From 700fb2d428c9f149e6311741206991859c4dc3c1 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Mon, 21 Mar 2022 14:09:03 +0800
Subject: [PATCH 1/5] Refractor build_arg_string to also deal with infile and
 outfile

---
 pygmt/helpers/utils.py | 6 +++++-
 pygmt/src/contour.py   | 3 +--
 pygmt/src/grdinfo.py   | 6 +++---
 pygmt/src/which.py     | 5 +++--
 4 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/pygmt/helpers/utils.py b/pygmt/helpers/utils.py
index ea7a89873e7..54ec746a3e1 100644
--- a/pygmt/helpers/utils.py
+++ b/pygmt/helpers/utils.py
@@ -119,7 +119,7 @@ def dummy_context(arg):
     yield arg
 
 
-def build_arg_string(kwargs):
+def build_arg_string(kwargs, infile=None, outfile=None):
     r"""
     Transform keyword arguments into a GMT argument string.
 
@@ -213,6 +213,10 @@ def build_arg_string(kwargs):
                 # remove any spaces in PROJ4 string
                 _value = str(kwargs[key]).replace(" ", "")
             gmt_args.append(rf"-{key}{_value}")
+    if infile:
+        gmt_args.append(str(infile))
+    if outfile:
+        gmt_args.append("->" + str(outfile))
     return " ".join(sorted(gmt_args))
 
 
diff --git a/pygmt/src/contour.py b/pygmt/src/contour.py
index f64cd5e0c15..17e275e6b70 100644
--- a/pygmt/src/contour.py
+++ b/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))
diff --git a/pygmt/src/grdinfo.py b/pygmt/src/grdinfo.py
index 8e5dbd22e3e..8057f21c74c 100644
--- a/pygmt/src/grdinfo.py
+++ b/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
diff --git a/pygmt/src/which.py b/pygmt/src/which.py
index 3a5afb3da1e..7e08a742c95 100644
--- a/pygmt/src/which.py
+++ b/pygmt/src/which.py
@@ -60,9 +60,10 @@ def which(fname, **kwargs):
         If the file is not found.
     """
     with GMTTempFile() as tmpfile:
-        arg_str = " ".join([fname, build_arg_string(kwargs), "->" + tmpfile.name])
         with Session() as lib:
-            lib.call_module("which", arg_str)
+            lib.call_module(
+                "which", build_arg_string(kwargs, infile=fname, outfile=tmpfile.name)
+            )
         path = tmpfile.read().strip()
     if not path:
         _fname = fname.replace(" ", "', '")

From 6c6dc3e17eb0a8f120a3ef48cee1cbb9368f5f9a Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Wed, 30 Mar 2022 16:00:12 +0800
Subject: [PATCH 2/5] Refactor more functions

---
 pygmt/helpers/utils.py      | 4 ++++
 pygmt/src/blockm.py         | 6 ++++--
 pygmt/src/grd2cpt.py        | 8 +++-----
 pygmt/src/grd2xyz.py        | 5 +++--
 pygmt/src/grdclip.py        | 3 +--
 pygmt/src/grdcontour.py     | 3 +--
 pygmt/src/grdcut.py         | 3 +--
 pygmt/src/grdfill.py        | 3 +--
 pygmt/src/grdfilter.py      | 3 +--
 pygmt/src/grdgradient.py    | 3 +--
 pygmt/src/grdhisteq.py      | 3 +--
 pygmt/src/grdimage.py       | 3 +--
 pygmt/src/grdlandmask.py    | 3 +--
 pygmt/src/grdproject.py     | 3 +--
 pygmt/src/grdsample.py      | 3 +--
 pygmt/src/grdtrack.py       | 6 +++---
 pygmt/src/grdview.py        | 3 +--
 pygmt/src/grdvolume.py      | 6 ++++--
 pygmt/src/histogram.py      | 3 +--
 pygmt/src/image.py          | 3 +--
 pygmt/src/info.py           | 5 ++---
 pygmt/src/legend.py         | 3 +--
 pygmt/src/makecpt.py        | 4 ++--
 pygmt/src/meca.py           | 3 +--
 pygmt/src/nearneighbor.py   | 5 +++--
 pygmt/src/plot.py           | 3 +--
 pygmt/src/plot3d.py         | 3 +--
 pygmt/src/project.py        | 6 ++----
 pygmt/src/rose.py           | 4 +---
 pygmt/src/select.py         | 6 ++++--
 pygmt/src/sph2grd.py        | 3 +--
 pygmt/src/sphdistance.py    | 4 +---
 pygmt/src/sphinterpolate.py | 5 +++--
 pygmt/src/surface.py        | 5 +++--
 pygmt/src/text.py           | 3 +--
 pygmt/src/triangulate.py    | 5 +++--
 pygmt/src/velo.py           | 3 +--
 pygmt/src/wiggle.py         | 3 +--
 pygmt/src/x2sys_cross.py    | 8 ++++++--
 pygmt/src/x2sys_init.py     | 3 +--
 pygmt/src/xyz2grd.py        | 3 +--
 41 files changed, 75 insertions(+), 89 deletions(-)

diff --git a/pygmt/helpers/utils.py b/pygmt/helpers/utils.py
index 54ec746a3e1..2b130773d73 100644
--- a/pygmt/helpers/utils.py
+++ b/pygmt/helpers/utils.py
@@ -140,6 +140,10 @@ def build_arg_string(kwargs, infile=None, outfile=None):
     ----------
     kwargs : dict
         Parsed keyword arguments.
+    infile : str or pathlib.Path
+        The input file.
+    outfile : str or pathlib.Path
+        The output file.
 
     Returns
     -------
diff --git a/pygmt/src/blockm.py b/pygmt/src/blockm.py
index 75693524d6c..f55f1bf36c7 100644
--- a/pygmt/src/blockm.py
+++ b/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
diff --git a/pygmt/src/grd2cpt.py b/pygmt/src/grd2cpt.py
index 2173fe30bc7..8e81fa4a14c 100644
--- a/pygmt/src/grd2cpt.py
+++ b/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)
diff --git a/pygmt/src/grd2xyz.py b/pygmt/src/grd2xyz.py
index 46797022abf..54f03fdc5ae 100644
--- a/pygmt/src/grd2xyz.py
+++ b/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
diff --git a/pygmt/src/grdclip.py b/pygmt/src/grdclip.py
index cd98e3a709b..f7c4d951d31 100644
--- a/pygmt/src/grdclip.py
+++ b/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
diff --git a/pygmt/src/grdcontour.py b/pygmt/src/grdcontour.py
index c3b63fbaefb..98a214a2fd3 100644
--- a/pygmt/src/grdcontour.py
+++ b/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))
diff --git a/pygmt/src/grdcut.py b/pygmt/src/grdcut.py
index 86334ca5ed9..5c4f34efe19 100644
--- a/pygmt/src/grdcut.py
+++ b/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
diff --git a/pygmt/src/grdfill.py b/pygmt/src/grdfill.py
index 0f44144e237..aa7623b9d5b 100644
--- a/pygmt/src/grdfill.py
+++ b/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
diff --git a/pygmt/src/grdfilter.py b/pygmt/src/grdfilter.py
index 0c8116ac708..6492f42fbbc 100644
--- a/pygmt/src/grdfilter.py
+++ b/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
diff --git a/pygmt/src/grdgradient.py b/pygmt/src/grdgradient.py
index b70c2cbf980..70200d9bc25 100644
--- a/pygmt/src/grdgradient.py
+++ b/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
diff --git a/pygmt/src/grdhisteq.py b/pygmt/src/grdhisteq.py
index 09555d05e94..c2d26a4ab56 100644
--- a/pygmt/src/grdhisteq.py
+++ b/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
diff --git a/pygmt/src/grdimage.py b/pygmt/src/grdimage.py
index 52cb637e32a..c50057cd640 100644
--- a/pygmt/src/grdimage.py
+++ b/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))
diff --git a/pygmt/src/grdlandmask.py b/pygmt/src/grdlandmask.py
index 93a9c369582..e6a39657bc2 100644
--- a/pygmt/src/grdlandmask.py
+++ b/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
diff --git a/pygmt/src/grdproject.py b/pygmt/src/grdproject.py
index 399d112b828..e27832876fb 100644
--- a/pygmt/src/grdproject.py
+++ b/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
diff --git a/pygmt/src/grdsample.py b/pygmt/src/grdsample.py
index f7b76cc469e..4e84e0827ee 100644
--- a/pygmt/src/grdsample.py
+++ b/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
diff --git a/pygmt/src/grdtrack.py b/pygmt/src/grdtrack.py
index 1f15161b99c..f0b9306ce6f 100644
--- a/pygmt/src/grdtrack.py
+++ b/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
diff --git a/pygmt/src/grdview.py b/pygmt/src/grdview.py
index 404fc490cc0..fca45686abd 100644
--- a/pygmt/src/grdview.py
+++ b/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))
diff --git a/pygmt/src/grdvolume.py b/pygmt/src/grdvolume.py
index 0beb3d4523f..6d088671382 100644
--- a/pygmt/src/grdvolume.py
+++ b/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
diff --git a/pygmt/src/histogram.py b/pygmt/src/histogram.py
index 93bf9e6721c..7e8af4057d3 100644
--- a/pygmt/src/histogram.py
+++ b/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))
diff --git a/pygmt/src/image.py b/pygmt/src/image.py
index 5b883722887..c0da5898861 100644
--- a/pygmt/src/image.py
+++ b/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))
diff --git a/pygmt/src/info.py b/pygmt/src/info.py
index 510723c95e2..00f8f7ed66e 100644
--- a/pygmt/src/info.py
+++ b/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"]):
diff --git a/pygmt/src/legend.py b/pygmt/src/legend.py
index 168f826ee68..6379b65e417 100644
--- a/pygmt/src/legend.py
+++ b/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))
diff --git a/pygmt/src/makecpt.py b/pygmt/src/makecpt.py
index bf52be37f80..ad0dc442a76 100644
--- a/pygmt/src/makecpt.py
+++ b/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)
diff --git a/pygmt/src/meca.py b/pygmt/src/meca.py
index 85bf48d97b7..c4b2ee9bfc3 100644
--- a/pygmt/src/meca.py
+++ b/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))
diff --git a/pygmt/src/nearneighbor.py b/pygmt/src/nearneighbor.py
index 1fe7e24bab8..641b5861703 100644
--- a/pygmt/src/nearneighbor.py
+++ b/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
diff --git a/pygmt/src/plot.py b/pygmt/src/plot.py
index adff9682295..82fd018760d 100644
--- a/pygmt/src/plot.py
+++ b/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))
diff --git a/pygmt/src/plot3d.py b/pygmt/src/plot3d.py
index faabf34395d..504daf6be04 100644
--- a/pygmt/src/plot3d.py
+++ b/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))
diff --git a/pygmt/src/project.py b/pygmt/src/project.py
index 1c3f422e638..21a0d8580db 100644
--- a/pygmt/src/project.py
+++ b/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
diff --git a/pygmt/src/rose.py b/pygmt/src/rose.py
index 842421067e7..02b03851aba 100644
--- a/pygmt/src/rose.py
+++ b/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))
diff --git a/pygmt/src/select.py b/pygmt/src/select.py
index c01560ae7d2..34d26850db8 100644
--- a/pygmt/src/select.py
+++ b/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
diff --git a/pygmt/src/sph2grd.py b/pygmt/src/sph2grd.py
index 0ca0eaf8c58..e16a368ee9a 100644
--- a/pygmt/src/sph2grd.py
+++ b/pygmt/src/sph2grd.py
@@ -82,7 +82,6 @@ def sph2grd(data, **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("sph2grd", arg_str)
+                lib.call_module("sph2grd", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None
diff --git a/pygmt/src/sphdistance.py b/pygmt/src/sphdistance.py
index 63abe94e6e6..c8ac83035b5 100644
--- a/pygmt/src/sphdistance.py
+++ b/pygmt/src/sphdistance.py
@@ -111,8 +111,6 @@ def sphdistance(data=None, x=None, y=None, **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)
-                arg_str = " ".join([infile, arg_str])
-                lib.call_module("sphdistance", arg_str)
+                lib.call_module("sphdistance", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None
diff --git a/pygmt/src/sphinterpolate.py b/pygmt/src/sphinterpolate.py
index 15f49904aaa..bf585440a02 100644
--- a/pygmt/src/sphinterpolate.py
+++ b/pygmt/src/sphinterpolate.py
@@ -63,7 +63,8 @@ def sphinterpolate(data, **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("sphinterpolate", arg_str)
+                lib.call_module(
+                    "sphinterpolate", build_arg_string(kwargs, infile=infile)
+                )
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None
diff --git a/pygmt/src/surface.py b/pygmt/src/surface.py
index c86ebc41e04..25273e1f2b7 100644
--- a/pygmt/src/surface.py
+++ b/pygmt/src/surface.py
@@ -101,7 +101,8 @@ def surface(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="surface", args=arg_str)
+                lib.call_module(
+                    module="surface", args=build_arg_string(kwargs, infile=infile)
+                )
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None
diff --git a/pygmt/src/text.py b/pygmt/src/text.py
index e7eac023cbd..2e81596c5aa 100644
--- a/pygmt/src/text.py
+++ b/pygmt/src/text.py
@@ -233,5 +233,4 @@ def text_(
                     np.atleast_1d(text).astype(str),
                 )
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("text", arg_str)
+            lib.call_module("text", build_arg_string(kwargs, infile=fname))
diff --git a/pygmt/src/triangulate.py b/pygmt/src/triangulate.py
index e50eb086269..3b540080033 100644
--- a/pygmt/src/triangulate.py
+++ b/pygmt/src/triangulate.py
@@ -134,8 +134,9 @@ def _triangulate(
                 # table output if outgrid is unset, else output to outgrid
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs.update({">": outfile})
-                arg_str = " ".join([infile, build_arg_string(kwargs)])
-                lib.call_module(module="triangulate", args=arg_str)
+                lib.call_module(
+                    module="triangulate", args=build_arg_string(kwargs, infile=infile)
+                )
 
         if output_type == "file":
             return None
diff --git a/pygmt/src/velo.py b/pygmt/src/velo.py
index c27128ee270..77d7115b974 100644
--- a/pygmt/src/velo.py
+++ b/pygmt/src/velo.py
@@ -252,5 +252,4 @@ def velo(self, data=None, **kwargs):
         file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
 
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("velo", arg_str)
+            lib.call_module("velo", build_arg_string(kwargs, infile=fname))
diff --git a/pygmt/src/wiggle.py b/pygmt/src/wiggle.py
index 5d7dbe6dea0..d3481e22276 100644
--- a/pygmt/src/wiggle.py
+++ b/pygmt/src/wiggle.py
@@ -113,5 +113,4 @@ def wiggle(self, data=None, x=None, y=None, z=None, **kwargs):
         )
 
         with file_context as fname:
-            arg_str = " ".join([fname, build_arg_string(kwargs)])
-            lib.call_module("wiggle", arg_str)
+            lib.call_module("wiggle", build_arg_string(kwargs, infile=fname))
diff --git a/pygmt/src/x2sys_cross.py b/pygmt/src/x2sys_cross.py
index de2cdcd2d19..24503ad49e8 100644
--- a/pygmt/src/x2sys_cross.py
+++ b/pygmt/src/x2sys_cross.py
@@ -220,8 +220,12 @@ def x2sys_cross(tracks=None, outfile=None, **kwargs):
                 fnames = [stack.enter_context(c) for c in file_contexts]
                 if outfile is None:
                     outfile = tmpfile.name
-                arg_str = " ".join([*fnames, build_arg_string(kwargs), "->" + outfile])
-                lib.call_module(module="x2sys_cross", args=arg_str)
+                lib.call_module(
+                    module="x2sys_cross",
+                    args=build_arg_string(
+                        kwargs, infile=" ".join(fname), outfile=outfile
+                    ),
+                )
 
             # Read temporary csv output to a pandas table
             if outfile == tmpfile.name:  # if outfile isn't set, return pd.DataFrame
diff --git a/pygmt/src/x2sys_init.py b/pygmt/src/x2sys_init.py
index 150188eef1c..cab1d4a9020 100644
--- a/pygmt/src/x2sys_init.py
+++ b/pygmt/src/x2sys_init.py
@@ -110,5 +110,4 @@ def x2sys_init(tag, **kwargs):
     {j}
     """
     with Session() as lib:
-        arg_str = " ".join([tag, build_arg_string(kwargs)])
-        lib.call_module(module="x2sys_init", args=arg_str)
+        lib.call_module(module="x2sys_init", args=build_arg_string(kwargs, infile=tag))
diff --git a/pygmt/src/xyz2grd.py b/pygmt/src/xyz2grd.py
index 7deb42778ab..4e0d9b7a220 100644
--- a/pygmt/src/xyz2grd.py
+++ b/pygmt/src/xyz2grd.py
@@ -160,7 +160,6 @@ def xyz2grd(data=None, x=None, y=None, z=None, **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("xyz2grd", arg_str)
+                lib.call_module("xyz2grd", build_arg_string(kwargs, infile=infile))
 
         return load_dataarray(outgrid) if outgrid == tmpfile.name else None

From 80ab6690ea28abf1795103db0421caa47ae23bf4 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Wed, 30 Mar 2022 16:13:04 +0800
Subject: [PATCH 3/5] Fix a typo in x2sys_cross.py

---
 pygmt/src/x2sys_cross.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygmt/src/x2sys_cross.py b/pygmt/src/x2sys_cross.py
index 24503ad49e8..5950be733a1 100644
--- a/pygmt/src/x2sys_cross.py
+++ b/pygmt/src/x2sys_cross.py
@@ -223,7 +223,7 @@ def x2sys_cross(tracks=None, outfile=None, **kwargs):
                 lib.call_module(
                     module="x2sys_cross",
                     args=build_arg_string(
-                        kwargs, infile=" ".join(fname), outfile=outfile
+                        kwargs, infile=" ".join(fnames), outfile=outfile
                     ),
                 )
 

From 074eee6e18e0e000e2391398cc23d08ff06fe65b Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Sat, 2 Apr 2022 12:54:30 +0800
Subject: [PATCH 4/5] Change kwargs to kwdict

---
 pygmt/helpers/utils.py | 42 ++++++++++++++++++++++++++----------------
 1 file changed, 26 insertions(+), 16 deletions(-)

diff --git a/pygmt/helpers/utils.py b/pygmt/helpers/utils.py
index 2b130773d73..c1da0a7ff5f 100644
--- a/pygmt/helpers/utils.py
+++ b/pygmt/helpers/utils.py
@@ -119,12 +119,12 @@ def dummy_context(arg):
     yield arg
 
 
-def build_arg_string(kwargs, infile=None, outfile=None):
+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
@@ -138,8 +138,8 @@ def build_arg_string(kwargs, infile=None, outfile=None):
 
     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
@@ -149,7 +149,8 @@ def build_arg_string(kwargs, infile=None, outfile=None):
     -------
     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
     --------
@@ -195,33 +196,42 @@ def build_arg_string(kwargs, infile=None, outfile=None):
     ...     )
     ... )
     -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",
+    ...         output="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}")
+    gmt_args = sorted(gmt_args)
     if infile:
-        gmt_args.append(str(infile))
+        gmt_args = [str(infile)] + gmt_args
     if outfile:
         gmt_args.append("->" + str(outfile))
-    return " ".join(sorted(gmt_args))
+    return " ".join(gmt_args)
 
 
 def is_nonstr_iter(value):

From c4ee94f33874d32e867a022edd1554c6e6484976 Mon Sep 17 00:00:00 2001
From: Dongdong Tian <seisman.info@gmail.com>
Date: Sat, 2 Apr 2022 23:15:08 +0800
Subject: [PATCH 5/5] Fix a typo

---
 pygmt/helpers/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygmt/helpers/utils.py b/pygmt/helpers/utils.py
index c1da0a7ff5f..0bd6aa60176 100644
--- a/pygmt/helpers/utils.py
+++ b/pygmt/helpers/utils.py
@@ -200,7 +200,7 @@ def build_arg_string(kwdict, infile=None, outfile=None):
     ...     build_arg_string(
     ...         dict(A="0", B=True, C="rainbow"),
     ...         infile="input.txt",
-    ...         output="output.txt",
+    ...         outfile="output.txt",
     ...     )
     ... )
     input.txt -A0 -B -Crainbow ->output.txt