Merge branch 'main' into slash-command-token

.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 pytest pytest-benchmark pytest-mpl
+                        geopandas 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

@@ -86,7 +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

@@ -25,7 +25,7 @@ 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/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

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/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

pygmt/figure.py

@@ -88,7 +88,9 @@ def __init__(self):
         self._activate_figure()
 
     def __del__(self):
-        # Clean up the temporary directory that stores the previews
+        """
+        Clean up the temporary directory that stores the previews.
+        """
         if hasattr(self, "_preview_dir"):
             self._preview_dir.cleanup()
 

pygmt/helpers/caching.py

@@ -0,0 +1,87 @@
+"""
+Functions for download remote data files as cache.
+"""
+from pygmt.src import which
+
+
+def cache_data():
+    """
+    Download GMT remote data files used in PyGMT tests and docs as cache files.
+    """
+    # List of datasets to download
+    datasets = [
+        # Earth relief grids
+        "@earth_gebco_01d_g",
+        "@earth_gebcosi_01d_g",
+        "@earth_gebcosi_15m_p",
+        "@earth_relief_01d_p",
+        "@earth_relief_01d_g",
+        "@earth_relief_30m_p",
+        "@earth_relief_30m_g",
+        "@earth_relief_10m_p",
+        "@earth_relief_10m_g",
+        "@earth_relief_05m_p",
+        "@earth_relief_05m_g",
+        "@earth_synbath_01d_g",
+        # List of tiles of 03s srtm data.
+        # Names like @N35E135.earth_relief_03s_g.nc are for internal use only.
+        # The naming scheme may change. DO NOT USE IT IN YOUR SCRIPTS.
+        "@N30W120.earth_relief_15s_p.nc",
+        "@N35E135.earth_relief_03s_g.nc",
+        "@N37W120.earth_relief_03s_g.nc",
+        "@N00W090.earth_relief_03m_p.nc",
+        "@N00E135.earth_relief_30s_g.nc",
+        "@N00W010.earth_relief_15s_p.nc",  # Specific grid for 15s test
+        "@N04W010.earth_relief_03s_g.nc",  # Specific grid for 03s test
+        # Earth synbath relief grid
+        "@S15W105.earth_synbath_30s_p.nc",
+        # Earth seafloor age grids
+        "@earth_age_01d_g",
+        "@N00W030.earth_age_01m_g.nc",  # Specific grid for 01m test
+        # Earth geoid grids
+        "@earth_geoid_01d_g",
+        "@N00W030.earth_geoid_01m_g.nc",  # Specific grid for 01m test
+        # Earth magnetic anomaly grids
+        "@earth_mag_01d_g",
+        "@S30W060.earth_mag_02m_p.nc",  # Specific grid for 02m test
+        "@earth_mag4km_01d_g",
+        "@S30W120.earth_mag4km_02m_p.nc",  # Specific grid for 02m test
+        # Earth mask grid
+        "@earth_mask_01d_g",
+        # Earth free-air anomaly grids
+        "@earth_faa_01d_g",
+        "@N00W030.earth_faa_01m_p.nc",  # Specific grid for 01m test
+        # Earth vertical gravity gradient grids
+        "@earth_vgg_01d_g",
+        "@N00W030.earth_vgg_01m_p.nc",  # Specific grid for 01m test
+        # Earth WDMAM grids
+        "@earth_wdmam_01d_g",
+        "@S90E000.earth_wdmam_03m_g.nc",  # Specific grid for 03m test
+        # Earth day/night grids
+        "@earth_day_01d_p",
+        # Other cache files
+        "@capitals.gmt",
+        "@circuit.png",
+        "@earth_relief_20m_holes.grd",
+        "@EGM96_to_36.txt",
+        "@MaunaLoa_CO2.txt",
+        "@RidgeTest.shp",
+        "@RidgeTest.shx",
+        "@RidgeTest.dbf",
+        "@RidgeTest.prj",
+        "@Table_5_11.txt",
+        "@Table_5_11_mean.xyz",
+        "@fractures_06.txt",
+        "@hotspots.txt",
+        "@ridge.txt",
+        "@mars370d.txt",
+        "@srtm_tiles.nc",  # needed for 03s and 01s relief data
+        "@static_earth_relief.nc",
+        "@ternary.txt",
+        "@test.dat.nc",
+        "@tut_bathy.nc",
+        "@tut_quakes.ngdc",
+        "@tut_ship.xyz",
+        "@usgs_quakes_22.txt",
+    ]
+    which(fname=datasets, download="a")

pygmt/helpers/decorators.py

@@ -445,7 +445,7 @@ def fmt_docstring(module_func):
     - J = projection
     - R = region
     <BLANKLINE>
-    """
+    """  # noqa: D410,D411
     filler_text = {}
 
     if hasattr(module_func, "aliases"):

pygmt/helpers/tempfile.py

@@ -62,9 +62,15 @@ def __init__(self, prefix="pygmt-", suffix=".txt"):
             self.name = tmpfile.name
 
     def __enter__(self):
+        """
+        Do nothing but return the object.
+        """
         return self
 
     def __exit__(self, *args):
+        """
+        Remove the temporary file.
+        """
         if os.path.exists(self.name):
             os.remove(self.name)