Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

docs: improve docstring based on group standards in diffraction_objects.py transforms.py #300

Merged
merged 5 commits into from
Dec 31, 2024
Merged

docs: improve docstring based on group standards in diffraction_objects.py transforms.py #300

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
13af9e2
docs: improve docstring based on group standards in diffraction_objec…
bobleesj Dec 31, 2024
ee5f3a3
chore: fix from a tuple to The tuple in docstring
bobleesj Dec 31, 2024
f29ad91
chore: removed np.nsarray return type, not needed
bobleesj Dec 31, 2024
6b78427
chore: resolve merge conflict
bobleesj Dec 31, 2024
5dfff33
chore: added news for docstring
bobleesj Dec 31, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 23 additions & 0 deletions news/docstrings-refactor.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
**Added:**

* Improved API documentation in `DiffractionObject` methods and properties using the NumPy docstring format and PEP 256

**Changed:**

* <news item>

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
119 changes: 85 additions & 34 deletions src/diffpy/utils/diffraction_objects.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -93,18 +93,18 @@ def __init__(
The dependent variable array corresponding to intensity values.
xtype : str
The type of the independent variable in `xarray`. Must be one of {*XQUANTITIES}.
wavelength : float, optional
The wavelength of the incoming beam, specified in angstroms (Å). Default is none.
scat_quantity : str, optional
The type of scattering experiment (e.g., "x-ray", "neutron"). Default is an empty string "".
name : str, optional
The name or label for the scattering data. Default is an empty string "".
metadata : dict, optional
The additional metadata associated with the diffraction object. Default is {}.
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 "".
The type of scattering experiment (e.g., "x-ray", "neutron").
name : str, optional, default is an empty string "".
The name or label for the scattering data.
metadata : dict, optional, default is an empty dictionary {}
The additional metadata associated with the diffraction object.

Examples
--------
Create a DiffractionObject for X-ray scattering data
Create a DiffractionObject for X-ray scattering data:
>>> import numpy as np
>>> from diffpy.utils.diffraction_objects import DiffractionObject
...
Expand Down Expand Up @@ -181,30 +181,32 @@ def __add__(self, other):

Parameters
----------
other : DiffractionObject or int or float
The object to add to the current DiffractionObject. If `other` is a scalar value,
it will be added to all yarray. The length of the yarray must match if `other` is
an instance of DiffractionObject.
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.

Returns
-------
DiffractionObject
The new and deep-copied DiffractionObject instance after adding values to the yarray.
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 length of the yarray of the two DiffractionObject instances do not match.
Raised when the xarrays of two DiffractionObject instances are not equal.
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

"not equal" feels more explicit and program-like, than "unequal" or "do not match"

TypeError
Raised when the type of `other` is not an instance of DiffractionObject, int, or float.
Raised when `other` is not an instance of DiffractionObject, int, or float.

Examples
--------
Add a scalar value to the yarray of the DiffractionObject instance:
Add a scalar value to the yarray of a DiffractionObject instance:
>>> new_do = my_do + 10.1
>>> new_do = 10.1 + my_do

Add the yarray of two DiffractionObject instances:
Combine the yarrays of two DiffractionObject instances:
>>> new_do = my_do_1 + my_do_2
"""

Expand All @@ -219,6 +221,21 @@ def __add__(self, other):
__radd__ = __add__

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.
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Since sub, mul, and truediv pretty much have the same docstrings, I asked them to refer to mul while the examples are still unique.

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:
>>> new_do = my_do - 10.1

Subtract the yarrays of two DiffractionObject instances:
>>> new_do = my_do_1 - my_do_2
"""

self._check_operation_compatibility(other)
subtracted_do = deepcopy(self)
if isinstance(other, (int, float)):
Expand All @@ -230,6 +247,21 @@ def __sub__(self, other):
__rsub__ = __sub__

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__`.

Examples
--------
Multiply a scalar value with the yarray of a DiffractionObject instance:
>>> new_do = my_do * 3.5

Multiply the yarrays of two DiffractionObject instances:
>>> new_do = my_do_1 * my_do_2
"""

self._check_operation_compatibility(other)
multiplied_do = deepcopy(self)
if isinstance(other, (int, float)):
Expand All @@ -241,6 +273,20 @@ def __mul__(self, other):
__rmul__ = __mul__

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__`.

Examples
--------
Divide the yarray of a DiffractionObject instance by a scalar value:
>>> new_do = my_do / 2.0

Divide the yarrays of two DiffractionObject instances:
>>> new_do = my_do_1 / my_do_2
"""
self._check_operation_compatibility(other)
divided_do = deepcopy(self)
if isinstance(other, (int, float)):
Expand Down Expand Up @@ -291,7 +337,7 @@ def input_xtype(self):

Returns
-------
str
input_xtype : str
The type of `xarray`, which must be one of {*XQUANTITIES}.
"""
return self._input_xtype
Expand All @@ -306,7 +352,7 @@ def uuid(self):

Returns
-------
uuid
uuid : UUID
The unique identifier of the DiffractionObject instance.
"""
return self._uuid
Expand All @@ -328,7 +374,7 @@ def get_array_index(self, xtype, xvalue):

Returns
-------
int
index : int
The index of the closest value in the array associated with the specified xtype and the value provided.
"""

Expand Down Expand Up @@ -381,7 +427,7 @@ def on_d(self):
return [self.all_arrays[:, 3], self.all_arrays[:, 0]]

def scale_to(self, target_diff_object, q=None, tth=None, d=None, offset=None):
"""Returns a new diffraction object which is the current object but
"""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.
Expand All @@ -403,12 +449,12 @@ def scale_to(self, target_diff_object, q=None, tth=None, d=None, offset=None):

Returns
-------
scaled : DiffractionObject
scaled_do : DiffractionObject
The rescaled DiffractionObject as a new object.
"""
if offset is None:
offset = 0
scaled = self.copy()
scaled_do = self.copy()
count = sum([q is not None, tth is not None, d is not None])
if count > 1:
raise ValueError(
Expand All @@ -419,8 +465,8 @@ def scale_to(self, target_diff_object, q=None, tth=None, d=None, offset=None):
if count == 0:
q_target_max = max(target_diff_object.on_q()[1])
q_self_max = max(self.on_q()[1])
scaled._all_arrays[:, 0] = scaled._all_arrays[:, 0] * q_target_max / q_self_max + offset
return scaled
scaled_do._all_arrays[:, 0] = scaled_do._all_arrays[:, 0] * q_target_max / q_self_max + offset
return scaled_do

xtype = "q" if q is not None else "tth" if tth is not None else "d"
data = self.on_xtype(xtype)
Expand All @@ -430,21 +476,26 @@ def scale_to(self, target_diff_object, q=None, tth=None, d=None, offset=None):

xindex_data = (np.abs(data[0] - xvalue)).argmin()
xindex_target = (np.abs(target[0] - xvalue)).argmin()
scaled._all_arrays[:, 0] = data[1] * target[1][xindex_target] / data[1][xindex_data] + offset
return scaled
scaled_do._all_arrays[:, 0] = data[1] * target[1][xindex_target] / data[1][xindex_data] + offset
return scaled_do

def on_xtype(self, xtype):
"""Return a list of two 1D np array with x and y data, raise an error
if the specified xtype is invalid.
"""Return a tuple of two 1D numpy arrays containing x and y data.

Parameters
----------
xtype str
the type of quantity for the independent variable from {*XQUANTITIES, }
xtype : str
The type of quantity for the independent variable chosen from {*XQUANTITIES, }

Raises
------
ValueError
Raised when the specified xtype is not among {*XQUANTITIES, }

Returns
-------
a list of two 1D np array with x and y data
(xarray, yarray) : tuple of ndarray
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 Down Expand Up @@ -485,6 +536,6 @@ def copy(self):
Returns
-------
DiffractionObject
A 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)
39 changes: 20 additions & 19 deletions src/diffpy/utils/tools.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,33 +11,33 @@
from diffpy.utils.parsers.loaddata import loadData


def _stringify(obj):
def _stringify(string_value):
"""Convert None to an empty string.

Parameters
----------
obj: str
The object to convert. If None, return an empty string.
string_value : str or None
The value to be converted. If None, an empty string is returned.

Returns
-------
str or None:
The converted string if obj is not None, otherwise an empty string.
str
The original string if string_value is not None, otherwise an empty string.
"""
return obj if obj is not None else ""
return string_value if string_value is not None else ""


def _load_config(file_path):
"""Load configuration from a .json file.

Parameters
----------
file_path: Path
file_path : Path
The path to the configuration file.

Returns
-------
dict:
config : dict
The configuration dictionary or {} if the config file does not exist.
"""
config_file = Path(file_path).resolve()
Expand All @@ -50,7 +50,7 @@ def _load_config(file_path):


def get_user_info(owner_name=None, owner_email=None, owner_orcid=None):
"""Get name, email and orcid of the owner/user from various sources and
"""Get name, email, and orcid of the owner/user from various sources and
return it as a metadata dictionary.

The function looks for the information in json format configuration files with the name 'diffpyconfig.json'.
Expand All @@ -71,16 +71,16 @@ def get_user_info(owner_name=None, owner_email=None, owner_orcid=None):

Parameters
----------
owner_name: string, optional, default is the value stored in the global or local config file.
owner_name : str, optional, default is the value stored in the global or local config file.
The name of the user who will show as owner in the metadata that is stored with the data
owner_email: string, optional, default is the value stored in the global or local config file.
owner_email : str, optional, default is the value stored in the global or local config file.
The email of the user/owner
owner_orcid: string, optional, default is the value stored in the global or local config file.
owner_orcid : str, optional, default is the value stored in the global or local config file.
The ORCID id of the user/owner

Returns
-------
dict:
user_info : dict
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

seems like numpy uses both (1) what's returned and (2) its type

Screenshot 2024-12-30 at 10 11 02 PM

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

https://numpydoc.readthedocs.io/en/latest/format.html#returns

The dictionary containing username, email and orcid of the user/owner, and any other information
stored in the global or local config files.
"""
Expand All @@ -97,7 +97,7 @@ def get_user_info(owner_name=None, owner_email=None, owner_orcid=None):


def check_and_build_global_config(skip_config_creation=False):
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Just minor prettification based on the standard

"""Checks for a global diffpu config file in user's home directory and
"""Check for a global diffpu config file in user's home directory and
creates one if it is missing.

The file it looks for is called diffpyconfig.json. This can contain anything in json format, but
Expand All @@ -116,12 +116,13 @@ def check_and_build_global_config(skip_config_creation=False):

Parameters
----------
skip_config_creation: bool, optional, Default is False
The bool that will override the creation workflow even if no config file exists.
skip_config_creation : bool, optional, default is False.
The boolean that will override the creation workflow even if no config file exists.

Returns
-------
bool: True if the file exists and False otherwise.
config_exists : bool
The boolean indicating whether the config file exists.
"""
config_exists = False
config_path = Path().home() / "diffpyconfig.json"
Expand Down Expand Up @@ -168,7 +169,7 @@ def check_and_build_global_config(skip_config_creation=False):


def get_package_info(package_names, metadata=None):
"""Fetches package version and updates it into (given) metadata.
"""Fetch package version and updates it into (given) metadata.

Package info stored in metadata as {'package_info': {'package_name': 'version_number'}}.

Expand All @@ -180,7 +181,7 @@ def get_package_info(package_names, metadata=None):

Returns
-------
dict:
metadata : dict
The updated metadata dict with package info inserted.
"""
if metadata is None:
Expand Down
Loading
Loading