diff --git a/.circleci/requirements-sphinx.txt b/.circleci/requirements-sphinx.txt index 58aac6fbf64..bf9104c0089 100644 --- a/.circleci/requirements-sphinx.txt +++ b/.circleci/requirements-sphinx.txt @@ -4,7 +4,7 @@ numpy rdflib reportlab scipy -sphinx==4.1.2 +sphinx>=4.2.0 numpydoc==1.0.0 pygments sphinx_rtd_theme diff --git a/Doc/api/conf.py b/Doc/api/conf.py index af866d1c061..54ae6d96b85 100644 --- a/Doc/api/conf.py +++ b/Doc/api/conf.py @@ -114,9 +114,7 @@ autodoc_preserve_defaults = True # To avoid import errors. -autodoc_mock_imports = ["MySQLdb", "Bio.Restriction.Restriction"] -if version > "1.77": - autodoc_mock_imports.append("Bio.Alphabet") +autodoc_mock_imports = ["MySQLdb"] # -- Options for HTML output ---------------------------------------------- @@ -305,7 +303,19 @@ def run_apidoc(_): # $ sphinx-apidoc -e -F -o /tmp/api/Bio Bio tmp_path = tempfile.mkdtemp() apidoc_main(["-e", "-F", "-o", tmp_path, "../../BioSQL"]) - apidoc_main(["-e", "-F", "-o", tmp_path, "../../Bio"]) + apidoc_main( + [ + "-e", + "-F", + "-o", + tmp_path, + # The input path: + "../../Bio", + # These are patterns to exclude: + "../../Bio/Alphabet/", + "../../Bio/Restriction/Restriction.py", + ] + ) os.remove(os.path.join(tmp_path, "index.rst")) # Using our own for filename in os.listdir(tmp_path): if filename.endswith(".rst"): diff --git a/ci-dependencies.txt b/ci-dependencies.txt index d98fae7dd55..44f2e8fe923 100644 --- a/ci-dependencies.txt +++ b/ci-dependencies.txt @@ -27,6 +27,6 @@ scipy ## Documentation numpydoc==1.0.0 pygments -sphinx==4.1.2 +sphinx>=4.2.0 sphinx_rtd_theme