Scikit image update from 0.21 to 0.23+ (#2049)

* changed importing of img_as_float32() to skimage.util

* silencing mypy error due to dynamic function call

* removing stale code and loading match_histograms from skimage.exposure

* output parameter in gaussian() is replaced by out

* replacing _GeometricTransform with SimilarityTransform

* updating requirements files

REQUIREMENTS.txt

@@ -12,8 +12,7 @@ mistune==0.8.4
 numpy<2
 read_roi
 regional
-# scikit-image is temporarily pinned as newer versions require updating module imports
-scikit-image==0.21
+scikit-image>0.22
 scikit-learn
 seaborn
 semantic_version

requirements/REQUIREMENTS-CI.txt

@@ -1,18 +1,18 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (requirements/REQUIREMENTS-CI.txt.in) and run make requirements/REQUIREMENTS-CI.txt
 alabaster==0.7.16
 asttokens==3.0.0
-attrs==24.2.0
+attrs==24.3.0
 babel==2.16.0
 backports.tarfile==1.2.0
 beautifulsoup4==4.12.3
 bleach==6.2.0
-boto3==1.35.38
-botocore==1.35.38
+boto3==1.35.86
+botocore==1.35.86
 build==1.2.2.post1
-certifi==2024.8.30
+certifi==2024.12.14
 cffi==1.17.1
 charset-normalizer==3.4.0
-click==8.1.7
+click==8.1.8
 commonmark==0.9.1
 contourpy==1.3.0
 coverage==7.6.9
@@ -29,10 +29,10 @@ executing==2.1.0
 fastjsonschema==2.21.1
 flake8==7.1.1
 flake8-import-order==0.18.2
-fonttools==4.54.1
+fonttools==4.55.3
 h5py==3.12.1
 idna==3.10
-imageio==2.35.1
+imageio==2.36.1
 imagesize==1.4.1
 importlib_metadata==8.5.0
 importlib_resources==6.4.5
@@ -68,20 +68,20 @@ more-itertools==10.5.0
 mpmath==1.3.0
 mypy==1.10.1
 mypy-extensions==1.0.0
-nbclient==0.10.1
+nbclient==0.10.2
 nbconvert==6.5.4
 nbencdec==0.0.10
 nbformat==5.10.4
 networkx==3.2.1
-nh3==0.2.19
+nh3==0.2.20
 numpy==1.26.4
 numpydoc==1.8.0
-packaging==24.1
+packaging==24.2
 pandas==2.2.3
 pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
-pillow==10.4.0
+pillow==11.0.0
 pkginfo==1.12.0
 platformdirs==4.3.6
 pluggy==1.5.0
@@ -92,15 +92,14 @@ pycodestyle==2.12.1
 pycparser==2.22
 pyflakes==3.2.0
 Pygments==2.18.0
-pyparsing==3.1.4
+pyparsing==3.2.0
 pyproject_hooks==1.2.0
 pyrsistent==0.20.0
 pytest==8.3.4
 pytest-cov==6.0.0
 pytest-xdist==3.6.1
 python-dateutil==2.9.0.post0
 pytz==2024.2
-PyWavelets==1.6.0
 PyYAML==6.0.2
 pyzmq==26.2.0
 read-roi==1.6.0
@@ -111,16 +110,16 @@ requests==2.32.3
 requests-toolbelt==1.0.0
 rfc3986==2.0.0
 rich==13.9.4
-s3transfer==0.10.3
-scikit-image==0.21.0
-scikit-learn==1.5.2
+s3transfer==0.10.4
+scikit-image==0.24.0
+scikit-learn==1.6.0
 scipy==1.13.1
 seaborn==0.13.2
 SecretStorage==3.3.3
 semantic-version==2.10.0
-setuptools==75.1.0
+setuptools==75.6.0
 showit==1.1.4
-six==1.16.0
+six==1.17.0
 slicedimage==4.1.1
 snowballstemmer==2.2.0
 soupsieve==2.6
@@ -145,13 +144,13 @@ tifffile==2024.8.30
 tinycss2==1.4.0
 tomli==2.2.1
 tornado==6.4.2
-tqdm==4.66.5
+tqdm==4.67.1
 trackpy==0.6.4
 traitlets==5.14.3
 twine==6.0.1
-types-PyYAML==6.0.12.20240917
+types-PyYAML==6.0.12.20241221
 types-requests==2.31.0.6
-types-setuptools==75.6.0.20241126
+types-setuptools==75.6.0.20241223
 types-urllib3==1.26.25.14
 typing_extensions==4.12.2
 tzdata==2024.2
@@ -160,4 +159,4 @@ validators==0.34.0
 wcwidth==0.2.13
 webencodings==0.5.1
 xarray==2023.8.0
-zipp==3.20.2
+zipp==3.21.0

requirements/REQUIREMENTS-JUPYTER.txt

@@ -1,51 +1,51 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (requirements/REQUIREMENTS-JUPYTER.txt.in) and run make requirements/REQUIREMENTS-JUPYTER.txt
-anyio==4.6.0
+anyio==4.7.0
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
 arrow==1.3.0
-asttokens==2.4.1
+asttokens==3.0.0
 async-lru==2.0.4
-attrs==24.2.0
+attrs==24.3.0
 babel==2.16.0
 beautifulsoup4==4.12.3
-bleach==6.1.0
-boto3==1.35.38
-botocore==1.35.38
-certifi==2024.8.30
+bleach==6.2.0
+boto3==1.35.86
+botocore==1.35.86
+certifi==2024.12.14
 cffi==1.17.1
 charset-normalizer==3.4.0
-click==8.1.7
+click==8.1.8
 comm==0.2.2
 contourpy==1.3.0
 cycler==0.12.1
-debugpy==1.8.7
+debugpy==1.8.11
 decorator==5.1.1
 defusedxml==0.7.1
 diskcache==5.6.3
 docutils==0.20.1
 entrypoints==0.4
 exceptiongroup==1.2.2
 executing==2.1.0
-fastjsonschema==2.20.0
-fonttools==4.54.1
+fastjsonschema==2.21.1
+fonttools==4.55.3
 fqdn==1.5.1
 h11==0.14.0
 h5py==3.12.1
-httpcore==1.0.6
-httpx==0.27.2
+httpcore==1.0.7
+httpx==0.28.1
 idna==3.10
-imageio==2.35.1
+imageio==2.36.1
 importlib_metadata==8.5.0
 importlib_resources==6.4.5
 ipykernel==6.29.5
 ipython==8.18.1
 ipywidgets==8.1.5
 isoduration==20.11.0
-jedi==0.19.1
+jedi==0.19.2
 Jinja2==3.1.5
 jmespath==1.0.1
 joblib==1.4.2
-json5==0.9.25
+json5==0.10.0
 jsonpointer==3.0.0
 jsonschema==4.17.3
 jupyter==1.1.1
@@ -64,12 +64,12 @@ kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
 lxml==5.3.0
-MarkupSafe==3.0.1
+MarkupSafe==3.0.2
 matplotlib==3.7.5
 matplotlib-inline==0.1.7
 mistune==0.8.4
 mpmath==1.3.0
-nbclient==0.10.0
+nbclient==0.10.2
 nbconvert==6.5.4
 nbformat==5.10.4
 nest-asyncio==1.6.0
@@ -78,43 +78,42 @@ notebook==7.1.3
 notebook_shim==0.2.4
 numpy==1.26.4
 overrides==7.7.0
-packaging==24.1
+packaging==24.2
 pandas==2.2.3
 pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
-pillow==10.4.0
+pillow==11.0.0
 platformdirs==4.3.6
-prometheus_client==0.21.0
+prometheus_client==0.21.1
 prompt_toolkit==3.0.48
-psutil==6.0.0
+psutil==6.1.1
 ptyprocess==0.7.0
 pure_eval==0.2.3
 pycparser==2.22
 Pygments==2.18.0
-pyparsing==3.1.4
+pyparsing==3.2.0
 pyrsistent==0.20.0
 python-dateutil==2.9.0.post0
-python-json-logger==2.0.7
+python-json-logger==3.2.1
 pytz==2024.2
-PyWavelets==1.6.0
 PyYAML==6.0.2
 pyzmq==26.2.0
 read-roi==1.6.0
 regional==1.1.2
 requests==2.32.3
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
-s3transfer==0.10.3
-scikit-image==0.21.0
-scikit-learn==1.5.2
+s3transfer==0.10.4
+scikit-image==0.24.0
+scikit-learn==1.6.0
 scipy==1.13.1
 seaborn==0.13.2
 semantic-version==2.10.0
 Send2Trash==1.8.3
-setuptools==75.1.0
+setuptools==75.6.0
 showit==1.1.4
-six==1.16.0
+six==1.17.0
 slicedimage==4.1.1
 sniffio==1.3.1
 soupsieve==2.6
@@ -123,22 +122,22 @@ sympy==1.13.3
 terminado==0.18.1
 threadpoolctl==3.5.0
 tifffile==2024.8.30
-tinycss2==1.3.0
-tomli==2.0.2
+tinycss2==1.4.0
+tomli==2.2.1
 tornado==6.4.2
-tqdm==4.66.5
+tqdm==4.67.1
 trackpy==0.6.4
 traitlets==5.14.3
-types-python-dateutil==2.9.0.20241003
+types-python-dateutil==2.9.0.20241206
 typing_extensions==4.12.2
 tzdata==2024.2
 uri-template==1.3.0
 urllib3==1.26.20
 validators==0.34.0
 wcwidth==0.2.13
-webcolors==24.8.0
+webcolors==24.11.1
 webencodings==0.5.1
 websocket-client==1.8.0
 widgetsnbextension==4.0.13
 xarray==2023.8.0
-zipp==3.20.2
+zipp==3.21.0