STYLE: Make documentation module consistent with Sphinx conventions

Make the documentation module consistent with Sphinx conventions:
- Rename the module to `docs`.
- Host the configuration file and index file in `docs/sources`. Change
  the makefile `SOURCEDIR` variable accordingly.

Change the bibliography references paths accordingly in the `README`
file.

.readthedocs.yaml

@@ -16,11 +16,11 @@ build:
   jobs:
     pre_build:
       - pip install --upgrade 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

README.md

@@ -115,7 +115,7 @@ This software is distributed under a particular license. Please see the
 [*LICENSE*](LICENSE) file for details.
 
 
-[FINTA]: ./doc/bibtex/Legarreta21_-_MIA_-_FINTA.bib "Filtering in tractography using autoencoders (FINTA)"
-[CINTA]: ./doc/bibtex/Legarreta22_-_MICCAI-CDMRI_-_CINTA.bib "Clustering in Tractography Using Autoencoders (CINTA)"
-[GESTA]: ./doc/bibtex/Legarreta23_-_MIA_-_GESTA.bib "Generative Sampling in Bundle Tractography using Autoencoders (GESTA)"
-[FIESTA]: ./doc/bibtex/Dumais23_-_Neuroimage_-_FIESTA.bib "FIESTA: Autoencoders for accurate fiber segmentation in tractography"
+[FINTA]: ./docs/bibtex/Legarreta21_-_MIA_-_FINTA.bib "Filtering in tractography using autoencoders (FINTA)"
+[CINTA]: ./docs/bibtex/Legarreta22_-_MICCAI-CDMRI_-_CINTA.bib "Clustering in Tractography Using Autoencoders (CINTA)"
+[GESTA]: ./docs/bibtex/Legarreta23_-_MIA_-_GESTA.bib "Generative Sampling in Bundle Tractography using Autoencoders (GESTA)"
+[FIESTA]: ./docs/bibtex/Dumais23_-_Neuroimage_-_FIESTA.bib "FIESTA: Autoencoders for accurate fiber segmentation in tractography"

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

@@ -11,16 +11,17 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
+import sys
 from datetime import datetime
 from importlib.metadata import version as vers
 
-# import sys
 import tomli
 
-# sys.path.insert(0, os.path.abspath('.'))
+# Location of files where Sphinx will look for docstrings
+sys.path.insert(0, os.path.abspath(".."))
 
 # Load the release info into a dict by explicit execution
-with open(os.path.join("..", "pyproject.toml"), "rb") as f:
+with open(os.path.join("../..", "pyproject.toml"), "rb") as f:
     info = tomli.load(f)
 
 # -- Project information -----------------------------------------------------