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xgarridosgiardie
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Add resources for documentation (#74)
* Add resources for documentation * start from empty directory * run notebook execution for the latest python compiler * fix again * double quote -> single quote * add missing readthedocs configuration * Hackish solution to badly formated pandas dataframe due to latex expression See jupyter-book/jupyter-book#1826 * don't need this one * fix missing dep * fix sacc tutorial link + add new project dependency for notebook compilation * split unit test and testing tutorial notebooks Both tests can be done in parallel and speed up the github actions time * Add API module (time for docstrings now) * fix missing mflike path * add mock imports * adding api reference * adding mflike.rst * fixing index.rst * fixing theoryforge.rst title * escape **kwargs arguments in documentation + kozmetix * change section order * fix import (was working but don't know how) --------- Co-authored-by: sgiardie <grdsrn1@unife.it>
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‎.github/workflows/notebooks.yml‎

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name: Testing tutorial notebooks
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on:
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pull_request:
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push:
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branches: [master]
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: ["3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies via pip
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run: |
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python -m pip install --upgrade pip
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python -m pip install .[notebook]
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- name: Test notebooks
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run: |
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cd docs/source/notebooks
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make

‎.github/workflows/testing.yml‎

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name: Testing
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name: Testing & coverage
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on:
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pull_request:
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- name: Report Coverage (codecov)
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if: matrix.os == 'ubuntu-latest'
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uses: codecov/codecov-action@v4
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- name: Test notebooks (Only on Linux for saving time)
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if: matrix.os == 'ubuntu-latest'
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run: |
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python -m pip install jupyter
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jupyter nbconvert --to notebook --execute notebooks/mflike_tutorial.ipynb

‎.readthedocs.yml‎

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# .readthedocs.yml
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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 version of Python 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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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/source/conf.py
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# Build documentation with MkDocs
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#mkdocs:
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# configuration: mkdocs.yml
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# Optionally build your docs in additional formats such as PDF and ePub
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formats: all
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# Optionally declare the Python requirements required to build your docs
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python:
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install:
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- requirements: docs/requirements.txt

‎README.rst‎

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.. image:: https://img.shields.io/github/actions/workflow/status/simonsobs/LAT_MFLike/testing.yml?branch=master
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:target: https://github.com/simonsobs/LAT_MFLike/actions
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.. image:: https://readthedocs.org/projects/lat-mflike/badge/?version=latest
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:target: https://lat-mflike.readthedocs.io/en/latest/?badge=latest
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.. image:: https://mybinder.org/badge_logo.svg
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:target: https://mybinder.org/v2/gh/simonsobs/LAT_MFLike/master?filepath=notebooks%2Fmflike_tutorial.ipynb
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.. image:: https://codecov.io/gh/simonsobs/LAT_MFLike/branch/master/graph/badge.svg?token=qrrVcbNCs5
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:target: https://codecov.io/gh/simonsobs/LAT_MFLike
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‎binder/requirements.txt‎

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matplotlib
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camb
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mflike
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seaborn

‎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 = source
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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/requirements.txt‎

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sphinx-book-theme
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sphinx-copybutton
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myst-nb
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cobaya

‎docs/source/_static/css/custom.css‎

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button.theme-switch-button {
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display: none !important;
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}
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.logo__title {
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font-size: 1.1rem !important;
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font-weight: bold !important;
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}

‎docs/source/_static/logo.png‎

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‎docs/source/conf.py‎

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from pkg_resources import DistributionNotFound, get_distribution
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try:
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__version__ = get_distribution("mflike").version
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except DistributionNotFound:
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__version__ = "unknown version"
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import os
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import sys
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sys.path.append(os.path.abspath("../.."))
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# autodoc_mock_imports = ["numpy", "cobaya"]
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# General stuff
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.intersphinx",
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"sphinx.ext.napoleon",
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"sphinx.ext.mathjax",
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"sphinx.ext.viewcode",
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"sphinx_copybutton",
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"myst_nb",
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]
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myst_enable_extensions = ["dollarmath", "colon_fence"]
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source_suffix = ".rst"
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master_doc = "index"
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project = "mflike"
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copyright = "2019 - 2024, Simons Observatory Collaboration Analysis Library Task Force"
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author = "Simons Observatory Collaboration Power Spectrum Group"
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language = "en"
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version = __version__
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release = __version__
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exclude_patterns = ["_build"]
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# HTML theme
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html_theme = "sphinx_book_theme"
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# Add paths to extra static html files from notebook conversion
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html_copy_source = True
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html_show_sourcelink = True
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html_sourcelink_suffix = ""
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html_title = "Multifrequency Likelihood for SO Large Aperture Telescope"
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html_favicon = "_static/logo.png"
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html_static_path = ["_static"]
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html_css_files = ["css/custom.css"]
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html_theme_options = {
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"logo": {
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"alt_text": "LAT_MFLike - Home",
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"text": html_title,
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"image_light": "_static/logo.png",
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},
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"path_to_docs": "docs",
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"repository_url": "https://github.com/simonsobs/LAT_MFLike",
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"repository_branch": "master",
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"launch_buttons": {
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"binderhub_url": "https://mybinder.org",
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"notebook_interface": "classic",
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},
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"use_edit_page_button": True,
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"use_issues_button": True,
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"use_repository_button": True,
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"use_download_button": True,
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}
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nb_execution_mode = "off"
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nb_execution_timeout = -1

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