🔖 Release 2.0.0

.github/workflows/docker-publish.yml

@@ -6,7 +6,7 @@ env:
   REGISTRY: ghcr.io
   IMAGE_NAME: TissueImageAnalytics/tiatoolbox
   image: ghcr.io/tissueimageanalytics/tiatoolbox
-  TOOLBOX_VER: 1.6.0
+  TOOLBOX_VER: 2.0.0
 
 jobs:
   build-and-push-image:

.github/workflows/pip-install.yml

@@ -34,142 +34,160 @@ jobs:
         python-version: ["3.10", "3.11", "3.12", "3.13"]
         os: [ubuntu-24.04, windows-latest, macos-latest]
 
+    # Force UTF-8 everywhere (Windows is the one that really needs it)
+    env:
+      PYTHONUTF8: "1"
+      PYTHONIOENCODING: "utf-8"
+
     steps:
-    - name: Checkout
-      uses: actions/checkout@v4
-
-    - name: Install Miniconda
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        channels: conda-forge
-        channel-priority: strict
-        auto-update-conda: true
-
-    # -------------------------------
-    # Create environment (Linux/macOS)
-    # -------------------------------
-    - name: Create conda environment (Linux/macOS)
-      if: runner.os != 'Windows'
-      shell: bash
-      run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda create -y -n test-env python=${{ matrix.python-version }}
-        conda activate test-env
-        conda install -y openjpeg sqlite
-
-    # -------------------------------
-    # Create environment (Windows)
-    # -------------------------------
-    - name: Create conda environment (Windows)
-      if: runner.os == 'Windows'
-      shell: pwsh
-      run: |
-        conda create -y -n test-env python=${{ matrix.python-version }}
-        conda activate test-env
-        conda install -y openjpeg sqlite
-
-    # -------------------------------
-    # Verify SQLite
-    # -------------------------------
-    - name: Verify SQLite (Linux/macOS)
-      if: runner.os != 'Windows'
-      shell: bash
-      run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate test-env
-        sqlite3 --version
-        sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
-
-    - name: Verify SQLite (Windows)
-      if: runner.os == 'Windows'
-      shell: pwsh
-      run: |
-        conda activate test-env
-        sqlite3 --version
-        sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
-
-    # -------------------------------
-    # Verify OpenJPEG
-    # -------------------------------
-    - name: Verify OpenJPEG (Linux/macOS)
-      if: runner.os != 'Windows'
-      shell: bash
-      run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate test-env
-        opj_dump -h || true  # This -h option exits with code 1 for some reason
-
-    - name: Verify OpenJPEG (Windows)
-      if: runner.os == 'Windows'
-      shell: pwsh
-      run: |
-        conda activate test-env
-        opj_dump -h || true  # This -h option exits with code 1 for some reason
-
-    # -------------------------------
-    # Install PyTorch
-    # -------------------------------
-    - name: Install CPU-only PyTorch (Linux/macOS)
-      if: runner.os != 'Windows'
-      shell: bash
-      run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate test-env
-        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-
-    - name: Install CPU-only PyTorch (Windows)
-      if: runner.os == 'Windows'
-      shell: pwsh
-      run: |
-        conda activate test-env
-        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-
-    # -------------------------------
-    # Install tiatoolbox
-    # -------------------------------
-    - name: Install tiatoolbox (Linux/macOS)
-      if: runner.os != 'Windows'
-      shell: bash
-      run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate test-env
-        pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_SHA}
-
-    - name: Install tiatoolbox (Windows)
-      if: runner.os == 'Windows'
-      shell: pwsh
-      run: |
-        conda activate test-env
-        pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_SHA
-
-    # -------------------------------
-    # Test Imports
-    # -------------------------------
-    - name: Test Imports (Linux/macOS)
-      if: runner.os != 'Windows'
-      shell: bash
-      run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate test-env
-        python - << 'EOF'
-        import tiatoolbox
-        print("tiatoolbox:", tiatoolbox.__version__)
-        import openslide
-        print("openslide:", openslide.__version__)
-        import torch
-        print("torch:", torch.__version__)
-        EOF
-
-    - name: Test Imports (Windows)
-      if: runner.os == 'Windows'
-      shell: pwsh
-      run: |
-        conda activate test-env
-        @"
-        import tiatoolbox
-        print("tiatoolbox:", tiatoolbox.__version__)
-        import openslide
-        print("openslide:", openslide.__version__)
-        import torch
-        print("torch:", torch.__version__)
-        "@ | python -
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          channels: conda-forge
+          channel-priority: strict
+          auto-update-conda: true
+
+      # -------------------------------
+      # Create environment (Linux/macOS)
+      # -------------------------------
+      - name: Create conda environment (Linux/macOS)
+        if: runner.os != 'Windows'
+        shell: bash
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda create -y -n test-env python=${{ matrix.python-version }}
+          conda activate test-env
+          conda install -y openjpeg sqlite
+          python -m pip install --upgrade pip setuptools wheel
+
+      # -------------------------------
+      # Create environment (Windows)
+      # -------------------------------
+      - name: Create conda environment (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          conda create -y -n test-env python=${{ matrix.python-version }}
+          conda activate test-env
+          conda install -y openjpeg sqlite
+          python -m pip install --upgrade pip setuptools wheel
+
+      # -------------------------------
+      # Verify SQLite
+      # -------------------------------
+      - name: Verify SQLite (Linux/macOS)
+        if: runner.os != 'Windows'
+        shell: bash
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate test-env
+          sqlite3 --version
+          sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
+
+      - name: Verify SQLite (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          conda activate test-env
+          sqlite3 --version
+          sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
+
+      # -------------------------------
+      # Verify OpenJPEG
+      # -------------------------------
+      - name: Verify OpenJPEG (Linux/macOS)
+        if: runner.os != 'Windows'
+        shell: bash
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate test-env
+          opj_dump -h || true  # -h exits with code 1 in some builds
+
+      - name: Verify OpenJPEG (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          conda activate test-env
+          opj_dump -h || true  # -h exits with code 1 in some builds
+
+      # -------------------------------
+      # Install PyTorch (CPU-only)
+      # -------------------------------
+      - name: Install CPU-only PyTorch (Linux/macOS)
+        if: runner.os != 'Windows'
+        shell: bash
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate test-env
+          pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+
+      - name: Install CPU-only PyTorch (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          conda activate test-env
+          pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+
+      # -------------------------------
+      # (Windows only) make console UTF-8 (extra safety)
+      # -------------------------------
+      - name: Ensure UTF-8 console (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          chcp 65001 > $null
+          [Console]::InputEncoding  = [System.Text.Encoding]::UTF8
+          [Console]::OutputEncoding = [System.Text.Encoding]::UTF8
+
+      # -------------------------------
+      # Install tiatoolbox from this commit
+      # -------------------------------
+      - name: Install tiatoolbox (Linux/macOS)
+        if: runner.os != 'Windows'
+        shell: bash
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate test-env
+          pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_SHA}
+
+      - name: Install tiatoolbox (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          conda activate test-env
+          pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_SHA
+
+      # -------------------------------
+      # Test Imports
+      # -------------------------------
+      - name: Test Imports (Linux/macOS)
+        if: runner.os != 'Windows'
+        shell: bash
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate test-env
+          python - << 'EOF'
+          import tiatoolbox
+          print("tiatoolbox:", tiatoolbox.__version__)
+          import openslide
+          print("openslide:", openslide.__version__)
+          import torch
+          print("torch:", torch.__version__)
+          EOF
+
+      - name: Test Imports (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          conda activate test-env
+          @"
+          import tiatoolbox
+          print("tiatoolbox:", tiatoolbox.__version__)
+          import openslide
+          print("openslide:", openslide.__version__)
+          import torch
+          print("torch:", torch.__version__)
+          "@ | python -

AUTHORS.md

@@ -2,28 +2,34 @@
 
 ## Development Lead
 
-- TIA Centre led by Nasir Rajpoot <TIA@warwick.ac.uk>
+- Tissue Image Analytics Centre <TIA@warwick.ac.uk>
 - Shan E Ahmed Raza \<@shaneahmed>
 - John Pocock \<@John-P>
 - Mark Eastwood \<@measty>
+- Jiaqi Lv \<@Jiaqi-Lv>
+- Mostafa Jahanifar \<@mostafajahanifar>
+- Adam Shephard \<@adamshephard>
 - Simon Graham \<@simongraham>
 - Dang Vu \<@vqdang>
-- Mostafa Jahanifar \<@mostafajahanifar>
 - David Epstein \<@DavidBAEpstein>
-- Adam Shephard \<@adamshephard>
 - Abdullah Alsalemi \<@Abdol>
 - Ruqayya Awan \<@ruqayya>
-- Jiaqi Lv \<@Jiaqi-Lv>
 - Dmitrii Blaginin \<@blaginin>
+- Yijie Zhu \<@YijieZhu15>
 - Srijay Deshpande \<@Srijay-lab>
 - George Hadjigeorgiou \<@ghadjigeorghiou>
+- Gozde Gunesli \<@gozdeg>
 - Abishekraj Vinayagar Gnanasambandam \<@AbishekRajVG>
 - Wenqi Lu \<@wenqi006>
 - Saad Bashir \<@rajasaad>
+- Behnaz Elhaminia \<@behnazelhaminia>
 
 ## Contributors
 
+- Nasir Rajpoot \<@nmrajpoot>
+- Fayyaz Minhas \<@foxtrotmike>
 - George Batchkala \<@GeorgeBatch>
+- Aleksandar Acic \<@aacic>
 - Rob Jewsbury \<@R-J96>
 - Mohsin Bilal \<@mbhahsmi>
-- Fayyaz Minhas \<@foxtrotmike>
+- Musraf Basheer \<mbasheer04>

CITATION.cff

@@ -44,7 +44,7 @@ authors:
   given-names: "Shan E Ahmed"
   orcid: "https://orcid.org/0000-0002-1097-1738"
 title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
-version: 1.6.0  # TIAToolbox version
+version: 2.0.0  # TIAToolbox version
 doi: 10.5281/zenodo.5802442
 date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"