Merge branch 'main' into timestamp/deprecate-justify

.github/workflows/check-links.yml

@@ -34,7 +34,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/[email protected].0
+      uses: lycheeverse/[email protected].1
       with:
         # 429: Too many requests
         args: >

.readthedocs.yaml

@@ -26,11 +26,7 @@ build:
         then
           exit 183;
         fi
-    pre_build:
-      # ReadTheDocs fails to download external resources.
-      # Temporarily delete the two files to make ReadTheDocs building work again.
-      - rm examples/gallery/lines/roads.py examples/gallery/maps/choropleth_map.py
-      # Generate api stub files before building
+    pre_build: # Generate api stub files before building
       - make -C doc api
 
 # Build documentation in the doc/ directory with Sphinx

doc/api/index.rst

@@ -307,6 +307,6 @@ Low level access (these are mostly used by the :mod:`pygmt.clib` package):
     clib.Session.put_strings
     clib.Session.put_vector
     clib.Session.write_data
-    clib.Session.open_virtual_file
+    clib.Session.open_virtualfile
     clib.Session.extract_region
     clib.Session.get_libgmt_func

pygmt/clib/session.py

@@ -1085,7 +1085,7 @@ def write_data(self, family, geometry, mode, wesn, output, data):
             raise GMTCLibError(f"Failed to write dataset to '{output}'")
 
     @contextlib.contextmanager
-    def open_virtual_file(self, family, geometry, direction, data):
+    def open_virtualfile(self, family, geometry, direction, data):
         """
         Open a GMT virtual file to pass data to and from a module.
 
@@ -1142,7 +1142,7 @@ def open_virtual_file(self, family, geometry, direction, data):
         ...     lib.put_vector(dataset, column=1, vector=y)
         ...     # Add the dataset to a virtual file
         ...     vfargs = (family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset)
-        ...     with lib.open_virtual_file(*vfargs) as vfile:
+        ...     with lib.open_virtualfile(*vfargs) as vfile:
         ...         # Send the output to a temp file so that we can read it
         ...         with GMTTempFile() as ofile:
         ...             args = f"{vfile} ->{ofile.name}"
@@ -1190,6 +1190,23 @@ def open_virtual_file(self, family, geometry, direction, data):
             if status != 0:
                 raise GMTCLibError(f"Failed to close virtual file '{vfname}'.")
 
+    def open_virtual_file(self, family, geometry, direction, data):
+        """
+        Open a GMT virtual file to pass data to and from a module.
+
+        .. deprecated: 0.11.0
+
+           Will be removed in v0.15.0. Use :meth:`pygmt.clib.Session.open_virtualfile`
+           instead.
+        """
+        msg = (
+            "API function `Session.open_virtual_file()' has been deprecated "
+            "since v0.11.0 and will be removed in v0.15.0. "
+            "Use `Session.open_virtualfile()' instead."
+        )
+        warnings.warn(msg, category=FutureWarning, stacklevel=2)
+        return self.open_virtualfile(family, geometry, direction, data)
+
     @contextlib.contextmanager
     def virtualfile_from_vectors(self, *vectors):
         """
@@ -1205,7 +1222,7 @@ def virtualfile_from_vectors(self, *vectors):
         Use this instead of creating the data container and virtual file by
         hand with :meth:`pygmt.clib.Session.create_data`,
         :meth:`pygmt.clib.Session.put_vector`, and
-        :meth:`pygmt.clib.Session.open_virtual_file`.
+        :meth:`pygmt.clib.Session.open_virtualfile`.
 
         If the arrays are C contiguous blocks of memory, they will be passed
         without copying to GMT. If they are not (e.g., they are columns of a
@@ -1286,7 +1303,7 @@ def virtualfile_from_vectors(self, *vectors):
                 dataset, family="GMT_IS_VECTOR|GMT_IS_DUPLICATE", strings=strings
             )
 
-        with self.open_virtual_file(
+        with self.open_virtualfile(
             family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset
         ) as vfile:
             yield vfile
@@ -1313,7 +1330,7 @@ def virtualfile_from_matrix(self, matrix):
         Use this instead of creating the data container and virtual file by
         hand with :meth:`pygmt.clib.Session.create_data`,
         :meth:`pygmt.clib.Session.put_matrix`, and
-        :meth:`pygmt.clib.Session.open_virtual_file`
+        :meth:`pygmt.clib.Session.open_virtualfile`
 
         The matrix must be C contiguous in memory. If it is not (e.g., it is a
         slice of a larger array), the array will be copied to make sure it is.
@@ -1366,7 +1383,7 @@ def virtualfile_from_matrix(self, matrix):
 
         self.put_matrix(dataset, matrix)
 
-        with self.open_virtual_file(
+        with self.open_virtualfile(
             family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset
         ) as vfile:
             yield vfile
@@ -1389,7 +1406,7 @@ def virtualfile_from_grid(self, grid):
         Use this instead of creating a data container and virtual file by hand
         with :meth:`pygmt.clib.Session.create_data`,
         :meth:`pygmt.clib.Session.put_matrix`, and
-        :meth:`pygmt.clib.Session.open_virtual_file`
+        :meth:`pygmt.clib.Session.open_virtualfile`.
 
         The grid data matrix must be C contiguous in memory. If it is not
         (e.g., it is a slice of a larger array), the array will be copied to
@@ -1453,7 +1470,7 @@ def virtualfile_from_grid(self, grid):
         )
         self.put_matrix(gmt_grid, matrix)
         args = (family, geometry, "GMT_IN|GMT_IS_REFERENCE", gmt_grid)
-        with self.open_virtual_file(*args) as vfile:
+        with self.open_virtualfile(*args) as vfile:
             yield vfile
 
     @fmt_docstring

pygmt/src/text.py

@@ -135,8 +135,8 @@ def text_(  # noqa: PLR0912
         [*dx/dy*][**+to**\|\ **O**\|\ **c**\|\ **C**].
         Adjust the clearance between the text and the surrounding box
         [Default is 15% of the font size]. Only used if ``pen`` or ``fill``
-        are specified. Append the unit you want (*c* for centimeters,
-        *i* for inches, or *p* for points; if not given we consult
+        are specified. Append the unit you want (**c** for centimeters,
+        **i** for inches, or **p** for points; if not given we consult
         :gmt-term:`PROJ_LENGTH_UNIT`) or *%* for a percentage of the font
         size. Optionally, use modifier **+t** to set the shape of the text
         box when using ``fill`` and/or ``pen``. Append lower case **o**

pygmt/src/tilemap.py

@@ -43,7 +43,7 @@ def tilemap(
     **kwargs,
 ):
     r"""
-    Plots an XYZ tile map.
+    Plot an XYZ tile map.
 
     This method loads XYZ tile maps from a tile server or local file using
     :func:`pygmt.datasets.load_tile_map` into a georeferenced form, and plots

pygmt/tests/test_clib_virtualfiles.py

@@ -67,7 +67,7 @@ def test_virtual_file(dtypes):
             lib.put_matrix(dataset, matrix=data)
             # Add the dataset to a virtual file and pass it along to gmt info
             vfargs = (family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset)
-            with lib.open_virtual_file(*vfargs) as vfile:
+            with lib.open_virtualfile(*vfargs) as vfile:
                 with GMTTempFile() as outfile:
                     lib.call_module("info", f"{vfile} ->{outfile.name}")
                     output = outfile.read(keep_tabs=True)
@@ -93,7 +93,7 @@ def test_virtual_file_fails():
     # virtual file.
     with clib.Session() as lib, mock(lib, "GMT_Open_VirtualFile", returns=1):
         with pytest.raises(GMTCLibError):
-            with lib.open_virtual_file(*vfargs):
+            with lib.open_virtualfile(*vfargs):
                 pass
 
     # Test the status check when closing the virtual file
@@ -103,7 +103,7 @@ def test_virtual_file_fails():
         lib, "GMT_Close_VirtualFile", returns=1
     ):
         with pytest.raises(GMTCLibError):
-            with lib.open_virtual_file(*vfargs):
+            with lib.open_virtualfile(*vfargs):
                 pass
 
 
@@ -119,7 +119,7 @@ def test_virtual_file_bad_direction():
             0,
         )
         with pytest.raises(GMTInvalidInput):
-            with lib.open_virtual_file(*vfargs):
+            with lib.open_virtualfile(*vfargs):
                 pass