--- a
+++ b/docs/conf.py
@@ -0,0 +1,186 @@
+#!/usr/bin/env python
+# mypy: ignore-errors
+
+import sys
+from datetime import datetime
+from importlib.metadata import metadata
+from pathlib import Path
+
+HERE = Path(__file__).parent
+sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
+
+needs_sphinx = "4.3"
+
+info = metadata("ehrapy")
+project_name = info["Name"]
+author = info["Author"]
+copyright = f"{datetime.now():%Y}, {author}."
+version = info["Version"]
+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
+repository_url = urls["Source"]
+release = info["Version"]
+github_repo = "ehrapy"
+
+extensions = [
+    "myst_parser",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "nbsphinx",
+    "nbsphinx_link",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",  # needs to be after napoleon
+    "sphinx.ext.autosummary",
+    "sphinx_copybutton",
+    "sphinx_gallery.load_style",
+    "sphinx_remove_toctrees",
+    "sphinx_design",
+]
+
+# remove_from_toctrees = ["tutorials/notebooks/*", "api/reference/*"]
+
+# for sharing urls with nice info
+ogp_site_url = "https://ehrapy.readthedocs.io/en/latest/"
+ogp_image = "https://ehrapy.readthedocs.io/en/latest//_static/logo.png"
+
+# nbsphinx specific settings
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "auto_*/**.ipynb",
+    "auto_*/**.md5",
+    "auto_*/**.py",
+    "**.ipynb_checkpoints",
+]
+nbsphinx_execute = "never"
+
+templates_path = ["_templates"]
+# source_suffix = ".md"
+
+autosummary_generate = True
+autodoc_member_order = "bysource"
+napoleon_google_docstring = True  # for pytorch lightning
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_use_rtype = True  # having a separate entry generally helps readability
+napoleon_use_param = True
+napoleon_custom_sections = [("Params", "Parameters")]
+todo_include_todos = False
+numpydoc_show_class_members = False
+annotate_defaults = True  # scanpydoc option, look into why we need this
+myst_enable_extensions = [
+    "colon_fence",
+    "dollarmath",
+    "amsmath",
+]
+
+master_doc = "index"
+
+intersphinx_mapping = {
+    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+    "ipython": ("https://ipython.readthedocs.io/en/stable/", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "python": ("https://docs.python.org/3", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
+    "pynndescent": ("https://pynndescent.readthedocs.io/en/latest/", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+    "torch": ("https://pytorch.org/docs/master/", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "pytorch_lightning": ("https://pytorch-lightning.readthedocs.io/en/stable/", None),
+    "pyro": ("http://docs.pyro.ai/en/stable/", None),
+    "pymde": ("https://pymde.org/", None),
+    "flax": ("https://flax.readthedocs.io/en/latest/", None),
+    "jax": ("https://jax.readthedocs.io/en/latest/", None),
+    "lamin": ("https://lamin.ai/docs", None),
+    "lifelines": ("https://lifelines.readthedocs.io/en/latest/", None),
+}
+
+language = "en"
+
+typehints_defaults = "comma"
+
+pygments_style = "default"
+pygments_dark_style = "native"
+
+
+# html_show_sourcelink = True
+html_theme = "furo"
+
+html_title = "ehrapy"
+html_logo = "_static/ehrapy_logos/ehrapy_pure.png"
+
+html_theme_options = {
+    "sidebar_hide_name": True,
+    "light_css_variables": {
+        "color-brand-primary": "#003262",
+        "color-brand-content": "#003262",
+        "admonition-font-size": "var(--font-size-normal)",
+        "admonition-title-font-size": "var(--font-size-normal)",
+        "code-font-size": "var(--font-size--small)",
+    },
+}
+html_static_path = ["_static"]
+html_css_files = ["css/overwrite.css", "css/sphinx_gallery.css"]
+html_show_sphinx = False
+
+
+nbsphinx_prolog = r"""
+.. raw:: html
+
+{{% set docname = env.doc2path(env.docname, base=None).split("/")[-1] %}}
+
+.. raw:: html
+
+    <style>
+        p {{
+            margin-bottom: 0.5rem;
+        }}
+        /* Main index page overview cards */
+        /* https://github.com/spatialaudio/nbsphinx/pull/635/files */
+        .jp-RenderedHTMLCommon table,
+        div.rendered_html table {{
+        border: none;
+        border-collapse: collapse;
+        border-spacing: 0;
+        font-size: 12px;
+        table-layout: fixed;
+        color: inherit;
+        }}
+
+        body:not([data-theme=light]) .jp-RenderedHTMLCommon tbody tr:nth-child(odd),
+        body:not([data-theme=light]) div.rendered_html tbody tr:nth-child(odd) {{
+        background: rgba(255, 255, 255, .1);
+        }}
+    </style>
+
+.. raw:: html
+
+    <div class="admonition note">
+        <p class="admonition-title">Note</p>
+        <p>
+        This page was generated from
+        <a class="reference external" href="https://github.com/theislab/ehrapy/tree/{version}/">{docname}</a>.
+        Some tutorial content may look better in light mode.
+        </p>
+    </div>
+""".format(version=version, docname="{{ docname|e }}")
+nbsphinx_thumbnails = {
+    "tutorials/notebooks/ehrapy_introduction": "_static/ehrapy_logos/ehrapy_pure.png",
+    "tutorials/notebooks/mimic_2_introduction": "_static/tutorials/catheter.png",
+    "tutorials/notebooks/mimic_2_fate": "_static/tutorials/fate.png",
+    "tutorials/notebooks/mimic_2_survival_analysis": "_static/tutorials/survival.png",
+    "tutorials/notebooks/mimic_2_effect_estimation": "_static/tutorials/effect_estimation.png",
+    "tutorials/notebooks/mimic_2_causal_inference": "_static/tutorials/causal_inference.png",
+    "tutorials/notebooks/medcat": "_static/tutorials/nlp.png",
+    "tutorials/notebooks/ml_usecases": "_static/tutorials/machine_learning.png",
+    "tutorials/notebooks/ontology_mapping": "_static/tutorials/ontology.png",
+    "tutorials/notebooks/fhir": "_static/tutorials/fhir.png",
+    "tutorials/notebooks/cohort_tracking": "_static/tutorials/cohort_tracking.png",
+    "tutorials/notebooks/bias": "_static/tutorials/bias.png",
+    "tutorials/notebooks/out_of_core": "_static/tutorials/out_of_core.png",
+    "tutorials/notebooks/patient_trajectory": "_static/tutorials/patient_trajectory.png",
+}