.

.readthedocs.yaml

@@ -1,35 +1,31 @@
-# Read the Docs configuration file for Sphinx projects
+# .readthedocs.yaml
+# Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
 version: 2
 
-# Set the OS, Python version and other tools you might need
+# Set the version of Python and other tools you might need
 build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.12"
-    # You can also specify other tool versions:
-    # nodejs: "20"
-    # rust: "1.70"
-    # golang: "1.20"
+   os: ubuntu-22.04
+   tools:
+     python: "3.10"
+     # You can also specify other tool versions:
+     # nodejs: "16"
+     # rust: "1.55"
+     # golang: "1.17"
 
-# Build documentation in the "docs/" directory with Sphinx
+# Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
-  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
-  # builder: "dirhtml"
-  # Fail on all warnings to avoid broken references
-  # fail_on_warning: true
+   configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF and ePub
+# If using Sphinx, optionally build your docs in additional formats such as PDF
 # formats:
-#   - pdf
-#   - epub
+#    - pdf
 
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#   install:
-#     - requirements: docs/requirements.txt
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .

docs/conf.py

@@ -4,6 +4,7 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+
 # -- Path setup --------------------------------------------------------------
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -12,24 +13,21 @@
 #
 # import os
 # import sys
-# sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath("."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'smaht-pipeline-utils'
-copyright = '2023, HMS DBMI'
-author = 'Michele Berselli, SMaHT Team'
+project = "smaht-pipeline-utils"
+copyright = "2023, HMS DBMI"
+author = "Michele Berselli, SMaHT Team"
 
 # The full version, including alpha/beta/rc tags
-release = '0.0.1'
+release = "0.0.1"
 
 
 # -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
+# -- General configuration
 extensions = [
     "sphinx.ext.duration",
     "sphinx.ext.doctest",
@@ -46,26 +44,27 @@
 
 intersphinx_disabled_domains = ["std"]
 
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
+
+# -- Options for EPUB output
+epub_show_urls = "footnote"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # 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,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]

docs/requirements.in

@@ -0,0 +1,2 @@
+Sphinx>=5,<6
+sphinx_rtd_theme

docs/requirements.txt

@@ -0,0 +1,58 @@
+#
+# This file is autogenerated by pip-compile with python 3.10
+# To update, run:
+#
+#    pip-compile docs/requirements.in
+#
+alabaster==0.7.12
+    # via sphinx
+babel==2.10.3
+    # via sphinx
+certifi==2022.6.15
+    # via requests
+charset-normalizer==2.1.0
+    # via requests
+docutils==0.17.1
+    # via
+    #   sphinx
+    #   sphinx-rtd-theme
+idna==3.3
+    # via requests
+imagesize==1.4.1
+    # via sphinx
+jinja2==3.1.2
+    # via sphinx
+markupsafe==2.1.1
+    # via jinja2
+packaging==21.3
+    # via sphinx
+pygments==2.12.0
+    # via sphinx
+pyparsing==3.0.9
+    # via packaging
+pytz==2022.1
+    # via babel
+requests==2.28.1
+    # via sphinx
+snowballstemmer==2.2.0
+    # via sphinx
+sphinx==5.0.2
+    # via
+    #   -r docs/requirements.in
+    #   sphinx-rtd-theme
+sphinx-rtd-theme==1.0.0
+    # via -r docs/requirements.in
+sphinxcontrib-applehelp==1.0.2
+    # via sphinx
+sphinxcontrib-devhelp==1.0.2
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.0
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.3
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.5
+    # via sphinx
+urllib3==1.26.9
+    # via requests