docs: clean up and add a real data XRD example (#191)

* refactor: move example data to docs/examples/data

* refactor: turn main.py into an example located in docs

* docs: add complete XRD example

* fix: clean up two more snmf references

* chore: add news item

* refactor: remove references to unused variable num_updates

* refactor: consistently label variables as private or fit-derived

* refactor: change remaining data files from underscores to dashes

* refactor: name files to sort correctly

* docs: add to API explanation of trailing underscores

---------

Co-authored-by: John Halloran <jhalloran@oxy.edu>

Author: john-halloran

AUTHORS.rst

@@ -7,4 +7,4 @@ Contributors
 ------------
 
 For a list of contributors, visit
-https://github.com/diffpy/diffpy.snmf/graphs/contributors
+https://github.com/diffpy/diffpy.stretched-nmf/graphs/contributors

docs/examples/XRD_MgMnO_YCl_real.py

@@ -0,0 +1,39 @@
+from pathlib import Path
+
+import numpy as np
+
+from diffpy.stretched_nmf.snmf_class import SNMFOptimizer
+
+# Input data
+DATA_DIR = Path(__file__).resolve().parent / "data/XRD-MgMnO-YCl-real"
+source_matrix_file = np.loadtxt(
+    DATA_DIR / "source-matrix.txt", dtype=float, skiprows=4
+)
+
+# Optional starting initialization
+# Without it, would need to provide n_components = 2 to get these results
+init_components_file = np.loadtxt(
+    DATA_DIR / "init-components.txt", dtype=float
+)
+init_stretch_file = np.loadtxt(DATA_DIR / "init-stretch.txt", dtype=float)
+init_weights_file = np.loadtxt(DATA_DIR / "init-weights.txt", dtype=float)
+
+my_model = SNMFOptimizer(
+    show_plots=True,
+    rho=1e12,
+    eta=610,
+)
+# Experimentally found best fit parameters for this data
+my_model.fit(
+    source_matrix=source_matrix_file,
+    init_weights=init_weights_file,
+    init_components=init_components_file,
+    init_stretch=init_stretch_file,
+)
+
+print("Done")
+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=" ")