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**Deprecation**: clib.Session.virtualfile_from_vectors now takes only one argument #3522

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**Deprecation**: clib.Session.virtualfile_from_vectors now takes only one argument #3522

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29bd3f8
**Breaking**: clib.Session.virtualfile_from_vectors now takes only on…
seisman Oct 16, 2024
f5b0e8e
Backward compatible with the old way
seisman Oct 16, 2024
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51 changes: 31 additions & 20 deletions pygmt/clib/session.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1330,7 +1330,7 @@ def open_virtual_file(self, family, geometry, direction, data):
return self.open_virtualfile(family, geometry, direction, data)

@contextlib.contextmanager
def virtualfile_from_vectors(self, *vectors):
def virtualfile_from_vectors(self, vectors, *args):
"""
Store 1-D arrays as columns of a table inside a virtual file.

Expand Down Expand Up @@ -1372,13 +1372,24 @@ def virtualfile_from_vectors(self, *vectors):
>>> y = np.array([4, 5, 6])
>>> z = pd.Series([7, 8, 9])
>>> with Session() as ses:
... with ses.virtualfile_from_vectors(x, y, z) as fin:
... with ses.virtualfile_from_vectors((x, y, z)) as fin:
... # Send the output to a file so that we can read it
... with GMTTempFile() as fout:
... ses.call_module("info", [fin, f"->{fout.name}"])
... print(fout.read().strip())
<vector memory>: N = 3 <1/3> <4/6> <7/9>
"""
if len(args) > 0:
warnings.warn(
"Passing multiple arguments to Session.virtualfile_fro_vectors is "
"deprecated since v0.14.0 and will be unsupported in v0.16.0. "
"Pass all vectors as a single tuple instead, e.g., "
"Use `with lib.virtualfile_from_vectors((x, y, z)) as vfile` "
"instead of `with lib.virtualfile_from_vectors(x, y, z) as vfile`.",
category=FutureWarning,
stacklevel=3,
)
vectors = (vectors, *args)
# Conversion to a C-contiguous array needs to be done here and not in
# put_vector or put_strings because we need to maintain a reference to
# the copy while it is being used by the C API. Otherwise, the array
Expand Down Expand Up @@ -1791,19 +1802,19 @@ def virtualfile_in( # noqa: PLR0912
"vectors": self.virtualfile_from_vectors,
}[kind]

# Ensure the data is an iterable (Python list or tuple).
# "_data" is the data that will be passed to the _virtualfile_from function.
# "_data" defaults to "data" but should be adjusted for some cases.
_data = data
match kind:
case "arg" | "file" | "geojson" | "grid" | "image" | "stringio":
_data = (data,)
if kind == "image" and data.dtype != "uint8":
msg = (
f"Input image has dtype: {data.dtype} which is unsupported, "
"and may result in an incorrect output. Please recast image "
"to a uint8 dtype and/or scale to 0-255 range, e.g. "
"using a histogram equalization function like "
"skimage.exposure.equalize_hist."
)
warnings.warn(message=msg, category=RuntimeWarning, stacklevel=2)
case "image" if data.dtype != "uint8":
msg = (
f"Input image has dtype: {data.dtype} which is unsupported, "
"and may result in an incorrect output. Please recast image "
"to a uint8 dtype and/or scale to 0-255 range, e.g. "
"using a histogram equalization function like "
"skimage.exposure.equalize_hist."
)
warnings.warn(message=msg, category=RuntimeWarning, stacklevel=2)
case "empty": # data is None, so data must be given via x/y/z.
_data = [x, y]
if z is not None:
Expand All @@ -1818,19 +1829,19 @@ def virtualfile_in( # noqa: PLR0912
else:
# Python list, tuple, numpy.ndarray, and pandas.Series types
_data = np.atleast_2d(np.asanyarray(data).T)
case "matrix":
case "matrix" if data.dtype.kind not in "iuf":
# GMT can only accept a 2-D matrix which are signed integer (i),
# unsigned integer (u) or floating point (f) types. For other data
# types, we need to use virtualfile_from_vectors instead, which turns
# the matrix into a list of vectors and allows for better handling of
# non-integer/float type inputs (e.g. for string or datetime data types)
_data = (data,)
if data.dtype.kind not in "iuf":
_virtualfile_from = self.virtualfile_from_vectors
_data = data.T
_virtualfile_from = self.virtualfile_from_vectors
_data = data.T
case _:
pass

# Finally create the virtualfile from the data, to be passed into GMT
file_context = _virtualfile_from(*_data)
file_context = _virtualfile_from(_data)
return file_context

def virtualfile_from_data(
Expand Down
37 changes: 30 additions & 7 deletions pygmt/tests/test_clib_virtualfile_from_vectors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ def test_virtualfile_from_vectors(dtypes):
y = np.arange(size, size * 2, 1, dtype=dtype)
z = np.arange(size * 2, size * 3, 1, dtype=dtype)
with clib.Session() as lib:
with lib.virtualfile_from_vectors(x, y, z) as vfile:
with lib.virtualfile_from_vectors((x, y, z)) as vfile:
with GMTTempFile() as outfile:
lib.call_module("info", [vfile, f"->{outfile.name}"])
output = outfile.read(keep_tabs=True)
Expand All @@ -64,7 +64,7 @@ def test_virtualfile_from_vectors_one_string_or_object_column(dtype):
y = np.arange(size, size * 2, 1, dtype=np.int32)
strings = np.array(["a", "bc", "defg", "hijklmn", "opqrst"], dtype=dtype)
with clib.Session() as lib:
with lib.virtualfile_from_vectors(x, y, strings) as vfile:
with lib.virtualfile_from_vectors((x, y, strings)) as vfile:
with GMTTempFile() as outfile:
lib.call_module("convert", [vfile, f"->{outfile.name}"])
output = outfile.read(keep_tabs=True)
Expand All @@ -86,7 +86,7 @@ def test_virtualfile_from_vectors_two_string_or_object_columns(dtype):
strings1 = np.array(["a", "bc", "def", "ghij", "klmnolooong"], dtype=dtype)
strings2 = np.array(["pqrst", "uvwx", "yz!", "@#", "$"], dtype=dtype)
with clib.Session() as lib:
with lib.virtualfile_from_vectors(x, y, strings1, strings2) as vfile:
with lib.virtualfile_from_vectors((x, y, strings1, strings2)) as vfile:
with GMTTempFile() as outfile:
lib.call_module("convert", [vfile, f"->{outfile.name}"])
output = outfile.read(keep_tabs=True)
Expand All @@ -105,7 +105,7 @@ def test_virtualfile_from_vectors_transpose(dtypes):
for dtype in dtypes:
data = np.arange(shape[0] * shape[1], dtype=dtype).reshape(shape)
with clib.Session() as lib:
with lib.virtualfile_from_vectors(*data.T) as vfile:
with lib.virtualfile_from_vectors(data.T) as vfile:
with GMTTempFile() as outfile:
lib.call_module("info", [vfile, "-C", f"->{outfile.name}"])
output = outfile.read(keep_tabs=True)
Expand All @@ -122,7 +122,7 @@ def test_virtualfile_from_vectors_diff_size():
y = np.arange(6)
with clib.Session() as lib:
with pytest.raises(GMTInvalidInput):
with lib.virtualfile_from_vectors(x, y):
with lib.virtualfile_from_vectors((x, y)):
pass


Expand All @@ -143,7 +143,7 @@ def test_virtualfile_from_vectors_pandas(dtypes_pandas):
dtype=dtype,
)
with clib.Session() as lib:
with lib.virtualfile_from_vectors(data.x, data.y, data.z) as vfile:
with lib.virtualfile_from_vectors((data.x, data.y, data.z)) as vfile:
with GMTTempFile() as outfile:
lib.call_module("info", [vfile, f"->{outfile.name}"])
output = outfile.read(keep_tabs=True)
Expand All @@ -163,10 +163,33 @@ def test_virtualfile_from_vectors_arraylike():
y = tuple(range(size, size * 2, 1))
z = range(size * 2, size * 3, 1)
with clib.Session() as lib:
with lib.virtualfile_from_vectors(x, y, z) as vfile:
with lib.virtualfile_from_vectors((x, y, z)) as vfile:
with GMTTempFile() as outfile:
lib.call_module("info", [vfile, f"->{outfile.name}"])
output = outfile.read(keep_tabs=True)
bounds = "\t".join([f"<{min(i):.0f}/{max(i):.0f}>" for i in (x, y, z)])
expected = f"<vector memory>: N = {size}\t{bounds}\n"
assert output == expected


def test_virtualfile_from_vectors_args():
"""
Test the backward compatibility of the deprecated syntax for passing multiple
vectors.

This test is the same as test_virtualfile_from_vectors_arraylike, but using the
old syntax.
"""
size = 13
x = list(range(0, size, 1))
y = tuple(range(size, size * 2, 1))
z = range(size * 2, size * 3, 1)
with pytest.warns(FutureWarning, match="virtualfile_from_vectors"):
with clib.Session() as lib:
with lib.virtualfile_from_vectors(x, y, z) as vfile:
with GMTTempFile() as outfile:
lib.call_module("info", [vfile, f"->{outfile.name}"])
output = outfile.read(keep_tabs=True)
bounds = "\t".join([f"<{min(i):.0f}/{max(i):.0f}>" for i in (x, y, z)])
expected = f"<vector memory>: N = {size}\t{bounds}\n"
assert output == expected