Add support for Python 3.11 and update dependencies

.github/workflows/docs.yml

@@ -33,7 +33,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       REQUIREMENTS: env/requirements-build.txt env/requirements-docs.txt
-      PYTHON: 3.9
+      PYTHON: 3.11
 
     steps:
       # Cancel any previous run of the test job
@@ -46,7 +46,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # Need to fetch more than the last commit so that setuptools-scm can
           # create the correct version string. If the number of commits since
@@ -117,7 +117,7 @@ jobs:
       # Store the docs as a build artifact so we can deploy it later
       - name: Upload HTML documentation as an artifact
         if: github.event_name == 'release' || github.event_name == 'push'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: docs-${{ github.sha }}
           path: doc/_build/html
@@ -131,17 +131,17 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       # Fetch the built docs from the "build" job
       - name: Download HTML documentation artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: docs-${{ github.sha }}
           path: doc/_build/html
 
       - name: Checkout the gh-pages branch in a separate folder
-        uses: actions/checkout@5a4ac9002d0be2fb38bd78e4b4dbde5606d7042f
+        uses: actions/checkout@v3
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/pypi.yml

@@ -33,7 +33,7 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # Need to fetch more than the last commit so that setuptools_scm can
           # create the correct version string. If the number of commits since
@@ -49,9 +49,9 @@ jobs:
         run: git fetch origin 'refs/tags/*:refs/tags/*'
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install requirements
         run: python -m pip install -r env/requirements-build.txt
@@ -81,7 +81,7 @@ jobs:
       - name: Upload archives as artifacts
         # Only if not a pull request
         if: success() && github.event_name != 'pull_request'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: pypi-${{ github.sha }}
           path: dist
@@ -96,23 +96,23 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # The GitHub token is preserved by default but this job doesn't need
           # to be able to push to GitHub.
           persist-credentials: false
 
       # Fetch the built archives from the "build" job
       - name: Download built archives artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: pypi-${{ github.sha }}
           path: dist
 
       - name: Publish to Test PyPI
         # Only publish to TestPyPI when a PR is merged (pushed to main)
         if: success() && github.event_name == 'push'
-        uses: pypa/gh-action-pypi-publish@bce3b74dbf8cc32833ffba9d15f83425c1a736e0
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_TOKEN}}
@@ -124,7 +124,7 @@ jobs:
       - name: Publish to PyPI
         # Only publish to PyPI when a release triggers the build
         if: success() && github.event_name == 'release'
-        uses: pypa/gh-action-pypi-publish@bce3b74dbf8cc32833ffba9d15f83425c1a736e0
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN}}

.github/workflows/style.yml

@@ -20,14 +20,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           persist-credentials: false
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install requirements
         run: python -m pip install -r env/requirements-style.txt
@@ -42,14 +42,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           persist-credentials: false
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install requirements
         run: python -m pip install -r env/requirements-style.txt

.github/workflows/test.yml

@@ -47,11 +47,11 @@ jobs:
           - optional
         include:
           - dependencies: oldest
-            python: "3.7"
+            python: "3.9"
           - dependencies: latest
-            python: "3.10"
+            python: "3.11"
           - dependencies: optional
-            python: "3.10"
+            python: "3.11"
     env:
       REQUIREMENTS: env/requirements-build.txt env/requirements-test.txt
       # Used to tag codecov submissions
@@ -70,7 +70,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # Need to fetch more than the last commit so that setuptools-scm can
           # create the correct version string. If the number of commits since

doc/conf.py

@@ -42,14 +42,14 @@
 # functions/classes
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
-    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "sklearn": ("https://scikit-learn.org/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
-    "xarray": ("https://xarray.pydata.org/en/stable/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
     "cartopy": ("https://scitools.org.uk/cartopy/docs/latest/", None),
     "pooch": ("https://www.fatiando.org/pooch/latest/", None),
-    "matplotlib": ("https://matplotlib.org/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
     "dask": ("https://docs.dask.org/en/latest/", None),
     "pygmt": ("https://www.pygmt.org/latest/", None),
 }
@@ -96,13 +96,13 @@
     # Insert links to documentation of objects in the examples
     "reference_url": {"verde": None},
     # Use the PyGMT image scraper
-    "image_scrapers": ("matplotlib", pygmt.sphinx_gallery.PyGMTScraper()),
+    "image_scrapers": (pygmt.sphinx_gallery.PyGMTScraper(), "matplotlib"),
 }
 
 # HTML output configuration
 # -----------------------------------------------------------------------------
 html_title = f'{project} <span class="project-version">{version}</span>'
-html_logo = "_static/verde-logo.png"
+# html_logo = "_static/verde-logo.png"
 html_favicon = "_static/favicon.png"
 html_last_updated_fmt = "%b %d, %Y"
 html_copy_source = True

doc/index.rst

@@ -5,6 +5,13 @@
     :margin: 5 5 0 0
     :padding: 0 0 0 0
 
+    .. grid-item::
+        :columns: 12 4 12 4
+
+        .. image:: ./_static/verde-logo.png
+            :width: 200px
+            :class: sd-m-auto dark-light
+
     .. grid-item::
         :columns: 12 8 12 8
 
@@ -16,19 +23,12 @@
 
                 .. raw:: html
 
-                    <h1 class="display-1"><img src="_static/verde-title.svg" alt="Verde"></h1>
+                    <h1 class="display-1"><img class="dark-light" src="_static/verde-title.png" alt="Verde"></h1>
 
         .. div:: sd-fs-3
 
             Processing and gridding spatial data, machine-learning style
 
-    .. grid-item::
-        :columns: 12 4 12 4
-
-        .. image:: ./_static/verde-logo.svg
-            :width: 200px
-            :class: sd-m-auto
-
 **Verde** is a Python library for processing spatial data (bathymetry,
 geophysics surveys, etc) and interpolating it on regular grids (i.e.,
 *gridding*).

doc/tutorials_src/chain.py

@@ -61,8 +61,8 @@
     cmap=True,
     style="c0.05c",
 )
-fig.basemap(frame=True)
 fig.colorbar(frame='af+l"bathymetric depth [m]"')
+fig.basemap(frame=True)
 fig.show()
 
 

env/requirements-docs.txt

@@ -1,11 +1,11 @@
-sphinx==4.5.*
-sphinx-book-theme==0.3.*
-sphinx-gallery==0.10.*
+sphinx==7.2.*
+sphinx-book-theme==1.1.*
+sphinx-gallery==0.15.*
 sphinx-copybutton==0.5.*
-sphinx-design==0.1.*
-matplotlib==3.5.*
+sphinx-design==0.5.*
+matplotlib==3.8.*
 cartopy>=0.20
 pyproj
-pygmt==0.6.*
-gmt==6.3.*
+pygmt==0.11.*
+gmt==6.5.*
 ipython

env/requirements-test.txt

@@ -3,4 +3,4 @@ pytest-cov
 pytest-mpl
 coverage
 matplotlib
-cartopy>=0.18
+cartopy>=0.20

environment.yml

@@ -3,7 +3,7 @@ channels:
     - conda-forge
     - defaults
 dependencies:
-    - python==3.10
+    - python==3.11
     - pip
     # Build
     - twine
@@ -20,21 +20,21 @@ dependencies:
     - pykdtree
     - numba
     # Test
-    - matplotlib==3.5.*
+    - matplotlib==3.8.*
     - cartopy>=0.20
     - pytest
     - pytest-cov
     - pytest-mpl
     - coverage
     # Documentation
-    - sphinx==4.5.*
-    - sphinx-book-theme==0.3.*
-    - sphinx-gallery==0.10.*
+    - sphinx==7.2.*
+    - sphinx-book-theme==1.1.*
+    - sphinx-gallery==0.15.*
     - sphinx-copybutton==0.5.*
-    - sphinx-design==0.1.*
+    - sphinx-design==0.5.*
     - pyproj
-    - pygmt==0.6.*
-    - gmt==6.3.*
+    - pygmt==0.11.*
+    - gmt==6.5.*
     - ipython
     # Style
     - black

setup.cfg

@@ -23,10 +23,10 @@ classifiers =
     Topic :: Scientific/Engineering
     Topic :: Software Development :: Libraries
     Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
 url = https://github.com/fatiando/verde
 project_urls =
     Documentation = https://www.fatiando.org/verde
@@ -40,17 +40,17 @@ include_package_data = True
 packages = find:
 python_requires = >=3.7
 install_requires =
-    numpy>=1.19
-    scipy>=1.5
-    pandas>=1.1
-    xarray>=0.16
-    scikit-learn>=0.24
+    numpy>=1.23
+    scipy>=1.8
+    pandas>=1.4
+    xarray>=2022.03
+    scikit-learn>=1.0
     pooch>=1.2
-    dask>=2021.05.0
+    dask>=2022.01.0
 
 [options.extras_require]
 fast =
-    numba>=0.52
+    numba>=0.55
     pykdtree>=1.3
 
 [options.package_data]