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seismanseisman
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Refractor build_arg_string to also deal with infile and outfile (#1837)
1 parent 4cfe813 commit a1924e8

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+111
-111
lines changed

‎pygmt/helpers/utils.py

+33-15
Original file line numberDiff line numberDiff line change
@@ -119,12 +119,12 @@ def dummy_context(arg):
119119
yield arg
120120

121121

122-
def build_arg_string(kwargs):
122+
def build_arg_string(kwdict, infile=None, outfile=None):
123123
r"""
124-
Transform keyword arguments into a GMT argument string.
124+
Convert a dict and optional input/output files into a GMT argument string.
125125
126-
Make sure all arguments have been previously converted to a string
127-
representation using the ``kwargs_to_strings`` decorator. The only
126+
Make sure all values in ``kwdict`` have been previously converted to a
127+
string representation using the ``kwargs_to_strings`` decorator. The only
128128
exceptions are True, False and None.
129129
130130
Any lists or tuples left will be interpreted as multiple entries for the
@@ -138,14 +138,19 @@ def build_arg_string(kwargs):
138138
139139
Parameters
140140
----------
141-
kwargs : dict
142-
Parsed keyword arguments.
141+
kwdict : dict
142+
A dict containing parsed keyword arguments.
143+
infile : str or pathlib.Path
144+
The input file.
145+
outfile : str or pathlib.Path
146+
The output file.
143147
144148
Returns
145149
-------
146150
args : str
147151
The space-delimited argument string with '-' inserted before each
148-
keyword. The arguments are sorted alphabetically.
152+
keyword. The arguments are sorted alphabetically, with optional input
153+
file at the begining and optioanl output file at the end.
149154
150155
Examples
151156
--------
@@ -191,29 +196,42 @@ def build_arg_string(kwargs):
191196
... )
192197
... )
193198
-BWSne+tBlank\040Space -Baf -F+t"Empty\040\040Spaces" -l'Void\040Space'
199+
>>> print(
200+
... build_arg_string(
201+
... dict(A="0", B=True, C="rainbow"),
202+
... infile="input.txt",
203+
... outfile="output.txt",
204+
... )
205+
... )
206+
input.txt -A0 -B -Crainbow ->output.txt
194207
"""
195208
gmt_args = []
196209

197-
for key in kwargs:
210+
for key in kwdict:
198211
if len(key) > 2: # raise an exception for unrecognized options
199212
raise GMTInvalidInput(f"Unrecognized parameter '{key}'.")
200-
if kwargs[key] is None or kwargs[key] is False:
213+
if kwdict[key] is None or kwdict[key] is False:
201214
pass # Exclude arguments that are None and False
202-
elif is_nonstr_iter(kwargs[key]):
203-
for value in kwargs[key]:
215+
elif is_nonstr_iter(kwdict[key]):
216+
for value in kwdict[key]:
204217
_value = str(value).replace(" ", r"\040")
205218
gmt_args.append(rf"-{key}{_value}")
206-
elif kwargs[key] is True:
219+
elif kwdict[key] is True:
207220
gmt_args.append(f"-{key}")
208221
else:
209222
if key != "J": # non-projection parameters
210-
_value = str(kwargs[key]).replace(" ", r"\040")
223+
_value = str(kwdict[key]).replace(" ", r"\040")
211224
else:
212225
# special handling if key == "J" (projection)
213226
# remove any spaces in PROJ4 string
214-
_value = str(kwargs[key]).replace(" ", "")
227+
_value = str(kwdict[key]).replace(" ", "")
215228
gmt_args.append(rf"-{key}{_value}")
216-
return " ".join(sorted(gmt_args))
229+
gmt_args = sorted(gmt_args)
230+
if infile:
231+
gmt_args = [str(infile)] + gmt_args
232+
if outfile:
233+
gmt_args.append("->" + str(outfile))
234+
return " ".join(gmt_args)
217235

218236

219237
def is_nonstr_iter(value):

‎pygmt/src/blockm.py

+4-2
Original file line numberDiff line numberDiff line change
@@ -51,8 +51,10 @@ def _blockm(block_method, data, x, y, z, outfile, **kwargs):
5151
with table_context as infile:
5252
if outfile is None:
5353
outfile = tmpfile.name
54-
arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
55-
lib.call_module(module=block_method, args=arg_str)
54+
lib.call_module(
55+
module=block_method,
56+
args=build_arg_string(kwargs, infile=infile, outfile=outfile),
57+
)
5658

5759
# Read temporary csv output to a pandas table
5860
if outfile == tmpfile.name: # if user did not set outfile, return pd.DataFrame

‎pygmt/src/contour.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -132,5 +132,4 @@ def contour(self, data=None, x=None, y=None, z=None, **kwargs):
132132
check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
133133
)
134134
with file_context as fname:
135-
arg_str = " ".join([fname, build_arg_string(kwargs)])
136-
lib.call_module("contour", arg_str)
135+
lib.call_module("contour", build_arg_string(kwargs, infile=fname))

‎pygmt/src/grd2cpt.py

+3-5
Original file line numberDiff line numberDiff line change
@@ -166,12 +166,10 @@ def grd2cpt(grid, **kwargs):
166166
file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
167167
with file_context as infile:
168168
if "H" not in kwargs: # if no output is set
169-
arg_str = " ".join([infile, build_arg_string(kwargs)])
169+
arg_str = build_arg_string(kwargs, infile=infile)
170170
if "H" in kwargs: # if output is set
171-
outfile = kwargs.pop("H")
171+
outfile, kwargs["H"] = kwargs["H"], True
172172
if not outfile or not isinstance(outfile, str):
173173
raise GMTInvalidInput("'output' should be a proper file name.")
174-
arg_str = " ".join(
175-
[infile, build_arg_string(kwargs), f"-H > {outfile}"]
176-
)
174+
arg_str = build_arg_string(kwargs, infile=infile, outfile=outfile)
177175
lib.call_module("grd2cpt", arg_str)

‎pygmt/src/grd2xyz.py

+3-2
Original file line numberDiff line numberDiff line change
@@ -178,8 +178,9 @@ def grd2xyz(grid, output_type="pandas", outfile=None, **kwargs):
178178
with file_context as infile:
179179
if outfile is None:
180180
outfile = tmpfile.name
181-
arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
182-
lib.call_module("grd2xyz", arg_str)
181+
lib.call_module(
182+
"grd2xyz", build_arg_string(kwargs, infile=infile, outfile=outfile)
183+
)
183184

184185
# Read temporary csv output to a pandas table
185186
if outfile == tmpfile.name: # if user did not set outfile, return pd.DataFrame

‎pygmt/src/grdclip.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -107,7 +107,6 @@ def grdclip(grid, **kwargs):
107107
if "G" not in kwargs: # if outgrid is unset, output to tempfile
108108
kwargs.update({"G": tmpfile.name})
109109
outgrid = kwargs["G"]
110-
arg_str = " ".join([infile, build_arg_string(kwargs)])
111-
lib.call_module("grdclip", arg_str)
110+
lib.call_module("grdclip", build_arg_string(kwargs, infile=infile))
112111

113112
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/grdcontour.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -100,5 +100,4 @@ def grdcontour(self, grid, **kwargs):
100100
with Session() as lib:
101101
file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
102102
with file_context as fname:
103-
arg_str = " ".join([fname, build_arg_string(kwargs)])
104-
lib.call_module("grdcontour", arg_str)
103+
lib.call_module("grdcontour", build_arg_string(kwargs, infile=fname))

‎pygmt/src/grdcut.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -109,7 +109,6 @@ def grdcut(grid, **kwargs):
109109
if "G" not in kwargs: # if outgrid is unset, output to tempfile
110110
kwargs.update({"G": tmpfile.name})
111111
outgrid = kwargs["G"]
112-
arg_str = " ".join([infile, build_arg_string(kwargs)])
113-
lib.call_module("grdcut", arg_str)
112+
lib.call_module("grdcut", build_arg_string(kwargs, infile=infile))
114113

115114
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/grdfill.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -72,7 +72,6 @@ def grdfill(grid, **kwargs):
7272
if "G" not in kwargs: # if outgrid is unset, output to tempfile
7373
kwargs.update({"G": tmpfile.name})
7474
outgrid = kwargs["G"]
75-
arg_str = " ".join([infile, build_arg_string(kwargs)])
76-
lib.call_module("grdfill", arg_str)
75+
lib.call_module("grdfill", build_arg_string(kwargs, infile=infile))
7776

7877
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/grdfilter.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -148,7 +148,6 @@ def grdfilter(grid, **kwargs):
148148
if "G" not in kwargs: # if outgrid is unset, output to tempfile
149149
kwargs.update({"G": tmpfile.name})
150150
outgrid = kwargs["G"]
151-
arg_str = " ".join([infile, build_arg_string(kwargs)])
152-
lib.call_module("grdfilter", arg_str)
151+
lib.call_module("grdfilter", build_arg_string(kwargs, infile=infile))
153152

154153
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/grdgradient.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -177,7 +177,6 @@ def grdgradient(grid, **kwargs):
177177
if "G" not in kwargs: # if outgrid is unset, output to tempfile
178178
kwargs.update({"G": tmpfile.name})
179179
outgrid = kwargs["G"]
180-
arg_str = " ".join([infile, build_arg_string(kwargs)])
181-
lib.call_module("grdgradient", arg_str)
180+
lib.call_module("grdgradient", build_arg_string(kwargs, infile=infile))
182181

183182
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/grdhisteq.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -112,8 +112,7 @@ def _grdhisteq(grid, output_type, **kwargs):
112112
with Session() as lib:
113113
file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
114114
with file_context as infile:
115-
arg_str = " ".join([infile, build_arg_string(kwargs)])
116-
lib.call_module("grdhisteq", arg_str)
115+
lib.call_module("grdhisteq", build_arg_string(kwargs, infile=infile))
117116

118117
if output_type == "file":
119118
return None

‎pygmt/src/grdimage.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -171,5 +171,4 @@ def grdimage(self, grid, **kwargs):
171171
kwargs["I"] = stack.enter_context(shading_context)
172172

173173
fname = stack.enter_context(file_context)
174-
arg_str = " ".join([fname, build_arg_string(kwargs)])
175-
lib.call_module("grdimage", arg_str)
174+
lib.call_module("grdimage", build_arg_string(kwargs, infile=fname))

‎pygmt/src/grdinfo.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -114,9 +114,9 @@ def grdinfo(grid, **kwargs):
114114
with Session() as lib:
115115
file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
116116
with file_context as infile:
117-
arg_str = " ".join(
118-
[infile, build_arg_string(kwargs), "->" + outfile.name]
117+
lib.call_module(
118+
"grdinfo",
119+
build_arg_string(kwargs, infile=infile, outfile=outfile.name),
119120
)
120-
lib.call_module("grdinfo", arg_str)
121121
result = outfile.read()
122122
return result

‎pygmt/src/grdlandmask.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -109,7 +109,6 @@ def grdlandmask(**kwargs):
109109
if "G" not in kwargs: # if outgrid is unset, output to tempfile
110110
kwargs.update({"G": tmpfile.name})
111111
outgrid = kwargs["G"]
112-
arg_str = build_arg_string(kwargs)
113-
lib.call_module("grdlandmask", arg_str)
112+
lib.call_module("grdlandmask", build_arg_string(kwargs))
114113

115114
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/grdproject.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -121,7 +121,6 @@ def grdproject(grid, **kwargs):
121121
if "G" not in kwargs: # if outgrid is unset, output to tempfile
122122
kwargs.update({"G": tmpfile.name})
123123
outgrid = kwargs["G"]
124-
arg_str = " ".join([infile, build_arg_string(kwargs)])
125-
lib.call_module("grdproject", arg_str)
124+
lib.call_module("grdproject", build_arg_string(kwargs, infile=infile))
126125

127126
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/grdsample.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -99,7 +99,6 @@ def grdsample(grid, **kwargs):
9999
if "G" not in kwargs: # if outgrid is unset, output to tempfile
100100
kwargs.update({"G": tmpfile.name})
101101
outgrid = kwargs["G"]
102-
arg_str = " ".join([infile, build_arg_string(kwargs)])
103-
lib.call_module("grdsample", arg_str)
102+
lib.call_module("grdsample", build_arg_string(kwargs, infile=infile))
104103

105104
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/grdtrack.py

+3-3
Original file line numberDiff line numberDiff line change
@@ -300,10 +300,10 @@ def grdtrack(points, grid, newcolname=None, outfile=None, **kwargs):
300300
kwargs.update({"G": grdfile})
301301
if outfile is None: # Output to tmpfile if outfile is not set
302302
outfile = tmpfile.name
303-
arg_str = " ".join(
304-
[csvfile, build_arg_string(kwargs), "->" + outfile]
303+
lib.call_module(
304+
module="grdtrack",
305+
args=build_arg_string(kwargs, infile=csvfile, outfile=outfile),
305306
)
306-
lib.call_module(module="grdtrack", args=arg_str)
307307

308308
# Read temporary csv output to a pandas table
309309
if outfile == tmpfile.name: # if user did not set outfile, return pd.DataFrame

‎pygmt/src/grdview.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -137,5 +137,4 @@ def grdview(self, grid, **kwargs):
137137
f"Unrecognized data type for drapegrid: {type(drapegrid)}"
138138
)
139139
fname = stack.enter_context(file_context)
140-
arg_str = " ".join([fname, build_arg_string(kwargs)])
141-
lib.call_module("grdview", arg_str)
140+
lib.call_module("grdview", build_arg_string(kwargs, infile=fname))

‎pygmt/src/grdvolume.py

+4-2
Original file line numberDiff line numberDiff line change
@@ -114,8 +114,10 @@ def grdvolume(grid, output_type="pandas", outfile=None, **kwargs):
114114
with file_context as infile:
115115
if outfile is None:
116116
outfile = tmpfile.name
117-
arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
118-
lib.call_module("grdvolume", arg_str)
117+
lib.call_module(
118+
"grdvolume",
119+
build_arg_string(kwargs, infile=infile, outfile=outfile),
120+
)
119121

120122
# Read temporary csv output to a pandas table
121123
if outfile == tmpfile.name: # if user did not set outfile, return pd.DataFrame

‎pygmt/src/histogram.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -148,5 +148,4 @@ def histogram(self, data, **kwargs):
148148
with Session() as lib:
149149
file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
150150
with file_context as infile:
151-
arg_str = " ".join([infile, build_arg_string(kwargs)])
152-
lib.call_module("histogram", arg_str)
151+
lib.call_module("histogram", build_arg_string(kwargs, infile=infile))

‎pygmt/src/image.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -64,5 +64,4 @@ def image(self, imagefile, **kwargs):
6464
"""
6565
kwargs = self._preprocess(**kwargs) # pylint: disable=protected-access
6666
with Session() as lib:
67-
arg_str = " ".join([imagefile, build_arg_string(kwargs)])
68-
lib.call_module("image", arg_str)
67+
lib.call_module("image", build_arg_string(kwargs, infile=imagefile))

‎pygmt/src/info.py

+2-3
Original file line numberDiff line numberDiff line change
@@ -85,10 +85,9 @@ def info(data, **kwargs):
8585
file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
8686
with GMTTempFile() as tmpfile:
8787
with file_context as fname:
88-
arg_str = " ".join(
89-
[fname, build_arg_string(kwargs), "->" + tmpfile.name]
88+
lib.call_module(
89+
"info", build_arg_string(kwargs, infile=fname, outfile=tmpfile.name)
9090
)
91-
lib.call_module("info", arg_str)
9291
result = tmpfile.read()
9392

9493
if any(arg in kwargs for arg in ["C", "I", "T"]):

‎pygmt/src/legend.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -87,5 +87,4 @@ def legend(self, spec=None, position="JTR+jTR+o0.2c", box="+gwhite+p1p", **kwarg
8787
specfile = spec
8888
else:
8989
raise GMTInvalidInput(f"Unrecognized data type: {type(spec)}")
90-
arg_str = " ".join([specfile, build_arg_string(kwargs)])
91-
lib.call_module("legend", arg_str)
90+
lib.call_module("legend", build_arg_string(kwargs, infile=specfile))

‎pygmt/src/makecpt.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -152,8 +152,8 @@ def makecpt(**kwargs):
152152
if "H" not in kwargs: # if no output is set
153153
arg_str = build_arg_string(kwargs)
154154
elif "H" in kwargs: # if output is set
155-
outfile = kwargs.pop("H")
155+
outfile, kwargs["H"] = kwargs.pop("H"), True
156156
if not outfile or not isinstance(outfile, str):
157157
raise GMTInvalidInput("'output' should be a proper file name.")
158-
arg_str = " ".join([build_arg_string(kwargs), f"-H > {outfile}"])
158+
arg_str = build_arg_string(kwargs, outfile=outfile)
159159
lib.call_module(module="makecpt", args=arg_str)

‎pygmt/src/meca.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -464,5 +464,4 @@ def update_pointers(data_pointers):
464464
else:
465465
raise GMTInvalidInput(f"Unrecognized data type: {type(spec)}")
466466
with file_context as fname:
467-
arg_str = " ".join([fname, build_arg_string(kwargs)])
468-
lib.call_module("meca", arg_str)
467+
lib.call_module("meca", build_arg_string(kwargs, infile=fname))

‎pygmt/src/nearneighbor.py

+3-2
Original file line numberDiff line numberDiff line change
@@ -142,7 +142,8 @@ def nearneighbor(data=None, x=None, y=None, z=None, **kwargs):
142142
if "G" not in kwargs: # if outgrid is unset, output to tmpfile
143143
kwargs.update({"G": tmpfile.name})
144144
outgrid = kwargs["G"]
145-
arg_str = " ".join([infile, build_arg_string(kwargs)])
146-
lib.call_module(module="nearneighbor", args=arg_str)
145+
lib.call_module(
146+
module="nearneighbor", args=build_arg_string(kwargs, infile=infile)
147+
)
147148

148149
return load_dataarray(outgrid) if outgrid == tmpfile.name else None

‎pygmt/src/plot.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -266,5 +266,4 @@ def plot(self, data=None, x=None, y=None, size=None, direction=None, **kwargs):
266266
)
267267

268268
with file_context as fname:
269-
arg_str = " ".join([fname, build_arg_string(kwargs)])
270-
lib.call_module("plot", arg_str)
269+
lib.call_module("plot", build_arg_string(kwargs, infile=fname))

‎pygmt/src/plot3d.py

+1-2
Original file line numberDiff line numberDiff line change
@@ -242,5 +242,4 @@ def plot3d(
242242
)
243243

244244
with file_context as fname:
245-
arg_str = " ".join([fname, build_arg_string(kwargs)])
246-
lib.call_module("plot3d", arg_str)
245+
lib.call_module("plot3d", build_arg_string(kwargs, infile=fname))

‎pygmt/src/project.py

+2-4
Original file line numberDiff line numberDiff line change
@@ -233,11 +233,9 @@ def project(data=None, x=None, y=None, z=None, outfile=None, **kwargs):
233233

234234
# Run project on the temporary (csv) data table
235235
with table_context as infile:
236-
arg_str = " ".join(
237-
[infile, build_arg_string(kwargs), "->" + outfile]
238-
)
236+
arg_str = build_arg_string(kwargs, infile=infile, outfile=outfile)
239237
else:
240-
arg_str = " ".join([build_arg_string(kwargs), "->" + outfile])
238+
arg_str = build_arg_string(kwargs, outfile=outfile)
241239
lib.call_module(module="project", args=arg_str)
242240

243241
# if user did not set outfile, return pd.DataFrame

‎pygmt/src/rose.py

+1-3
Original file line numberDiff line numberDiff line change
@@ -211,6 +211,4 @@ def rose(self, data=None, length=None, azimuth=None, **kwargs):
211211
)
212212

213213
with file_context as fname:
214-
arg_str = " ".join([fname, build_arg_string(kwargs)])
215-
216-
lib.call_module("rose", arg_str)
214+
lib.call_module("rose", build_arg_string(kwargs, infile=fname))

‎pygmt/src/select.py

+4-2
Original file line numberDiff line numberDiff line change
@@ -167,8 +167,10 @@ def select(data=None, outfile=None, **kwargs):
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with table_context as infile:
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if outfile is None:
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outfile = tmpfile.name
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arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
171-
lib.call_module(module="gmtselect", args=arg_str)
170+
lib.call_module(
171+
module="gmtselect",
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args=build_arg_string(kwargs, infile=infile, outfile=outfile),
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)
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# Read temporary csv output to a pandas table
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if outfile == tmpfile.name: # if user did not set outfile, return pd.DataFrame

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