Update Sphinx & optional dependencies version pin

Updated Sphinx and optional dependencies packages pinned versions in
`environment-dev.yaml`, `environment-test.yaml`, and `environment-rtd.yaml` in
preparation for Python 3.13 environment.

envs/environment-dev.yaml

@@ -44,9 +44,9 @@ dependencies:
   - tomli
 
   # For documentation
-  - sphinx=7.2.6
-  - sphinx-notfound-page=1.0.0
-  - sphinx-rtd-theme=2.0.0
+  - sphinx==8.1.3
+  - sphinx-notfound-page==1.0.4
+  - sphinx-rtd-theme==3.0.0
 
   - pip:
     # install of Reshapr package in editable mode

envs/environment-rtd.yaml

@@ -11,9 +11,9 @@ dependencies:
   - python=3.12
 
   # Sphinx and extensions
-  - sphinx=7.2.6
-  - sphinx-notfound-page=1.0.0
-  - sphinx-rtd-theme=2.0.0
+  - sphinx==8.1.3
+  - sphinx-notfound-page==1.0.4
+  - sphinx-rtd-theme==3.0.0
 
   # readthedocs build system packages
   - mock

envs/environment-test.yaml

@@ -33,9 +33,9 @@ dependencies:
   - tomli
 
   # For documentation links checking
-  - sphinx=7.2.6
-  - sphinx-notfound-page=1.0.0
-  - sphinx-rtd-theme=2.0.0
+  - sphinx==8.1.3
+  - sphinx-notfound-page==1.0.4
+  - sphinx-rtd-theme==3.0.0
 
   - pip:
     # install Reshapr package in editable mode

envs/requirements.txt

@@ -3,135 +3,135 @@
 # Create/update this file with:
 #   (reshapr-dev)$ python -m pip list --format=freeze >> envs/requirements.txt
 
-alabaster==0.7.16
-anyio==4.3.0
+alabaster==1.0.0
+anyio==4.6.2.post1
 arrow==1.3.0
 Babel==2.14.0
 backports.tarfile==1.0.0
-black==24.4.2
-bokeh==3.4.1
-Bottleneck==1.3.8
+black==24.10.0
+bokeh==3.6.0
+Bottleneck==1.4.2
 Brotli==1.1.0
 cached-property==1.5.2
-certifi==2024.7.4
-cffi==1.16.0
+certifi==2024.8.30
+cffi==1.17.1
 cfgv==3.3.1
-cftime==1.6.3
-charset-normalizer==3.3.2
+cftime==1.6.4
+charset-normalizer==3.4.0
 click==8.1.7
-cloudpickle==3.0.0
+cloudpickle==3.1.0
 colorama==0.4.6
-contourpy==1.2.1
-coverage==7.5.1
-cryptography==43.0.1
-cytoolz==0.12.3
-dask==2024.5.1
-dask-expr==1.1.1
-distlib==0.3.8
-distributed==2024.5.1
-docutils==0.20.1
+contourpy==1.3.0
+coverage==7.6.4
+cryptography==43.0.3
+cytoolz==1.0.0
+dask==2024.10.0
+dask-expr==1.1.16
+distlib==0.3.9
+distributed==2024.10.0
+docutils==0.21.2
 editables==0.5
-exceptiongroup==1.2.0
-filelock==3.14.0
-flox==0.9.7
-fsspec==2024.5.0
+exceptiongroup==1.2.2
+filelock==3.16.1
+flox==0.9.12
+fsspec==2024.10.0
 h11==0.14.0
 h2==4.1.0
-h5netcdf==1.3.0
-h5py==3.11.0
-hatch==1.11.1
-hatchling==1.24.2
+h5netcdf==1.4.0
+h5py==3.12.1
+hatch==1.13.0
+hatchling==1.25.0
 hpack==4.0.0
-httpcore==1.0.5
-httpx==0.27.0
+httpcore==1.0.6
+httpx==0.27.2
 hyperframe==6.0.1
 hyperlink==21.0.0
-identify==2.5.36
-idna==3.7
+identify==2.6.1
+idna==3.10
 imagesize==1.4.1
-importlib_metadata==7.1.0
-importlib_resources==6.4.0
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
 iniconfig==2.0.0
 jaraco.classes==3.4.0
 jaraco.context==5.3.0
 jaraco.functools==4.0.0
 jeepney==0.8.0
 Jinja2==3.1.4
-keyring==25.2.1
+keyring==25.5.0
 locket==1.0.0
 lz4==4.3.3
 markdown-it-py==3.0.0
-MarkupSafe==2.1.5
+MarkupSafe==3.0.2
 mdurl==0.1.2
-more-itertools==10.2.0
-msgpack==1.0.8
+more-itertools==10.5.0
+msgpack==1.1.0
 mypy-extensions==1.0.0
-netCDF4==1.6.5
-nodeenv==1.8.0
-numpy==1.26.4
-numpy-groupies==0.11.1
-packaging==24.0
-pandas==2.2.2
+netCDF4==1.7.1
+nodeenv==1.9.1
+numpy==2.1.3
+numpy-groupies==0.11.2
+packaging==24.1
+pandas==2.2.3
 partd==1.4.2
 pathspec==0.12.1
 pexpect==4.9.0
-pillow==10.3.0
-pip==24.0
-platformdirs==4.2.2
+pillow==11.0.0
+pip==24.3.1
+platformdirs==4.3.6
 pluggy==1.5.0
-pre_commit==3.7.1
-psutil==5.9.8
+pre_commit==4.0.1
+psutil==6.1.0
 ptyprocess==0.7.0
-pyarrow==15.0.2
-pyarrow-hotfix==0.6
+pyarrow==18.0.0
 pycparser==2.22
 Pygments==2.18.0
 PySocks==1.7.1
-pytest==8.2.1
-pytest-cov==5.0.0
+pytest==8.3.3
+pytest-cov==6.0.0
 pytest-randomly==3.15.0
 python-dateutil==2.9.0
 pytz==2024.1
-PyYAML==6.0.1
-requests==2.32.2
-rich==13.7.1
-scipy==1.13.1
+PyYAML==6.0.2
+requests==2.32.3
+Reshapr==24.1.dev0
+rich==13.9.4
+scipy==1.14.1
 SecretStorage==3.3.3
-setuptools==70.0.0
+setuptools==75.3.0
 shellingham==1.5.4
 six==1.16.0
 sniffio==1.3.1
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
-Sphinx==7.2.6
-sphinx-notfound-page==1.0.0
-sphinx-rtd-theme==2.0.0
-sphinxcontrib-applehelp==1.0.8
-sphinxcontrib-devhelp==1.0.6
-sphinxcontrib-htmlhelp==2.0.5
+Sphinx==8.1.3
+sphinx-notfound-page==1.0.4
+sphinx_rtd_theme==3.0.0
+sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.7
+sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==1.1.10
-structlog==24.1.0
+structlog==24.4.0
 tblib==3.0.0
 toml==0.10.2
-tomli==2.0.1
-tomli_w==1.0.0
-tomlkit==0.12.5
-toolz==0.12.1
+tomli==2.0.2
+tomli_w==1.1.0
+tomlkit==0.13.2
+toolz==1.0.0
 tornado==6.4.1
-trove-classifiers==2024.5.22
-types-python-dateutil==2.9.0.20240316
-typing_extensions==4.11.0
-tzdata==2024.1
+trove-classifiers==2024.10.21.16
+types-python-dateutil==2.9.0.20241003
+typing_extensions==4.12.2
+tzdata==2024.2
 ukkonen==1.0.1
-urllib3==2.2.2
+urllib3==2.2.3
 userpath==1.7.0
-virtualenv==20.26.2
-wheel==0.43.0
-xarray==2024.5.0
-xyzservices==2024.4.0
+virtualenv==20.27.1
+wheel==0.44.0
+xarray==2024.10.0
+xyzservices==2024.9.0
 zict==3.0.0
-zipp==3.19.1
-zstandard==0.22.0
+zipp==3.20.2
+zstandard==0.23.0