Skip to content

Commit

Permalink
style: manual split long string, comment and docs
Browse files Browse the repository at this point in the history
  • Loading branch information
@ycexiao
ycexiao committed Feb 2, 2025
1 parent e2f789c commit 476fac5
Show file tree
Hide file tree
Showing 14 changed files with 473 additions and 269 deletions.
23 changes: 23 additions & 0 deletions news/linelength79.rst
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
**Added:**

* update isort, flake8 and black to set line limit to 79

**Changed:**

* <news item>

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
123 changes: 78 additions & 45 deletions src/diffpy/utils/diffraction_objects.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,16 @@
]

x_values_not_equal_emsg = (
"The two objects have different values in x arrays (my_do.all_arrays[:, [1, 2, 3]]). "
"Please ensure the x values of the two objects are identical by re-instantiating "
"the DiffractionObject with the correct x value inputs."
"The two objects have different values in x arrays "
"my_do.all_arrays[:, [1, 2, 3]]). Please ensure the x values of the two "
"objects are identical by re-instantiating the DiffractionObject with the "
"correct x value inputs."
)

invalid_add_type_emsg = (
"You may only add a DiffractionObject with another DiffractionObject or a scalar value. "
"Please rerun by adding another DiffractionObject instance or a scalar value. "
"You may only add a DiffractionObject with another DiffractionObject or a"
"scalar value. Please rerun by adding another DiffractionObject or "
"a scalar value. "
"e.g., my_do_1 + my_do_2 or my_do + 10 or 10 + my_do"
)

Expand Down Expand Up @@ -70,11 +72,14 @@ class DiffractionObject:
Attributes
----------
scat_quantity : str
The type of scattering experiment (e.g., "x-ray", "neutron"). Default is an empty string "".
The type of scattering experiment (e.g., "x-ray", "neutron").
Default is an empty string "".
wavelength : float
The wavelength of the incoming beam, specified in angstroms (Å). Default is none.
The wavelength of the incoming beam, specified in angstroms (Å).
Default is none.
name: str
The name or label for the scattering data. Default is an empty string "".
The name or label for the scattering data. Default is an empty
string "".
qmin : float
The minimum q value.
qmax : float
Expand Down Expand Up @@ -104,11 +109,13 @@ def __init__(
Parameters
----------
xarray : ndarray
The independent variable array containing "q", "tth", or "d" values.
The independent variable array containing "q", "tth", or "d"
values.
yarray : ndarray
The dependent variable array corresponding to intensity values.
xtype : str
The type of the independent variable in `xarray`. Must be one of {*XQUANTITIES}.
The type of the independent variable in `xarray`.
Must be one of {*XQUANTITIES}.
wavelength : float, optional, default is None.
The wavelength of the incoming beam, specified in angstroms (Å)
scat_quantity : str, optional, default is an empty string "".
Expand All @@ -124,7 +131,8 @@ def __init__(
>>> import numpy as np
>>> from diffpy.utils.diffraction_objects import DiffractionObject
...
>>> x = np.array([0.12, 0.24, 0.31, 0.4]) # independent variable (e.g., q)
>>> # independent variable (e.g., q)
>>> x = np.array([0.12, 0.24, 0.31, 0.4])
>>> y = np.array([10, 20, 40, 60]) # intensity values
>>> metadata = {
... "sample": "rock salt from the beach",
Expand Down Expand Up @@ -211,23 +219,28 @@ def __add__(self, other):
Parameters
----------
other : DiffractionObject, int, or float
The item to be added. If `other` is a scalar value, this value will be added to each element of the
yarray of this DiffractionObject instance. If `other` is another DiffractionObject, the yarrays of the
two DiffractionObjects will be combined element-wise. The result is a new DiffractionObject instance,
representing the addition and using the xarray from the left-hand side DiffractionObject.
The item to be added. If `other` is a scalar value, this value will
be added to each element of the yarray of this DiffractionObject
instance. If `other` is another DiffractionObject, the yarrays of
the two DiffractionObjects will be combined element-wise.The result
is a new DiffractionObject instance,representing the addition and
using the xarray from the left-hand side DiffractionObject.
Returns
-------
DiffractionObject
The new DiffractionObject instance with modified yarray values. This instance is a deep copy of the
original with the additions applied.
The new DiffractionObject instance with modified yarray values.
This instance is a deep copy of the original with the additions
applied.
Raises
------
ValueError
Raised when the xarrays of two DiffractionObject instances are not equal.
Raised when the xarrays of two DiffractionObject instances are not
equal.
TypeError
Raised when `other` is not an instance of DiffractionObject, int, or float.
Raised when `other` is not an instance of DiffractionObject, int,
or float.
Examples
--------
Expand All @@ -253,12 +266,14 @@ def __sub__(self, other):
"""Subtract scalar value or another DiffractionObject to the yarray of
the DiffractionObject.
This method behaves similarly to the `__add__` method, but performs subtraction instead of addition.
For details on parameters, returns, and exceptions, refer to the documentation for `__add__`.
This method behaves similarly to the `__add__` method, but performs
subtraction instead of addition.For details on parameters, returns, and
exceptions, refer to the documentation for `__add__`.
Examples
--------
Subtract a scalar value from the yarray of a DiffractionObject instance:
Subtract a scalar value from the yarray of a DiffractionObject
instance:
>>> new_do = my_do - 10.1
Subtract the yarrays of two DiffractionObject instances:
Expand All @@ -279,12 +294,14 @@ def __mul__(self, other):
"""Multiply a scalar value or another DiffractionObject with the yarray
of this DiffractionObject.
This method behaves similarly to the `__add__` method, but performs multiplication instead of addition.
For details on parameters, returns, and exceptions, refer to the documentation for `__add__`.
This method behaves similarly to the `__add__` method, but performs
multiplication instead of addition. For details on parameters, returns,
and exceptions, refer to the documentation for `__add__`.
Examples
--------
Multiply a scalar value with the yarray of a DiffractionObject instance:
Multiply a scalar value with the yarray of a DiffractionObject
instance:
>>> new_do = my_do * 3.5
Multiply the yarrays of two DiffractionObject instances:
Expand All @@ -305,8 +322,9 @@ def __truediv__(self, other):
"""Divide the yarray of this DiffractionObject by a scalar value or
another DiffractionObject.
This method behaves similarly to the `__add__` method, but performs division instead of addition.
For details on parameters, returns, and exceptions, refer to the documentation for `__add__`.
This method behaves similarly to the `__add__` method, but performs
division instead of addition.For details on parameters, returns, and
exceptions, refer to the documentation for `__add__`.
Examples
--------
Expand Down Expand Up @@ -344,7 +362,8 @@ def all_arrays(self):
Returns
-------
ndarray
The shape (len(data), 4) 2D array with columns containing the `yarray` (intensity)
The shape (len(data), 4) 2D array with columns containing the
`yarray` (intensity)
and the `xarray` values in q, tth, and d.
Examples
Expand Down Expand Up @@ -399,21 +418,26 @@ def get_array_index(self, xtype, xvalue):
Parameters
----------
xtype : str
The type of the independent variable in `xarray`. Must be one of {*XQUANTITIES}.
The type of the independent variable in `xarray`. Must be one of
{*XQUANTITIES}.
xvalue : float
The value of the xtype to find the closest index for.
Returns
-------
index : int
The index of the closest value in the array associated with the specified xtype and the value provided.
The index of the closest value in the array associated with the
specified xtype and the value provided.
"""

xtype = self._input_xtype
xarray = self.on_xtype(xtype)[0]
if len(xarray) == 0:
raise ValueError(
f"The '{xtype}' array is empty. Please ensure it is initialized."
(
f"The '{xtype}' array is empty. "
f"Please ensure it is initialized."
)
)
index = (np.abs(xarray - xvalue)).argmin()
return index
Expand Down Expand Up @@ -486,19 +510,22 @@ def scale_to(
"""Return a new diffraction object which is the current object but
rescaled in y to the target.
By default, if `q`, `tth`, or `d` are not provided, scaling is based on the max intensity from each object.
Otherwise, y-value in the target at the closest specified x-value will be used as the factor to scale to.
The entire array is scaled by this factor so that one object places on top of the other at that point.
If multiple values of `q`, `tth`, or `d` are provided, an error will be raised.
By default, if `q`, `tth`, or `d` are not provided, scaling is based on
the max intensity from each object. Otherwise, y-value in the target at
the closest specified x-value will be used as the factor to scale to.
The entire array is scaled by this factor so that one object places on
top of the other at that point.If multiple values of `q`, `tth`, or `d`
are provided, an error will be raised.
Parameters
----------
target_diff_object: DiffractionObject
The diffraction object you want to scale the current one onto.
q, tth, d : float, optional, default is None
The value of the x-array where you want the curves to line up vertically.
Specify a value on one of the allowed grids, q, tth, or d), e.g., q=10.
The value of the x-array where you want the curves to line up
vertically. Specify a value on one of the allowed grids, q, tth,
or d), e.g., q=10.
offset : float, optional, default is None
The offset to add to the scaled y-values.
Expand Down Expand Up @@ -546,7 +573,8 @@ def on_xtype(self, xtype):
Parameters
----------
xtype : str
The type of quantity for the independent variable chosen from {*XQUANTITIES, }
The type of quantity for the independent variable chosen from
{*XQUANTITIES, }
Raises
------
Expand All @@ -556,7 +584,8 @@ def on_xtype(self, xtype):
Returns
-------
(xarray, yarray) : tuple of ndarray
The tuple containing two 1D numpy arrays with x and y data for the specified xtype.
The tuple containing two 1D numpy arrays with x and y data for the
specified xtype.
"""
if xtype.lower() in ANGLEQUANTITIES:
return self.on_tth()
Expand All @@ -576,12 +605,13 @@ def dump(self, filepath, xtype=None):
filepath : str
The filepath where the diffraction object will be dumped
xtype : str, optional, default is q
The type of quantity for the independent variable chosen from {*XQUANTITIES, }
The type of quantity for the independent variable chosen from
{*XQUANTITIES, }
Examples
--------
To save a diffraction object to a file named "diffraction_data.chi" in the current directory
with the independent variable 'q':
To save a diffraction object to a file named "diffraction_data.chi" in
the current directory with the independent variable 'q':
>>> file = "diffraction_data.chi"
>>> do.dump(file, xtype="q")
Expand All @@ -591,7 +621,8 @@ def dump(self, filepath, xtype=None):
>>> file = "./output/diffraction_data.chi"
>>> do.dump(file, xtype="q")
To save the diffraction data with a different independent variable, such as 'tth':
To save the diffraction data with a different independent variable,
such as 'tth':
>>> file = "diffraction_data_tth.chi"
>>> do.dump(file, xtype="tth")
Expand All @@ -615,7 +646,8 @@ def dump(self, filepath, xtype=None):

with open(filepath, "w") as f:
f.write(
f"[DiffractionObject]\nname = {self.name}\nwavelength = {self.wavelength}\n"
f"[DiffractionObject]\nname = {self.name}\n"
f"wavelength = {self.wavelength}\n"
f"scat_quantity = {self.scat_quantity}\n"
)
for key, value in self.metadata.items():
Expand All @@ -629,6 +661,7 @@ def copy(self):
Returns
-------
DiffractionObject
The new instance of DiffractionObject, which is a deep copy of the current instance.
The new instance of DiffractionObject, which is a deep copy of the
current instance.
"""
return deepcopy(self)
Loading

0 comments on commit 476fac5

Please sign in to comment.