Merge pull request #16 from DavidStirling/compat-4-2-ai

Update 4.2 AI build

.github/workflows/release.yml

@@ -4,7 +4,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ macos-10.15, windows-2019 ]
+        os: [ macos-latest, windows-2019 ]
         python-version: [ "3.8" ]
       fail-fast: false
     steps:
@@ -17,92 +17,98 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: pip
           cache-dependency-path: setup.py
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v3
         name: Install Java
         with:
-          java-version: '14.0.1' # The JDK version to make available on the path.
+          distribution: "temurin"
+          java-version: "11" # The JDK version to make available on the path.
           java-package: jdk
           architecture: x64
+
       - name: Install build-time dependencies
         run: |
           pip install --upgrade wheel pip
           pip install setuptools==49
-          pip install numpy==1.20.1
-          pip install pyinstaller==4.10
-          pip install imageio==2.9.0
+          pip install numpy==1.23.1
+          pip install pyinstaller-hooks-contrib==2024.2
+          pip install pyinstaller==5.13.2
+          pip install imageio==2.34.0
+          pip install cython
+          pip install lxml
       - env:
           LDFLAGS: -L/usr/local/opt/openssl/lib
           CERTIFICATE_OSX_APPLICATION: ${{ secrets.CERTIFICATE_OSX_APPLICATION }}
           CERTIFICATE_PASSWORD: ${{ secrets.CERTIFICATE_PASSWORD }}
-        if: ${{ matrix.os == 'macos-10.15' }}
+        if: startsWith(matrix.os, 'macos')
         name: MacOS dependency install
         run: |
-          brew install mysql
-          brew install create-dmg
-          pip install centrosome==1.2.0 --no-cache-dir --no-build-isolation
+          brew install graphicsmagick imagemagick
+          npm install --global create-dmg
+          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
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
           pip install --editable . --upgrade --no-use-pep517
           cd ..
           pip install --editable . --no-use-pep517
       - env:
-          JDK_HOME: C:\hostedtoolcache\windows\jdk\14.0.1\x64
-        if: ${{ matrix.os == 'windows-2019' }}
+          JDK_HOME: ${{ env.JAVA_HOME }}
+        if: startsWith(matrix.os, 'windows')
         name: Windows dependency install
         run: |
-          pip install cython
-          pip install mysqlclient==1.4.6
-          pip install centrosome==1.2.0 --no-cache-dir --no-build-isolation
+          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
           git clone https://github.com/glencoesoftware/core.git
           cd core
           git checkout compat-4-2
           pip install --editable . --upgrade --no-use-pep517
           cd ..
           pip install --editable . --no-use-pep517
+          pip install wxpython==4.1.1
       - name: Install plugins
         run: |
-          pip install torch==1.11.0
-          pip install cellpose==2.1.0
-          pip install csbdeep==0.7.2
+          pip install torch==2.2.1
+          pip install cellpose==3.0.5
+          pip install csbdeep==0.7.4
           pip install stardist==0.8.1
-          pip install tensorflow==2.10.0
+          pip install tensorflow==2.12.1
           pip install markupsafe==2.0.1
-          pip install h5py==3.2.1
+          pip install h5py==3.6.0
       - name: Display installed packages
         run: pip list
-      - if: ${{ matrix.os == 'windows-2019' }}
+      - if: startsWith(matrix.os, 'windows')
         name: Windows pyinstaller build and package
         run: |
           pyinstaller distribution/windows/cellprofiler.spec
-          iscc /dMyAppVersion="4.2.10002-ai" "distribution/windows/cellprofiler.iss"
-      - if: ${{ matrix.os == 'macos-10.15' }}
+          rm ./dist/CellProfiler/jvm.dll
+          iscc /dMyAppVersion="4.2.60001-ai" "distribution/windows/cellprofiler.iss"
+      - if: startsWith(matrix.os, 'macos')
         name: MacOS pyinstaller build and package
         run: |
           pyinstaller -y ./distribution/macos/CellProfiler.spec
-          create-dmg \
-            --volname "CellProfiler" \
-            --window-pos 200 120 \
-            --window-size 800 529 \
-            --icon-size 130 \
-            --text-size 14 \
-            --icon "CellProfiler+AI.app" 260 250 \
-            --app-drop-link 540 250 \
-            --hdiutil-quiet \
-            "./dist/CellProfiler-macOS-4.2.10002-ai.dmg" \
-            "./dist/CellProfiler+AI.app"
-      - if: ${{ matrix.os == 'macos-10.15' }}
-        uses: actions/upload-artifact@v1
-        name: MacOS artifact upload
+      - 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"
+      - if: startsWith(matrix.os, 'macos')
+        uses: actions/upload-artifact@v4
+        name: MacOS dmg upload
         with:
-          name: CellProfiler-macOS-4.2.10002-ai.dmg
-          path: ./dist/CellProfiler-macOS-4.2.10002-ai.dmg
-      - if: ${{ matrix.os == 'windows-2019' }}
-        uses: actions/upload-artifact@v2
+          name: CellProfiler-macOS-4.2.60001-ai.dmg
+          path: ./dist/*.dmg
+      - if: startsWith(matrix.os, 'windows')
+        uses: actions/upload-artifact@v4
         name: Windows artifact upload
         with:
-          name: CellProfiler-Windows-4.2.10002-ai.exe
-          path: ./distribution/windows/Output/CellProfiler-Windows-4.2.10002-ai.exe
+          name: CellProfiler-Windows-4.2.60001-ai.exe
+          path: ./distribution/windows/Output/*.exe
   upload:
     name: upload
     needs: build
@@ -121,27 +127,27 @@ jobs:
           tag_name: ${{ github.ref }}
       - uses: actions/download-artifact@v1
         with:
-          name: CellProfiler-macOS-4.2.10002-ai.dmg
+          name: CellProfiler-macOS-4.2.60001-ai.dmg
           path: ./
       - uses: actions/download-artifact@v1
         with:
-          name: CellProfiler-Windows-4.2.10002-ai.exe
+          name: CellProfiler-Windows-4.2.60001-ai.exe
           path: ./
       - env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         uses: actions/upload-release-asset@v1
         with:
           asset_content_type: application/zip
-          asset_name: CellProfiler-macOS-4.2.10002-ai.dmg
-          asset_path: /home/runner/work/CellProfiler/CellProfiler/CellProfiler-macOS-4.2.10002-ai.dmg
+          asset_name: CellProfiler-macOS-4.2.60001-ai.dmg
+          asset_path: /home/runner/work/CellProfiler/CellProfiler/CellProfiler-macOS-4.2.60001-ai.dmg
           upload_url: ${{ steps.create_release.outputs.upload_url }}
       - env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         uses: actions/upload-release-asset@v1
         with:
           asset_content_type: application/exe
-          asset_name: CellProfiler-Windows-4.2.10002-ai.exe
-          asset_path: /home/runner/work/CellProfiler/CellProfiler/CellProfiler-Windows-4.2.10002-ai.exe
+          asset_name: CellProfiler-Windows-4.2.60001-ai.exe
+          asset_path: /home/runner/work/CellProfiler/CellProfiler/CellProfiler-Windows-4.2.60001-ai.exe
           upload_url: ${{ steps.create_release.outputs.upload_url }}
 name: create-release
 on:
@@ -150,3 +156,6 @@ on:
       - compat-4-2-ai
     tags:
       - "v*"
+  pull_request:
+    branches:
+      - compat-4-2-ai

CITATION

@@ -1,6 +1,35 @@
 When using CellProfiler, please cite one of the following papers.
 See also: http://cellprofiler.org/citations/
 
+CellProfiler 4: 
+
+@article{Stirling_2021,
+	doi = {10.1186/s12859-021-04344-9},
+	url = {https://doi.org/10.1186%2Fs12859-021-04344-9},
+	year = 2021,
+	month = {sep},
+	publisher = {Springer Science and Business Media {LLC}},
+	volume = {22},
+	number = {1},
+	author = {David R. Stirling and Madison J. Swain-Bowden and Alice M. Lucas and Anne E. Carpenter and Beth A. Cimini and Allen Goodman},
+	title = {{CellProfiler} 4: improvements in speed, utility and usability},
+	journal = {{BMC} Bioinformatics}
+
+CellProfiler 3: 
+
+@misc{McQuin_Goodman_Chernyshev_Kamentsky_Cimini_Karhohs_Doan_Ding_Rafelski_Thirstrup_et al._2018, 
+    doi={10.1371/journal.pbio.2005970}, 
+    url={http://dx.doi.org/10.1371/journal.pbio.2005970}, 
+    year={2018}, 
+    month={Jul}, 
+    publisher={Public Library of Science (PLoS)},
+    volume={16}, 
+    number={7}, 
+    author={McQuin, Claire and Goodman, Allen and Chernyshev, Vasiliy and Kamentsky, Lee and Cimini, Beth A. and Karhohs, Kyle W. and Doan, Minh and Ding, Liya and Rafelski, Susanne M. and Thirstrup, Derek and Wiegraebe, Winfried and Singh, Shantanu and Becker, Tim and Caicedo, Juan C. and Carpenter, Anne E.},
+    title={CellProfiler 3.0: Next-generation image processing for biology}, 
+    journal={PLOS Biology},  
+    editor={Misteli, Tom}, pages={e2005970}, language={en} }
+
 
 CellProfiler for cells:
 
@@ -77,24 +106,4 @@ CellProfiler for other biological images:
     year = {2007}
 }
 
-
-CellProfiler Analyst software in general:
-
-@article{Jones2008,
-    abstract = {Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment.},
-    author = {Jones, Thouis R. and Kang, In Han and Wheeler, Douglas B. and Lindquist, Robert A. and Papallo, Adam and Sabatini, David M. and Golland, Polina and Carpenter, Anne E.},
-    day = {15},
-    doi = {10.1186/1471-2105-9-482},
-    issn = {1471-2105},
-    journal = {BMC Bioinformatics},
-    month = nov,
-    number = {1},
-    pages = {482},
-    title = {{{CellProfiler Analyst}}: Data Exploration and Analysis Software for Complex Image-Based Screens},
-    url = {https://doi.org/10.1186/1471-2105-9-482},
-    volume = {9},
-    year = {2008}
-}
-
-
 Please find the CellProfiler Analyst's BibTeX snippets in  https://github.com/CellProfiler/CellProfiler-Analyst/blob/master/CITATION

README.md

@@ -1,7 +1,7 @@
 ![CellProfiler](cellprofiler/data/images/splash.png)
 
-[![Version](https://img.shields.io/badge/version-4.2.1-green.svg)](https://cellprofiler.org/releases)
-[![Docs](https://img.shields.io/badge/documentation-4.2.1-brightgreen.svg)](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.1/index.html)
+[![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)
 [![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).

cellprofiler/__init__.py

@@ -1,3 +1,3 @@
 __test__ = False
 
-__version__ = "4.2.10002"
+__version__ = "4.2.60001"