Add doc/conf.py

.readthedocs.yaml

@@ -9,9 +9,13 @@ build:
   tools:
     python: "mambaforge-4.10"
 
-conda:
-  environment: doc/rtd-environment.yml
+# conda:
+  # environment: doc/rtd-environment.yml
 
 sphinx:
   configuration: doc/conf.py
   fail_on_warning: true
+
+python:
+   install:
+   - requirements: docs/requirements.txt

doc/conf.py

@@ -0,0 +1,360 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# 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 os
+import pathlib
+import warnings
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+needs_sphinx = '1.8.3'
+
+# 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.mathjax',
+              'matplotlib.sphinxext.plot_directive',
+              'sphinx.ext.autodoc',
+              'sphinx.ext.todo',
+              'sphinx.ext.doctest',
+              'sphinx.ext.autosummary',
+              'numpydoc',
+              'sphinx.ext.extlinks',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.ifconfig',
+              'sphinx.ext.napoleon',
+              'sphinx_gallery.gen_gallery',
+              'sphinxcontrib.bibtex']
+
+# Add any paths that contain templates here, relative to this directory.
+# templates_path = ['templates']
+
+# This is needed for ipython @savefig
+# Otherwise it just puts the png in the root dir
+savefig_dir = '_images'
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'QuTiP-Jax: Jax support for QuTiP'
+author = ', '.join([
+    'S. Ahmed',
+    'A, Galicia',
+    'and E. Giguère'
+])
+
+copyright = '2022, QuTiP developers and contributors'
+
+
+def _check_source_folder_and_imported_qutip_match():
+    """ Warn if the imported qutip and the source folder the documentation
+        is being built from don't match.
+
+        The generated documentation contains material from both the
+        source folder (e.g. ``.rst`` files) and from the imported qutip
+        (e.g. docstrings), so if the two don't match the generated
+        documentation will be a chimera.
+    """
+    import qutip_jax
+    qutip_folder = pathlib.Path(qutip_jax.__file__).absolute().parent.parent
+    source_folder = pathlib.Path(__file__).absolute().parent.parent
+    if qutip_folder != source_folder:
+        warnings.warn(
+            "The documentation source and imported qutip package are"
+            " not from the same source folder. This may result in the"
+            " documentation containing text from different sources."
+            " Documentation source: {!r}."
+            " Qutip-jax package source: {!r}.".format(
+                str(source_folder), str(qutip_folder)
+            )
+        )
+
+
+_check_source_folder_and_imported_qutip_match()
+
+
+def qutip_jax_version():
+    """ Retrieve the QuTiP version from ``../VERSION``.
+    """
+    src_folder_root = pathlib.Path(__file__).absolute().parent.parent
+    version = src_folder_root.joinpath(
+        "VERSION"
+    ).read_text().strip()
+    return version
+
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+# The full version, including alpha/beta/rc tags.
+release = qutip_jax_version()
+# The short X.Y version.
+version = ".".join(release.split(".")[:2])
+# 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 = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+add_function_parentheses = False
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+add_module_names = False
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+show_authors = True
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+todo_include_todos = True
+
+numpydoc_show_class_members = False
+napoleon_numpy_docstring = True
+napoleon_use_admonition_for_notes = True
+
+# sphinxcontrib.bixtex options
+bibtex_bibfiles = []
+
+# -- 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'
+full_logo= True
+
+
+# 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 themes here, relative to this directory.
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+html_title = 'QuTiP-Jax {} Documentation'.format(version)
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+html_short_title = 'QuTiP-Jax'
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+html_favicon = 'figures/favicon.ico'
+
+# 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']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {'sidebar': ['localtoc.html', 'sourcelink.html', 'searchbox.html']}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+html_show_sourcelink = False
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+html_css_files = [
+    'site.css',
+]
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'QuTiPdoc'
+
+
+# -- Configure MathJax for maths output in HTML targets
+
+# Currently (2021-04-10) Sphinx 3.5.3 loads MathJax 2.7, which does not have
+# support for the 'physics' package.  MathJax 3 does, so once Sphinx is using
+# that (should be in Sphinx 4), you will be able to swap to using that.  In the
+# meantime, we just have to define all the functions we're going to use.
+#
+# See:
+# - https://docs.mathjax.org/en/v3.0-latest/input/tex/extensions/physics.html
+mathjax3_config = {
+    'TeX': {
+        'Macros': {
+            'bra': [r'\left\langle{#1}\right\rvert', 1],
+            'ket': [r'\left\lvert{#1}\right\rangle', 1],
+            'tr': r'\operatorname{tr}',
+        },
+    },
+}
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    'papersize': 'a4paper',
+    'pointsize': '10pt',
+    'classoptions': '',
+    'babel': '\\usepackage[english]{babel}',
+    'fncychap': '',
+    'figure_align': 'H',
+    # This preamble is inserted into the build tools for the latex make targets
+    # but not any others.  Be sure to change mathjax_config too if you need to
+    # define more commands.
+    'preamble': r"\usepackage{physics}",
+}
+
+# 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 = [
+  ('index', 'qutip.tex', project, author, 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = 'figures/logo.png'
+
+# Sometimes make might suggest setting this to False.
+# It screws a few things up if you do - don't be tempted.
+latex_keep_old_macro_names=True
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = True
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'qutip', project, [author], 1)
+]
+
+# -- Doctest Setup ---------------------------------------
+
+# os_nt = False
+# if os.name == "nt":
+#     os_nt = True
+
+
+# doctest_global_setup = '''
+# import matplotlib.pyplot as plt
+# import numpy as np
+# import os
+# import warnings
+# warnings.filterwarnings("ignore")
+# from qutip import *
+# os_nt = {}
+# '''.format(os_nt)
+
+
+# -- Options for plot directive ---------------------------------------
+
+# plot_working_directory = "./"
+# plot_pre_code = """
+# import numpy as np
+# import matplotlib.pyplot as plt
+# from qutip import *
+# plt.close("all")
+# """
+# plot_include_source = True
+# plot_html_show_source_link = False
+# plot_html_show_formats = False
+
+# -- Options 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 = [
+    (master_doc, 'qutip_jax', project,
+     author, 'QuTiP-Jax',
+     'Jax support for QuTiP',
+     'Miscellaneous'),
+]
+
+autodoc_member_order = 'alphabetical'
+
+## EXTLINKS CONFIGURATION ######################################################
+
+extlinks = {
+    'arxiv': ('https://arxiv.org/abs/%s', 'arXiv:%s'),
+    'doi': ('https://dx.doi.org/%s', 'doi:%s'),
+}
+
+# configuration declares the location of the examples directory for
+# Sphinx Gallery
+
+sphinx_gallery_conf = {
+     'examples_dirs': 'gallery/src',   # path to your example scripts
+     'gallery_dirs': 'gallery/build',  # save generated examples
+     'abort_on_example_error': True  # abort if exception occurs
+}
+
+ipython_strict_fail = False