Merge pull request uibcdf#19 from dprada/main

Documentation first version

devtools/conda-envs/development_env.yaml

@@ -18,4 +18,6 @@ dependencies:
 - sphinx_rtd_theme
 - sphinxcontrib-bibtex
 - myst-nb
+- sphinx-copybutton
+- sphinx-remove-toctrees
 - jupyterlab

devtools/conda-envs/docs_env.yaml

@@ -14,3 +14,5 @@ dependencies:
 - sphinx_rtd_theme
 - sphinxcontrib-bibtex
 - myst-nb
+- sphinx-copybutton
+- sphinx-remove-toctrees

devtools/requirements.yaml

@@ -37,6 +37,8 @@ docs:
     - sphinx_rtd_theme
     - sphinxcontrib-bibtex
     - myst-nb
+    - sphinx-copybutton
+    - sphinx-remove-toctrees
 
 development:
   channels:

docs/Makefile

@@ -0,0 +1,22 @@
+# Minimal makefile for Sphinx documentation
+#
+
+export SPHINXWORKING=True
+
+# You can set these variables from the command line.
+SPHINXOPTS    = -j auto
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = openpocket
+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/_static/README.md

@@ -0,0 +1,16 @@
+# Static Doc Directory
+
+Add any paths that contain custom static files (such as style sheets) here,
+relative to the `conf.py` file's directory. 
+They are copied after the builtin static files,
+so a file named "default.css" will overwrite the builtin "default.css".
+
+The path to this folder is set in the Sphinx `conf.py` file in the line: 
+```python
+templates_path = ['_static']
+```
+
+## Examples of file to add to this directory
+* Custom Cascading Style Sheets
+* Custom JavaScript code
+* Static logo images

docs/_static/custom.css

@@ -0,0 +1,10 @@
+.wy-nav-content {
+    max-width: 100% !important;
+}
+
+/* To change the left bar of executable cells in markdown and executable cells in jupyter notebooks */
+/* See https://github.com/executablebooks/meta/discussions/667 */
+div.cell div.cell_input {
+    border-left-color: #C9C9C9;
+}
+

docs/_templates/README.md

@@ -0,0 +1,14 @@
+# Templates Doc Directory
+
+Add any paths that contain templates here, relative to  
+the `conf.py` file's directory.
+They are copied after the builtin template files,
+so a file named "page.html" will overwrite the builtin "page.html".
+
+The path to this folder is set in the Sphinx `conf.py` file in the line: 
+```python
+html_static_path = ['_templates']
+```
+
+## Examples of file to add to this directory
+* HTML extensions of stock pages like `page.html` or `layout.html`

docs/_templates/layout.html

@@ -0,0 +1,8 @@
+{% extends '!layout.html' %}
+{% block document %}
+{{super()}}
+    <a href="https://github.com/uibcdf/openpocket">
+        <img style="position: absolute; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png" alt="Fork me on GitHub">
+    </a>
+{% endblock %}
+

docs/api/developers/api_developers.rst

@@ -0,0 +1,8 @@
+Developers
+==========
+
+.. toctree::
+   :name: developers
+   :caption: Developers
+   :maxdepth: 2
+

docs/api/users/api_users.rst

@@ -0,0 +1,8 @@
+Users
+=====
+
+.. toctree::
+   :name: users
+   :caption: Users
+   :maxdepth: 2
+

docs/conf.py

@@ -0,0 +1,234 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+import os
+import sys
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+import openpocket
+
+# -- Project information -----------------------------------------------------
+
+project = 'OpenPocket'
+copyright = ("2022, UIBCDF Lab at the Mexico City Childrens Hospital Federico Gomez and authors."
+             "Computational Molecular Science Python Cookiecutter version 1.5")
+author = 'UIBCDF Lab'
+
+# The short X.Y version
+version = openpocket.__version__.split('+')[0]
+# The full version, including alpha/beta/rc tags
+release = openpocket.__version__
+
+print(f'version {version}, release {release}')
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.todo',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.githubpages',
+    'sphinxcontrib.bibtex',
+    'sphinx.ext.extlinks',
+    'sphinx_remove_toctrees',
+    'sphinx_copybutton',
+    'myst_nb'
+]
+
+autosummary_generate = True
+napoleon_google_docstring = False
+napoleon_use_param = False
+napoleon_use_ivar = True
+
+# sphinxcontrib-bibtex
+bibtex_bibfiles = ['bibliography.bib'] # list of *.bib files
+bibtex_default_style = 'alpha'
+bibtex_encoding = 'utf-8-sig'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+
+source_parsers={
+}
+
+source_suffix = ['.rst', '.md', '.ipynb']
+
+# 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 was edited to use sphinx-intl
+language = 'en'
+# These next two variables were incluede to use sphinx-intl
+locale_dirs =  ['_locale/']
+gettext_compact = False
+
+# 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', '**.ipynb_checkpoints', 'old_api', 'freezer']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'default'
+
+# Remove from toctrees
+remove_from_toctrees = []
+for directory in os.walk('api'):
+    if directory[0].endswith('/autosummary'):
+        remove_from_toctrees.append(directory[0]+'/*')
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# 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 = {}
+html_theme_options = {
+    'canonical_url': '',
+    'analytics_id': '',
+    'logo_only': False,
+    'display_version': True,
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': False,
+    # Toc options
+    'collapse_navigation': False,
+    'sticky_navigation': False,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': True
+}
+
+# Add any paths that contain custom themes here, relative to this directory.
+html_theme_path = []
+
+# 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']
+
+#### I should check
+#### https://github.com/lotharschulz/sphinx-pages/blob/master/conf.py for more
+#### options
+
+# Custom css
+
+html_css_files = [
+    'custom.css',
+]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+html_show_sourcelink = False
+
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'openpocketdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+]
+
+
+# -- 1 for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+]
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+#intersphinx_mapping = {'https://docs.python.org/': None}
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+

docs/contents/about/citation.md

@@ -0,0 +1,3 @@
+# Citation
+
+To be written soon...

docs/contents/about/installation.md

@@ -0,0 +1,3 @@
+# Installation
+
+To be written soon...

docs/contents/about/showcase/index.md

@@ -0,0 +1,3 @@
+# Showcase
+
+To be written soon...

docs/contents/about/what.md

@@ -0,0 +1,3 @@
+# What
+
+To be written soon...

docs/contents/developer/intro/index.md

@@ -0,0 +1 @@
+# Introduction

docs/contents/user/intro/index.md

@@ -0,0 +1 @@
+# Introduction

docs/contents/user/tools/index.md

@@ -0,0 +1 @@
+# Tools