diff --git a/diffpy/__init__.py b/diffpy/__init__.py
deleted file mode 100644
index 7170a04..0000000
--- a/diffpy/__init__.py
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env python
-########################################################################
-#
-# diffpy            by DANSE Diffraction group
-#                   Simon J. L. Billinge
-#                   (c) 2008 The Trustees of Columbia University
-#                   in the City of New York.  All rights reserved.
-#
-# File coded by:    Pavol Juhas
-#
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE_DANSE.txt for license information.
-#
-########################################################################
-
-
-"""diffpy - tools for structure analysis by diffraction.
-
-Blank namespace package.
-"""
-
-
-__import__("pkg_resources").declare_namespace(__name__)
-
-
-# End of file
diff --git a/diffpy/srmise/__init__.py b/diffpy/srmise/__init__.py
deleted file mode 100644
index dc7bb07..0000000
--- a/diffpy/srmise/__init__.py
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-##############################################################################
-#
-# SrMise            by Luke Granlund
-#                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
-#                   All rights reserved.
-#
-# File coded by:    Luke Granlund
-#
-# See LICENSE.txt for license information.
-#
-##############################################################################
-
-"""Tools for peak extraction from PDF."""
-
-
-from diffpy.srmise.version import __version__
-
-# silence the pyflakes syntax checker
-assert __version__ or True
diff --git a/diffpy/srmise/version.py b/diffpy/srmise/version.py
deleted file mode 100644
index 094af4a..0000000
--- a/diffpy/srmise/version.py
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-##############################################################################
-#
-# SrMise            by Luke Granlund
-#                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
-#                   All rights reserved.
-#
-# File coded by:    Luke Granlund
-#
-# See LICENSE.txt for license information.
-#
-##############################################################################
-
-"""Definition of __version__, __date__, __gitsha__.
-"""
-
-from ConfigParser import SafeConfigParser
-from pkg_resources import resource_stream
-
-# obtain version information from the version.cfg file
-cp = SafeConfigParser()
-cp.readfp(resource_stream(__name__, "version.cfg"))
-
-__version__ = cp.get("DEFAULT", "version")
-__date__ = cp.get("DEFAULT", "date")
-__gitsha__ = cp.get("DEFAULT", "commit")
-
-del cp
-
-# End of file
diff --git a/pyproject.toml b/pyproject.toml
index 897eb5a..3c8f23b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,6 +7,7 @@ name = "diffpy.srmise"
 dynamic=['version']
 authors = [
   { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+        {name="Luke Granlund", email="granlund@pa.msu.edu"},
 ]
 maintainers = [
   { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
new file mode 100644
index 0000000..377a0f9
--- /dev/null
+++ b/src/diffpy/__init__.py
@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srmise/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Blank namespace package for module diffpy."""
+
+
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)
+
+# End of file
diff --git a/src/diffpy/srmise/__init__.py b/src/diffpy/srmise/__init__.py
new file mode 100644
index 0000000..65eb42b
--- /dev/null
+++ b/src/diffpy/srmise/__init__.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srmise/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Peak extraction and peak fitting tool for atomic pair distribution functions."""
+
+# package version
+from diffpy.srmise.version import __version__
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file
diff --git a/diffpy/srmise/applications/__init__.py b/src/diffpy/srmise/applications/__init__.py
similarity index 100%
rename from diffpy/srmise/applications/__init__.py
rename to src/diffpy/srmise/applications/__init__.py
diff --git a/diffpy/srmise/applications/extract.py b/src/diffpy/srmise/applications/extract.py
similarity index 100%
rename from diffpy/srmise/applications/extract.py
rename to src/diffpy/srmise/applications/extract.py
diff --git a/diffpy/srmise/applications/plot.py b/src/diffpy/srmise/applications/plot.py
similarity index 100%
rename from diffpy/srmise/applications/plot.py
rename to src/diffpy/srmise/applications/plot.py
diff --git a/diffpy/srmise/basefunction.py b/src/diffpy/srmise/basefunction.py
similarity index 100%
rename from diffpy/srmise/basefunction.py
rename to src/diffpy/srmise/basefunction.py
diff --git a/diffpy/srmise/baselines/__init__.py b/src/diffpy/srmise/baselines/__init__.py
similarity index 100%
rename from diffpy/srmise/baselines/__init__.py
rename to src/diffpy/srmise/baselines/__init__.py
diff --git a/diffpy/srmise/baselines/arbitrary.py b/src/diffpy/srmise/baselines/arbitrary.py
similarity index 100%
rename from diffpy/srmise/baselines/arbitrary.py
rename to src/diffpy/srmise/baselines/arbitrary.py
diff --git a/diffpy/srmise/baselines/base.py b/src/diffpy/srmise/baselines/base.py
similarity index 100%
rename from diffpy/srmise/baselines/base.py
rename to src/diffpy/srmise/baselines/base.py
diff --git a/diffpy/srmise/baselines/fromsequence.py b/src/diffpy/srmise/baselines/fromsequence.py
similarity index 100%
rename from diffpy/srmise/baselines/fromsequence.py
rename to src/diffpy/srmise/baselines/fromsequence.py
diff --git a/diffpy/srmise/baselines/nanospherical.py b/src/diffpy/srmise/baselines/nanospherical.py
similarity index 100%
rename from diffpy/srmise/baselines/nanospherical.py
rename to src/diffpy/srmise/baselines/nanospherical.py
diff --git a/diffpy/srmise/baselines/polynomial.py b/src/diffpy/srmise/baselines/polynomial.py
similarity index 100%
rename from diffpy/srmise/baselines/polynomial.py
rename to src/diffpy/srmise/baselines/polynomial.py
diff --git a/diffpy/srmise/dataclusters.py b/src/diffpy/srmise/dataclusters.py
similarity index 100%
rename from diffpy/srmise/dataclusters.py
rename to src/diffpy/srmise/dataclusters.py
diff --git a/diffpy/srmise/modelcluster.py b/src/diffpy/srmise/modelcluster.py
similarity index 100%
rename from diffpy/srmise/modelcluster.py
rename to src/diffpy/srmise/modelcluster.py
diff --git a/diffpy/srmise/modelevaluators/__init__.py b/src/diffpy/srmise/modelevaluators/__init__.py
similarity index 100%
rename from diffpy/srmise/modelevaluators/__init__.py
rename to src/diffpy/srmise/modelevaluators/__init__.py
diff --git a/diffpy/srmise/modelevaluators/aic.py b/src/diffpy/srmise/modelevaluators/aic.py
similarity index 100%
rename from diffpy/srmise/modelevaluators/aic.py
rename to src/diffpy/srmise/modelevaluators/aic.py
diff --git a/diffpy/srmise/modelevaluators/aicc.py b/src/diffpy/srmise/modelevaluators/aicc.py
similarity index 100%
rename from diffpy/srmise/modelevaluators/aicc.py
rename to src/diffpy/srmise/modelevaluators/aicc.py
diff --git a/diffpy/srmise/modelevaluators/base.py b/src/diffpy/srmise/modelevaluators/base.py
similarity index 100%
rename from diffpy/srmise/modelevaluators/base.py
rename to src/diffpy/srmise/modelevaluators/base.py
diff --git a/src/diffpy/srmise/modelparts.py b/src/diffpy/srmise/modelparts.py
new file mode 100644
index 0000000..37d6e0c
--- /dev/null
+++ b/src/diffpy/srmise/modelparts.py
@@ -0,0 +1,610 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# SrMise            by Luke Granlund
+#                   (c) 2014 trustees of the Michigan State University
+#                   (c) 2024 trustees of Columia University in the City of New York
+#                   All rights reserved.
+#
+# File coded by:    Luke Granlund
+#
+# See LICENSE.txt for license information.
+#
+##############################################################################
+"""Module for representing instances of mathematical functions.
+
+Classes
+-------
+ModelPart: Superclass of Peak and Baseline
+ModelParts: Collection (list) of ModelPart instances.
+"""
+
+import logging
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+# Output of scipy.optimize.leastsq for a single parameter changed in scipy 0.8.0
+# Before it returned a scalar, later it returned an array of length 1.
+import pkg_resources as pr
+from scipy.optimize import leastsq
+
+from diffpy.srmise import srmiselog
+from diffpy.srmise.srmiseerrors import SrMiseFitError, SrMiseStaticOwnerError, SrMiseUndefinedCovarianceError
+
+logger = logging.getLogger("diffpy.srmise")
+__spv__ = pr.get_distribution("scipy").version
+__oldleastsqbehavior__ = pr.parse_version(__spv__) < pr.parse_version("0.8.0")
+
+
+class ModelParts(list):
+    """A collection of ModelPart instances.
+
+    Methods
+    -------
+    copy: Return deep copy
+    fit: Fit to given data
+    npars: Return total number of parameters
+    pack_freepars: Update free parameters with values in given sequence
+    residual: Return residual of model
+    residual_jacobian: Return jacobian of residual of model
+    transform: Change format of parameters.
+    value: Return value of model
+    unpack_freepars: Return sequence containing value of all free parameters
+    """
+
+    def __init__(self, *args, **kwds):
+        list.__init__(self, *args, **kwds)
+
+    def fit(
+        self,
+        r,
+        y,
+        y_error,
+        range=None,
+        ntrials=0,
+        cov=None,
+        cov_format="default_output",
+    ):
+        """Chi-square fit of all free parameters to given data.
+
+        There must be at least as many free parameters as data points.
+        Fitting is performed with the MINPACK leastsq() routine exposed by scipy.
+
+        Parameters
+        r - Sequence of r values over which to fit
+        y - Sequence of y values over which to fit
+        y_error - Sequence of uncertainties in y
+        range - Slice object specifying region of r and y over which to fit.
+                Fits over all the data by default.
+        ntrials - The maximum number of function evaluations while fitting.
+        cov - Optional ModelCovariance object preserves covariance information.
+        cov_format - Parameterization to use in cov.
+        """
+        freepars = self.unpack_freepars()
+        if len(freepars) >= len(r):
+            emsg = (
+                "Cannot fit model with "
+                + str(len(freepars))
+                + " free parametersbut only "
+                + str(len(r))
+                + " data points."
+            )
+            raise SrMiseFitError(emsg)
+        if len(freepars) == 0:
+            # emsg = "Cannot fit model with no free parameters."
+            # raise SrMiseFitError(emsg)
+            return
+
+        if range is None:
+            range = slice(None)
+
+        args = (r, y, y_error, range)
+
+        if srmiselog.liveplots:
+            plt.figure(1)
+            plt.ioff()
+            plt.subplot(211)
+            plt.cla()
+            plt.title("Before")
+            plt.plot(r, y, label="_nolabel_")
+            plt.plot(
+                r,
+                (y - self.value(r, range=range)) - 1.1 * (max(y) - min(y)),
+                label="_nolabel_",
+            )
+            for p in self:
+                plt.plot(r, p.value(r, range=range), label=str(p))
+            plt.ion()
+
+        try:
+            f = leastsq(
+                self.residual,  # minimize this function
+                freepars,  # initial parameters
+                args=args,  # arguments to residual, residual_jacobian
+                Dfun=self.residual_jacobian,  # explicit Jacobian
+                col_deriv=1,  # order of derivatives in Jacobian
+                full_output=1,
+                maxfev=ntrials,
+            )
+        except NotImplementedError:
+            # TODO: Figure out if is worth checking for residual_jacobian
+            # before leastsq().  This exception will either occur almost never
+            # or extremely frequently, and the extra evaluations will add up.
+            logger.info("One or more functions do not define residual_jacobian().")
+            f = leastsq(
+                self.residual,  # minimize this function
+                freepars,  # initial parameters
+                args=args,  # arguments to residual
+                col_deriv=1,  # order of derivatives in Jacobian
+                full_output=1,
+                maxfev=ntrials,
+            )
+        except Exception:
+            # Sadly, KeyboardInterrupt, etc. is reraised as minpack.error
+            # Not much I can do about that, though.
+            import traceback
+
+            emsg = (
+                "Unexpected error in modelparts.fit().  Original exception:\n"
+                + traceback.format_exc()
+                + "End original exception."
+            )
+            raise SrMiseFitError(emsg)
+
+        result = f[0]
+        if __oldleastsqbehavior__ and len(freepars) == 1:
+            # leastsq returns a scalar when there is only one parameter
+            result = np.array([result])
+
+        self.pack_freepars(result)
+
+        if srmiselog.liveplots:
+            plt.draw()
+            plt.ioff()
+            plt.figure(1)
+            plt.subplot(212)
+            plt.cla()
+            plt.title("After")
+            plt.ion()
+            plt.plot(
+                r,
+                y,
+                r,
+                (y - self.value(r, range=range)) - 1.1 * (max(y) - min(y)),
+                *[i for sublist in [[r, p.value(r, range=range)] for p in self] for i in sublist],
+            )
+            plt.draw()
+
+            if srmiselog.wait:
+                print(
+                    "Press 'Enter' to continue...",
+                )
+                input()
+
+        if f[4] not in (1, 2, 3, 4):
+            emsg = "Fit did not succeed -- " + str(f[3])
+            raise SrMiseFitError(emsg)
+
+        # clean up parameters
+        for p in self:
+            p.pars = p.owner().transform_parameters(p.pars, in_format="internal", out_format="internal")
+
+        # Supply estimated covariance matrix if requested.
+        # The precise relationship between f[1] and estimated covariance matrix is a little unclear from
+        # the documentation of leastsq.  This is the interpretation given by scipy.optimize.curve_fit,
+        # which is a wrapper around leastsq.
+        if cov is not None:
+            pcov = f[1]
+            fvec = f[2]["fvec"]
+            dof = len(r) - len(freepars)
+            cov.setcovariance(self, pcov * np.sum(fvec**2) / dof)
+            try:
+                cov.transform(in_format="internal", out_format=cov_format)
+            except SrMiseUndefinedCovarianceError:
+                logger.warn("Covariance not defined.  Fit may not have converged.")
+
+        return
+
+    # # Notes on the fit f
+    # f[0] = solution
+    # f[1] = Uses the fjac and ipvt optional outputs to construct an estimate of the jacobian around the solution.
+    #        None if a singular matrix encountered (indicates very flat curvature in some direction).
+    #        This matrix must be multiplied by the residual variance to get the covariance of the parameter
+    #        estimates - see curve fit.
+    # f[2] = dictionary{nfev: int, fvec: array(), fjac: array(), ipvt: array(), qtf: array()}
+    #        nfev - The number of function calls made
+    #        fvec - function (residual) evaluated at solution
+    #        fjac - "a permutation of the R matrix of a QR factorization of the final Jacobian."
+    #        ipvt - integer array defining a permutation matrix P such that fjac*P=QR
+    #        qtf - transpose(q)*fvec
+    # f[3] = message about results of fit
+    # f[4] = integer flag.  Fit was successful on 1,2,3, or 4.  Otherwise unsuccessful.
+
+    def npars(self, count_fixed=True):
+        """Return total number of parameters in all parts.
+
+        Parameters
+        count_fixed - Boolean which determines if fixed parameters are
+                      are included in the count.
+        """
+        n = 0
+        for p in self:
+            n += p.npars(count_fixed=count_fixed)
+        return n
+
+    def pack_freepars(self, freepars):
+        """Update parameters with values from sequence of freepars."""
+        if np.isnan(freepars).any():
+            emsg = "Non-numeric free parameters."
+            raise ValueError(emsg)
+        freeidx = 0
+        for p in self:
+            freeidx += p.update(freepars[freeidx:])
+
+    def residual(self, freepars, r, y_expected, y_error, range=None):
+        """Calculate residual of all parameters.
+
+        Parameters
+        freepars - sequence of free parameters
+        r - the input domain
+        y_expected - sequence of expected values
+        y_error - sequence of uncertainties in y-variable
+        range - Slice object specifying region of r and y over which to fit.
+                All the data by default.
+        """
+        self.pack_freepars(freepars)
+        total = self.value(r, range)
+        try:
+            if range is None:
+                range = slice(0, len(r))
+            return (y_expected[range] - total[range]) / y_error[range]
+        except TypeError:
+            return (y_expected - total) / y_error
+
+    def residual_jacobian(self, freepars, r, y_expected, y_error, range=None):
+        """Calculate the Jacobian of freepars.
+
+        Parameters
+        freepars - sequence of free parameters
+        r - the input domain
+        y_expected - sequence of expected values
+        y_error - sequence of uncertainties in y-variable
+        range - Slice object specifying region of r and y over which to fit.
+                All the data by default.
+        """
+        if len(freepars) == 0:
+            raise ValueError(
+                "Argument freepars has length 0.  The Jacobian " "is only defined with >=1 free parameters."
+            )
+
+        self.pack_freepars(freepars)
+        tempJac = []
+        for p in self:
+            tempJac[len(tempJac) :] = p.jacobian(r, range)
+        # Since the residual is (expected - calculated) the jacobian
+        # of the residual has a minus sign.
+        jac = -np.array([j for j in tempJac if j is not None])
+        try:
+            if range is None:
+                range = slice(0, len(r))
+            return jac[:, range] / y_error[range]
+        except TypeError:
+            return jac / y_error
+
+    def value(self, r, range=None):
+        """Calculate total value of all parts over range.
+
+        Parameters
+        r - the input domain
+        range - Slice object specifying region of r and y over which to fit.
+                All the data by default.
+        """
+        total = r * 0.0
+        for p in self:
+            total += p.value(r, range)
+        return total
+
+    def unpack_freepars(self):
+        """Return array of all free parameters."""
+        # To check: ravel() sometimes returns a reference and othertimes a copy.
+        #          Do I need to use flatten() instead?
+        return np.concatenate([p.compress() for p in self]).ravel()
+
+    def covariance(self, format="internal", **kwds):
+        """Return estimated covariance matrix of the model.
+
+        The covariance matrix may be given in terms of any parameterization
+        defined by the formats for each individual ModelPart.
+
+        Parameters
+        format - The format ("internal" by default) to use for all ModelParts.
+                 This may be overridden for specific peaks as shown below.
+
+        Keywords
+        f0 - The format of the 0th ModelPart
+        f1 - The format of the 1st ModelPart
+        etc.
+        """
+        formats = [format for p in self]
+
+        for k, v in kwds.items():
+            try:
+                int(k[1:])
+            except ValueError:
+                emsg = "Invalid format keyword '%s'.  They must be specified as 'f0', 'f1', etc." % k
+                raise ValueError(emsg)
+
+            formats[int(k[1:])] = v
+
+        return
+
+    def copy(self):
+        """Return deep copy of this ModelParts.
+
+        The original and the copy are completely independent, except each
+        ModelPart and its copy still reference the same owner."""
+        return type(self).__call__([p.copy() for p in self])
+
+    def __str__(self):
+        """Return string representation of this ModelParts."""
+        return "".join([str(p) + "\n" for p in self])
+
+    def __getslice__(self, i, j):
+        """Extends list.__getslice__"""
+        return self.__class__(list.__getslice__(self, i, j))
+
+    def transform(self, in_format="internal", out_format="internal"):
+        """Transforms format of parameters in this modelpart.
+
+        Parameters
+        in_format - The format the parameters are already in.
+        out_format - The format the parameters are transformed to.
+        """
+        for p in self:
+            try:
+                p.pars = p.owner().transform_parameters(p.pars, in_format, out_format)
+            except ValueError:
+                logger.info(
+                    "Invalid parameter transformation: Ignoring %s->%s for function of type %s."
+                    % (in_format, out_format, p.owner().getmodule())
+                )
+
+
+# End of class ModelParts
+
+
+class ModelPart(object):
+    """Represents a single part (instance of some function) of a model.
+
+    Members
+    -------
+    pars - Array containing the parameters of this model part
+    free - Array containing boolean values defining whether the corresponding parameter
+           is free or not.
+    removable - Boolean determining whether or not this model part can be
+                removed during extraction.
+    static_owner - Boolean determines if owner can be changed with changeowner()
+
+    Methods
+    -------
+    changeowner - Change the owner of self
+    copy - Return deep copy of self
+    compress - Return parameters with non-free parameters removed
+    jacobian - Return jacobian
+    getfree - Return free parameter by index or keyword define by owner
+    npars - Return number of parameters in self
+    owner - Return self.owner
+    setfree - Set a free parameter by index or keyword defined by owner
+    update - Update free parameters with values in given sequence
+    value - Return value
+    writestr - Return string representation of self
+    """
+
+    def __init__(self, owner, pars, free=None, removable=True, static_owner=False):
+        """Set instance members.
+
+        Parameters
+        owner - an instance of a BaseFunction subclass
+        pars - Sequence of parameters which specify the function explicitly
+        free - Sequence of Boolean variables.  If False, the corresponding
+               parameter will not be changed.
+        removable - Boolean determines whether this part can be removed.
+        static_owner - Whether or not the part can be changed with
+                       changeowner()
+
+        Note that free and removable are not mutually exclusive.  If any
+        pars are not free but removable=True then the part may be removed, but
+        the held parameters for this part will remain unchanged until then.
+        """
+        self._owner = owner
+
+        if len(pars) != owner.npars:
+            emsg = "The length of pars must equal the number of parameters " + "specified by the model part owner."
+            raise ValueError(emsg)
+        self.pars = np.array(pars[:])  # pars[:] in case pars is a ModelPart
+
+        if free is None:
+            self.free = np.array([True for p in pars], dtype=bool)
+        else:
+            self.free = np.array(free, dtype=bool)
+        if len(self.free) != owner.npars:
+            emsg = (
+                "The length of free must be equal to the number of "
+                + "parameters specified by the model part owner."
+            )
+            raise ValueError(emsg)
+
+        self.removable = removable
+        self.static_owner = static_owner
+
+    def changeowner(self, owner):
+        """Change the owner of this part.
+
+        Does not change the parameters associated with this model part. Raises
+        SrMiseStaticOwnerError if this peak has been declared to have a static
+        owner, or if the number of parameters is incompatible.
+
+        Parameters
+        owner - an instance of a BaseFunction subclass
+        """
+        if self.static_owner and self._owner is not owner:
+            emsg = "Cannot change owner if static_owner is True."
+            raise SrMiseStaticOwnerError(emsg)
+        if self._owner.npars != owner.npars:
+            emsg = "New owner specifies different number of parameters than " + "original owner."
+            raise SrMiseStaticOwnerError(emsg)
+        self._owner = owner
+
+    def compress(self):
+        """Return part parameters with non-free values removed."""
+        return self.pars[self.free]
+
+    def jacobian(self, r, range=None):
+        """Return jacobian of this part over r.
+
+        Parameters
+        r - the input domain
+        range - Slice object specifying region of r and y over which to fit.
+                All the data by default.
+        """
+        return self._owner.jacobian(self, r, range)
+
+    def owner(self):
+        """Return the BaseFunction subclass instance which owns this part."""
+        return self._owner
+
+    def update(self, freepars):
+        """Sequentially update free parameters from freepars.
+
+        Parameters
+        freepars - sequence of new parameter values.  May contain more
+                   parameters than can actually be updated.
+
+        Return number of parameters updated from freepars.
+        """
+        numfree = self.npars(count_fixed=False)
+        if len(freepars) < numfree:
+            pass  # raise "freepars does not have enough elements to
+            # update every unheld parameter."
+        # TODO: Check if I need to make copies here, or if references
+        #       to parameters are safe.
+        self.pars[self.free] = freepars[:numfree]
+        return numfree
+
+    def value(self, r, range=None):
+        """Return value of peak over r.
+
+        Parameters
+        r - the input domain
+        range - Slice object specifying region of r and y over which to fit.
+                All the data by default.
+        """
+        return self._owner.value(self, r, range)
+
+    def copy(self):
+        """Return a deep copy of this ModelPart.
+
+        The original and the copy are completely independent, except they both
+        reference the same owner."""
+        return type(self).__call__(self._owner, self.pars, self.free, self.removable, self.static_owner)
+
+    def __getitem__(self, key_or_idx):
+        """Return parameter of peak corresponding with key_or_idx.
+
+        Parameters
+        key_or_idx - An integer index, slice, or key from owner's parameter
+                     dictionary.
+        """
+        if key_or_idx in self._owner.parameterdict:
+            return self.pars[self._owner.parameterdict[key_or_idx]]
+        else:
+            return self.pars[key_or_idx]
+
+    def getfree(self, key_or_idx):
+        """Return value of free corresponding with key_or_idx.
+
+        Parameters
+        key_or_idx - An integer index, slice, or key from owner's parameter
+                     dictionary."""
+        if key_or_idx in self._owner.parameterdict:
+            return self.free[self._owner.parameterdict[key_or_idx]]
+        else:
+            return self.free[key_or_idx]
+
+    def setfree(self, key_or_idx, value):
+        """Set value of free corresponding with key_or_idx.
+
+        Parameters
+        key_or_idx - An integer index, slice, or key from owner's parameter
+                     dictionary.
+        value: A boolean"""
+        if key_or_idx in self._owner.parameterdict:
+            self.free[self._owner.parameterdict[key_or_idx]] = value
+        else:
+            self.free[key_or_idx] = value
+
+    def __len__(self):
+        """Return number of parameters, including any fixed ones."""
+        return self._owner.npars
+
+    def npars(self, count_fixed=True):
+        """Return total number of parameters in all parts.
+
+        Parameters
+        count_fixed - Boolean which determines if fixed parameters are
+                      are included in the count."""
+        if count_fixed:
+            return self._owner.npars
+        else:
+            return (self.free is True).sum()
+
+    def __str__(self):
+        """Return string representation of ModelPart parameters."""
+        return str(self._owner.transform_parameters(self.pars, in_format="internal", out_format="default_output"))
+
+    def __eq__(self, other):
+        """ """
+        if hasattr(other, "_owner"):
+            return (
+                (self._owner is other._owner)
+                and np.all(self.pars == other.pars)
+                and np.all(self.free == other.free)
+                and self.removable == other.removable
+            )
+        else:
+            return False
+
+    def __ne__(self, other):
+        """ """
+        return not self == other
+
+    def writestr(self, ownerlist):
+        """Return string representation of ModelPart.
+
+        The value of owner is determined by its index in ownerlist.
+
+        Parameters
+        ownerlist - List of owner functions
+        """
+        if self._owner not in ownerlist:
+            emsg = "ownerlist does not contain this ModelPart's owner."
+            raise ValueError(emsg)
+        lines = []
+        lines.append("owner=%s" % repr(ownerlist.index(self._owner)))
+
+        # Lists/numpy arrays don't give full representation of long lists
+        lines.append("pars=[%s]" % ", ".join([repr(p) for p in self.pars]))
+        lines.append("free=[%s]" % ", ".join([repr(f) for f in self.free]))
+        lines.append("removable=%s" % repr(self.removable))
+        lines.append("static_owner=%s" % repr(self.static_owner))
+        datastring = "\n".join(lines) + "\n"
+        return datastring
+
+
+# End of class ModelPart
+
+# simple test code
+if __name__ == "__main__":
+
+    pass
diff --git a/diffpy/srmise/multimodelselection.py b/src/diffpy/srmise/multimodelselection.py
similarity index 100%
rename from diffpy/srmise/multimodelselection.py
rename to src/diffpy/srmise/multimodelselection.py
diff --git a/diffpy/srmise/pdfdataset.py b/src/diffpy/srmise/pdfdataset.py
similarity index 100%
rename from diffpy/srmise/pdfdataset.py
rename to src/diffpy/srmise/pdfdataset.py
diff --git a/diffpy/srmise/pdfpeakextraction.py b/src/diffpy/srmise/pdfpeakextraction.py
similarity index 100%
rename from diffpy/srmise/pdfpeakextraction.py
rename to src/diffpy/srmise/pdfpeakextraction.py
diff --git a/diffpy/srmise/peakextraction.py b/src/diffpy/srmise/peakextraction.py
similarity index 100%
rename from diffpy/srmise/peakextraction.py
rename to src/diffpy/srmise/peakextraction.py
diff --git a/diffpy/srmise/peaks/__init__.py b/src/diffpy/srmise/peaks/__init__.py
similarity index 100%
rename from diffpy/srmise/peaks/__init__.py
rename to src/diffpy/srmise/peaks/__init__.py
diff --git a/diffpy/srmise/peaks/base.py b/src/diffpy/srmise/peaks/base.py
similarity index 100%
rename from diffpy/srmise/peaks/base.py
rename to src/diffpy/srmise/peaks/base.py
diff --git a/diffpy/srmise/peaks/gaussian.py b/src/diffpy/srmise/peaks/gaussian.py
similarity index 100%
rename from diffpy/srmise/peaks/gaussian.py
rename to src/diffpy/srmise/peaks/gaussian.py
diff --git a/diffpy/srmise/peaks/gaussianoverr.py b/src/diffpy/srmise/peaks/gaussianoverr.py
similarity index 100%
rename from diffpy/srmise/peaks/gaussianoverr.py
rename to src/diffpy/srmise/peaks/gaussianoverr.py
diff --git a/diffpy/srmise/peaks/terminationripples.py b/src/diffpy/srmise/peaks/terminationripples.py
similarity index 100%
rename from diffpy/srmise/peaks/terminationripples.py
rename to src/diffpy/srmise/peaks/terminationripples.py
diff --git a/diffpy/srmise/peakstability.py b/src/diffpy/srmise/peakstability.py
similarity index 100%
rename from diffpy/srmise/peakstability.py
rename to src/diffpy/srmise/peakstability.py
diff --git a/diffpy/srmise/srmiseerrors.py b/src/diffpy/srmise/srmiseerrors.py
similarity index 100%
rename from diffpy/srmise/srmiseerrors.py
rename to src/diffpy/srmise/srmiseerrors.py
diff --git a/diffpy/srmise/srmiselog.py b/src/diffpy/srmise/srmiselog.py
similarity index 100%
rename from diffpy/srmise/srmiselog.py
rename to src/diffpy/srmise/srmiselog.py
diff --git a/src/diffpy/srmise/tests/__init__.py b/src/diffpy/srmise/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/diffpy/srmise/tests/conftest.py b/src/diffpy/srmise/tests/conftest.py
new file mode 100644
index 0000000..e3b6313
--- /dev/null
+++ b/src/diffpy/srmise/tests/conftest.py
@@ -0,0 +1,19 @@
+import json
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def user_filesystem(tmp_path):
+    base_dir = Path(tmp_path)
+    home_dir = base_dir / "home_dir"
+    home_dir.mkdir(parents=True, exist_ok=True)
+    cwd_dir = base_dir / "cwd_dir"
+    cwd_dir.mkdir(parents=True, exist_ok=True)
+
+    home_config_data = {"username": "home_username", "email": "home@email.com"}
+    with open(home_dir / "diffpyconfig.json", "w") as f:
+        json.dump(home_config_data, f)
+
+    yield tmp_path
diff --git a/src/diffpy/srmise/tests/debug.py b/src/diffpy/srmise/tests/debug.py
new file mode 100644
index 0000000..313b120
--- /dev/null
+++ b/src/diffpy/srmise/tests/debug.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srmise/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""
+Convenience module for debugging the unit tests using
+
+python -m diffpy.srmise.tests.debug
+
+Exceptions raised by failed tests or other errors are not caught.
+"""
+
+
+if __name__ == "__main__":
+    import sys
+
+    from diffpy.srmise.tests import testsuite
+
+    pattern = sys.argv[1] if len(sys.argv) > 1 else ""
+    suite = testsuite(pattern)
+    suite.debug()
+
+
+# End of file
diff --git a/src/diffpy/srmise/tests/run.py b/src/diffpy/srmise/tests/run.py
new file mode 100644
index 0000000..afe4bbf
--- /dev/null
+++ b/src/diffpy/srmise/tests/run.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srmise/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Convenience module for executing all unit tests with
+python -m diffpy.srmise.tests.run
+"""
+
+import sys
+
+import pytest
+
+if __name__ == "__main__":
+    # show output results from every test function
+    args = ["-v"]
+    # show the message output for skipped and expected failure tests
+    if len(sys.argv) > 1:
+        args.extend(sys.argv[1:])
+    print("pytest arguments: {}".format(args))
+    # call pytest and exit with the return code from pytest
+    exit_res = pytest.main(args)
+    sys.exit(exit_res)
+
+# End of file
diff --git a/src/diffpy/srmise/version.py b/src/diffpy/srmise/version.py
new file mode 100644
index 0000000..304027c
--- /dev/null
+++ b/src/diffpy/srmise/version.py
@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srmise/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Definition of __version__."""
+
+#  We do not use the other three variables, but can be added back if needed.
+#  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
+
+# obtain version information
+from importlib.metadata import version
+
+__version__ = version("diffpy.srmise")
+
+# End of file