Add initial documentation

Add synthetic data tutorial
Add read the docs setup

.gitignore

@@ -3,3 +3,5 @@ tests/__pycache__/*
 
 build/*
 src/AMBER.egg-info/*
+source/tutorials/.ipynb_checkpoints/*
+make.bat

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu
+  tools:
+    python: "3.13"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: source/conf.py
+
+python:
+   install:
+   - requirements: docs/requirements.txt

Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

README.md

@@ -1,14 +1,7 @@
 AMBER
 =====
 
-
-
-[![Test status](https://gitea.psi.ch/lass_j/AMBER/actions/workflows/test.yaml/badge.svg)]()
-
-
-General introduction
-
-## Installation
+## Quick Installation
 
 ```
 pip install AMBER
@@ -22,7 +15,7 @@ python3 -m pip install AMBER
 
 
 ## Documentation and Tutorials
-
+The documentation for AMBER can be found at 
 
 
 ## Contribute

source/conf.py

@@ -0,0 +1,37 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+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 = '0.0.2'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'nbsphinx', # allows notebooks
+    'myst_parser' # allows markdown
+]
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
+}
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'pyramid'
+html_static_path = ['_static']
+
+output_dir = ''

source/index.rst

@@ -0,0 +1,94 @@
+.. AMBER documentation master file, created by
+   sphinx-quickstart on Fri Apr 11 10:48:14 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+AMBER documentation
+===================
+
+This is the documentation for the **A** lgorithm for **M** ultiplexing spectrometer
+**B** ackground **E** stimation with **R** otation-independence **AMBER** which is a method to estimate and background within 3D data sets. 
+
+This software is the result of the collaboration between the instrument responsible at the `CAMEA <https://www.psi.ch/en/sinq/camea>`_ beamline at SINQ, at the 
+`Paul Scherrer Institut <https://psi.ch/>`_ with the `Swiss Data Science Center <https://www.datascience.ch/>`_ through the "Data Science for Multiplexing Spectrometers" (DS4MS) project supported by 
+the fifth call for Collaborative Research Data Science Projects. 
+
+
+Badges
+------
+
+.. image:: https://gitea.psi.ch/lass_j/AMBER/actions/workflows/test.yaml/badge.svg
+  :width: 200
+  :alt: Test Status
+
+
+
+
+
+
+Installation
+------------
+Installation can be done through PyPI using
+
+.. code-block::
+
+   python -m pip install AMBER
+
+Alternatively, the newest version can be installed directly from the source repository through
+
+.. code-block::
+
+   python -m pip install git https://gitea.psi.ch/lass_j/AMBER.git@master
+
+
+General Introduction
+--------------------
+
+
+**AMBER** has been developed with multiplexing neutron spectrometers in mind, i.e. a novel version of the triple axis instrument which acquires multiple data points simultaneously. 
+However, the algorithm is more general and can be utilized on data with other origins. 
+
+The main requirements of the data are
+
+#. Rotation independence of the background in two out of three directions.
+#. Smooth change of background along all directions 
+#. The signal is sparse but continuous in all directions
+
+**AMBER** minimizes the following cost function for the signal and background given the set of parameters :math:`\lambda`, :math:`\beta`, and :math:`\mu` on a voxelated data set:
+
+.. math::
+    \min_{X,b} \frac{1}{2}\lVert Y-X-\mathcal{R}b\rVert_{2}^2+\lambda\vert| X |\vert_{1} +\frac{\beta}{2} \mathrm{Tr} \left( b^T L_{b} b \right) +\frac{\mu}{2} \boldsymbol{1}_{n_x}^TX^T L_{\omega} X\boldsymbol{1}_{n_y}
+
+where :math:`Y`, :math:`X`, and :math:`b` are the measured signal, the subtracted signal and the rotation independent background, respectively. :math:`\mathcal{R}` is a rotation operator taking
+the radial :math:`b` to the full space. These three parameters constitute the fitting term while the rest are denoted penalty terms. :math:`\lambda` controls the weighing of sparcity of the subtracted signal gauge through the L-1 norm
+:math:`\vert| X |\vert_{1}`, :math:`\beta` controls the smoothness of the background while :math:`\mu` the smoothness of the subtracted signal. 
+
+For further details, see the the paper. 
+
+
+
+
+
+Documentation & Tutorials
+-------------------------
+
+For **AMBER** the following tutorials have been created
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+   tutorials/index.rst
+
+
+Contribute
+----------
+
+
+
+Contact
+-------
+
+

source/requirements.txt

@@ -0,0 +1,4 @@
+docutils<0.18
+ipykernel
+nbsphinx
+sphinx>5

source/tutorials/index.md

@@ -0,0 +1,11 @@
+# Tutorials
+
+Below is a list of tutorials utilizing __AMBER__ to perform a background determination and background subtraction. Some of these require additional packages and data to function. For those notebooks, links to the and installation requirements are highlighted. 
+
+```{toctree}
+---
+maxdepth: 1
+caption: Tutorials:
+---
+simulated_data.ipynb
+```