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Henry Webel
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Merge pull request #3 from RasmussenLab/docs
Add Sphinx template
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‎.gitignore‎

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@@ -15,6 +15,12 @@ build/
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dist/
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**.egg-info
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# Sphinx documenter creates these
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_build
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_static
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_templates
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/docs/reference
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# MacOS automatically creates these files
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.DS_Store
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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: "3.11"
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# You can also specify other tool versions:
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# nodejs: "19"
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# rust: "1.64"
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# golang: "1.19"
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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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pip install -e .
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```
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## TestPyPI
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Install vom [TestPyPI](https://test.pypi.org/project/rasmussenlab-mockup):
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```
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pip install -i https://test.pypi.org/simple/ rasmussenlab-mockup
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```
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> The package on PyPI is call `rasmussenlab-mockup` and not `mockup` as the package name is already taken. The import is still `import mockup`.
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## Readthedocs
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The documentation is build using readthedocs automatically. See
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[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/).
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- make sure to enable build from PRs in the settings (advanded settings)
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- checkout configuration file: [`.readthedocs.yaml`](.readthedocs.yaml)

‎docs/Makefile‎

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎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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```
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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/mockup
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# build docs
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sphinx-build -n -W --keep-going -b html ./ ./_build/
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```

‎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 = "mockup"
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copyright = "2024, Jakob Nybo Nissen, Henry Webel"
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author = "Jakob Nybo Nissen, Henry Webel"
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PACKAGE_VERSION = metadata.version("rasmussenlab-mockup")
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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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# 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 = ["_build", "Thumbs.db", ".DS_Store"]
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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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# "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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}
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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/RasmussenLab/python_package",
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"repository_url": "https://github.com/RasmussenLab/python_package",
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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" / "mockup"
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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.rst‎

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.. mockup documentation master file, created by
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sphinx-quickstart on Mon Aug 28 14:09:15 2023.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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The mockup package
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==================================
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Mockup is a Python package with some simple example code.
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To get started, explore the :class:`mockup.Circle` class.
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.. toctree::
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:maxdepth: 2
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:caption: Tutorial
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tutorial/tutorial
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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reference/modules
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.. toctree::
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:hidden:
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:caption: Technical notes
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README.md
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎docs/tutorial/tutorial.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Mockup tutorial"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from mockup import mockup"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"mockup.add_one(-11)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"list(mockup.flatten_ints([[9, 11], [12], [4, 5]]))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"c2 = mockup.Circle.from_circumference(100)\n",
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"round(c2.radius, 3)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"c2 # repr"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "pathways",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.4"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

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