Merge branch 'master' into columns-plot3d

Author: seisman

.github/workflows/ci_tests.yaml

@@ -144,7 +144,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1.5.0
+        uses: codecov/codecov-action@v1.5.2
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

CONTRIBUTING.md

@@ -162,10 +162,6 @@
     )
 html_context = {
     "menu_links": [
-        (
-            '<i class="fa fa-users fa-fw"></i> Contributing',
-            f"{repository_url}/blob/master/CONTRIBUTING.md",
-        ),
         (
             '<i class="fa fa-gavel fa-fw"></i> Code of Conduct',
             f"{repository_url}/blob/master/CODE_OF_CONDUCT.md",

doc/conf.py

@@ -58,4 +58,5 @@
 
     api/index.rst
     changes.md
+    contributing.md
     maintenance.md

doc/contributing.md

@@ -8,6 +8,7 @@
 import functools
 import textwrap
 import warnings
+from inspect import Parameter, signature
 
 import numpy as np
 from pygmt.exceptions import GMTInvalidInput
@@ -322,6 +323,30 @@ def fmt_docstring(module_func):
     return module_func
 
 
+def _insert_alias(module_func, default_value=None):
+    """
+    Function to insert PyGMT long aliases into the signature of a method.
+    """
+
+    # Get current signature and parameters
+    sig = signature(module_func)
+    wrapped_params = list(sig.parameters.values())
+    kwargs_param = wrapped_params.pop(-1)
+    # Add new parameters from aliases
+    for alias in module_func.aliases.values():
+        if alias not in sig.parameters.keys():
+            new_param = Parameter(
+                alias, kind=Parameter.KEYWORD_ONLY, default=default_value
+            )
+            wrapped_params = wrapped_params + [new_param]
+    all_params = wrapped_params + [kwargs_param]
+    # Update method signature
+    sig_new = sig.replace(parameters=all_params)
+    module_func.__signature__ = sig_new
+
+    return module_func
+
+
 def use_alias(**aliases):
     """
     Decorator to add aliases to keyword arguments of a function.
@@ -359,7 +384,7 @@ def use_alias(**aliases):
     Traceback (most recent call last):
       ...
     pygmt.exceptions.GMTInvalidInput:
-        Arguments in short-form (J) and long-form (projection) can't coexist
+        Parameters in short-form (J) and long-form (projection) can't coexist.
     """
 
     def alias_decorator(module_func):
@@ -372,17 +397,26 @@ def new_module(*args, **kwargs):
             """
             New module that parses and replaces the registered aliases.
             """
-            for arg, alias in aliases.items():
-                if alias in kwargs and arg in kwargs:
+            for short_param, long_alias in aliases.items():
+                if long_alias in kwargs and short_param in kwargs:
                     raise GMTInvalidInput(
-                        f"Arguments in short-form ({arg}) and long-form ({alias}) can't coexist"
+                        f"Parameters in short-form ({short_param}) and "
+                        f"long-form ({long_alias}) can't coexist."
                     )
-                if alias in kwargs:
-                    kwargs[arg] = kwargs.pop(alias)
+                if long_alias in kwargs:
+                    kwargs[short_param] = kwargs.pop(long_alias)
+                elif short_param in kwargs:
+                    msg = (
+                        f"Short-form parameter ({short_param}) is not recommended. "
+                        f"Use long-form parameter '{long_alias}' instead."
+                    )
+                    warnings.warn(msg, category=SyntaxWarning, stacklevel=2)
             return module_func(*args, **kwargs)
 
         new_module.aliases = aliases
 
+        new_module = _insert_alias(new_module)
+
         return new_module
 
     return alias_decorator

doc/index.rst

@@ -4,6 +4,7 @@
 
 import xarray as xr
 from pygmt.clib import Session
+from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers import (
     GMTTempFile,
     build_arg_string,
@@ -18,6 +19,7 @@
     A="mode",
     G="outgrid",
     R="region",
+    V="verbose",
 )
 @kwargs_to_strings(R="sequence")
 def grdfill(grid, **kwargs):
@@ -45,8 +47,12 @@ def grdfill(grid, **kwargs):
         constant fill and append the constant value, **n** for nearest
         neighbor (and optionally append a search radius in
         pixels [default radius is :math:`r^2 = \sqrt{{ X^2 + Y^2 }}`,
-        where (*X,Y*) are the node dimensions of the grid]).
+        where (*X,Y*) are the node dimensions of the grid]), or
+        **s** for bicubic spline (optionally append a *tension*
+        parameter [Default is no tension]).
+
     {R}
+    {V}
 
     Returns
     -------
@@ -57,6 +63,8 @@ def grdfill(grid, **kwargs):
         - None if ``outgrid`` is set (grid output will be stored in file set by
           ``outgrid``)
     """
+    if "A" not in kwargs.keys() and "L" not in kwargs.keys():
+        raise GMTInvalidInput("At least parameter 'mode' or 'L' must be specified.")
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
             file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)

pygmt/helpers/decorators.py

@@ -80,7 +80,7 @@ def plot(self, x=None, y=None, data=None, size=None, direction=None, **kwargs):
     data : str or {table-like}
         Pass in either a file name to an ASCII data table, a 2D
         {table-classes}.
-        Use parameter ``columns`` to choose which columns are x, y, color, and
+        Use parameter ``incols`` to choose which columns are x, y, color, and
         size, respectively.
     size : 1d array
         The size of the data points in units specified using ``style``.

pygmt/src/grdfill.py

@@ -1,5 +1,5 @@
 """
-Tests for grdclip.
+Tests for grdfill.
 """
 import os
 
@@ -8,6 +8,7 @@
 import xarray as xr
 from pygmt import grdfill, grdinfo
 from pygmt.datasets import load_earth_relief
+from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers import GMTTempFile
 
 
@@ -47,3 +48,11 @@ def test_grdfill_file_out(grid):
         assert os.path.exists(path=tmpfile.name)  # check that outgrid exists
         result = grdinfo(tmpfile.name, per_column=True).strip()
         assert result == "-5 5 -5 5 -5130.5 inf 1 1 10 10 1 1"
+
+
+def test_grdfill_required_args(grid):
+    """
+    Test that grdfill fails without arguments for `mode` and `L`.
+    """
+    with pytest.raises(GMTInvalidInput):
+        grdfill(grid=grid)