diffpy · danielsirakov · May 31, 2026 · May 31, 2026 · Jun 20, 2026 · Jun 20, 2026
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
@@ -21,31 +21,31 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.5.1
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 9.0.0a3
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
@@ -58,8 +58,8 @@ repos:
         additional_dependencies:
           - "prettier@^3.2.4"
   # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.8
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]

diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -1,5 +1,5 @@
 Authors
-=======
+-------
 
 Christopher Farrow, Pavol Juhas, Simon J. L. Billinge, and members of the Billinge Group
 

diff --git a/docs/examples/coreshellnp.py b/docs/examples/coreshellnp.py
@@ -37,7 +37,6 @@
 
 def makeRecipe(stru1, stru2, datname):
     """Create a fitting recipe for crystalline PDF data."""
-
     # The Profile
     profile = Profile()
 
@@ -133,7 +132,6 @@ def makeRecipe(stru1, stru2, datname):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     r = recipe.cdszns.profile.x
     g = recipe.cdszns.profile.y
@@ -157,7 +155,6 @@ def plotResults(recipe):
 
 def main():
     """Set up and refine the recipe."""
-
     # Make the data and the recipe
     cdsciffile = "data/CdS.cif"
     znsciffile = "data/ZnS.cif"

diff --git a/docs/examples/crystalpdf.py b/docs/examples/crystalpdf.py
@@ -42,7 +42,6 @@
 
 def makeRecipe(ciffile, datname):
     """Create a fitting recipe for crystalline PDF data."""
-
     # The Profile
     # This will be used to store the observed and calculated PDF profile.
     profile = Profile()
@@ -131,7 +130,6 @@ def makeRecipe(ciffile, datname):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     r = recipe.nickel.profile.x
     g = recipe.nickel.profile.y

diff --git a/docs/examples/crystalpdfall.py b/docs/examples/crystalpdfall.py
@@ -56,7 +56,6 @@ def makeRecipe(
     ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si, xdata_sini
 ):
     """Create a fitting recipe for crystalline PDF data."""
-
     # The Profiles
     # We need a profile for each data set.
     xprofile_ni = makeProfile(xdata_ni)
@@ -146,7 +145,6 @@ def makeRecipe(
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     xnickel = recipe.xnickel
     xr_ni = xnickel.profile.x

diff --git a/docs/examples/crystalpdfobjcryst.py b/docs/examples/crystalpdfobjcryst.py
@@ -37,7 +37,6 @@
 
 def makeRecipe(ciffile, datname):
     """Create a fitting recipe for crystalline PDF data."""
-
     # The Profile
     # This will be used to store the observed and calculated PDF profile.
     profile = Profile()

diff --git a/docs/examples/crystalpdftwodata.py b/docs/examples/crystalpdftwodata.py
@@ -38,7 +38,6 @@
 
 def makeRecipe(ciffile, xdatname, ndatname):
     """Create a fitting recipe for crystalline PDF data."""
-
     # The Profiles
     # We need a profile for each data set. This means that we will need two
     # FitContributions as well.
@@ -137,7 +136,6 @@ def makeRecipe(ciffile, xdatname, ndatname):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     xr = recipe.xnickel.profile.x
     xg = recipe.xnickel.profile.y

diff --git a/docs/examples/crystalpdftwophase.py b/docs/examples/crystalpdftwophase.py
@@ -38,7 +38,6 @@
 
 def makeRecipe(niciffile, siciffile, datname):
     """Create a fitting recipe for crystalline PDF data."""
-
     # The Profile
     profile = Profile()
 
@@ -142,7 +141,6 @@ def makeRecipe(niciffile, siciffile, datname):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     r = recipe.nisi.profile.x
     g = recipe.nisi.profile.y

diff --git a/docs/examples/debyemodel.py b/docs/examples/debyemodel.py
@@ -84,7 +84,6 @@ def makeRecipe():
     optimize for the data/equation pair. This can be modified, but we
     won't do that here.
     """
-
     # The Profile
     # Create a Profile to hold the experimental and calculated signal.
     profile = Profile()
@@ -159,7 +158,6 @@ def makeRecipe():
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # Plot this.
     # Note that since the contribution was given the name "pb", it is
     # accessible from the recipe with this name. This is a useful way to
@@ -182,7 +180,6 @@ def plotResults(recipe):
 
 def main():
     """The workflow of creating, running and inspecting a fit."""
-
     # Create the recipe
     recipe = makeRecipe()
 

diff --git a/docs/examples/debyemodelII.py b/docs/examples/debyemodelII.py
@@ -54,7 +54,6 @@ def makeRecipeII():
     constrain the Debye temperature in each FitContribution to be the
     same.
     """
-
     # We'll throw these away. We just want the FitContributions that are
     # configured within the recipes.
     m1 = makeRecipe()
@@ -95,7 +94,6 @@ def makeRecipeII():
 
 def plotResults(recipe):
     """Display the results contained within a refined FitRecipe."""
-
     # The variable values are returned in the order in which the variables were
     # added to the FitRecipe.
     lowToffset, highToffset, thetaD = recipe.getValues()

diff --git a/docs/examples/ellipsoidsas.py b/docs/examples/ellipsoidsas.py
@@ -30,7 +30,6 @@
 
 def makeRecipe(datname):
     """Create a fitting recipe for ellipsoidal SAS data."""
-
     # The Profile
     # This will be used to store the observed and calculated I(Q) data.
     profile = Profile()
@@ -89,7 +88,6 @@ def makeRecipe(datname):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     r = recipe.ellipsoid.profile.x
     y = recipe.ellipsoid.profile.y

diff --git a/docs/examples/gaussiangenerator.py b/docs/examples/gaussiangenerator.py
@@ -124,7 +124,6 @@ def makeRecipe():
     This will create a FitContribution that uses the GaussianGenerator,
     associate this with a Profile, and use this to define a FitRecipe.
     """
-
     # The Profile
     # Create a Profile to hold the experimental and calculated signal.
     profile = Profile()

diff --git a/docs/examples/gaussianrecipe.py b/docs/examples/gaussianrecipe.py
@@ -58,7 +58,6 @@
 
 def main():
     """The workflow of creating, running and inspecting a fit."""
-
     # Start by creating the recipe. The recipe describes the data to be fit,
     # the profile generator used to simulate the data and the variables that
     # will be tuned by the optimizer.
@@ -95,7 +94,6 @@ def makeRecipe():
     Once we define the FitRecipe, we can send it an optimizer to be
     optimized. See the 'scipyOptimize' function.
     """
-
     # The Profile
     # Create a Profile to hold the experimental and calculated signal.
     profile = Profile()
@@ -168,7 +166,6 @@ def scipyOptimize(recipe):
     we can be minimized using a scipy optimizer. The details are
     described in the source.
     """
-
     # We're going to use the least-squares (Levenberg-Marquardt) optimizer from
     # scipy. We simply have to give it the function to minimize
     # (recipe.residual) and the starting values of the Variables
@@ -183,7 +180,6 @@ def scipyOptimize(recipe):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # We can access the data and fit profile through the Profile we created
     # above. We get to it through our FitContribution, which we named "g1".
     #

diff --git a/docs/examples/npintensity.py b/docs/examples/npintensity.py
@@ -181,7 +181,6 @@ def makeRecipe(strufile, datname):
     This will create a FitContribution that uses the IntensityGenerator,
     associate this with a Profile, and use this to define a FitRecipe.
     """
-
     # The Profile
     # Create a Profile. This will hold the experimental and calculated signal.
     profile = Profile()
@@ -336,7 +335,6 @@ def main():
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     q = recipe.bucky.profile.x
 
@@ -484,7 +482,6 @@ def makeData(strufile, q, datname, scale, a, Uiso, sig, bkgc, nl=1):
     bkgc    --  A parameter that gives minor control of the background.
     nl      --  Noise level (0, inf), default 1, larger -> less noise.
     """
-
     from diffpy.structure import Structure
 
     S = Structure()

diff --git a/docs/examples/npintensityII.py b/docs/examples/npintensityII.py
@@ -62,7 +62,6 @@ def makeRecipe(strufile, datname1, datname2):
     (which is generated by the IntensityGenerator when we load the
     structure) in both generators.
     """
-
     # The Profiles
     # Create two Profiles for the two FitContributions.
     profile1 = Profile()
@@ -187,7 +186,6 @@ def gaussian(q, q0, width):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # plotting song and dance
     q = recipe.bucky1.profile.x
 

diff --git a/docs/examples/nppdfcrystal.py b/docs/examples/nppdfcrystal.py
@@ -38,7 +38,6 @@
 
 def makeRecipe(ciffile, grdata):
     """Make a recipe to model a crystal-like nanoparticle PDF."""
-
     # Set up a PDF fit as has been done in other examples.
     pdfprofile = Profile()
 
@@ -83,7 +82,6 @@ def makeRecipe(ciffile, grdata):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     r = recipe.pdf.profile.x
     g = recipe.pdf.profile.y

diff --git a/docs/examples/nppdfobjcryst.py b/docs/examples/nppdfobjcryst.py
@@ -34,7 +34,6 @@
 
 def makeRecipe(molecule, datname):
     """Create a recipe that uses the DebyePDFGenerator."""
-
     # The Profile
     profile = Profile()
 
@@ -110,7 +109,6 @@ def makeRecipe(molecule, datname):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # Plot this.
     r = recipe.bucky.profile.x
     g = recipe.bucky.profile.y
@@ -221,7 +219,6 @@ def main():
 
 def makeC60():
     """Make the C60 molecule using pyobjcryst."""
-
     from pyobjcryst.crystal import Crystal
     from pyobjcryst.molecule import Molecule
     from pyobjcryst.scatteringpower import ScatteringPowerAtom

diff --git a/docs/examples/nppdfsas.py b/docs/examples/nppdfsas.py
@@ -43,7 +43,6 @@ def makeRecipe(ciffile, grdata, iqdata):
     The fit I(q) is fed into the calculation of G(r), which provides
     feedback for the fit parameters of both.
     """
-
     # Create a PDF contribution as before
     pdfprofile = Profile()
     pdfparser = PDFParser()
@@ -120,7 +119,6 @@ def makeRecipe(ciffile, grdata, iqdata):
 
 def fitRecipe(recipe):
     """We refine in stages to help the refinement converge."""
-
     # Tune SAS.
     recipe.setWeight(recipe.pdf, 0)
     recipe.fix("all")
@@ -147,7 +145,6 @@ def fitRecipe(recipe):
 
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
-
     # All this should be pretty familiar by now.
     r = recipe.pdf.profile.x
     g = recipe.pdf.profile.y

diff --git a/docs/examples/simplepdf.py b/docs/examples/simplepdf.py
@@ -31,7 +31,6 @@
 
 def makeRecipe(ciffile, datname):
     """Create a fitting recipe for crystalline PDF data."""
-
     # Work directly with a custom PDFContribution to load the data
     contribution = PDFContribution("nickel")
     contribution.loadData(datname)

diff --git a/docs/examples/simplepdftwophase.py b/docs/examples/simplepdftwophase.py
@@ -27,7 +27,6 @@
 
 def makeRecipe(niciffile, siciffile, datname):
     """Create a fitting recipe for crystalline PDF data."""
-
     # Load data and add it to the profile
     contribution = PDFContribution("nisi")
     contribution.loadData(datname)

diff --git a/docs/examples/simplerecipe.py b/docs/examples/simplerecipe.py
@@ -27,7 +27,6 @@
 
 def main():
     """Set up a simple recipe in a few lines."""
-
     # The SimpleRecipe class is a type of FitRecipe. It provides attribute-like
     # access to variables and a residual function that can be minimized.
     recipe = SimpleRecipe()
-Original file line number
+Diff line change
@@ -1,5 +1,5 @@
     Authors
-    =======
+    -------
     Christopher Farrow, Pavol Juhas, Simon J. L. Billinge, and members of the Billinge Group
@@ Expand Down @@