clib: Change the parameter order and set output_type to pandas in virtualfile_to_dataset (#3124)

seisman · weiji14 · web-flow · commit 7fd8253acead · 2024-03-20T09:18:09.000+08:00
Co-authored-by: Wei Ji &lt;23487320+weiji14@users.noreply.github.com&gt;
diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
@@ -1740,8 +1740,8 @@ def read_virtualfile(
 
     def virtualfile_to_dataset(
         self,
-        output_type: Literal["pandas", "numpy", "file"],
         vfname: str,
+        output_type: Literal["pandas", "numpy", "file"] = "pandas",
         column_names: list[str] | None = None,
     ) -> pd.DataFrame | np.ndarray | None:
         """
@@ -1751,15 +1751,15 @@ def virtualfile_to_dataset(
 
         Parameters
         ----------
+        vfname
+            The virtual file name that stores the result data. Required for ``"pandas"``
+            and ``"numpy"`` output type.
         output_type
             Desired output type of the result data.
 
             - ``"pandas"`` will return a :class:`pandas.DataFrame` object.
             - ``"numpy"`` will return a :class:`numpy.ndarray` object.
             - ``"file"`` means the result was saved to a file and will return ``None``.
-        vfname
-            The virtual file name that stores the result data. Required for ``"pandas"``
-            and ``"numpy"`` output type.
         column_names
             The column names for the :class:`pandas.DataFrame` output.
 
@@ -1795,7 +1795,7 @@ def virtualfile_to_dataset(
         ...             ) as vouttbl:
         ...                 lib.call_module("read", f"{tmpfile.name} {vouttbl} -Td")
         ...                 result = lib.virtualfile_to_dataset(
-        ...                     output_type="file", vfname=vouttbl
+        ...                     vfname=vouttbl, output_type="file"
         ...                 )
         ...                 assert result is None
         ...                 assert Path(outtmp.name).stat().st_size > 0
@@ -1805,7 +1805,7 @@ def virtualfile_to_dataset(
         ...         with lib.virtualfile_out(kind="dataset") as vouttbl:
         ...             lib.call_module("read", f"{tmpfile.name} {vouttbl} -Td")
         ...             outnp = lib.virtualfile_to_dataset(
-        ...                 output_type="numpy", vfname=vouttbl
+        ...                 vfname=vouttbl, output_type="numpy"
         ...             )
         ...     assert isinstance(outnp, np.ndarray)
         ...
@@ -1814,7 +1814,7 @@ def virtualfile_to_dataset(
         ...         with lib.virtualfile_out(kind="dataset") as vouttbl:
         ...             lib.call_module("read", f"{tmpfile.name} {vouttbl} -Td")
         ...             outpd = lib.virtualfile_to_dataset(
-        ...                 output_type="pandas", vfname=vouttbl
+        ...                 vfname=vouttbl, output_type="pandas"
         ...             )
         ...     assert isinstance(outpd, pd.DataFrame)
         ...
@@ -1823,8 +1823,8 @@ def virtualfile_to_dataset(
         ...         with lib.virtualfile_out(kind="dataset") as vouttbl:
         ...             lib.call_module("read", f"{tmpfile.name} {vouttbl} -Td")
         ...             outpd2 = lib.virtualfile_to_dataset(
-        ...                 output_type="pandas",
         ...                 vfname=vouttbl,
+        ...                 output_type="pandas",
         ...                 column_names=["col1", "col2", "col3", "coltext"],
         ...             )
         ...     assert isinstance(outpd2, pd.DataFrame)
diff --git a/pygmt/src/blockm.py b/pygmt/src/blockm.py
@@ -64,7 +64,7 @@ def _blockm(
                 args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),
             )
             return lib.virtualfile_to_dataset(
-                output_type=output_type, vfname=vouttbl, column_names=column_names
+                vfname=vouttbl, output_type=output_type, column_names=column_names
             )
 
 
diff --git a/pygmt/src/filter1d.py b/pygmt/src/filter1d.py
@@ -123,4 +123,4 @@ def filter1d(
                 module="filter1d",
                 args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),
             )
-        return lib.virtualfile_to_dataset(output_type=output_type, vfname=vouttbl)
+        return lib.virtualfile_to_dataset(vfname=vouttbl, output_type=output_type)
diff --git a/pygmt/src/grd2xyz.py b/pygmt/src/grd2xyz.py
@@ -168,5 +168,5 @@ def grd2xyz(
                 args=build_arg_string(kwargs, infile=vingrd, outfile=vouttbl),
             )
             return lib.virtualfile_to_dataset(
-                output_type=output_type, vfname=vouttbl, column_names=column_names
+                vfname=vouttbl, output_type=output_type, column_names=column_names
             )
diff --git a/pygmt/src/grdhisteq.py b/pygmt/src/grdhisteq.py
@@ -239,8 +239,8 @@ def compute_bins(
                 )
 
             result = lib.virtualfile_to_dataset(
-                output_type=output_type,
                 vfname=vouttbl,
+                output_type=output_type,
                 column_names=["start", "stop", "bin_id"],
             )
             if output_type == "pandas":
diff --git a/pygmt/src/grdtrack.py b/pygmt/src/grdtrack.py
@@ -318,7 +318,7 @@ def grdtrack(
                 args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),
             )
         return lib.virtualfile_to_dataset(
-            output_type=output_type,
             vfname=vouttbl,
+            output_type=output_type,
             column_names=column_names,
         )
diff --git a/pygmt/src/grdvolume.py b/pygmt/src/grdvolume.py
@@ -111,4 +111,4 @@ def grdvolume(
                 module="grdvolume",
                 args=build_arg_string(kwargs, infile=vingrd, outfile=vouttbl),
             )
-            return lib.virtualfile_to_dataset(output_type=output_type, vfname=vouttbl)
+            return lib.virtualfile_to_dataset(vfname=vouttbl, output_type=output_type)
diff --git a/pygmt/src/project.py b/pygmt/src/project.py
@@ -256,7 +256,7 @@ def project(
                 args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),
             )
         return lib.virtualfile_to_dataset(
-            output_type=output_type,
             vfname=vouttbl,
+            output_type=output_type,
             column_names=column_names,
         )
diff --git a/pygmt/src/select.py b/pygmt/src/select.py
@@ -221,7 +221,7 @@ def select(
                 args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),
             )
         return lib.virtualfile_to_dataset(
-            output_type=output_type,
             vfname=vouttbl,
+            output_type=output_type,
             column_names=column_names,
         )
diff --git a/pygmt/src/triangulate.py b/pygmt/src/triangulate.py
@@ -249,4 +249,4 @@ def delaunay_triples(
                     module="triangulate",
                     args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),
                 )
-            return lib.virtualfile_to_dataset(output_type=output_type, vfname=vouttbl)
+            return lib.virtualfile_to_dataset(vfname=vouttbl, output_type=output_type)

Original file line number	Diff line number	Diff line change
`@@ -64,7 +64,7 @@ def _blockm(`
`64`	`64`	`args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),`
`65`	`65`	`)`
`66`	`66`	`return lib.virtualfile_to_dataset(`
`67`		`- output_type=output_type, vfname=vouttbl, column_names=column_names`
	`67`	`+ vfname=vouttbl, output_type=output_type, column_names=column_names`
`68`	`68`	`)`
`69`	`69`
`70`	`70`
Original file line number	Diff line number	Diff line change
`@@ -123,4 +123,4 @@ def filter1d(`
`123`	`123`	`module="filter1d",`
`124`	`124`	`args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),`
`125`	`125`	`)`
`126`		`- return lib.virtualfile_to_dataset(output_type=output_type, vfname=vouttbl)`
	`126`	`+ return lib.virtualfile_to_dataset(vfname=vouttbl, output_type=output_type)`
Original file line number	Diff line number	Diff line change
`@@ -168,5 +168,5 @@ def grd2xyz(`
`168`	`168`	`args=build_arg_string(kwargs, infile=vingrd, outfile=vouttbl),`
`169`	`169`	`)`
`170`	`170`	`return lib.virtualfile_to_dataset(`
`171`		`- output_type=output_type, vfname=vouttbl, column_names=column_names`
	`171`	`+ vfname=vouttbl, output_type=output_type, column_names=column_names`
`172`	`172`	`)`
Original file line number	Diff line number	Diff line change
`@@ -239,8 +239,8 @@ def compute_bins(`
`239`	`239`	`)`
`240`	`240`
`241`	`241`	`result = lib.virtualfile_to_dataset(`
`242`		`- output_type=output_type,`
`243`	`242`	`vfname=vouttbl,`
	`243`	`+ output_type=output_type,`
`244`	`244`	`column_names=["start", "stop", "bin_id"],`
`245`	`245`	`)`
`246`	`246`	`if output_type == "pandas":`
Original file line number	Diff line number	Diff line change
`@@ -318,7 +318,7 @@ def grdtrack(`
`318`	`318`	`args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),`
`319`	`319`	`)`
`320`	`320`	`return lib.virtualfile_to_dataset(`
`321`		`- output_type=output_type,`
`322`	`321`	`vfname=vouttbl,`
	`322`	`+ output_type=output_type,`
`323`	`323`	`column_names=column_names,`
`324`	`324`	`)`
Original file line number	Diff line number	Diff line change
`@@ -111,4 +111,4 @@ def grdvolume(`
`111`	`111`	`module="grdvolume",`
`112`	`112`	`args=build_arg_string(kwargs, infile=vingrd, outfile=vouttbl),`
`113`	`113`	`)`
`114`		`- return lib.virtualfile_to_dataset(output_type=output_type, vfname=vouttbl)`
	`114`	`+ return lib.virtualfile_to_dataset(vfname=vouttbl, output_type=output_type)`
Original file line number	Diff line number	Diff line change
`@@ -256,7 +256,7 @@ def project(`
`256`	`256`	`args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),`
`257`	`257`	`)`
`258`	`258`	`return lib.virtualfile_to_dataset(`
`259`		`- output_type=output_type,`
`260`	`259`	`vfname=vouttbl,`
	`260`	`+ output_type=output_type,`
`261`	`261`	`column_names=column_names,`
`262`	`262`	`)`
Original file line number	Diff line number	Diff line change
`@@ -221,7 +221,7 @@ def select(`
`221`	`221`	`args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),`
`222`	`222`	`)`
`223`	`223`	`return lib.virtualfile_to_dataset(`
`224`		`- output_type=output_type,`
`225`	`224`	`vfname=vouttbl,`
	`225`	`+ output_type=output_type,`
`226`	`226`	`column_names=column_names,`
`227`	`227`	`)`
Original file line number	Diff line number	Diff line change
`@@ -249,4 +249,4 @@ def delaunay_triples(`
`249`	`249`	`module="triangulate",`
`250`	`250`	`args=build_arg_string(kwargs, infile=vintbl, outfile=vouttbl),`
`251`	`251`	`)`
`252`		`- return lib.virtualfile_to_dataset(output_type=output_type, vfname=vouttbl)`
	`252`	`+ return lib.virtualfile_to_dataset(vfname=vouttbl, output_type=output_type)`