Rename virtualfile_from_data to virtualfile_in

Author: seisman

doc/api/index.rst

@@ -288,11 +288,11 @@ conversion of Python variables to GMT virtual files:
 
 .. autosummary::
     :toctree: generated
-
-    clib.Session.virtualfile_from_data
+    
     clib.Session.virtualfile_from_matrix
     clib.Session.virtualfile_from_vectors
     clib.Session.virtualfile_from_grid
+    clib.Session.virtualfile_in
     clib.Session.virtualfile_out
 
 

pygmt/clib/session.py

@@ -1478,7 +1478,7 @@ def virtualfile_from_grid(self, grid):
             yield vfile
 
     @fmt_docstring
-    def virtualfile_from_data(  # noqa: PLR0912
+    def virtualfile_in(  # noqa: PLR0912
         self,
         check_kind=None,
         data=None,
@@ -1535,7 +1535,7 @@ def virtualfile_from_data(  # noqa: PLR0912
         ...     ),
         ... )
         >>> with Session() as ses:
-        ...     with ses.virtualfile_from_data(check_kind="vector", data=data) as fin:
+        ...     with ses.virtualfile_in(check_kind="vector", data=data) as fin:
         ...         # Send the output to a file so that we can read it
         ...         with GMTTempFile() as fout:
         ...             ses.call_module("info", fin + " ->" + fout.name)
@@ -1609,6 +1609,9 @@ def virtualfile_from_data(  # noqa: PLR0912
 
         return file_context
 
+    # virtualfile_from_data is the old name for virtualfile_in
+    virtualfile_from_data = virtualfile_in
+
     @contextlib.contextmanager
     def virtualfile_out(
         self, kind: Literal["dataset", "grid"] = "dataset", fname: str | None = None

pygmt/src/binstats.py

@@ -111,7 +111,7 @@ def binstats(data, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
+            file_context = lib.virtualfile_in(check_kind="vector", data=data)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/blockm.py

@@ -43,7 +43,7 @@ def _blockm(block_method, data, x, y, z, outfile, **kwargs):
     """
     with GMTTempFile(suffix=".csv") as tmpfile:
         with Session() as lib:
-            table_context = lib.virtualfile_from_data(
+            table_context = lib.virtualfile_in(
                 check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
             )
             # Run blockm* on data table

pygmt/src/contour.py

@@ -115,7 +115,7 @@ def contour(self, data=None, x=None, y=None, z=None, **kwargs):
     kwargs = self._preprocess(**kwargs)
 
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(
+        file_context = lib.virtualfile_in(
             check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
         )
         with file_context as fname:

pygmt/src/dimfilter.py

@@ -151,7 +151,7 @@ def dimfilter(grid, **kwargs):
 
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/filter1d.py

@@ -119,7 +119,7 @@ def filter1d(data, output_type="pandas", outfile=None, **kwargs):
 
     with GMTTempFile() as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
+            file_context = lib.virtualfile_in(check_kind="vector", data=data)
             with file_context as infile:
                 if outfile is None:
                     outfile = tmpfile.name

pygmt/src/grd2cpt.py

@@ -184,7 +184,7 @@ def grd2cpt(grid, **kwargs):
     if kwargs.get("W") is not None and kwargs.get("Ww") is not None:
         raise GMTInvalidInput("Set only categorical or cyclic to True, not both.")
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+        file_context = lib.virtualfile_in(check_kind="raster", data=grid)
         with file_context as infile:
             if kwargs.get("H") is None:  # if no output is set
                 arg_str = build_arg_string(kwargs, infile=infile)

pygmt/src/grd2xyz.py

@@ -158,7 +158,7 @@ def grd2xyz(grid, output_type="pandas", outfile=None, **kwargs):
 
     with GMTTempFile() as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if outfile is None:
                     outfile = tmpfile.name

pygmt/src/grdclip.py

@@ -97,7 +97,7 @@ def grdclip(grid, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/grdcontour.py

@@ -122,7 +122,7 @@ def grdcontour(self, grid, **kwargs):
     """
     kwargs = self._preprocess(**kwargs)
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+        file_context = lib.virtualfile_in(check_kind="raster", data=grid)
         with file_context as fname:
             lib.call_module(
                 module="grdcontour", args=build_arg_string(kwargs, infile=fname)

pygmt/src/grdcut.py

@@ -101,7 +101,7 @@ def grdcut(grid, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/grdfill.py

@@ -79,7 +79,7 @@ def grdfill(grid, **kwargs):
         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)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/grdfilter.py

@@ -134,7 +134,7 @@ def grdfilter(grid, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/grdgradient.py

@@ -169,7 +169,7 @@ def grdgradient(grid, **kwargs):
                 azimuth, direction, or radiance"""
             )
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/grdhisteq.py

@@ -107,7 +107,7 @@ def _grdhisteq(grid, output_type, **kwargs):
         """
 
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 lib.call_module(
                     module="grdhisteq", args=build_arg_string(kwargs, infile=infile)

pygmt/src/grdimage.py

@@ -163,9 +163,9 @@ def grdimage(self, grid, **kwargs):
         )
 
     with Session() as lib:
-        with lib.virtualfile_from_data(
+        with lib.virtualfile_in(
             check_kind="raster", data=grid
-        ) as fname, lib.virtualfile_from_data(
+        ) as fname, lib.virtualfile_in(
             check_kind="raster", data=kwargs.get("I"), required_data=False
         ) as shadegrid:
             kwargs["I"] = shadegrid

pygmt/src/grdinfo.py

@@ -111,7 +111,7 @@ def grdinfo(grid, **kwargs):
     """
     with GMTTempFile() as outfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 lib.call_module(
                     module="grdinfo",

pygmt/src/grdproject.py

@@ -112,7 +112,7 @@ def grdproject(grid, **kwargs):
         raise GMTInvalidInput("The projection must be specified.")
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/grdsample.py

@@ -89,7 +89,7 @@ def grdsample(grid, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/grdtrack.py

@@ -292,9 +292,9 @@ def grdtrack(grid, points=None, newcolname=None, outfile=None, **kwargs):
 
     with GMTTempFile(suffix=".csv") as tmpfile:
         with Session() as lib:
-            with lib.virtualfile_from_data(
+            with lib.virtualfile_in(
                 check_kind="raster", data=grid
-            ) as grdfile, lib.virtualfile_from_data(
+            ) as grdfile, lib.virtualfile_in(
                 check_kind="vector", data=points, required_data=False
             ) as csvfile:
                 kwargs["G"] = grdfile

pygmt/src/grdview.py

@@ -144,9 +144,9 @@ def grdview(self, grid, **kwargs):
     """
     kwargs = self._preprocess(**kwargs)
     with Session() as lib:
-        with lib.virtualfile_from_data(
+        with lib.virtualfile_in(
             check_kind="raster", data=grid
-        ) as fname, lib.virtualfile_from_data(
+        ) as fname, lib.virtualfile_in(
             check_kind="raster", data=kwargs.get("G"), required_data=False
         ) as drapegrid:
             kwargs["G"] = drapegrid

pygmt/src/grdvolume.py

@@ -104,7 +104,7 @@ def grdvolume(grid, output_type="pandas", outfile=None, **kwargs):
 
     with GMTTempFile() as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="raster", data=grid)
+            file_context = lib.virtualfile_in(check_kind="raster", data=grid)
             with file_context as infile:
                 if outfile is None:
                     outfile = tmpfile.name

pygmt/src/histogram.py

@@ -134,7 +134,7 @@ def histogram(self, data, **kwargs):
     """
     kwargs = self._preprocess(**kwargs)
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
+        file_context = lib.virtualfile_in(check_kind="vector", data=data)
         with file_context as infile:
             lib.call_module(
                 module="histogram", args=build_arg_string(kwargs, infile=infile)

pygmt/src/info.py

@@ -80,7 +80,7 @@ def info(data, **kwargs):
         - str if none of the above parameters are used.
     """
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
+        file_context = lib.virtualfile_in(check_kind="vector", data=data)
         with GMTTempFile() as tmpfile:
             with file_context as fname:
                 lib.call_module(

pygmt/src/meca.py

@@ -488,6 +488,6 @@ def meca(  # noqa: PLR0912, PLR0913, PLR0915
     # Assemble -S flag
     kwargs["S"] = f"{data_format}{scale}"
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(check_kind="vector", data=spec)
+        file_context = lib.virtualfile_in(check_kind="vector", data=spec)
         with file_context as fname:
             lib.call_module(module="meca", args=build_arg_string(kwargs, infile=fname))

pygmt/src/nearneighbor.py

@@ -145,7 +145,7 @@ def nearneighbor(data=None, x=None, y=None, z=None, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            table_context = lib.virtualfile_from_data(
+            table_context = lib.virtualfile_in(
                 check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
             )
             with table_context as infile:

pygmt/src/plot.py

@@ -250,7 +250,7 @@ def plot(  # noqa: PLR0912
             kwargs[flag] = ""
 
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(
+        file_context = lib.virtualfile_in(
             check_kind="vector", data=data, x=x, y=y, extra_arrays=extra_arrays
         )
 

pygmt/src/plot3d.py

@@ -225,7 +225,7 @@ def plot3d(  # noqa: PLR0912
             kwargs[flag] = ""
 
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(
+        file_context = lib.virtualfile_in(
             check_kind="vector",
             data=data,
             x=x,

pygmt/src/project.py

@@ -227,7 +227,7 @@ def project(data=None, x=None, y=None, z=None, outfile=None, **kwargs):
             outfile = tmpfile.name
         with Session() as lib:
             if kwargs.get("G") is None:
-                table_context = lib.virtualfile_from_data(
+                table_context = lib.virtualfile_in(
                     check_kind="vector", data=data, x=x, y=y, z=z, required_z=False
                 )
 

pygmt/src/rose.py

@@ -200,7 +200,7 @@ def rose(self, data=None, length=None, azimuth=None, **kwargs):
     kwargs = self._preprocess(**kwargs)
 
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(
+        file_context = lib.virtualfile_in(
             check_kind="vector", data=data, x=length, y=azimuth
         )
 

pygmt/src/select.py

@@ -198,7 +198,7 @@ def select(data=None, outfile=None, **kwargs):
 
     with GMTTempFile(suffix=".csv") as tmpfile:
         with Session() as lib:
-            table_context = lib.virtualfile_from_data(check_kind="vector", data=data)
+            table_context = lib.virtualfile_in(check_kind="vector", data=data)
             with table_context as infile:
                 if outfile is None:
                     outfile = tmpfile.name

pygmt/src/sph2grd.py

@@ -73,7 +73,7 @@ def sph2grd(data, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
+            file_context = lib.virtualfile_in(check_kind="vector", data=data)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/sphdistance.py

@@ -117,9 +117,7 @@ def sphdistance(data=None, x=None, y=None, **kwargs):
         raise GMTInvalidInput("Both 'region' and 'spacing' must be specified.")
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(
-                check_kind="vector", data=data, x=x, y=y
-            )
+            file_context = lib.virtualfile_in(check_kind="vector", data=data, x=x, y=y)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/sphinterpolate.py

@@ -67,7 +67,7 @@ def sphinterpolate(data, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
+            file_context = lib.virtualfile_in(check_kind="vector", data=data)
             with file_context as infile:
                 if (outgrid := kwargs.get("G")) is None:
                     kwargs["G"] = outgrid = tmpfile.name  # output to tmpfile

pygmt/src/surface.py

@@ -159,7 +159,7 @@ def surface(data=None, x=None, y=None, z=None, **kwargs):
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
         with Session() as lib:
-            file_context = lib.virtualfile_from_data(
+            file_context = lib.virtualfile_in(
                 check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
             )
             with file_context as infile:

pygmt/src/ternary.py

@@ -86,7 +86,7 @@ def ternary(self, data, alabel=None, blabel=None, clabel=None, **kwargs):
         data = data.to_numpy()
 
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(check_kind="vector", data=data)
+        file_context = lib.virtualfile_in(check_kind="vector", data=data)
         with file_context as infile:
             lib.call_module(
                 module="ternary",

pygmt/src/text.py

@@ -236,7 +236,7 @@ def text_(  # noqa: PLR0912
         )
 
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(
+        file_context = lib.virtualfile_in(
             check_kind="vector", data=textfiles, x=x, y=y, extra_arrays=extra_arrays
         )
         with file_context as fname:

pygmt/src/tilemap.py

@@ -163,7 +163,7 @@ def tilemap(
         kwargs["R"] = "/".join(str(coordinate) for coordinate in region)
 
     with Session() as lib:
-        file_context = lib.virtualfile_from_data(check_kind="raster", data=raster)
+        file_context = lib.virtualfile_in(check_kind="raster", data=raster)
         with file_context as infile:
             lib.call_module(
                 module="grdimage", args=build_arg_string(kwargs, infile=infile)

pygmt/src/triangulate.py

@@ -123,7 +123,7 @@ def _triangulate(
               ``outgrid`` or ``outfile``)
         """
         with Session() as lib:
-            table_context = lib.virtualfile_from_data(
+            table_context = lib.virtualfile_in(
                 check_kind="vector", data=data, x=x, y=y, z=z, required_z=False
             )
             with table_context as infile: