Merge branch 'main' into pytest/mark-benchmark-part2

.github/workflows/benchmarks.yml

@@ -61,7 +61,7 @@ jobs:
           echo $CONDA/bin >> $GITHUB_PATH
           conda install --solver=libmamba gmt=6.4.0 python=3.12 \
                         numpy pandas xarray netCDF4 packaging \
-                        geopandas pyarrow pytest pytest-benchmark pytest-mpl
+                        geopandas pyarrow pytest pytest-mpl
           python -m pip install -U pytest-codspeed setuptools
 
       # Download cached remote files (artifacts) from GitHub

.github/workflows/cache_data.yaml

@@ -1,18 +1,21 @@
-# Cache GMT remote data files and uploads as artifacts
+# Cache GMT remote data files and upload as artifacts
 #
 # This workflow downloads data files needed by PyGMT tests/documentation from
 # the GMT data server and uploads as workflow artifacts which can be accessed
 # by other GitHub Actions workflows.
 #
 # It is scheduled to run every Sunday at 12:00 (UTC). If new remote files are
-# needed urgently, maintainers can manually uncomment the 'pull_request:' line
-# below to refresh the cache.
+# needed urgently, maintainers can update the workflow file or
+# 'pygmt/helpers/caching.py' file to refresh the cache.
 #
 name: Cache data
 
 on:
-  # Uncomment the 'pull_request' line below to manually re-cache data artifacts
-  # pull_request:
+  pull_request:
+    # Make any changes to the following files to refresh the cache
+    paths:
+      - 'pygmt/helpers/caching.py'
+      - '.github/workflows/cache_data.yaml'
   # Schedule runs on 12 noon every Sunday
   schedule:
     - cron: '0 12 * * 0'
@@ -61,7 +64,7 @@ jobs:
       # Download remote files
       - name: Download remote data
         run: |
-          python -c "from pygmt.helpers.testing import download_test_data; download_test_data()"
+          python -c "from pygmt.helpers.caching import cache_data; cache_data()"
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub

.github/workflows/ci_docs.yml

@@ -72,7 +72,7 @@ jobs:
             channels:
               - conda-forge
               - nodefaults
-          cache-downloads: true
+          cache-downloads: false
           cache-environment: true
           create-args: >-
             python=3.12

.github/workflows/ci_tests.yaml

@@ -101,7 +101,7 @@ jobs:
             channels:
               - conda-forge
               - nodefaults
-          cache-downloads: true
+          cache-downloads: false
           cache-environment: true
           create-args: >-
             python=${{ matrix.python-version }}${{ matrix.optional-packages }}

.github/workflows/ci_tests_dev.yaml

@@ -57,31 +57,22 @@ jobs:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
-      # Generate token from GenericMappingTools bot
-      - name: Generate token from GenericMappingTools bot
-        uses: tibdex/github-app-token@v2
-        if: github.event_name == 'repository_dispatch'
-        id: generate-token
-        with:
-          app_id: ${{ secrets.APP_ID }}
-          private_key: ${{ secrets.APP_PRIVATE_KEY }}
-
       # Checkout the pull request branch
       - name: Checkout
         uses: actions/[email protected]
         if: github.event_name == 'repository_dispatch'
         with:
-          token: ${{ steps.generate-token.outputs.token }}
+          token: ${{ secrets.GITHUB_TOKEN }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
           ref: ${{ github.event.client_payload.pull_request.head.ref }}
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
 
       - name: Show job URL
         uses: peter-evans/[email protected]
-        if: github.event_name == 'repository_dispatch' && (matrix.os == 'ubuntu-latest')
+        if: github.event_name == 'repository_dispatch' && runner.os == 'Linux'
         with:
-          token: ${{ steps.generate-token.outputs.token }}
+          token: ${{ secrets.GITHUB_TOKEN }}
           repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
           comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
           body: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
@@ -95,7 +86,7 @@ jobs:
             channels:
               - conda-forge
               - nodefaults
-          cache-downloads: true
+          cache-downloads: false
           cache-environment: true
           create-args: >-
             python=3.12

.github/workflows/ci_tests_legacy.yaml

@@ -59,7 +59,7 @@ jobs:
             channels:
               - conda-forge
               - nodefaults
-          cache-downloads: true
+          cache-downloads: false
           cache-environment: true
           create-args: >-
             python=3.9

.github/workflows/format-command.yml

@@ -32,7 +32,7 @@ jobs:
       # Install formatting tools
       - name: Install formatting tools
         run: |
-          python -m pip install docformatter ruff
+          python -m pip install ruff
           python -m pip list
           sudo apt-get install dos2unix
 

.github/workflows/slash-command-dispatch.yml

@@ -13,17 +13,10 @@ jobs:
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
     steps:
-      # Generate token from GenericMappingTools bot
-      - uses: tibdex/github-app-token@v2
-        id: generate-token
-        with:
-          app_id: ${{ secrets.APP_ID }}
-          private_key: ${{ secrets.APP_PRIVATE_KEY }}
-
       - name: Slash Command Dispatch
         uses: peter-evans/slash-command-dispatch@v3
         with:
-          token: ${{ steps.generate-token.outputs.token }}
+          token: ${{ secrets.GITHUB_TOKEN }}
           commands: |
             format
             test-gmt-dev

.github/workflows/style_checks.yaml

@@ -34,11 +34,11 @@ jobs:
 
       - name: Install packages
         run: |
-          python -m pip install docformatter ruff
+          python -m pip install ruff
           python -m pip list
           sudo apt-get install dos2unix
 
-      - name: Formatting check (docformatter, ruff)
+      - name: Formatting check (ruff)
         run: make check
 
       - name: Ensure files use UNIX line breaks and have 644 permission

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2017-2023 The PyGMT Developers
+Copyright (c) 2017-2024 The PyGMT Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

Makefile

@@ -15,8 +15,8 @@ help:
 	@echo "  fulltest       run the test suite (including all doctests)"
 	@echo "  doctest        run the doctests only"
 	@echo "  test_no_images run the test suite (including all doctests) but skip image comparisons"
-	@echo "  format         run docformatter and ruff to automatically format the code"
-	@echo "  check          run code style and quality checks (docformatter and ruff)"
+	@echo "  format         run ruff to automatically format the code"
+	@echo "  check          run ruff to check code style and quality"
 	@echo "  codespell      run codespell to check common misspellings"
 	@echo "  typecheck      run mypy for static type check"
 	@echo "  clean          clean up build and generated files"
@@ -60,12 +60,10 @@ test_no_images: PYTEST_ARGS=-o addopts="--verbose --durations=0 --durations-min=
 test_no_images: _runtest
 
 format:
-	docformatter --in-place $(FORMAT_FILES)
 	ruff check --fix $(FORMAT_FILES)
 	ruff format $(FORMAT_FILES)
 
 check:
-	docformatter --check $(FORMAT_FILES)
 	ruff check $(FORMAT_FILES)
 	ruff format --check $(FORMAT_FILES)
 

doc/contributing.md

@@ -406,7 +406,7 @@ arguments and return values.
 
 While the maximum line length for code is automatically set by ruff, docstrings
 must be formatted manually. To play nicely with Jupyter and IPython, **keep docstrings
-limited to 79 characters** per line.
+limited to 88 characters** per line.
 
 ### Standards for Example Code
 
@@ -471,14 +471,10 @@ code, be sure to follow the general guidelines in the
 
 ### Code Style
 
-We use some tools to format the code so we don't have to think about it:
-
-- [docformatter](https://github.com/myint/docformatter)
-- [ruff](https://docs.astral.sh/ruff)
-
-These tools loosely follow the [PEP8](http://pep8.org) guide but with a few
-differences. Regardless, you won't have to worry about formatting the code yourself.
-Before committing, run it to automatically format your code:
+We use the [ruff](https://docs.astral.sh/ruff) tool to format the code, so we
+don't have to think about it. It loosely follow the [PEP8](http://pep8.org) guide
+but with a few differences. Regardless, you won't have to worry about formatting
+the code yourself. Before committing, run it to automatically format your code:
 
 ```bash
 make format
@@ -511,7 +507,7 @@ The [`Makefile`](https://github.com/GenericMappingTools/pygmt/blob/main/Makefile
 contains rules for running the linter checks:
 
 ```bash
-make check   # Runs docformatter and ruff (in check mode)
+make check   # Runs ruff in check mode
 ```
 
 ### Testing your Code

environment.yml

@@ -24,7 +24,6 @@ dependencies:
     - pip
     # Dev dependencies (style checks)
     - codespell
-    - docformatter>=1.7.2
     - ruff>=0.1.9
     # Dev dependencies (unit testing)
     - matplotlib

examples/gallery/3d_plots/grdview_surface.py

@@ -23,6 +23,9 @@
 # Define an interesting function of two variables, see:
 # https://en.wikipedia.org/wiki/Ackley_function
 def ackley(x, y):
+    """
+    Ackley function.
+    """
     return (
         -20 * np.exp(-0.2 * np.sqrt(0.5 * (x**2 + y**2)))
         - np.exp(0.5 * (np.cos(2 * np.pi * x) + np.cos(2 * np.pi * y)))

examples/gallery/images/grdgradient_shading.py

@@ -59,6 +59,6 @@
                 panel=True,
             )
 
-fig.colorbar(position="JBC+w10c/0.25c+h", frame="a2000f500+lElevation (m)")
+fig.colorbar(position="JBC+w10c/0.25c+h", frame="xa2000f500+lElevation (m)")
 
 fig.show()

examples/gallery/lines/vector_styles.py

@@ -4,9 +4,7 @@
 
 The :meth:`pygmt.Figure.plot` method can plot Cartesian, circular, and
 geographic vectors. The ``style`` parameter controls vector attributes.
-See also
-:doc:`Vector attributes example </gallery/lines/vector_heads_tails>`.
-
+See also :doc:`Vector attributes example </gallery/lines/vector_heads_tails>`.
 """
 
 # %%

examples/tutorials/advanced/working_with_panel.py

@@ -73,9 +73,11 @@
 )
 
 
-# Define a function for plotting the single slices
 @pn.depends(central_lon=slider_lon)
 def view(central_lon):
+    """
+    Define a function for plotting the single slices.
+    """
     # Create a new instance or object of the pygmt.Figure() class
     fig = pygmt.Figure()
     fig.coast(
@@ -112,9 +114,11 @@ def view(central_lon):
 )
 
 
-# Define a function for plotting the single slices
 @pn.depends(central_lon=slider_lon)
 def view(central_lon):
+    """
+    Define a function for plotting the single slices.
+    """
     # Create a new instance or object of the pygmt.Figure() class
     fig = pygmt.Figure()
     # Set up a colormap for the elevation in meters

examples/tutorials/basics/plot.py

@@ -90,7 +90,7 @@
     style="cc",
     pen="black",
 )
-fig.colorbar(frame="af+lDepth (km)")
+fig.colorbar(frame="xaf+lDepth (km)")
 fig.show()
 
 # sphinx_gallery_thumbnail_number = 3

pygmt/__init__.py

@@ -1,10 +1,10 @@
 """
 PyGMT is a library for processing geospatial and geophysical data and making
-publication-quality maps and figures. It provides a Pythonic interface for the
-Generic Mapping Tools (GMT), a command-line program widely used across the
-Earth, Ocean, and Planetary sciences and beyond. Besides making GMT more
-accessible to new users, PyGMT aims to provide integration with the PyData
-ecosystem as well as support for rich display in Jupyter notebooks.
+publication-quality maps and figures. It provides a Pythonic interface for the Generic
+Mapping Tools (GMT), a command-line program widely used across the Earth, Ocean, and
+Planetary sciences and beyond. Besides making GMT more accessible to new users, PyGMT
+aims to provide integration with the PyData ecosystem as well as support for rich
+display in Jupyter notebooks.
 
 Main Features
 -------------
@@ -93,8 +93,7 @@ def print_clib_info(file=sys.stdout):
 
 def show_versions(file=sys.stdout):
     """
-    Print various dependency versions which are useful when submitting bug
-    reports.
+    Print various dependency versions which are useful when submitting bug reports.
 
     This includes information about:
 

pygmt/accessors.py

@@ -150,8 +150,7 @@ def registration(self, value):
     @property
     def gtype(self):
         """
-        Coordinate system type of the grid, either 0 (Cartesian) or 1
-        (Geographic).
+        Coordinate system type of the grid, either 0 (Cartesian) or 1 (Geographic).
         """
         return self._gtype
 

pygmt/clib/__init__.py

@@ -1,8 +1,8 @@
 """
 Low-level wrapper for the GMT C API.
 
-The pygmt.clib.Session class wraps the GMT C shared library (libgmt) with a
-Pythonic interface. Access to the C library is done through ctypes.
+The pygmt.clib.Session class wraps the GMT C shared library (libgmt) with a Pythonic
+interface. Access to the C library is done through ctypes.
 """
 
 from pygmt.clib.session import Session

pygmt/clib/conversion.py

@@ -126,8 +126,7 @@ def dataarray_to_matrix(grid):
 
 def vectors_to_arrays(vectors):
     """
-    Convert 1-D vectors (lists, arrays, or pandas.Series) to C contiguous 1-D
-    arrays.
+    Convert 1-D vectors (lists, arrays, or pandas.Series) to C contiguous 1-D arrays.
 
     Arrays must be in C contiguous order for us to pass their memory pointers
     to GMT. If any are not, convert them to C order (which requires copying the

pygmt/clib/loading.py

@@ -1,8 +1,8 @@
 """
 Utility functions to load libgmt as ctypes.CDLL.
 
-The path to the shared library can be found automatically by ctypes or set
-through the GMT_LIBRARY_PATH environment variable.
+The path to the shared library can be found automatically by ctypes or set through the
+GMT_LIBRARY_PATH environment variable.
 """
 import ctypes
 import os