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NF: Add keyword_only decorator to enforce keyword-only arguments (fur…
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…y-gl#888)

* parent 4baa99d
author WassCodeur <[email protected]> 1716302141 +0000
committer WassCodeur <[email protected]> 1717549770 +0000

NF: Add keyword_only decorator to enforce keyword-only arguments

RF: Refactor keyword-only  code and Add keyword-only arguments to functions

TEST: Add test for keyword_only" decorator

Refactor code to use keyword-only arguments in several functions

NF: remove some doctest and add a short comment on line 111 to explain what the loop does in fury/decorators.py

RF: Refactor keyword-only  code and Add keyword-only arguments to functions

Refactor code to use keyword-only arguments in several functions

* NF: Add keyword_only decorator to enforce keyword-only arguments

* NF: Add keyword_only decorator to enforce keyword-only arguments

* RF: Refactor keyword-only  code and Add keyword-only arguments to functions

* TEST: Add test for keyword_only" decorator

* Refactor interactor.py and molecular.py

* RF: Rename and update decorator for version checks

- Renamed `keyword-only` decorator to `warn_on_args_to_kwargs` for greater clarity.
- Updated `warn_on_args_to_kwargs` to include version parameters `from_version` and `until_version`.
- Added logic to raise a RuntimeError if the current version of FURY_VERSION is greater than `until_version`.
- Moved `__version__` definition to a new `fury/version.py` module to avoid circular import problems.
- Updated all functions using the decorator to reflect the new name and parameters.
- Adjusted import declarations and ensured compatibility across the code base.

* RF: Refactor the code by removing version constraints in the call to the warn_on_args_to_kwargs decorator

* RF: Refactor warn_on_args_to_kwargs  code and Add warn_on_args_to_kwargs arguments to functions in window.py and actor.py

* RF: update the version checks in the decorator: warn_on_args_to_kwargs and update the unittest

* RF: warn_on_args_to_kwargs decorator

parent 4baa99d
author WassCodeur <[email protected]> 1716302141 +0000
committer WassCodeur <[email protected]> 1717549770 +0000

NF: Add keyword_only decorator to enforce keyword-only arguments

RF: Refactor keyword-only  code and Add keyword-only arguments to functions

TEST: Add test for keyword_only" decorator

Refactor code to use keyword-only arguments in several functions

NF: remove some doctest and add a short comment on line 111 to explain what the loop does in fury/decorators.py

RF: Refactor keyword-only  code and Add keyword-only arguments to functions

Refactor code to use keyword-only arguments in several functions

NF: Add keyword_only decorator to enforce keyword-only arguments

RF: Refactor keyword-only  code and Add keyword-only arguments to functions

Refactor interactor.py and molecular.py

RF: Rename and update decorator for version checks

- Renamed `keyword-only` decorator to `warn_on_args_to_kwargs` for greater clarity.
- Updated `warn_on_args_to_kwargs` to include version parameters `from_version` and `until_version`.
- Added logic to raise a RuntimeError if the current version of FURY_VERSION is greater than `until_version`.
- Moved `__version__` definition to a new `fury/version.py` module to avoid circular import problems.
- Updated all functions using the decorator to reflect the new name and parameters.
- Adjusted import declarations and ensured compatibility across the code base.

RF: update the version checks in the decorator: warn_on_args_to_kwargs and update the unittest

RF: warn_on_args_to_kwargs decorator
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@WassCodeur
WassCodeur committed Jul 11, 2024
1 parent 7651a24 commit bea3c6c
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Showing 42 changed files with 1,393 additions and 463 deletions.
259 changes: 182 additions & 77 deletions fury/actor.py
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4 changes: 2 additions & 2 deletions fury/actors/odf_slicer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -254,14 +254,14 @@ def _generate_color_for_vertices(self, sf):
if self.colormap is None:
raise IOError("if global_cm=True, colormap must be defined.")
else:
all_colors = create_colormap(sf.ravel(), self.colormap) * 255
all_colors = create_colormap(sf.ravel(), name=self.colormap) * 255
elif self.colormap is not None:
if isinstance(self.colormap, str):
# Map ODFs values [min, max] to [0, 1] for each ODF
range_sf = sf.max(axis=-1) - sf.min(axis=-1)
rescaled = sf - sf.min(axis=-1, keepdims=True)
rescaled[range_sf > 0] /= range_sf[range_sf > 0][..., None]
all_colors = create_colormap(rescaled.ravel(), self.colormap) * 255
all_colors = create_colormap(rescaled.ravel(), name=self.colormap) * 255
else:
all_colors = np.tile(
np.array(self.colormap).reshape(1, 3),
Expand Down
28 changes: 19 additions & 9 deletions fury/colormap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
from scipy import linalg

from fury.data import DATA_DIR
from fury.decorators import warn_on_args_to_kwargs
from fury.lib import LookupTable

# Allow import, but disable doctests if we don't have matplotlib
Expand All @@ -14,7 +15,9 @@
cm, have_matplotlib, _ = optional_package("matplotlib.cm")


@warn_on_args_to_kwargs()
def colormap_lookup_table(
*,
scale_range=(0, 1),
hue_range=(0.8, 0),
saturation_range=(1, 1),
Expand Down Expand Up @@ -242,7 +245,8 @@ def orient2rgb(v):
return orient


def line_colors(streamlines, cmap="rgb_standard"):
@warn_on_args_to_kwargs()
def line_colors(streamlines, *, cmap="rgb_standard"):
"""Create colors for streamlines to be used in actor.line.
Parameters
Expand Down Expand Up @@ -308,7 +312,8 @@ def simple_cmap(v):
return simple_cmap


def create_colormap(v, name="plasma", auto=True):
@warn_on_args_to_kwargs()
def create_colormap(v, *, name="plasma", auto=True):
"""Create colors from a specific colormap and return it
as an array of shape (N,3) where every row gives the corresponding
r,g,b value. The colormaps we use are similar with those of matplotlib.
Expand Down Expand Up @@ -511,7 +516,8 @@ def _lab2rgb(lab):
return _xyz2rgb(tmp)


def distinguishable_colormap(bg=(0, 0, 0), exclude=None, nb_colors=None):
@warn_on_args_to_kwargs()
def distinguishable_colormap(*, bg=(0, 0, 0), exclude=None, nb_colors=None):
"""Generate colors that are maximally perceptually distinct.
This function generates a set of colors which are distinguishable
Expand Down Expand Up @@ -903,7 +909,8 @@ def get_xyz_coords(illuminant, observer):
) from err


def xyz2lab(xyz, illuminant="D65", observer="2"):
@warn_on_args_to_kwargs()
def xyz2lab(xyz, *, illuminant="D65", observer="2"):
"""XYZ to CIE-LAB color space conversion.
Parameters
Expand Down Expand Up @@ -950,7 +957,8 @@ def xyz2lab(xyz, illuminant="D65", observer="2"):
return np.concatenate([x[..., np.newaxis] for x in [L, a, b]], axis=-1)


def lab2xyz(lab, illuminant="D65", observer="2"):
@warn_on_args_to_kwargs()
def lab2xyz(lab, *, illuminant="D65", observer="2"):
"""CIE-LAB to XYZcolor space conversion.
Parameters
Expand Down Expand Up @@ -1001,7 +1009,8 @@ def lab2xyz(lab, illuminant="D65", observer="2"):
return out


def rgb2lab(rgb, illuminant="D65", observer="2"):
@warn_on_args_to_kwargs()
def rgb2lab(rgb, *, illuminant="D65", observer="2"):
"""Conversion from the sRGB color space (IEC 61966-2-1:1999)
to the CIE Lab colorspace under the given illuminant and observer.
Expand All @@ -1028,10 +1037,11 @@ def rgb2lab(rgb, illuminant="D65", observer="2"):
This implementation might have been modified.
"""
return xyz2lab(rgb2xyz(rgb), illuminant, observer)
return xyz2lab(rgb2xyz(rgb), illuminant=illuminant, observer=observer)


def lab2rgb(lab, illuminant="D65", observer="2"):
@warn_on_args_to_kwargs()
def lab2rgb(lab, *, illuminant="D65", observer="2"):
"""Lab to RGB color space conversion.
Parameters
Expand All @@ -1057,4 +1067,4 @@ def lab2rgb(lab, illuminant="D65", observer="2"):
This implementation might have been modified.
"""
return xyz2rgb(lab2xyz(lab, illuminant, observer))
return xyz2rgb(lab2xyz(lab, illuminant=illuminant, observer=observer))
10 changes: 8 additions & 2 deletions fury/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,13 @@

import numpy as np

from fury.decorators import warn_on_args_to_kwargs
from fury.io import load_image


@warn_on_args_to_kwargs()
def matplotlib_figure_to_numpy(
fig, dpi=100, fname=None, flip_up_down=True, transparent=False
fig, *, dpi=100, fname=None, flip_up_down=True, transparent=False
):
"""Convert a Matplotlib figure to a 3D numpy array with RGBA channels.
Expand Down Expand Up @@ -54,7 +56,11 @@ def matplotlib_figure_to_numpy(
arr = load_image(fname)
else:
fig.savefig(
fname, dpi=dpi, transparent=transparent, bbox_inches="tight", pad_inches=0
fname,
dpi=dpi,
transparent=transparent,
bbox_inches="tight",
pad_inches=0,
)
arr = load_image(fname)

Expand Down
161 changes: 161 additions & 0 deletions fury/decorators.py
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,15 @@
"""Decorators for FURY tests."""

from functools import wraps
from inspect import signature
import platform
import re
import sys
from warnings import warn

from packaging import version

import fury

skip_linux = is_linux = platform.system().lower() == "linux"
skip_osx = is_osx = platform.system().lower() == "darwin"
Expand Down Expand Up @@ -43,3 +50,157 @@ def doctest_skip_parser(func):
new_lines.append(code)
func.__doc__ = "\n".join(new_lines)
return func


def warn_on_args_to_kwargs(
from_version="0.1.0",
until_version="0.11.0",
):
"""Decorator to enforce keyword-only arguments.
This decorator enforces that all arguments after the first one are
keyword-only arguments. It also checks that all keyword arguments are
expected by the function.
Parameters
----------
from_version: str, optional
The version of fury from which the function was supported.
until_version: str, optional
The version of fury until which the function was supported.
Returns
-------
decorator: Callable
Decorator function.
Examples
--------
>>> from fury.decorators import warn_on_args_to_kwargs
>>> import fury
>>> @warn_on_args_to_kwargs()
... def f(a, b, *, c, d=1, e=1):
... return a + b + c + d + e
>>> CURRENT_VERSION = fury.__version__
>>> fury.__version__ = "0.11.0"
>>> f(1, 2, 3, 4, 5)
15
>>> f(1, 2, c=3, d=4, e=5)
15
>>> f(1, 2, 2, 4, e=5)
14
>>> f(1, 2, c=3, d=4)
11
>>> f(1, 2, d=3, e=5)
Traceback (most recent call last):
...
TypeError: f() missing 1 required keyword-only argument: 'c'
>>> fury.__version__ = "0.12.0"
>>> f(1, 2, 3, 4, e=5)
Traceback (most recent call last):
...
TypeError: f() takes 2 positional arguments but 4 positional arguments (and 1 keyword-only argument) were given
>>> fury.__version__ = CURRENT_VERSION
""" # noqa: E501

def decorator(func):
"""Decorator function. This function enforces that all arguments after
the first one are keyword-only arguments. It also checks that all
keyword arguments are expected by the function.
Parameters
----------
func: function
Function to be decorated.
Returns
-------
wrapper: Callable
Decorated function.
"""

@wraps(func)
def wrapper(*args, **kwargs):
sig = signature(func)
params = sig.parameters
#
KEYWORD_ONLY_ARGS = [
arg.name for arg in params.values() if arg.kind == arg.KEYWORD_ONLY
]
POSITIONAL_ARGS = [
arg.name
for arg in params.values()
if arg.kind in (arg.POSITIONAL_OR_KEYWORD, arg.POSITIONAL_ONLY)
]

# Keyword-only arguments that do not have default values and not in kwargs
missing_kwargs = [
arg
for arg in KEYWORD_ONLY_ARGS
if arg not in kwargs and params[arg].default == params[arg].empty
]

# Keyword-only arguments that have default values
ARG_DEFAULT = [
arg
for arg in KEYWORD_ONLY_ARGS
if arg not in kwargs and params[arg].default != params[arg].empty
]
func_params_sample = []

# Create a sample of the function parameters
for arg in params.values():
if arg.kind in (arg.POSITIONAL_OR_KEYWORD, arg.POSITIONAL_ONLY):
func_params_sample.append(f"{arg.name}_value")
elif arg.kind == arg.KEYWORD_ONLY:
func_params_sample.append(f"{arg.name}='value'")
func_params_sample = ", ".join(func_params_sample)
args_kwargs_len = len(args) + len(kwargs)
params_len = len(params)
try:
return func(*args, **kwargs)
except TypeError as e:
FURY_CURRENT_VERSION = fury.__version__

if ARG_DEFAULT:
missing_kwargs += ARG_DEFAULT
if missing_kwargs and params_len >= args_kwargs_len:
# if the version of fury is greater than until_version,
# an error should be displayed,
if version.parse(FURY_CURRENT_VERSION) > version.parse(
until_version
):
raise TypeError(e) from e

positional_args_len = len(POSITIONAL_ARGS)
args_k = list(args[positional_args_len:])
args = list(args[:positional_args_len])
kwargs.update(dict(zip(missing_kwargs, args_k)))
result = func(*args, **kwargs)

# if from_version is less or equal to fury.__version__ and,
# less or equal to until_version
# a warning should be displayed.
if (
version.parse(from_version)
<= version.parse(FURY_CURRENT_VERSION)
<= version.parse(until_version)
):
warn(
f"We'll no longer accept the way you call the "
f"{func.__name__} function in future versions of FURY.\n\n"
"Here's how to call the Function {}: {}({})\n".format(
func.__name__, func.__name__, func_params_sample
),
UserWarning,
stacklevel=3,
)

# if the current version of fury is less than from_version,
# the function should be called without any changes.

return result

return wrapper

return decorator
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