diffpy.utils 3.6.0rc3__py3-none-any.whl → 3.6.1rc0__py3-none-any.whl

diffpy/utils/parsers/serialization.py

@@ -47,16 +47,19 @@ def serialize_data(
     data_table: list or ndarray
         Data table.
     dt_colnames: list
-        Names of each column in data_table. Every name in data_table_cols will be put into the Dictionary
-        as a key with a value of that column in data_table (stored as a List). Put None for columns
-        without names. If dt_cols has less non-None entries than columns in data_table,
-        the pair {'data table': data_table} will be put in the dictionary.
-        (Default None: only entry {'data table': data_table} will be added to dictionary.)
+        Names of each column in data_table. Every name in data_table_cols
+        will be put into the Dictionary as a key with a value of that column
+        in data_table (stored as a List). Put None for columns without names.
+        If dt_cols has less non-None entries than columns in data_table, the
+        pair {'data table': data_table} will be put in the dictionary.
+        (Default None: only entry {'data table': data_table} will be added to
+        dictionary.)
     show_path: bool
-        include a path element in the database entry (default True). If 'path' is not included in hddata,
-         extract path from filename.
+        include a path element in the database entry (default True). If
+        'path' is not included in hddata, extract path from filename.
     serial_file
-        Serial language file to dump dictionary into. If None (default), no dumping will occur.
+        Serial language file to dump dictionary into. If None (default), no
+        dumping will occur.
 
     Returns
     -------
@@ -79,32 +82,44 @@ def serialize_data(
     data.update(hdata)
 
     # second add named columns in dt_cols
-    # performed second to prioritize overwriting hdata entries with data_table column entries
+    # performed second to prioritize overwriting hdata entries with data_
+    # table column entries
     named_columns = 0  # initial value
     max_columns = 1  # higher than named_columns to trigger 'data table' entry
     if dt_colnames is not None:
         num_columns = [len(row) for row in data_table]
         max_columns = max(num_columns)
         num_col_names = len(dt_colnames)
-        if max_columns < num_col_names:  # assume numpy.loadtxt gives non-irregular array
-            raise ImproperSizeError("More entries in dt_colnames than columns in data_table.")
+        if (
+            max_columns < num_col_names
+        ):  # assume numpy.loadtxt gives non-irregular array
+            raise ImproperSizeError(
+                "More entries in dt_colnames than columns in data_table."
+            )
         named_columns = 0
         for idx in range(num_col_names):
             colname = dt_colnames[idx]
             if colname is not None:
                 if colname in hdata.keys():
                     warnings.warn(
-                        f"Entry '{colname}' in hdata has been overwritten by a data_table entry.",
+                        (
+                            f"Entry '{colname}' in hdata has been "
+                            "overwritten by a data_table entry."
+                        ),
                         RuntimeWarning,
                     )
                 data.update({colname: list(data_table[:, idx])})
                 named_columns += 1
 
-    # finally add data_table as an entry named 'data table' if not all columns were parsed
+    # finally add data_table as an entry named 'data table' if not all
+    # columns were parsed
     if named_columns < max_columns:
         if "data table" in data.keys():
             warnings.warn(
-                "Entry 'data table' in hdata has been overwritten by data_table.",
+                (
+                    "Entry 'data table' in hdata has been "
+                    "overwritten by data_table."
+                ),
                 RuntimeWarning,
             )
         data.update({"data table": data_table})

diffpy/utils/resampler.py

@@ -22,11 +22,11 @@ import numpy as np
 def wsinterp(x, xp, fp, left=None, right=None):
     """One-dimensional Whittaker-Shannon interpolation.
 
-    Reconstruct a continuous signal from discrete data points by utilizing sinc functions
-    as interpolation kernels. This function interpolates the values of fp (array),
-    which are defined over xp (array), at new points x (array or float).
-    The implementation is based on E. T. Whittaker's 1915 paper
-    (https://doi.org/10.1017/S0370164600017806).
+    Reconstruct a continuous signal from discrete data points by utilizing
+    sinc functions as interpolation kernels. This function interpolates the
+    values of fp (array), which are defined over xp (array), at new points x
+    (array or float). The implementation is based on E. T. Whittaker's 1915
+    paper (https://doi.org/10.1017/S0370164600017806).
 
     Parameters
     ----------
@@ -37,17 +37,18 @@ def wsinterp(x, xp, fp, left=None, right=None):
     fp: ndarray
         The array of y values associated with xp.
     left: float
-        If given, set fp for x < xp[0] to left. Otherwise, if left is None (default) or not given,
-        set fp for x < xp[0] to fp evaluated at xp[-1].
+        If given, set fp for x < xp[0] to left. Otherwise, if left is None
+        (default) or not given, set fp for x < xp[0] to fp evaluated at xp[-1].
     right: float
-        If given, set fp for x > xp[-1] to right. Otherwise, if right is None (default) or not given, set fp for
-        x > xp[-1] to fp evaluated at xp[-1].
+        If given, set fp for x > xp[-1] to right. Otherwise, if right is None
+        (default) or not given, set fp for x > xp[-1] to fp evaluated at
+        xp[-1].
 
     Returns
     -------
     ndarray or float
-        The interpolated values at points x. Returns a single float if x is a scalar,
-        otherwise returns a numpy.ndarray.
+        The interpolated values at points x. Returns a single float if x is a
+        scalar, otherwise returns a numpy.ndarray.
     """
     scalar = np.isscalar(x)
     if scalar:
@@ -82,10 +83,11 @@ def nsinterp(xp, fp, qmin=0, qmax=25, left=None, right=None):
     """One-dimensional Whittaker-Shannon interpolation onto the Nyquist-Shannon
     grid.
 
-    Takes a band-limited function fp and original grid xp and resamples fp on the NS grid.
-    Uses the minimum number of points N required by the Nyquist sampling theorem.
-    N = (qmax-qmin)(rmax-rmin)/pi, where rmin and rmax are the ends of the real-space ranges.
-    fp must be finite, and the user inputs qmin and qmax of the frequency-domain.
+    Takes a band-limited function fp and original grid xp and resamples fp on
+    the NS grid. Uses the minimum number of points N required by the Nyquist
+    sampling theorem. N = (qmax-qmin)(rmax-rmin)/pi, where rmin and rmax are
+    the ends of the real-space ranges. fp must be finite, and the user inputs
+    qmin and qmax of the frequency-domain.
 
     Parameters
     ----------
@@ -103,8 +105,8 @@ def nsinterp(xp, fp, qmin=0, qmax=25, left=None, right=None):
     x: ndarray
         The Nyquist-Shannon grid computed for the given qmin and qmax.
     fp_at_x: ndarray
-        The interpolated values at points x. Returns a single float if x is a scalar,
-        otherwise returns a numpy.ndarray.
+        The interpolated values at points x. Returns a single float if x is a
+        scalar, otherwise returns a numpy.ndarray.
     """
     # Ensure numpy array
     xp = np.array(xp)
@@ -122,8 +124,9 @@ def nsinterp(xp, fp, qmin=0, qmax=25, left=None, right=None):
 def resample(r, s, dr):
     """Resample a PDF on a new grid.
 
-    This uses the Whittaker-Shannon interpolation formula to put s1 on a new grid if dr is less than the sampling
-    interval of r1, or linear interpolation if dr is greater than the sampling interval of r1.
+    This uses the Whittaker-Shannon interpolation formula to put s1 on a new
+    grid if dr is less than the sampling interval of r1, or linear
+    interpolation if dr is greater than the sampling interval of r1.
 
     Parameters
     ----------
@@ -140,8 +143,12 @@ def resample(r, s, dr):
     """
 
     warnings.warn(
-        "The 'resample' function is deprecated and will be removed in a future release (3.8.0). \n"
-        "'resample' has been renamed 'wsinterp' to better reflect functionality. Please use 'wsinterp' instead.",
+        (
+            "The 'resample' function is deprecated and will be removed "
+            "in a future release (3.8.0). \n"
+            "'resample' has been renamed 'wsinterp' to better reflect "
+            "functionality. Please use 'wsinterp' instead."
+        ),
         DeprecationWarning,
         stacklevel=2,
     )

diffpy/utils/tools.py

@@ -22,7 +22,8 @@ def _stringify(string_value):
     Returns
     -------
     str
-        The original string if string_value is not None, otherwise an empty string.
+        The original string if string_value is not None, otherwise an empty
+        string.
     """
     return string_value if string_value is not None else ""
 
@@ -53,38 +54,46 @@ 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
     return it as a metadata dictionary.
 
-    The function looks for the information in json format configuration files with the name 'diffpyconfig.json'.
-    These can be in the user's home directory and in the current working directory.  The information in the
-    config files are combined, with the local config overriding the home-directory one.  Values for
-    owner_name, owner_email, and owner_orcid may be passed in to the function and these override the values
-    in the config files.
-
-    A template for the config file is below.  Create a text file called 'diffpyconfig.json' in your home directory
-    and copy-paste the template into it, editing it with your real information.
+    The function looks for the information in json format configuration files
+    with the name 'diffpyconfig.json'. These can be in the user's home
+    directory and in the current working directory.  The information in the
+    config files are combined, with the local config overriding the
+    home- directory one.  Values for owner_name, owner_email, and owner_orcid
+    may be passed in to the function and these override the values in the
+    config files.
+
+    A template for the config file is below.  Create a text file called '
+    diffpyconfig.json' in your home directory and copy-paste the template
+    into it, editing it with your real information.
     {
       "owner_name": "<your name as you would like it stored with your data>>",
       "owner_email": "<your_associated_email>>@email.com",
-      "owner_orcid": "<your_associated_orcid if you would like this stored with your data>>"
+      "owner_orcid": "<your_associated_orcid if you would like this stored with your data>>"  # noqa: E501
     }
-    You may also store any other global-level information that you would like associated with your
-    diffraction data in this file
+    You may also store any other global-level information that you would like
+    associated with your diffraction data in this file
 
     Parameters
     ----------
-    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 : str, optional, default is the value stored in the global or local config file.
-        The email of the user/owner
-    owner_orcid : str, optional, default is the value stored in the global or local config file.
-        The ORCID id of the user/owner
+    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 : str, optional, default is the value stored in the global or
+        local config file. The email of the user/owner
+    owner_orcid : str, optional, default is the value stored in the global or
+        local config file. The ORCID id of the user/owner
 
     Returns
     -------
     user_info : dict
-        The dictionary containing username, email and orcid of the user/owner, and any other information
-        stored in the global or local config files.
+        The dictionary containing username, email and orcid of the user/owner
+        , and any other information stored in the global or local config files.
     """
-    runtime_info = {"owner_name": owner_name, "owner_email": owner_email, "owner_orcid": owner_orcid}
+    runtime_info = {
+        "owner_name": owner_name,
+        "owner_email": owner_email,
+        "owner_orcid": owner_orcid,
+    }
     for key, value in copy(runtime_info).items():
         if value is None or value == "":
             del runtime_info[key]
@@ -100,24 +109,27 @@ def check_and_build_global_config(skip_config_creation=False):
     """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
-    minimally contains information about the computer owner.  The information is used
-    when diffpy objects are created and saved to files or databases to retain ownership information
-    of datasets.  For example, it is used by diffpy.utils.tools.get_user_info().
+    The file it looks for is called diffpyconfig.json.  This can contain
+    anything in json format, but minimally contains information about the
+    computer owner.  The information is used when diffpy objects are created
+    and saved to files or databases to retain ownership information of
+    datasets.  For example, it is used by diffpy.utils.tools.get_user_info().
 
-    If the function finds no config file in the user's home directory it interrupts execution
-    and prompts the user for name, email, and orcid information.  It then creates the config file
-    with this information inside it.
+    If the function finds no config file in the user's home directory it
+    interrupts execution and prompts the user for name, email, and orcid
+    information.  It then creates the config file with this information
+    inside it.
 
     The function returns True if the file exists and False otherwise.
 
-    If you would like to check for a file but not run the file creation workflow you can set
-    the optional argument skip_config_creation to True.
+    If you would like to check for a file but not run the file creation
+    workflow you can set the optional argument skip_config_creation to True.
 
     Parameters
     ----------
     skip_config_creation : bool, optional, default is False.
-        The boolean that will override the creation workflow even if no config file exists.
+        The boolean that will override the creation workflow even if no
+        config file exists.
 
     Returns
     -------
@@ -132,16 +144,19 @@ def check_and_build_global_config(skip_config_creation=False):
     if skip_config_creation:
         return config_exists
     intro_text = (
-        "No global configuration file was found containing information about the user to "
-        "associate with the data.\n By following the prompts below you can add your name "
-        "and email to this file on the current "
-        "computer and your name will be automatically associated with subsequent diffpy data by default.\n"
-        "This is not recommended on a shared or public computer. "
-        "You will only have to do that once.\n"
-        "For more information, please refer to www.diffpy.org/diffpy.utils/examples/toolsexample.html"
+        "No global configuration file was found containing information about "
+        "the user to associate with the data.\n By following the prompts "
+        "below you can add your name and email to this file on the current "
+        "computer and your name will be automatically associated with "
+        "subsequent diffpy data by default.\n This is not recommended on a "
+        "shared or public computer. You will only have to do that once.\n "
+        "For more information, please refer to www.diffpy.org/diffpy.utils/ "
+        "examples/toolsexample.html "
     )
     print(intro_text)
-    username = input("Please enter the name you would want future work to be credited to: ").strip()
+    username = input(
+        "Please enter the name you would want future work to be credited to: "
+    ).strip()
     email = input("Please enter your email: ").strip()
     orcid = input("Please enter your orcid ID if you know it: ").strip()
     config = {
@@ -154,14 +169,15 @@ def check_and_build_global_config(skip_config_creation=False):
         with open(config_path, "w") as f:
             f.write(json.dumps(config))
         outro_text = (
-            f"The config file at {Path().home() / 'diffpyconfig.json'} has been created. "
-            f"The values  {config} were entered.\n"
-            f"These values will be inserted as metadata with your data in apps that use "
-            f"diffpy.get_user_info(). If you would like to update these values, either "
-            f"delete the config file and this workflow will rerun next time you run this "
-            f"program.  Or you may open the config file in a text editor and manually edit the"
-            f"entries.  For more information, see: "
-            f"https://diffpy.github.io/diffpy.utils/examples/tools_example.html"
+            f"The config file at {Path().home() / 'diffpyconfig.json'} has "
+            f"been created. The values  {config} were entered.\n These values "
+            "will be inserted as metadata with your data in apps that use "
+            "diffpy.get_user_info(). If you would like to update these values "
+            ", either delete the config file and this workflow will rerun "
+            "next time you run this program.  Or you may open the config "
+            "file in a text editor and manually edit the entries.  For more "
+            "information, see: "
+            "https://diffpy.github.io/diffpy.utils/examples/tools_example.html"
         )
         print(outro_text)
         config_exists = True
@@ -171,13 +187,15 @@ def check_and_build_global_config(skip_config_creation=False):
 def get_package_info(package_names, metadata=None):
     """Fetch package version and updates it into (given) metadata.
 
-    Package info stored in metadata as {'package_info': {'package_name': 'version_number'}}.
+    Package info stored in metadata as
+    {'package_info': {'package_name': 'version_number'}}.
 
     ----------
     package_name : str or list
         The name of the package(s) to retrieve the version number for.
     metadata : dict
-        The dictionary to store the package info. If not provided, a new dictionary will be created.
+        The dictionary to store the package info. If not provided, a new
+        dictionary will be created.
 
     Returns
     -------
@@ -202,18 +220,22 @@ def get_density_from_cloud(sample_composition, mp_token=""):
     It is not implemented yet.
     """
     raise NotImplementedError(
-        "So sorry, density computation from composition is not implemented right now. "
+        "So sorry, density computation from composition is not implemented "
+        "right now. "
         "We hope to have this implemented in the next release. "
         "Please rerun specifying a sample mass density."
     )
 
 
-def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None, packing_fraction=None):
+def compute_mu_using_xraydb(
+    sample_composition, energy, sample_mass_density=None, packing_fraction=None
+):
     """Compute the attenuation coefficient (mu) using the XrayDB database.
 
     Computes mu based on the sample composition and energy.
     User should provide a sample mass density or a packing fraction.
-    If neither density nor packing fraction is specified, or if both are specified, a ValueError will be raised.
+    If neither density nor packing fraction is specified,
+    or if both are specified, a ValueError will be raised.
     Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu.
 
     Parameters
@@ -237,13 +259,24 @@ def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density=None
         sample_mass_density is not None and packing_fraction is not None
     ):
         raise ValueError(
-            "You must specify either sample_mass_density or packing_fraction, but not both. "
+            "You must specify either sample_mass_density or packing_fraction, "
+            "but not both. "
             "Please rerun specifying only one."
         )
     if packing_fraction is not None:
-        sample_mass_density = get_density_from_cloud(sample_composition) * packing_fraction
+        sample_mass_density = (
+            get_density_from_cloud(sample_composition) * packing_fraction
+        )
     energy_eV = energy * 1000
-    mu = material_mu(sample_composition, energy_eV, density=sample_mass_density, kind="total") / 10
+    mu = (
+        material_mu(
+            sample_composition,
+            energy_eV,
+            density=sample_mass_density,
+            kind="total",
+        )
+        / 10
+    )
     return mu
 
 
@@ -257,8 +290,10 @@ def _model_function(z, diameter, z0, I0, mud, slope):
     """
     Compute the model function with the following steps:
     1. Let dz = z-z0, so that dz is centered at 0
-    2. Compute length l that is the effective length for computing intensity I = I0 * e^{-mu * l}:
-    - For dz within the capillary diameter, l is the chord length of the circle at position dz
+    2. Compute length l that is the effective length for computing intensity
+       I = I0 * e^{-mu * l}:
+    - For dz within the capillary diameter, l is the chord length of
+      the circle at position dz
     - For dz outside this range, l = 0
     3. Apply a linear adjustment to I0 by taking I0 as I0 - slope * z
     """
@@ -267,7 +302,11 @@ def _model_function(z, diameter, z0, I0, mud, slope):
     dz = z - z0
     length = np.piecewise(
         dz,
-        [dz < min_radius, (min_radius <= dz) & (dz <= max_radius), dz > max_radius],
+        [
+            dz < min_radius,
+            (min_radius <= dz) & (dz <= max_radius),
+            dz > max_radius,
+        ],
         [0, lambda dz: 2 * np.sqrt((diameter / 2) ** 2 - dz**2), 0],
     )
     return (I0 - slope * z) * np.exp(-mud / diameter * length)
@@ -278,12 +317,16 @@ def _extend_z_and_convolve(z, diameter, half_slit_width, z0, I0, mud, slope):
     convolution), then perform convolution (note that the convolved I values
     are the same as modeled I values if slit width is close to 0)"""
     n_points = len(z)
-    z_left_pad = np.linspace(z.min() - n_points * (z[1] - z[0]), z.min(), n_points)
-    z_right_pad = np.linspace(z.max(), z.max() + n_points * (z[1] - z[0]), n_points)
+    z_left_pad = np.linspace(
+        z.min() - n_points * (z[1] - z[0]), z.min(), n_points
+    )
+    z_right_pad = np.linspace(
+        z.max(), z.max() + n_points * (z[1] - z[0]), n_points
+    )
     z_extended = np.concatenate([z_left_pad, z, z_right_pad])
     I_extended = _model_function(z_extended, diameter, z0, I0, mud, slope)
     kernel = _top_hat(z_extended - z_extended.mean(), half_slit_width)
-    I_convolved = I_extended  # this takes care of the case where slit width is close to 0
+    I_convolved = I_extended  # this takes care of the case where slit width is close to 0  # noqa: E501
     if kernel.sum() != 0:
         kernel /= kernel.sum()
         I_convolved = convolve(I_extended, kernel, mode="same")
@@ -296,7 +339,9 @@ def _objective_function(params, z, observed_data):
     observed/experimental data by minimizing the sum of squared residuals
     between the observed data and the convolved model data."""
     diameter, half_slit_width, z0, I0, mud, slope = params
-    convolved_model_data = _extend_z_and_convolve(z, diameter, half_slit_width, z0, I0, mud, slope)
+    convolved_model_data = _extend_z_and_convolve(
+        z, diameter, half_slit_width, z0, I0, mud, slope
+    )
     residuals = observed_data - convolved_model_data
     return np.sum(residuals**2)
 
@@ -304,16 +349,27 @@ def _objective_function(params, z, observed_data):
 def _compute_single_mud(z_data, I_data):
     """Perform dual annealing optimization and extract the parameters."""
     bounds = [
-        (1e-5, z_data.max() - z_data.min()),  # diameter: [small positive value, upper bound]
-        (0, (z_data.max() - z_data.min()) / 2),  # half slit width: [0, upper bound]
+        (
+            1e-5,
+            z_data.max() - z_data.min(),
+        ),  # diameter: [small positive value, upper bound]
+        (
+            0,
+            (z_data.max() - z_data.min()) / 2,
+        ),  # half slit width: [0, upper bound]
         (z_data.min(), z_data.max()),  # z0: [min z, max z]
-        (1e-5, I_data.max()),  # I0: [small positive value, max observed intensity]
+        (
+            1e-5,
+            I_data.max(),
+        ),  # I0: [small positive value, max observed intensity]
         (1e-5, 20),  # muD: [small positive value, upper bound]
         (-100000, 100000),  # slope: [lower bound, upper bound]
     ]
     result = dual_annealing(_objective_function, bounds, args=(z_data, I_data))
     diameter, half_slit_width, z0, I0, mud, slope = result.x
-    convolved_fitted_signal = _extend_z_and_convolve(z_data, diameter, half_slit_width, z0, I0, mud, slope)
+    convolved_fitted_signal = _extend_z_and_convolve(
+        z_data, diameter, half_slit_width, z0, I0, mud, slope
+    )
     residuals = I_data - convolved_fitted_signal
     rmse = np.sqrt(np.mean(residuals**2))
     return mud, rmse
@@ -325,11 +381,13 @@ def compute_mud(filepath):
 
     This function loads z-scan data and fits it to a model
     that convolves a top-hat function with I = I0 * e^{-mu * l}.
-    The fitting procedure is run multiple times, and we return the best-fit parameters based on the lowest rmse.
+    The fitting procedure is run multiple times, and we return the best-fit
+    parameters based on the lowest rmse.
 
     The full mathematical details are described in the paper:
-    An ad hoc Absorption Correction for Reliable Pair-Distribution Functions from Low Energy x-ray Sources,
-    Yucong Chen, Till Schertenleib, Andrew Yang, Pascal Schouwink, Wendy L. Queen and Simon J. L. Billinge,
+    An ad hoc Absorption Correction for Reliable Pair-Distribution Functions
+    from Low Energy x-ray Sources, Yucong Chen, Till Schertenleib, Andrew Yang
+    , Pascal Schouwink, Wendy L. Queen and Simon J. L. Billinge,
     in preparation.
 
     Parameters
@@ -343,5 +401,8 @@ def compute_mud(filepath):
         The best-fit mu*D value.
     """
     z_data, I_data = loadData(filepath, unpack=True)
-    best_mud, _ = min((_compute_single_mud(z_data, I_data) for _ in range(20)), key=lambda pair: pair[1])
+    best_mud, _ = min(
+        (_compute_single_mud(z_data, I_data) for _ in range(20)),
+        key=lambda pair: pair[1],
+    )
     return best_mud

diffpy/utils/transforms.py

@@ -4,18 +4,23 @@ from copy import copy
 import numpy as np
 
 wavelength_warning_emsg = (
-    "No wavelength has been specified. You can continue to use the DiffractionObject, but "
-    "some of its powerful features will not be available. "
-    "To specify a wavelength, if you have do = DiffractionObject(xarray, yarray, 'tth'), "
-    "you may set do.wavelength = 1.54 for a wavelength of 1.54 angstroms."
+    "No wavelength has been specified. You can continue to use the "
+    "DiffractionObject, but some of its powerful features will not be "
+    "available. To specify a wavelength, if you have "
+    "do = DiffractionObject(xarray, yarray, 'tth'), you may set "
+    "do.wavelength = 1.54 for a wavelength of 1.54 angstroms. "
+)
+invalid_tth_emsg = (
+    "Two theta exceeds 180 degrees. Please check the input values for errors."
 )
-invalid_tth_emsg = "Two theta exceeds 180 degrees. Please check the input values for errors."
 invalid_q_or_d_or_wavelength_emsg = (
-    "The supplied input array and wavelength will result in an impossible two-theta. "
-    "Please check these values and re-instantiate the DiffractionObject with correct values."
+    "The supplied input array and wavelength will result in an impossible "
+    "two-theta. Please check these values and re-instantiate the "
+    "DiffractionObject with correct values. "
 )
 inf_output_imsg = (
-    "INFO: The largest output value in the array is infinite. This is allowed, but it will not be plotted."
+    "INFO: The largest output value in the array is infinite. "
+    "This is allowed, but it will not be plotted."
 )
 
 
@@ -73,7 +78,8 @@ def q_to_tth(q, wavelength):
 def tth_to_q(tth, wavelength):
     r"""Helper function to convert two-theta to q on independent variable axis.
 
-    If wavelength is missing, returns independent variable axis as integer indexes.
+    If wavelength is missing, returns independent variable axis as integer
+    indexes.
 
     By definition the relationship is:
 
@@ -100,7 +106,8 @@ def tth_to_q(tth, wavelength):
     -------
     q : ndarray
         The 1D array of :math:`q` values np.array([qs]).
-        The units for the q-values are the inverse of the units of the provided wavelength.
+        The units for the q-values are the inverse of the units of the
+        provided wavelength.
     """
     tth.astype(float)
     if np.any(np.deg2rad(tth) > np.pi):
@@ -139,7 +146,8 @@ def q_to_d(q):
 def tth_to_d(tth, wavelength):
     r"""Helper function to convert two-theta to d on independent variable axis.
 
-    The formula is .. math:: d = \frac{\lambda}{2 \sin\left(\frac{2\theta}{2}\right)}.
+    The formula is ..
+    math:: d = \frac{\lambda}{2 \sin\left(\frac{2\theta}{2}\right)}.
 
     Here we convert tth to q first, then to d.
 
@@ -191,7 +199,8 @@ def d_to_q(d):
 def d_to_tth(d, wavelength):
     r"""Helper function to convert d to two-theta on independent variable axis.
 
-    The formula is .. math:: 2\theta = 2 \arcsin\left(\frac{\lambda}{2d}\right).
+    The formula is ..
+    math:: 2\theta = 2 \arcsin\left(\frac{\lambda}{2d}\right).
 
     Here we convert d to q first, then to tth.
 

diffpy/utils/validators.py

@@ -1,8 +1,9 @@
 def is_number(string):
     """Check if the provided string can be converted to a float.
 
-    Since integers can be converted to floats, this function will return True for integers as well.
-    Hence, we can use this function to check if a string is a number.
+    Since integers can be converted to floats, this function will return True
+    for integers as well. Hence, we can use this function to check if a
+    string is a number.
 
     Parameters
     ----------

diffpy/utils/version.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
-# File coded by: Billinge Group members and community contributors.
+# File coded by: Simon Billinge, Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.utils/graphs/contributors
@@ -21,3 +21,5 @@
 from importlib.metadata import version
 
 __version__ = version("diffpy.utils")
+
+# End of file