Merge branch 'main' into alias-system

seisman · web-flow · commit 1c08e311964b · 2024-07-12T18:55:56.000+08:00
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -69,8 +69,6 @@ jobs:
             pytest
             pytest-codspeed
             pytest-mpl
-            pytest-rerunfailures
-            pytest-xdist
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -93,4 +91,4 @@ jobs:
         with:
           # 'bash -el -c' is needed to use the custom shell.
           # See https://github.com/CodSpeedHQ/action/issues/65.
-          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P -n auto --reruns 2 --pyargs pygmt --codspeed"
+          run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed"
diff --git a/.github/workflows/format-command.yml b/.github/workflows/format-command.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Generate token from GenericMappingTools bot
-      - uses: actions/create-github-app-token@v1.10.1
+      - uses: actions/create-github-app-token@v1.10.3
         id: generate-token
         with:
           app-id: ${{ secrets.APP_ID }}
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -75,10 +75,10 @@ jobs:
         ls -lh dist/
 
     - name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@v1.8.14
+      uses: pypa/gh-action-pypi-publish@v1.9.0
       with:
         repository-url: https://test.pypi.org/legacy/
 
     - name: Publish to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@v1.8.14
+      uses: pypa/gh-action-pypi-publish@v1.9.0
diff --git a/AUTHORS.md b/AUTHORS.md
@@ -6,7 +6,7 @@ with [Paul Wessel](https://www.soest.hawaii.edu/wessel) at the University of
 Hawaiʻi at Mānoa.
 
 The following people have contributed code and/or documentation to the project
-(alphabetical by name) and are considered to be "PyGMT Developers":
+(alphabetically by name) and are considered to be "PyGMT Developers":
 
 * [Abhishek Anant](https://twitter.com/itsabhianant) | [0000-0002-5751-2010](https://orcid.org/0000-0002-5751-2010) | Unaffiliated
 * [Andre L. Belem](https://github.com/andrebelem) | [0000-0002-8865-6180](https://orcid.org/0000-0002-8865-6180) | Fluminense Federal University, Brazil
diff --git a/examples/gallery/basemaps/double_y_axes.py b/examples/gallery/basemaps/double_y_axes.py
@@ -1,5 +1,5 @@
 """
-Double Y axes graph
+Double Y-axes graph
 ===================
 
 The ``frame`` parameter of the plotting methods of the :class:`pygmt.Figure`
diff --git a/examples/gallery/basemaps/ternary.py b/examples/gallery/basemaps/ternary.py
@@ -42,5 +42,5 @@
 
 # Add a colorbar indicating the values given in the fourth column of
 # the input dataset
-fig.colorbar(position="JBC+o0c/1.5c", frame=["x+lPermittivity"])
+fig.colorbar(position="JBC+o0c/1.5c", frame="x+lPermittivity")
 fig.show()
diff --git a/examples/gallery/embellishments/inset.py b/examples/gallery/embellishments/inset.py
@@ -18,7 +18,7 @@
 fig.coast(region="MG+r2", land="brown", water="lightblue", shorelines="thin", frame="a")
 # Create an inset, setting the position to top left, the width to 3.5 cm, and
 # the x- and y-offsets to 0.2 cm. The margin is set to 0, and the border is
-# "gold" with a pen size of 1.5p.
+# "gold" with a pen size of 1.5 points.
 with fig.inset(position="jTL+w3.5c+o0.2c", margin=0, box="+p1.5p,gold"):
     # Create a figure in the inset using coast. This example uses the azimuthal
     # orthogonal projection centered at 47E, 20S. The land color is set to
diff --git a/pygmt/accessors.py b/pygmt/accessors.py
@@ -141,7 +141,7 @@ def registration(self):
 
     @registration.setter
     def registration(self, value):
-        if value not in (0, 1):
+        if value not in {0, 1}:
             raise GMTInvalidInput(
                 f"Invalid grid registration value: {value}, should be either "
                 "0 for Gridline registration or 1 for Pixel registration."
@@ -157,7 +157,7 @@ def gtype(self):
 
     @gtype.setter
     def gtype(self, value):
-        if value not in (0, 1):
+        if value not in {0, 1}:
             raise GMTInvalidInput(
                 f"Invalid coordinate system type: {value}, should be "
                 "either 0 for Cartesian or 1 for Geographic."
diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
@@ -944,7 +944,7 @@ def put_vector(self, dataset, column, vector):
         )
 
         gmt_type = self._check_dtype_and_dim(vector, ndim=1)
-        if gmt_type in (self["GMT_TEXT"], self["GMT_DATETIME"]):
+        if gmt_type in {self["GMT_TEXT"], self["GMT_DATETIME"]}:
             if gmt_type == self["GMT_DATETIME"]:
                 vector = np.datetime_as_string(array_to_datetime(vector))
             vector_pointer = strings_to_ctypes_array(vector)
@@ -1622,7 +1622,7 @@ def virtualfile_in(  # noqa: PLR0912
         }[kind]
 
         # Ensure the data is an iterable (Python list or tuple)
-        if kind in ("geojson", "grid", "image", "file", "arg"):
+        if kind in {"geojson", "grid", "image", "file", "arg"}:
             if kind == "image" and data.dtype != "uint8":
                 msg = (
                     f"Input image has dtype: {data.dtype} which is unsupported, "
@@ -1849,7 +1849,7 @@ def read_virtualfile(
         # _GMT_DATASET).
         if kind is None:  # Return the ctypes void pointer
             return pointer
-        if kind in ["image", "cube"]:
+        if kind in {"image", "cube"}:
             raise NotImplementedError(f"kind={kind} is not supported yet.")
         dtype = {"dataset": _GMT_DATASET, "grid": _GMT_GRID}[kind]
         return ctp.cast(pointer, ctp.POINTER(dtype))
diff --git a/pygmt/datasets/load_remote_dataset.py b/pygmt/datasets/load_remote_dataset.py
@@ -387,7 +387,7 @@ def _load_remote_dataset(
     if registration is None:
         # Use gridline registration unless only pixel registration is available
         registration = "gridline" if "gridline" in resinfo.registrations else "pixel"
-    elif registration in ("pixel", "gridline"):
+    elif registration in {"pixel", "gridline"}:
         if registration not in resinfo.registrations:
             raise GMTInvalidInput(
                 f"{registration} registration is not available for the "
diff --git a/pygmt/datasets/tile_map.py b/pygmt/datasets/tile_map.py
@@ -3,6 +3,7 @@
 :class:`xarray.DataArray`.
 """
 
+import contextlib
 from typing import Literal
 
 from packaging.version import Version
@@ -16,6 +17,10 @@
     TileProvider = None
     _HAS_CONTEXTILY = False
 
+with contextlib.suppress(ImportError):
+    # rioxarray is needed to register the rio accessor
+    import rioxarray  # noqa: F401
+
 import numpy as np
 import xarray as xr
 
@@ -113,16 +118,20 @@ def load_tile_map(
     Frozen({'band': 3, 'y': 256, 'x': 512})
     >>> raster.coords  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
     Coordinates:
-      * band    (band) uint8 ... 0 1 2
-      * y       (y) float64 ... -7.081e-10 -7.858e+04 ... -1.996e+07 ...
-      * x       (x) float64 ... -2.004e+07 -1.996e+07 ... 1.996e+07 2.004e+07
+      * band         (band) uint8 ... 1 2 3
+      * y            (y) float64 ... -7.081e-10 -7.858e+04 ... -1.996e+07 -2.004e+07
+      * x            (x) float64 ... -2.004e+07 -1.996e+07 ... 1.996e+07 2.004e+07
+        spatial_ref  int64 ... 0
+    >>> # CRS is set only if rioxarray is available
+    >>> if hasattr(raster, "rio"):
+    ...     raster.rio.crs
+    CRS.from_epsg(3857)
     """
     if not _HAS_CONTEXTILY:
         raise ImportError(
             "Package `contextily` is required to be installed to use this function. "
             "Please use `python -m pip install contextily` or "
-            "`mamba install -c conda-forge contextily` "
-            "to install the package."
+            "`mamba install -c conda-forge contextily` to install the package."
         )
 
     contextily_kwargs = {}
@@ -157,7 +166,7 @@ def load_tile_map(
     dataarray = xr.DataArray(
         data=rgb_image,
         coords={
-            "band": np.array(object=[0, 1, 2], dtype=np.uint8),  # Red, Green, Blue
+            "band": np.array(object=[1, 2, 3], dtype=np.uint8),  # Red, Green, Blue
             "y": np.linspace(start=top, stop=bottom, num=rgb_image.shape[1]),
             "x": np.linspace(start=left, stop=right, num=rgb_image.shape[2]),
         },
@@ -166,6 +175,6 @@ def load_tile_map(
 
     # If rioxarray is installed, set the coordinate reference system
     if hasattr(dataarray, "rio"):
-        dataarray = dataarray.rio.set_crs(input_crs="EPSG:3857")
+        dataarray = dataarray.rio.write_crs(input_crs="EPSG:3857")
 
     return dataarray
diff --git a/pygmt/figure.py b/pygmt/figure.py
@@ -236,7 +236,7 @@ def psconvert(self, **kwargs):
             kwargs["A"] = ""
 
         prefix = kwargs.get("F")
-        if prefix in ["", None, False, True]:
+        if prefix in {"", None, False, True}:
             raise GMTInvalidInput(
                 "The 'prefix' parameter must be specified with a valid value."
             )
@@ -363,7 +363,7 @@ def savefig(  # noqa: PLR0912
             kwargs["Qg"] = 2
 
         if worldfile:
-            if ext in ["eps", "kml", "pdf", "tiff"]:
+            if ext in {"eps", "kml", "pdf", "tiff"}:
                 raise GMTInvalidInput(
                     f"Saving a world file is not supported for '{ext}' format."
                 )
@@ -444,7 +444,7 @@ def show(self, dpi=300, width=500, method=None, waiting=0.5, **kwargs):
         if method is None:
             method = SHOW_CONFIG["method"]
 
-        if method not in ["external", "notebook", "none"]:
+        if method not in {"external", "notebook", "none"}:
             raise GMTInvalidInput(
                 f"Invalid display method '{method}', "
                 "should be either 'notebook', 'external', or 'none'."
@@ -584,7 +584,7 @@ def set_display(method=None):
     >>> pygmt.set_display(method=None)
     >>> fig.show()  # again, will show a PNG image in the current notebook
     """
-    if method in ["notebook", "external", "none"]:
+    if method in {"notebook", "external", "none"}:
         SHOW_CONFIG["method"] = method
     elif method is not None:
         raise GMTInvalidInput(
diff --git a/pygmt/helpers/tempfile.py b/pygmt/helpers/tempfile.py
@@ -148,15 +148,15 @@ def tempfile_from_geojson(geojson):
                 geojson = geojson.reset_index(drop=False)
                 schema = gpd.io.file.infer_schema(geojson)
                 for col, dtype in schema["properties"].items():
-                    if dtype in ("int", "int64"):
+                    if dtype in {"int", "int64"}:
                         overflow = geojson[col].abs().max() > 2**31 - 1
                         schema["properties"][col] = "float" if overflow else "int32"
                 ogrgmt_kwargs["schema"] = schema
             else:  # GeoPandas v1.x.
                 # The default engine "pyogrio" doesn't support the 'schema' parameter
                 # but we can change the dtype directly.
                 for col in geojson.columns:
-                    if geojson[col].dtype in ("int", "int64", "Int64"):
+                    if geojson[col].dtype.name in {"int", "int64", "Int64"}:
                         overflow = geojson[col].abs().max() > 2**31 - 1
                         dtype = "float" if overflow else "int32"
                         geojson[col] = geojson[col].astype(dtype)
diff --git a/pygmt/helpers/validators.py b/pygmt/helpers/validators.py
@@ -49,7 +49,7 @@ def validate_output_table_type(
     ...     assert len(w) == 1
     'file'
     """
-    if output_type not in ["file", "numpy", "pandas"]:
+    if output_type not in {"file", "numpy", "pandas"}:
         raise GMTInvalidInput(
             "Must specify 'output_type' either as 'file', 'numpy', or 'pandas'."
         )
diff --git a/pygmt/src/meca.py b/pygmt/src/meca.py
@@ -95,7 +95,7 @@ def convention_code(convention, component="full"):
                 f"Invalid component '{component}' for convention '{convention}'."
             )
         return codes2[convention][component]
-    if convention in ["a", "c", "m", "d", "z", "p", "x", "y", "t"]:
+    if convention in {"a", "c", "m", "d", "z", "p", "x", "y", "t"}:
         return convention
     raise GMTInvalidInput(f"Invalid convention '{convention}'.")
 
diff --git a/pygmt/src/plot.py b/pygmt/src/plot.py
@@ -247,7 +247,7 @@ def plot(  # noqa: PLR0912
             kwargs["S"] = "s0.2c"
         elif kind == "file" and str(data).endswith(".gmt"):  # OGR_GMT file
             try:
-                with Path(which(data)).open() as file:
+                with Path(which(data)).open(encoding="utf-8") as file:
                     line = file.readline()
                 if "@GMULTIPOINT" in line or "@GPOINT" in line:
                     kwargs["S"] = "s0.2c"
diff --git a/pygmt/src/plot3d.py b/pygmt/src/plot3d.py
@@ -223,7 +223,7 @@ def plot3d(  # noqa: PLR0912
             kwargs["S"] = "u0.2c"
         elif kind == "file" and str(data).endswith(".gmt"):  # OGR_GMT file
             try:
-                with Path(which(data)).open() as file:
+                with Path(which(data)).open(encoding="utf-8") as file:
                     line = file.readline()
                 if "@GMULTIPOINT" in line or "@GPOINT" in line:
                     kwargs["S"] = "u0.2c"
diff --git a/pygmt/src/tilemap.py b/pygmt/src/tilemap.py
@@ -146,7 +146,7 @@ def tilemap(
 
     # Only set region if no_clip is None or False, so that plot is clipped to exact
     # bounding box region
-    if kwargs.get("N") in [None, False]:
+    if kwargs.get("N") in {None, False}:
         kwargs["R"] = "/".join(str(coordinate) for coordinate in region)
 
     with Session() as lib:
diff --git a/pygmt/tests/test_clib.py b/pygmt/tests/test_clib.py
@@ -529,7 +529,7 @@ def test_get_default():
     Make sure get_default works without crashing and gives reasonable results.
     """
     with clib.Session() as lib:
-        assert lib.get_default("API_GRID_LAYOUT") in ["rows", "columns"]
+        assert lib.get_default("API_GRID_LAYOUT") in {"rows", "columns"}
         assert int(lib.get_default("API_CORES")) >= 1
         assert Version(lib.get_default("API_VERSION")) >= Version("6.3.0")
         assert lib.get_default("PROJ_LENGTH_UNIT") == "cm"
diff --git a/pygmt/tests/test_clib_loading.py b/pygmt/tests/test_clib_loading.py
@@ -131,7 +131,7 @@ def _mock_ctypes_cdll_return(self, libname):
         # libname is a loaded GMT library
         return self.loaded_libgmt
 
-    @pytest.fixture()
+    @pytest.fixture
     def _mock_ctypes(self, monkeypatch):
         """
         Patch the ctypes.CDLL function.
diff --git a/pygmt/tests/test_datatypes_dataset.py b/pygmt/tests/test_datatypes_dataset.py
@@ -57,7 +57,7 @@ def test_dataset():
     Test the basic functionality of GMT_DATASET.
     """
     with GMTTempFile(suffix=".txt") as tmpfile:
-        with Path(tmpfile.name).open(mode="w") as fp:
+        with Path(tmpfile.name).open(mode="w", encoding="utf-8") as fp:
             print(">", file=fp)
             print("1.0 2.0 3.0 TEXT1 TEXT23", file=fp)
             print("4.0 5.0 6.0 TEXT4 TEXT567", file=fp)
@@ -75,7 +75,7 @@ def test_dataset_empty():
     Make sure that an empty DataFrame is returned if a file contains no data.
     """
     with GMTTempFile(suffix=".txt") as tmpfile:
-        with Path(tmpfile.name).open(mode="w") as fp:
+        with Path(tmpfile.name).open(mode="w", encoding="utf-8") as fp:
             print("# This is a comment line.", file=fp)
 
         df = dataframe_from_gmt(tmpfile.name)
@@ -89,7 +89,7 @@ def test_dataset_header():
     Test parsing column names from dataset header.
     """
     with GMTTempFile(suffix=".txt") as tmpfile:
-        with Path(tmpfile.name).open(mode="w") as fp:
+        with Path(tmpfile.name).open(mode="w", encoding="utf-8") as fp:
             print("# lon lat z text", file=fp)
             print("1.0 2.0 3.0 TEXT1 TEXT23", file=fp)
             print("4.0 5.0 6.0 TEXT4 TEXT567", file=fp)
@@ -109,7 +109,7 @@ def test_dataset_header_greater_than_nheaders():
     Test passing a header line number that is greater than the number of header lines.
     """
     with GMTTempFile(suffix=".txt") as tmpfile:
-        with Path(tmpfile.name).open(mode="w") as fp:
+        with Path(tmpfile.name).open(mode="w", encoding="utf-8") as fp:
             print("# lon lat z text", file=fp)
             print("1.0 2.0 3.0 TEXT1 TEXT23", file=fp)
             print("4.0 5.0 6.0 TEXT4 TEXT567", file=fp)
@@ -127,7 +127,7 @@ def test_dataset_header_too_many_names():
     Test passing a header line with more column names than the number of columns.
     """
     with GMTTempFile(suffix=".txt") as tmpfile:
-        with Path(tmpfile.name).open(mode="w") as fp:
+        with Path(tmpfile.name).open(mode="w", encoding="utf-8") as fp:
             print("# lon lat z text1 text2", file=fp)
             print("1.0 2.0 3.0 TEXT1 TEXT23", file=fp)
             print("4.0 5.0 6.0 TEXT4 TEXT567", file=fp)
diff --git a/pygmt/tests/test_helpers.py b/pygmt/tests/test_helpers.py
@@ -132,7 +132,7 @@ def test_gmttempfile_read():
     Make sure GMTTempFile.read() works.
     """
     with GMTTempFile() as tmpfile:
-        Path(tmpfile.name).write_text("in.dat: N = 2\t<1/3>\t<2/4>\n")
+        Path(tmpfile.name).write_text("in.dat: N = 2\t<1/3>\t<2/4>\n", encoding="utf-8")
         assert tmpfile.read() == "in.dat: N = 2 <1/3> <2/4>\n"
         assert tmpfile.read(keep_tabs=True) == "in.dat: N = 2\t<1/3>\t<2/4>\n"
 
diff --git a/pygmt/tests/test_legend.py b/pygmt/tests/test_legend.py
@@ -97,7 +97,7 @@ def test_legend_specfile():
 """
 
     with GMTTempFile() as specfile:
-        Path(specfile.name).write_text(specfile_contents)
+        Path(specfile.name).write_text(specfile_contents, encoding="utf-8")
         fig = Figure()
         fig.basemap(projection="x6i", region=[0, 1, 0, 1], frame=True)
         fig.legend(specfile.name, position="JTM+jCM+w5i")
diff --git a/pygmt/tests/test_meca.py b/pygmt/tests/test_meca.py
@@ -74,7 +74,7 @@ def test_meca_spec_single_focalmecha_file():
     fig = Figure()
     fig.basemap(region=[-1, 1, 4, 6], projection="M8c", frame=2)
     with GMTTempFile() as temp:
-        Path(temp.name).write_text("0 5 0 0 90 0 5")
+        Path(temp.name).write_text("0 5 0 0 90 0 5", encoding="utf-8")
         fig.meca(spec=temp.name, convention="aki", scale="2.5c")
     return fig
 
diff --git a/pygmt/tests/test_plot.py b/pygmt/tests/test_plot.py
@@ -487,7 +487,7 @@ def test_plot_ogrgmt_file_multipoint_default_style(func):
 # FEATURE_DATA
 1 2
         """
-        Path(tmpfile.name).write_text(gmt_file)
+        Path(tmpfile.name).write_text(gmt_file, encoding="utf-8")
         fig = Figure()
         fig.plot(
             data=func(tmpfile.name), region=[0, 2, 1, 3], projection="X2c", frame=True
@@ -506,7 +506,7 @@ def test_plot_ogrgmt_file_multipoint_non_default_style():
 # FEATURE_DATA
 1 2
         """
-        Path(tmpfile.name).write_text(gmt_file)
+        Path(tmpfile.name).write_text(gmt_file, encoding="utf-8")
         fig = Figure()
         fig.plot(
             data=tmpfile.name,
diff --git a/pygmt/tests/test_plot3d.py b/pygmt/tests/test_plot3d.py
diff --git a/pygmt/tests/test_text.py b/pygmt/tests/test_text.py
diff --git a/pyproject.toml b/pyproject.toml
