pylint 2.7.0 breaks the style check

[seisman]

Description of the problem

See the "Style Checks" runs in #944 for details.

[weiji14]

Lots of duplicate-code recommendations in the error message log:

pylint pygmt setup.py doc/conf.py
************* Module conf
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.src.plot3d:166
==pygmt.src.plot:203
    extra_arrays = []
    if "S" in kwargs and kwargs["S"][0] in "vV" and direction is not None:
        extra_arrays.extend(direction)
    if "G" in kwargs and not isinstance(kwargs["G"], str):
        if kind != "vectors":
            raise GMTInvalidInput(
                "Can't use arrays for color if data is matrix or file."
            )
        extra_arrays.append(kwargs["G"])
        del kwargs["G"]
    if sizes is not None:
        if kind != "vectors":
            raise GMTInvalidInput(
                "Can't use arrays for sizes if data is matrix or file."
            )
        extra_arrays.append(sizes)

    if "t" in kwargs and is_nonstr_iter(kwargs["t"]):
        extra_arrays.append(kwargs["t"])
        kwargs["t"] = ""

    with Session() as lib:
        # Choose how data will be passed in to the module
        if kind == "file":
            file_context = dummy_context(data)
        elif kind == "matrix":
            file_context = lib.virtualfile_from_matrix(data)
        elif kind == "vectors":
            file_context = lib.virtualfile_from_vectors( (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.tests.test_contour:12
==pygmt.tests.test_plot:16
TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), "data")
POINTS_DATA = os.path.join(TEST_DATA_DIR, "points.txt")


@pytest.fixture(scope="module")
def data():
    """
    Load the point data from the test file.
    """
    return np.loadtxt(POINTS_DATA)


@pytest.fixture(scope="module")
def region():
    """
    The data region.
    """
    return [10, 70, -5, 10]

 (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.src.plot3d:3
==pygmt.src.plot:3
import numpy as np
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    is_nonstr_iter,
    kwargs_to_strings,
    use_alias,
)


@fmt_docstring
@use_alias(
    A="straight_line",
    B="frame",
    C="cmap",
    D="offset", (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.src.contour:4
==pygmt.src.grdcontour:3
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    kwargs_to_strings,
    use_alias,
)


@fmt_docstring
@use_alias(
    A="annotation",
    B="frame", (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 3 files
==pygmt.src.plot3d:3
==pygmt.src.plot:3
==pygmt.src.text:3
import numpy as np
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    is_nonstr_iter,
    kwargs_to_strings,
    use_alias,
)


@fmt_docstring
@use_alias( (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.src.grdcut:90
==pygmt.src.grdfilter:143
    kind = data_kind(grid)

    with GMTTempFile(suffix=".nc") as tmpfile:
        with Session() as lib:
            if kind == "file":
                file_context = dummy_context(grid)
            elif kind == "grid":
                file_context = lib.virtualfile_from_grid(grid)
            else:
                raise GMTInvalidInput("Unrecognized data type: {}".format(type(grid)))

            with file_context as infile:
                if "G" not in kwargs.keys():  # if outgrid is unset, output to tempfile
                    kwargs.update({"G": tmpfile.name})
                outgrid = kwargs["G"]
                arg_str = " ".join([infile, build_arg_string(kwargs)]) (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.src.grdcut:4
==pygmt.src.grdfilter:4
import xarray as xr
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    GMTTempFile,
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    kwargs_to_strings,
    use_alias,
)


@fmt_docstring
@use_alias( (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.src.basemap:4
==pygmt.src.coast:4
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    args_in_kwargs,
    build_arg_string,
    fmt_docstring,
    kwargs_to_strings,
    use_alias,
)


@fmt_docstring
@use_alias(
    R="region",
    J="projection", (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 3 files
==pygmt.src.grdcut:5
==pygmt.src.grdfilter:5
==pygmt.src.grdinfo:3
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    GMTTempFile,
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    kwargs_to_strings,
    use_alias,
)


@fmt_docstring
@use_alias( (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 3 files
==pygmt.src.grdcut:4
==pygmt.src.grdfilter:4
==pygmt.src.surface:4
import xarray as xr
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    GMTTempFile,
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    kwargs_to_strings,
    use_alias,
)


@fmt_docstring (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.src.grdview:7
==pygmt.src.meca:8
from pygmt.helpers import (
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    kwargs_to_strings,
    use_alias,
)


@fmt_docstring
@use_alias(
    R="region",
    J="projection", (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 5 files
==pygmt.src.contour:4
==pygmt.src.grd2cpt:4
==pygmt.src.grdcontour:3
==pygmt.src.grdimage:3
==pygmt.src.grdview:5
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    kwargs_to_strings,
            file_context = dummy_context(data)
        elif kind == "matrix":
            file_context = lib.virtualfile_from_matrix(data)
        elif kind == "vectors": (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.tests.test_clib:7
==pygmt.tests.test_info:5
import numpy as np
import numpy.testing as npt
import pandas as pd
import pytest
import xarray as xr (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 7 files
==pygmt.src.contour:7
==pygmt.src.grd2cpt:7
==pygmt.src.grdcontour:6
==pygmt.src.grdimage:6
==pygmt.src.grdview:8
==pygmt.src.meca:9
==pygmt.x2sys:12
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring,
    kwargs_to_strings, (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 4 files
==pygmt.src.meca:8
==pygmt.src.plot3d:6
==pygmt.src.plot:6
==pygmt.src.text:6
from pygmt.helpers import (
    build_arg_string,
    data_kind,
    dummy_context,
    fmt_docstring, (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 9 files
==pygmt.src.contour:4
==pygmt.src.grd2cpt:4
==pygmt.src.grdcontour:3
==pygmt.src.grdimage:3
==pygmt.src.grdview:5
==pygmt.src.legend:4
==pygmt.src.plot3d:4
==pygmt.src.plot:4
==pygmt.src.text:4
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
    build_arg_string,
    data_kind, (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 3 files
==pygmt.src.colorbar:8
==pygmt.src.meca:18
==pygmt.src.text:17
@fmt_docstring
@use_alias(
    R="region",
    J="projection",
    B="frame", (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 2 files
==pygmt.src.contour:27
==pygmt.src.text:26
    V="verbose",
    W="pen",
    X="xshift",
    Y="yshift",
    c="panel", (duplicate-code)
doc/conf.py:1:0: R0801: Similar lines in 3 files
==pygmt.src.basemap:25
==pygmt.src.coast:30
==pygmt.src.logo:15
    U="timestamp",
    V="verbose",
    X="xshift",
    Y="yshift",
    c="panel", (duplicate-code)

------------------------------------
Your code has been rated at 10.00/10

make: *** [Makefile:54: lint] Error 8
Error: Process completed with exit code 2.

The docs at http://pylint.pycqa.org/en/2.7/technical_reference/features.html#similarities-checker-messages says:

Similar lines in %s files Indicates that a set of similar lines has been detected among multiple file. This usually means that the code should be refactored to avoid this duplication.

So we should tweak our .pylintrc file a bit following https://stackoverflow.com/questions/29206482/pylint-duplicate-code-false-positive (using ignore-imports=yes should fix most warnings).

Also take this as a cue to refactor some of the duplicate code. I was going to create a virtualfile_from_data() function to replace this common block of code in our functions:

    with Session() as lib:
        # Choose how data will be passed in to the module
        if kind == "file":
            file_context = dummy_context(data)
        elif kind == "matrix":
            file_context = lib.virtualfile_from_matrix(data)
        elif kind == "vectors":
            file_context = lib.virtualfile_from_vectors()

[seisman]

Still a lot of warnings after setting ignore-imports=yes. Perhaps better to disable duplicate-code and try to refactor later.

[weiji14]

Yes, I'll open a separate issue for refactoring. Do you want to go ahead and update .pylintrc?