Use TODO comments to track deprecations and workarounds

[seisman]

Description of proposed changes

See #3705 for context.

A simple grep to find all TODOs:

$ grep '# TODO' **/*.py
pygmt/clib/conversion.py:    # TODO(pandas>=2.2): Remove the workaround for pandas<2.2.
pygmt/clib/session.py:            # TODO(GMT>6.5.0): Remove the workaround for upstream bug in GMT<=6.5.0.
pygmt/clib/session.py:    # TODO(PyGMT>=0.15.0): Remove the deprecated open_virtual_file method.
pygmt/clib/session.py:        # TODO(PyGMT>=0.16.0): Remove the "*args" parameter and related codes.
pygmt/clib/session.py:    # TODO(PyGMT>=0.15.0): Remove the deprecated virtualfile_from_data method.
pygmt/conftest.py:# TODO(NumPy>=2.0): Remove the conftest.py file.
pygmt/datasets/tile_map.py:    # TODO(contextily>=1.5.0): Remove the check for the 'zoom_adjust' parameter.
pygmt/figure.py:        # TODO(GMT>=6.5.0): Remve the workaround for upstream bug in GMT<6.5.0.
pygmt/helpers/tempfile.py:            # TODO(GeoPandas>=1.0): Remove the workaround for GeoPandas < 1.
pygmt/src/ternary.py:    # TODO(GMT>=6.5.0): Remove the patch for upstream bug fixed in GMT 6.5.0.
pygmt/src/timestamp.py:    # TODO(GMT>=6.5.0): Remove the patch for upstream bug fixed in GMT 6.5.0.
pygmt/src/timestamp.py:        # TODO(GMT>=6.5.0): Remove the workaround for the new '+t' modifier.
pygmt/tests/test_accessor.py:# TODO(GMT>=6.5.0): Remove the xfail marker for GMT>=6.5.0.
pygmt/tests/test_clib_to_numpy.py:        # TODO(NumPy>=2.0): Remove the if-else statement after NumPy>=2.0.
pygmt/tests/test_clib_to_numpy.py:    # TODO(pandas>=2.2): Remove the workaround for float16 dtype in pandas<2.2.
pygmt/tests/test_clib_to_numpy.py:    # TODO(pandas>=2.2): Remove the workaround for float16 dtype in pandas<2.2.
pygmt/tests/test_clib_to_numpy.py:                # TODO(pandas>=2.1): Remove the skipif marker for pandas<2.1.
pygmt/tests/test_clib_to_numpy.py:            # TODO(pyarrow>=16): Remove the skipif marker for pyarrow<16.
pygmt/tests/test_clib_virtualfile_from_vectors.py:# TODO(PyGMT>=0.16.0): Remove this test in PyGMT v0.16.0 in which the "*args" parameter
pygmt/tests/test_clib_virtualfile_in.py:# TODO(GMT>6.5.0): Remove the xfail marker for GMT<=6.5.0.
pygmt/tests/test_clib_virtualfile_in.py:# TODO(PyGMT>=0.16.0): Remove this test in PyGMT v0.16.0 in which the old usage of
pygmt/tests/test_clib_virtualfiles.py:# TODO(PyGMT>=0.15.0): Remove the test after removing the deprecated open_virtual_file
pygmt/tests/test_datasets_earth_relief.py:# TODO(GMT X.Y.Z): Upstream bug which is not fixed yet.
pygmt/tests/test_grdimage.py:# TODO(GMT>6.5.0): Remove the xfail marker for GMT<=6.5.0.
pygmt/tests/test_meca.py:# TODO(GMT>=6.5.0): Remove the skipif condition for GMT>=6.5.0.
pygmt/tests/test_meca.py:# TODO(GMT>=6.5.0): Remove the skipif marker for GMT>=6.5.0.
pygmt/tests/test_x2sys_cross.py:# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.
pygmt/tests/test_x2sys_cross.py:# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.
pygmt/tests/test_x2sys_cross.py:# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.
pygmt/tests/test_x2sys_cross.py:# TODO(GMT>=6.5.0): Remove the xfail marker for the upstream bug fixed in GMT 6.5.0.