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🔖 REL: Release 1.3.0 (#523)
# 1.3.1 (2022-12-20) ### Major Updates and Feature Improvements - Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449 - Adds Annotation Store Reader #476 - Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510 ### Changes to API - Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517 ### Bug Fixes and Other Changes - Simplifies example notebook for image reading for better readability - Restricts Shapely version to \<2.0.0 for compatibility ### Development related changes - Adds GitHub workflow for automatic generation of docker image - Updates dependencies - Updates bump2version config - Enables flake8 E800 checks for commented codes. - Fixes several errors generated by DeepSource. - Prevent test dumping file to root - Removes duplicate functions to generate parameterized test scenarios Co-authored-by: John Pocock <[email protected]> Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: Ruqayya Awan <[email protected]> Co-authored-by: Mostafa Jahanifar <[email protected]> Co-authored-by: kesixu <[email protected]> Co-authored-by: David Epstein <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: Simon Graham <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Roger Trullo <[email protected]>
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‎.github/workflows/docker-publish.yml‎

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name: Publish Dockers
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on:
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workflow_dispatch
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env:
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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: 1.3.1
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jobs:
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build-and-push-image:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: true
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matrix:
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include:
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- dockerfile: ./docker/3.7/Debian/Dockerfile
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mtag: py3.7-debian
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- dockerfile: ./docker/3.8/Debian/Dockerfile
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mtag: py3.8-debian
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- dockerfile: ./docker/3.9/Debian/Dockerfile
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mtag: py3.9-debian
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- dockerfile: ./docker/3.9/Ubuntu/Dockerfile
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mtag: py3.9-ubuntu
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- dockerfile: ./docker/3.10/Debian/Dockerfile
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mtag: py3.10-debian
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- dockerfile: ./docker/3.10/Ubuntu/Dockerfile
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mtag: py3.10-ubuntu
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- dockerfile: ./docker/3.10/Ubuntu/Dockerfile
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mtag: latest
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permissions:
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contents: read
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packages: write
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id-token: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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- name: Log in to the Container registry
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uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Publishing with 'latest' tag
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if: contains(matrix.mtag, 'latest')
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uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
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with:
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context: .
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file: ${{ matrix.dockerfile }}
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push: true
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tags: "${{ env.image }}:${{ matrix.mtag }}"
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- name: Publishing with explicit tags
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if: ${{ !contains(matrix.mtag, 'latest') }}
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uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
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with:
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context: .
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file: ${{ matrix.dockerfile }}
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push: true
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tags: "${{ env.image }}:${{ env.TOOLBOX_VER }}-${{ matrix.mtag }}"

‎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: 1.3.0
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version: 1.3.1 # 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"

‎HISTORY.md‎

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# History
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# 1.3.1 (2022-12-20)
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### Major Updates and Feature Improvements
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- Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449
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- Adds Annotation Store Reader #476
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- Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510
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### Changes to API
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- Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517
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### Bug Fixes and Other Changes
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- Simplifies example notebook for image reading for better readability
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- Restricts Shapely version to \<2.0.0 for compatibility
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### Development related changes
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- Adds GitHub workflow for automatic generation of docker image
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- Updates dependencies
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- Updates bump2version config
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- Enables flake8 E800 checks for commented codes.
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- Fixes several errors generated by DeepSource.
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- Prevent test dumping file to root
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- Removes duplicate functions to generate parameterized test scenarios
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## 1.3.0 (2022-10-20)
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### Major Updates and Feature Improvements

‎docker/3.10/Debian/Dockerfile‎

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FROM python:3.10-slim-bullseye
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#get linux packages
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RUN apt-get -y update && apt-get -y install --no-install-recommends \
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libopenjp2-7-dev libopenjp2-tools \
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openslide-tools \
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libgl1 \
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build-essential \
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&& pip3 --no-cache-dir install tiatoolbox \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*

‎docker/3.10/Ubuntu/Dockerfile‎

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FROM ubuntu:22.04 AS builder-image
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# To avoid tzdata blocking the build with frontend questions
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ENV DEBIAN_FRONTEND=noninteractive
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# Install python3.10
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RUN : \
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&& apt-get update && apt upgrade \
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&& apt install software-properties-common -y \
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&& add-apt-repository ppa:deadsnakes/ppa -y && apt update \
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&& apt-get install -y --no-install-recommends python3.10-venv \
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&& apt-get install libpython3.10-de -y \
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&& apt-get install python3.10-dev -y \
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&& apt-get install build-essential -y \
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&& apt-get clean \
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&& :
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# Add env to PATH
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RUN python3.10 -m venv /venv
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ENV PATH=/venv/bin:$PATH
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# install TIAToolbox and its requirements
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RUN apt-get update && apt-get install --no-install-recommends -y \
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libopenjp2-7-dev libopenjp2-tools \
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openslide-tools \
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libgl1 \
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&& apt-get clean && rm -rf /var/lib/apt/lists/*
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RUN pip install --no-cache-dir tiatoolbox
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# activate virtual environment
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ENV VIRTUAL_ENV=/opt/venv
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ENV PATH="/opt/venv/bin:$PATH"

‎docker/3.7/Debian/Dockerfile‎

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FROM python:3.7-slim-bullseye
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#get linux packages
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RUN apt-get -y update && apt-get -y install --no-install-recommends \
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libopenjp2-7-dev libopenjp2-tools \
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openslide-tools \
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libgl1 \
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build-essential \
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&& pip3 --no-cache-dir install tiatoolbox \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*

‎docker/3.8/Debian/Dockerfile‎

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FROM python:3.8-slim-bullseye
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#get linux packages
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RUN apt-get -y update && apt-get -y install --no-install-recommends \
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libopenjp2-7-dev libopenjp2-tools \
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openslide-tools \
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libgl1 \
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build-essential \
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&& pip3 --no-cache-dir install tiatoolbox \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*

‎docker/3.9/Debian/Dockerfile‎

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FROM python:3.9-slim-bullseye
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#get linux packages
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RUN apt-get -y update && apt-get -y install --no-install-recommends \
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libopenjp2-7-dev libopenjp2-tools \
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openslide-tools \
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libgl1 \
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build-essential \
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&& pip3 --no-cache-dir install tiatoolbox \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*

‎docker/3.9/Ubuntu/Dockerfile‎

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FROM ubuntu:22.04 AS builder-image
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# To avoid tzdata blocking the build with frontend questions
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ENV DEBIAN_FRONTEND=noninteractive
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# Install python3.9
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RUN : \
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&& apt-get update && apt upgrade \
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&& apt install software-properties-common -y \
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&& add-apt-repository ppa:deadsnakes/ppa -y && apt update \
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&& apt-get install -y --no-install-recommends python3.9-venv \
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&& apt-get install libpython3.9-de -y \
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&& apt-get install python3.9-dev -y \
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&& apt-get install build-essential -y \
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&& apt-get clean \
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&& :
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# Add env to PATH
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RUN python3.9 -m venv /venv
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ENV PATH=/venv/bin:$PATH
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# install TIAToolbox and its requirements
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RUN apt-get update && apt-get install --no-install-recommends -y \
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libopenjp2-7-dev libopenjp2-tools \
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openslide-tools \
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libgl1 \
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&& apt-get clean && rm -rf /var/lib/apt/lists/*
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RUN pip install --no-cache-dir tiatoolbox
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# activate virtual environment
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ENV VIRTUAL_ENV=/opt/venv
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ENV PATH="/opt/venv/bin:$PATH"
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CMD ["python"]

‎docs/images/wsi-registration.png‎

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