Numpy 1.26 update to support Python 3.12 (#2025)

* np.product is deprecated in numpy 1.25. Use np.prod instead.

* np.NINF is deprecated in numpy 2.0. Use -np.inf instead.

* updating requirements files for numpy==1.26.4

* Updating tests as quicksort (default) is not stable for columns with same values

REQUIREMENTS.txt

@@ -8,8 +8,8 @@ jsonschema<4.18
 matplotlib<3.8
 # pinning mistune for m2r2 in CI requirements
 mistune==0.8.4
-# numpy 1.25 slightly changes values in three tests causing them to fail
-numpy<1.25
+# numpy 2.0 breaks code and migration requires additional work
+numpy<2
 read_roi
 regional
 # scikit-image is temporarily pinned as newer versions require updating module imports

requirements/REQUIREMENTS-CI.txt

@@ -6,15 +6,15 @@ babel==2.16.0
 backports.tarfile==1.2.0
 beautifulsoup4==4.12.3
 bleach==6.1.0
-boto3==1.35.13
-botocore==1.35.13
+boto3==1.35.38
+botocore==1.35.38
 certifi==2024.8.30
 cffi==1.17.1
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 click==8.1.7
 commonmark==0.9.1
 contourpy==1.3.0
-coverage==7.6.1
+coverage==7.6.2
 cryptography==43.0.1
 cycler==0.12.1
 decorator==5.1.1
@@ -28,36 +28,36 @@ executing==2.1.0
 fastjsonschema==2.20.0
 flake8==7.1.1
 flake8-import-order==0.18.2
-fonttools==4.53.1
-h5py==3.11.0
-idna==3.8
+fonttools==4.54.1
+h5py==3.12.1
+idna==3.10
 imageio==2.35.1
 imagesize==1.4.1
-importlib_metadata==8.4.0
-importlib_resources==6.4.4
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
 iniconfig==2.0.0
 ipython==8.18.1
 jaraco.classes==3.4.0
 jaraco.context==6.0.1
-jaraco.functools==4.0.2
+jaraco.functools==4.1.0
 jedi==0.19.1
 jeepney==0.8.0
 Jinja2==3.1.4
 jmespath==1.0.1
 joblib==1.4.2
 jsonschema==4.17.3
-jupyter_client==8.6.2
+jupyter_client==8.6.3
 jupyter_core==5.7.2
 jupyterlab_pygments==0.3.0
-keyring==25.3.0
+keyring==25.4.1
 kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
 lxml==5.3.0
-lxml_html_clean==0.2.2
+lxml_html_clean==0.3.1
 m2r2==0.3.3.post2
 markdown-it-py==3.0.0
-MarkupSafe==2.1.5
+MarkupSafe==3.0.1
 matplotlib==3.7.5
 matplotlib-inline==0.1.7
 mccabe==0.7.0
@@ -73,18 +73,18 @@ nbencdec==0.0.10
 nbformat==5.10.4
 networkx==3.2.1
 nh3==0.2.18
-numpy==1.24.4
+numpy==1.26.4
 numpydoc==1.8.0
 packaging==24.1
-pandas==2.2.2
+pandas==2.2.3
 pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
 pillow==10.4.0
 pkginfo==1.10.0
-platformdirs==4.2.2
+platformdirs==4.3.6
 pluggy==1.5.0
-prompt_toolkit==3.0.47
+prompt_toolkit==3.0.48
 ptyprocess==0.7.0
 pure_eval==0.2.3
 pycodestyle==2.12.1
@@ -93,11 +93,11 @@ pyflakes==3.2.0
 Pygments==2.18.0
 pyparsing==3.1.4
 pyrsistent==0.20.0
-pytest==8.3.2
+pytest==8.3.3
 pytest-cov==5.0.0
 pytest-xdist==3.6.1
 python-dateutil==2.9.0.post0
-pytz==2024.1
+pytz==2024.2
 PyWavelets==1.6.0
 PyYAML==6.0.2
 pyzmq==26.2.0
@@ -108,15 +108,15 @@ regional==1.1.2
 requests==2.32.3
 requests-toolbelt==1.0.0
 rfc3986==2.0.0
-rich==13.8.0
-s3transfer==0.10.2
+rich==13.9.2
+s3transfer==0.10.3
 scikit-image==0.21.0
-scikit-learn==1.5.1
+scikit-learn==1.5.2
 scipy==1.13.1
 seaborn==0.13.2
 SecretStorage==3.3.3
 semantic-version==2.10.0
-setuptools==74.1.2
+setuptools==75.1.0
 showit==1.1.4
 six==1.16.0
 slicedimage==4.1.1
@@ -125,8 +125,8 @@ soupsieve==2.6
 Sphinx==7.4.7
 sphinx-autodoc-typehints==2.3.0
 sphinx-bootstrap-theme==0.8.1
-sphinx-gallery==0.17.1
-sphinx-rtd-theme==2.0.0
+sphinx-gallery==0.18.0
+sphinx-rtd-theme==3.0.1
 sphinxcontrib-applehelp==2.0.0
 sphinxcontrib-devhelp==2.0.0
 sphinxcontrib-htmlhelp==2.1.0
@@ -136,26 +136,26 @@ sphinxcontrib-programoutput==0.17
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 stack-data==0.6.3
-sympy==1.13.2
+sympy==1.13.3
 tabulate==0.9.0
 threadpoolctl==3.5.0
 tifffile==2024.8.30
 tinycss2==1.3.0
-tomli==2.0.1
+tomli==2.0.2
 tornado==6.4.1
 tqdm==4.66.5
 trackpy==0.6.4
 traitlets==5.14.3
 twine==5.1.1
-types-PyYAML==6.0.12.20240808
+types-PyYAML==6.0.12.20240917
 types-requests==2.31.0.6
-types-setuptools==74.1.0.20240906
+types-setuptools==75.1.0.20240917
 types-urllib3==1.26.25.14
 typing_extensions==4.12.2
-tzdata==2024.1
+tzdata==2024.2
 urllib3==1.26.20
 validators==0.34.0
 wcwidth==0.2.13
 webencodings==0.5.1
 xarray==2023.8.0
-zipp==3.20.1
+zipp==3.20.2

requirements/REQUIREMENTS-JUPYTER.txt

@@ -1,5 +1,5 @@
 # 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==4.4.0
+anyio==4.6.0
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
 arrow==1.3.0
@@ -9,16 +9,16 @@ attrs==24.2.0
 babel==2.16.0
 beautifulsoup4==4.12.3
 bleach==6.1.0
-boto3==1.35.13
-botocore==1.35.13
+boto3==1.35.38
+botocore==1.35.38
 certifi==2024.8.30
 cffi==1.17.1
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 click==8.1.7
 comm==0.2.2
 contourpy==1.3.0
 cycler==0.12.1
-debugpy==1.8.5
+debugpy==1.8.7
 decorator==5.1.1
 defusedxml==0.7.1
 diskcache==5.6.3
@@ -27,16 +27,16 @@ entrypoints==0.4
 exceptiongroup==1.2.2
 executing==2.1.0
 fastjsonschema==2.20.0
-fonttools==4.53.1
+fonttools==4.54.1
 fqdn==1.5.1
 h11==0.14.0
-h5py==3.11.0
-httpcore==1.0.5
+h5py==3.12.1
+httpcore==1.0.6
 httpx==0.27.2
-idna==3.8
+idna==3.10
 imageio==2.35.1
-importlib_metadata==8.4.0
-importlib_resources==6.4.4
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
 ipykernel==6.29.5
 ipython==8.18.1
 ipywidgets==8.1.5
@@ -52,7 +52,7 @@ jupyter==1.1.1
 jupyter-console==6.6.3
 jupyter-events==0.6.3
 jupyter-lsp==2.2.5
-jupyter_client==8.6.2
+jupyter_client==8.6.3
 jupyter_core==5.7.2
 jupyter_server==2.10.0
 jupyter_server_terminals==0.5.3
@@ -64,7 +64,7 @@ kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
 lxml==5.3.0
-MarkupSafe==2.1.5
+MarkupSafe==3.0.1
 matplotlib==3.7.5
 matplotlib-inline==0.1.7
 mistune==0.8.4
@@ -76,17 +76,17 @@ nest-asyncio==1.6.0
 networkx==3.2.1
 notebook==7.1.3
 notebook_shim==0.2.4
-numpy==1.24.4
+numpy==1.26.4
 overrides==7.7.0
 packaging==24.1
-pandas==2.2.2
+pandas==2.2.3
 pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
 pillow==10.4.0
-platformdirs==4.2.2
-prometheus_client==0.20.0
-prompt_toolkit==3.0.47
+platformdirs==4.3.6
+prometheus_client==0.21.0
+prompt_toolkit==3.0.48
 psutil==6.0.0
 ptyprocess==0.7.0
 pure_eval==0.2.3
@@ -96,7 +96,7 @@ pyparsing==3.1.4
 pyrsistent==0.20.0
 python-dateutil==2.9.0.post0
 python-json-logger==2.0.7
-pytz==2024.1
+pytz==2024.2
 PyWavelets==1.6.0
 PyYAML==6.0.2
 pyzmq==26.2.0
@@ -105,33 +105,33 @@ regional==1.1.2
 requests==2.32.3
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
-s3transfer==0.10.2
+s3transfer==0.10.3
 scikit-image==0.21.0
-scikit-learn==1.5.1
+scikit-learn==1.5.2
 scipy==1.13.1
 seaborn==0.13.2
 semantic-version==2.10.0
 Send2Trash==1.8.3
-setuptools==74.1.2
+setuptools==75.1.0
 showit==1.1.4
 six==1.16.0
 slicedimage==4.1.1
 sniffio==1.3.1
 soupsieve==2.6
 stack-data==0.6.3
-sympy==1.13.2
+sympy==1.13.3
 terminado==0.18.1
 threadpoolctl==3.5.0
 tifffile==2024.8.30
 tinycss2==1.3.0
-tomli==2.0.1
+tomli==2.0.2
 tornado==6.4.1
 tqdm==4.66.5
 trackpy==0.6.4
 traitlets==5.14.3
-types-python-dateutil==2.9.0.20240906
+types-python-dateutil==2.9.0.20241003
 typing_extensions==4.12.2
-tzdata==2024.1
+tzdata==2024.2
 uri-template==1.3.0
 urllib3==1.26.20
 validators==0.34.0
@@ -141,4 +141,4 @@ webencodings==0.5.1
 websocket-client==1.8.0
 widgetsnbextension==4.0.13
 xarray==2023.8.0
-zipp==3.20.1
+zipp==3.20.2