diffpy.utils 3.6.1rc1__py3-none-any.whl → 3.7.0__py3-none-any.whl

diffpy/utils/tools.py

@@ -8,7 +8,7 @@ from scipy.optimize import dual_annealing
 from scipy.signal import convolve
 from xraydb import material_mu
 
-from diffpy.utils.parsers.loaddata import loadData
+from diffpy.utils.parsers import load_data
 
 
 def _stringify(string_value):
@@ -51,43 +51,46 @@ 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
-    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.
-    {
-      "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>>"  # noqa: E501
-    }
+    """Get name, email, and ORCID of the owner/user from various sources
+    and return it as a metadata dictionary.
+
+    The function looks for information in JSON configuration files named
+    ``diffpyconfig.json``. These can be in the user's home directory and in
+    the current working directory. The information in the config files is
+    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 config files.
+
+    A template for the config file is below. Create a text file called
+    ``diffpyconfig.json`` in your home directory and 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>" # noqa: E501
+        }
+
     You may also store any other global-level information that you would like
-    associated with your diffraction data in this file
+    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 stored in metadata.
+    owner_email : str, ``optional``
+        Default is the value stored in the global or local config file.
+        The email address 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.
+        Dictionary containing username, email, ORCID, and any other
+        information stored in global or local config files.
     """
     runtime_info = {
         "owner_name": owner_name,
@@ -106,8 +109,8 @@ def get_user_info(owner_name=None, owner_email=None, owner_orcid=None):
 
 
 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.
+    """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
@@ -127,9 +130,9 @@ def check_and_build_global_config(skip_config_creation=False):
 
     Parameters
     ----------
-    skip_config_creation : bool, optional, default is False.
+    skip_config_creation : bool, ``optional``
         The boolean that will override the creation workflow even if no
-        config file exists.
+        config file exists. Default is False.
 
     Returns
     -------
@@ -190,6 +193,7 @@ def get_package_info(package_names, metadata=None):
     Package info stored in metadata as
     {'package_info': {'package_name': 'version_number'}}.
 
+    Parameters
     ----------
     package_name : str or list
         The name of the package(s) to retrieve the version number for.
@@ -227,46 +231,30 @@ def get_density_from_cloud(sample_composition, mp_token=""):
     )
 
 
-def compute_mu_using_xraydb(
-    sample_composition, energy, sample_mass_density=None, packing_fraction=None
-):
-    """Compute the attenuation coefficient (mu) using the XrayDB database.
+def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density):
+    """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.
-    Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu.
+    Computes mu based on the sample composition, X-ray energy, and
+    sample mass density.
+
+    Reference:
+    https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu
 
     Parameters
     ----------
     sample_composition : str
         The chemical formula of the material.
     energy : float
-        The energy of the incident x-rays in keV.
-    sample_mass_density : float, optional, Default is None
-        The mass density of the packed powder/sample in g/cm*3.
-    packing_fraction : float, optional, Default is None
-        The fraction of sample in the capillary (between 0 and 1).
-        Specify either sample_mass_density or packing_fraction but not both.
+        The energy of the incident X-rays in keV.
+    sample_mass_density : float
+        The mass density of the sample in g/cm^3.
 
     Returns
     -------
     mu : float
-        The attenuation coefficient mu in mm^{-1}.
+        The attenuation coefficient μ in mm⁻¹.
     """
-    if (sample_mass_density is None and packing_fraction is None) or (
-        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. "
-            "Please rerun specifying only one."
-        )
-    if packing_fraction is not None:
-        sample_mass_density = (
-            get_density_from_cloud(sample_composition) * packing_fraction
-        )
     energy_eV = energy * 1000
     mu = (
         material_mu(
@@ -281,8 +269,8 @@ def compute_mu_using_xraydb(
 
 
 def _top_hat(z, half_slit_width):
-    """Create a top-hat function, return 1.0 for values within the specified
-    slit width and 0 otherwise."""
+    """Create a top-hat function, return 1.0 for values within the
+    specified slit width and 0 otherwise."""
     return np.where((z >= -half_slit_width) & (z <= half_slit_width), 1.0, 0.0)
 
 
@@ -313,9 +301,10 @@ def _model_function(z, diameter, z0, I0, mud, slope):
 
 
 def _extend_z_and_convolve(z, diameter, half_slit_width, z0, I0, mud, slope):
-    """Extend z values and I values for padding (so that we don't have tails in
-    convolution), then perform convolution (note that the convolved I values
-    are the same as modeled I values if slit width is close to 0)"""
+    """Extend z values and I values for padding (so that we don't have
+    tails in 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
@@ -336,8 +325,8 @@ def _extend_z_and_convolve(z, diameter, half_slit_width, z0, I0, mud, slope):
 
 def _objective_function(params, z, observed_data):
     """Compute the objective function for fitting a model to the
-    observed/experimental data by minimizing the sum of squared residuals
-    between the observed data and the convolved model 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
@@ -347,7 +336,8 @@ def _objective_function(params, z, observed_data):
 
 
 def _compute_single_mud(z_data, I_data):
-    """Perform dual annealing optimization and extract the parameters."""
+    """Perform dual annealing optimization and extract the
+    parameters."""
     bounds = [
         (
             1e-5,
@@ -376,8 +366,8 @@ def _compute_single_mud(z_data, I_data):
 
 
 def compute_mud(filepath):
-    """Compute the best-fit mu*D value from a z-scan file, removing the sample
-    holder effect.
+    """Compute the best-fit mu*D value from a z-scan file, removing the
+    sample holder effect.
 
     This function loads z-scan data and fits it to a model
     that convolves a top-hat function with I = I0 * e^{-mu * l}.
@@ -400,7 +390,7 @@ def compute_mud(filepath):
     mu*D : float
         The best-fit mu*D value.
     """
-    z_data, I_data = loadData(filepath, unpack=True)
+    z_data, I_data = load_data(filepath, unpack=True)
     best_mud, _ = min(
         (_compute_single_mud(z_data, I_data) for _ in range(20)),
         key=lambda pair: pair[1],

diffpy/utils/transforms.py

@@ -52,7 +52,7 @@ def q_to_tth(q, wavelength):
 
     Parameters
     ----------
-    q : ndarray
+    q : ``ndarray``
         The 1D array of :math:`q` values numpy.array([qs]).
         The units of q must be reciprocal of the units of wavelength.
 
@@ -61,7 +61,7 @@ def q_to_tth(q, wavelength):
 
     Returns
     -------
-    tth : ndarray
+    tth : ``ndarray``
         The 1D array of :math:`2\theta` values in degrees numpy.array([tths]).
     """
     _validate_inputs(q, wavelength)
@@ -76,7 +76,8 @@ 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.
+    r"""Helper function to convert two-theta to q on independent variable
+    axis.
 
     If wavelength is missing, returns independent variable axis as integer
     indexes.
@@ -95,7 +96,7 @@ def tth_to_q(tth, wavelength):
 
     Parameters
     ----------
-    tth : ndarray
+    tth : ``ndarray``
         The 1D array of :math:`2\theta` values np.array([tths]).
         The units of tth are expected in degrees.
 
@@ -104,7 +105,7 @@ def tth_to_q(tth, wavelength):
 
     Returns
     -------
-    q : ndarray
+    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.
@@ -124,18 +125,18 @@ def tth_to_q(tth, wavelength):
 
 
 def q_to_d(q):
-    r"""Helper function to convert q to d on independent variable axis, using
-    :math:`d = \frac{2 \pi}{q}`.
+    r"""Helper function to convert q to d on independent variable axis,
+    using :math:`d = \frac{2 \pi}{q}`.
 
     Parameters
     ----------
-    q : ndarray
+    q : ``ndarray``
         The 1D array of :math:`q` values np.array([qs]).
         The units of q must be reciprocal of the units of wavelength.
 
     Returns
     -------
-    d : ndarray
+    d : ``ndarray``
         The 1D array of :math:`d` values np.array([ds]).
     """
     if 0 in q:
@@ -144,7 +145,8 @@ def q_to_d(q):
 
 
 def tth_to_d(tth, wavelength):
-    r"""Helper function to convert two-theta to d on independent variable axis.
+    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)}.
@@ -153,7 +155,7 @@ def tth_to_d(tth, wavelength):
 
     Parameters
     ----------
-    tth : nsarray
+    tth : ``nsarray``
         The 1D array of :math:`2\theta` values np.array([tths]).
         The units of tth are expected in degrees.
 
@@ -162,7 +164,7 @@ def tth_to_d(tth, wavelength):
 
     Returns
     -------
-    d : nsarray
+    d : ``nsarray``
         The 1D array of :math:`d` values np.array([ds]).
     """
     q = tth_to_q(tth, wavelength)
@@ -178,16 +180,17 @@ def tth_to_d(tth, wavelength):
 
 
 def d_to_q(d):
-    r"""Helper function to convert q to d using :math:`d = \frac{2 \pi}{q}`.
+    r"""Helper function to convert q to d using :math:`d = \frac{2
+    \pi}{q}`.
 
     Parameters
     ----------
-    d : nsarray
+    d : ``nsarray``
         The 1D array of :math:`d` values np.array([ds]).
 
     Returns
     -------
-    q : nsarray
+    q : ``nsarray``
         The 1D array of :math:`q` values np.array([qs]).
         The units of q must be reciprocal of the units of wavelength.
     """
@@ -197,7 +200,8 @@ def d_to_q(d):
 
 
 def d_to_tth(d, wavelength):
-    r"""Helper function to convert d to two-theta on independent variable axis.
+    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).
@@ -206,7 +210,7 @@ def d_to_tth(d, wavelength):
 
     Parameters
     ----------
-    d : nsarray
+    d : ``nsarray``
         The 1D array of :math:`d` values np.array([ds]).
 
     wavelength : float
@@ -214,7 +218,7 @@ def d_to_tth(d, wavelength):
 
     Returns
     -------
-    tth : nsarray
+    tth : ``nsarray``
         The 1D array of :math:`2\theta` values np.array([tths]).
         The units of tth are expected in degrees.
     """

diffpy/utils/utils_app.py

@@ -0,0 +1,33 @@
+import argparse
+
+from diffpy.utils.version import __version__  # noqa
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="diffpy.utils",
+        description=(
+            "Shared utilities for diffpy packages.\n\n"
+            "For more information, visit: "
+            "https://github.com/diffpy/diffpy.utils/"
+        ),
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    parser.add_argument(
+        "--version",
+        action="store_true",
+        help="Show the program's version number and exit",
+    )
+
+    args = parser.parse_args()
+
+    if args.version:
+        print(f"diffpy.utils {__version__}")
+    else:
+        # Default behavior when no arguments are given
+        parser.print_help()
+
+
+if __name__ == "__main__":
+    main()

diffpy/utils/version.py

@@ -18,8 +18,9 @@
 #  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
 
 # obtain version information
-from importlib.metadata import version
+from importlib.metadata import PackageNotFoundError, version
 
-__version__ = version("diffpy.utils")
-
-# End of file
+try:
+    __version__ = version("diffpy.utils")
+except PackageNotFoundError:
+    __version__ = "unknown"

diffpy/utils/wx/gridutils.py

@@ -146,9 +146,9 @@ def quickResizeColumns(grid, indices):
 
 
 def _indicesToBlocks(indices):
-    """Convert a list of integer indices to a list of (start, stop) tuples. The
-    (start, stop) tuple defines a continuous block, where the stop index is
-    included in the block.
+    """Convert a list of integer indices to a list of (start, stop)
+    tuples. The (start, stop) tuple defines a continuous block, where
+    the stop index is included in the block.
 
     Parameters
     ----------

{diffpy_utils-3.6.1rc1.dist-info → diffpy_utils-3.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffpy.utils
-Version: 3.6.1rc1
+Version: 3.7.0
 Summary: General utilities for analyzing diffraction data
 Author-email: Simon Billinge <sb2896@columbia.edu>
 Maintainer-email: Simon Billinge <sb2896@columbia.edu>
@@ -16,12 +16,12 @@ Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: <3.14,>=3.11
+Requires-Python: <3.15,>=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
 License-File: LICENSE_DANSE.txt
@@ -58,6 +58,7 @@ Dynamic: license-file
         :target: https://anaconda.org/conda-forge/diffpy.utils
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.utils/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.utils
         :target: https://pypi.org/project/diffpy.utils/
@@ -68,8 +69,7 @@ Dynamic: license-file
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
         :target: https://github.com/diffpy/diffpy.utils/issues
 
-diffpy.utils Package
-========================================================================
+Shared utilities for diffpy packages.
 
 General utilities for analyzing diffraction data
 

diffpy_utils-3.7.0.dist-info/RECORD

@@ -0,0 +1,24 @@
+diffpy/__init__.py,sha256=PLQx_UmkmhCTu5bPeYdp9nQBx-OJGP0s4Pz-lLQhKsU,926
+diffpy/utils/__init__.py,sha256=CtxZ5VpVDjhWlvoGLIEjkBGtXn1Pnb4lrdhpIfzmYYc,704
+diffpy/utils/_deprecator.py,sha256=12F5wxSBZ3WPJbFa_K5WzVqyUfJywG0k5ZyntOv2ajU,5716
+diffpy/utils/diffraction_objects.py,sha256=wBxD-tFsV0KrKg6LIjBUOnjZdqLkOmr3Wfdlfivcqmc,23406
+diffpy/utils/resampler.py,sha256=m6dCsaxieizjAbWftIJyxlfVLnr1AsoyefUvJixjJ58,5980
+diffpy/utils/tools.py,sha256=gDAZJ9Da_5Fz1ps1OLAn8ykWF5-_8XC7n-W1GHKnRXs,14208
+diffpy/utils/transforms.py,sha256=q4L17QZp0eQrvghx6AzbQlXmqbieYUrD22u7TN_kp-4,6209
+diffpy/utils/utils_app.py,sha256=0ofHWceSaz4Sj8TtrfW0pXpVOZdecOCFZHIhnDr-mzA,779
+diffpy/utils/validators.py,sha256=JOtQBXbmke4ShMrBKy3-Ia1rc_0qrDBJ6gf66-9ukgA,901
+diffpy/utils/version.py,sha256=bSLZJHvxtxaB1QMgGMUl1F2DvE5wKO7spgo1od52lzA,898
+diffpy/utils/parsers/__init__.py,sha256=gojPo8UTIHsXzTqvLxizRreJVJ4H_aJxfeKTeR_ylRs,934
+diffpy/utils/parsers/custom_exceptions.py,sha256=aWFm1AJA_3dprNeBxb_SfQ7Mw2s3ENdzxxCy3QiZM5c,1737
+diffpy/utils/parsers/loaddata.py,sha256=dRjd25LJYbYqEAltBsft2ApJuDuq18KlZvBHE_yyoRY,13972
+diffpy/utils/parsers/serialization.py,sha256=GsCBNPzD3rDHaQtt4u2S5q7rzZVOKmw9PYuEutMVVZA,6856
+diffpy/utils/wx/__init__.py,sha256=dyVlLVVqqn3pBhCTyWr3zvvIcmQjqzUCOjWAaZ2lkX4,586
+diffpy/utils/wx/gridutils.py,sha256=mor8QT8xE3SZN74CwboLnSBfYM3PEHRzZ-AX3ZmlJfM,5158
+diffpy_utils-3.7.0.dist-info/licenses/AUTHORS.rst,sha256=vSJE4eFlrvgzwe0UiB5nnuqWVi7HO1aTzavOgqH1ngE,181
+diffpy_utils-3.7.0.dist-info/licenses/LICENSE.rst,sha256=Fic68qk6_MHLTR4fTua4ufK3iZH7ioQJ0x9STJAjkyk,6011
+diffpy_utils-3.7.0.dist-info/licenses/LICENSE_DANSE.txt,sha256=mPt7YHs0xQgff18u_MPvAFqHRTTF0x9ecqubGy6Fxjs,2160
+diffpy_utils-3.7.0.dist-info/METADATA,sha256=OXjglx56ZAmJhQrSc0hhKPi8Xx2Zq3h2p89liMt57EU,7566
+diffpy_utils-3.7.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+diffpy_utils-3.7.0.dist-info/entry_points.txt,sha256=k8fC_YuQDSsgvst9b-qgOB-9lRE88howBp6Tb0i3T-M,55
+diffpy_utils-3.7.0.dist-info/top_level.txt,sha256=34qLZyi9mxikpHepVDTMHrrNbe8VoOuz3ShYeiWA7KA,7
+diffpy_utils-3.7.0.dist-info/RECORD,,

{diffpy_utils-3.6.1rc1.dist-info → diffpy_utils-3.7.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

diffpy_utils-3.7.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+diffpy-utils = diffpy.utils_app:main

diffpy_utils-3.6.1rc1.dist-info/RECORD

@@ -1,21 +0,0 @@
-diffpy/__init__.py,sha256=PLQx_UmkmhCTu5bPeYdp9nQBx-OJGP0s4Pz-lLQhKsU,926
-diffpy/utils/__init__.py,sha256=CtxZ5VpVDjhWlvoGLIEjkBGtXn1Pnb4lrdhpIfzmYYc,704
-diffpy/utils/diffraction_objects.py,sha256=Qj3ka5DE-XswAo1jI3FhRYwyFrfCOWvkhBhrcBdrgj8,23294
-diffpy/utils/resampler.py,sha256=7M5VfH9Wddpy4j3SzSiCp1txUQwLPfwC1GcdYLdjyzE,5948
-diffpy/utils/tools.py,sha256=rAxjUrcnkQReT6uSu2X7GzqqLiEsaNArKkr-cfdkCTA,15161
-diffpy/utils/transforms.py,sha256=FW8vJB8Ft8TM4_vwRPMwTLZBiTxgZnLn9sbW8Nz0Ef4,6145
-diffpy/utils/validators.py,sha256=JOtQBXbmke4ShMrBKy3-Ia1rc_0qrDBJ6gf66-9ukgA,901
-diffpy/utils/version.py,sha256=b4ZYUji9mSEb7KDhiqdJoM17rJ9mQ9IJA21joYoCvtE,825
-diffpy/utils/parsers/__init__.py,sha256=nfOvZXjWN0nx4Yqt6BYspqdXjTeBLJcsm5X2-3SMhb4,612
-diffpy/utils/parsers/custom_exceptions.py,sha256=aWFm1AJA_3dprNeBxb_SfQ7Mw2s3ENdzxxCy3QiZM5c,1737
-diffpy/utils/parsers/loaddata.py,sha256=YQ7bAMHx0sGuE123BYNpg8npfruNEd4P8ZBma7Jmr48,13257
-diffpy/utils/parsers/serialization.py,sha256=6huTN8R4zkF2V30DeQxs-knHn7ZwotKaVN5kaEM-h9c,6851
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