Drop support of old versions and removed deprecated codes for v0.16.0

[seisman]

Following our quarterly release plan, we expect to release v0.16.0 in June 2025. As per the SPEC0 policy, we should

• Remove deprecated codes for PyGMT v0.16.0 [Session.virtualfile_from_vectors: Remove the deprecated '*args' parameter [deprecated since v0.14.0] #3893]
• Bump to NumPy>=1.26 [SPEC 0: Bump minimum supported versions to NumPy 1.26 #3916]
• Bump to pandas>=2.1 [SPEC 0: Bump minimum supported version to pandas>=2.1 #3895]
• Bump to xarray>=2023.7 [SPEC 0: Bump minimum supported version to xarray>=2023.07 #3918]

As for optional dependencies, we agreed to "maintain support for optional dependencies for at least 1 year after their initial release.". So we also need to decide if we want to drop these optional dependencies:

• Bump to contextily>=1.5. https://github.com/geopandas/contextily/tags. v1.4 was released in Oct. 2023 and v1.5 in Dec. 2023. Bump minimum supported version to contextily>=1.5 #3912
• Bump to GeoPandas>=1.0. https://geopandas.org/en/stable/docs/changelog.html. 0.14.4 was released in April, 2024, v1.0 in June, 2024. Bump minimum supported version to geopandas>=1.0 #3908
• Bump to pyarrow>=16. https://arrow.apache.org/release/. v15 was released in Mar. 2024 and v16 in Apr. 2024. Bump minimum supported version to pyarrow>=16 #3917

Here are the related TODO comments:

pygmt/clib/conversion.py:        # TODO(pandas>=2.1): Remove the workaround for pandas<2.1.
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(pandas>=2.1): Simplify the if-else statement.
pygmt/clib/session.py:        # TODO(PyGMT>=0.16.0): Remove the "*args" parameter and related codes.
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/datasets/tile_map.py:    # TODO(contextily>=1.5.0): Remove the check for the 'zoom_adjust' parameter.
pygmt/helpers/tempfile.py:            # TODO(GeoPandas>=1.0): Remove the workaround for GeoPandas < 1.
pygmt/tests/test_clib_to_numpy.py:            # TODO(pyarrow>=16): Remove the skipif marker for pyarrow<16.

[weiji14]

• Bump to contextily>=1.5. https://github.com/geopandas/contextily/tags. v1.4 was released in Oct. 2023 and v1.5 in Dec. 2023.

Sounds fair, this would allow us to remove the note here:

pygmt/pygmt/src/tilemap.py

Lines 106 to 107 in fd92fb7

	.. note::
	The ``zoom_adjust`` parameter requires ``contextily>=1.5.0``.

• Bump to GeoPandas>=1.0. https://geopandas.org/en/stable/docs/changelog.html. 0.14.4 was released in April, 2024, v1.0 in June, 2024.

Agree. The PR at #3639 is currently failing with an AttributeError: module 'fiona' has no attribute 'path' error, which I think should be resolved with geopandas>1.0 that switched to pyogrio as the default backend engine.

• Bump to pyarrow>=16. https://arrow.apache.org/release/. v15 was released in Mar. 2024 and v16 in Apr. 2024.

Yep, this means we won't need to add pytest.mark.skipif as mentioned at #3639 (comment).