Merge pull request #46 from broadinstitute/dp-scaffold

docbuild fixes, viral-core bump

.readthedocs.yml

@@ -7,7 +7,7 @@ version: 2
 
 # Set the version of Python
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
     python: "3.10"
 
@@ -25,6 +25,5 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.10
   install:
     - requirements: docs/requirements.txt

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.3.1
+FROM quay.io/broadinstitute/viral-core:2.3.2
 
 LABEL maintainer "[email protected]"
 

docs/Makefile

@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = --jobs auto
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build

docs/conf.py

@@ -70,7 +70,7 @@ def _get_viral_core():
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.imgmath', 'sphinxarg.ext',]
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.imgmath', 'sphinxarg.ext', 'sphinx_rtd_theme']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -139,7 +139,7 @@ def _get_viral_core():
 # a list of builtin themes.
 on_rtd = os.environ.get('READTHEDOCS') == 'True'
 if on_rtd:
-    html_theme = 'default'
+    html_theme = 'sphinx_rtd_theme'
 else:
     import sphinx_rtd_theme
     html_theme = "sphinx_rtd_theme"

docs/requirements.txt

@@ -1,8 +1,8 @@
-jinja2==3.1.2 # https://github.com/readthedocs/readthedocs.org/issues/9037#issuecomment-1077818554
-Sphinx==5.3.0 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies
-sphinx-argparse
-sphinx-rtd-theme==1.1.1
+jinja2==3.1.4 # https://github.com/readthedocs/readthedocs.org/issues/9037#issuecomment-1077818554
+Sphinx==7.4.7 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies
+sphinx-argparse==0.5.2
+sphinx-rtd-theme>=2.0.0
 matplotlib>=2.2.4
-PyYAML==6.0
+PyYAML==6.0.1
 mock==5.0.1
 recommonmark