style: convert variables to lowercase (#159)

* style: Convert variables to lowercase

* chore: Add news item

* style: lowercase remaining variables

* style: fix indentation on docstrings

* style: rename and make public certain attributes

* style: update docstring defaults

---------

Co-authored-by: John Halloran <[email protected]>

Author: john-halloran

news/lowercasing.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Conform variable names to PEP-8
+
+**Security:**
+
+* <news item>

src/diffpy/snmf/main.py

@@ -1,14 +1,20 @@
 import numpy as np
 from snmf_class import SNMFOptimizer
 
-X0 = np.loadtxt("input/X0.txt", dtype=float)
-MM = np.loadtxt("input/MM.txt", dtype=float)
-A0 = np.loadtxt("input/A0.txt", dtype=float)
-Y0 = np.loadtxt("input/W0.txt", dtype=float)
-N, M = MM.shape
+# Example input files (not provided)
+init_components_file = np.loadtxt("input/init_components.txt", dtype=float)
+source_matrix_file = np.loadtxt("input/source_matrix.txt", dtype=float)
+init_stretch_file = np.loadtxt("input/init_stretch.txt", dtype=float)
+init_weights_file = np.loadtxt("input/init_weights.txt", dtype=float)
+
+my_model = SNMFOptimizer(
+    source_matrix=source_matrix_file,
+    init_weights=init_weights_file,
+    init_components=init_components_file,
+    init_stretch=init_stretch_file,
+)
 
-my_model = SNMFOptimizer(MM=MM, Y0=Y0, X0=X0, A0=A0)
 print("Done")
-np.savetxt("my_norm_X.txt", my_model.X, fmt="%.6g", delimiter=" ")
-np.savetxt("my_norm_Y.txt", my_model.Y, fmt="%.6g", delimiter=" ")
-np.savetxt("my_norm_A.txt", my_model.A, fmt="%.6g", delimiter=" ")
+np.savetxt("my_norm_components.txt", my_model.components, fmt="%.6g", delimiter=" ")
+np.savetxt("my_norm_weights.txt", my_model.weights, fmt="%.6g", delimiter=" ")
+np.savetxt("my_norm_stretch.txt", my_model.stretch, fmt="%.6g", delimiter=" ")