Update of tutorial

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 77.0.3"]
+requires = ["setuptools"]# >= 77.0.3"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
@@ -8,7 +8,7 @@ package-dir = {"" = "src"}
 
 [project]
 name = "AMBER-ds4ms"
-version = "1.0.0"
+version = "1.0.1"
 dependencies = [
   "numpy>=1.14",
   "scipy>=1.7",
@@ -27,7 +27,7 @@ maintainers = [
 ]
 description = "AMBER: Algorithm for Multiplexing spectrometer Background Estimation with Rotation-independence"
 readme = "README.md"
-license-files = ["LICENSE"]
+#license-files = ["LICENSE"]
 keywords = ["Machine Learning", "Signal Segmentation", "Background Determination"]
 classifiers = [
   "Development Status :: 4 - Beta",

source/conf.py

@@ -9,14 +9,15 @@
 project = 'AMBER'
 copyright = '2025, J. Lass, V. Cohen, B. B. Haro, & D. G. Mazzone'
 author = 'J. Lass, V. Cohen, B. B. Haro, & D. G. Mazzone'
-release = '1.0.0'
+release = '1.0.1'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
     'nbsphinx', # allows notebooks
-    'myst_parser' # allows markdown
+    'myst_parser', # allows markdown
+    'IPython.sphinxext.ipython_console_highlighting',
 ]
 source_suffix = {
     '.rst': 'restructuredtext',
@@ -24,7 +25,7 @@ source_suffix = {
     '.md': 'markdown',
 }
 templates_path = ['_templates']
-exclude_patterns = []
+exclude_patterns = ['**.ipynb_checkpoints']
 
 
 

src/AMBER/background.py

@@ -613,11 +613,10 @@ class background():
 
         # Loss function
         loss = []#np.zeros(n_epochs, dtype=self.dtype)
-        old_loss = 2000000
-        new_loss = 1000000
+        old_loss = 0
+        new_loss = 0
         k = 0
-
-        while (old_loss - new_loss > 1e-3) and (k < n_epochs):
+        while ((old_loss - new_loss > 1e-3) and (k < n_epochs)) or k < 2:
             # Compute A = Y - B by filling the nans with 0s
             A = np.where(np.isnan(Y_r - b_tmp) == True, 0.0, Y_r - b_tmp)