STYLE: Make doc module consistent with Sphinx conventions

.readthedocs.yaml

@@ -16,11 +16,11 @@ build:
   jobs:
     pre_build:
       - pip install --upgrade myst-parser furo
-      - sphinx-apidoc -f -o doc .
+      - sphinx-apidoc -f -o docs/source .
 
 # Build documentation in the doc/ directory with Sphinx
 sphinx:
-  configuration: doc/conf.py
+  configuration: docs/source/conf.py
 
 # We recommend specifying your dependencies to enable reproducible builds:
 # https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html

doc/Makefile → docs/Makefile

@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = doc
+SOURCEDIR     = source
 BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".

doc/conf.py → docs/source/conf.py

@@ -27,7 +27,7 @@
 # Load the release info into a dict by explicit execution
 info = {}
 with open(os.path.abspath(os.path.join(
-        os.path.dirname(__file__), "..", "setup.py")), "r") as f:
+        os.path.dirname(__file__), "../..", "setup.py")), "r") as f:
     for line in f:
         if line.startswith(name_setup_str):
             project = (
@@ -93,8 +93,8 @@
 #
 html_theme = "furo"
 
-html_favicon = "_static/icon/favicon.ico"
-html_logo = "_static/wma_small_alpha.png"
+html_favicon = "../_static/icon/favicon.ico"
+html_logo = "../_static/wma_small_alpha.png"
 
 # 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,

setup.py

@@ -35,7 +35,7 @@
     version='0.3.0',
     author='Fan Zhang and Lauren O\'Donnell',
     author_email='[email protected]',
-    packages=find_packages(exclude=["doc"]),
+    packages=find_packages(exclude=["docs"]),
     license='LICENSE.txt',
     description='Processing of whole-brain streamline tractography.',
     long_description=open('README.md').read(),