diffpy.utils 3.2.7__tar.gz → 3.3.1__tar.gz

{diffpy.utils-3.2.7 → diffpy.utils-3.3.1}/PKG-INFO

@@ -1,14 +1,12 @@
 Metadata-Version: 2.1
 Name: diffpy.utils
-Version: 3.2.7
+Version: 3.3.1
 Summary: Shared utilities for diffpy packages.
-Home-page: https://github.com/diffpy/diffpy.utils/
-Author: Simon J.L. Billinge group
-Author-email: sb2896@columbia.edu
-Maintainer: Simon J.L. Billinge group
-Maintainer-email: sb2896@columbia.edu
-License: BSD-style license
-Keywords: text data parsers wx grid
+Author-email: "Simon J.L. Billinge group" <simon.billinge@gmail.com>
+Maintainer-email: "Simon J.L. Billinge group" <simon.billinge@gmail.com>
+Project-URL: Homepage, https://github.com/diffpy/diffpy.utils/
+Project-URL: Issues, https://github.com/diffpy/diffpy.utils/issues
+Keywords: text data parsers,wx grid,diffraction objects
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
@@ -19,10 +17,12 @@ Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
 Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 License-File: LICENSE_DANSE.txt
@@ -87,7 +87,7 @@ If you prefer to install from sources, after installing the dependencies, obtain
 `GitHub <https://github.com/diffpy/diffpy.utils/>`_. Once installed, ``cd`` into your ``diffpy.utils`` directory
 and run the following ::
 
-   pip install -e .
+   pip install .
 
 To check the installation integrity, if the following passes all checks, you are good! ::
 
@@ -105,9 +105,12 @@ https://github.com/diffpy/diffpy.utils.
 
 Feel free to fork the project and contribute.  To install diffpy.utils
 in a development mode, with its sources being directly used by Python
-rather than copied to a package directory, use ::
+rather than copied to a package directory, use the following in the root
+directory ::
+
+   pip install -e .
 
-   python setup.py develop --user
+Note that this is only supported for `setuptools` version 62.0 and above.
 
 
 CONTACTS

{diffpy.utils-3.2.7 → diffpy.utils-3.3.1}/README.rst

@@ -57,7 +57,7 @@ If you prefer to install from sources, after installing the dependencies, obtain
 `GitHub <https://github.com/diffpy/diffpy.utils/>`_. Once installed, ``cd`` into your ``diffpy.utils`` directory
 and run the following ::
 
-   pip install -e .
+   pip install .
 
 To check the installation integrity, if the following passes all checks, you are good! ::
 
@@ -75,9 +75,12 @@ https://github.com/diffpy/diffpy.utils.
 
 Feel free to fork the project and contribute.  To install diffpy.utils
 in a development mode, with its sources being directly used by Python
-rather than copied to a package directory, use ::
+rather than copied to a package directory, use the following in the root
+directory ::
+
+   pip install -e .
 
-   python setup.py develop --user
+Note that this is only supported for `setuptools` version 62.0 and above.
 
 
 CONTACTS

diffpy.utils-3.3.1/pyproject.toml

@@ -0,0 +1,50 @@
+[build-system]
+requires = ["setuptools>=62.0", "setuptools-git-versioning<2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "diffpy.utils"
+dynamic=['version']
+authors = [
+  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+]
+maintainers = [
+  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+]
+description = "Shared utilities for diffpy packages."
+keywords = ["text data parsers", "wx grid", "diffraction objects"]
+readme = "README.rst"
+requires-python = ">=3.9"
+classifiers = [
+        'Development Status :: 5 - Production/Stable',
+        'Environment :: Console',
+        'Intended Audience :: Developers',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: BSD License',
+        'Operating System :: MacOS :: MacOS X',
+        'Operating System :: Microsoft :: Windows',
+        'Operating System :: POSIX',
+        'Operating System :: Unix',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Topic :: Scientific/Engineering :: Physics',
+]
+
+[project.urls]
+Homepage = "https://github.com/diffpy/diffpy.utils/"
+Issues = "https://github.com/diffpy/diffpy.utils/issues"
+
+[tool.setuptools-git-versioning]
+enabled = true
+template = "{tag}"
+dev_template = "{tag}"
+dirty_template = "{tag}"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["diffpy*"]  # package names should match these glob patterns (["*"] by default)
+exclude = ["diffpy.utils.tests*"]  # exclude packages matching these glob patterns (empty by default)
+namespaces = false  # to disable scanning PEP 420 namespaces (true by default)

diffpy.utils-3.3.1/src/diffpy/utils/scattering_objects/__init__.py

@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# diffpy.utils      by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2010 The Trustees of Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:    Simon Billinge
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE_DANSE.txt for license information.
+#
+##############################################################################
+
+"""Scattering objects
+"""
+
+# End of file

diffpy.utils-3.3.1/src/diffpy/utils/scattering_objects/diffraction_objects.py

@@ -0,0 +1,428 @@
+import uuid
+from copy import deepcopy
+
+import numpy as np
+from numpy import array
+
+QQUANTITIES = ["q"]
+ANGLEQUANTITIES = ["angle","tth", "twotheta", "2theta"]
+DQUANTITIES = ["d", "dspace"]
+XQUANTITIES = ANGLEQUANTITIES + DQUANTITIES + QQUANTITIES
+XUNITS = ["degrees","radians","rad","deg","inv_angs","inv_nm","nm-1","A-1"]
+
+class Diffraction_object():
+    def __init__(self, name='', wavelength=None):
+        self.name = name
+        self.wavelength = wavelength
+        self.scat_quantity = ""
+        self.on_q = [np.empty(1), np.empty(1)]
+        self.on_tth = [np.empty(1), np.empty(1)]
+        self.on_d = [np.empty(1), np.empty(1)]
+        self._all_arrays = [self.on_q, self.on_tth]
+        self.metadata = {}
+
+    def __add__(self, other):
+        summed = deepcopy(self)
+        if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
+            summed.on_tth[1] = self.on_tth[1] + other
+            summed.on_q[1] = self.on_q[1] + other
+        elif not isinstance(other, Diffraction_object):
+            raise TypeError(f"I only know how to sum two Diffraction_object objects")
+        elif self.on_tth[0].all() != other.on_tth[0].all():
+            raise RuntimeError(f"objects are not on the same x-grid. You may add them using the self.add method and"
+                               f"specifying how to handle the mismatch.")
+        else:
+            summed.on_tth[1] = self.on_tth[1] + other.on_tth[1]
+            summed.on_q[1] = self.on_q[1] + other.on_q[1]
+        return summed
+    def __radd__(self, other):
+        summed = deepcopy(self)
+        if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
+            summed.on_tth[1] = self.on_tth[1] + other
+            summed.on_q[1] = self.on_q[1] + other
+        elif not isinstance(other, Diffraction_object):
+            raise TypeError(f"I only know how to sum two Scattering_object objects")
+        elif self.on_tth[0].all() != other.on_tth[0].all():
+            raise RuntimeError(f"objects are not on the same x-grid. You may add them using the self.add method and"
+                               f"specifying how to handle the mismatch.")
+        else:
+            summed.on_tth[1] = self.on_tth[1] + other.on_tth[1]
+            summed.on_q[1] = self.on_q[1] + other.on_q[1]
+        return summed
+
+    def __sub__(self, other):
+        subtracted = deepcopy(self)
+        if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
+            subtracted.on_tth[1] = self.on_tth[1] - other
+            subtracted.on_q[1] = self.on_q[1] - other
+        elif not isinstance(other, Diffraction_object):
+            raise TypeError(f"I only know how to subtract two Scattering_object objects")
+        elif self.on_tth[0].all() != other.on_tth[0].all():
+            raise RuntimeError(
+                f"objects are not on the same x-grid. You may subtract them using the self.add method and"
+                f"specifying how to handle the mismatch.")
+        else:
+            subtracted.on_tth[1] = self.on_tth[1] - other.on_tth[1]
+            subtracted.on_q[1] = self.on_q[1] - other.on_q[1]
+        return subtracted
+
+    def __rsub__(self, other):
+        subtracted = deepcopy(self)
+        if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
+            subtracted.on_tth[1] = other - self.on_tth[1]
+            subtracted.on_q[1] = other - self.on_q[1]
+        elif not isinstance(other, Diffraction_object):
+            raise TypeError(f"I only know how to subtract two Scattering_object objects")
+        elif self.on_tth[0].all() != other.on_tth[0].all():
+            raise RuntimeError(
+                f"objects are not on the same x-grid. You may subtract them using the self.add method and"
+                f"specifying how to handle the mismatch.")
+        else:
+            subtracted.on_tth[1] =  other.on_tth[1] - self.on_tth[1]
+            subtracted.on_q[1] = other.on_q[1] - self.on_q[1]
+        return subtracted
+
+    def __mul__(self, other):
+        multiplied = deepcopy(self)
+        if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
+            multiplied.on_tth[1] = other * self.on_tth[1]
+            multiplied.on_q[1] = other * self.on_q[1]
+        elif not isinstance(other, Diffraction_object):
+            raise TypeError(f"I only know how to multiply two Scattering_object objects")
+        elif self.on_tth[0].all() != other.on_tth[0].all():
+            raise RuntimeError(
+                f"objects are not on the same x-grid. You may multiply them using the self.add method and"
+                f"specifying how to handle the mismatch.")
+        else:
+            multiplied.on_tth[1] = self.on_tth[1] * other.on_tth[1]
+            multiplied.on_q[1] = self.on_q[1] * other.on_q[1]
+        return multiplied
+
+    def __rmul__(self, other):
+        multiplied = deepcopy(self)
+        if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
+            multiplied.on_tth[1] = other * self.on_tth[1]
+            multiplied.on_q[1] = other * self.on_q[1]
+        elif self.on_tth[0].all() != other.on_tth[0].all():
+            raise RuntimeError(
+                f"objects are not on the same x-grid. You may multiply them using the self.add method and"
+                f"specifying how to handle the mismatch.")
+        else:
+            multiplied.on_tth[1] = self.on_tth[1] * other.on_tth[1]
+            multiplied.on_q[1] = self.on_q[1] * other.on_q[1]
+        return multiplied
+
+    def __truediv__(self, other):
+        divided = deepcopy(self)
+        if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
+            divided.on_tth[1] = other / self.on_tth[1]
+            divided.on_q[1] = other / self.on_q[1]
+        elif not isinstance(other, Diffraction_object):
+            raise TypeError(f"I only know how to multiply two Scattering_object objects")
+        elif self.on_tth[0].all() != other.on_tth[0].all():
+            raise RuntimeError(
+                f"objects are not on the same x-grid. You may multiply them using the self.add method and"
+                f"specifying how to handle the mismatch.")
+        else:
+            divided.on_tth[1] = self.on_tth[1] / other.on_tth[1]
+            divided.on_q[1] = self.on_q[1] / other.on_q[1]
+        return divided
+
+
+    def __rtruediv__(self, other):
+        divided = deepcopy(self)
+        if isinstance(other, int) or isinstance(other, float) or isinstance(other, np.ndarray):
+            divided.on_tth[1] = other / self.on_tth[1]
+            divided.on_q[1] = other / self.on_q[1]
+        elif self.on_tth[0].all() != other.on_tth[0].all():
+            raise RuntimeError(
+                f"Diffraction objects are not on the same x-grid. You may multiply them using the self.add method and"
+                f"specifying how to handle the mismatch.")
+        else:
+            divided.on_tth[1] = other.on_tth[1] / self.on_tth[1]
+            divided.on_q[1] = other.on_q[1] / self.on_q[1]
+        return divided
+
+
+    def set_angles_from_list(self, angles_list):
+            self.angles = angles_list
+            self.n_steps = len(angles_list) - 1.
+            self.begin_angle = self.angles[0]
+            self.end_angle = self.angles[-1]
+
+    def set_qs_from_range(self, begin_q, end_q, step_size=None, n_steps=None):
+        '''
+        create an array of linear spaced Q-values
+
+        Parameters
+        ----------
+        begin_q float
+          the beginning angle
+        end_q float
+          the ending angle
+        step_size float
+          the size of the step between points.  Only specify step_size or n_steps, not both
+        n_steps integer
+          the number of steps.  Odd numbers are preferred. Only specify step_size or n_steps, not both
+
+        Returns
+        -------
+        Sets self.qs
+        self.qs array of floats
+          the q values in the independent array
+
+        '''
+        self.qs = self._set_array_from_range(begin_q, end_q, step_size=step_size, n_steps=n_steps)
+
+
+    def set_angles_from_range(self, begin_angle, end_angle, step_size=None, n_steps=None):
+        '''
+        create an array of linear spaced angle-values
+
+        Parameters
+        ----------
+        begin_angle float
+          the beginning angle
+        end_angle float
+          the ending angle
+        step_size float
+          the size of the step between points.  Only specify step_size or n_steps, not both
+        n_steps integer
+          the number of steps.  Odd numbers are preferred. Only specify step_size or n_steps, not both
+
+        Returns
+        -------
+        Sets self.angles
+        self.angles array of floats
+          the q values in the independent array
+
+        '''
+        self.angles = self._set_array_from_range(begin_angle, end_angle, step_size=step_size, n_steps=n_steps)
+
+
+    def _set_array_from_range(self, begin, end, step_size=None, n_steps=None):
+        if step_size is not None and n_steps is not None:
+            print(
+                "WARNING: both step_size and n_steps have been given.  n_steps will be used and step_size will be "
+                "reset.")
+            array = np.linspace(begin, end, n_steps)
+        elif step_size is not None:
+            array = np.arange(begin, end, step_size)
+        elif n_steps is not None:
+            array = np.linspace(begin, end, n_steps)
+        return array
+
+    def get_angle_index(self, angle):
+        count = 0
+        for i, target in enumerate(self.angles):
+            if angle == target:
+                return i
+            else:
+                count += 1
+        if count >= len(self.angles):
+            raise IndexError(f"WARNING: no angle {angle} found in angles list")
+
+    def insert_scattering_quantity(self, xarray, yarray, xtype, metadata={},
+                                   scat_quantity=None, name=None, wavelength=None):
+        f"""
+        insert a new scattering quantity into the scattering object
+        
+        Parameters
+        ----------
+        xarray array-like of floats
+          the independent variable array
+        yarray array-like of floats
+          the dependent variable array
+        xtype string
+          the type of quantity for the independent variable from {*XQUANTITIES,}
+        metadata: dict
+          the metadata in the form of a dictionary of user-supplied key:value pairs
+        
+        Returns
+        -------
+
+        """
+        self.input_xtype = xtype
+        # empty attributes have been defined in the __init__ method so only
+        # set the attributes that are not empty to avoid emptying them by mistake
+        if metadata: self.metadata = metadata
+        if scat_quantity is not None: self.scat_quantity = scat_quantity
+        if name is not None: self.name = name
+        if wavelength is not None: self.wavelength = wavelength
+        if xtype.lower() in QQUANTITIES:
+            self.on_q = [np.array(xarray),np.array(yarray)]
+        elif xtype.lower() in ANGLEQUANTITIES:
+            self.on_tth = [np.array(xarray),np.array(yarray)]
+        elif xtype.lower() in DQUANTITIES:
+            self.on_tth = [np.array(xarray),np.array(yarray)]
+        self.set_all_arrays()
+    def q_to_tth(self):
+        r"""
+        Helper function to convert q to two-theta.
+
+        By definition the relationship is:
+
+        .. math::
+
+            \sin\left(\frac{2\theta}{2}\right) = \frac{\lambda q}{4 \pi}
+
+        thus
+
+        .. math::
+
+            2\theta_n = 2 \arcsin\left(\frac{\lambda q}{4 \pi}\right)
+
+        Parameters
+        ----------
+        q : array
+            An array of :math:`q` values
+
+        wavelength : float
+            Wavelength of the incoming x-rays
+
+        Function adapted from scikit-beam.  Thanks to those developers
+
+        Returns
+        -------
+        two_theta : array
+            An array of :math:`2\theta` values in radians
+        """
+        q = self.on_q[0]
+        q = np.asarray(q)
+        wavelength = float(self.wavelength)
+        pre_factor = wavelength / (4 * np.pi)
+        return np.rad2deg(2. * np.arcsin(q * pre_factor))
+
+    def tth_to_q(self):
+        r"""
+        Helper function to convert two-theta to q
+
+        By definition the relationship is
+
+        .. math::
+
+            \sin\left(\frac{2\theta}{2}\right) = \frac{\lambda q}{4 \pi}
+
+        thus
+
+        .. math::
+
+            q = \frac{4 \pi \sin\left(\frac{2\theta}{2}\right)}{\lambda}
+
+
+
+        Parameters
+        ----------
+        two_theta : array
+            An array of :math:`2\theta` values in units of degrees
+
+        wavelength : float
+            Wavelength of the incoming x-rays
+
+        Function adapted from scikit-beam.  Thanks to those developers.
+
+        Returns
+        -------
+        q : array
+            An array of :math:`q` values in the inverse of the units
+            of ``wavelength``
+        """
+        two_theta = np.asarray(np.deg2rad(self.on_tth[0]))
+        wavelength = float(self.wavelength)
+        pre_factor = (4 * np.pi) / wavelength
+        return pre_factor * np.sin(two_theta / 2)
+
+    def set_all_arrays(self):
+        master_array, xtype = self._get_original_array()
+        if xtype == "q":
+            self.on_tth[0] = self.q_to_tth()
+            self.on_tth[1] = master_array[1]
+        if xtype == "tth":
+            self.on_q[0] = self.tth_to_q()
+            self.on_q[1] = master_array[1]
+        self.tthmin = self.on_tth[0][0]
+        self.tthmax = self.on_tth[0][-1]
+        self.qmin = self.on_q[0][0]
+        self.qmax = self.on_q[0][-1]
+
+
+    def _get_original_array(self):
+        if self.input_xtype in QQUANTITIES:
+            return self.on_q, "q"
+        elif self.input_xtype in ANGLEQUANTITIES:
+            return self.on_tth, "tth"
+        elif self.input_xtype in DQUANTITIES:
+            return self.on_d, "d"
+
+    def scale_to(self, target_diff_object, xtype=None, xvalue=None):
+        f"""
+        returns a new diffraction object which is the current object but recaled in y to the target
+
+        Parameters
+        ----------
+        target_diff_object: Diffraction_object
+          the diffractoin object you want to scale the current one on to
+        xtype: string, optional.  Default is Q
+          the xtype, from {XQUANTITIES}, that you will specify a point from to scale to
+        xvalue: float. Default is the midpoint of the array
+          the y-value in the target at this x-value will be used as the factor to scale to.
+          The entire array is scaled be the factor that places on on top of the other at that point.
+          xvalue does not have to be in the x-array, the point closest to this point will be used for the scaling.
+
+        Returns
+        -------
+        the rescaled Diffraction_object as a new object
+
+        """
+        scaled = deepcopy(self)
+        if xtype is None:
+            xtype = "q"
+
+        data = self.on_xtype(xtype)
+        target = target_diff_object.on_xtype(xtype)
+        if xvalue is None:
+            xvalue = data[0][0] + (data[0][-1] - data[0][0]) / 2.
+
+        xindex = (np.abs(data[0] - xvalue)).argmin()
+        ytarget = target[1][xindex]
+        yself = data[1][xindex]
+        scaled.on_tth[1] = data[1]*ytarget/yself
+        scaled.on_q[1] = data[1]*ytarget/yself
+        return scaled
+
+    def on_xtype(self, xtype):
+        '''
+        return a 2D np array with x in the first column and y in the second for x of type type
+        Parameters
+        ----------
+        xtype
+
+        Returns
+        -------
+
+        '''
+        if xtype.lower() in ANGLEQUANTITIES:
+            return self.on_tth
+        elif xtype.lower() in QQUANTITIES:
+            return self.on_q
+        elif xtype.lower() in DQUANTITIES:
+            return self.on_d
+        pass
+
+    def dump(self, filepath, xtype=None):
+        if xtype is None:
+            xtype = " q"
+        if xtype == "q":
+            data_to_save = np.column_stack((self.on_q[0], self.on_q[1]))
+        elif xtype == "tth":
+            data_to_save = np.column_stack((self.on_tth[0], self.on_tth[1]))
+        else:
+            print(f"WARNING: cannot handle the xtype '{xtype}'")
+
+        with open(filepath, 'w') as f:
+            f.write(f"[Diffraction_object]\nname = {self.name}\nwavelength = {self.wavelength}\n"
+                    f"scat_quantity = {self.scat_quantity}\n")
+            for key, value in self.metadata.items():
+                f.write(f"{key} = {value}\n")
+            f.write("\n#### start data\n")
+            np.savetxt(f, data_to_save, delimiter=" ")

diffpy.utils-3.3.1/src/diffpy/utils/tests/test_diffraction_objects.py

@@ -0,0 +1,25 @@
+import numpy as np
+from pathlib import Path
+from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
+
+def test_dump(tmp_path):
+	x, y = np.linspace(0, 10, 11), np.linspace(0, 10, 11)
+	directory = Path(tmp_path)
+	file = directory / "testfile"
+	test = Diffraction_object()
+	test.wavelength = 1.54
+	test.name = "test"
+	test.scat_quantity = "x-ray"
+	test.insert_scattering_quantity(x, y, "q", metadata={"thing1": 1, "thing2": "thing2"})
+	test.dump(file, "q")
+	with open(file, "r") as f:
+		actual = f.read()
+	expected = ("[Diffraction_object]\nname = test\nwavelength = 1.54\nscat_quantity = x-ray\nthing1 = 1\n"
+				"thing2 = thing2\n\n#### start data\n0.000000000000000000e+00 0.000000000000000000e+00\n"
+				"1.000000000000000000e+00 1.000000000000000000e+00\n2.000000000000000000e+00 2.000000000000000000e+00\n"
+				"3.000000000000000000e+00 3.000000000000000000e+00\n4.000000000000000000e+00 4.000000000000000000e+00\n"
+				"5.000000000000000000e+00 5.000000000000000000e+00\n"
+				"6.000000000000000000e+00 6.000000000000000000e+00\n7.000000000000000000e+00 7.000000000000000000e+00\n"
+				"8.000000000000000000e+00 8.000000000000000000e+00\n9.000000000000000000e+00 9.000000000000000000e+00\n"
+				"1.000000000000000000e+01 1.000000000000000000e+01\n")
+	assert actual == expected

{diffpy.utils-3.2.7 → diffpy.utils-3.3.1}/src/diffpy/utils/version.py

@@ -36,7 +36,7 @@ if __package__ is not None:
     with as_file(ref) as fcfg:
         if not os.path.isfile(fcfg):    # pragma: no cover
             from warnings import warn
-            warn('Package metadata not found, execute "./setup.py egg_info".')
+            warn('Package metadata not found.')
             fcfg = os.devnull
         with open(fcfg) as fp:
             kwords = [[w.strip() for w in line.split(' = ', 1)]

{diffpy.utils-3.2.7 → diffpy.utils-3.3.1}/src/diffpy.utils.egg-info/PKG-INFO

@@ -1,14 +1,12 @@
 Metadata-Version: 2.1
 Name: diffpy.utils
-Version: 3.2.7
+Version: 3.3.1
 Summary: Shared utilities for diffpy packages.
-Home-page: https://github.com/diffpy/diffpy.utils/
-Author: Simon J.L. Billinge group
-Author-email: sb2896@columbia.edu
-Maintainer: Simon J.L. Billinge group
-Maintainer-email: sb2896@columbia.edu
-License: BSD-style license
-Keywords: text data parsers wx grid
+Author-email: "Simon J.L. Billinge group" <simon.billinge@gmail.com>
+Maintainer-email: "Simon J.L. Billinge group" <simon.billinge@gmail.com>
+Project-URL: Homepage, https://github.com/diffpy/diffpy.utils/
+Project-URL: Issues, https://github.com/diffpy/diffpy.utils/issues
+Keywords: text data parsers,wx grid,diffraction objects
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
@@ -19,10 +17,12 @@ Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
 Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 License-File: LICENSE_DANSE.txt
@@ -87,7 +87,7 @@ If you prefer to install from sources, after installing the dependencies, obtain
 `GitHub <https://github.com/diffpy/diffpy.utils/>`_. Once installed, ``cd`` into your ``diffpy.utils`` directory
 and run the following ::
 
-   pip install -e .
+   pip install .
 
 To check the installation integrity, if the following passes all checks, you are good! ::
 
@@ -105,9 +105,12 @@ https://github.com/diffpy/diffpy.utils.
 
 Feel free to fork the project and contribute.  To install diffpy.utils
 in a development mode, with its sources being directly used by Python
-rather than copied to a package directory, use ::
+rather than copied to a package directory, use the following in the root
+directory ::
+
+   pip install -e .
 
-   python setup.py develop --user
+Note that this is only supported for `setuptools` version 62.0 and above.
 
 
 CONTACTS

{diffpy.utils-3.2.7 → diffpy.utils-3.3.1}/src/diffpy.utils.egg-info/SOURCES.txt

@@ -3,12 +3,11 @@ LICENSE.txt
 LICENSE_DANSE.txt
 MANIFEST.in
 README.rst
-setup.py
+pyproject.toml
 src/diffpy/__init__.py
 src/diffpy.utils.egg-info/PKG-INFO
 src/diffpy.utils.egg-info/SOURCES.txt
 src/diffpy.utils.egg-info/dependency_links.txt
-src/diffpy.utils.egg-info/not-zip-safe
 src/diffpy.utils.egg-info/top_level.txt
 src/diffpy/utils/__init__.py
 src/diffpy/utils/version.cfg
@@ -18,9 +17,12 @@ src/diffpy/utils/parsers/custom_exceptions.py
 src/diffpy/utils/parsers/loaddata.py
 src/diffpy/utils/parsers/resample.py
 src/diffpy/utils/parsers/serialization.py
+src/diffpy/utils/scattering_objects/__init__.py
+src/diffpy/utils/scattering_objects/diffraction_objects.py
 src/diffpy/utils/tests/__init__.py
 src/diffpy/utils/tests/debug.py
 src/diffpy/utils/tests/run.py
+src/diffpy/utils/tests/test_diffraction_objects.py
 src/diffpy/utils/tests/test_loaddata.py
 src/diffpy/utils/tests/test_resample.py
 src/diffpy/utils/tests/test_serialization.py

diffpy.utils-3.2.7/setup.py

@@ -1,127 +0,0 @@
-#!/usr/bin/env python
-
-"""utils - small shared utilities for other diffpy packages
-
-Packages:   diffpy.utils
-"""
-
-import os
-import re
-import sys
-from setuptools import setup, find_packages
-
-# Use this version when git data are not available, like in git zip archive.
-# Update when tagging a new release.
-FALLBACK_VERSION = '3.2.4'
-
-# versioncfgfile holds version data for git commit hash and date.
-# It must reside in the same directory as version.py.
-MYDIR = os.path.dirname(os.path.abspath(__file__))
-versioncfgfile = os.path.join(MYDIR, 'src/diffpy/utils/version.cfg')
-gitarchivecfgfile = os.path.join(MYDIR, '.gitarchive.cfg')
-
-# determine if we run with Python 3.
-PY3 = (sys.version_info[0] == 3)
-
-
-def gitinfo():
-    from subprocess import Popen, PIPE
-    kw = dict(stdout=PIPE, cwd=MYDIR, universal_newlines=True)
-    proc = Popen(['git', 'describe', '--tags', '--match=[v,V,[:digit:]]*'], **kw)
-    desc = proc.stdout.read()
-    proc = Popen(['git', 'log', '-1', '--format=%H %ct %ci'], **kw)
-    glog = proc.stdout.read()
-    rv = {}
-    rv['version'] = '.post'.join(desc.strip().split('-')[:2]).lstrip('v').lstrip('V')
-    rv['commit'], rv['timestamp'], rv['date'] = glog.strip().split(None, 2)
-    return rv
-
-
-def getversioncfg():
-    if PY3:
-        from configparser import RawConfigParser
-    else:
-        from ConfigParser import RawConfigParser
-    vd0 = dict(version=FALLBACK_VERSION, commit='', date='', timestamp=0)
-    # first fetch data from gitarchivecfgfile, ignore if it is unexpanded
-    g = vd0.copy()
-    cp0 = RawConfigParser(vd0)
-    cp0.read(gitarchivecfgfile)
-    if len(cp0.get('DEFAULT', 'commit')) > 20:
-        g = cp0.defaults()
-        mx = re.search(r'\btag: [vV]?(\d[^,]*)', g.pop('refnames'))
-        if mx:
-            g['version'] = mx.group(1)
-    # then try to obtain version data from git.
-    gitdir = os.path.join(MYDIR, '.git')
-    if os.path.exists(gitdir) or 'GIT_DIR' in os.environ:
-        try:
-            g = gitinfo()
-        except OSError:
-            pass
-    if len(g['version']) == 0:
-        g['version'] = FALLBACK_VERSION
-
-    # finally, check and update the active version file
-    cp = RawConfigParser()
-    cp.read(versioncfgfile)
-    d = cp.defaults()
-    rewrite = not d or (g['commit'] and (
-        g['version'] != d.get('version') or g['commit'] != d.get('commit')))
-    if rewrite:
-        cp.set('DEFAULT', 'version', g['version'])
-        cp.set('DEFAULT', 'commit', g['commit'])
-        cp.set('DEFAULT', 'date', g['date'])
-        cp.set('DEFAULT', 'timestamp', g['timestamp'])
-        with open(versioncfgfile, 'w') as fp:
-            cp.write(fp)
-    return cp
-
-versiondata = getversioncfg()
-
-with open(os.path.join(MYDIR, 'README.rst')) as fp:
-    long_description = fp.read()
-
-# define distribution
-setup_args = dict(
-    name = "diffpy.utils",
-    version = versiondata.get('DEFAULT', 'version'),
-    packages = find_packages(os.path.join(MYDIR, 'src')),
-    package_dir = {'' : 'src'},
-    test_suite = 'diffpy.utils.tests',
-    include_package_data = True,
-    zip_safe = False,
-    author = 'Simon J.L. Billinge group',
-    author_email = 'sb2896@columbia.edu',
-    maintainer = 'Simon J.L. Billinge group',
-    maintainer_email = 'sb2896@columbia.edu',
-    description = "Shared utilities for diffpy packages.",
-    long_description = long_description,
-    long_description_content_type = 'text/x-rst',
-    license = 'BSD-style license',
-    url = "https://github.com/diffpy/diffpy.utils/",
-    keywords = "text data parsers wx grid",
-    classifiers = [
-        # List of possible values at
-        # http://pypi.python.org/pypi?:action=list_classifiers
-        'Development Status :: 5 - Production/Stable',
-        'Environment :: Console',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: Microsoft :: Windows',
-        'Operating System :: POSIX',
-        'Operating System :: Unix',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3.11',
-        'Programming Language :: Python :: 3.12',
-        'Topic :: Scientific/Engineering :: Physics',
-    ],
-)
-
-if __name__ == '__main__':
-    setup(**setup_args)
-
-# End of file

diffpy.utils-3.2.7/src/diffpy.utils.egg-info/not-zip-safe

@@ -1 +0,0 @@
-