diff --git a/.readthedocs.yml b/.readthedocs.yml index 187ea55c..a428a7cc 100644 --- a/.readthedocs.yml +++ b/.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 \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index dcda7937..55c51268 100644 --- a/Dockerfile +++ b/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 "viral-ngs@broadinstitute.org" diff --git a/docs/Makefile b/docs/Makefile index b4c06bc2..4c0907b4 100644 --- a/docs/Makefile +++ b/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 diff --git a/docs/conf.py b/docs/conf.py index 477f12cf..209387ee 100644 --- a/docs/conf.py +++ b/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" diff --git a/docs/requirements.txt b/docs/requirements.txt index 20bf937d..8144c8fd 100644 --- a/docs/requirements.txt +++ b/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