Merge branch 'develop' into pre-commit-ci-update-config

Author: shaneahmed

docs/requirements.txt

@@ -1,7 +1,6 @@
-furo>=2022.6.21
-jinja2>=3.0.3, <3.1.0
+furo>=2022.12.7
 myst-nb>=0.17.1
 myst-parser>=0.18.1
-sphinx-copybutton>=0.5.0
-sphinx-toolbox>=3.1.2
+sphinx-copybutton>=0.5.1
+sphinx-toolbox>=3.2.0
 sphinx_design>=0.3.0

requirements.txt

@@ -4,28 +4,28 @@ albumentations>=1.3.0
 Click>=8.1.3
 defusedxml>=0.7.1
 flask>=2.2.2
-glymur>=0.11.7
-imagecodecs>=2021.11.20
-jupyterlab>=3.4.8
-matplotlib>=3.5.3
-numpy>=1.21.6
+glymur>=0.12.1
+imagecodecs>=2022.9.26
+jupyterlab>=3.5.2
+matplotlib>=3.6.2
+numpy>=1.23.5
 opencv-python>=4.6.0
 openslide-python>=1.2.0
-pandas>=1.3.5
-pillow>=9.2.0
-pydicom>=2.3.0 # Used by wsidicom
+pandas>=1.5.2
+pillow>=9.3.0
+pydicom>=2.3.1 # Used by wsidicom
 pyyaml>=6.0
 requests>=2.28.1
 scikit-image>=0.19.3
-scikit-learn>=1.0.2
-scipy>=1.7.3
+scikit-learn>=1.2.0
+scipy>=1.9.3
 shapely>=1.8.5, <2.0.0 # Remove 2.0.0 once AnnotationStore is compatible
-SimpleITK>=2.1.1
-sphinx>=4.3.2
-tifffile>=2021.11.2
-torch>=1.13.0
-torchvision>=0.13.0
+SimpleITK>=2.2.1
+sphinx>=5.3.0
+tifffile>=2022.10.10
+torch>=1.13.1
+torchvision>=0.14.1
 tqdm>=4.64.1
 umap-learn>=0.5.3
-wsidicom>=0.3.2
-zarr>=2.12.0
+wsidicom>=0.5.0
+zarr>=2.13.3

requirements_dev.txt

@@ -1,17 +1,19 @@
 -r requirements.txt
 -r docs/requirements.txt
-black>=22.10.0
+black>=22.12.0
 bump2version>=1.0.1
-coverage>=6.5.0
-docutils>=0.17.1
+coverage>=7.0.0
+docutils>=0.18.1
 flake8>=5.0.4
-flake8-bugbear>=22.9.23
+flake8-bugbear>=22.10.27
+isort>=5.11.4
+jinja2>=3.0.3, <3.1.0
 pip>=22.3
 pre-commit>=2.20.0
-pytest>=7.1.3
+pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 toml>=0.10.2
-tox>=3.26.0
+tox>=3.27.1
 twine>=4.0.1
 wheel>=0.37.1