🔖 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 <John-P@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> 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 <rogertrullo@hotmail.com>
shaneahmed · May 5, 2023 · Oct 21, 2022 · Dec 20, 2022 · Dec 20, 2022 · Dec 20, 2022
commit 075c47299148b3f502c526b44b99748fd563e173
diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
@@ -0,0 +1,64 @@
+name: Publish Dockers
+on:
+  workflow_dispatch
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: TissueImageAnalytics/tiatoolbox
+  image: ghcr.io/tissueimageanalytics/tiatoolbox
+  TOOLBOX_VER: 1.3.1
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - dockerfile: ./docker/3.7/Debian/Dockerfile
+            mtag: py3.7-debian
+          - dockerfile: ./docker/3.8/Debian/Dockerfile
+            mtag: py3.8-debian
+          - dockerfile: ./docker/3.9/Debian/Dockerfile
+            mtag: py3.9-debian
+          - dockerfile: ./docker/3.9/Ubuntu/Dockerfile
+            mtag: py3.9-ubuntu
+          - dockerfile: ./docker/3.10/Debian/Dockerfile
+            mtag: py3.10-debian
+          - dockerfile: ./docker/3.10/Ubuntu/Dockerfile
+            mtag: py3.10-ubuntu
+          - dockerfile: ./docker/3.10/Ubuntu/Dockerfile
+            mtag: latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN  }}
+
+      - name: Publishing with 'latest' tag
+        if: contains(matrix.mtag, 'latest')
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          file: ${{ matrix.dockerfile }}
+          push: true
+          tags: "${{ env.image }}:${{ matrix.mtag }}"
+
+      - name: Publishing with explicit tags
+        if: ${{ !contains(matrix.mtag, 'latest') }}
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          file: ${{ matrix.dockerfile }}
+          push: true
+          tags: "${{ env.image }}:${{ env.TOOLBOX_VER }}-${{ matrix.mtag }}"
diff --git a/CITATION.cff b/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: 1.3.0
+version: 1.3.1  # TIAToolbox version
 doi: 10.5281/zenodo.5802442
 date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"

diff --git a/HISTORY.md b/HISTORY.md
@@ -1,5 +1,32 @@
 # History
 
+# 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
+
 ## 1.3.0 (2022-10-20)
 
 ### Major Updates and Feature Improvements

diff --git a/docker/3.10/Debian/Dockerfile b/docker/3.10/Debian/Dockerfile
@@ -0,0 +1,11 @@
+FROM python:3.10-slim-bullseye
+
+#get linux packages
+RUN apt-get -y update && apt-get -y install --no-install-recommends \
+    libopenjp2-7-dev libopenjp2-tools \
+    openslide-tools \
+    libgl1 \
+    build-essential \
+    && pip3 --no-cache-dir install tiatoolbox \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
diff --git a/docker/3.10/Ubuntu/Dockerfile b/docker/3.10/Ubuntu/Dockerfile
@@ -0,0 +1,32 @@
+FROM ubuntu:22.04 AS builder-image
+
+# To avoid tzdata blocking the build with frontend questions
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install python3.10
+RUN : \
+    && apt-get update && apt upgrade \
+    && apt install software-properties-common -y \
+    && add-apt-repository ppa:deadsnakes/ppa -y && apt update \
+    && apt-get install -y --no-install-recommends python3.10-venv \
+    && apt-get install libpython3.10-de -y \
+    && apt-get install python3.10-dev -y \
+    && apt-get install build-essential -y \
+    && apt-get clean \
+    && :
+
+# Add env to PATH
+RUN python3.10 -m venv /venv
+ENV PATH=/venv/bin:$PATH
+
+# install TIAToolbox and its requirements
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    libopenjp2-7-dev libopenjp2-tools \
+    openslide-tools \
+    libgl1 \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+RUN pip install --no-cache-dir tiatoolbox
+
+# activate virtual environment
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
diff --git a/docker/3.7/Debian/Dockerfile b/docker/3.7/Debian/Dockerfile
@@ -0,0 +1,11 @@
+FROM python:3.7-slim-bullseye
+
+#get linux packages
+RUN apt-get -y update && apt-get -y install --no-install-recommends \
+    libopenjp2-7-dev libopenjp2-tools \
+    openslide-tools \
+    libgl1 \
+    build-essential \
+    && pip3 --no-cache-dir install tiatoolbox \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
diff --git a/docker/3.8/Debian/Dockerfile b/docker/3.8/Debian/Dockerfile
@@ -0,0 +1,11 @@
+FROM python:3.8-slim-bullseye
+
+#get linux packages
+RUN apt-get -y update && apt-get -y install --no-install-recommends \
+    libopenjp2-7-dev libopenjp2-tools \
+    openslide-tools \
+    libgl1 \
+    build-essential \
+    && pip3 --no-cache-dir install tiatoolbox \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
diff --git a/docker/3.9/Debian/Dockerfile b/docker/3.9/Debian/Dockerfile
@@ -0,0 +1,11 @@
+FROM python:3.9-slim-bullseye
+
+#get linux packages
+RUN apt-get -y update && apt-get -y install --no-install-recommends \
+    libopenjp2-7-dev libopenjp2-tools \
+    openslide-tools \
+    libgl1 \
+    build-essential \
+    && pip3 --no-cache-dir install tiatoolbox \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
diff --git a/docker/3.9/Ubuntu/Dockerfile b/docker/3.9/Ubuntu/Dockerfile
@@ -0,0 +1,34 @@
+FROM ubuntu:22.04 AS builder-image
+
+# To avoid tzdata blocking the build with frontend questions
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install python3.9
+RUN : \
+    && apt-get update && apt upgrade \
+    && apt install software-properties-common -y \
+    && add-apt-repository ppa:deadsnakes/ppa -y && apt update \
+    && apt-get install -y --no-install-recommends python3.9-venv \
+    && apt-get install libpython3.9-de -y \
+    && apt-get install python3.9-dev -y \
+    && apt-get install build-essential -y \
+    && apt-get clean \
+    && :
+
+# Add env to PATH
+RUN python3.9 -m venv /venv
+ENV PATH=/venv/bin:$PATH
+
+# install TIAToolbox and its requirements
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    libopenjp2-7-dev libopenjp2-tools \
+    openslide-tools \
+    libgl1 \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+RUN pip install --no-cache-dir tiatoolbox
+
+# activate virtual environment
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+
+CMD ["python"]
diff --git a/docs/images/wsi-registration.png b/docs/images/wsi-registration.png
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,8 +1,7 @@
-docutils>=0.17.1
 furo>=2022.6.21
-jinja2<3.1.0
-myst-nb>=0.16.0
-myst-parser>=0.17.0
+jinja2>=3.0.3, <3.1.0
+myst-nb>=0.17.1
+myst-parser>=0.18.1
 sphinx-copybutton>=0.5.0
 sphinx-toolbox>=3.1.2
 sphinx_design>=0.3.0