chore: change email and instruction

.pre-commit-config.yaml

@@ -57,10 +57,9 @@ repos:
       - id: prettier
         additional_dependencies:
           - "prettier@^3.2.4"
-  # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+  # ruff - An extremely fast Python linter and code formatter, written in Rust.
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.12
     hooks:
-      - id: docformatter
-        additional_dependencies: [tomli]
-        args: [--in-place, --config, ./pyproject.toml]
+      - id: ruff-check
+        args: [--fix]

CODE-OF-CONDUCT.rst

@@ -67,7 +67,7 @@ Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-sb2896@columbia.edu. All complaints will be reviewed and investigated promptly and fairly.
+sbillinge@ucsb.edu. All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
 reporter of any incident.

LICENSE-PDFgui.rst

@@ -24,7 +24,7 @@ program by citing the following paper in your publication:
 For more information please visit the diffpy web-page at
     http://www.diffpy.org
 or email Luke Granlund at luke.r.granlund@gmail.com, or Prof. Simon
-Billinge at sb2896@columbia.edu.
+Billinge at sbillinge@ucsb.edu.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

LICENSE.rst

@@ -17,7 +17,7 @@ program by citing the following paper in your publication:
 For more information please visit the diffpy web-page at
     http://www.diffpy.org
 or email Luke Granlund at luke.r.granlund@gmail.com, or Prof. Simon
-Billinge at sb2896@columbia.edu.
+Billinge at sbillinge@ucsb.edu.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

README.rst

@@ -102,7 +102,9 @@ The following creates and activates a new environment named ``diffpy.srmise_env`
         conda create -n diffpy.srmise_env diffpy.srmise
         conda activate diffpy.srmise_env
 
-The output should print the latest version displayed on the badges above.
+You can also install diffpy.srmise in another activated environment with ::
+
+        conda install -c conda-forge diffpy.srmise
 
 If the above does not work, you can use ``pip`` to download and install the latest release from
 `Python Package Index <https://pypi.python.org>`_.
@@ -120,6 +122,7 @@ This package also provides command-line utilities. To check the software has bee
 
         diffpy.srmise --version
 
+The output should print the latest version displayed on the badges above.
 You can also type the following command to verify the installation. ::
 
         python -c "import diffpy.srmise; print(diffpy.srmise.__version__)"

docs/examples/multimodel-unknown-dG2.py

@@ -140,7 +140,7 @@ def run(plot=True):
         dG = ms.dgs[np.argmax(cls_probs)]
         best_dGs.append(dG)
 
-    print("\n--------- Best models for at least one dG ---------" % dG)
+    print(f"\n--------- Best models for at least one dG: {dG} ---------")
     print("   Best dG  Model  Class  Free       AIC     Prob  File")
     for dG in best_dGs:
 

docs/source/license.rst

@@ -29,7 +29,7 @@ program by citing the following paper in your publication:
 For more information please visit the diffpy web-page at
     http://www.diffpy.org
 or email Luke Granlund at luke.r.granlund@gmail.com, or Prof. Simon
-Billinge at sb2896@columbia.edu.
+Billinge at sbillinge@ucsb.edu.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

news/email.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No News Added: change email to the right one and add instruction to install in existing env
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -60,10 +60,11 @@ exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat"
 
-[tool.docformatter]
-recursive = true
-wrap-summaries = 72
-wrap-descriptions = 72
+[tool.ruff]
+line-length = 115
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
 
 [tool.black]
 line-length = 115

src/diffpy/srmise/__init__.py

@@ -13,7 +13,8 @@
 #
 ##############################################################################
 """Peak extraction and peak fitting tool for atomic pair distribution
-functions."""
+functions.
+"""
 
 # package version
 from diffpy.srmise.version import __version__  # noqa

src/diffpy/srmise/applications/extract.py

@@ -35,7 +35,6 @@ def _baseline_namespace():
 
 def main():
     """Default SrMise entry-point."""
-
     usage = (
         "usage: %prog pdf_file [options]\n"
         "pdf_file is a file containing a PDF (accepts several "
@@ -624,7 +623,8 @@ def parsepars(mp, parseq):
     a float with the character 'c' appended.  If 'c' is appended,
     that parameter will be fixed.
 
-    Parameters:
+    Parameters
+    ----------
     mp - A ModelPart instance
     parseq - A sequence of string
     """

src/diffpy/srmise/applications/plot.py

@@ -556,8 +556,8 @@ def on_draw(event):
 
 def readcompare(filename):
     """Returns a list of distances read from filename, otherwise
-    None."""
-
+    None.
+    """
     # TODO: Make this safer
     try:
         datastring = open(filename, "rb").read()

src/diffpy/srmise/basefunction.py

@@ -12,7 +12,8 @@
 #
 ##############################################################################
 """Defines BaseFunction, the base class for mathematical functions in
-srmise."""
+srmise.
+"""
 
 import logging
 import re
@@ -30,7 +31,7 @@ class BaseFunction(object):
     sequences.
 
     Attributes
-    -------------
+    ----------
     parameterdict : dict
         The dictionary mapping string keys to their index in the
         sequence of parameters.  These keys apply only to the
@@ -102,7 +103,6 @@ def __init__(
             The class (not instance) which implements caching of BaseFunction
             evaluations.
         """
-
         self.parameterdict = parameterdict
         self.npars = len(self.parameterdict)
 
@@ -448,6 +448,7 @@ def factory(functionstr, baselist):
             The list of BaseFunction (or subclass) instances.
 
         Returns
+        -------
         Basefunction instance
             The BaseFunction instance based on the parameter strings
         """
@@ -505,6 +506,7 @@ def safefunctionlist(fs):
         is guaranteed to be safe for saving/reinstantiating peak functions.
 
         Parameters
+        ----------
         fs: List of BaseFunction instances.
         """
         fsafe = []

src/diffpy/srmise/baselines/base.py

@@ -128,14 +128,15 @@ def getmodule(self):
 
 class Baseline(ModelPart):
     """Represents a baseline associated with a BaselineFunction
-    subclass."""
+    subclass.
+    """
 
     def __init__(self, owner, pars, free=None, removable=False, static_owner=False):
         """Initialize the BaselineComponent instance with specified
         configurations.
 
-            Parameters
-            ----------
+        Parameters
+        ----------
             owner : BaselineFunction subclass instance
                 The owner object which is an instance of a subclass of BaselineFunction.
             pars : array-like
@@ -151,8 +152,8 @@ def __init__(self, owner, pars, free=None, removable=False, static_owner=False):
                 Determines if the owner of the baseline can be altered using the
         `       changeowner()` method. Defaults to False.
 
-            Notes
-            -----
+        Notes
+        -----
             - The `free` and `removable` parameters are independent; a baseline can be marked
             as removable even if some of its parameters are fixed (`free` is False). In such
             cases, the baseline may be removed during peak extraction, but the fixed
@@ -171,7 +172,6 @@ def factory(baselinestr, ownerlist):
         ownerlist : array-like
             The list of BaseFunctions that owner is in
         """
-
         data = baselinestr.strip().splitlines()
 
         # dictionary of parameters

src/diffpy/srmise/baselines/polynomial.py

@@ -24,7 +24,8 @@
 
 class Polynomial(BaselineFunction):
     """Methods for evaluation and parameter estimation of a polynomial
-    baseline."""
+    baseline.
+    """
 
     def __init__(self, degree, Cache=None):
         """Initialize a polynomial function of degree d.
@@ -166,6 +167,7 @@ def _transform_parametersraw(self, pars, in_format, out_format):
         """Convert parameter values from in_format to out_format.
 
         Parameters
+        ----------
         pars : array-like
             The sequence of parameters
         in_format : str

src/diffpy/srmise/dataclusters.py

@@ -12,7 +12,8 @@
 #
 ##############################################################################
 """Defines class to partition sequences representing the x and y axis
-into peak-like clusters."""
+into peak-like clusters.
+"""
 
 import logging
 
@@ -434,6 +435,7 @@ def cut(self, idx):
         """Return slice(s) for data given cluster index (or indices).
 
         Parameters
+        ----------
         idx - Cluster index (or sequence of indices).
         """
         data_ids = self.clusters[idx]

src/diffpy/srmise/modelcluster.py

@@ -266,11 +266,11 @@ def getvalue(self, i):
         """Return value of parameter i.
 
         The variable may be specified as an integer, or as a two-
-        component tuple of integers (l, m) which indicate the mth
-        parameter of modelpart l.
+        component tuple of integers ``(part_idx, param_idx)`` indicating
+        the ``param_idx``-th parameter of model part ``part_idx``.
         """
-        (l, m) = i if i in self.pmap else self.ipmap[i]
-        return self.model[l][m]
+        part_idx, param_idx = i if i in self.pmap else self.ipmap[i]
+        return self.model[part_idx][param_idx]
 
     def getuncertainty(self, i):
         """Return uncertainty of parameter i.
@@ -288,7 +288,7 @@ def getuncertainty(self, i):
         float
             The uncertainty of variable at index i.
         """
-        (l, m) = i if i in self.pmap else self.ipmap[i]
+        part_idx, param_idx = i if i in self.pmap else self.ipmap[i]
         return np.sqrt(self.getcovariance(i, i))
 
     def getcovariance(self, i, j):
@@ -369,7 +369,8 @@ def correlationwarning(self, threshold=0.8):
 
     def __str__(self):
         """Return string of value (uncertainty) pairs for all
-        parameters."""
+        parameters.
+        """
         if self.model is None or self.cov is None:
             return "Model and/or Covariance matrix undefined."
         lines = []
@@ -799,16 +800,16 @@ def join_adjacent(m1, m2):
             The new ModelCluster instance between m1 and m2.
         """
         # Check for members that must be shared.
-        if not (m1.r_data is m2.r_data):
+        if m1.r_data is not m2.r_data:
             emsg = "Cannot join ModelClusters that do not share r_data."
             raise ValueError(emsg)
-        if not (m1.y_data is m2.y_data):
+        if m1.y_data is not m2.y_data:
             emsg = "Cannot join ModelClusters that do not share y_data."
             raise ValueError(emsg)
-        if not (m1.y_error is m2.y_error):
+        if m1.y_error is not m2.y_error:
             emsg = "Cannot join ModelClusters that do not share y_error."
             raise ValueError(emsg)
-        if not (m1.error_method is m2.error_method):
+        if m1.error_method is not m2.error_method:
             emsg = "Cannot join ModelClusters that do not share error_method."
             raise ValueError(emsg)
         if not (m1.baseline == m2.baseline):

src/diffpy/srmise/modelevaluators/aic.py

@@ -103,7 +103,6 @@ def minpoints(self, npars):
         int
             The minimum number of points required to make an estimate of a model's quality.
         """
-
         return 1
 
     def parpenalty(self, k):
@@ -120,7 +119,6 @@ def parpenalty(self, k):
         float
             The penalty cost for adding k parameters to the current model cluster.
         """
-
         # Weight the penalty for additional parameters.
         # If this isn't 1 there had better be a good reason.
         fudgefactor = 1.0
@@ -151,7 +149,6 @@ def growth_justified(self, fit, k_prime):
         bool
             Whether adding k_prime parameters to the given model is justified.
         """
-
         if self.chisq is None:
             self.chisq = self.chi_squared(fit.value(), fit.y_cluster, fit.error_cluster)
 
@@ -187,7 +184,6 @@ def akaikeweights(aics):
         array-like
             The sequence of Akaike weights
         """
-
         aic_stats = np.array([aic.stat for aic in aics])
         aic_min = min(aic_stats)
         return np.exp(-(aic_stats - aic_min) / 2.0)