rolling back to Sphinx v5 as v6-8 introduce issues on ReadTheDocs wit…

…h navbar logo and sub-menus

REQUIREMENTS.txt

@@ -1,6 +1,7 @@
 click
-# docutils introduces an AttributeError: module 'docutils.nodes' has no attribute 'reprunicode'
-docutils<0.21
+# docutils 0.22 introduces an AttributeError: module 'docutils.nodes' has no attribute 'reprunicode'
+# sphinx 5.3.0 requires docutils<0.20
+docutils<0.20
 h5py
 # jsonschema 4.18.0 made RefResolver deprecated
 jsonschema<4.18

requirements/REQUIREMENTS-CI.txt

@@ -1,41 +1,42 @@
 # 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==24.3.0
-babel==2.16.0
+attrs==25.1.0
+babel==2.17.0
 backports.tarfile==1.2.0
-beautifulsoup4==4.12.3
+beautifulsoup4==4.13.3
 bleach==6.2.0
-boto3==1.35.86
-botocore==1.35.86
+boto3==1.36.15
+botocore==1.36.15
 build==1.2.2.post1
-certifi==2024.12.14
+certifi==2025.1.31
 cffi==1.17.1
-charset-normalizer==3.4.0
+charset-normalizer==3.4.1
 click==8.1.8
 commonmark==0.9.1
 contourpy==1.3.0
-coverage==7.6.9
+coverage==7.6.10
 cryptography==44.0.0
 cycler==0.12.1
 decorator==5.1.1
 defusedxml==0.7.1
 diskcache==5.6.3
-docutils==0.20.1
+docutils==0.19
 entrypoints==0.4
 exceptiongroup==1.2.2
 execnet==2.1.1
-executing==2.1.0
+executing==2.2.0
 fastjsonschema==2.21.1
 flake8==7.1.1
 flake8-import-order==0.18.2
-fonttools==4.55.3
+fonttools==4.56.0
 h5py==3.12.1
+id==1.5.0
 idna==3.10
-imageio==2.36.1
+imageio==2.37.0
 imagesize==1.4.1
-importlib_metadata==8.5.0
-importlib_resources==6.4.5
+importlib_metadata==8.6.1
+importlib_resources==6.5.2
 iniconfig==2.0.0
 ipython==8.18.1
 jaraco.classes==3.4.0
@@ -50,7 +51,7 @@ jsonschema==4.17.3
 jupyter_client==8.6.3
 jupyter_core==5.7.2
 jupyterlab_pygments==0.3.0
-keyring==25.5.0
+keyring==25.6.0
 kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
@@ -64,7 +65,7 @@ matplotlib-inline==0.1.7
 mccabe==0.7.0
 mdurl==0.1.2
 mistune==0.8.4
-more-itertools==10.5.0
+more-itertools==10.6.0
 mpmath==1.3.0
 mypy==1.10.1
 mypy-extensions==1.0.0
@@ -75,33 +76,32 @@ nbformat==5.10.4
 networkx==3.2.1
 nh3==0.2.20
 numpy==1.26.4
-numpydoc==1.8.0
+numpydoc==1.6.0
 packaging==24.2
 pandas==2.2.3
 pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
-pillow==11.0.0
-pkginfo==1.12.0
+pillow==11.1.0
 platformdirs==4.3.6
 pluggy==1.5.0
-prompt_toolkit==3.0.48
+prompt_toolkit==3.0.50
 ptyprocess==0.7.0
 pure_eval==0.2.3
 pycodestyle==2.12.1
 pycparser==2.22
 pyflakes==3.2.0
-Pygments==2.18.0
-pyparsing==3.2.0
+Pygments==2.19.1
+pyparsing==3.2.1
 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
+pytz==2025.1
 PyYAML==6.0.2
-pyzmq==26.2.0
+pyzmq==26.2.1
 read-roi==1.6.0
 readme_renderer==43.0
 recommonmark==0.7.1
@@ -110,24 +110,24 @@ requests==2.32.3
 requests-toolbelt==1.0.0
 rfc3986==2.0.0
 rich==13.9.4
-s3transfer==0.10.4
+s3transfer==0.11.2
 scikit-image==0.24.0
-scikit-learn==1.6.0
+scikit-learn==1.6.1
 scipy==1.13.1
 seaborn==0.13.2
 SecretStorage==3.3.3
 semantic-version==2.10.0
-setuptools==75.6.0
+setuptools==75.8.0
 showit==1.1.4
 six==1.17.0
 slicedimage==4.1.1
 snowballstemmer==2.2.0
 soupsieve==2.6
-Sphinx==7.4.7
-sphinx-autodoc-typehints==2.3.0
+Sphinx==5.3.0
+sphinx-autodoc-typehints==1.23.0
 sphinx-bootstrap-theme==0.8.1
 sphinx-gallery==0.18.0
-sphinx-rtd-theme==3.0.2
+sphinx-rtd-theme==2.0.0
 sphinxcontrib-applehelp==2.0.0
 sphinxcontrib-devhelp==2.0.0
 sphinxcontrib-htmlhelp==2.1.0
@@ -147,13 +147,13 @@ tornado==6.4.2
 tqdm==4.67.1
 trackpy==0.6.4
 traitlets==5.14.3
-twine==6.0.1
-types-PyYAML==6.0.12.20241221
+twine==6.1.0
+types-PyYAML==6.0.12.20241230
 types-requests==2.31.0.6
-types-setuptools==75.6.0.20241223
+types-setuptools==75.8.0.20250110
 types-urllib3==1.26.25.14
 typing_extensions==4.12.2
-tzdata==2024.2
+tzdata==2025.1
 urllib3==1.26.20
 validators==0.34.0
 wcwidth==0.2.13

requirements/REQUIREMENTS-CI.txt.in

@@ -17,7 +17,7 @@ pytest-cov>=2.5.1
 pytest-xdist
 recommonmark
 requests
-sphinx
+sphinx>5,<6
 sphinx_autodoc_typehints
 sphinx_bootstrap_theme
 sphinxcontrib-programoutput

starfish/REQUIREMENTS-STRICT.txt

@@ -1,19 +1,19 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (REQUIREMENTS.txt) and run make starfish/REQUIREMENTS-STRICT.txt
-attrs==24.3.0
-boto3==1.35.86
-botocore==1.35.86
-certifi==2024.12.14
-charset-normalizer==3.4.0
+attrs==25.1.0
+boto3==1.36.15
+botocore==1.36.15
+certifi==2025.1.31
+charset-normalizer==3.4.1
 click==8.1.8
 contourpy==1.3.0
 cycler==0.12.1
 diskcache==5.6.3
-docutils==0.20.1
-fonttools==4.55.3
+docutils==0.19
+fonttools==4.56.0
 h5py==3.12.1
 idna==3.10
-imageio==2.36.1
-importlib_resources==6.4.5
+imageio==2.37.0
+importlib_resources==6.5.2
 jmespath==1.0.1
 joblib==1.4.2
 jsonschema==4.17.3
@@ -27,22 +27,22 @@ networkx==3.2.1
 numpy==1.26.4
 packaging==24.2
 pandas==2.2.3
-pillow==11.0.0
-pyparsing==3.2.0
+pillow==11.1.0
+pyparsing==3.2.1
 pyrsistent==0.20.0
 python-dateutil==2.9.0.post0
-pytz==2024.2
+pytz==2025.1
 PyYAML==6.0.2
 read-roi==1.6.0
 regional==1.1.2
 requests==2.32.3
-s3transfer==0.10.4
+s3transfer==0.11.2
 scikit-image==0.24.0
-scikit-learn==1.6.0
+scikit-learn==1.6.1
 scipy==1.13.1
 seaborn==0.13.2
 semantic-version==2.10.0
-setuptools==75.6.0
+setuptools==75.8.0
 showit==1.1.4
 six==1.17.0
 slicedimage==4.1.1
@@ -51,7 +51,7 @@ threadpoolctl==3.5.0
 tifffile==2024.8.30
 tqdm==4.67.1
 trackpy==0.6.4
-tzdata==2024.2
+tzdata==2025.1
 urllib3==1.26.20
 validators==0.34.0
 xarray==2023.8.0