Merge branch 'main' into clib/load-libgmt

Author: seisman

.github/workflows/ci_tests_dev.yaml

@@ -120,7 +120,7 @@ jobs:
         run: curl https://raw.githubusercontent.com/GenericMappingTools/gmt/master/ci/build-gmt.sh | bash
         env:
           GMT_GIT_REF: ${{ matrix.gmt_git_ref }}
-          GMT_INSTALL_DIR: ${{ github.workspace }}/gmt-install-dir
+          GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
         if: runner.os != 'Windows'
 
       - name: Install GMT ${{ matrix.gmt_git_ref }} branch (Windows)
@@ -139,13 +139,15 @@ jobs:
             -DGMT_USE_THREADS=TRUE
           cmake --build .
           cmake --build . --target install
+          cd ..
+          rm -rf gmt/
         env:
           GMT_GIT_REF: ${{ matrix.gmt_git_ref }}
-          GMT_INSTALL_DIR: ${{ github.workspace }}/gmt-install-dir
+          GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
         if: runner.os == 'Windows'
 
       - name: Add GMT's bin to PATH
-        run: echo '${{ github.workspace }}/gmt-install-dir/bin' >> $GITHUB_PATH
+        run: echo '${{ runner.temp }}/gmt-install-dir/bin' >> $GITHUB_PATH
 
       # Install dependencies from PyPI
       - name: Install dependencies
@@ -163,7 +165,7 @@ jobs:
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
-        run: dvc pull && ls -lhR pygmt/tests/baseline/
+        run: dvc pull --verbose && ls -lhR pygmt/tests/baseline/
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -191,7 +193,7 @@ jobs:
       - name: Test with pytest
         run: make test PYTEST_EXTRA="-r P"
         env:
-          GMT_LIBRARY_PATH: ${{ github.workspace }}/gmt-install-dir/lib
+          GMT_LIBRARY_PATH: ${{ runner.temp }}/gmt-install-dir/lib
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails

doc/contributing.md

@@ -320,24 +320,24 @@ Open `doc/_build/html/index.html` in your browser to view the pages. Follow the
 Many of the PyGMT functions have example code in their documentation. To contribute an
 example, add an "Example" header and put the example code below it. Have all lines
 begin with `>>>`.  To keep this example code from being run during testing, add the code
-`__doctest_skip__ = [function name]` to the top of the module.
+`__doctest_skip__ = ["function_name"]` to the top of the module.
 
 **Inline code example**
 
 Below the import statements at the top of the file
 
-``
-__doctest_skip__ = ["module_name"]
-``
-
-At the end of the function's docstring
+```python
+__doctest_skip__ = ["function_name"]
 
-    Example
-    -------
-    >>> import pygmt
-    >>> # Comment describing what is happening
-    >>> Code example
+At the end of the function's docstring:
 
+```python
+Example
+-------
+>>> import pygmt
+>>> # Comment describing what is happening
+>>> Code example
+```
 
 ### Contributing Gallery Plots
 
@@ -580,7 +580,9 @@ returning the `pygmt.Figure` object:
 ```python
 @pytest.mark.mpl_image_compare
 def test_my_plotting_case():
-    "Test that my plotting method works"
+    """
+    Test that my plotting method works.
+    """
     fig = Figure()
     fig.basemap(region=[0, 360, -90, 90], projection="W15c", frame=True)
     return fig
@@ -675,20 +677,22 @@ summarized as follows:
     dvc push  # Run before git push to enable automated testing with the new images
     git push
 
-#### Using check_figures_equal
+#### Using `check_figures_equal`
 
 This approach draws the same figure using two different methods (the reference
 method and the tested method), and checks that both of them are the same.
-It takes two `pygmt.Figure` objects ('fig_ref' and 'fig_test'), generates a png
+It takes two `pygmt.Figure` objects (`fig_ref` and `fig_test`), generates a png
 image, and checks for the Root Mean Square (RMS) error between the two.
 Here's an example:
 
 ```python
 @check_figures_equal()
 def test_my_plotting_case():
-  "Test that my plotting method works"
-  fig_ref, fig_test = Figure(), Figure()
-  fig_ref.grdimage("@earth_relief_01d_g", projection="W120/15c", cmap="geo")
-  fig_test.grdimage(grid, projection="W120/15c", cmap="geo")
-  return fig_ref, fig_test
+    """
+    Test that my plotting method works.
+    """
+    fig_ref, fig_test = Figure(), Figure()
+    fig_ref.grdimage("@earth_relief_01d_g", projection="W120/15c", cmap="geo")
+    fig_test.grdimage(grid, projection="W120/15c", cmap="geo")
+    return fig_ref, fig_test
 ```

pygmt/datasets/samples.py

@@ -26,7 +26,7 @@ def _load_japan_quakes():
     return pd.read_csv(
         fname,
         header=1,
-        delim_whitespace=True,
+        sep=r"\s+",
         names=[
             "year",
             "month",
@@ -52,7 +52,7 @@ def _load_ocean_ridge_points():
     fname = which("@ridge.txt", download="c")
     return pd.read_csv(
         fname,
-        delim_whitespace=True,
+        sep=r"\s+",
         names=["longitude", "latitude"],
         skiprows=1,
         comment=">",
@@ -102,9 +102,7 @@ def _load_fractures_compilation():
         the fractures.
     """
     fname = which("@fractures_06.txt", download="c")
-    data = pd.read_csv(
-        fname, header=None, delim_whitespace=True, names=["azimuth", "length"]
-    )
+    data = pd.read_csv(fname, header=None, sep=r"\s+", names=["azimuth", "length"])
     return data[["length", "azimuth"]]
 
 
@@ -167,7 +165,7 @@ def _load_rock_sample_compositions():
     fname = which("@ternary.txt", download="c")
     return pd.read_csv(
         fname,
-        delim_whitespace=True,
+        sep=r"\s+",
         header=None,
         names=["limestone", "water", "air", "permittivity"],
     )
@@ -183,7 +181,7 @@ def _load_notre_dame_topography():
         The data table with columns "x", "y", and "z".
     """
     fname = which("@Table_5_11.txt", download="c")
-    return pd.read_csv(fname, delim_whitespace=True, header=None, names=["x", "y", "z"])
+    return pd.read_csv(fname, sep=r"\s+", header=None, names=["x", "y", "z"])
 
 
 def _load_maunaloa_co2():
@@ -197,7 +195,7 @@ def _load_maunaloa_co2():
     """
     fname = which("@MaunaLoa_CO2.txt", download="c")
     return pd.read_csv(
-        fname, header=None, skiprows=1, delim_whitespace=True, names=["date", "co2_ppm"]
+        fname, header=None, skiprows=1, sep=r"\s+", names=["date", "co2_ppm"]
     )
 
 

pygmt/tests/test_contour.py

@@ -18,7 +18,7 @@ def fixture_data():
     """
     Load the point data from the test file.
     """
-    return pd.read_table(POINTS_DATA, header=None, delim_whitespace=True)
+    return pd.read_table(POINTS_DATA, header=None, sep=r"\s+")
 
 
 @pytest.fixture(scope="module", name="region")

pygmt/tests/test_grdtrack.py

@@ -51,7 +51,7 @@ def fixture_dataframe():
     Load a pandas DataFrame with points.
     """
     return pd.read_csv(
-        POINTS_DATA, delim_whitespace=True, header=None, names=["longitude", "latitude"]
+        POINTS_DATA, sep=r"\s+", header=None, names=["longitude", "latitude"]
     )
 
 

pygmt/tests/test_surface.py

@@ -18,7 +18,7 @@ def fixture_data():
     """
     fname = which("@Table_5_11_mean.xyz", download="c")
     return pd.read_csv(
-        fname, delim_whitespace=True, header=None, names=["x", "y", "z"], skiprows=1
+        fname, sep=r"\s+", header=None, names=["x", "y", "z"], skiprows=1
     )
 
 

pygmt/tests/test_triangulate.py

@@ -19,7 +19,7 @@ def fixture_dataframe():
     """
     fname = which("@Table_5_11_mean.xyz", download="c")
     return pd.read_csv(
-        fname, delim_whitespace=True, header=None, names=["x", "y", "z"], skiprows=1
+        fname, sep=r"\s+", header=None, names=["x", "y", "z"], skiprows=1
     )[:10]