diff --git a/doc/source/api.rst b/doc/source/api.rst
new file mode 100644
index 0000000..8c71620
--- /dev/null
+++ b/doc/source/api.rst
@@ -0,0 +1,8 @@
+API
+===
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   filter_functions
diff --git a/doc/source/conf.py b/doc/source/conf.py
index cf630d8..89e80c7 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -38,6 +38,7 @@
     'nbsphinx',
     'sphinx.ext.mathjax',
     'sphinx.ext.todo',
+    'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'numpydoc',
     'sphinx.ext.extlinks',
@@ -45,13 +46,12 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.napoleon',
     'sphinx.ext.intersphinx',
-    #'sphinxcontrib.apidoc',
+    'sphinxcontrib.apidoc',
     #'IPython.sphinxext.ipython_console_highlighting',
     #'IPython.sphinxext.ipython_directive',
     #'matplotlib.sphinxext.only_directives',
     #'matplotlib.sphinxext.plot_directive',
     #'matplotlib.sphinxext.mathmpl',
-    #'sphinx.ext.autodoc',
     #'sphinx.ext.doctest',
 ]
 
@@ -59,6 +59,7 @@
 apidoc_module_dir = '../../filter_functions'
 apidoc_excluded_paths = ['../tests']
 apidoc_separate_modules = True
+apidoc_module_first = True
 
 # Numpydoc settings
 numpydoc_show_inherited_class_members = False
diff --git a/doc/source/filter_functions.rst b/doc/source/filter_functions.rst
deleted file mode 100644
index 0c4efd6..0000000
--- a/doc/source/filter_functions.rst
+++ /dev/null
@@ -1,85 +0,0 @@
-filter\_functions package
-=========================
-
-Submodules
-----------
-
-filter\_functions.analytic module
----------------------------------
-
-.. automodule:: filter_functions.analytic
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-filter\_functions.basis module
-------------------------------
-
-.. automodule:: filter_functions.basis
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-filter\_functions.gradient module
----------------------------------
-
-.. automodule:: filter_functions.gradient
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-filter\_functions.numeric module
---------------------------------
-
-.. automodule:: filter_functions.numeric
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-filter\_functions.plotting module
----------------------------------
-
-.. automodule:: filter_functions.plotting
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-filter\_functions.pulse\_sequence module
-----------------------------------------
-
-.. automodule:: filter_functions.pulse_sequence
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-filter\_functions.superoperator module
---------------------------------------
-
-.. automodule:: filter_functions.superoperator
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-filter\_functions.types module
-------------------------------
-
-.. automodule:: filter_functions.types
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-filter\_functions.util module
------------------------------
-
-.. automodule:: filter_functions.util
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: filter_functions
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 1101d48..b787bc9 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -23,7 +23,7 @@ Documentation
    :numbered:
 
    examples/examples
-   filter_functions API Documentation <filter_functions>
+   filter_functions API Documentation <api>
 
 Indices and tables
 ==================
diff --git a/environment.yml b/environment.yml
index 60f7de2..2c97499 100644
--- a/environment.yml
+++ b/environment.yml
@@ -6,6 +6,7 @@ channels:
 dependencies:
   - python >= 3.9
   - qutip
+  - pandoc
   - pip
 
 prefix: /home/docs/.conda/envs/filter_functions
diff --git a/setup.py b/setup.py
index 4e0e643..dabcadf 100644
--- a/setup.py
+++ b/setup.py
@@ -19,7 +19,7 @@ def extract_version(version_file):
 extras_require = {'plotting': ['matplotlib'],
                   'bloch_sphere_visualization': ['qutip', 'matplotlib'],
                   'doc': ['jupyter', 'nbsphinx', 'numpydoc', 'sphinx', 'sphinx_rtd_theme',
-                          'ipympl', 'qutip-qip', 'qutip-qtrl', 'numpy<2'],
+                          'sphinxcontrib-apidoc', 'ipympl', 'qutip-qip', 'qutip-qtrl', 'numpy<2'],
                   'tests': ['pytest>=4.6', 'pytest-cov', 'codecov']}
 
 extras_require['all'] = list({dep for deps in extras_require.values() for dep in deps})