I've looked at numerous tutorials and videos taking one through the process of generating documentation using Sphinx, and at this point I am convinced that there is something wrong with my project structure. I am running Windows 10 Pro, 2004; Python 3.7.9; Sphinx 3.3.0. I created a completely fresh project sphinx_test to test my Sphinx skills by following these steps: Create a new virtualenv python -m virtualenv sphinxtest Activate it sphinxtest\Scripts\activate Install Sphinx and requirements pip install sphinx Create a new project folder mkdir sphinx_test and navigate into it cd sphinx_test Create subdirectory for source code and all sub-modules to come mkdir src Create some silly sample *.py files with random docstrings (nopes.py and sqrer.py) Create the docs directory mkdir docs and navigate into it cd docs Execute sphinx-quickstart --ext-autodoc, choosing separate build and source directories Modify conf.py, adding ./src/ to the PATH Modify index.rst, adding modules beneath toctree group: Run sphinx-apidoc -o .\source\ ..\src\ from inside the docs directory. Run make html and get the following: Running Sphinx v3.3.0 loading pickled environment... done building [mo]: targets for 0 po files that are out of date building HTML: : targets for 2 source files that are out of date updating environment: 0 added, 2 changed, 0 removed reading sources... [100%] src WARNING: autodoc: failed to import module 'nopes' from module 'src'; the following exception was raised: No module named 'src' WARNING: autodoc: failed to import module 'sqrer' from module 'src'; the following exception was raised: No module named 'src' WARNING: autodoc: failed to import module 'src'; the following exception was raised: No module named 'src' looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [100%] src generating indices... genindex done writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 3 warnings. The HTML pages are in build\html. This is the folder structure at present: C:. ├───docs │ │ make.bat │ │ Makefile │ │ │ ├───build │ │ ├───doctrees │ │ │ environment.pickle │ │ │ index.doctree │ │ │ modules.doctree │ │ │ src.doctree │ │ │ │ │ └───html │ │ │ .buildinfo │ │ │ genindex.html │ │ │ index.html │ │ │ modules.html │ │ │ objects.inv │ │ │ search.html │ │ │ searchindex.js │ │ │ src.html │ │ │ │ │ ├───_sources │ │ │ index.rst.txt │ │ │ modules.rst.txt │ │ │ src.rst.txt │ │ │ │ │ └───_static │ │ alabaster.css │ │ basic.css │ │ custom.css │ │ doctools.js │ │ documentation_options.js │ │ file.png │ │ jquery-3.5.1.js │ │ jquery.js │ │ language_data.js │ │ minus.png │ │ plus.png │ │ pygments.css │ │ searchtools.js │ │ underscore-1.3.1.js │ │ underscore.js │ │ │ └───source │ │ conf.py │ │ index.rst │ │ modules.rst │ │ src.rst │ │ │ ├───_static │ └───_templates └───src nopes.py sqrer.py __init__.py And here is my conf.py: # Configuration file for the Sphinx documentation builder. # # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. import os import sys import pathlib path = pathlib.Path(__file__).resolve() / '..' / '..' / '..' / 'src' # sys.path.insert(0, os.path.abspath('..\src')) sys.path.insert(0, os.path.abspath(path)) # -- Project information ----------------------------------------------------- project = 'TEST PROJECT' copyright = '2020, Cerberton' author = 'Cerberton' # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', ] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = [] # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'alabaster' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # -- Extension configuration ------------------------------------------------- [url="https://stackoverflow.com/questions/64687973/how-to-correctly-set-up-a-project-directory-for-sphinx"]Continue reading...[/url]