ci: add docformatter config to pyproject.toml and apply them to the files (#156)

* ci: add docformatter config block and run pre-commit to apply them to files

* chore: add news file for this change

Author: zmx27

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>

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?$'

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.

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.

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