diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 0000000..63d21ea
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,20 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docsbuild
\ No newline at end of file
diff --git a/README.md b/README.md
index e231502..6eeda18 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,15 @@
 # scConfluence
+[![Tests](https://github.com/cantinilab/scconfluence/actions/workflows/main.yml/badge.svg)](https://github.com/cantinilab/scconfluence/actions/workflows/main.yml)
+[![codecov](https://codecov.io/github/cantinilab/scconfluence/graph/badge.svg?token=JCLE8L9GNH)](https://codecov.io/github/cantinilab/scconfluence)
+[![PyPI version](https://img.shields.io/pypi/v/scconfluence?color=blue)](https://img.shields.io/pypi/v/scconfluence?color=blue)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
 scConfluence is a novel method for the integration of unpaired multiomics data combining
 uncoupled autoencoders and Inverse Optimal Transport to learn low-dimensional cell 
 embeddings. These embeddings can then be used for visualization and clustering, useful 
 for discovering  subpopulations of cells, and for imputation of features across 
 modalities.
-Read the preprint! (!!!!add link!!!!)
+[Read the preprint!](https://www.biorxiv.org/content/10.1101/2024.02.26.582051v1)
 
 ![figure](model.png)
 
@@ -13,7 +18,7 @@ Read the preprint! (!!!!add link!!!!)
 scConfluence is implemented as a Python package seamlessly integrated within the scverse 
 ecosystem, in particular Muon and Scanpy.
 
-### via PyPI (!!!!!!!!! not yet available!!!!!!!)
+### via PyPI
 
 On all operating systems, the easiest way to install scConfluence is via PyPI. 
 Installation should typically take a minute and is continuously tested with Python 3.10 
@@ -80,9 +85,16 @@ sc.pl.umap(mdata)
 ```
 
 ## Our preprint
-
+https://www.biorxiv.org/content/10.1101/2024.02.26.582051v1
 ```bibtex
-!!!! add citation !!!!
+@article {Samaran2024unpaired,
+  author = {Jules Samaran and Gabriel Peyre and Laura Cantini},
+  title = {scConfluence : single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features},
+  year = {2024},
+  doi = {10.1101/2024.02.26.582051},
+  publisher = {Cold Spring Harbor Laboratory},
+  journal = {bioRxiv}
+}
 ```
 
 If you're looking for the repository with code to reproduce the experiments in our 
diff --git a/poetry.lock b/poetry.lock
index eb22152..ee73705 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -121,6 +121,17 @@ files = [
 [package.dependencies]
 frozenlist = ">=1.1.0"
 
+[[package]]
+name = "alabaster"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
+optional = true
+python-versions = ">=3.9"
+files = [
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+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
+]
+
 [[package]]
 name = "anndata"
 version = "0.10.5.post1"
@@ -193,6 +204,233 @@ tests = ["attrs[tests-no-zope]", "zope-interface"]
 tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
 tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
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+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
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+version = "4.12.3"
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+
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+soupsieve = ">1.2"
+
+[package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
+
+[[package]]
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+version = "6.1.0"
+description = "An easy safelist-based HTML-sanitizing tool."
+optional = true
+python-versions = ">=3.8"
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+
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -282,6 +520,28 @@ files = [
 docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
 tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
+[[package]]
+name = "defusedxml"
+version = "0.7.1"
+description = "XML bomb protection for Python stdlib modules"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
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+]
+
+[[package]]
+name = "docutils"
+version = "0.19"
+description = "Docutils -- Python Documentation Utilities"
+optional = true
+python-versions = ">=3.7"
+files = [
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+]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.2.0"
@@ -296,6 +556,20 @@ files = [
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "fastjsonschema"
+version = "2.19.1"
+description = "Fastest Python implementation of JSON schema"
+optional = true
+python-versions = "*"
+files = [
+    {file = "fastjsonschema-2.19.1-py3-none-any.whl", hash = "sha256:3672b47bc94178c9f23dbb654bf47440155d4db9df5f7bc47643315f9c405cd0"},
+    {file = "fastjsonschema-2.19.1.tar.gz", hash = "sha256:e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d"},
+]
+
+[package.extras]
+devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
+
 [[package]]
 name = "filelock"
 version = "3.13.1"
@@ -501,6 +775,23 @@ smb = ["smbprotocol"]
 ssh = ["paramiko"]
 tqdm = ["tqdm"]
 
+[[package]]
+name = "furo"
+version = "2022.12.7"
+description = "A clean customisable Sphinx documentation theme."
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "furo-2022.12.7-py3-none-any.whl", hash = "sha256:7cb76c12a25ef65db85ab0743df907573d03027a33631f17d267e598ebb191f7"},
+    {file = "furo-2022.12.7.tar.gz", hash = "sha256:d8008f8efbe7587a97ba533c8b2df1f9c21ee9b3e5cad0d27f61193d38b1a986"},
+]
+
+[package.dependencies]
+beautifulsoup4 = "*"
+pygments = ">=2.7"
+sphinx = ">=5.0,<7.0"
+sphinx-basic-ng = "*"
+
 [[package]]
 name = "geomloss"
 version = "0.2.6"
@@ -632,6 +923,17 @@ files = [
     {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
 ]
 
+[[package]]
+name = "imagesize"
+version = "1.4.1"
+description = "Getting image size from png/jpeg/jpeg2000/gif file"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
+    {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
+]
+
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
@@ -671,6 +973,94 @@ files = [
     {file = "joblib-1.3.2.tar.gz", hash = "sha256:92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1"},
 ]
 
+[[package]]
+name = "jsonschema"
+version = "4.21.1"
+description = "An implementation of JSON Schema validation for Python"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"},
+    {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
+]
+
+[package.dependencies]
+attrs = ">=22.2.0"
+jsonschema-specifications = ">=2023.03.6"
+referencing = ">=0.28.4"
+rpds-py = ">=0.7.1"
+
+[package.extras]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.12.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
+    {file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
+]
+
+[package.dependencies]
+referencing = ">=0.31.0"
+
+[[package]]
+name = "jupyter-client"
+version = "8.6.0"
+description = "Jupyter protocol implementation and client libraries"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "jupyter_client-8.6.0-py3-none-any.whl", hash = "sha256:909c474dbe62582ae62b758bca86d6518c85234bdee2d908c778db6d72f39d99"},
+    {file = "jupyter_client-8.6.0.tar.gz", hash = "sha256:0642244bb83b4764ae60d07e010e15f0e2d275ec4e918a8f7b80fbbef3ca60c7"},
+]
+
+[package.dependencies]
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+python-dateutil = ">=2.8.2"
+pyzmq = ">=23.0"
+tornado = ">=6.2"
+traitlets = ">=5.3"
+
+[package.extras]
+docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
+
+[[package]]
+name = "jupyter-core"
+version = "5.7.1"
+description = "Jupyter core package. A base package on which Jupyter projects rely."
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "jupyter_core-5.7.1-py3-none-any.whl", hash = "sha256:c65c82126453a723a2804aa52409930434598fd9d35091d63dfb919d2b765bb7"},
+    {file = "jupyter_core-5.7.1.tar.gz", hash = "sha256:de61a9d7fc71240f688b2fb5ab659fbb56979458dc66a71decd098e03c79e218"},
+]
+
+[package.dependencies]
+platformdirs = ">=2.5"
+pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
+traitlets = ">=5.3"
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
+test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "jupyterlab-pygments"
+version = "0.3.0"
+description = "Pygments theme using JupyterLab CSS variables"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "jupyterlab_pygments-0.3.0-py3-none-any.whl", hash = "sha256:841a89020971da1d8693f1a99997aefc5dc424bb1b251fd6322462a1b8842780"},
+    {file = "jupyterlab_pygments-0.3.0.tar.gz", hash = "sha256:721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d"},
+]
+
 [[package]]
 name = "kiwisolver"
 version = "1.4.5"
@@ -967,6 +1357,17 @@ pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
+[[package]]
+name = "mistune"
+version = "3.0.2"
+description = "A sane and fast Markdown parser with useful plugins and renderers"
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "mistune-3.0.2-py3-none-any.whl", hash = "sha256:71481854c30fdbc938963d3605b72501f5c10a9320ecd412c121c163a1c7d205"},
+    {file = "mistune-3.0.2.tar.gz", hash = "sha256:fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8"},
+]
+
 [[package]]
 name = "mpmath"
 version = "1.3.0"
@@ -1149,6 +1550,105 @@ files = [
 fast = ["fastnumbers (>=2.0.0)"]
 icu = ["PyICU (>=1.0.0)"]
 
+[[package]]
+name = "nbclient"
+version = "0.9.0"
+description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
+optional = true
+python-versions = ">=3.8.0"
+files = [
+    {file = "nbclient-0.9.0-py3-none-any.whl", hash = "sha256:a3a1ddfb34d4a9d17fc744d655962714a866639acd30130e9be84191cd97cd15"},
+    {file = "nbclient-0.9.0.tar.gz", hash = "sha256:4b28c207877cf33ef3a9838cdc7a54c5ceff981194a82eac59d558f05487295e"},
+]
+
+[package.dependencies]
+jupyter-client = ">=6.1.12"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+nbformat = ">=5.1"
+traitlets = ">=5.4"
+
+[package.extras]
+dev = ["pre-commit"]
+docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
+test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
+
+[[package]]
+name = "nbconvert"
+version = "7.16.1"
+description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "nbconvert-7.16.1-py3-none-any.whl", hash = "sha256:3188727dffadfdc9c6a1c7250729063d7bc78b355ad7aa023138afa030d1cd07"},
+    {file = "nbconvert-7.16.1.tar.gz", hash = "sha256:e79e6a074f49ba3ed29428ed86487bf51509d9aab613bd8522ac08f6d28fd7fd"},
+]
+
+[package.dependencies]
+beautifulsoup4 = "*"
+bleach = "!=5.0.0"
+defusedxml = "*"
+jinja2 = ">=3.0"
+jupyter-core = ">=4.7"
+jupyterlab-pygments = "*"
+markupsafe = ">=2.0"
+mistune = ">=2.0.3,<4"
+nbclient = ">=0.5.0"
+nbformat = ">=5.7"
+packaging = "*"
+pandocfilters = ">=1.4.1"
+pygments = ">=2.4.1"
+tinycss2 = "*"
+traitlets = ">=5.1"
+
+[package.extras]
+all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"]
+docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"]
+qtpdf = ["nbconvert[qtpng]"]
+qtpng = ["pyqtwebengine (>=5.15)"]
+serve = ["tornado (>=6.1)"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7.5)", "pytest"]
+webpdf = ["playwright"]
+
+[[package]]
+name = "nbformat"
+version = "5.9.2"
+description = "The Jupyter Notebook format"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "nbformat-5.9.2-py3-none-any.whl", hash = "sha256:1c5172d786a41b82bcfd0c23f9e6b6f072e8fb49c39250219e4acfff1efe89e9"},
+    {file = "nbformat-5.9.2.tar.gz", hash = "sha256:5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192"},
+]
+
+[package.dependencies]
+fastjsonschema = "*"
+jsonschema = ">=2.6"
+jupyter-core = "*"
+traitlets = ">=5.1"
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["pep440", "pre-commit", "pytest", "testpath"]
+
+[[package]]
+name = "nbsphinx"
+version = "0.8.12"
+description = "Jupyter Notebook Tools for Sphinx"
+optional = true
+python-versions = ">=3.6"
+files = [
+    {file = "nbsphinx-0.8.12-py3-none-any.whl", hash = "sha256:c15b681c7fce287000856f91fe1edac50d29f7b0c15bbc746fbe55c8eb84750b"},
+    {file = "nbsphinx-0.8.12.tar.gz", hash = "sha256:76570416cdecbeb21dbf5c3d6aa204ced6c1dd7ebef4077b5c21b8c6ece9533f"},
+]
+
+[package.dependencies]
+docutils = "*"
+jinja2 = "*"
+nbconvert = "!=5.4"
+nbformat = "*"
+sphinx = ">=1.8"
+traitlets = ">=5"
+
 [[package]]
 name = "networkx"
 version = "3.2.1"
@@ -1470,6 +1970,17 @@ sql-other = ["SQLAlchemy (>=2.0.0)", "adbc-driver-postgresql (>=0.8.0)", "adbc-d
 test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"]
 xml = ["lxml (>=4.9.2)"]
 
+[[package]]
+name = "pandocfilters"
+version = "1.5.1"
+description = "Utilities for writing pandoc filters in python"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "pandocfilters-1.5.1-py2.py3-none-any.whl", hash = "sha256:93be382804a9cdb0a7267585f157e5d1731bbe5545a85b268d6f5fe6232de2bc"},
+    {file = "pandocfilters-1.5.1.tar.gz", hash = "sha256:002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e"},
+]
+
 [[package]]
 name = "patsy"
 version = "0.5.6"
@@ -1573,6 +2084,21 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 typing = ["typing-extensions"]
 xmp = ["defusedxml"]
 
+[[package]]
+name = "platformdirs"
+version = "4.2.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "platformdirs-4.2.0-py3-none-any.whl", hash = "sha256:0614df2a2f37e1a662acbd8e2b25b92ccf8632929bc6d43467e17fe89c75e068"},
+    {file = "platformdirs-4.2.0.tar.gz", hash = "sha256:ef0cc731df711022c174543cb70a9b5bd22e5a9337c8624ef2c2ceb8ddad8768"},
+]
+
+[package.extras]
+docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
+
 [[package]]
 name = "pluggy"
 version = "1.4.0"
@@ -1662,6 +2188,32 @@ files = [
     {file = "protobuf-4.25.3.tar.gz", hash = "sha256:25b5d0b42fd000320bd7830b349e3b696435f3b329810427a6bcce6a5492cc5c"},
 ]
 
+[[package]]
+name = "pycparser"
+version = "2.21"
+description = "C parser in Python"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "pycparser-2.21-py2.py3-none-any.whl", hash = "sha256:8ee45429555515e1f6b185e78100aea234072576aa43ab53aefcae078162fca9"},
+    {file = "pycparser-2.21.tar.gz", hash = "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"},
+]
+
+[[package]]
+name = "pygments"
+version = "2.17.2"
+description = "Pygments is a syntax highlighting package written in Python."
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "pygments-2.17.2-py3-none-any.whl", hash = "sha256:b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c"},
+    {file = "pygments-2.17.2.tar.gz", hash = "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"},
+]
+
+[package.extras]
+plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
+
 [[package]]
 name = "pynndescent"
 version = "0.5.11"
@@ -1772,6 +2324,29 @@ files = [
     {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
 ]
 
+[[package]]
+name = "pywin32"
+version = "306"
+description = "Python for Window Extensions"
+optional = true
+python-versions = "*"
+files = [
+    {file = "pywin32-306-cp310-cp310-win32.whl", hash = "sha256:06d3420a5155ba65f0b72f2699b5bacf3109f36acbe8923765c22938a69dfc8d"},
+    {file = "pywin32-306-cp310-cp310-win_amd64.whl", hash = "sha256:84f4471dbca1887ea3803d8848a1616429ac94a4a8d05f4bc9c5dcfd42ca99c8"},
+    {file = "pywin32-306-cp311-cp311-win32.whl", hash = "sha256:e65028133d15b64d2ed8f06dd9fbc268352478d4f9289e69c190ecd6818b6407"},
+    {file = "pywin32-306-cp311-cp311-win_amd64.whl", hash = "sha256:a7639f51c184c0272e93f244eb24dafca9b1855707d94c192d4a0b4c01e1100e"},
+    {file = "pywin32-306-cp311-cp311-win_arm64.whl", hash = "sha256:70dba0c913d19f942a2db25217d9a1b726c278f483a919f1abfed79c9cf64d3a"},
+    {file = "pywin32-306-cp312-cp312-win32.whl", hash = "sha256:383229d515657f4e3ed1343da8be101000562bf514591ff383ae940cad65458b"},
+    {file = "pywin32-306-cp312-cp312-win_amd64.whl", hash = "sha256:37257794c1ad39ee9be652da0462dc2e394c8159dfd913a8a4e8eb6fd346da0e"},
+    {file = "pywin32-306-cp312-cp312-win_arm64.whl", hash = "sha256:5821ec52f6d321aa59e2db7e0a35b997de60c201943557d108af9d4ae1ec7040"},
+    {file = "pywin32-306-cp37-cp37m-win32.whl", hash = "sha256:1c73ea9a0d2283d889001998059f5eaaba3b6238f767c9cf2833b13e6a685f65"},
+    {file = "pywin32-306-cp37-cp37m-win_amd64.whl", hash = "sha256:72c5f621542d7bdd4fdb716227be0dd3f8565c11b280be6315b06ace35487d36"},
+    {file = "pywin32-306-cp38-cp38-win32.whl", hash = "sha256:e4c092e2589b5cf0d365849e73e02c391c1349958c5ac3e9d5ccb9a28e017b3a"},
+    {file = "pywin32-306-cp38-cp38-win_amd64.whl", hash = "sha256:e8ac1ae3601bee6ca9f7cb4b5363bf1c0badb935ef243c4733ff9a393b1690c0"},
+    {file = "pywin32-306-cp39-cp39-win32.whl", hash = "sha256:e25fd5b485b55ac9c057f67d94bc203f3f6595078d1fb3b458c9c28b7153a802"},
+    {file = "pywin32-306-cp39-cp39-win_amd64.whl", hash = "sha256:39b61c15272833b5c329a2989999dcae836b1eed650252ab1b7bfbe1d59f30f4"},
+]
+
 [[package]]
 name = "pyyaml"
 version = "6.0.1"
@@ -1832,6 +2407,255 @@ files = [
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
+[[package]]
+name = "pyzmq"
+version = "25.1.2"
+description = "Python bindings for 0MQ"
+optional = true
+python-versions = ">=3.6"
+files = [
+    {file = "pyzmq-25.1.2-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:e624c789359f1a16f83f35e2c705d07663ff2b4d4479bad35621178d8f0f6ea4"},
+    {file = "pyzmq-25.1.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:49151b0efece79f6a79d41a461d78535356136ee70084a1c22532fc6383f4ad0"},
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+    {file = "rpds_py-0.18.0-pp39-pypy39_pp73-musllinux_1_2_i686.whl", hash = "sha256:bc362ee4e314870a70f4ae88772d72d877246537d9f8cb8f7eacf10884862432"},
+    {file = "rpds_py-0.18.0-pp39-pypy39_pp73-musllinux_1_2_x86_64.whl", hash = "sha256:4832d7d380477521a8c1644bbab6588dfedea5e30a7d967b5fb75977c45fd77f"},
+    {file = "rpds_py-0.18.0.tar.gz", hash = "sha256:42821446ee7a76f5d9f71f9e33a4fb2ffd724bb3e7f93386150b61a43115788d"},
+]
+
 [[package]]
 name = "scanpy"
 version = "1.9.8"
@@ -2026,6 +2850,173 @@ files = [
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
 
+[[package]]
+name = "snowballstemmer"
+version = "2.2.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+optional = true
+python-versions = "*"
+files = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
+    {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
+]
+
+[[package]]
+name = "soupsieve"
+version = "2.5"
+description = "A modern CSS selector implementation for Beautiful Soup."
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
+    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
+]
+
+[[package]]
+name = "sphinx"
+version = "6.2.1"
+description = "Python documentation generator"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "Sphinx-6.2.1.tar.gz", hash = "sha256:6d56a34697bb749ffa0152feafc4b19836c755d90a7c59b72bc7dfd371b9cc6b"},
+    {file = "sphinx-6.2.1-py3-none-any.whl", hash = "sha256:97787ff1fa3256a3eef9eda523a63dbf299f7b47e053cfcf684a1c2a8380c912"},
+]
+
+[package.dependencies]
+alabaster = ">=0.7,<0.8"
+babel = ">=2.9"
+colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.18.1,<0.20"
+imagesize = ">=1.3"
+Jinja2 = ">=3.0"
+packaging = ">=21.0"
+Pygments = ">=2.13"
+requests = ">=2.25.0"
+snowballstemmer = ">=2.0"
+sphinxcontrib-applehelp = "*"
+sphinxcontrib-devhelp = "*"
+sphinxcontrib-htmlhelp = ">=2.0.0"
+sphinxcontrib-jsmath = "*"
+sphinxcontrib-qthelp = "*"
+sphinxcontrib-serializinghtml = ">=1.1.5"
+
+[package.extras]
+docs = ["sphinxcontrib-websupport"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"]
+test = ["cython", "filelock", "html5lib", "pytest (>=4.6)"]
+
+[[package]]
+name = "sphinx-basic-ng"
+version = "1.0.0b2"
+description = "A modern skeleton for Sphinx themes."
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "sphinx_basic_ng-1.0.0b2-py3-none-any.whl", hash = "sha256:eb09aedbabfb650607e9b4b68c9d240b90b1e1be221d6ad71d61c52e29f7932b"},
+    {file = "sphinx_basic_ng-1.0.0b2.tar.gz", hash = "sha256:9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9"},
+]
+
+[package.dependencies]
+sphinx = ">=4.0"
+
+[package.extras]
+docs = ["furo", "ipython", "myst-parser", "sphinx-copybutton", "sphinx-inline-tabs"]
+
+[[package]]
+name = "sphinxcontrib-applehelp"
+version = "1.0.8"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_applehelp-1.0.8-py3-none-any.whl", hash = "sha256:cb61eb0ec1b61f349e5cc36b2028e9e7ca765be05e49641c97241274753067b4"},
+    {file = "sphinxcontrib_applehelp-1.0.8.tar.gz", hash = "sha256:c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-devhelp"
+version = "1.0.6"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_devhelp-1.0.6-py3-none-any.whl", hash = "sha256:6485d09629944511c893fa11355bda18b742b83a2b181f9a009f7e500595c90f"},
+    {file = "sphinxcontrib_devhelp-1.0.6.tar.gz", hash = "sha256:9893fd3f90506bc4b97bdb977ceb8fbd823989f4316b28c3841ec128544372d3"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.5"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl", hash = "sha256:393f04f112b4d2f53d93448d4bce35842f62b307ccdc549ec1585e950bc35e04"},
+    {file = "sphinxcontrib_htmlhelp-2.0.5.tar.gz", hash = "sha256:0dc87637d5de53dd5eec3a6a01753b1ccf99494bd756aafecd74b4fa9e729015"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
+test = ["html5lib", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-jsmath"
+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
+optional = true
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
+
+[package.extras]
+test = ["flake8", "mypy", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-qthelp"
+version = "1.0.7"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_qthelp-1.0.7-py3-none-any.whl", hash = "sha256:e2ae3b5c492d58fcbd73281fbd27e34b8393ec34a073c792642cd8e529288182"},
+    {file = "sphinxcontrib_qthelp-1.0.7.tar.gz", hash = "sha256:053dedc38823a80a7209a80860b16b722e9e0209e32fea98c90e4e6624588ed6"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-serializinghtml"
+version = "1.1.10"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl", hash = "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7"},
+    {file = "sphinxcontrib_serializinghtml-1.1.10.tar.gz", hash = "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
+test = ["pytest"]
+
 [[package]]
 name = "statsmodels"
 version = "0.14.1"
@@ -2155,6 +3146,24 @@ files = [
     {file = "threadpoolctl-3.3.0.tar.gz", hash = "sha256:5dac632b4fa2d43f42130267929af3ba01399ef4bd1882918e92dbc30365d30c"},
 ]
 
+[[package]]
+name = "tinycss2"
+version = "1.2.1"
+description = "A tiny CSS parser"
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "tinycss2-1.2.1-py3-none-any.whl", hash = "sha256:2b80a96d41e7c3914b8cda8bc7f705a4d9c49275616e886103dd839dfc847847"},
+    {file = "tinycss2-1.2.1.tar.gz", hash = "sha256:8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627"},
+]
+
+[package.dependencies]
+webencodings = ">=0.4"
+
+[package.extras]
+doc = ["sphinx", "sphinx_rtd_theme"]
+test = ["flake8", "isort", "pytest"]
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
@@ -2252,6 +3261,26 @@ text = ["ipadic (>=1.0.0)", "mecab-ko (>=1.0.0)", "mecab-ko-dic (>=1.0.0)", "mec
 typing = ["mypy (==1.8.0)", "torch (==2.2.0)", "types-PyYAML", "types-emoji", "types-protobuf", "types-requests", "types-setuptools", "types-six", "types-tabulate"]
 visual = ["SciencePlots (>=2.0.0)", "matplotlib (>=3.3.0)"]
 
+[[package]]
+name = "tornado"
+version = "6.4"
+description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
+optional = true
+python-versions = ">= 3.8"
+files = [
+    {file = "tornado-6.4-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:02ccefc7d8211e5a7f9e8bc3f9e5b0ad6262ba2fbb683a6443ecc804e5224ce0"},
+    {file = "tornado-6.4-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:27787de946a9cffd63ce5814c33f734c627a87072ec7eed71f7fc4417bb16263"},
+    {file = "tornado-6.4-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f7894c581ecdcf91666a0912f18ce5e757213999e183ebfc2c3fdbf4d5bd764e"},
+    {file = "tornado-6.4-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e43bc2e5370a6a8e413e1e1cd0c91bedc5bd62a74a532371042a18ef19e10579"},
+    {file = "tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f0251554cdd50b4b44362f73ad5ba7126fc5b2c2895cc62b14a1c2d7ea32f212"},
+    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:fd03192e287fbd0899dd8f81c6fb9cbbc69194d2074b38f384cb6fa72b80e9c2"},
+    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_i686.whl", hash = "sha256:88b84956273fbd73420e6d4b8d5ccbe913c65d31351b4c004ae362eba06e1f78"},
+    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:71ddfc23a0e03ef2df1c1397d859868d158c8276a0603b96cf86892bff58149f"},
+    {file = "tornado-6.4-cp38-abi3-win32.whl", hash = "sha256:6f8a6c77900f5ae93d8b4ae1196472d0ccc2775cc1dfdc9e7727889145c45052"},
+    {file = "tornado-6.4-cp38-abi3-win_amd64.whl", hash = "sha256:10aeaa8006333433da48dec9fe417877f8bcc21f48dda8d661ae79da357b2a63"},
+    {file = "tornado-6.4.tar.gz", hash = "sha256:72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee"},
+]
+
 [[package]]
 name = "tqdm"
 version = "4.66.2"
@@ -2272,6 +3301,21 @@ notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
+[[package]]
+name = "traitlets"
+version = "5.14.1"
+description = "Traitlets Python configuration system"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "traitlets-5.14.1-py3-none-any.whl", hash = "sha256:2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74"},
+    {file = "traitlets-5.14.1.tar.gz", hash = "sha256:8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e"},
+]
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
+
 [[package]]
 name = "triton"
 version = "2.2.0"
@@ -2340,6 +3384,34 @@ parametric-umap = ["tensorflow (>=2.1)", "tensorflow-probability (>=0.10)"]
 plot = ["bokeh", "colorcet", "datashader", "holoviews", "matplotlib", "pandas", "scikit-image", "seaborn"]
 tbb = ["tbb (>=2019.0)"]
 
+[[package]]
+name = "urllib3"
+version = "2.2.1"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
+    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+]
+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "webencodings"
+version = "0.5.1"
+description = "Character encoding aliases for legacy web content"
+optional = true
+python-versions = "*"
+files = [
+    {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"},
+    {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"},
+]
+
 [[package]]
 name = "werkzeug"
 version = "3.0.1"
@@ -2463,4 +3535,4 @@ multidict = ">=4.0"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "1a5413553bbf7d1dbd4f42a0e2a690c4db05e07916b400df25b39f0e9ee2540a"
+content-hash = "ee765706ba288f302dc0d931f1424555abde31673f9fbf515e1b0ef48549d0ee"
diff --git a/pyproject.toml b/pyproject.toml
index eeb1926..ba7e0a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,6 +16,8 @@ geomloss = "^0.2"
 pot = "^0.9.1"
 tensorboard = "^2.12.0"
 muon = "^0.1.0"
+nbsphinx = {version = "^0.8.12", optional = true, extras = ["docsbuild"]}
+furo = {version = "^2022.12.7", optional = true, extras = ["docsbuild"]}
 
 
 
diff --git a/scconfluence/distributions.py b/scconfluence/distributions.py
index 8decc0d..f12ba8d 100644
--- a/scconfluence/distributions.py
+++ b/scconfluence/distributions.py
@@ -37,7 +37,8 @@ def log_zinb_positive(
     -----
     We parametrize the bernoulli using the logits, hence the softplus functions appearing.
     """
-    # theta is the dispersion rate. If .ndimension() == 1, it is shared for all cells (regardless of batch or labels)
+    # theta is the dispersion rate. If .ndimension() == 1, it is shared for all cells
+    # (regardless of batch or labels)
     if theta.ndimension() == 1:
         theta = theta.view(
             1, theta.size(0)
@@ -224,7 +225,7 @@ def variance(self):
 
     def sample(
         self, sample_shape: Union[torch.Size, Tuple] = torch.Size()
-    ) -> torch.Tensor:
+    ) -> torch.Tensor:  # pragma: no cover
         with torch.no_grad():
             gamma_d = self._gamma()
             p_means = gamma_d.sample(sample_shape)
@@ -330,7 +331,7 @@ def zi_probs(self) -> torch.Tensor:
 
     def sample(
         self, sample_shape: Union[torch.Size, Tuple] = torch.Size()
-    ) -> torch.Tensor:
+    ) -> torch.Tensor:  # pragma: no cover
         with torch.no_grad():
             samp = super().sample(sample_shape=sample_shape)
             is_zero = torch.rand_like(samp) <= self.zi_probs