Sphinx auto-doc not rendering the .rst for the milliontrees modules.

[bw4sz]

@henrykironde can you assist me in trying to get sphinx and readthedocs to render the milliontrees source? Just like for DeepForest

https://deepforest.readthedocs.io/en/latest/source/modules.html

What i've done so far.

1. Readthedocs builds and interprets the index.rst file, builds the table of contents and associated other .md files.

https://milliontrees.readthedocs.io/en/latest/

2. Updated the docs/conf.py to have the correct extensions.

MillionTrees/docs/conf.py

Line 25 in 2a03edd

extensions = ['myst_parser', 'sphinx.ext.autodoc',"sphinx.ext.napoleon"]

3. Add the extensions to a requirements file so they are installed.

https://github.com/weecology/MillionTrees/blob/main/docs/requirements.txt

But I see nothing rendering, not locally when you can make html and look in _build or on readthedocs. It all works if you call sphinx-api-doc, it generates .rst files for each the modules, but its not like we do that everytime for deepforest.

Some links that i've been looking at

https://eikonomega.medium.com/getting-started-with-sphinx-autodoc-part-1-2cebbbca5365

https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html

https://stackoverflow.com/questions/65487163/python-sphinx-autodoc-not-rendering-on-readthedocs

I do not see anything in readthedocs log, plus it doesn't do it locally, so that's the first step.

Read the Docs build information
Build id: 25259385
Project: milliontrees
Version: latest
Commit: 2a03edd5e7b024742aa9824cebbc2f004a0fcf18
Date: 2024-08-09T00:04:39.993114Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-08-09T00:04:40.610733Z, end-time: 2024-08-09T00:04:42.014038Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/weecology/MillionTrees.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-08-09T00:04:42.040822Z, end-time: 2024-08-09T00:04:42.733879Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main


[rtd-command-info] start-time: 2024-08-09T00:04:42.836660Z, end-time: 2024-08-09T00:04:42.911281Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: switching to 'origin/main'.

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 2a03edd change to index.rst

[rtd-command-info] start-time: 2024-08-09T00:04:42.935376Z, end-time: 2024-08-09T00:04:42.994095Z, duration: 0, exit-code: 0
cat .readthedocs.yaml
# Read the Docs configuration file for Sphinx projects
# 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
build:
  os: ubuntu-22.04
  tools:
    python: "3.11"
    # You can also specify other tool versions:
    # nodejs: "20"
    # rust: "1.70"
    # golang: "1.20"

# 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

# Optionally build your docs in additional formats such as PDF and ePub
# formats:
#   - pdf
#   - epub

# 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
submodules:
  include: all

[rtd-command-info] start-time: 2024-08-09T00:04:49.262281Z, end-time: 2024-08-09T00:04:49.346196Z, duration: 0, exit-code: 0
asdf global python 3.11.9


[rtd-command-info] start-time: 2024-08-09T00:04:50.137957Z, end-time: 2024-08-09T00:04:51.327764Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.9.final.0-64 in 815ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/milliontrees/envs/latest, 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: 2024-08-09T00:04:51.375226Z, end-time: 2024-08-09T00:05:07.238492Z, duration: 15, 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/milliontrees/envs/latest/lib/python3.11/site-packages (23.1)
Collecting pip
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/milliontrees/envs/latest/lib/python3.11/site-packages (67.6.1)
Collecting setuptools
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      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-72.1.0

[rtd-command-info] start-time: 2024-08-09T00:05:07.264738Z, end-time: 2024-08-09T00:05:15.898935Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
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Installing collected packages: snowballstemmer, 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, sphinx
Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.7.4 charset-normalizer-3.3.2 docutils-0.21.2 idna-3.7 imagesize-1.4.1 packaging-24.1 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.0.2 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.2.2

[rtd-command-info] start-time: 2024-08-09T00:05:15.923136Z, end-time: 2024-08-09T00:05:19.179062Z, duration: 3, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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[rtd-command-info] start-time: 2024-08-09T00:05:19.260441Z, end-time: 2024-08-09T00:05:19.335699Z, duration: 0, exit-code: 0
cat docs/conf.py
# Configuration file for the Sphinx documentation builder.
import os
import sys

curr_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
sys.path.insert(0, os.path.join(curr_path, '..'))
sys.path.insert(0, os.path.abspath('..'))

# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

project = 'MillionTrees'
copyright = '2024, Ben Weinstein'
author = 'Ben Weinstein'
release = '0.y.z'

master_doc = 'index'

# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

extensions = ['myst_parser', 'sphinx.ext.autodoc',"sphinx.ext.napoleon"]

templates_path = ['_templates']
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

html_theme = 'furo'
html_static_path = ['_static']

source_suffix = {
    '.rst': 'restructuredtext',
    '.md': 'markdown',
}

[rtd-command-info] start-time: 2024-08-09T00:05:19.374082Z, end-time: 2024-08-09T00:05:21.072300Z, duration: 1, exit-code: 0
python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.0.2
loading translations [en]... done
making output directory... done
WARNING: html_static_path entry '_static' does not exist
myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 6 source files that are out of date
updating environment: [new config] 6 added, 0 changed, 0 removed
reading sources... [ 17%] Contributing
reading sources... [ 33%] Dataset_Structure
reading sources... [ 50%] Datasets
reading sources... [ 67%] Getting_Started
reading sources... [ 83%] Leaderboard
reading sources... [100%] index

looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/milliontrees/checkouts/latest/docs/Dataset_Structure.md: WARNING: document isn't included in any toctree
done
preparing documents... done
copying assets... 
copying static files... done
copying extra files... done
copying assets: done
writing output... [ 17%] Contributing
writing output... [ 33%] Dataset_Structure
writing output... [ 50%] Datasets
writing output... [ 67%] Getting_Started
writing output... [ 83%] Leaderboard
writing output... [100%] index

generating indices... genindex py-modindex done
writing additional pages... search done
copying images... [100%] public/open_drone_example.png

dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 2 warnings.

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