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`. Chang the makefile `SOURCEDIR` variable accordingly. Change the bibliography references paths accordingly in the `README` file.
scil-vital · Oct 28, 2023 · a6eb2c1 · a6eb2c1
1 parent 4980b83
commit a6eb2c1
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Showing 11 changed files with 8 additions and 8 deletions.
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -15,11 +15,11 @@ build:
     - liblapack-dev
   jobs:
     pre_build:
-      - sphinx-apidoc -f -o doc .
+      - sphinx-apidoc -f -o docs .
 
 # 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

diff --git a/README.md b/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"
diff --git a/doc/Makefile → docs/Makefile b/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".

diff --git a/...bibtex/Dumais23_-_Neuroimage_-_FIESTA.bib → ...bibtex/Dumais23_-_Neuroimage_-_FIESTA.bib b/...bibtex/Dumais23_-_Neuroimage_-_FIESTA.bib → ...bibtex/Dumais23_-_Neuroimage_-_FIESTA.bib
diff --git a/doc/bibtex/Legarreta21_-_MIA_-_FINTA.bib → docs/bibtex/Legarreta21_-_MIA_-_FINTA.bib b/doc/bibtex/Legarreta21_-_MIA_-_FINTA.bib → docs/bibtex/Legarreta21_-_MIA_-_FINTA.bib
diff --git a/...ex/Legarreta22_-_MICCAI-CDMRI_-_CINTA.bib → ...ex/Legarreta22_-_MICCAI-CDMRI_-_CINTA.bib b/...ex/Legarreta22_-_MICCAI-CDMRI_-_CINTA.bib → ...ex/Legarreta22_-_MICCAI-CDMRI_-_CINTA.bib
diff --git a/doc/bibtex/Legarreta23_-_MIA_-_GESTA.bib → docs/bibtex/Legarreta23_-_MIA_-_GESTA.bib b/doc/bibtex/Legarreta23_-_MIA_-_GESTA.bib → docs/bibtex/Legarreta23_-_MIA_-_GESTA.bib
diff --git a/doc/devel/coding_style_guideline.rst → docs/devel/coding_style_guideline.rst b/doc/devel/coding_style_guideline.rst → docs/devel/coding_style_guideline.rst
diff --git a/doc/make.bat → docs/make.bat b/doc/make.bat → docs/make.bat
diff --git a/doc/conf.py → docs/source/conf.py b/doc/conf.py → docs/source/conf.py
@@ -20,7 +20,7 @@
 # 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 -----------------------------------------------------

diff --git a/doc/index.rst → docs/source/index.rst b/doc/index.rst → docs/source/index.rst