REL: Release 1.3.0 (#496)

### Major Updates and Feature Improvements

- Adds an AnnotationTileGenerator and AnnotationRenderer which allows serving of tiles rendered directly from an annotation store.
- Adds [DFBR](https://arxiv.org/abs/2202.09971) registration model and jupyter notebook example
  - Adds DICE metric
- Adds [SCCNN](https://doi.org/10.1109/tmi.2016.2525803) architecture. \[[read the docs](https://tia-toolbox.readthedocs.io/en/develop/_autosummary/tiatoolbox.models.architecture.sccnn.SCCNN.html)\]
- Adds [MapDe](https://arxiv.org/abs/1806.06970) architecture. \[[read the docs](https://tia-toolbox.readthedocs.io/en/develop/_autosummary/tiatoolbox.models.architecture.mapde.MapDe.html)\]
- Adds support for reading MPP metadata from  NGFF v0.4
- Adds enhancements to tiatoolbox.annotation.storage that are useful when using an AnnotationStore for visualization purposes.

### Changes to API

- None

### Bug Fixes and Other Changes

- Fixes colorbar_params #410
- Fixes Jupyter notebooks for better read the docs rendering
  - Fixes typos, metadata and links
- Fixes nucleus_segmentor_engine for boundary artefacts
- Fixes the colorbar cropping in tests
- Adds citation in README.md and CITATION.cff to Nature Communications Medicine paper
- Fixes a bug #452 raised by @rogertrullo  where only the numerator of the TIFF resolution tags was being read.
- Fixes HoVer-Net+ post-processing to be inline with original work.
- Fixes a bug where an exception would be raised if the OME XML is missing objective power.

### Development related changes

- Uses Furo theme for readthedocs
- Replaces nbgallery and nbsphinx with myst-nb for jupyter notebook rendering
- Uses myst for markdown parsing
- Uses requirements.txt to define dependencies for requirements consistency
- Adds notebook AST pre-commit hook
- Adds check to validate python examples in the code
- Adds check to resolve imports
- Fixes an error in a docstring which triggered the failing test.
- Adds pre-commit hooks to format markdown and notebook markdown
- Adds pip install workflow to resolve dependencies when requirements file is updated
- Improves TIAToolbox import using LazyLoader

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

Author: shaneahmed

.github/ISSUE_TEMPLATE.md

@@ -1,6 +1,6 @@
-* TIA Toolbox version:
-* Python version:
-* Operating System:
+- TIA Toolbox version:
+- Python version:
+- Operating System:
 
 ### Description
 

.github/workflows/conda-env-create.yml

@@ -4,9 +4,9 @@ name: Solve Conda Environment
 
 on:
   push:
-    paths: [ "requirements*.yml", "conda-env-create.yml" ]
+    paths: [ "requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
   pull_request:
-    paths: [ "requirements*.yml", "conda-env-create.yml" ]
+    paths: [ "requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
   schedule: # Run on the 1st of every month at midnight
     - cron: "0 0 1 * *"
 
@@ -16,15 +16,30 @@ jobs:
       fail-fast: true
       matrix:
         os: [ubuntu-latest, windows-latest]
+        kind: ["dev", "prod"]
         include:
           - os: ubuntu-latest
+            kind: prod
             requirements: requirements.conda.yml
+          - os: ubuntu-latest
+            kind: dev
+            requirements: requirements.dev.conda.yml
           - os: windows-latest
+            kind: prod
             requirements: requirements.win64.conda.yml
+          - os: windows-latest
+            kind: dev
+            requirements: requirements.win64.dev.conda.yml
     runs-on: ${{ matrix.os }}
     timeout-minutes: 20
     steps:
       - uses: actions/checkout@v2
+      - name: Copy requirements files
+        shell: bash
+        run: |
+          cp ./requirements*.txt /tmp/
+          mkdir /tmp/docs/
+          cp ./docs/requirements*.txt /tmp/docs/
       - uses: mamba-org/provision-with-micromamba@main
         with:
           environment-name: tiatoolbox

.github/workflows/pip-install.yml

@@ -0,0 +1,89 @@
+# This workflow will install the package as is on the github default branch using pip
+
+name: pip Install
+
+on:
+    push:
+        paths: [ "requirements*.yml", "conda-env-create.yml", "requirement*.txt", "setup*py", "setup*cfg", "pytproject*toml", "MANIFEST*in"]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: [ubuntu-22.04, windows-latest, macos-latest]
+    steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: 🐧 Install OpenSlide & OpenJPEG
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt update
+        sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
+        python -m pip install --upgrade pip
+    - name: 🍎 Install OpenSlide & OpenJPEG
+      if: runner.os == 'macOS'
+      run: |
+        brew install openslide openjpeg
+        python -m pip install --upgrade pip
+    - name: 🪟 Install OpenJPEG
+      if: runner.os == 'Windows'
+      run: |
+        # Install OpenJPEG
+        git clone https://github.com/uclouvain/openjpeg.git
+        cd openjpeg
+        mkdir build
+        cd build
+        cmake -G "MinGW Makefiles" .. -DCMAKE_BUILD_TYPE=Release
+        ls
+        make -j4
+        make install
+        make clean
+    - name: 🪟 Install OpenSlide
+      if: runner.os == 'Windows'
+      run: |
+        choco install wget --no-progress
+        wget https://github.com/openslide/openslide-winbuild/releases/download/v20220811/openslide-win64-20220811.zip
+        7z x openslide-win64-20220811.zip
+        ls openslide-win64-20220811
+        # Add to PATH
+        echo "$(realpath ./openslide-win64-20220811/bin)" >> $GITHUB_PATH
+        echo "$(realpath ./openslide-win64-20220811/lib)" >> $GITHUB_PATH
+        # Install
+        mkdir "C:\Program Files\openslide"
+        Copy-Item -Path ".\openslide-win64-20220811\*" -Destination "C:\Program Files\openslide" -Recurse
+        ls "C:/Program Files/openslide"
+    - name: 🪟 Install SQLite Shell
+      if: runner.os == 'Windows'
+      run: choco install sqlite.shell --no-progress
+    - name: SQLite Version Information
+      run: |
+        sqlite3 --version
+        sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
+    - name: OpenSlide Version Information
+      if: runner.os == 'Linux'
+      run: openslide-quickhash1sum --version
+    - name: OpenJPEG Version Information
+      continue-on-error: true  # This -h option has exit code 1 for some reason
+      run: opj_dump -h
+    - name: pip Install From GitHub Repo on Linux and macOS
+      if: runner.os != 'Windows'
+      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_REF_NAME}
+    - name: pip Install From GitHub on Windows
+      if: runner.os == 'Windows'
+      run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_REF_NAME
+    - name: Test TIAToolbox Import
+      shell: python
+      run: |
+        import os
+        if hasattr(os, "add_dll_directory"):
+          # Required for Python>=3.8 on Windows
+          with os.add_dll_directory(r"D:\a\tiatoolbox\tiatoolbox\openslide-win64-20220811\bin"):
+            import tiatoolbox
+        else:
+          os.environ["PATH"] = r"D:\a\tiatoolbox\tiatoolbox\openslide-win64-20220811\bin;"
+          import tiatoolbox

.pre-commit-config.yaml

@@ -1,4 +1,36 @@
 repos:
+  - repo: local
+    hooks:
+      - id: pytest-changed-files
+        name: pytest-changed-files
+        entry: pytest
+        files: tests/.*\btest_\w*.py
+        require_serial: true
+        language: system
+        stages: [push]
+      - id: notebook-check-ast
+        name: check notebook ast
+        entry: python pre-commit/notebook_check_ast.py
+        types_or: [jupyter]
+        language: python
+      - id: notebook-markdown-format
+        name: notebook markdown format
+        entry: python pre-commit/notebook_markdown_format.py
+        require_serial: true
+        types_or: [jupyter]
+        language: python
+        additional_dependencies:
+        - mdformat
+        - mdformat-black
+        - mdformat-myst
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.16
+    hooks:
+    - id: mdformat
+      # Optionally add plugins
+      additional_dependencies:
+      - mdformat-gfm  # GitHub flavoured markdown
+      - mdformat-black  # Black formatting for python verbatim blocks
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
     hooks:
@@ -32,15 +64,15 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 22.6.0 # Replace with any tag/version: https://github.com/psf/black/tags
+    rev: 22.10.0 # Replace with any tag/version: https://github.com/psf/black/tags
     hooks:
       - id: black
         language_version: python3 # Should be a command that runs python3.7+
         additional_dependencies: ['click==8.0.4']  # Currently >8.0.4 breaks black
       - id: black-jupyter
         language: python
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 5.0.4
     hooks:
       - id: flake8
         additional_dependencies: [
@@ -59,24 +91,6 @@ repos:
           flake8-return, # Check return statements
           flake8-simplify, # Suggestions to simplify code
           flake8-spellcheck, # Spelling checker
-          flake8-sql, # Check SQL statement style
           flake8-use-fstring, # Encourages use of f-strings vs old style
           pep8-naming, # Check PEP8 class naming
         ]
-  - repo: local
-    hooks:
-      - id: pytest-changed-files
-        name: pytest-changed-files
-        entry: pytest
-        files: tests/.*\btest_\w*.py
-        language: system
-        stages: [push]
-  - repo: local
-    hooks:
-      - id: requirements-consistency
-        name: check requirements are consistent
-        entry: python pre-commit/requirements_consistency.py
-        files: "(requirements.*.(txt|yml|yaml)|setup.py)$"
-        pass_filenames: false
-        language: python
-        additional_dependencies: [pyyaml]

.readthedocs.yml

@@ -5,29 +5,26 @@
 # Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  apt_packages:
+    - openslide-tools
+    - libopenjp2-7-dev
+    - libopenjp2-tools
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-# mkdocs:
-#  configuration: mkdocs.yml
-
 # Optionally build your docs in additional formats such as PDF
 formats:
   - pdf
-  - epub
-
-# Install apt packages
-build:
-  apt_packages:
-    - openslide-tools
-    - libopenjp2-7-dev
-    - libopenjp2-tools
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: "3.8"
   install:
       - requirements: requirements.txt
       - requirements: docs/requirements.txt

AUTHORS.md

@@ -1,26 +1,24 @@
-Credits
-=======
+# Credits
 
-Development Lead
-----------------
+## Development Lead
 
 - TIA Centre led by Nasir Rajpoot <tia@dcs.warwick.ac.uk>
-- Shan E Ahmed Raza  <shaneahmed>
-- John Pocock <John-P>
-- Simon Graham <simongraham>
-- Dang Vu <vqdang>
-- Mostafa Jahanifar <mostafajahanifar>
-- David Epstein <DavidBAEpstein>
-- Srijay Deshpande <Srijay-lab>
-- George Hadjigeorgiou <ghadjigeorghiou>
-- Adam Shephard <adamshephard>
-- Mark Eastwood <measty>
-- Wenqi Lu <wenqi006>
-- Saad Bashir <rajasaad>
+- Shan E Ahmed Raza \<@shaneahmed>
+- John Pocock \<@John-P>
+- Simon Graham \<@simongraham>
+- Dang Vu \<@vqdang>
+- Mostafa Jahanifar \<@mostafajahanifar>
+- David Epstein \<@DavidBAEpstein>
+- Mark Eastwood \<@measty>
+- Srijay Deshpande \<@Srijay-lab>
+- Ruqayya Awan \<@ruqayya>
+- Adam Shephard \<@adamshephard>
+- George Hadjigeorgiou \<@ghadjigeorghiou>
+- Wenqi Lu \<@wenqi006>
+- Saad Bashir \<@rajasaad>
 
-Contributors
-------------
+## Contributors
 
-- Rob Jewsbury <R-J96>
-- Mohsin Bilal <mbhahsmi>
-- Fayyaz Minhas <foxtrotmike>
+- Rob Jewsbury \<@R-J96>
+- Mohsin Bilal \<@mbhahsmi>
+- Fayyaz Minhas \<@foxtrotmike>

CITATION.cff

@@ -43,10 +43,10 @@ authors:
 - family-names: "Raza"
   given-names: "Shan E Ahmed"
   orcid: "https://orcid.org/0000-0002-1097-1738"
-title: "TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics"
-version: 1.2.1
+title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
+version: 1.3.0
 doi: 10.5281/zenodo.5802442
-date-released: 2022-07-07
+date-released: 2022-10-20
 url: "https://github.com/TissueImageAnalytics/tiatoolbox"
 preferred-citation:
   type: article
@@ -93,8 +93,8 @@ preferred-citation:
   - family-names: "Raza"
     given-names: "Shan E Ahmed"
     orcid: "https://orcid.org/0000-0002-1097-1738"
-  doi: "10.1101/2021.12.23.474029"
-  journal: "bioRxiv"
-  month: 12
-  title: "TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics"
-  year: 2021
+  doi: "10.1038/s43856-022-00186-5"
+  journal: "Communications Medicine"
+  month: 09
+  title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
+  year: 2022