Remove deprecated codes after dropping GMT 6.4 support (#4128)

Author: seisman

pygmt/figure.py

@@ -269,12 +269,6 @@ def savefig(
         kwargs.pop("metadata", None)
         self.psconvert(prefix=prefix, fmt=fmts[ext], crop=crop, **kwargs)
 
-        # TODO(GMT>=6.5.0): Remove the workaround for upstream bug in GMT<6.5.0.
-        # Remove the .pgw world file if exists. Not necessary after GMT 6.5.0.
-        # See upstream fix https://github.com/GenericMappingTools/gmt/pull/7865
-        if ext == "tiff":
-            fname.with_suffix(".pgw").unlink(missing_ok=True)
-
         # Rename if file extension doesn't match the input file suffix.
         if ext != suffix[1:]:
             fname.with_suffix("." + ext).rename(fname)

pygmt/src/ternary.py

@@ -5,11 +5,9 @@
 from collections.abc import Sequence
 from typing import Literal
 
-import pandas as pd
-from packaging.version import Version
 from pygmt._typing import PathLike, TableLike
 from pygmt.alias import Alias, AliasSystem
-from pygmt.clib import Session, __gmt_version__
+from pygmt.clib import Session
 from pygmt.helpers import build_arg_list, fmt_docstring, kwargs_to_strings, use_alias
 
 
@@ -107,11 +105,6 @@ def ternary(
     )
     aliasdict.merge(kwargs)
 
-    # TODO(GMT>=6.5.0): Remove the patch for upstream bug fixed in GMT 6.5.0.
-    # See https://github.com/GenericMappingTools/pygmt/pull/2138
-    if Version(__gmt_version__) < Version("6.5.0") and isinstance(data, pd.DataFrame):
-        data = data.to_numpy()
-
     with Session() as lib:
         with lib.virtualfile_in(check_kind="vector", data=data) as vintbl:
             lib.call_module(

pygmt/src/timestamp.py

@@ -5,10 +5,9 @@
 import warnings
 from collections.abc import Sequence
 
-from packaging.version import Version
 from pygmt._typing import AnchorCode
 from pygmt.alias import Alias, AliasSystem
-from pygmt.clib import Session, __gmt_version__
+from pygmt.clib import Session
 from pygmt.helpers import build_arg_list
 
 __doctest_skip__ = ["timestamp"]
@@ -52,8 +51,7 @@ def timestamp(
     font
         Font of the timestamp and the optional label. Since the GMT logo has a fixed
         height, the font sizes are fixed to be 8-point for the timestamp and 7-point for
-        the label. The parameter can't change the font color for GMT<=6.4.0, only the
-        font style.
+        the label.
     timefmt
         Format string for the UNIX timestamp. The format string is parsed by the C
         function ``strftime``, so that virtually any text can be used (even not
@@ -84,20 +82,6 @@ def timestamp(
         warnings.warn(message=msg, category=RuntimeWarning, stacklevel=2)
         text = str(text)[:64]
 
-    # TODO(GMT>=6.5.0): Remove the patch for upstream "offset" bug fixed in GMT 6.5.0.
-    # TODO(GMT>=6.5.0): Remove the workaround for the '+t' modifier added in GMT 6.5.0.
-    # Related issues:
-    # - https://github.com/GenericMappingTools/gmt/issues/7107
-    # - https://github.com/GenericMappingTools/gmt/pull/7127
-    if Version(__gmt_version__) < Version("6.5.0"):
-        if "/" not in str(offset):  # Giving a single offset doesn't work in GMT<6.5.0
-            offset = f"{offset}/{offset}"
-        if text is not None:
-            # Workaround for GMT<6.5.0 by overriding the 'timefmt' parameter and
-            # unsetting 'text'.
-            timefmt = str(text)
-            text = None
-
     aliasdict = AliasSystem(
         U=[
             Alias(label, name="label"),

pygmt/tests/test_binstats.py

@@ -6,9 +6,7 @@
 
 import numpy.testing as npt
 import pytest
-from packaging.version import Version
 from pygmt import binstats
-from pygmt.clib import __gmt_version__
 from pygmt.enums import GridRegistration, GridType
 from pygmt.helpers import GMTTempFile
 
@@ -53,11 +51,6 @@ def test_binstats_no_outgrid():
     npt.assert_allclose(temp_grid.mean(), 4227489)
 
 
-# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.
-@pytest.mark.xfail(
-    condition=Version(__gmt_version__) < Version("6.5.0"),
-    reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/8243",
-)
 def test_binstats_quantile():
     """
     Test binstats quantile statistic functionality.

pygmt/tests/test_meca.py

@@ -7,9 +7,7 @@
 import numpy as np
 import pandas as pd
 import pytest
-from packaging.version import Version
 from pygmt import Figure
-from pygmt.clib import __gmt_version__
 from pygmt.exceptions import GMTInvalidInput, GMTValueError
 from pygmt.helpers import GMTTempFile
 
@@ -143,21 +141,10 @@ def test_meca_spec_multiple_focalmecha(inputtype):
     return fig
 
 
-# TODO(GMT>=6.5.0): Remove the skipif condition for GMT>=6.5.0.
 @pytest.mark.mpl_image_compare(filename="test_meca_offset.png")
 @pytest.mark.parametrize(
     "inputtype",
-    [
-        "args",
-        "dict",
-        pytest.param(
-            "ndarray",
-            marks=pytest.mark.skipif(
-                condition=Version(__gmt_version__) < Version("6.5.0"),
-                reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/7557",
-            ),
-        ),
-    ],
+    ["args", "dict", "ndarray"],
 )
 def test_meca_offset(inputtype):
     """
@@ -202,22 +189,10 @@ def test_meca_offset(inputtype):
     return fig
 
 
-# TODO(GMT>=6.5.0): Remove the skipif marker for GMT>=6.5.0.
-# Passing event names via pandas doesn't work for GMT<=6.4.
-# See https://github.com/GenericMappingTools/pygmt/issues/2524.
 @pytest.mark.mpl_image_compare(filename="test_meca_eventname.png")
 @pytest.mark.parametrize(
     "inputtype",
-    [
-        "args",
-        pytest.param(
-            "dataframe",
-            marks=pytest.mark.skipif(
-                condition=Version(__gmt_version__) < Version("6.5.0"),
-                reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/7557",
-            ),
-        ),
-    ],
+    ["args", "dataframe"],
 )
 def test_meca_eventname(inputtype):
     """

pygmt/tests/test_subplot.py

@@ -104,9 +104,7 @@ def test_subplot_nrows_ncols_less_than_one_error():
             pass
 
 
-# Increase tolerance for compatibility with GMT 6.4, see
-# https://github.com/GenericMappingTools/pygmt/pull/2454
-@pytest.mark.mpl_image_compare(tolerance=4.0)
+@pytest.mark.mpl_image_compare()
 def test_subplot_outside_plotting_positioning():
     """
     Plotting calls are correctly positioned after exiting subplot.

pygmt/tests/test_x2sys_cross.py

@@ -12,9 +12,7 @@
 import numpy.testing as npt
 import pandas as pd
 import pytest
-from packaging.version import Version
 from pygmt import config, x2sys_cross, x2sys_init
-from pygmt.clib import __gmt_version__
 from pygmt.datasets import load_sample_data
 from pygmt.exceptions import GMTTypeError
 
@@ -38,12 +36,7 @@ def fixture_tracks():
     return [dataframe.query(expr="z > -20")]  # reduce size of dataset
 
 
-# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.
 @pytest.mark.usefixtures("mock_x2sys_home")
-@pytest.mark.xfail(
-    condition=Version(__gmt_version__) < Version("6.5.0"),
-    reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/8188",
-)
 def test_x2sys_cross_input_file_output_file():
     """
     Run x2sys_cross by passing in a filename, and output internal crossovers to an ASCII
@@ -68,12 +61,7 @@ def test_x2sys_cross_input_file_output_file():
         npt.assert_allclose(result["i_1"].max(), 82945.9370, rtol=1.0e-4)
 
 
-# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.
 @pytest.mark.usefixtures("mock_x2sys_home")
-@pytest.mark.xfail(
-    condition=Version(__gmt_version__) < Version("6.5.0"),
-    reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/8188",
-)
 def test_x2sys_cross_input_file_output_dataframe():
     """
     Run x2sys_cross by passing in a filename, and output internal crossovers to a
@@ -247,12 +235,7 @@ def test_x2sys_cross_invalid_tracks_input_type(tracks):
         x2sys_cross(tracks=[invalid_tracks])
 
 
-# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.
 @pytest.mark.usefixtures("mock_x2sys_home")
-@pytest.mark.xfail(
-    condition=Version(__gmt_version__) < Version("6.5.0"),
-    reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/8188",
-)
 def test_x2sys_cross_region_interpolation_numpoints():
     """
     Test that x2sys_cross's region (R), interpolation (l) and numpoints (W) arguments
@@ -283,12 +266,7 @@ def test_x2sys_cross_region_interpolation_numpoints():
             npt.assert_allclose(output.z_M.mean(), -2896.875915, rtol=1e-4)
 
 
-# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.
 @pytest.mark.usefixtures("mock_x2sys_home")
-@pytest.mark.xfail(
-    condition=Version(__gmt_version__) < Version("6.5.0"),
-    reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/8188",
-)
 def test_x2sys_cross_trackvalues():
     """
     Test that x2sys_cross's trackvalues (Z) argument work.

pygmt/tests/test_xarray_accessor.py

@@ -3,14 +3,11 @@
 """
 
 import importlib
-import sys
 from pathlib import Path
 
 import pytest
 import xarray as xr
-from packaging.version import Version
 from pygmt import which
-from pygmt.clib import __gmt_version__
 from pygmt.datasets import load_earth_relief
 from pygmt.enums import GridRegistration, GridType
 from pygmt.exceptions import GMTValueError
@@ -113,12 +110,7 @@ def test_xarray_accessor_set_invalid_registration_and_gtype():
         grid.gmt.gtype = "geographic"
 
 
-# TODO(GMT>=6.5.0): Remove the xfail marker for GMT>=6.5.0.
 @pytest.mark.skipif(condition=not _HAS_NETCDF4, reason="netCDF4 is not installed")
-@pytest.mark.xfail(
-    condition=sys.platform == "win32" and Version(__gmt_version__) < Version("6.5.0"),
-    reason="Upstream bug fixed in https://github.com/GenericMappingTools/gmt/pull/7573",
-)
 def test_xarray_accessor_sliced_datacube():
     """
     Check that a 2-D grid which is sliced from an n-dimensional datacube works with