Refractor build_arg_string to also deal with infile and outfile (Gene…

…ricMappingTools#1837)

pygmt/helpers/utils.py

@@ -119,12 +119,12 @@ def dummy_context(arg):
     yield arg
 
 
-def build_arg_string(kwargs):
+def build_arg_string(kwdict, infile=None, outfile=None):
     r"""
-    Transform keyword arguments into a GMT argument string.
+    Convert a dict and optional input/output files into a GMT argument string.
 
-    Make sure all arguments have been previously converted to a string
-    representation using the ``kwargs_to_strings`` decorator. The only
+    Make sure all values in ``kwdict`` have been previously converted to a
+    string representation using the ``kwargs_to_strings`` decorator. The only
     exceptions are True, False and None.
 
     Any lists or tuples left will be interpreted as multiple entries for the
@@ -138,14 +138,19 @@ def build_arg_string(kwargs):
 
     Parameters
     ----------
-    kwargs : dict
-        Parsed keyword arguments.
+    kwdict : dict
+        A dict containing parsed keyword arguments.
+    infile : str or pathlib.Path
+        The input file.
+    outfile : str or pathlib.Path
+        The output file.
 
     Returns
     -------
     args : str
         The space-delimited argument string with '-' inserted before each
-        keyword. The arguments are sorted alphabetically.
+        keyword. The arguments are sorted alphabetically, with optional input
+        file at the begining and optioanl output file at the end.
 
     Examples
     --------
@@ -191,29 +196,42 @@ def build_arg_string(kwargs):
     ...     )
     ... )
     -BWSne+tBlank\040Space -Baf -F+t"Empty\040\040Spaces" -l'Void\040Space'
+    >>> print(
+    ...     build_arg_string(
+    ...         dict(A="0", B=True, C="rainbow"),
+    ...         infile="input.txt",
+    ...         outfile="output.txt",
+    ...     )
+    ... )
+    input.txt -A0 -B -Crainbow ->output.txt
     """
     gmt_args = []
 
-    for key in kwargs:
+    for key in kwdict:
         if len(key) > 2:  # raise an exception for unrecognized options
             raise GMTInvalidInput(f"Unrecognized parameter '{key}'.")
-        if kwargs[key] is None or kwargs[key] is False:
+        if kwdict[key] is None or kwdict[key] is False:
             pass  # Exclude arguments that are None and False
-        elif is_nonstr_iter(kwargs[key]):
-            for value in kwargs[key]:
+        elif is_nonstr_iter(kwdict[key]):
+            for value in kwdict[key]:
                 _value = str(value).replace(" ", r"\040")
                 gmt_args.append(rf"-{key}{_value}")
-        elif kwargs[key] is True:
+        elif kwdict[key] is True:
             gmt_args.append(f"-{key}")
         else:
             if key != "J":  # non-projection parameters
-                _value = str(kwargs[key]).replace(" ", r"\040")
+                _value = str(kwdict[key]).replace(" ", r"\040")
             else:
                 # special handling if key == "J" (projection)
                 # remove any spaces in PROJ4 string
-                _value = str(kwargs[key]).replace(" ", "")
+                _value = str(kwdict[key]).replace(" ", "")
             gmt_args.append(rf"-{key}{_value}")
-    return " ".join(sorted(gmt_args))
+    gmt_args = sorted(gmt_args)
+    if infile:
+        gmt_args = [str(infile)] + gmt_args
+    if outfile:
+        gmt_args.append("->" + str(outfile))
+    return " ".join(gmt_args)
 
 
 def is_nonstr_iter(value):

pygmt/src/blockm.py

@@ -51,8 +51,10 @@ def _blockm(block_method, data, x, y, z, outfile, **kwargs):
             with table_context as infile:
                 if outfile is None:
                     outfile = tmpfile.name
-                arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
-                lib.call_module(module=block_method, args=arg_str)
+                lib.call_module(
+                    module=block_method,
+                    args=build_arg_string(kwargs, infile=infile, outfile=outfile),
+                )
 
         # Read temporary csv output to a pandas table
         if outfile == tmpfile.name:  # if user did not set outfile, return pd.DataFrame

pygmt/src/contour.py

@@ -132,5 +132,4 @@ def contour(self, data=None, x=None, y=None, z=None, **kwargs):
             check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
         )
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("contour", arg_str)
+            lib.call_module("contour", build_arg_string(kwargs, infile=fname))

pygmt/src/grd2cpt.py

@@ -166,12 +166,10 @@ def grd2cpt(grid, **kwargs):
         file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
         with file_context as infile:
             if "H" not in kwargs:  # if no output is set
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
+                arg_str = build_arg_string(kwargs, infile=infile)
             if "H" in kwargs:  # if output is set
-                outfile = kwargs.pop("H")
+                outfile, kwargs["H"] = kwargs["H"], True
                 if not outfile or not isinstance(outfile, str):
                     raise GMTInvalidInput("'output' should be a proper file name.")
-                arg_str = " ".join(
-                    [infile, build_arg_string(kwargs), f"-H > {outfile}"]
-                )
+                arg_str = build_arg_string(kwargs, infile=infile, outfile=outfile)
             lib.call_module("grd2cpt", arg_str)

pygmt/src/grd2xyz.py

@@ -178,8 +178,9 @@ def grd2xyz(grid, output_type="pandas", outfile=None, **kwargs):
             with file_context as infile:
                 if outfile is None:
                     outfile = tmpfile.name
-                arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
-                lib.call_module("grd2xyz", arg_str)
+                lib.call_module(
+                    "grd2xyz", build_arg_string(kwargs, infile=infile, outfile=outfile)
+                )
 
         # Read temporary csv output to a pandas table
         if outfile == tmpfile.name:  # if user did not set outfile, return pd.DataFrame

pygmt/src/grdclip.py

@@ -107,7 +107,6 @@ def grdclip(grid, **kwargs):
                 if "G" not in kwargs:  # if outgrid is unset, output to tempfile
                     kwargs.update({"G": tmpfile.name})
                 outgrid = kwargs["G"]
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module("grdclip", arg_str)
+                lib.call_module("grdclip", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/grdcontour.py

@@ -100,5 +100,4 @@ def grdcontour(self, grid, **kwargs):
     with Session() as lib:
         file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("grdcontour", arg_str)
+            lib.call_module("grdcontour", build_arg_string(kwargs, infile=fname))

pygmt/src/grdcut.py

@@ -109,7 +109,6 @@ def grdcut(grid, **kwargs):
                 if "G" not in kwargs:  # if outgrid is unset, output to tempfile
                     kwargs.update({"G": tmpfile.name})
                 outgrid = kwargs["G"]
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module("grdcut", arg_str)
+                lib.call_module("grdcut", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/grdfill.py

@@ -72,7 +72,6 @@ def grdfill(grid, **kwargs):
                 if "G" not in kwargs:  # if outgrid is unset, output to tempfile
                     kwargs.update({"G": tmpfile.name})
                 outgrid = kwargs["G"]
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module("grdfill", arg_str)
+                lib.call_module("grdfill", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/grdfilter.py

@@ -148,7 +148,6 @@ def grdfilter(grid, **kwargs):
                 if "G" not in kwargs:  # if outgrid is unset, output to tempfile
                     kwargs.update({"G": tmpfile.name})
                 outgrid = kwargs["G"]
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module("grdfilter", arg_str)
+                lib.call_module("grdfilter", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/grdgradient.py

@@ -177,7 +177,6 @@ def grdgradient(grid, **kwargs):
                 if "G" not in kwargs:  # if outgrid is unset, output to tempfile
                     kwargs.update({"G": tmpfile.name})
                 outgrid = kwargs["G"]
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module("grdgradient", arg_str)
+                lib.call_module("grdgradient", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/grdhisteq.py

@@ -112,8 +112,7 @@ def _grdhisteq(grid, output_type, **kwargs):
         with Session() as lib:
             file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
             with file_context as infile:
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module("grdhisteq", arg_str)
+                lib.call_module("grdhisteq", build_arg_string(kwargs, infile=infile))
 
         if output_type == "file":
             return None

pygmt/src/grdimage.py

@@ -171,5 +171,4 @@ def grdimage(self, grid, **kwargs):
                 kwargs["I"] = stack.enter_context(shading_context)
 
             fname = stack.enter_context(file_context)
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("grdimage", arg_str)
+            lib.call_module("grdimage", build_arg_string(kwargs, infile=fname))

pygmt/src/grdinfo.py

@@ -114,9 +114,9 @@ def grdinfo(grid, **kwargs):
         with Session() as lib:
             file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
             with file_context as infile:
-                arg_str = " ".join(
-                    [infile, build_arg_string(kwargs), "->" + outfile.name]
+                lib.call_module(
+                    "grdinfo",
+                    build_arg_string(kwargs, infile=infile, outfile=outfile.name),
                 )
-                lib.call_module("grdinfo", arg_str)
         result = outfile.read()
     return result

pygmt/src/grdlandmask.py

@@ -109,7 +109,6 @@ def grdlandmask(**kwargs):
             if "G" not in kwargs:  # if outgrid is unset, output to tempfile
                 kwargs.update({"G": tmpfile.name})
             outgrid = kwargs["G"]
-            arg_str = build_arg_string(kwargs)
-            lib.call_module("grdlandmask", arg_str)
+            lib.call_module("grdlandmask", build_arg_string(kwargs))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/grdproject.py

@@ -121,7 +121,6 @@ def grdproject(grid, **kwargs):
                 if "G" not in kwargs:  # if outgrid is unset, output to tempfile
                     kwargs.update({"G": tmpfile.name})
                 outgrid = kwargs["G"]
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module("grdproject", arg_str)
+                lib.call_module("grdproject", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/grdsample.py

@@ -99,7 +99,6 @@ def grdsample(grid, **kwargs):
                 if "G" not in kwargs:  # if outgrid is unset, output to tempfile
                     kwargs.update({"G": tmpfile.name})
                 outgrid = kwargs["G"]
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module("grdsample", arg_str)
+                lib.call_module("grdsample", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/grdtrack.py

@@ -300,10 +300,10 @@ def grdtrack(points, grid, newcolname=None, outfile=None, **kwargs):
                     kwargs.update({"G": grdfile})
                     if outfile is None:  # Output to tmpfile if outfile is not set
                         outfile = tmpfile.name
-                    arg_str = " ".join(
-                        [csvfile, build_arg_string(kwargs), "->" + outfile]
+                    lib.call_module(
+                        module="grdtrack",
+                        args=build_arg_string(kwargs, infile=csvfile, outfile=outfile),
                     )
-                    lib.call_module(module="grdtrack", args=arg_str)
 
         # Read temporary csv output to a pandas table
         if outfile == tmpfile.name:  # if user did not set outfile, return pd.DataFrame

pygmt/src/grdview.py

@@ -137,5 +137,4 @@ def grdview(self, grid, **kwargs):
                         f"Unrecognized data type for drapegrid: {type(drapegrid)}"
                     )
             fname = stack.enter_context(file_context)
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("grdview", arg_str)
+            lib.call_module("grdview", build_arg_string(kwargs, infile=fname))

pygmt/src/grdvolume.py

@@ -114,8 +114,10 @@ def grdvolume(grid, output_type="pandas", outfile=None, **kwargs):
             with file_context as infile:
                 if outfile is None:
                     outfile = tmpfile.name
-                arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
-                lib.call_module("grdvolume", arg_str)
+                lib.call_module(
+                    "grdvolume",
+                    build_arg_string(kwargs, infile=infile, outfile=outfile),
+                )
 
         # Read temporary csv output to a pandas table
         if outfile == tmpfile.name:  # if user did not set outfile, return pd.DataFrame

pygmt/src/histogram.py

@@ -148,5 +148,4 @@ def histogram(self, data, **kwargs):
     with Session() as lib:
         file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
         with file_context as infile:
-            arg_str = " ".join([infile, build_arg_string(kwargs)])
-            lib.call_module("histogram", arg_str)
+            lib.call_module("histogram", build_arg_string(kwargs, infile=infile))

pygmt/src/image.py

@@ -64,5 +64,4 @@ def image(self, imagefile, **kwargs):
     """
     kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
     with Session() as lib:
-        arg_str = " ".join([imagefile, build_arg_string(kwargs)])
-        lib.call_module("image", arg_str)
+        lib.call_module("image", build_arg_string(kwargs, infile=imagefile))

pygmt/src/info.py

@@ -85,10 +85,9 @@ def info(data, **kwargs):
         file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
         with GMTTempFile() as tmpfile:
             with file_context as fname:
-                arg_str = " ".join(
-                    [fname, build_arg_string(kwargs), "->" + tmpfile.name]
+                lib.call_module(
+                    "info", build_arg_string(kwargs, infile=fname, outfile=tmpfile.name)
                 )
-                lib.call_module("info", arg_str)
             result = tmpfile.read()
 
         if any(arg in kwargs for arg in ["C", "I", "T"]):

pygmt/src/legend.py

@@ -87,5 +87,4 @@ def legend(self, spec=None, position="JTR+jTR+o0.2c", box="+gwhite+p1p", **kwarg
             specfile = spec
         else:
             raise GMTInvalidInput(f"Unrecognized data type: {type(spec)}")
-        arg_str = " ".join([specfile, build_arg_string(kwargs)])
-        lib.call_module("legend", arg_str)
+        lib.call_module("legend", build_arg_string(kwargs, infile=specfile))

pygmt/src/makecpt.py

@@ -152,8 +152,8 @@ def makecpt(**kwargs):
         if "H" not in kwargs:  # if no output is set
             arg_str = build_arg_string(kwargs)
         elif "H" in kwargs:  # if output is set
-            outfile = kwargs.pop("H")
+            outfile, kwargs["H"] = kwargs.pop("H"), True
             if not outfile or not isinstance(outfile, str):
                 raise GMTInvalidInput("'output' should be a proper file name.")
-            arg_str = " ".join([build_arg_string(kwargs), f"-H > {outfile}"])
+            arg_str = build_arg_string(kwargs, outfile=outfile)
         lib.call_module(module="makecpt", args=arg_str)

pygmt/src/meca.py

@@ -464,5 +464,4 @@ def update_pointers(data_pointers):
         else:
             raise GMTInvalidInput(f"Unrecognized data type: {type(spec)}")
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("meca", arg_str)
+            lib.call_module("meca", build_arg_string(kwargs, infile=fname))

pygmt/src/nearneighbor.py

@@ -142,7 +142,8 @@ def nearneighbor(data=None, x=None, y=None, z=None, **kwargs):
                 if "G" not in kwargs:  # if outgrid is unset, output to tmpfile
                     kwargs.update({"G": tmpfile.name})
                 outgrid = kwargs["G"]
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module(module="nearneighbor", args=arg_str)
+                lib.call_module(
+                    module="nearneighbor", args=build_arg_string(kwargs, infile=infile)
+                )
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

pygmt/src/plot.py

@@ -266,5 +266,4 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs):
         )
 
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("plot", arg_str)
+            lib.call_module("plot", build_arg_string(kwargs, infile=fname))

pygmt/src/plot3d.py

@@ -242,5 +242,4 @@ def plot3d(
         )
 
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("plot3d", arg_str)
+            lib.call_module("plot3d", build_arg_string(kwargs, infile=fname))

pygmt/src/project.py

@@ -233,11 +233,9 @@ def project(data=None, x=None, y=None, z=None, outfile=None, **kwargs):
 
                 # Run project on the temporary (csv) data table
                 with table_context as infile:
-                    arg_str = " ".join(
-                        [infile, build_arg_string(kwargs), "->" + outfile]
-                    )
+                    arg_str = build_arg_string(kwargs, infile=infile, outfile=outfile)
             else:
-                arg_str = " ".join([build_arg_string(kwargs), "->" + outfile])
+                arg_str = build_arg_string(kwargs, outfile=outfile)
             lib.call_module(module="project", args=arg_str)
 
         # if user did not set outfile, return pd.DataFrame

pygmt/src/rose.py

@@ -211,6 +211,4 @@ def rose(self, data=None, length=None, azimuth=None, **kwargs):
         )
 
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-
-            lib.call_module("rose", arg_str)
+            lib.call_module("rose", build_arg_string(kwargs, infile=fname))

pygmt/src/select.py

@@ -167,8 +167,10 @@ def select(data=None, outfile=None, **kwargs):
             with table_context as infile:
                 if outfile is None:
                     outfile = tmpfile.name
-                arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
-                lib.call_module(module="gmtselect", args=arg_str)
+                lib.call_module(
+                    module="gmtselect",
+                    args=build_arg_string(kwargs, infile=infile, outfile=outfile),
+                )
 
         # Read temporary csv output to a pandas table
         if outfile == tmpfile.name:  # if user did not set outfile, return pd.DataFrame