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Merge branch 'develop' into fix-zarr-check
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‎.github/workflows/conda-env-create.yml‎

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name: Solve Conda Environment
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permissions:
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contents: read
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on:
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push:
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paths: [ "requirements/requirements*.yml", "conda-env-create.yml", "requirement*.txt"]

‎.github/workflows/docker-publish.yml‎

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REGISTRY: ghcr.io
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IMAGE_NAME: TissueImageAnalytics/tiatoolbox
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image: ghcr.io/tissueimageanalytics/tiatoolbox
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TOOLBOX_VER: 1.6.0
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TOOLBOX_VER: 2.0.0
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jobs:
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build-and-push-image:

‎.github/workflows/mypy-type-check.yml‎

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# This workflow will perform code type checking using mypy
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name: mypy type checking
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permissions:
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contents: read
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on:
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push:

‎.github/workflows/pip-install.yml‎

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

‎.github/workflows/python-package.yml‎

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name: Python package
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permissions:
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contents: read
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branches: [ develop, pre-release, master, main ]

‎AUTHORS.md‎

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

‎CITATION.cff‎

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

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