DOC: Fix highlighting, typos, etc. - Part I (#3574)

Author: yvonnefroehlich

pygmt/src/binstats.py

@@ -72,7 +72,7 @@ def binstats(data, outgrid: str | None = None, **kwargs) -> xr.DataArray | None:
         Set the value assigned to empty nodes [Default is NaN].
     normalize : bool
         Normalize the resulting grid values by the area represented by the
-        search *radius* [no normalization].
+        search *radius* [Default is no normalization].
     search_radius : float or str
         Set the *search_radius* that determines which data points are
         considered close to a node. Append the distance unit.
@@ -98,7 +98,7 @@ def binstats(data, outgrid: str | None = None, **kwargs) -> xr.DataArray | None:
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
     """
     with Session() as lib:

pygmt/src/blockm.py

@@ -244,7 +244,7 @@ def blockmedian(
     ret
         Return type depends on ``outfile`` and ``output_type``:
 
-        - ``None`` if ``outfile`` is set (output will be stored in file set by
+        - ``None`` if ``outfile`` is set (output will be stored in the file set by
           ``outfile``)
         - :class:`pandas.DataFrame` or :class:`numpy.ndarray` if ``outfile`` is not set
           (depends on ``output_type``)
@@ -342,7 +342,7 @@ def blockmode(
     ret
         Return type depends on ``outfile`` and ``output_type``:
 
-        - ``None`` if ``outfile`` is set (output will be stored in file set by
+        - ``None`` if ``outfile`` is set (output will be stored in the file set by
           ``outfile``)
         - :class:`pandas.DataFrame` or :class:`numpy.ndarray` if ``outfile`` is not set
           (depends on ``output_type``)

pygmt/src/dimfilter.py

@@ -98,12 +98,12 @@ def dimfilter(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | None
     spacing : str or list
         *x_inc* [and optionally *y_inc*] is the output increment. Append
         **m** to indicate minutes, or **c** to indicate seconds. If the new
-        *x_inc*, *y_inc* are NOT integer multiples of the old ones (in the
+        *x_inc*, *y_inc* are **not** integer multiples of the old ones (in the
         input data), filtering will be considerably slower. [Default is same
-        as input.]
+        as the input.]
     region : str or list
         [*xmin*, *xmax*, *ymin*, *ymax*].
-        Define the region of the output points [Default is same as input].
+        Define the region of the output points [Default is the same as the input].
     {verbose}
 
     Returns
@@ -112,7 +112,7 @@ def dimfilter(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | None
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
     Example

pygmt/src/filter1d.py

@@ -105,7 +105,8 @@ def filter1d(
     ret
         Return type depends on ``outfile`` and ``output_type``:
 
-        - None if ``outfile`` is set (output will be stored in file set by ``outfile``)
+        - ``None`` if ``outfile`` is set (output will be stored in the file set by
+          ``outfile``)
         - :class:`pandas.DataFrame` or :class:`numpy.ndarray` if ``outfile`` is not set
           (depends on ``output_type``)
     """

pygmt/src/grd2xyz.py

@@ -121,7 +121,8 @@ def grd2xyz(
     ret
         Return type depends on ``outfile`` and ``output_type``:
 
-        - None if ``outfile`` is set (output will be stored in file set by ``outfile``)
+        - ``None`` if ``outfile`` is set (output will be stored in the file set by
+          ``outfile``)
         - :class:`pandas.DataFrame` or :class:`numpy.ndarray` if ``outfile`` is not set
           (depends on ``output_type``)
 
@@ -133,7 +134,7 @@ def grd2xyz(
     >>> grid = pygmt.datasets.load_earth_relief(
     ...     resolution="30m", region=[10, 30, 15, 25]
     ... )
-    >>> # Create a pandas DataFrame with the xyz data from an input grid
+    >>> # Create a pandas.DataFrame with the xyz data from an input grid
     >>> xyz_dataframe = pygmt.grd2xyz(grid=grid, output_type="pandas")
     >>> xyz_dataframe.head(n=2)
         lon   lat          z

pygmt/src/grdclip.py

@@ -67,7 +67,7 @@ def grdclip(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | None:
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
     Example

pygmt/src/grdcontour.py

@@ -40,7 +40,7 @@ def grdcontour(self, grid, **kwargs):
     r"""
     Convert grids or images to contours and plot them on maps.
 
-    Takes a grid file name or an xarray.DataArray object as input.
+    Takes a grid file name or an :class:`xarray.DataArray` object as input.
 
     Full option list at :gmt-docs:`grdcontour.html`
 

pygmt/src/grdcut.py

@@ -85,7 +85,7 @@ def grdcut(grid, **kwargs) -> xr.DataArray | None:
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
     Example

pygmt/src/grdfill.py

@@ -56,7 +56,7 @@ def grdfill(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | None:
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
     Example

pygmt/src/grdfilter.py

@@ -102,7 +102,7 @@ def grdfilter(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | None
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
     Examples

pygmt/src/grdgradient.py

@@ -143,7 +143,7 @@ def grdgradient(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | No
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
 

pygmt/src/grdhisteq.py

@@ -99,9 +99,8 @@ def equalize_grid(
         ret
             Return type depends on the ``outgrid`` parameter:
 
-            - xarray.DataArray if ``outgrid`` is None
-            - None if ``outgrid`` is a str (grid output is stored in
-              ``outgrid``)
+            - :class:`xarray.DataArray` if ``outgrid`` is ``None``
+            - ``None`` if ``outgrid`` is a str (grid output is stored in ``outgrid``)
 
         Example
         -------

pygmt/src/grdimage.py

@@ -103,7 +103,7 @@ def grdimage(self, grid, **kwargs):
         paint the mask with the given color. Append **+b** to paint the
         background pixels (1) or **+f** for the foreground pixels
         [Default is **+f**].
-    shading : str or xarray.DataArray
+    shading : str or :class:`xarray.DataArray`
         [*intensfile*\|\ *intensity*\|\ *modifiers*].
         Give the name of a grid file or a DataArray with intensities in the
         (-1,+1) range, or a constant intensity to apply everywhere (affects the

pygmt/src/grdinfo.py

@@ -30,7 +30,7 @@ def grdinfo(grid, **kwargs):
     r"""
     Get information about a grid.
 
-    Can read the grid from a file or given as an xarray.DataArray grid.
+    Can read the grid from a file or given as an :class:`xarray.DataArray` grid.
 
     Full option list at :gmt-docs:`grdinfo.html`
 

pygmt/src/grdlandmask.py

@@ -85,7 +85,7 @@ def grdlandmask(outgrid: str | None = None, **kwargs) -> xr.DataArray | None:
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
     Example

pygmt/src/grdproject.py

@@ -53,8 +53,8 @@ def grdproject(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | Non
     {grid}
     {outgrid}
     inverse : bool
-        When set to ``True`` transforms grid from rectangular to
-        geographical [Default is False].
+        When set to ``True`` transforms grid from rectangular to geographical
+        [Default is ``False``].
     {projection}
     {region}
     center : str or list
@@ -63,7 +63,7 @@ def grdproject(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | Non
         is relative to lower left corner]. Optionally, add offsets in the
         projected units to be added (or subtracted when ``inverse`` is set) to
         (from) the projected coordinates, such as false eastings and
-        northings for particular projection zones [0/0].
+        northings for particular projection zones [Default is ``[0, 0]``].
     {spacing}
     dpi : int
         Set the resolution for the new grid in dots per inch.
@@ -89,7 +89,7 @@ def grdproject(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | Non
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
     Example

pygmt/src/grdsample.py

@@ -65,7 +65,7 @@ def grdsample(grid, outgrid: str | None = None, **kwargs) -> xr.DataArray | None
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray` if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
 
     Example

pygmt/src/grdtrack.py

@@ -191,7 +191,7 @@ def grdtrack(
     {region}
     no_skip : bool
         Do *not* skip points that fall outside the domain of the grid(s)
-        [Default only output points within grid domain].
+        [Default only output points within the grid domain].
     stack : str or list
         *method*/*modifiers*.
         In conjunction with ``crossprofile``, compute a single stacked profile

pygmt/src/grdview.py

@@ -61,7 +61,7 @@ def grdview(self, grid, **kwargs):
     {frame}
     cmap : str
         The name of the color palette table to use.
-    drapegrid : str or xarray.DataArray
+    drapegrid : str or :class:`xarray.DataArray`
         The file name or a DataArray of the image grid to be draped on top
         of the relief provided by ``grid`` [Default determines colors from grid].
         Note that ``zscale`` and ``plane`` always refer to the grid.

pygmt/src/histogram.py

@@ -1,5 +1,5 @@
 """
-Histogram - Create a histogram
+Histogram - Create a histogram.
 """
 
 from pygmt.clib import Session

pygmt/src/info.py

@@ -34,12 +34,12 @@ def info(data, **kwargs):
     the number of columns vary from record to record. As an option, it will
     find the extent of the first two columns rounded up and down to the nearest
     multiple of the supplied increments given by ``spacing``. Such output will
-    be in a numpy.ndarray form [*w*, *e*, *s*, *n*], which can be used
+    be in a :class:`numpy.ndarray` form [*w*, *e*, *s*, *n*], which can be used
     directly as the ``region`` parameter for other modules (hence only *dx*
     and *dy* are needed). If the ``per_column`` parameter is combined with
-    ``spacing``, then the numpy.ndarray output will be rounded up/down for as
+    ``spacing``, then the :class:`numpy.ndarray` output will be rounded up/down for as
     many columns as there are increments provided in ``spacing``. A similar
-    parameter ``nearest_multiple`` will provide a numpy.ndarray in the form
+    parameter ``nearest_multiple`` will provide a :class:`numpy.ndarray` in the form
     of [*zmin*, *zmax*, *dz*] for makecpt.
 
     Full option list at :gmt-docs:`gmtinfo.html`
@@ -73,7 +73,7 @@ def info(data, **kwargs):
 
     Returns
     -------
-    output : np.ndarray or str
+    output : :class:`numpy.ndarray` or str
         Return type depends on whether any of the ``per_column``,
         ``spacing``, or ``nearest_multiple`` parameters are set.
 

pygmt/src/meca.py

@@ -227,7 +227,7 @@ def meca(  # noqa: PLR0912, PLR0913, PLR0915
 
     Parameters
     ----------
-    spec : str, 1-D array, 2-D array, dict, or pd.DataFrame
+    spec : str, 1-D array, 2-D array, dict, or :class:`pandas.DataFrame`
         Data that contain focal mechanism parameters.
 
         ``spec`` can be specified in either of the following types:
@@ -250,9 +250,10 @@ def meca(  # noqa: PLR0912, PLR0913, PLR0915
           The meanings of columns are the same as above.
         - *2-D array*: focal mechanism parameters of multiple events.
           The meanings of columns are the same as above.
-        - *dictionary or pd.DataFrame*: The dictionary keys or pd.DataFrame
-          column names determine the focal mechanism convention. For
-          different conventions, the following combination of keys are allowed:
+        - *dictionary or :class:`pandas.DataFrame`*: The dictionary keys or
+          :class:`pandas.DataFrame` column names determine the focal mechanism
+          convention. For different conventions, the following combination of
+          keys are allowed:
 
           - ``"aki"``: *strike, dip, rake, magnitude*
           - ``"gcmt"``: *strike1, dip1, rake1, strike2, dip2, rake2, mantissa,*
@@ -265,13 +266,13 @@ def meca(  # noqa: PLR0912, PLR0913, PLR0915
           A dictionary may contain values for a single focal mechanism or
           lists of values for multiple focal mechanisms.
 
-          Both dictionary and pd.DataFrame may optionally contain
+          Both dictionary and :class:`pandas.DataFrame` may optionally contain
           keys/column names: ``latitude``, ``longitude``, ``depth``,
           ``plot_longitude``, ``plot_latitude``, and/or ``event_name``.
 
         If ``spec`` is either a str, a 1-D array or a 2-D array, the
         ``convention`` parameter is required so we know how to interpret the
-        columns. If ``spec`` is a dictionary or a pd.DataFrame,
+        columns. If ``spec`` is a dictionary or a :class:`pandas.DataFrame`,
         ``convention`` is not needed and is ignored if specified.
     scale : float or str
         *scale*\ [**+a**\ *angle*][**+f**\ *font*][**+j**\ *justify*]\
@@ -299,7 +300,7 @@ def meca(  # noqa: PLR0912, PLR0913, PLR0915
         - ``"partial"`` (partial focal mechanism)
         - ``"principal_axis"`` (principal axis)
 
-        Ignored if ``spec`` is a dictionary or pd.DataFrame.
+        Ignored if ``spec`` is a dictionary or :class:`pandas.DataFrame`.
     component : str
         The component of the seismic moment tensor to plot.
 
@@ -310,28 +311,28 @@ def meca(  # noqa: PLR0912, PLR0913, PLR0915
     longitude : float, list, or 1-D numpy array
         Longitude(s) of event location(s). Must be the same length as the
         number of events. Will override the ``longitude`` values
-        in ``spec`` if ``spec`` is a dictionary or pd.DataFrame.
+        in ``spec`` if ``spec`` is a dictionary or :class:`pandas.DataFrame`.
     latitude : float, list, or 1-D numpy array
         Latitude(s) of event location(s). Must be the same length as the
         number of events. Will override the ``latitude`` values
-        in ``spec`` if ``spec`` is a dictionary or pd.DataFrame.
+        in ``spec`` if ``spec`` is a dictionary or :class:`pandas.DataFrame`.
     depth : float, list, or 1-D numpy array
         Depth(s) of event location(s) in kilometers. Must be the same length
         as the number of events. Will override the ``depth`` values in ``spec``
-        if ``spec`` is a dictionary or pd.DataFrame.
+        if ``spec`` is a dictionary or :class:`pandas.DataFrame`.
     plot_longitude : float, str, list, or 1-D numpy array
         Longitude(s) at which to place beachball(s). Must be the same length
         as the number of events. Will override the ``plot_longitude`` values
-        in ``spec`` if ``spec`` is a dictionary or pd.DataFrame.
+        in ``spec`` if ``spec`` is a dictionary or :class:`pandas.DataFrame`.
     plot_latitude : float, str, list, or 1-D numpy array
         Latitude(s) at which to place beachball(s). List must be the same
         length as the number of events. Will override the ``plot_latitude``
-        values in ``spec`` if ``spec`` is a dictionary or pd.DataFrame.
+        values in ``spec`` if ``spec`` is a dictionary or :class:`pandas.DataFrame`.
     event_name : str, list of str, or 1-D numpy array
         Text string(s), e.g., event name(s) to appear near the beachball(s).
         List must be the same length as the number of events. Will override
         the ``event_name`` labels in ``spec`` if ``spec`` is a dictionary
-        or pd.DataFrame.
+        or :class:`pandas.DataFrame`.
     labelbox : bool or str
         [*fill*].
         Draw a box behind the label if given. Use *fill* to give a fill color

pygmt/src/nearneighbor.py

@@ -122,7 +122,7 @@ def nearneighbor(
         Return type depends on whether the ``outgrid`` parameter is set:
 
         - :class:`xarray.DataArray`: if ``outgrid`` is not set
-        - None if ``outgrid`` is set (grid output will be stored in file set by
+        - ``None`` if ``outgrid`` is set (grid output will be stored in the file set by
           ``outgrid``)
     Example
     -------