Add isort to sort imports alphabetically

[seisman]

Description of proposed changes

This PR adds isort to automatically sort imports.

Notes:

• profile = "black" is added to pyproject.toml for compatibility between black and isort, which requires isort>=5
• pylint also depends on isort. Thus when we install pylint, isort is already installed.

References:

• https://black.readthedocs.io/en/stable/compatible_configs.html#isort
• https://pycqa.github.io/isort/docs/configuration/profiles/

Reminders

• Run make format and make check to make sure the code follows the style guide.
• Add tests for new features or tests that would have caught the bug that you're fixing.
• Add new public functions/methods/classes to doc/api/index.rst.
• Write detailed docstrings for all functions/methods.
• If adding new functionality, add an example to docstrings or tutorials.

Notes

• You can write /format in the first line of a comment to lint the code automatically

[weiji14]

I've used isort and quite like it, but I've found different isort versions to apply the sort styles rather inconsistently (specifically the standard lib/firstparty/thirdparty sections, see https://pycqa.github.io/isort/#custom-sections-and-ordering). Does this "black" profile keep things simple?

[seisman]

Does this "black" profile keep things simple?

No, profile = "black" is equivalent to the following settings:

multi_line_output: 3
include_trailing_comma: True
force_grid_wrap: 0
use_parentheses: True
ensure_newline_before_comments: True
line_length: 88

As for section orders, the default order (https://pycqa.github.io/isort/docs/configuration/options/#sections) is:

('FUTURE', 'STDLIB', 'THIRDPARTY', 'FIRSTPARTY', 'LOCALFOLDER')

Do you mean the default values change in different isort versions?

[weiji14]

I think there was a point where they separated well known third-party libaries (e.g. numpy and pandas) from other third-party libraries. Maybe that has changed now with newer isort versions, but I'm not too sure.

Do you think we should add other configuration options? I'm looking at xarray's at pydata/xarray#4518 and they have some extra ones besides black.

[seisman]

OK, I will look at these options later.

[seisman]

Most of our examples import some of the four packages: pygmt, numpy, pandas and xarray.

Currently, isort sorts them like

import numpy as np
import pandas as pd
import xarray as xr

import pygmt

because numpy, pandas, and xarray are known third-party packages, and pygmt is first-party package (not sure if I understand it correctly).

I don't think I like it. We can add options:

known_third_party = "pygmt"
force_to_top = "pygmt

so that they will be sorted like:

import pygmt
import numpy as np
import pandas as pd
import xarray as xr

[seisman]

After reading through all the isort options, I added the following ones to pyproject.toml, similar to pydata/xarray#4518:

skip_gitignore = true
force_to_top = "pygmt"
known_third_party = "pygmt"

the only exception is default_section = THIRDPARTY, as I don't understand what it is, and adding it doesn't change the codes at all.

[seisman]

I have to remove force_to_top, otherwise pylint will complain.