(self, workspace):
 
         # In volumetric case the 3D image stack gets converted to a long 2D image and gets analyzed
         if ground_truth_image.volumetric:
+
+            orig_shape = ground_truth_pixels.shape
+            
             ground_truth_pixels = ground_truth_pixels.reshape(
                 -1, ground_truth_pixels.shape[-1]
             )
@@ -451,6 +454,15 @@ def run(self, workspace):
             )
 
         if self.show_window:
+
+            workspace.display_data.dimensions = test_image.dimensions
+
+            if ground_truth_image.volumetric:
+                true_positives = true_positives.reshape(orig_shape)
+                true_negatives = true_negatives.reshape(orig_shape)
+                false_positives = false_positives.reshape(orig_shape)
+                false_negatives = false_negatives.reshape(orig_shape)
+
             workspace.display_data.true_positives = true_positives
 
             workspace.display_data.true_negatives = true_negatives
@@ -741,7 +753,7 @@ def get_weights(self, i, j, labels_mask):
 
     def display(self, workspace, figure):
         """Display the image confusion matrix & statistics"""
-        figure.set_subplots((3, 2))
+        figure.set_subplots((3, 2),dimensions=workspace.display_data.dimensions)
 
         for x, y, image, label in (
             (0, 0, workspace.display_data.true_positives, "True positives"),

From a700ec06a8f4a9b0191113386fc4d505395489eb Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Tue, 23 Jul 2024 15:33:46 -0400
Subject: [PATCH 04/35] fix measurment specification

---
 cellprofiler/modules/measureimageskeleton.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cellprofiler/modules/measureimageskeleton.py b/cellprofiler/modules/measureimageskeleton.py
index 7290a06cb8..9e07e941a7 100644
--- a/cellprofiler/modules/measureimageskeleton.py
+++ b/cellprofiler/modules/measureimageskeleton.py
@@ -199,8 +199,8 @@ def get_measurements(self, pipeline, object_name, category):
 
         if object_name == "Image" and category == "Skeleton":
             return [
-                "Skeleton_Branches_{}".format(name),
-                "Skeleton_Endpoints_{}".format(name),
+                "Branches",
+                "Endpoints"
             ]
 
         return []

From 0473eb335a29b443bc9de76c8a776b17ee7e879e Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Thu, 25 Jul 2024 14:02:25 -0400
Subject: [PATCH 05/35] fix bad tests

---
 tests/modules/test_measureimageskeleton.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/test_measureimageskeleton.py b/tests/modules/test_measureimageskeleton.py
index 24f6ffaeca..e69865251a 100644
--- a/tests/modules/test_measureimageskeleton.py
+++ b/tests/modules/test_measureimageskeleton.py
@@ -87,7 +87,7 @@ def test_get_measurement_columns(module, pipeline):
 def test_get_measurements_image_skeleton(module, pipeline):
     module.skeleton_name.value = "example"
 
-    expected_measurements = ["Skeleton_Branches_example", "Skeleton_Endpoints_example"]
+    expected_measurements = ["Branches", "Endpoints"]
 
     measurements = module.get_measurements(
         pipeline, "Image", "Skeleton"
@@ -127,7 +127,7 @@ def test_get_measurement_images(module, pipeline):
         pipeline,
         "Image",
         "Skeleton",
-        "Skeleton_Branches_example",
+        "Branches",
     )
 
     assert images == expected_images

From ce762ae262dfee5195543b2a76256fd933071ffd Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Tue, 23 Jul 2024 18:46:28 -0400
Subject: [PATCH 06/35] scale value

---
 cellprofiler/modules/measureimagequality.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cellprofiler/modules/measureimagequality.py b/cellprofiler/modules/measureimagequality.py
index b1192a56b7..44e695f25d 100644
--- a/cellprofiler/modules/measureimagequality.py
+++ b/cellprofiler/modules/measureimagequality.py
@@ -1036,7 +1036,7 @@ def get_measurement_scales(
                         if image_names in self.images_to_process(
                             image_group, None, pipeline
                         ):
-                            result += [scale_group.scale]
+                            result += [scale_group.scale.value]
                 return result
             if measurement.startswith(F_THRESHOLD):
                 result = []

From aaa863da6b206f63ad13cc997114d329a73a596c Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Thu, 25 Jul 2024 08:22:05 -0400
Subject: [PATCH 07/35] remove tuple wrapping of labels

---
 cellprofiler/modules/classifyobjects.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cellprofiler/modules/classifyobjects.py b/cellprofiler/modules/classifyobjects.py
index 61028209b7..352bc2f78e 100644
--- a/cellprofiler/modules/classifyobjects.py
+++ b/cellprofiler/modules/classifyobjects.py
@@ -1080,7 +1080,7 @@ def run_two_measurements(self, workspace):
 
         if self.show_window:
             workspace.display_data.in_high_class = in_high_class
-            workspace.display_data.labels = (objects.segmented,)
+            workspace.display_data.labels = objects.segmented
             workspace.display_data.saved_values = saved_values
 
     def display_two_measurements(self, workspace, figure):

From 2547a5e296691a371408a6a5a7ba0d0f9143cc69 Mon Sep 17 00:00:00 2001
From: Beth Cimini <bethac07@users.noreply.github.com>
Date: Tue, 23 Jul 2024 19:07:13 -0400
Subject: [PATCH 08/35] Update runimagejmacro.py

---
 cellprofiler/modules/runimagejmacro.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cellprofiler/modules/runimagejmacro.py b/cellprofiler/modules/runimagejmacro.py
index 25e9f2d9ba..6ec2d519d0 100644
--- a/cellprofiler/modules/runimagejmacro.py
+++ b/cellprofiler/modules/runimagejmacro.py
@@ -292,7 +292,7 @@ def run(self, workspace):
 
             cmd += [self.stringify_metadata(tempdir)]
 
-            result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)
+            result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True, errors='backslashreplace')
             for image_group in self.image_groups_out:
                 if not os.path.exists(os.path.join(tempdir, image_group.input_filename.value)):
                     # Cleanup the error logs for display, we want to remove less-useful lines to keep it succinct.

From 4254cd898d0504bd9773a5f465dbcc2bddced167 Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Thu, 25 Jul 2024 10:45:40 -0400
Subject: [PATCH 09/35] tell workers to pull the dictionary from disk

---
 cellprofiler/modules/flagimage.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/cellprofiler/modules/flagimage.py b/cellprofiler/modules/flagimage.py
index 55200082ae..bb9979a714 100644
--- a/cellprofiler/modules/flagimage.py
+++ b/cellprofiler/modules/flagimage.py
@@ -716,6 +716,10 @@ def load_classifier(self, measurement_group):
                 d[path_] = joblib.load(path_)
         return d[path_]
 
+    def get_dictionary_for_worker(self):
+        # Sklearn models can't be serialized, so workers will need to read them from disk.
+        return {}
+
     def get_classifier(self, measurement_group):
         return self.load_classifier(measurement_group)[0]
 

From a4f3aa63f086416a90b98e4cecdf6134c5eb159b Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Thu, 25 Jul 2024 11:48:46 -0400
Subject: [PATCH 10/35] check for case of mixed 0s and nans

---
 cellprofiler/modules/threshold.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/cellprofiler/modules/threshold.py b/cellprofiler/modules/threshold.py
index c9ed0b882d..c94ab8f62b 100644
--- a/cellprofiler/modules/threshold.py
+++ b/cellprofiler/modules/threshold.py
@@ -932,6 +932,10 @@ def get_local_threshold(self, image, mask, volumetric):
         elif numpy.all(image_data == image_data[0]):
             local_threshold = numpy.full_like(image_data, image_data[0])
 
+        elif numpy.unique(numpy.where(numpy.isnan(image_data),0,image_data)).shape == (1,):
+            #test if all values are a mixture of 0 or nan
+            local_threshold = numpy.zeros_like(image_data)
+
         elif self.threshold_operation == TM_LI:
             local_threshold = self._run_local_threshold(
                 image_data,

From 7563623749dfca1f791109d58eaa3099f0fd5bd3 Mon Sep 17 00:00:00 2001
From: Beth Cimini <bethac07@users.noreply.github.com>
Date: Thu, 25 Jul 2024 16:56:38 -0400
Subject: [PATCH 11/35] Update threshold.py

---
 cellprofiler/modules/threshold.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cellprofiler/modules/threshold.py b/cellprofiler/modules/threshold.py
index c94ab8f62b..edc8c52689 100644
--- a/cellprofiler/modules/threshold.py
+++ b/cellprofiler/modules/threshold.py
@@ -932,7 +932,7 @@ def get_local_threshold(self, image, mask, volumetric):
         elif numpy.all(image_data == image_data[0]):
             local_threshold = numpy.full_like(image_data, image_data[0])
 
-        elif numpy.unique(numpy.where(numpy.isnan(image_data),0,image_data)).shape == (1,):
+        elif numpy.all((image_data == 0) | numpy.isnan(image_data)):
             #test if all values are a mixture of 0 or nan
             local_threshold = numpy.zeros_like(image_data)
 

From 04c6d3902aeb6f9678ce2712c9fc78673606ac91 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Fri, 26 Jul 2024 16:38:18 +0100
Subject: [PATCH 12/35] Bump to 4.2.7

---
 .github/workflows/release.yml | 8 ++++----
 README.md                     | 4 ++--
 cellprofiler/__init__.py      | 2 +-
 docs/source/conf.py           | 2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 9083af8147..9a0c794794 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -47,7 +47,7 @@ jobs:
           brew install mysql@8.0
           brew link mysql@8.0
           pip install mysqlclient==2.0.3
-          pip install centrosome==1.2.2 --no-cache-dir --no-build-isolation
+          pip install centrosome==1.2.3 --no-cache-dir --no-build-isolation
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
@@ -85,7 +85,7 @@ jobs:
         run: |
           pyinstaller distribution/windows/cellprofiler.spec
           rm ./dist/CellProfiler/jvm.dll
-          iscc /dMyAppVersion="4.2.60001-ai" "distribution/windows/cellprofiler.iss"
+          iscc /dMyAppVersion="4.2.70001-ai" "distribution/windows/cellprofiler.iss"
       - if: startsWith(matrix.os, 'macos')
         name: MacOS pyinstaller build and package
         run: |
@@ -101,13 +101,13 @@ jobs:
         uses: actions/upload-artifact@v4
         name: MacOS dmg upload
         with:
-          name: CellProfiler-macOS-4.2.60001-ai.dmg
+          name: CellProfiler-macOS-4.2.70001-ai.dmg
           path: ./dist/*.dmg
       - if: startsWith(matrix.os, 'windows')
         uses: actions/upload-artifact@v4
         name: Windows artifact upload
         with:
-          name: CellProfiler-Windows-4.2.60001-ai.exe
+          name: CellProfiler-Windows-4.2.70001-ai.exe
           path: ./distribution/windows/Output/*.exe
   upload:
     name: upload
diff --git a/README.md b/README.md
index 8816179945..28b6893b3a 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 ![CellProfiler](cellprofiler/data/images/splash.png)
 
-[![Version](https://img.shields.io/badge/version-4.2.6-green.svg)](https://cellprofiler.org/releases)
-[![Docs](https://img.shields.io/badge/documentation-4.2.6-brightgreen.svg)](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.6/index.html)
+[![Version](https://img.shields.io/badge/version-4.2.7-green.svg)](https://cellprofiler.org/releases)
+[![Docs](https://img.shields.io/badge/documentation-4.2.7-brightgreen.svg)](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.7/index.html)
 [![Image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftag%2Fcellprofiler.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/cellprofiler)
 
 **CellProfiler** is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the [CellProfiler Wiki](https://github.com/CellProfiler/CellProfiler/wiki).
diff --git a/cellprofiler/__init__.py b/cellprofiler/__init__.py
index 34e8de27ad..cdbfe3c4a2 100644
--- a/cellprofiler/__init__.py
+++ b/cellprofiler/__init__.py
@@ -1,3 +1,3 @@
 __test__ = False
 
-__version__ = "4.2.60001"
+__version__ = "4.2.70001"
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 553d44f0e4..7b7ddb488d 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -67,7 +67,7 @@
 # The short X.Y version.
 version = "4.2"
 # The full version, including alpha/beta/rc tags.
-release = "4.2.6"
+release = "4.2.7"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

From 88614d9e5bfa8b5027bc6c8b8f1a9a888329eed8 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Mon, 29 Jul 2024 20:59:42 +0100
Subject: [PATCH 13/35] [CI fix] pin exact java version to match distribution

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

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 9a0c794794..d65bdad548 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -21,7 +21,7 @@ jobs:
         name: Install Java
         with:
           distribution: "temurin"
-          java-version: "11" # The JDK version to make available on the path.
+          java-version: "11.0.20-8" # The JDK version to make available on the path.
           java-package: jdk
           architecture: x64
 

From c57cdfc14b8c0ec8890f62bc5f4e50453c563fa9 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Mon, 29 Jul 2024 21:05:42 +0100
Subject: [PATCH 14/35] [CI fix] Adjust macos version and fix java specifier

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

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index d65bdad548..496e4fd0b8 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -21,7 +21,7 @@ jobs:
         name: Install Java
         with:
           distribution: "temurin"
-          java-version: "11.0.20-8" # The JDK version to make available on the path.
+          java-version: "11.0.20+8" # The JDK version to make available on the path.
           java-package: jdk
           architecture: x64
 

From 7d2831e90363be47e41a608d83a6d470b93f9645 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Mon, 29 Jul 2024 21:52:52 +0100
Subject: [PATCH 15/35] [CI fix] place working dir for distribution in correct
 step

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

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 496e4fd0b8..d2bd15cd1f 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -56,6 +56,8 @@ jobs:
           pip install --editable . --no-use-pep517
       - env:
           JDK_HOME: ${{ env.JAVA_HOME }}
+          CPPFLAGS: -I/usr/local/opt/mysql@8.0/include
+          LDFLAGS: "-L/usr/local/opt/mysql@8.0/lib -L/usr/local/opt/openssl/lib"
         if: startsWith(matrix.os, 'windows')
         name: Windows dependency install
         run: |

From 8509434e51efd11fe4a6afd8ee15e1c035133580 Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Mon, 5 Aug 2024 14:37:28 -0400
Subject: [PATCH 16/35] fix label assignment when different objects are
 neighbors

---
 cellprofiler/modules/measureobjectneighbors.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/cellprofiler/modules/measureobjectneighbors.py b/cellprofiler/modules/measureobjectneighbors.py
index 2f0fcfdee9..3b566fcbf4 100644
--- a/cellprofiler/modules/measureobjectneighbors.py
+++ b/cellprofiler/modules/measureobjectneighbors.py
@@ -323,9 +323,9 @@ def run(self, workspace):
             neighbor_has_pixels = has_pixels
         else:
             _, neighbor_numbers = neighbor_objects.relate_labels(
-                neighbor_labels, neighbor_objects.small_removed_segmented
+                neighbor_labels, neighbor_kept_labels
             )
-            neighbor_has_pixels = numpy.bincount(neighbor_labels.ravel())[1:] > 0
+            neighbor_has_pixels = numpy.bincount(neighbor_kept_labels.ravel())[1:] > 0
         neighbor_count = numpy.zeros((nobjects,))
         pixel_count = numpy.zeros((nobjects,))
         first_object_number = numpy.zeros((nobjects,), int)
@@ -703,6 +703,7 @@ def run(self, workspace):
             )
 
         labels = kept_labels
+        neighbor_labels = neighbor_kept_labels
 
         neighbor_count_image = numpy.zeros(labels.shape, int)
         object_mask = objects.segmented != 0

From bd023262796b897812901d3ca2bb2675054bcba1 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Mon, 26 Aug 2024 23:34:41 +0100
Subject: [PATCH 17/35] Pin and bump versions

---
 .github/workflows/test.yml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000000..e69de29bb2

From b39416cc9d957f2953729c5835070ae68ac05892 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Mon, 26 Aug 2024 22:52:12 +0000
Subject: [PATCH 18/35] Move to non-broken pytest

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d56a5f5edb..80c218e582 100644
--- a/setup.py
+++ b/setup.py
@@ -59,7 +59,7 @@ def package_data():
     extras_require={
         "build": ["black", "pre-commit", "pyinstaller", "twine"],
         "docs": ["Sphinx>=3.1.1", "sphinx-rtd-theme>=0.5.0"],
-        "test": ["pytest>=3.3.2,<4"],
+        "test": ["pytest~=7.4.1"],
     },
     install_requires=[
         "boto3>=1.12.28",

From 5fae3cda9cf5b57ff35e7078b90d762329a07dd6 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Fri, 13 Sep 2024 20:01:30 +0100
Subject: [PATCH 19/35] Bump to 4.2.8

---
 .github/workflows/release.yml | 6 +++---
 README.md                     | 4 ++--
 cellprofiler/__init__.py      | 2 +-
 docs/source/conf.py           | 2 +-
 setup.py                      | 9 +++++----
 5 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index d2bd15cd1f..1f0975ab8e 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -87,7 +87,7 @@ jobs:
         run: |
           pyinstaller distribution/windows/cellprofiler.spec
           rm ./dist/CellProfiler/jvm.dll
-          iscc /dMyAppVersion="4.2.70001-ai" "distribution/windows/cellprofiler.iss"
+          iscc /dMyAppVersion="4.2.80001-ai" "distribution/windows/cellprofiler.iss"
       - if: startsWith(matrix.os, 'macos')
         name: MacOS pyinstaller build and package
         run: |
@@ -103,13 +103,13 @@ jobs:
         uses: actions/upload-artifact@v4
         name: MacOS dmg upload
         with:
-          name: CellProfiler-macOS-4.2.70001-ai.dmg
+          name: CellProfiler-macOS-4.2.80001-ai.dmg
           path: ./dist/*.dmg
       - if: startsWith(matrix.os, 'windows')
         uses: actions/upload-artifact@v4
         name: Windows artifact upload
         with:
-          name: CellProfiler-Windows-4.2.70001-ai.exe
+          name: CellProfiler-Windows-4.2.80001-ai.exe
           path: ./distribution/windows/Output/*.exe
   upload:
     name: upload
diff --git a/README.md b/README.md
index 28b6893b3a..87a4d4d57f 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 ![CellProfiler](cellprofiler/data/images/splash.png)
 
-[![Version](https://img.shields.io/badge/version-4.2.7-green.svg)](https://cellprofiler.org/releases)
-[![Docs](https://img.shields.io/badge/documentation-4.2.7-brightgreen.svg)](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.7/index.html)
+[![Version](https://img.shields.io/badge/version-4.2.8-green.svg)](https://cellprofiler.org/releases)
+[![Docs](https://img.shields.io/badge/documentation-4.2.8-brightgreen.svg)](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.8/index.html)
 [![Image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftag%2Fcellprofiler.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/cellprofiler)
 
 **CellProfiler** is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the [CellProfiler Wiki](https://github.com/CellProfiler/CellProfiler/wiki).
diff --git a/cellprofiler/__init__.py b/cellprofiler/__init__.py
index cdbfe3c4a2..9b37a08b65 100644
--- a/cellprofiler/__init__.py
+++ b/cellprofiler/__init__.py
@@ -1,3 +1,3 @@
 __test__ = False
 
-__version__ = "4.2.70001"
+__version__ = "4.2.80001"
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 7b7ddb488d..6e06e661d9 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -67,7 +67,7 @@
 # The short X.Y version.
 version = "4.2"
 # The full version, including alpha/beta/rc tags.
-release = "4.2.7"
+release = "4.2.8"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/setup.py b/setup.py
index 80c218e582..80c047050f 100644
--- a/setup.py
+++ b/setup.py
@@ -51,19 +51,20 @@ def package_data():
         "Operating System :: OS Independent",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Image Recognition",
         "Topic :: Scientific/Engineering",
     ],
     entry_points={"console_scripts": ["cellprofiler=cellprofiler.__main__:main"]},
     extras_require={
-        "build": ["black", "pre-commit", "pyinstaller", "twine"],
+        "build": ["pyinstaller", "twine"],
         "docs": ["Sphinx>=3.1.1", "sphinx-rtd-theme>=0.5.0"],
         "test": ["pytest~=7.4.1"],
     },
     install_requires=[
         "boto3>=1.12.28",
-        "cellprofiler-core==4.2.7",
+        "cellprofiler-core==4.2.8",
         "centrosome==1.2.3",
         "docutils==0.15.2",
         "h5py==3.6.0",
@@ -88,8 +89,8 @@ def package_data():
         "scikit-learn==0.24.1",
         "scipy==1.9.0",
         "six",
-        "tifffile==2023.2.3",
-        "wxPython==4.2.1",
+        "tifffile<2022.4.22",
+        "wxPython>=4.1.0,<5",
     ],
     license="BSD",
     name="CellProfiler",

From 0d125062672a6eac0d7416ec7c1ff65e111e6fa8 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Tue, 17 Sep 2024 16:34:38 -0400
Subject: [PATCH 20/35] [build] Pin markupsafe for jinja

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 80c047050f..b681ed6b5e 100644
--- a/setup.py
+++ b/setup.py
@@ -59,7 +59,7 @@ def package_data():
     entry_points={"console_scripts": ["cellprofiler=cellprofiler.__main__:main"]},
     extras_require={
         "build": ["pyinstaller", "twine"],
-        "docs": ["Sphinx>=3.1.1", "sphinx-rtd-theme>=0.5.0"],
+        "docs": ["Sphinx>=3.1.1", "sphinx-rtd-theme>=0.5.0", "markupsafe<2.0.1"],
         "test": ["pytest~=7.4.1"],
     },
     install_requires=[

From 29fdc51b153beaed880772229dcfd1b3f112dd94 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Thu, 26 Sep 2024 14:33:52 -0400
Subject: [PATCH 21/35] [CI] allow manual trigger

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

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 1f0975ab8e..913a4f5948 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -132,6 +132,7 @@ jobs:
 
 name: create-release
 on:
+  workflow_dispatch:
   push:
     branches:
       - compat-4-2-ai

From 08d8ec77f0306c441ca149b17ef19b24b99ce2d7 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Thu, 26 Sep 2024 20:14:39 +0100
Subject: [PATCH 22/35] [CI] Switch to macos 13

homebrew no longer supports macos 12, and macsos 13 is still intel
---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 913a4f5948..363155210a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -4,7 +4,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ macos-12, windows-2019 ]
+        os: [ macos-13, windows-2019 ]
         python-version: [ "3.8" ]
       fail-fast: false
     steps:

From e44f8e86c8bd43871a86d77a731f855c1db33378 Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Thu, 26 Sep 2024 15:51:45 -0400
Subject: [PATCH 23/35] Make pep 517 compat

---
 pyproject.toml | 20 +++-----------------
 1 file changed, 3 insertions(+), 17 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2109152172..fed528d4a7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,17 +1,3 @@
-[tool.black]
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | build
-    | dist
-  )/
-)
-'''
-target_version = ['py38']
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"

From 90e8f2ee2a0be0a195a8b0d17bcdec72c5b8d5fe Mon Sep 17 00:00:00 2001
From: Nodar Gogoberidze <gnodar01@gmail.com>
Date: Thu, 26 Sep 2024 19:14:02 -0400
Subject: [PATCH 24/35] Add tmate

---
 .github/workflows/release.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 363155210a..6c14b35fd9 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -132,7 +132,6 @@ jobs:
 
 name: create-release
 on:
-  workflow_dispatch:
   push:
     branches:
       - compat-4-2-ai

From 893f9c2989a4b079f7de7e3c8b4728cbf76287b9 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 14:16:24 +0100
Subject: [PATCH 25/35] Test modified java deps

---
 .github/workflows/release.yml | 6 ++++--
 .github/workflows/test.yml    | 0
 setup.py                      | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)
 delete mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 6c14b35fd9..aea70f7709 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -47,7 +47,8 @@ jobs:
           brew install mysql@8.0
           brew link mysql@8.0
           pip install mysqlclient==2.0.3
-          pip install centrosome==1.2.3 --no-cache-dir --no-build-isolation
+          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
+          pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
@@ -63,7 +64,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools wheel
           pip install mysqlclient==2.0.3
-          pip install centrosome==1.2.2 --no-cache-dir --no-build-isolation
+          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
+          pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/setup.py b/setup.py
index b681ed6b5e..5719307c7c 100644
--- a/setup.py
+++ b/setup.py
@@ -65,7 +65,7 @@ def package_data():
     install_requires=[
         "boto3>=1.12.28",
         "cellprofiler-core==4.2.8",
-        "centrosome==1.2.3",
+        "centrosome~=1.2.3",
         "docutils==0.15.2",
         "h5py==3.6.0",
         "imageio==2.34.0",
@@ -80,7 +80,7 @@ def package_data():
         "opencv-python-headless==4.5.3.56",
         "Pillow==8.3.2",
         "prokaryote==2.4.4",
-        "python-bioformats==4.0.7",
+        "python-bioformats~=4.1.10001",
         "python-javabridge==4.0.3",
         "pyzmq==22.3.0",
         "sentry-sdk==0.18.0",

From 8fbd162ed634d73ccca29e79d3b0506bbbe8f6d0 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 14:23:50 +0100
Subject: [PATCH 26/35] Disabling PEP 517 no longer supported

---
 .github/workflows/release.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index aea70f7709..71b990770c 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -52,9 +52,9 @@ jobs:
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
-          pip install --editable . --upgrade --no-use-pep517
+          pip install --editable . --upgrade
           cd ..
-          pip install --editable . --no-use-pep517
+          pip install --editable .
       - env:
           JDK_HOME: ${{ env.JAVA_HOME }}
           CPPFLAGS: -I/usr/local/opt/mysql@8.0/include
@@ -69,9 +69,9 @@ jobs:
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
-          pip install --editable . --upgrade --no-use-pep517
+          pip install --editable . --upgrade
           cd ..
-          pip install --editable . --no-use-pep517
+          pip install --editable .
           pip install wxpython==4.1.1
       - name: Install plugins
         run: |

From e7bd732798a677fdb64560f765e827fa0370e880 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 14:30:31 +0100
Subject: [PATCH 27/35] Do bf after core

---
 .github/workflows/release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 71b990770c..eddb457beb 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -47,13 +47,13 @@ jobs:
           brew install mysql@8.0
           brew link mysql@8.0
           pip install mysqlclient==2.0.3
-          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
           pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
           pip install --editable . --upgrade
           cd ..
+          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
           pip install --editable .
       - env:
           JDK_HOME: ${{ env.JAVA_HOME }}
@@ -64,13 +64,13 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools wheel
           pip install mysqlclient==2.0.3
-          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
           pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
           pip install --editable . --upgrade
           cd ..
+          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
           pip install --editable .
           pip install wxpython==4.1.1
       - name: Install plugins

From f873b4aed988de95d9827a11d6010e132b9ce7bb Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 14:38:35 +0100
Subject: [PATCH 28/35] Override bf manually

---
 .github/workflows/release.yml | 4 ++--
 setup.py                      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index eddb457beb..39bb75daba 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -53,8 +53,8 @@ jobs:
           git checkout compat-4-2
           pip install --editable . --upgrade
           cd ..
-          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
           pip install --editable .
+          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
       - env:
           JDK_HOME: ${{ env.JAVA_HOME }}
           CPPFLAGS: -I/usr/local/opt/mysql@8.0/include
@@ -70,9 +70,9 @@ jobs:
           git checkout compat-4-2
           pip install --editable . --upgrade
           cd ..
-          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
           pip install --editable .
           pip install wxpython==4.1.1
+          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
       - name: Install plugins
         run: |
           pip install torch==2.2.1
diff --git a/setup.py b/setup.py
index 5719307c7c..815b56eaed 100644
--- a/setup.py
+++ b/setup.py
@@ -80,7 +80,7 @@ def package_data():
         "opencv-python-headless==4.5.3.56",
         "Pillow==8.3.2",
         "prokaryote==2.4.4",
-        "python-bioformats~=4.1.10001",
+        "python-bioformats~=4.1.0",
         "python-javabridge==4.0.3",
         "pyzmq==22.3.0",
         "sentry-sdk==0.18.0",

From 3f5ad5f858bd59d3d8a9695733cb46e19917c012 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 14:49:38 +0100
Subject: [PATCH 29/35] Bump javabridge

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 815b56eaed..587f6b0b6e 100644
--- a/setup.py
+++ b/setup.py
@@ -81,7 +81,7 @@ def package_data():
         "Pillow==8.3.2",
         "prokaryote==2.4.4",
         "python-bioformats~=4.1.0",
-        "python-javabridge==4.0.3",
+        "python-javabridge==4.0.4",
         "pyzmq==22.3.0",
         "sentry-sdk==0.18.0",
         "requests==2.22",

From 3f2cf4a8ee88e4e383dd7ba6c1f6d5da56aa2829 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 15:04:19 +0100
Subject: [PATCH 30/35] Force prokaryote too

---
 .github/workflows/release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 39bb75daba..a0e1f76866 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -47,13 +47,13 @@ jobs:
           brew install mysql@8.0
           brew link mysql@8.0
           pip install mysqlclient==2.0.3
-          pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
           pip install --editable . --upgrade
           cd ..
           pip install --editable .
+          pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
       - env:
           JDK_HOME: ${{ env.JAVA_HOME }}
@@ -64,7 +64,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools wheel
           pip install mysqlclient==2.0.3
-          pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
@@ -72,6 +71,7 @@ jobs:
           cd ..
           pip install --editable .
           pip install wxpython==4.1.1
+          pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
       - name: Install plugins
         run: |

From b00b65aa62e65f5dff307ec25882a20edba5ea72 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 15:32:12 +0100
Subject: [PATCH 31/35] Force include core

---
 distribution/macos/CellProfiler.spec   | 1 +
 distribution/windows/CellProfiler.spec | 1 +
 2 files changed, 2 insertions(+)

diff --git a/distribution/macos/CellProfiler.spec b/distribution/macos/CellProfiler.spec
index 88e1baa59f..5e89810085 100644
--- a/distribution/macos/CellProfiler.spec
+++ b/distribution/macos/CellProfiler.spec
@@ -50,6 +50,7 @@ hiddenimports += PyInstaller.utils.hooks.collect_submodules("wx")
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler.gui')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler.modules')
+hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler_core')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler_core.modules')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('skimage.io._plugins')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules("skimage.feature")
diff --git a/distribution/windows/CellProfiler.spec b/distribution/windows/CellProfiler.spec
index 776d2848a6..5ca95965a3 100644
--- a/distribution/windows/CellProfiler.spec
+++ b/distribution/windows/CellProfiler.spec
@@ -27,6 +27,7 @@ hiddenimports = []
 
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('centrosome')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler.modules')
+hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler_core')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler_core.modules')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler.utilities')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules("scipy")

From 66f13189774ebffd1aeeba1695cd345c8afa9928 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 15:36:14 +0100
Subject: [PATCH 32/35] Use tar for macos app

---
 .github/workflows/release.yml | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index a0e1f76866..d73710d986 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -95,18 +95,14 @@ jobs:
         run: |
           pyinstaller -y ./distribution/macos/CellProfiler.spec
       - if: startsWith(matrix.os, 'macos')
-        name: MacOS dmg package
-        continue-on-error: true
-        run: |
-          cd dist
-          echo Creating DMG
-          create-dmg 'CellProfiler+AI.app' --dmg-title "CellProfiler+AI.dmg"
+        name: MacOS tar package
+        run: tar -cvf dist/CellProfiler+AI.tar dist/CellProfiler+AI.app
       - if: startsWith(matrix.os, 'macos')
         uses: actions/upload-artifact@v4
-        name: MacOS dmg upload
+        name: MacOS tar upload
         with:
-          name: CellProfiler-macOS-4.2.80001-ai.dmg
-          path: ./dist/*.dmg
+          name: CellProfiler-macOS-4.2.80001-ai.tar
+          path: ./dist/*.tar
       - if: startsWith(matrix.os, 'windows')
         uses: actions/upload-artifact@v4
         name: Windows artifact upload

From ec5046e2a93ce87624950fa9c534f2d0b63803a5 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 16:12:57 +0100
Subject: [PATCH 33/35] Use wheel for core

---
 .github/workflows/release.yml | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index d73710d986..7bb0880640 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -47,11 +47,7 @@ jobs:
           brew install mysql@8.0
           brew link mysql@8.0
           pip install mysqlclient==2.0.3
-          git clone https://github.com/glencoesoftware/core.git
-          cd core
-          git checkout compat-4-2
-          pip install --editable . --upgrade
-          cd ..
+          pip install https://github.com/glencoesoftware/core/releases/download/v4.2.80001/cellprofiler_core-4.2.8-py3-none-any.whl
           pip install --editable .
           pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
@@ -64,11 +60,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools wheel
           pip install mysqlclient==2.0.3
-          git clone https://github.com/glencoesoftware/core.git
-          cd core
-          git checkout compat-4-2
-          pip install --editable . --upgrade
-          cd ..
+          pip install https://github.com/glencoesoftware/core/releases/download/v4.2.80001/cellprofiler_core-4.2.8-py3-none-any.whl
           pip install --editable .
           pip install wxpython==4.1.1
           pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
@@ -96,7 +88,8 @@ jobs:
           pyinstaller -y ./distribution/macos/CellProfiler.spec
       - if: startsWith(matrix.os, 'macos')
         name: MacOS tar package
-        run: tar -cvf dist/CellProfiler+AI.tar dist/CellProfiler+AI.app
+        run: tar -cvf CellProfiler+AI.tar CellProfiler+AI.app
+        working-directory: ./dist
       - if: startsWith(matrix.os, 'macos')
         uses: actions/upload-artifact@v4
         name: MacOS tar upload

From 7dfbd1096207ee8260f02e089a1534d03450ac79 Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Mon, 21 Oct 2024 16:24:14 +0100
Subject: [PATCH 34/35] No editable installs

---
 .github/workflows/release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 7bb0880640..c3db1d9f15 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -48,7 +48,7 @@ jobs:
           brew link mysql@8.0
           pip install mysqlclient==2.0.3
           pip install https://github.com/glencoesoftware/core/releases/download/v4.2.80001/cellprofiler_core-4.2.8-py3-none-any.whl
-          pip install --editable .
+          pip install .
           pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
       - env:
@@ -61,7 +61,7 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
           pip install mysqlclient==2.0.3
           pip install https://github.com/glencoesoftware/core/releases/download/v4.2.80001/cellprofiler_core-4.2.8-py3-none-any.whl
-          pip install --editable .
+          pip install .
           pip install wxpython==4.1.1
           pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
           pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl

From 17781ed47b34b6199dfb755e5b60e8c19c3cefea Mon Sep 17 00:00:00 2001
From: David Stirling <dstirling@glencoesoftware.com>
Date: Tue, 22 Oct 2024 10:34:27 +0100
Subject: [PATCH 35/35] Disable auto update checker and fix version processor

---
 cellprofiler/gui/checkupdate.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/cellprofiler/gui/checkupdate.py b/cellprofiler/gui/checkupdate.py
index fe5e027a25..ebf5c42df3 100644
--- a/cellprofiler/gui/checkupdate.py
+++ b/cellprofiler/gui/checkupdate.py
@@ -7,10 +7,10 @@
 
 
 def check_update(parent, force=False):
-    if not force and not check_date():
+    if not force:
         return
     try:
-        response = requests.get("https://api.github.com/repos/cellprofiler/cellprofiler/releases/latest", timeout=0.25)
+        response = requests.get("https://api.github.com/repos/glencoesoftware/cellprofiler/releases/latest", timeout=0.25)
     except:
         response = False
         message = "CellProfiler was unable to connect to GitHub to check for updates"
@@ -19,6 +19,8 @@ def check_update(parent, force=False):
         response = response.json()
         if status == 200 and 'name' in response:
             latest_version = response['name'][1:]
+            if '-' in latest_version:
+                latest_version = latest_version.split('-')[0]
             if current_version < latest_version or len(current_version) != len(latest_version):
                 body_text = response['body']
                 if len(body_text) > 1000: