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✨ first rudementary API documentation (#9)
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‎.readthedocs.yaml

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# .readthedocs.yaml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Set the OS, Python version and other tools you might need
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build:
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os: ubuntu-22.04
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tools:
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python: "3.12"
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# apt_packages:
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# - some-package
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# Build documentation in the "docs/" directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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# Optionally build your docs in additional formats such as PDF and ePub
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# formats:
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# - pdf
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# - epub
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# Optional but recommended, declare the Python requirements required
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# to build your documentation
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# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
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python:
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install:
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- method: pip
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path: .
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extra_requirements:
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- docs

‎README.md

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# vcore
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Visualization library for omics data
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# Visualization Core (vuecore) library
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Visualization library for omics data.
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See also acore and vuegen.
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## Installation
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### Latest stable release from PyPI
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```bash
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pip install vuecore
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```
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### Latest development version from GitHub
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Clone this repository and then install using pip the development version in
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editable mode:
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```bash
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# git clone https://github.com/Multiomics-Analytics-Group/vuecore.git
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# cd vuecore
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pip install -e '.[dev]'
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```

‎docs/.gitignore

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# apidocs
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reference
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# builds
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_build
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jupyter_execute

‎docs/README.md

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# Docs creation
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In order to build the docs you need to
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1. install sphinx and additional support packages
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2. build the package reference files
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3. run sphinx to create a local html version
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The documentation is build using readthedocs automatically.
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Install the docs dependencies of the package (as speciefied in toml):
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```bash
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# in main folder
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# pip install ".[docs]"
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poetry install --with docs
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```
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## Build docs using Sphinx command line tools
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Command to be run from `path/to/docs`, i.e. from within the `docs` package folder:
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Options:
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- `--separate` to build separate pages for each (sub-)module
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```bash
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# pwd: docs
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# apidoc
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sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuecore
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# build docs
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sphinx-build -n -W --keep-going -b html ./ ./_build/
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```
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## Include repo README.md into docs
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Relative links are used in the main README, which need to be resolved when building. It's
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possible to include the a `relative-docs` option if one uses `index.md` ([see docs](https://myst-parser.readthedocs.io/en/latest/faq/index.html#include-a-file-from-outside-the-docs-folder-like-readme-md)). This does not work
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with `href` links, only native markdown links.

‎docs/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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from importlib import metadata
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# -- Project information -----------------------------------------------------
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project = "vuecore"
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copyright = "2024, Multiomics-Analytics-Group"
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author = (
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"Multiomics-Analytics-Group, Sebastián Ayala Ruano, Henry Webel, Alberto Santos"
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)
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PACKAGE_VERSION = metadata.version("vuecore")
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version = PACKAGE_VERSION
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release = PACKAGE_VERSION
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.autodoc.typehints",
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"sphinx.ext.viewcode",
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"sphinx.ext.napoleon",
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"sphinx.ext.intersphinx",
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"sphinx_new_tab_link",
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"myst_nb",
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]
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# https://myst-nb.readthedocs.io/en/latest/computation/execute.html
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nb_execution_mode = "auto"
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myst_enable_extensions = ["dollarmath", "amsmath"]
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# Plolty support through require javascript library
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# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly
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html_js_files = [
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"https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
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]
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# https://myst-nb.readthedocs.io/en/latest/configuration.html
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# Execution
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nb_execution_raise_on_error = True
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# Rendering
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nb_merge_streams = True
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# maximum execution time per cell in seconds
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nb_execution_timeout = 120
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# https://myst-nb.readthedocs.io/en/latest/authoring/custom-formats.html#write-custom-formats
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# ! if you use it, then you cannot directly execute the notebook in the browser in colab
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# (the file needs to be fetched from the repository)
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# just keep both syncing it using papermill
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# nb_custom_formats = {".py": ["jupytext.reads", {"fmt": "py:percent"}]}
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ["_templates"]
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = [
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"_build",
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"Thumbs.db",
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".DS_Store",
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"jupyter_execute",
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"conf.py",
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]
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# Intersphinx options
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3", None),
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"networkx": ("https://networkx.org/documentation/stable/", None),
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"pyvis": ("https://pyvis.readthedocs.io/en/stable/", None),
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"pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
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# "scikit-learn": ("https://scikit-learn.org/stable/", None),
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"matplotlib": ("https://matplotlib.org/stable/", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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}
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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# See:
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# https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py
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# html_title = ""
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html_theme = "sphinx_book_theme"
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# html_logo = "_static/logo-wide.svg"
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# html_favicon = "_static/logo-square.svg"
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html_theme_options = {
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"github_url": "https://github.com/Multiomics-Analytics-Group/vuecore",
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"repository_url": "https://github.com/Multiomics-Analytics-Group/vuecore",
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"repository_branch": "main",
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"home_page_in_toc": True,
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"path_to_docs": "docs",
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"show_navbar_depth": 1,
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"use_edit_page_button": True,
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"use_repository_button": True,
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"use_download_button": True,
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"launch_buttons": {
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"colab_url": "https://colab.research.google.com"
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# "binderhub_url": "https://mybinder.org",
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# "notebook_interface": "jupyterlab",
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},
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"navigation_with_keys": False,
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}
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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# html_static_path = ["_static"]
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# -- Setup for sphinx-apidoc -------------------------------------------------
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# Read the Docs doesn't support running arbitrary commands like tox.
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# sphinx-apidoc needs to be called manually if Sphinx is running there.
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# https://github.com/readthedocs/readthedocs.org/issues/1139
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if os.environ.get("READTHEDOCS") == "True":
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from pathlib import Path
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PROJECT_ROOT = Path(__file__).parent.parent
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PACKAGE_ROOT = PROJECT_ROOT / "src" / "vuecore"
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def run_apidoc(_):
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from sphinx.ext import apidoc
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apidoc.main(
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[
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"--force",
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"--implicit-namespaces",
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"--module-first",
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"--separate",
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"-o",
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str(PROJECT_ROOT / "docs" / "reference"),
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str(PACKAGE_ROOT),
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str(PACKAGE_ROOT / "*.c"),
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str(PACKAGE_ROOT / "*.so"),
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]
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)
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def setup(app):
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app.connect("builder-inited", run_apidoc)

‎docs/index.md

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<!-- https://myst-parser.readthedocs.io/en/latest/faq/index.html
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#include-a-file-from-outside-the-docs-folder-like-readme-md -->
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```{include} ../README.md
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:start-line: 0
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:relative-docs: docs
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:relative-images:
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```
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```{toctree}
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:maxdepth: 2
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:caption: Modules
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:hidden:
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reference/vuecore
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```
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```{toctree}
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:maxdepth: 1
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:caption: MISC:
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:hidden:
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README.md
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```

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