diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 765fce3f..9a08cd3f 100644 --- a/.readthedocs.yaml +++ b/.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 diff --git a/doc/Makefile b/docs/Makefile similarity index 96% rename from doc/Makefile rename to docs/Makefile index 26217e7e..d0c3cbf1 100644 --- a/doc/Makefile +++ b/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/doc/_static/icon/favicon.ico b/docs/_static/icon/favicon.ico similarity index 100% rename from doc/_static/icon/favicon.ico rename to docs/_static/icon/favicon.ico diff --git a/doc/_static/wma_small.jpg b/docs/_static/wma_small.jpg similarity index 100% rename from doc/_static/wma_small.jpg rename to docs/_static/wma_small.jpg diff --git a/doc/_static/wma_small_alpha.png b/docs/_static/wma_small_alpha.png similarity index 100% rename from doc/_static/wma_small_alpha.png rename to docs/_static/wma_small_alpha.png diff --git a/doc/make.bat b/docs/make.bat similarity index 100% rename from doc/make.bat rename to docs/make.bat diff --git a/doc/bundles.md b/docs/source/bundles.md similarity index 100% rename from doc/bundles.md rename to docs/source/bundles.md diff --git a/doc/conf.py b/docs/source/conf.py similarity index 95% rename from doc/conf.py rename to docs/source/conf.py index bd535b3d..bbe05b5b 100644 --- a/doc/conf.py +++ b/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, diff --git a/doc/index.rst b/docs/source/index.rst similarity index 100% rename from doc/index.rst rename to docs/source/index.rst diff --git a/doc/subject-specific-tractography-parcellation.md b/docs/source/subject-specific-tractography-parcellation.md similarity index 100% rename from doc/subject-specific-tractography-parcellation.md rename to docs/source/subject-specific-tractography-parcellation.md diff --git a/doc/tutorial-pics/fig_csv_clusters.png b/docs/source/tutorial-pics/fig_csv_clusters.png similarity index 100% rename from doc/tutorial-pics/fig_csv_clusters.png rename to docs/source/tutorial-pics/fig_csv_clusters.png diff --git a/doc/tutorial-pics/fig_csv_tracts.png b/docs/source/tutorial-pics/fig_csv_tracts.png similarity index 100% rename from doc/tutorial-pics/fig_csv_tracts.png rename to docs/source/tutorial-pics/fig_csv_tracts.png diff --git a/doc/tutorial-pics/fig_ini_fiber_clusters.jpg b/docs/source/tutorial-pics/fig_ini_fiber_clusters.jpg similarity index 100% rename from doc/tutorial-pics/fig_ini_fiber_clusters.jpg rename to docs/source/tutorial-pics/fig_ini_fiber_clusters.jpg diff --git a/doc/tutorial-pics/fig_qc_ana_tracts.png b/docs/source/tutorial-pics/fig_qc_ana_tracts.png similarity index 100% rename from doc/tutorial-pics/fig_qc_ana_tracts.png rename to docs/source/tutorial-pics/fig_qc_ana_tracts.png diff --git a/doc/tutorial-pics/fig_qc_ini_clusters.png b/docs/source/tutorial-pics/fig_qc_ini_clusters.png similarity index 100% rename from doc/tutorial-pics/fig_qc_ini_clusters.png rename to docs/source/tutorial-pics/fig_qc_ini_clusters.png diff --git a/doc/tutorial-pics/fig_qc_input_overlap.jpg b/docs/source/tutorial-pics/fig_qc_input_overlap.jpg similarity index 100% rename from doc/tutorial-pics/fig_qc_input_overlap.jpg rename to docs/source/tutorial-pics/fig_qc_input_overlap.jpg diff --git a/doc/tutorial-pics/fig_qc_input_tract.png b/docs/source/tutorial-pics/fig_qc_input_tract.png similarity index 100% rename from doc/tutorial-pics/fig_qc_input_tract.png rename to docs/source/tutorial-pics/fig_qc_input_tract.png diff --git a/doc/tutorial-pics/fig_qc_outlier_removed.png b/docs/source/tutorial-pics/fig_qc_outlier_removed.png similarity index 100% rename from doc/tutorial-pics/fig_qc_outlier_removed.png rename to docs/source/tutorial-pics/fig_qc_outlier_removed.png diff --git a/doc/tutorial-pics/fig_qc_reg_overlap.jpg b/docs/source/tutorial-pics/fig_qc_reg_overlap.jpg similarity index 100% rename from doc/tutorial-pics/fig_qc_reg_overlap.jpg rename to docs/source/tutorial-pics/fig_qc_reg_overlap.jpg diff --git a/doc/tutorial-pics/fig_separated_clusters.png b/docs/source/tutorial-pics/fig_separated_clusters.png similarity index 100% rename from doc/tutorial-pics/fig_separated_clusters.png rename to docs/source/tutorial-pics/fig_separated_clusters.png diff --git a/doc/tutorial-pics/fig_terminal_env.png b/docs/source/tutorial-pics/fig_terminal_env.png similarity index 100% rename from doc/tutorial-pics/fig_terminal_env.png rename to docs/source/tutorial-pics/fig_terminal_env.png diff --git a/doc/tutorial-pics/fig_tract_reg_folder.png b/docs/source/tutorial-pics/fig_tract_reg_folder.png similarity index 100% rename from doc/tutorial-pics/fig_tract_reg_folder.png rename to docs/source/tutorial-pics/fig_tract_reg_folder.png diff --git a/doc/tutorial-pics/fig_tutorial_data.png b/docs/source/tutorial-pics/fig_tutorial_data.png similarity index 100% rename from doc/tutorial-pics/fig_tutorial_data.png rename to docs/source/tutorial-pics/fig_tutorial_data.png diff --git a/setup.py b/setup.py index 7ab54191..b0fae485 100755 --- a/setup.py +++ b/setup.py @@ -35,7 +35,7 @@ version='0.3.0', author='Fan Zhang and Lauren O\'Donnell', author_email='odonnell@bwh.harvard.edu', - 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(),