Configure documentation

.readthedocs.yml

@@ -20,4 +20,3 @@ python:
       path: .
       extra_requirements:
         - doc
-  system_packages: true

README.rst

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+physioQC
+==========
+
+.. image:: https://img.shields.io/github/v/release/physiopy/physioqc?style=flat&logo=github&sort=semver
+   :target: https://github.com/physiopy/physioqc/releases
+.. image:: https://readthedocs.org/projects/physioqc/badge/?version=latest
+   :target: http://physioqc.readthedocs.io/en/latest
+.. image:: https://img.shields.io/badge/license-Apache%202-blue.svg
+   :target: http://www.apache.org/licenses/LICENSE-2.0
+.. image:: https://img.shields.io/codecov/c/gh/physiopy/physioqc?style=flat&label=codecov&logo=codecov
+   :target: https://codecov.io/gh/physiopy/physioqc
+.. image:: https://img.shields.io/circleci/build/github/physiopy/physioqc?style=flat&label=circleci&logo=circleci
+   :target: https://circleci.com/gh/physiopy/physioqc
+.. image:: https://img.shields.io/badge/python-3.7+-blue.svg
+   :target: https://www.python.org/downloads/
+
+
+``physioQC`` is a toolbox for physiological data (Automagic) Quality Control.
+
+.. _licensing:
+
+License
+-------
+
+This template is released under The Unlicense. Commented here below a copy of the Apache 2.0 Licence, adopted by Physiopy.
+Remember to change the licence of your repository as soon as you adopt the template.

docs/Makefile

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

docs/api.rst

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+.. _api_ref:
+
+API
+===
+
+.. py:module:: physioqc

docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+import os
+import sys
+
+from datetime import datetime
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "physioqc"
+author = "the {} developers".format(project)
+copyright = "2019-{}, {}".format(datetime.now().year, author)
+
+# Import project to get version info
+sys.path.insert(0, os.path.abspath(os.path.pardir))
+import physioqc  # noqa
+
+# The short X.Y version
+version = physioqc.__version__
+# The full version, including alpha/beta/rc tags
+release = physioqc.__version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+]
+
+# Generate the API documentation when building
+autosummary_generate = True
+numpydoc_show_class_members = False
+autoclass_content = "class"
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+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 = None
+
+# 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 = "sphinx"
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+import sphinx_rtd_theme  # noqa
+
+html_theme = "sphinx_rtd_theme"
+html_show_sourcelink = False
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "physioqc"
+
+# -- Extension configuration -------------------------------------------------
+intersphinx_mapping = {
+    "matplotlib": ("https://matplotlib.org", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+}
+
+plot_include_source = True
+plot_formats = [("png", 90)]
+plot_html_show_formats = False
+plot_html_show_source_link = False

docs/index.rst

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+
+.. include:: ../README.rst
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 1
+
+   installation
+   api

docs/installation.rst

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+.. _installation_setup:
+
+Installation and setup
+======================