Read the Docs build information
Build id: 2500903
Project: tiledb-inc-tiledb-py
Version: dev
Commit: 31a2ce978247130212cd519f10c52c9f482b4239
Date: 2024-09-23T16:26:59.391668Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-09-23T16:27:00.980129Z, end-time: 2024-09-23T16:27:01.571289Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/TileDB-Inc/TileDB-Py.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-09-23T16:27:01.715723Z, end-time: 2024-09-23T16:27:02.678297Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/dev:refs/remotes/origin/dev
From https://github.com/TileDB-Inc/TileDB-Py
 * [new tag]         0.31.0     -> 0.31.0
 * [new tag]         0.31.1     -> 0.31.1
 * [new tag]         0.32.0     -> 0.32.0
 * [new tag]         0.32.1     -> 0.32.1

[rtd-command-info] start-time: 2024-09-23T16:27:02.836769Z, end-time: 2024-09-23T16:27:02.910916Z, duration: 0, exit-code: 0
git checkout --force origin/dev
Note: switching to 'origin/dev'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 31a2ce9 Move `PackedBuffer` and `pack_metadata_val` to pure Python, and wrap `tiledb_datatype_size` with pybind (#2072)

[rtd-command-info] start-time: 2024-09-23T16:27:03.001154Z, end-time: 2024-09-23T16:27:03.064547Z, duration: 0, exit-code: 0
cat .readthedocs.yml
# Don't build any extra formats
formats: []

# Use RTD config version 2
# https://docs.readthedocs.io/en/stable/config-file/v2.html
version: 2

# Set build OS to avoid build failures with old compiler
build:
  os: "ubuntu-22.04"
  tools:
    python: "3.8"

sphinx:
  configuration: doc/source/conf.py

python:
  install:
    - method: pip
      path: .
      extra_requirements:
        - doc

[rtd-command-info] start-time: 2024-09-23T16:27:08.241227Z, end-time: 2024-09-23T16:27:08.322917Z, duration: 0, exit-code: 0
asdf global python 3.8.19


[rtd-command-info] start-time: 2024-09-23T16:27:08.761004Z, end-time: 2024-09-23T16:27:10.046271Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.8.19.final.0-64 in 911ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-09-23T16:27:10.139359Z, end-time: 2024-09-23T16:27:19.857329Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages (23.1)
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Installing collected packages: setuptools, pip
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      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-24.2 setuptools-75.1.0

[rtd-command-info] start-time: 2024-09-23T16:27:19.954558Z, end-time: 2024-09-23T16:27:28.733080Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Installing collected packages: snowballstemmer, pytz, zipp, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-0.7.13 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.10 imagesize-1.4.1 importlib-metadata-8.5.0 packaging-24.1 pytz-2024.2 readthedocs-sphinx-ext-2.2.5 requests-2.32.3 snowballstemmer-2.2.0 sphinx-7.1.2 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 urllib3-2.2.3 zipp-3.20.2

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python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/checkouts/dev
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
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  Installing backend dependencies: started
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  Preparing metadata (pyproject.toml): started
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Collecting numpy>=1.17 (from tiledb==0.32.2.dev2+g31a2ce9)
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Collecting jinja2==3.0.0 (from tiledb==0.32.2.dev2+g31a2ce9)
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Collecting sphinx-rtd-theme==2.0.0 (from tiledb==0.32.2.dev2+g31a2ce9)
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Building wheels for collected packages: tiledb
  Building wheel for tiledb (pyproject.toml): started
  Building wheel for tiledb (pyproject.toml): still running...
  Building wheel for tiledb (pyproject.toml): still running...
  Building wheel for tiledb (pyproject.toml): still running...
  Building wheel for tiledb (pyproject.toml): finished with status 'done'
  Created wheel for tiledb: filename=tiledb-0.32.2.dev2+g31a2ce9-cp38-cp38-linux_x86_64.whl size=16704695 sha256=d1ed7e33c443a972bd4b6f057013a6b021ae31b56750b79674c71e8d68cbcb7c
  Stored in directory: /tmp/pip-ephem-wheel-cache-qz5szywm/wheels/ff/fb/1d/eb4170597e293eba00c65773f2ed98dc1fabca482d94802730
Successfully built tiledb
Installing collected packages: numpy, jinja2, tiledb, sphinxcontrib-jquery, breathe, sphinx-rtd-theme
  Attempting uninstall: jinja2
    Found existing installation: Jinja2 3.1.4
    Uninstalling Jinja2-3.1.4:
      Successfully uninstalled Jinja2-3.1.4
Successfully installed breathe-4.35.0 jinja2-3.0.0 numpy-1.24.4 sphinx-rtd-theme-2.0.0 sphinxcontrib-jquery-4.1 tiledb-0.32.2.dev2+g31a2ce9

[rtd-command-info] start-time: 2024-09-23T16:31:03.137792Z, end-time: 2024-09-23T16:31:03.200868Z, duration: 0, exit-code: 0
cat doc/source/conf.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#

# -- Imports configuration -------------------------------------------------

import os
import sys
from os.path import abspath, dirname, join
import sphinx_rtd_theme
from importlib.metadata import version as get_version

sys.path.insert(0, abspath(join(dirname(__file__))))

# -- ReadTheDocs configuration ---------------------------------------------

# Special handling on ReadTheDocs builds.
# Some of this code is from https://github.com/robotpy/robotpy-docs/blob/master/conf.py
readthedocs = os.environ.get("READTHEDOCS", None) == "True"
rtd_version = os.environ.get("READTHEDOCS_VERSION", "latest")
rtd_version = rtd_version if rtd_version in ["stable", "latest"] else "stable"

# -- Project information -----------------------------------------------------

project = "TileDB-Py"
copyright = "2024, TileDB, Inc."
author = "TileDB, Inc."

# The full version, including alpha/beta/rc tags
release: str = get_version("tiledb")
# The short X.Y version
version: str = ".".join(release.split(".")[:2])


# -- General configuration ---------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# 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.intersphinx"]

# Mapping for linking between RTD subprojects.
if readthedocs:
    intersphinx_mapping = {
        "tiledb": (
            "https://tiledb-inc-tiledb.readthedocs-hosted.com/en/%s/" % rtd_version,
            None,
        ),
        "tiledb-py": (
            "https://tiledb-inc-tiledb.readthedocs-hosted.com/projects/python-api/en/%s/"
            % rtd_version,
            None,
        ),
        "python": ("https://docs.python.org/", None),
    }

# Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"]

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = ".rst"

# The master toctree document.
master_doc = "index"

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = "en"

# 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"]

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = "friendly"


# -- Options for HTML output -------------------------------------------------

html_static_path = ["_static"]
html_title = "TileDB Python API Reference — TileDB-Py %s documentation" % version
html_logo = "_static/tiledb-logo_color_no_margin_@4x.png"
html_favicon = "_static/favicon.ico"

html_theme = "sphinx_rtd_theme"
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = "TileDB-Pydoc"


# -- Options for LaTeX output ------------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',
    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',
    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',
    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, "TileDB-Py.tex", "TileDB-Py Documentation", "TileDB, Inc.", "manual")
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [(master_doc, "tiledb-py", "TileDB-Py Documentation", [author], 1)]


# -- Options for Texinfo output ----------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (
        master_doc,
        "TileDB-Py",
        "TileDB-Py Documentation",
        author,
        "TileDB-Py",
        "One line description of project.",
        "Miscellaneous",
    )
]

# -- Custom Document processing ----------------------------------------------

# Generate the sidebar automatically so that it is identical across all subprojects.
# This (and gensidebar.py) from https://github.com/robotpy/robotpy-docs
import gensidebar

gensidebar.generate_sidebar(
    {"on_rtd": readthedocs, "rtd_version": rtd_version}, "tiledb-py"
)

# -- Custom setup -----------------------------------------------------------


def setup(app):
    app.add_css_file("custom.css")




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Define this variable in case it's not defined by the user.
# It defaults to `alabaster` which is the default from Sphinx.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme
html_theme = globals().get('html_theme', 'alabaster')

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "dev",
    'version_slug': "dev",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("release-0.6", "/en/release-0.6/"),
    ("dev", "/en/dev/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'tiledb-inc-tiledb-py',
    'name': u'TileDB-Py',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': '',
    'analytics_code': 'G-W0J7K3XGLY',
    'single_version': False,
    'conf_py_path': '/doc/source/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'TileDB-Inc',
    'proxied_api_host': '/_',
    'github_repo': 'TileDB-Py',
    'github_version': 'dev',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'dev',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'dev',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': 'G-W0J7K3XGLY',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '31a2ce97',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/tiledb-inc-tiledb-py/builds/2500903/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2024-09-23T16:31:03.319600Z, end-time: 2024-09-23T16:31:08.450105Z, duration: 5, exit-code: 0
python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.1.2
making output directory... done
loading intersphinx inventory from https://tiledb-inc-tiledb.readthedocs-hosted.com/en/stable/objects.inv...
loading intersphinx inventory from https://tiledb-inc-tiledb.readthedocs-hosted.com/projects/python-api/en/stable/objects.inv...
loading intersphinx inventory from https://docs.python.org/objects.inv...
intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://tiledb-inc-tiledb.readthedocs-hosted.com/projects/python-api/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 404 Client Error: Not Found for url: https://tiledb-inc-tiledb.readthedocs-hosted.com/projects/python-api/en/stable/objects.inv
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 2 source files that are out of date
updating environment: [new config] 2 added, 0 changed, 0 removed
reading sources... [ 50%] index
reading sources... [100%] python-api
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/__init__.py:docstring of tiledb.libtiledb.DenseArrayImpl.query:22: ERROR: Unexpected indentation.
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/__init__.py:docstring of tiledb.libtiledb.DenseArrayImpl.query:23: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/group.py:docstring of tiledb.group.Group.GroupMetadata:1: WARNING: duplicate object description of tiledb.Group.GroupMetadata, other instance in python-api, use :noindex: for one of them
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/group.py:docstring of tiledb.group.Group.GroupMetadata:1: WARNING: duplicate object description of tiledb.group.Group.GroupMetadata, other instance in python-api, use :noindex: for one of them
WARNING: autodoc: failed to import method 'Group.GroupMetadata.__keys__' from module 'tiledb'; the following exception was raised:
No module named 'tiledb.Group'
WARNING: autodoc: failed to import method 'Group.GroupMetadata.__values__' from module 'tiledb'; the following exception was raised:
No module named 'tiledb.Group'
WARNING: autodoc: failed to import method 'Group.GroupMetadata.__items__' from module 'tiledb'; the following exception was raised:
No module named 'tiledb.Group'
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/group.py:docstring of tiledb.group.Group.GroupMetadata.clear:1: WARNING: duplicate object description of tiledb.Group.GroupMetadata.clear, other instance in python-api, use :noindex: for one of them
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/group.py:docstring of tiledb.group.Group.GroupMetadata.dump:1: WARNING: duplicate object description of tiledb.Group.GroupMetadata.dump, other instance in python-api, use :noindex: for one of them
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/group.py:docstring of tiledb.group.Group.GroupMetadata.pop:1: WARNING: duplicate object description of tiledb.Group.GroupMetadata.pop, other instance in python-api, use :noindex: for one of them
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/group.py:docstring of tiledb.group.Group.GroupMetadata.popitem:1: WARNING: duplicate object description of tiledb.Group.GroupMetadata.popitem, other instance in python-api, use :noindex: for one of them
/home/docs/checkouts/readthedocs.org/user_builds/tiledb-inc-tiledb-py/envs/dev/lib/python3.8/site-packages/tiledb/group.py:docstring of tiledb.group.Group.GroupMetadata.setdefault:1: WARNING: duplicate object description of tiledb.Group.GroupMetadata.setdefault, other instance in python-api, use :noindex: for one of them
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
writing output... [ 50%] index
writing output... [100%] python-api
generating indices... genindex done
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
Updating searchtools for Read the Docs search... build succeeded, 13 warnings.

The HTML pages are in ../../_readthedocs/html.