diff --git a/cookiecutter.json b/src/cookiecutter.json
similarity index 95%
rename from cookiecutter.json
rename to src/cookiecutter.json
index 7830ed87..0a351692 100644
--- a/cookiecutter.json
+++ b/src/cookiecutter.json
@@ -6,7 +6,6 @@
   "version": "0.1.0",
   "github_organization": "<my-github-organization>",
   "license": ["Apache Software License 2.0", "MIT license", "BSD license", "ISC license", "GNU General Public License v3 or later", "Not open source"],
-  "apidoc": ["no", "yes"],
   "full_name": "John Smith",
   "email": "yourname@esciencecenter.nl",
   "copyright_holder": "Netherlands eScience Center",
diff --git a/hooks/post_gen_project.py b/src/hooks/post_gen_project.py
similarity index 100%
rename from hooks/post_gen_project.py
rename to src/hooks/post_gen_project.py
diff --git a/hooks/pre_gen_project.py b/src/hooks/pre_gen_project.py
similarity index 100%
rename from hooks/pre_gen_project.py
rename to src/hooks/pre_gen_project.py
diff --git a/{{cookiecutter.project_name}}/.bumpversion.cfg b/src/{{cookiecutter.project_name}}/.bumpversion.cfg
similarity index 100%
rename from {{cookiecutter.project_name}}/.bumpversion.cfg
rename to src/{{cookiecutter.project_name}}/.bumpversion.cfg
diff --git a/{{cookiecutter.project_name}}/.editorconfig b/src/{{cookiecutter.project_name}}/.editorconfig
similarity index 100%
rename from {{cookiecutter.project_name}}/.editorconfig
rename to src/{{cookiecutter.project_name}}/.editorconfig
diff --git a/{{cookiecutter.project_name}}/.githooks/pre-commit b/src/{{cookiecutter.project_name}}/.githooks/pre-commit
similarity index 100%
rename from {{cookiecutter.project_name}}/.githooks/pre-commit
rename to src/{{cookiecutter.project_name}}/.githooks/pre-commit
diff --git a/{{cookiecutter.project_name}}/.github/workflows/build.yml b/src/{{cookiecutter.project_name}}/.github/workflows/build.yml
similarity index 100%
rename from {{cookiecutter.project_name}}/.github/workflows/build.yml
rename to src/{{cookiecutter.project_name}}/.github/workflows/build.yml
diff --git a/{{cookiecutter.project_name}}/.github/workflows/cffconvert.yml b/src/{{cookiecutter.project_name}}/.github/workflows/cffconvert.yml
similarity index 100%
rename from {{cookiecutter.project_name}}/.github/workflows/cffconvert.yml
rename to src/{{cookiecutter.project_name}}/.github/workflows/cffconvert.yml
diff --git a/{{cookiecutter.project_name}}/.github/workflows/pypi.yml b/src/{{cookiecutter.project_name}}/.github/workflows/pypi.yml
similarity index 100%
rename from {{cookiecutter.project_name}}/.github/workflows/pypi.yml
rename to src/{{cookiecutter.project_name}}/.github/workflows/pypi.yml
diff --git a/{{cookiecutter.project_name}}/.github/workflows/quality.yml b/src/{{cookiecutter.project_name}}/.github/workflows/quality.yml
similarity index 100%
rename from {{cookiecutter.project_name}}/.github/workflows/quality.yml
rename to src/{{cookiecutter.project_name}}/.github/workflows/quality.yml
diff --git a/{{cookiecutter.project_name}}/.gitignore b/src/{{cookiecutter.project_name}}/.gitignore
similarity index 100%
rename from {{cookiecutter.project_name}}/.gitignore
rename to src/{{cookiecutter.project_name}}/.gitignore
diff --git a/{{cookiecutter.project_name}}/.prospector.yml b/src/{{cookiecutter.project_name}}/.prospector.yml
similarity index 100%
rename from {{cookiecutter.project_name}}/.prospector.yml
rename to src/{{cookiecutter.project_name}}/.prospector.yml
diff --git a/{{cookiecutter.project_name}}/CHANGELOG.md b/src/{{cookiecutter.project_name}}/CHANGELOG.md
similarity index 100%
rename from {{cookiecutter.project_name}}/CHANGELOG.md
rename to src/{{cookiecutter.project_name}}/CHANGELOG.md
diff --git a/{{cookiecutter.project_name}}/CITATION.cff b/src/{{cookiecutter.project_name}}/CITATION.cff
similarity index 100%
rename from {{cookiecutter.project_name}}/CITATION.cff
rename to src/{{cookiecutter.project_name}}/CITATION.cff
diff --git a/{{cookiecutter.project_name}}/CODE_OF_CONDUCT.md b/src/{{cookiecutter.project_name}}/CODE_OF_CONDUCT.md
similarity index 100%
rename from {{cookiecutter.project_name}}/CODE_OF_CONDUCT.md
rename to src/{{cookiecutter.project_name}}/CODE_OF_CONDUCT.md
diff --git a/{{cookiecutter.project_name}}/CONTRIBUTING.md b/src/{{cookiecutter.project_name}}/CONTRIBUTING.md
similarity index 100%
rename from {{cookiecutter.project_name}}/CONTRIBUTING.md
rename to src/{{cookiecutter.project_name}}/CONTRIBUTING.md
diff --git a/{{cookiecutter.project_name}}/LICENSE b/src/{{cookiecutter.project_name}}/LICENSE
similarity index 100%
rename from {{cookiecutter.project_name}}/LICENSE
rename to src/{{cookiecutter.project_name}}/LICENSE
diff --git a/{{cookiecutter.project_name}}/MANIFEST.in b/src/{{cookiecutter.project_name}}/MANIFEST.in
similarity index 100%
rename from {{cookiecutter.project_name}}/MANIFEST.in
rename to src/{{cookiecutter.project_name}}/MANIFEST.in
diff --git a/{{cookiecutter.project_name}}/NOTICE b/src/{{cookiecutter.project_name}}/NOTICE
similarity index 100%
rename from {{cookiecutter.project_name}}/NOTICE
rename to src/{{cookiecutter.project_name}}/NOTICE
diff --git a/{{cookiecutter.project_name}}/README.dev.rst b/src/{{cookiecutter.project_name}}/README.dev.rst
similarity index 100%
rename from {{cookiecutter.project_name}}/README.dev.rst
rename to src/{{cookiecutter.project_name}}/README.dev.rst
diff --git a/{{cookiecutter.project_name}}/README.md b/src/{{cookiecutter.project_name}}/README.md
similarity index 100%
rename from {{cookiecutter.project_name}}/README.md
rename to src/{{cookiecutter.project_name}}/README.md
diff --git a/{{cookiecutter.project_name}}/docs/Makefile b/src/{{cookiecutter.project_name}}/docs/Makefile
similarity index 100%
rename from {{cookiecutter.project_name}}/docs/Makefile
rename to src/{{cookiecutter.project_name}}/docs/Makefile
diff --git a/{{cookiecutter.project_name}}/docs/_static/theme_overrides.css b/src/{{cookiecutter.project_name}}/docs/_static/theme_overrides.css
similarity index 100%
rename from {{cookiecutter.project_name}}/docs/_static/theme_overrides.css
rename to src/{{cookiecutter.project_name}}/docs/_static/theme_overrides.css
diff --git a/{{cookiecutter.project_name}}/docs/_templates/.gitignore b/src/{{cookiecutter.project_name}}/docs/_templates/.gitignore
similarity index 100%
rename from {{cookiecutter.project_name}}/docs/_templates/.gitignore
rename to src/{{cookiecutter.project_name}}/docs/_templates/.gitignore
diff --git a/{{cookiecutter.project_name}}/docs/conf.py b/src/{{cookiecutter.project_name}}/docs/conf.py
similarity index 99%
rename from {{cookiecutter.project_name}}/docs/conf.py
rename to src/{{cookiecutter.project_name}}/docs/conf.py
index 39cbd1f4..d18ab35e 100644
--- a/{{cookiecutter.project_name}}/docs/conf.py
+++ b/src/{{cookiecutter.project_name}}/docs/conf.py
@@ -78,7 +78,6 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
-{% if cookiecutter.apidoc == "yes" %}
 # -- Run apidoc plug-in manually, as readthedocs doesn't support it -------
 # See https://github.com/rtfd/readthedocs.org/issues/1139
 def run_apidoc(_):
@@ -110,7 +109,6 @@ def run_apidoc(_):
 
 def setup(app):
     app.connect("builder-inited", run_apidoc)
-{% endif %}
 
 # -- Options for HTML output ----------------------------------------------
 
diff --git a/{{cookiecutter.project_name}}/docs/index.rst b/src/{{cookiecutter.project_name}}/docs/index.rst
similarity index 92%
rename from {{cookiecutter.project_name}}/docs/index.rst
rename to src/{{cookiecutter.project_name}}/docs/index.rst
index e71f8a14..d8ef571c 100644
--- a/{{cookiecutter.project_name}}/docs/index.rst
+++ b/src/{{cookiecutter.project_name}}/docs/index.rst
@@ -10,7 +10,6 @@ Welcome to {{ cookiecutter.package_name }}'s documentation!
   :maxdepth: 2
   :caption: Contents:
 
-{% if cookiecutter.apidoc == 'yes' %}
 API Reference
 =============
 
@@ -18,7 +17,6 @@ API Reference
   :maxdepth: 2
 
   {{ cookiecutter.package_name }} <apidocs/{{ cookiecutter.package_name }}.rst>
-{% endif %}
 
 Indices and tables
 ==================
diff --git a/{{cookiecutter.project_name}}/docs/make.bat b/src/{{cookiecutter.project_name}}/docs/make.bat
similarity index 100%
rename from {{cookiecutter.project_name}}/docs/make.bat
rename to src/{{cookiecutter.project_name}}/docs/make.bat
diff --git a/{{cookiecutter.project_name}}/project_setup.md b/src/{{cookiecutter.project_name}}/project_setup.md
similarity index 100%
rename from {{cookiecutter.project_name}}/project_setup.md
rename to src/{{cookiecutter.project_name}}/project_setup.md
diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/src/{{cookiecutter.project_name}}/pyproject.toml
similarity index 100%
rename from {{cookiecutter.project_name}}/pyproject.toml
rename to src/{{cookiecutter.project_name}}/pyproject.toml
diff --git a/{{cookiecutter.project_name}}/setup.cfg b/src/{{cookiecutter.project_name}}/setup.cfg
similarity index 100%
rename from {{cookiecutter.project_name}}/setup.cfg
rename to src/{{cookiecutter.project_name}}/setup.cfg
diff --git a/{{cookiecutter.project_name}}/setup.py b/src/{{cookiecutter.project_name}}/setup.py
similarity index 100%
rename from {{cookiecutter.project_name}}/setup.py
rename to src/{{cookiecutter.project_name}}/setup.py
diff --git a/{{cookiecutter.project_name}}/sonar-project.properties b/src/{{cookiecutter.project_name}}/sonar-project.properties
similarity index 100%
rename from {{cookiecutter.project_name}}/sonar-project.properties
rename to src/{{cookiecutter.project_name}}/sonar-project.properties
diff --git a/{{cookiecutter.project_name}}/tests/__init__.py b/src/{{cookiecutter.project_name}}/tests/__init__.py
similarity index 100%
rename from {{cookiecutter.project_name}}/tests/__init__.py
rename to src/{{cookiecutter.project_name}}/tests/__init__.py
diff --git a/{{cookiecutter.project_name}}/tests/test_my_module.py b/src/{{cookiecutter.project_name}}/tests/test_my_module.py
similarity index 100%
rename from {{cookiecutter.project_name}}/tests/test_my_module.py
rename to src/{{cookiecutter.project_name}}/tests/test_my_module.py
diff --git a/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__init__.py b/src/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__init__.py
similarity index 65%
rename from {{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__init__.py
rename to src/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__init__.py
index b874d2c0..418484ea 100644
--- a/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__init__.py
+++ b/src/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__init__.py
@@ -1,4 +1,4 @@
-{% if cookiecutter.apidoc == "yes" %}"""Documentation about {{ cookiecutter.package_name }}"""{% endif %}
+"""Documentation about {{ cookiecutter.package_name }}"""
 import logging
 from .__version__ import __version__
 
diff --git a/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__version__.py b/src/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__version__.py
similarity index 100%
rename from {{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__version__.py
rename to src/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/__version__.py
diff --git a/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/my_module.py b/src/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/my_module.py
similarity index 60%
rename from {{cookiecutter.project_name}}/{{cookiecutter.package_name}}/my_module.py
rename to src/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/my_module.py
index fcf8ae8e..3479f21b 100644
--- a/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/my_module.py
+++ b/src/{{cookiecutter.project_name}}/{{cookiecutter.package_name}}/my_module.py
@@ -1,4 +1,4 @@
-{%-if cookiecutter.apidoc == "yes" %}"""Documentation about the {{ cookiecutter.package_name }} module."""{% endif %}
+"""Documentation about the {{ cookiecutter.package_name }} module."""
 import logging