diff --git a/.github/workflows/auto-accept-ci-changes.yml b/.github/workflows/auto-accept-ci-changes.yml
index 3c9a34d8..4908e999 100644
--- a/.github/workflows/auto-accept-ci-changes.yml
+++ b/.github/workflows/auto-accept-ci-changes.yml
@@ -33,6 +33,8 @@ jobs:
         uses: dependabot/fetch-metadata@ffa630c65fa7e0ecfa0625b5ceda64399aea1b36 # v3.0.0
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
+          permission-contents: write
+          permission-pull-requests: write
 
       - name: Stop workflow if not minor update or patch update
         id: skip-condition
diff --git a/.github/workflows/cache_cleaner.yml b/.github/workflows/cache_cleaner.yml
index 7403251d..78486309 100644
--- a/.github/workflows/cache_cleaner.yml
+++ b/.github/workflows/cache_cleaner.yml
@@ -27,6 +27,8 @@ jobs:
 
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Cleanup
         run: |
diff --git a/.github/workflows/first_pull_request.yml b/.github/workflows/first_pull_request.yml
index 50a52446..c99a3a11 100644
--- a/.github/workflows/first_pull_request.yml
+++ b/.github/workflows/first_pull_request.yml
@@ -20,6 +20,7 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8.0.0
         with:
           script: |
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7ca44ee4..0bc9f058 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -35,24 +35,29 @@ jobs:
             files.pythonhosted.org:443
             github.com:443
             pypi.org:443
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
+
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+
       - name: Environment Caching
         uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
         with:
           path: |
             .tox
           key: ${{ runner.os }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-lint-${{ env.ESGF_TEST_DATA_VERSION }}
+
       - name: Run linting suite
         run: |
           python -m tox -e lint
@@ -71,22 +76,27 @@ jobs:
         with:
           disable-sudo: false
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
+
       - name: Install HDF5 (Linux)
         run: |
           sudo apt-get update
           sudo apt-get install -y libhdf5-dev
+
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+
       - name: Environment Caching
         uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
         with:
@@ -95,6 +105,7 @@ jobs:
             ~/.cache/xclim-testdata
             .tox
           key: ${{ runner.os }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-Python${{ matrix.python-version }}-${{ env.ESGF_TEST_DATA_VERSION }}
+
       - name: Test with tox
         run: |
           python -m tox
@@ -112,7 +123,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.11", "3.12", "3.13" ]
+        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
     defaults:
       run:
         shell: bash -l {0}
@@ -122,10 +133,12 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
@@ -134,10 +147,11 @@ jobs:
           environment-file: environment.yml
           create-args: >-
             python=${{ matrix.python-version }}
-            pytest-timeout
+
       - name: Install CLISOPS
         run: |
           python -m pip install --no-user --no-deps --editable .
+
       - name: Test Data Caching
         uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4
         with:
@@ -145,13 +159,16 @@ jobs:
             ~/.cache/mini-esgf-data
             ~/.cache/xclim-testdata
           key: ${{ runner.os }}-${{ hashFiles('pyproject.toml', 'tox.ini') }}-conda-Python${{ matrix.python-version }}-${{ env.ESGF_TEST_DATA_VERSION }}
+
       - name: Check versions
         run: |
           micromamba list
           python -m pip check || true
+
       - name: Test with conda
         run: |
-          python -m pytest -m "not slow" --timeout=300 --numprocesses=logical --durations=10 --cov=clisops --cov-report=lcov
+          python -m pytest -m "not slow" --numprocesses=logical --durations=10 --cov=clisops --cov-report=lcov
+
       - name: Report Coverage
         uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
         with:
@@ -170,6 +187,7 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Coveralls Finished
         uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
         with:
diff --git a/.github/workflows/prepare-release.yml b/.github/workflows/prepare-release.yml
index 64d3a1f0..5044f1ff 100644
--- a/.github/workflows/prepare-release.yml
+++ b/.github/workflows/prepare-release.yml
@@ -21,10 +21,12 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Create Release
         uses: softprops/action-gh-release@153bb8e04406b158c6c84fc1615b65b24149a1fe # v2.6.1
         env:
diff --git a/.github/workflows/publish-pypi-production.yml b/.github/workflows/publish-pypi-production.yml
index 5fd40d30..ae4afca4 100644
--- a/.github/workflows/publish-pypi-production.yml
+++ b/.github/workflows/publish-pypi-production.yml
@@ -25,19 +25,24 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: "${{ matrix.python-version }}"
+
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+
       - name: Build a binary wheel and a source tarball
         run: |
           python -m flit build
+
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
diff --git a/.github/workflows/tag-testpypi-staging.yml b/.github/workflows/tag-testpypi-staging.yml
index 4a3cb289..71e8cc56 100644
--- a/.github/workflows/tag-testpypi-staging.yml
+++ b/.github/workflows/tag-testpypi-staging.yml
@@ -25,20 +25,25 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
+
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: "${{ matrix.python-version }}"
+
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+
       - name: Build a binary wheel and a source tarball
         run: |
           python -m flit build
+
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
         with:
diff --git a/.github/workflows/upstream.yml b/.github/workflows/upstream.yml
index 5f69af74..9cb9162d 100644
--- a/.github/workflows/upstream.yml
+++ b/.github/workflows/upstream.yml
@@ -42,11 +42,13 @@ jobs:
         with:
           disable-sudo: true
           egress-policy: audit
+
       - name: Checkout Repository
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
           persist-credentials: false
+
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
@@ -56,21 +58,26 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             pytest-reportlog
+
       - name: Install CLISOPS
         run: |
           python -m pip install --no-deps --no-user --editable .
+
       - name: Install upstream versions
         run: |
           python -m pip install -r CI/requirements_upstream.txt
+
       - name: Check versions
         run: |
           micromamba list
           python -m pip check || true
+
       - name: Run Tests
         if: success()
         id: status
         run: |
           python -m pytest --durations=10 --cov=clisops --cov-report=term-missing --report-log output-${{ matrix.python-version }}-log.jsonl
+
       - name: Generate and publish the report
         if: |
           failure()
diff --git a/.gitignore b/.gitignore
index c7348c05..00bf926c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -43,7 +43,7 @@ htmlcov/
 .coverage.*
 .cache
 nosetests.xml
-coverage.xml
+coverage.*
 *.cover
 .hypothesis/
 .pytest_cache/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 99f2058f..d1e1a94a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,17 +10,21 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
-      - id: end-of-file-fixer
-      - id: fix-byte-order-marker
       - id: check-merge-conflict
+      - id: check-json
       - id: check-toml
       - id: check-yaml
       - id: debug-statements
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
       - id: mixed-line-ending
-      - id: no-commit-to-branch
-        args: [ '--branch', 'main' ]
       - id: name-tests-test
         args: [ '--pytest-test-first' ]
+      - id: no-commit-to-branch
+        args: [ '--branch', 'main' ]
+      - id: pretty-format-json
+        args: [ '--autofix', '--no-ensure-ascii', '--no-sort-keys' ]
+        exclude: .ipynb
       - id: trailing-whitespace
   - repo: https://github.com/pappasam/toml-sort
     rev: v0.24.4
@@ -32,7 +36,7 @@ repos:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.9
+    rev: v0.15.15
     hooks:
       - id: ruff-check
         args: [ '--fix', '--show-fixes' ]
@@ -69,11 +73,11 @@ repos:
       - id: numpydoc-validation
         exclude: ^docs/|^tests/
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.30.0
+    rev: v8.30.1
     hooks:
       - id: gitleaks
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.37.1
+    rev: 0.37.2
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs
diff --git a/.readthedocs.yml b/.readthedocs.yml
index 1d12bd33..d6e0ba8a 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -12,9 +12,9 @@ sphinx:
 
 # Build configuration
 build:
-  os: ubuntu-24.04
+  os: "ubuntu-26.04"
   tools:
-    python: "mambaforge-23.11"
+    python: "miniforge3-25.11"
   jobs:
     post_create_environment:
       - mamba install --quiet --name ${READTHEDOCS_VERSION} -c conda-forge "python>=3.12,<3.13" "psy-maps>=1.5.0"
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 0bec879b..be67007a 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -86,34 +86,35 @@ Ready to contribute? Here's how to set up `clisops` for local development.
     Now you can make your changes locally!
 
 #.
-    When you are done making changes, check that you verify your changes with `flake8` and `black` and run the tests, including testing other Python versions with `tox`:
+    When you are done making changes, check that you verify your changes with `deptry`, `flake8`, and `ruff` and run the tests, including testing other Python versions with `tox`:
 
     .. code-block:: shell
 
         # For virtualenv environments:
-        $ pip install flake8 black pytest pytest-loguru tox
+        $ pip install flake8 ruff deptry pytest pytest-loguru tox
 
         # For Anaconda/Miniconda environments:
         $ conda install -c conda-forge flake8 black pytest pytest-loguru tox
 
-        $ flake8 clisops tests
-        $ black clisops tests
+        $ ruff check clisops tests
+	    $ flake8 --config=.flake8 clisops tests
+	    $ deptry .
         $ pytest
         $ tox
 
 #.
-    Before committing your changes, we ask that you install `pre-commit` in your virtualenv. `Pre-commit` runs git hooks that ensure that your code resembles that of the project and catches and corrects any small errors or inconsistencies when you `git commit`:
+    Before committing your changes, we ask that you install `prek` in your virtualenv. `prek` runs git hooks that ensure that your code resembles that of the project and catches and corrects any small errors or inconsistencies when you `git commit`:
 
     .. code-block:: shell
 
         # For virtualenv environments:
-        $ pip install pre-commit
+        $ pip install prek
 
         # For Anaconda/Miniconda environments:
-        $ conda install -c conda-forge pre-commit
+        $ conda install -c conda-forge prek
 
-        $ pre-commit install
-        $ pre-commit run --all-files
+        $ prek install
+        $ prek run --all-files
 
 #.
     Commit your changes and push your branch to GitHub:
diff --git a/HISTORY.rst b/HISTORY.rst
index 3c2fb9fa..1cc883e9 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -1,14 +1,40 @@
 Version History
 ===============
 
-
-v0.17.0 (2025-12-16)
+v0.18.0 (unreleased)
 --------------------
 
 New Features
 ^^^^^^^^^^^^
 * Added support for a data mask in `subset_gridpoint` where the subsetted grid points but be within the mask (True) (#493).
 * Allows choice between using true world distance (`distance`) or nearest neighbour based on lat, lon (`geographic`) methods for subsetting both regular and irregular grids (#493).
+
+Bug Fixes
+^^^^^^^^^
+* The `regrid.ipynb` notebook had malformed Python examples that were causing issues when building with `sphinx-codeautolink`. The issues have been addressed. (#498).
+
+Breaking Changes
+^^^^^^^^^^^^^^^^
+* Default method for `subset_gridpoint` using regular lat,lon grids is now `distance` instead of previously employing the equivalent of the new `geographic` method (#493).
+* Many development dependencies have been updated to more modern versions; `pytest` (v9.0+), `sphinx` (v8.2+), `matplotlib` (v3.8+), `tox` (v4.52.0+) and others. (#498).
+* The pin on `numpy` (`<2.3.0`) has been lifted. (#498).
+
+Internal Changes
+^^^^^^^^^^^^^^^^
+* Added a workflow to automatically accept patch and minor updates to CI dependencies via Dependabot. (#479).
+* Adjusted GitHub Workflows security by constraining token and job permissions to stricter defaults. (#498).
+* `pre-commit` has been replaced by `prek`. `prek` is a Rust-built reimplementation of `pre-commit` that runs very fast and is low on resources. (#498).
+* `sphinx-autobuild` is now a development dependency, used for the `$ make servedocs` recipe (`make livehtml`). (#498).
+* `pytest-timeout` is now a development dependency, used to prevent stalled tests from freezing CI builds (timeout default: 300 seconds). (#498).
+* `pretty-format-json` hook for `pre-commit` has been enabled. (#498).
+* ReadTheDocs build images have been updated to modern versions: OS `ubuntu-26.04` and Python `miniforge3-25.11`. (#498).
+* Tests marked "outdated" have been removed from the testing suite. (#498).
+
+v0.17.0 (2025-12-16)
+--------------------
+
+New Features
+^^^^^^^^^^^^
 * Added an `engine` argument to `Grid.ds.to_netcdf()` to allow users to specify the engine used for writing NetCDF files (#439).
 * Coding conventions have been updated to use Python 3.10+ features (#439).
 * `Weights` will now use `post_mask_source='domain_edge'` introduced in `xesmf` version 0.9 when remapping a regional grid via nearest-neighbour to avoid extrapolation beyond the source domain (#447).
@@ -27,7 +53,6 @@ Bug Fixes
 
 Breaking Changes
 ^^^^^^^^^^^^^^^^
-* Default method for `subset_gridpoint` using regular lat,lon grids is now `distance` instead of previously employing the equivalent of the new `geographic` method (#493).
 * Support for Python 3.10 has been dropped. `numpy >=1.26` is the new minimum supported version (#469).
 * `Grid.detect_extent()` now returns a tuple `(lon_extent, lat_extent)` instead of only `lon_extent` (#447).
 * `Grid.extent` now represents the combined lon/lat extent: `"global"` if both are global; otherwise `"regional"`. The new `Grid.extent_lon` and `Grid.extent_lat` attributes provide axis-specific extent information (#447).
diff --git a/Makefile b/Makefile
index 38e54642..ad50de21 100644
--- a/Makefile
+++ b/Makefile
@@ -78,14 +78,16 @@ coverage: ## check code coverage quickly with the default Python
 autodoc: clean-docs ## create sphinx-apidoc files:
 	env SPHINX_APIDOC_OPTIONS="members,undoc-members,show-inheritance,no-index" sphinx-apidoc -o docs/apidoc --private --module-first clisops
 
-docs: autodoc ## generate Sphinx HTML documentation, including API docs
+build-docs: autodoc ## generate Sphinx HTML documentation, including API docs
 	$(MAKE) -C docs html
+
+docs: build-docs ## open the built documentation in a web browser
 ifndef READTHEDOCS
 	$(BROWSER) docs/_build/html/index.html
 endif
 
-servedocs: docs ## compile the docs watching for changes
-	watchmedo shell-command -p '*.md' -c '$(MAKE) -C docs html' -R -D .
+servedocs: autodoc ## compile the docs watching for changes
+	$(MAKE) -C docs livehtml
 
 dist: clean ## builds source and wheel package
 	python -m flit build
@@ -95,10 +97,11 @@ release: dist ## package and upload a release
 	python -m flit publish dist/*
 
 install: clean ## install the package to the active Python's site-packages
-	python -m flit install
+	python -m pip install
 
 develop: clean ## install the package and development dependencies in editable mode to the active Python's site-packages
-	python -m flit install --no-user --symlink
+	python -m pip install --no-user --editable ".[dev]""
+	prek install
 
 upstream: develop ## install the GitHub-based development branches of dependencies in editable mode to the active Python's site-packages
 	python -m pip install --no-user --requirement requirements_upstream.txt
diff --git a/README.rst b/README.rst
index f585a383..74e6994d 100644
--- a/README.rst
+++ b/README.rst
@@ -9,7 +9,7 @@ clisops - climate simulation operations
 +----------------------------+---------------------------------+
 | Open Source                | |license|                       |
 +----------------------------+---------------------------------+
-| Coding Standards           | |ruff| |pre-commit|             |
+| Coding Standards           | |ruff| |prek| |pre-commit-ci|   |
 +----------------------------+---------------------------------+
 | Development Status         | |status| |build| |coveralls|    |
 +----------------------------+---------------------------------+
@@ -87,10 +87,14 @@ This package was created with ``Cookiecutter`` and the ``audreyr/cookiecutter-py
         :target: https://github.com/roocs/clisops/blob/master/LICENSE
         :alt: License
 
-.. |pre-commit| image:: https://results.pre-commit.ci/badge/github/roocs/clisops/master.svg
+.. |pre-commit-ci| image:: https://results.pre-commit.ci/badge/github/roocs/clisops/master.svg
         :target: https://results.pre-commit.ci/latest/github/roocs/clisops/master
         :alt: pre-commit.ci status
 
+.. |prek| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/j178/prek/master/docs/assets/badge-v0.json
+        :target: https://github.com/j178/prek
+        :alt: prek
+
 .. |pypi| image:: https://img.shields.io/pypi/v/clisops.svg
         :target: https://pypi.python.org/pypi/clisops
         :alt: Python Package Index Build
diff --git a/docs/Makefile b/docs/Makefile
index 1d231a51..91e1c009 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -18,3 +18,7 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+
+livehtml:
+	sphinx-autobuild --port 54345 --open-browser --delay 3 --re-ignore "$(BUILDDIR)|apidoc|Makefile|__pycache__" "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/conf.py b/docs/conf.py
index dea76e64..0c593ed7 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -47,7 +47,7 @@
     "nbsphinx",
     # sphinx_autodoc_typehints must always be listed after sphinx.ext.napoleon
     "sphinx_autodoc_typehints",
-    # "sphinx_codeautolink",
+    "sphinx_codeautolink",
     "sphinx_copybutton",
     "IPython.sphinxext.ipython_console_highlighting",
 ]
diff --git a/docs/index.rst b/docs/index.rst
index ae52784b..f316ccb0 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -21,8 +21,15 @@ Welcome to clisops's documentation!
 
    apidoc/modules
 
-Indices and tables
-==================
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+.. toctree::
+   :caption: GitHub Repository
+
+   roocs/clisops <https://github.com/roocs/clisops>
+
+.. only:: html
+
+    Indices and tables
+    ==================
+    * :ref:`genindex`
+    * :ref:`modindex`
+    * :ref:`search`
diff --git a/docs/notebooks/regrid.ipynb b/docs/notebooks/regrid.ipynb
index bdb9886b..965d1857 100644
--- a/docs/notebooks/regrid.ipynb
+++ b/docs/notebooks/regrid.ipynb
@@ -86,9 +86,7 @@
     "    *,\n",
     "    method: Optional[str] = \"nearest_s2d\",\n",
     "    adaptive_masking_threshold: Optional[Union[int, float]] = 0.5,\n",
-    "    grid: Optional[\n",
-    "        Union[xr.Dataset, xr.DataArray, int, float, tuple, str]\n",
-    "    ] = \"adaptive\",\n",
+    "    grid: Optional[Union[xr.Dataset, xr.DataArray, int, float, tuple, str]] = \"adaptive\",\n",
     "    output_dir: Optional[Union[str, Path]] = None,\n",
     "    output_type: Optional[str] = \"netcdf\",\n",
     "    split_method: Optional[str] = \"time:auto\",\n",
@@ -979,6 +977,7 @@
     "    adaptive_masking_threshold: Optional[float] = 0.5,\n",
     "    keep_attrs: Optional[bool] = True,\n",
     "):\n",
+    "    pass\n",
     "```\n",
     "\n",
     "*  `grid_in` and `grid_out` are `Grid` objects, `weights` is a `Weights` object.\n",
@@ -988,7 +987,6 @@
     "  *  `False` : The resulting `xarray.Dataset` will have no attributes despite attributes generated by the regridding process.\n",
     "  *  `\"target\"` : The resulting `xarray.Dataset` will have all attributes of `grid_out.ds.attrs`, despite attributes generated by the regridding process. Not recommended.\n",
     "\n",
-    "\n",
     "### In the following an example showing the function application and the effect of the adaptive masking."
    ]
   },
diff --git a/docs/readme.rst b/docs/readme.rst
index 929943b4..72a33558 100644
--- a/docs/readme.rst
+++ b/docs/readme.rst
@@ -1,5 +1 @@
-===========
-Quick Guide
-===========
-
 .. include:: ../README.rst
diff --git a/environment.yml b/environment.yml
index 9fa922eb..96d9fd7a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,9 +2,9 @@ name: clisops
 channels:
  - conda-forge
 dependencies:
- - python >=3.11,<3.14
+ - python >=3.11,<3.15
  - flit >=3.11.0,<4.0
- - pip >=25.0
+ - pip >=25.2
  - aiohttp # Needed for HTTPFileSystem
  - bottleneck >=1.3.1
  - cartopy >=0.23.0
@@ -18,7 +18,8 @@ dependencies:
  - geopandas >=1.0
  - jinja2 >=2.11
  - loguru >=0.5.3
- - numpy >=1.26.0,<2.3.0
+ - numcodecs <0.16.0 # FIXME: Pin required for zarr v2.x compatibility
+ - numpy >=1.26.0
  - packaging >=23.2
  - pandas >=2.2.0
  - platformdirs >=4.0
@@ -36,30 +37,33 @@ dependencies:
  # Extras
  - xesmf >=0.9.2
 #  # Dev tools and testing
- - bump-my-version >=1.2.0
+ - bump-my-version >=1.3.0
  - coverage >=7.5.0
- - deptry >=0.23.0
- - flake8 >=7.2.0
- - flake8-rst-docstrings >=0.3.0
+ - deptry >=0.25.1
+ - flake8 >=7.3.0
+ - flake8-rst-docstrings >=0.4.0
  - h5netcdf >=1.5.0
- - pre-commit >=3.5.0
- - pytest >=8.0.0
- - pytest-cov >=5.0.0
- - pytest-loguru >=0.3.0
- - pytest-xdist >=3.2
- - ruff >=0.12.0
- - tox >=4.24.1
- - watchdog >=4.0.0
+ - h5py
+ - prek >=0.4.0
+ - pytest >=9.0.0
+ - pytest-cov >=7.0.0
+ - pytest-loguru >=0.4.1
+ - pytest-timeout >=2.4.0
+ - pytest-xdist >=3.2.0
+ - ruff >=0.15.9
+ - tox >=4.52.0
+ - watchdog >=6.0.0
 # # Documentation
  - ipykernel
- - ipython >=8.5.0
+ - ipython >=8.15.0
  - ipython_genutils
  - jupyter_client
- - matplotlib-base >=3.6.0
+ - matplotlib-base >=3.8.0
  - nbconvert >=7.14.0
- - nbsphinx >=0.9.5
- - sphinx >=7.1.0,<8.2.0 # pinned until nbsphinx supports sphinx 8.2
- - sphinx-autodoc-typehints
- - sphinx-codeautolink
- - sphinx-copybutton
+ - nbsphinx >=0.9.8
+ - sphinx >=8.2.0
+ - sphinx-autobuild >=2024.4.16
+ - sphinx-autodoc-typehints >=3.5.0
+ - sphinx-codeautolink >=0.16.2
+ - sphinx-copybutton >=0.5.2
  - sphinx-rtd-theme >=1.0
diff --git a/pyproject.toml b/pyproject.toml
index 18c7fa2c..5f2c6c74 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,13 +17,13 @@ maintainers = [
 readme = {file = "README.rst", content-type = "text/x-rst"}
 requires-python = ">=3.11.0"
 keywords = ["clisops", "xarray", "climate", "gis", "subsetting", "operations"]
-license = {file = "LICENSE"}
+license = "BSD-3-Clause"
+license-files = ["LICENSE"]
 classifiers = [
   "Development Status :: 5 - Production/Stable",
   "Intended Audience :: Developers",
   "Intended Audience :: System Administrators",
   "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: BSD License",
   "Natural Language :: English",
   "Operating System :: OS Independent",
   "Programming Language :: Python",
@@ -55,7 +55,8 @@ dependencies = [
   "geopandas >=1.0",
   "jinja2 >=2.11",
   "loguru >=0.5.3",
-  "numpy >=1.26.0,<2.3.0",
+  "numcodecs <0.16.0", # FIXME: Pin required for zarr v2.x compatibility
+  "numpy >=1.26.0",
   "packaging >=23.2",
   "pandas >=2.2.0",
   "platformdirs >=4.0",
@@ -74,34 +75,37 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
   # Dev tools and testing
-  "bump-my-version >=1.2.0",
+  "bump-my-version >=1.3.0",
   "coverage[toml] >=7.5.0",
-  "deptry >=0.23.1",
+  "deptry >=0.25.1",
   "flake8 >=7.3.0",
   "flake8-rst-docstrings >=0.4.0",
   "h5netcdf >=1.5.0",
+  "h5py",
   "pip >=25.2",
-  "pre-commit >=3.5.0",
-  "pytest >=8.0.0",
-  "pytest-cov >=5.0.0",
-  "pytest-loguru >=0.3.0",
+  "prek >=0.4.0",
+  "pytest >=9.0.0",
+  "pytest-cov >=7.0.0",
+  "pytest-loguru >=0.4.1",
+  "pytest-timeout >=2.4.0",
   "pytest-xdist[psutil] >=3.2",
-  "ruff >=0.14.3",
-  "tox >=4.30.3",
-  "watchdog >=4.0.0"
+  "ruff >=0.15.9",
+  "tox >=4.52.0",
+  "watchdog >=6.0.0"
 ]
 docs = [
   "ipykernel",
-  "ipython >=8.5.0",
+  "ipython >=8.15.0",
   "ipython_genutils",
   "jupyter_client",
-  "matplotlib >=3.6.0",
+  "matplotlib >=3.8.0",
   "nbconvert >=7.14.0",
-  "nbsphinx >=0.9.5",
-  "sphinx >=7.1.0,<8.2", # pinned until nbsphinx supports sphinx 8.2
-  "sphinx-autodoc-typehints",
-  "sphinx-codeautolink",
-  "sphinx-copybutton",
+  "nbsphinx >=0.9.8",
+  "sphinx >=8.2",
+  "sphinx-autobuild >=2024.4.16",
+  "sphinx-autodoc-typehints >=3.5.0",
+  "sphinx-codeautolink >=0.16.2",
+  "sphinx-copybutton >=0.5.2",
   "sphinx-rtd-theme >=1.0"
 ]
 extras = [
@@ -136,7 +140,7 @@ search = "version = \"{current_version}\""
 replace = "version = \"{new_version}\""
 
 [tool.codespell]
-ignore-words-list = "scrip,nam,te,mye,bu,lik,tread,fo"
+ignore-words-list = "bu,fo,lik,mye,nam,scrip,te,tread"
 
 [tool.coverage.paths]
 source = ["clisops", "*/site-packages/clisops/"]
@@ -147,13 +151,13 @@ omit = ["*/tests/*.py"]
 source = ["clisops"]
 
 [tool.deptry]
+known_first_party = ["clisops"]
 extend_exclude = ["docs"]
 ignore_notebooks = true
 pep621_dev_dependency_groups = ["dev", "docs", "extras"]
 
 [tool.deptry.per_rule_ignores]
-DEP002 = ["aiohttp", "bottleneck", "cartopy", "fastparquet", "netcdf4", "requests", "s3fs", "zarr"]
-DEP003 = ["clisops"] # should be removed when restructuring to src layout
+DEP002 = ["aiohttp", "bottleneck", "cartopy", "fastparquet", "netcdf4", "numcodecs", "requests", "s3fs", "zarr"]
 DEP004 = ["xesmf"]
 
 [tool.flit.sdist]
@@ -220,8 +224,8 @@ override_SS05 = [
   '^Statistics '
 ]
 
-[tool.pytest.ini_options]
-minversion = "7.0"
+[tool.pytest]
+minversion = "9.0"
 addopts = [
   "-ra",
   "--verbose",
@@ -229,8 +233,8 @@ addopts = [
   "--numprocesses=0",
   "--maxprocesses=8",
   "--dist=worksteal",
-  "--strict-config",
-  "--strict-markers"
+  "--strict",
+  "--timeout=300"
 ]
 filterwarnings = ["ignore::UserWarning"]
 markers = [
diff --git a/tests/data/meridian.json b/tests/data/meridian.json
index 6b638c68..995dff56 100644
--- a/tests/data/meridian.json
+++ b/tests/data/meridian.json
@@ -9,7 +9,7 @@
         "coordinates": [
           [
             [
-              5.8671874999999996,
+              5.8671875,
               57.326521225217064
             ],
             [
@@ -33,7 +33,7 @@
               52.482780222078226
             ],
             [
-              5.8671874999999996,
+              5.8671875,
               57.326521225217064
             ]
           ]
diff --git a/tests/data/meridian_multi.json b/tests/data/meridian_multi.json
index afaa1887..fbefd70b 100644
--- a/tests/data/meridian_multi.json
+++ b/tests/data/meridian_multi.json
@@ -1,67 +1,67 @@
 {
-    "type": "FeatureCollection",
-    "features": [
-        {
-            "id": "0",
-            "type": "Feature",
-            "properties": {},
-            "geometry": {
-                "type": "MultiPolygon",
-                "coordinates": [
-                    [
-                        [
-                            [
-                                -22.148437499999996,
-                                54.16243396806779
-                            ],
-                            [
-                                -29.003906249999996,
-                                53.85252660044951
-                            ],
-                            [
-                                -29.70703125,
-                                48.22467264956519
-                            ],
-                            [
-                                -27.773437499999996,
-                                42.8115217450979
-                            ],
-                            [
-                                -16.34765625,
-                                47.39834920035926
-                            ],
-                            [
-                                -22.148437499999996,
-                                54.16243396806779
-                            ]
-                        ]
-                    ],
-                    [
-                        [
-                            [
-                                -23.73046875,
-                                58.44773280389084
-                            ],
-                            [
-                                10.1953125,
-                                58.26328705248601
-                            ],
-                            [
-                                8.0859375,
-                                65.29346780107583
-                            ],
-                            [
-                                -21.26953125,
-                                64.77412531292873
-                            ],
-                            [
-                                -23.73046875,
-                                58.44773280389084
-                            ]
-                        ]
-                    ]
-                ]
-            }
-        }
-    ]
+  "type": "FeatureCollection",
+  "features": [
+    {
+      "id": "0",
+      "type": "Feature",
+      "properties": {},
+      "geometry": {
+        "type": "MultiPolygon",
+        "coordinates": [
+          [
+            [
+              [
+                -22.148437499999996,
+                54.16243396806779
+              ],
+              [
+                -29.003906249999996,
+                53.85252660044951
+              ],
+              [
+                -29.70703125,
+                48.22467264956519
+              ],
+              [
+                -27.773437499999996,
+                42.8115217450979
+              ],
+              [
+                -16.34765625,
+                47.39834920035926
+              ],
+              [
+                -22.148437499999996,
+                54.16243396806779
+              ]
+            ]
+          ],
+          [
+            [
+              [
+                -23.73046875,
+                58.44773280389084
+              ],
+              [
+                10.1953125,
+                58.26328705248601
+              ],
+              [
+                8.0859375,
+                65.29346780107583
+              ],
+              [
+                -21.26953125,
+                64.77412531292873
+              ],
+              [
+                -23.73046875,
+                58.44773280389084
+              ]
+            ]
+          ]
+        ]
+      }
+    }
+  ]
 }
diff --git a/tests/data/multi_regions.json b/tests/data/multi_regions.json
index 8c0d9a7a..f5d797b1 100644
--- a/tests/data/multi_regions.json
+++ b/tests/data/multi_regions.json
@@ -3,7 +3,9 @@
   "features": [
     {
       "type": "Feature",
-      "properties": {"id": "Québec"},
+      "properties": {
+        "id": "Québec"
+      },
       "geometry": {
         "type": "Polygon",
         "coordinates": [
@@ -46,7 +48,9 @@
     },
     {
       "type": "Feature",
-      "properties": {"id": "Europe"},
+      "properties": {
+        "id": "Europe"
+      },
       "geometry": {
         "type": "Polygon",
         "coordinates": [
@@ -121,7 +125,9 @@
     },
     {
       "type": "Feature",
-      "properties": {"id": "Newfoundland"},
+      "properties": {
+        "id": "Newfoundland"
+      },
       "geometry": {
         "type": "Polygon",
         "coordinates": [
diff --git a/tests/test_project_utils.py b/tests/test_project_utils.py
index 91baffdb..13369f0b 100644
--- a/tests/test_project_utils.py
+++ b/tests/test_project_utils.py
@@ -3,7 +3,7 @@
 import pytest
 import xarray as xr
 
-from clisops import config, project_utils
+from clisops import project_utils
 
 
 @pytest.fixture(scope="module")
@@ -79,12 +79,6 @@ def test_get_project_name(self, mini_esgf_data):
         project = project_utils.get_project_name(dset)
         assert project in ["c3s-ipcc-ar6-atlas", "c3s-ipcc-atlas"]
 
-    @pytest.mark.xfail(reason="outdated")
-    def test_get_project_name_badc(self):
-        dset = "/badc/cmip5/data/cmip5/output1/MOHC/HadGEM2-ES/rcp85/mon/atmos/Amon/r1i1p1/latest/tas/*.nc"
-        project = project_utils.get_project_name(dset)
-        assert project == "cmip5"
-
     def test_get_project_base_dir(self):
         cmip5_base_dir = project_utils.get_project_base_dir("cmip5")
         assert cmip5_base_dir == "/mnt/lustre/work/kd0956/CMIP5/data/cmip5"
@@ -128,41 +122,6 @@ def test_files(self):
             "/siconc_SImon_CESM2_historical_r1i1p1f1_gn_185001-201412.nc"
         ]
 
-    @pytest.mark.xfail(reason="outdated")
-    def test_fixed_path_mappings(self, write_roocs_cfg, monkeypatch):
-        # reload the roocs_config
-        monkeypatch.setenv("ROOCS_CONFIG", write_roocs_cfg)
-        project_utils.CONFIG = config.reload_config()
-
-        dsm = project_utils.DatasetMapper("proj_test.my.first.test")
-        assert dsm._data_path == "/projects/test/proj/first/test/something.nc"
-        assert dsm.files == []  # because these do not exist when globbed
-
-        dsm = project_utils.DatasetMapper("proj_test.my.second.test")
-        assert dsm._data_path == "/projects/test/proj/second/test/data_*.txt"
-        assert dsm.files == []  # because these do not exist when globbed
-
-        dsm = project_utils.DatasetMapper("proj_test.my.unknown")
-        assert dsm._data_path == "/projects/test/proj/my/unknown"
-
-        # reset the config
-        monkeypatch.delenv("ROOCS_CONFIG")
-        project_utils.CONFIG = config.reload_config()
-
-    @pytest.mark.xfail(reason="outdated")
-    def test_fixed_path_modifiers(self, write_roocs_cfg, monkeypatch):
-        """Tests how modifiers can change the fixed path mappings."""
-        # reload the roocs_config
-        monkeypatch.setenv("ROOCS_CONFIG", write_roocs_cfg)
-        project_utils.CONFIG = config.reload_config()
-
-        dsm = project_utils.DatasetMapper("proj_test.another.sun.test")
-        assert dsm._data_path == "/projects/test/proj/good/test/sun.nc"
-
-        # reset the config
-        monkeypatch.delenv("ROOCS_CONFIG")
-        project_utils.CONFIG = config.reload_config()
-
 
 @pytest.mark.skipif(os.path.isdir("/badc") is False, reason="data not available")
 def test_get_filepaths():
@@ -203,70 +162,6 @@ def test_get_filepaths():
     )
 
 
-class TestDset:
-    @pytest.mark.xfail(reason="outdated")
-    def test_derive_dset(self):
-        from clisops.project_utils import derive_dset
-
-        # c3s-cmip6
-        dset = "c3s-cmip6.CMIP.MIROC.MIROC6.historical.r1i1p1f1.SImon.siconc.gn.latest"
-        ds_id = derive_dset(dset)
-
-        assert ds_id == "/badc/cmip6/data/CMIP6/CMIP/MIROC/MIROC6/historical/r1i1p1f1/SImon/siconc/gn/latest"
-
-        # cmip5
-        dset = "cmip5.output1.ICHEC.EC-EARTH.historical.day.atmos.day.r1i1p1.tas.v20131231"
-        ds_id = derive_dset(dset)
-
-        assert ds_id == "/badc/cmip5/data/cmip5/output1/ICHEC/EC-EARTH/historical/day/atmos/day/r1i1p1/tas/v20131231"
-
-        # c3s-cmip6-decadal
-        dset = "c3s-cmip6-decadal.DCPP.MOHC.HadGEM3-GC31-MM.dcppA-hindcast.s1995-r1i1p1f2.Amon.tas.gn.v20200417"
-        ds_id = derive_dset(dset)
-
-        assert (
-            ds_id
-            == "/badc/cmip6/data/CMIP6/DCPP/MOHC/HadGEM3-GC31-MM/dcppA-hindcast/s1995-r1i1p1f2/Amon/tas/gn/v20200417"
-        )
-
-        # c3s-cica-atlas
-        dset = "c3s-cica-atlas.cd.CMIP6.historical.yr"
-        ds_id = derive_dset(dset)
-
-        assert ds_id == "/pool/data/c3s-cica-atlas/cd/CMIP6/historical/yr"
-
-        # c3s-ipcc-ar6-atlas
-        dset = "c3s-ipcc-ar6-atlas.cd.CMIP6.historical.yr"
-        ds_id = derive_dset(dset)
-
-        assert ds_id == "/pool/data/c3s-ipcc-ar6-atlas/cd/CMIP6/historical/yr"
-
-    @pytest.mark.xfail(reason="outdated")
-    def test_switch_dset(self):
-        from clisops.project_utils import switch_dset
-
-        dset = "/badc/cmip6/data/CMIP6/CMIP/MIROC/MIROC6/historical/r1i1p1f1/SImon/siconc/gn/latest/*.nc"
-        ds_id = switch_dset(dset)
-
-        assert ds_id == "c3s-cmip6.CMIP.MIROC.MIROC6.historical.r1i1p1f1.SImon.siconc.gn.latest"
-
-    @pytest.mark.xfail(reason="outdated")
-    def test_switch_dset_modified_config(self, write_roocs_cfg, monkeypatch):
-        # reload the roocs_config
-        monkeypatch.setenv("ROOCS_CONFIG", write_roocs_cfg)
-        project_utils.CONFIG = config.reload_config()
-
-        dset = "/badc/cmip6/data/CMIP6/CMIP/MIROC/MIROC6/historical/r1i1p1f1/SImon/siconc/gn/latest/*.nc"
-        ds_id = project_utils.switch_dset(dset)
-
-        # The first match is returned when parsing the projects within the roocs.ini file
-        assert ds_id == "c3s-cmip6-decadal.CMIP.MIROC.MIROC6.historical.r1i1p1f1.SImon.siconc.gn.latest"
-
-        # reset the config
-        monkeypatch.delenv("ROOCS_CONFIG")
-        project_utils.CONFIG = config.reload_config()
-
-
 def test_unknown_fpath_force():
     dset = "/tmp/tmpxi6d78ng/subset_tttaum9d/rlds_Amon_IPSL-CM6A-LR_historical_r1i1p1f1_gr_19850116-20141216.nc"
 
@@ -324,20 +219,3 @@ def test_filemapper(self):
         ]
         assert dm.data_path == "/badc/cmip6/data/CMIP6/CMIP/MIROC/MIROC6/amip/r1i1p1f1/day/tas/gn/latest"
         assert dm.ds_id == "c3s-cmip6.CMIP.MIROC.MIROC6.amip.r1i1p1f1.day.tas.gn.latest"
-
-
-@pytest.mark.xfail(reason="outdated")
-def test_url_to_file_path(cds_domain):
-    from clisops.project_utils import url_to_file_path
-
-    url = (
-        f"{cds_domain}/thredds/fileServer/esg_c3s-cmip6/CMIP/E3SM-Project/E3SM-1-1"
-        "/historical/r1i1p1f1/Amon/rlus/gr/v20191211/rlus_Amon_E3SM-1-1_historical_r1i1p1f1_gr_200001-200912.nc"
-    )
-    fpath = url_to_file_path(url)
-
-    assert (
-        fpath == "/badc/cmip6/data/CMIP6/CMIP/E3SM-Project/E3SM-1-1"
-        "/historical/r1i1p1f1/Amon/rlus/gr/v20191211"
-        "/rlus_Amon_E3SM-1-1_historical_r1i1p1f1_gr_200001-200912.nc"
-    )
diff --git a/tox.ini b/tox.ini
index 1dfff6ec..083506ba 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,32 +1,30 @@
 [tox]
-min_version = 4.30.3
 envlist =
-    py{3.11,3.12,3.13}
+    py3.{11,12,13,14}
     lint
     docs
-requires =
-    flit >=3.11.0,<4.0
-    pip >=25.2
 opts = -v
 
 [gh]
 python =
-    3.11 = py3.11-coverage
-    3.12 = py3.12-netcdf4-coverage
+    3.11 = py3.11
+    3.12 = py3.12-netcdf4
     3.13 = py3.13
+    3.14 = py3.14
 
 [testenv:lint]
 skip_install = True
 basepython = python
 deps =
-    deptry >=0.23.1
+    deptry >=0.25.1
     flake8 >=7.3.0
     flake8-rst-docstrings >=0.4.0
-    ruff >=0.14.3
+    ruff >=0.15.9
 commands_pre =
     pip list
 commands =
     make lint
+commands_post =
 allowlist_externals =
     make
 
@@ -37,12 +35,13 @@ extras = docs
 deps =
 commands =
     make docs
+commands_post =
 allowlist_externals =
     make
 
 [testenv]
 setenv =
-    PYTEST_ADDOPTS = -m "not slow" --numprocesses=logical --durations=10 --cov=clisops --cov-report=term-missing
+    PYTEST_ADDOPTS = -m "not slow" --numprocesses=logical --durations=10 --cov=clisops --cov-report=lcov
     PYTHONPATH = {toxinidir}
 passenv =
     CI
@@ -53,15 +52,12 @@ extras = dev
 install_command = python -m pip install --no-user {opts} {packages}
 download = True
 deps =
-    coverage: coveralls >=4.0.1
     netcdf4: netcdf4 >=1.6.3
     upstream: -r CI/requirements_upstream.txt
 commands_pre =
     python -m pip list
     python -m pip check
 commands =
-    ; Recompile h5py to avoid issues with different numpy versions
-    python -m pip install --no-user --upgrade --no-deps --force-reinstall --no-binary h5py h5py>=3.12.1
     pytest {posargs}
-commands_post:
-    coverage: - coveralls
+commands_post =
+    coverage report