From e1302bb141f7acb85885c8b87482ea663d16ddb7 Mon Sep 17 00:00:00 2001
From: Zhi Ming Xu <zhimingx27@gmail.com>
Date: Wed, 18 Jun 2025 13:26:36 -0400
Subject: [PATCH 1/2] ci: add docformatter config block and run pre-commit to
 apply them to files

---
 pyproject.toml                 |  5 +++++
 src/diffpy/snmf/io.py          |  7 ++++---
 src/diffpy/snmf/optimizers.py  |  4 ++--
 src/diffpy/snmf/subroutines.py | 11 ++++++-----
 4 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6a914219..e30a9dea 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,6 +59,11 @@ 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.black]
 line-length = 115
 include = '\.pyi?$'
diff --git a/src/diffpy/snmf/io.py b/src/diffpy/snmf/io.py
index 62614d05..18c3ca39 100644
--- a/src/diffpy/snmf/io.py
+++ b/src/diffpy/snmf/io.py
@@ -7,7 +7,8 @@
 
 
 def initialize_variables(data_input, number_of_components, data_type, sparsity=1, smoothness=1e18):
-    """Determines the variables and initial values used in the SNMF algorithm.
+    """Determines the variables and initial values used in the SNMF
+    algorithm.
 
     Parameters
     ----------
@@ -73,8 +74,8 @@ def initialize_variables(data_input, number_of_components, data_type, sparsity=1
 
 
 def load_input_signals(file_path=None):
-    """Processes a directory of a series of PDF/XRD patterns into a usable
-    format.
+    """Processes a directory of a series of PDF/XRD patterns into a
+    usable format.
 
     Constructs a 2d array out of a directory of PDF/XRD patterns containing each files dependent variable
     column in a new column. Constructs a 1d array containing the grid values.
diff --git a/src/diffpy/snmf/optimizers.py b/src/diffpy/snmf/optimizers.py
index 81a1b6da..ea4ecff1 100644
--- a/src/diffpy/snmf/optimizers.py
+++ b/src/diffpy/snmf/optimizers.py
@@ -8,8 +8,8 @@ def get_weights(
     lower_bound,
     upper_bound,
 ):
-    """Finds the weights of stretched component signals under a two-sided
-    constraint.
+    """Finds the weights of stretched component signals under a two-
+    sided constraint.
 
     Solves min J(y) = (linear_coefficient)' * y + (1/2) * y' * (quadratic coefficient) * y where
     lower_bound <= y <= upper_bound and stretched_component_gram_matrix is symmetric positive definite.
diff --git a/src/diffpy/snmf/subroutines.py b/src/diffpy/snmf/subroutines.py
index 9d6a6562..19abc6d5 100644
--- a/src/diffpy/snmf/subroutines.py
+++ b/src/diffpy/snmf/subroutines.py
@@ -211,8 +211,8 @@ def reconstruct_signal(components, signal_idx):
 
 
 def initialize_arrays(number_of_components, number_of_moments, signal_length):
-    """Generates the initial guesses for the weight, stretching, and component
-    matrices.
+    """Generates the initial guesses for the weight, stretching, and
+    component matrices.
 
     Calculates the initial guesses for the component matrix, stretching factor matrix, and weight matrix. The
     initial guess for the component matrix is a random (signal_length) x (number_of_components) matrix where
@@ -255,7 +255,8 @@ def objective_function(
     component_matrix,
     sparsity,
 ):
-    """Defines the objective function of the algorithm and returns its value.
+    """Defines the objective function of the algorithm and returns its
+    value.
 
     Calculates the value of '(||residual_matrix||_F) ** 2 + smoothness * (||smoothness_term *
     stretching_factor_matrix.T||)**2 + sparsity * sum(component_matrix ** .5)' and returns its value.
@@ -437,8 +438,8 @@ def get_residual_matrix(
     component_amount,
     signal_length,
 ):
-    """Obtains the residual matrix between the experimental data and calculated
-    data.
+    """Obtains the residual matrix between the experimental data and
+    calculated data.
 
     Calculates the difference between the experimental data and the reconstructed experimental data created from
     the calculated components, weights, and stretching factors. For each experimental pattern, the stretched and

From df35349093cdaeb2b2a256803a0c924f09659757 Mon Sep 17 00:00:00 2001
From: Zhi Ming Xu <zhimingx27@gmail.com>
Date: Wed, 18 Jun 2025 13:28:25 -0400
Subject: [PATCH 2/2] chore: add news file for this change

---
 news/add-docformatter.rst | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 news/add-docformatter.rst

diff --git a/news/add-docformatter.rst b/news/add-docformatter.rst
new file mode 100644
index 00000000..0df46db0
--- /dev/null
+++ b/news/add-docformatter.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* Add docformatter config block to the end of the pyproject.toml file.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>