diff --git a/pyproject.toml b/pyproject.toml
index d4a19d5..1ecd685 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ urls.Documentation = "https://embedding-scvi.readthedocs.io/"
 urls.Source = "https://github.com/YosefLab/embedding-scvi"
 urls.Home-page = "https://github.com/YosefLab/embedding-scvi"
 dependencies = [
-    "anndata",
+    "scvi-tools>=1.0.0",
     # for debug logging (referenced from the issue template)
     "session-info"
 ]
diff --git a/src/embedding_scvi/__init__.py b/src/embedding_scvi/__init__.py
index 654906f..b18539a 100644
--- a/src/embedding_scvi/__init__.py
+++ b/src/embedding_scvi/__init__.py
@@ -1,7 +1,3 @@
 from importlib.metadata import version
 
-from . import pl, pp, tl
-
-__all__ = ["pl", "pp", "tl"]
-
 __version__ = version("embedding-scvi")
diff --git a/src/embedding_scvi/pl/__init__.py b/src/embedding_scvi/pl/__init__.py
deleted file mode 100644
index c2315dd..0000000
--- a/src/embedding_scvi/pl/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from .basic import BasicClass, basic_plot
diff --git a/src/embedding_scvi/pl/basic.py b/src/embedding_scvi/pl/basic.py
deleted file mode 100644
index ed390ef..0000000
--- a/src/embedding_scvi/pl/basic.py
+++ /dev/null
@@ -1,63 +0,0 @@
-from anndata import AnnData
-
-
-def basic_plot(adata: AnnData) -> int:
-    """Generate a basic plot for an AnnData object.
-
-    Parameters
-    ----------
-    adata
-        The AnnData object to preprocess.
-
-    Returns
-    -------
-    Some integer value.
-    """
-    print("Import matplotlib and implement a plotting function here.")
-    return 0
-
-
-class BasicClass:
-    """A basic class.
-
-    Parameters
-    ----------
-    adata
-        The AnnData object to preprocess.
-    """
-
-    my_attribute: str = "Some attribute."
-    my_other_attribute: int = 0
-
-    def __init__(self, adata: AnnData):
-        print("Implement a class here.")
-
-    def my_method(self, param: int) -> int:
-        """A basic method.
-
-        Parameters
-        ----------
-        param
-            A parameter.
-
-        Returns
-        -------
-        Some integer value.
-        """
-        print("Implement a method here.")
-        return 0
-
-    def my_other_method(self, param: str) -> str:
-        """Another basic method.
-
-        Parameters
-        ----------
-        param
-            A parameter.
-
-        Returns
-        -------
-        Some integer value.
-        """
-        print("Implement a method here.")
-        return ""
diff --git a/src/embedding_scvi/pp/__init__.py b/src/embedding_scvi/pp/__init__.py
deleted file mode 100644
index 5e7e293..0000000
--- a/src/embedding_scvi/pp/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from .basic import basic_preproc
diff --git a/src/embedding_scvi/pp/basic.py b/src/embedding_scvi/pp/basic.py
deleted file mode 100644
index 5db1ec0..0000000
--- a/src/embedding_scvi/pp/basic.py
+++ /dev/null
@@ -1,17 +0,0 @@
-from anndata import AnnData
-
-
-def basic_preproc(adata: AnnData) -> int:
-    """Run a basic preprocessing on the AnnData object.
-
-    Parameters
-    ----------
-    adata
-        The AnnData object to preprocess.
-
-    Returns
-    -------
-    Some integer value.
-    """
-    print("Implement a preprocessing function here.")
-    return 0
diff --git a/src/embedding_scvi/tl/__init__.py b/src/embedding_scvi/tl/__init__.py
deleted file mode 100644
index 95a32cd..0000000
--- a/src/embedding_scvi/tl/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from .basic import basic_tool
diff --git a/src/embedding_scvi/tl/basic.py b/src/embedding_scvi/tl/basic.py
deleted file mode 100644
index d215ade..0000000
--- a/src/embedding_scvi/tl/basic.py
+++ /dev/null
@@ -1,17 +0,0 @@
-from anndata import AnnData
-
-
-def basic_tool(adata: AnnData) -> int:
-    """Run a tool on the AnnData object.
-
-    Parameters
-    ----------
-    adata
-        The AnnData object to preprocess.
-
-    Returns
-    -------
-    Some integer value.
-    """
-    print("Implement a tool to run on the AnnData object.")
-    return 0