skpkg: add scaffold, moved over .git. docs, test

.flake8

@@ -1,3 +1,5 @@
+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
 [flake8]
 exclude =
     .git,

.isort.cfg

@@ -1,4 +1,5 @@
 [settings]
+# Keep import statement below line_length character limit
 line_length = 115
 multi_line_output = 3
 include_trailing_comma = True

.pre-commit-config.yaml

@@ -50,3 +50,9 @@ repos:
     - id: codespell
       additional_dependencies:
         - tomli
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+    - id: docformatter
+      additional_dependencies: [tomli]
+      args: [--in-place, --wrap-summaries, "115", --wrap-descriptions, "115"] #--config, ./pyproject.toml]

doc/examples/fit_initial.py

@@ -12,12 +12,11 @@
 ##############################################################################
 """Example of peak fitting C60 PDF (unnormalized) with unreliable uncertainties.
 
-Peak fitting in SrMise means fitting a model of initial peaks, which may be
-specified manually or estimated with a clustering-based convenience function,
-just as with specifying initial peaks for peak extraction.  Unlike peak
-extraction, it does not attempt to add or remove peaks, apply termination
-ripples, or otherwise do anything beyond chi-square fitting using the specified
-grid."""
+Peak fitting in SrMise means fitting a model of initial peaks, which may be specified manually or estimated with a
+clustering-based convenience function, just as with specifying initial peaks for peak extraction.  Unlike peak
+extraction, it does not attempt to add or remove peaks, apply termination ripples, or otherwise do anything beyond
+chi-square fitting using the specified grid.
+"""
 
 import matplotlib.pyplot as plt
 

doc/examples/multimodel_known_dG1.py

@@ -10,8 +10,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""Extract multiple models from crystalline PDF with known uncertainties for
-use in later AIC-driven multimodeling analysis.
+"""Extract multiple models from crystalline PDF with known uncertainties for use in later AIC-driven multimodeling
+analysis.
 
 The multimodel approach generates many models of varying complexity by assuming
 a range of experimental uncertainties are physically plausible.  This example

doc/examples/multimodel_unknown_dG1.py

@@ -10,8 +10,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""Extract multiple models from nanoparticle PDF with unknown uncertainties for
-use in later AIC-driven multimodeling analysis.
+"""Extract multiple models from nanoparticle PDF with unknown uncertainties for use in later AIC-driven
+multimodeling analysis.
 
 The multimodel approach generates many models of varying complexity by assuming
 a range of experimental uncertainties are physically plausible.  This example

doc/examples/multimodel_unknown_dG2.py

@@ -10,8 +10,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""AIC-driven multimodel analysis of nanoparticle PDF with unknown
-uncertainties.
+"""AIC-driven multimodel analysis of nanoparticle PDF with unknown uncertainties.
 
 The multimodel approach generates many models of varying complexity by assuming
 a range of experimental uncertainties are physically plausible.  This example

doc/examples/parameter_summary.py

@@ -25,7 +25,8 @@
 nyquist (whether to use Nyquist sampling)
 supersample (minimum amount to oversample during initial stages)
 cres (clustering resolution)
-initial_peaks (peaks already assumed to exist during extraction)"""
+initial_peaks (peaks already assumed to exist during extraction)
+"""
 
 import matplotlib.pyplot as plt
 

pyproject.toml

@@ -6,22 +6,20 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.srmise"
 dynamic=['version', 'dependencies']
 authors = [
-  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
-        {name="Luke Granlund", email="granlund@pa.msu.edu"},
+  { name="Simon Billinge", email="sb2896@columbia.edu" },
 ]
 maintainers = [
-  { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
+  { name="Simon Billinge", email="sb2896@columbia.edu" },
 ]
 description = "Peak extraction and peak fitting tool for atomic pair distribution functions."
-keywords = ['peak extraction fitting PDF AIC multimodeling']
+keywords = ['peak extraction', 'fitting', 'PDF', 'AIC', 'multimodeling']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"
 classifiers = [
-        'Development Status :: 3 - Alpha',
+        'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
         'Intended Audience :: Developers',
         'Intended Audience :: Science/Research',
-        'Intended Audience :: Education',
         'License :: OSI Approved :: BSD License',
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: Microsoft :: Windows',
@@ -32,7 +30,6 @@ classifiers = [
         'Programming Language :: Python :: 3.13',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
-        'Topic :: Software Development :: Libraries',
 ]
 
 [project.urls]
@@ -45,9 +42,6 @@ template = "{tag}"
 dev_template = "{tag}"
 dirty_template = "{tag}"
 
-[project.scripts]
-srmise = "diffpy.srmise.applications.extract:main"
-
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)

src/diffpy/__init__.py

@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Blank namespace package for module diffpy."""
 
 

src/diffpy/srmise/__init__.py

@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Peak extraction and peak fitting tool for atomic pair distribution functions."""
 
 # package version

src/diffpy/srmise/applications/plot.py

@@ -11,7 +11,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""plot extracted peaks and comparison to ideal distances (if given)"""
+"""Plot extracted peaks and comparison to ideal distances (if given)"""
 
 import optparse
 import sys
@@ -175,7 +175,7 @@ def labelallsubplots():
 
 
 def makeplot(ppe_or_stability, ip=None, **kwds):
-    """Plot stuff"""
+    """Plot stuff."""
     if isinstance(ppe_or_stability, PeakStability):
         stability = ppe_or_stability
         ppe = stability.ppe

src/diffpy/srmise/basefunction.py

@@ -76,7 +76,7 @@ def __init__(
         base=None,
         Cache=None,
     ):
-        """Set parameterdict defined by subclass
+        """Set parameterdict defined by subclass.
 
         Parameters
         ----------
@@ -159,32 +159,50 @@ def __init__(
     # "Virtual" class methods ####
 
     def actualize(self, *args, **kwds):
-        """Create ModelPart instance of self with given parameters.  ("Virtual" method)"""
+        """Create ModelPart instance of self with given parameters.
+
+        ("Virtual" method)
+        """
         emsg = "actualize() must be implemented in a BaseFunction subclass."
         raise NotImplementedError(emsg)
 
     def estimate_parameters(self, *args, **kwds):
-        """Estimate BaseFunction parameters from supplied data. ("Virtual" method)"""
+        """Estimate BaseFunction parameters from supplied data.
+
+        ("Virtual" method)
+        """
         emsg = "estimate_parameters() must be implemented in a BaseFunction subclass."
         raise NotImplementedError(emsg)
 
     def _jacobianraw(self, *args, **kwds):
-        """Calculate the jacobian. ("Virtual" method)"""
+        """Calculate the jacobian.
+
+        ("Virtual" method)
+        """
         emsg = "_jacobianraw() must be implemented in a BaseFunction subclass."
         raise NotImplementedError(emsg)
 
     def _transform_derivativesraw(self, *args, **kwds):
-        """Convert BaseFunction parameters to another form. ("Virtual" method)"""
+        """Convert BaseFunction parameters to another form.
+
+        ("Virtual" method)
+        """
         emsg = "transform_parameters() must be implemented in a BaseFunction subclass."
         raise NotImplementedError(emsg)
 
     def _transform_parametersraw(self, *args, **kwds):
-        """Convert BaseFunction parameters to another form. ("Virtual" method)"""
+        """Convert BaseFunction parameters to another form.
+
+        ("Virtual" method)
+        """
         emsg = "transform_parameters() must be implemented in a BaseFunction subclass."
         raise NotImplementedError(emsg)
 
     def _valueraw(self, *args, **kwds):
-        """Calculate value of function. ("Virtual" method)"""
+        """Calculate value of function.
+
+        ("Virtual" method)
+        """
         emsg = "_valueraw must() be implemented in a BaseFunction subclass."
         raise NotImplementedError(emsg)
 
@@ -373,7 +391,7 @@ def pgradient(self, p, format):
         return
 
     def getmodule(self):
-        """Return 'diffpy.srmise.basefunction'"""
+        """Return 'diffpy.srmise.basefunction'."""
         return "diffpy.srmise.basefunction"
 
     def writestr(self, baselist):
@@ -480,7 +498,8 @@ def safefunctionlist(fs):
         is guaranteed to be safe for saving/reinstantiating peak functions.
 
         Parameters
-        fs: List of BaseFunction instances."""
+        fs: List of BaseFunction instances.
+        """
         fsafe = []
         for f in fs:
             BaseFunction.safefunction(f, fsafe)

src/diffpy/srmise/baselines/arbitrary.py

@@ -26,17 +26,12 @@
 class Arbitrary(BaselineFunction):
     """Methods for evaluating a baseline from an arbitrary function.
 
-    Supports baseline calculations with arbitrary functions.  These functions,
-    if implemented, must have the following signatures and return values:
-    valuef(pars, x) ==> numpy.array of length x if x is a sequence
-                  ==> number if x is a number
-    jacobianf(pars, x, free) ==> list, each element a numpy.array of length x if
-                                x is a sequence or None if value of free for
-                                that parameter is False.
-                            ==> list, each element a number if x is a number
-                                or None if value of free for that parameter is
-                                False
-    estimatef(x, y) ==> numpy.array of length npars
+    Supports baseline calculations with arbitrary functions.  These functions, if implemented, must have the
+    following signatures and return values: valuef(pars, x) ==> numpy.array of length x if x is a sequence
+    ==> number if x is a number jacobianf(pars, x, free) ==> list, each element a numpy.array of length x if
+    x is a sequence or None if value of free for                             that parameter is False.
+    ==> list, each element a number if x is a number                             or None if value of free for that
+    parameter is                             False estimatef(x, y) ==> numpy.array of length npars
     """
 
     def __init__(self, npars, valuef, jacobianf=None, estimatef=None, Cache=None):
@@ -117,7 +112,8 @@ def estimate_parameters(self, r, y):
         The numpy array of parameters in the default internal format.
 
         we raise NotImplementedError if no estimation routine is defined, and
-        SrMiseEstimationError if parameters cannot be estimated for any other."""
+        SrMiseEstimationError if parameters cannot be estimated for any other.
+        """
         if self.estimatef is None:
             emsg = "No estimation routine provided to Arbitrary."
             raise NotImplementedError(emsg)

src/diffpy/srmise/baselines/base.py

@@ -71,7 +71,7 @@ def __init__(
         base=None,
         Cache=None,
     ):
-        """Set parameterdict defined by subclass
+        """Set parameterdict defined by subclass.
 
         parameterdict : dict
             The dictionary mapping string keys to their index in a
@@ -91,7 +91,8 @@ def __init__(
             additional functionality.
         Cache : class
             The class (not instance) which implements caching of BaseFunction
-            evaluations."""
+            evaluations.
+        """
         BaseFunction.__init__(self, parameterdict, parformats, default_formats, metadict, base, Cache)
 
     # "Virtual" class methods ####

src/diffpy/srmise/baselines/fromsequence.py

@@ -25,9 +25,9 @@
 class FromSequence(BaselineFunction):
     """Methods for evaluation of a baseline from discrete data via interpolation.
 
-    FromSequence uses cubic spline interpolation (no smoothing) on discrete
-    points to approximate the baseline at arbitrary points within the
-    interpolation domain.  This baseline function permits no free parameters."""
+    FromSequence uses cubic spline interpolation (no smoothing) on discrete points to approximate the baseline at
+    arbitrary points within the interpolation domain.  This baseline function permits no free parameters.
+    """
 
     def __init__(self, *args, **kwds):
         """Initialize a baseline object based on input sequences `x` and `y`.
@@ -233,7 +233,7 @@ def xyrepr(self, var):
         return "[%s]" % ", ".join([repr(v) for v in var])
 
     def readxy(self, filename):
-        """ """
+        """"""
         from diffpy.srmise.srmiseerrors import SrMiseDataFormatError
 
         # TODO: Make this safer

src/diffpy/srmise/baselines/nanospherical.py

@@ -267,7 +267,7 @@ def _valueraw2(self, pars, r):
         return -s * r * (1 - (3.0 / 4.0) * rdivR + (1.0 / 16.0) * rdivR**3)
 
     def _getdomain(self, pars, r):
-        """Return slice object for which r > 0 and r < twice the radius
+        """Return slice object for which r > 0 and r < twice the radius.
 
         Parameters
         ----------

src/diffpy/srmise/dataclusters.py

@@ -53,7 +53,7 @@ class DataClusters:
     """
 
     def __init__(self, x, y, res):
-        """Constructor
+        """Constructor.
 
         Parameters
         ----------
@@ -102,8 +102,7 @@ def __eq__(self, other):
         )
 
     def _clear(self):
-        """
-        Clear all data and reset the cluster object to a transient initial state.
+        """Clear all data and reset the cluster object to a transient initial state.
 
         The purpose of this method is to provide a clean state before creating new clustering operations.
         The object is updated in-place and no new instance is returned.
@@ -175,8 +174,8 @@ def _setdata(self, x, y, res):
     def __next__(self):
         """Cluster point with largest y-coordinate left, returning self.
 
-        next() always adds at least one additional point to the existing
-        cluster, or raises an exception if all points have been clustered.
+        next() always adds at least one additional point to the existing cluster, or raises an exception if all
+        points have been clustered.
         """
         if self.status == self.INIT:
             raise Exception("Cannot cluster next point while status is INIT.")
@@ -465,7 +464,10 @@ def plot(self, *args, **kwds):
         return
 
     def animate(self):
-        """Animate clustering.  Restores state when complete."""
+        """Animate clustering.
+
+        Restores state when complete.
+        """
         clusters = self.clusters
         current_idx = self.current_idx
         lastcluster_idx = self.lastcluster_idx