conf.py

# -*- coding: utf-8 -*-
"""
pyGIMLi sphinx configuration file.
"""
import warnings

warnings.filterwarnings("ignore", category=UserWarning,
                        message="Matplotlib is currently using agg, which is a"
                                " non-GUI backend, so cannot show the figure.")

import random
import datetime
import os
import re
import sys
from os import path
from os.path import join
sys.path.insert(0, os.path.abspath("."))

import numpy as np
# for doc rendering on headless machines (jenkins server)
import matplotlib
matplotlib.use("Agg")
import pkg_resources
import sphinx

import pygimli


from sidebar_gallery import make_gallery

try:
    # from _build.doc.conf_environment import *
    from conf_environment import *
    pygimli.boxprint("Building documentation out-of-source. Good.")
    in_source = False
    print("DOXY_BUILD_DIR", DOXY_BUILD_DIR)
except ImportError:
    TRUNK_PATH = ".."
    SPHINXDOC_PATH = "."
    DOC_BUILD_DIR = ""
    DOXY_BUILD_DIR = ""
    in_source = True
    pygimli.boxprint("Building documentation in-source. Don't forget to make clean.")

sys.path.append(os.path.abspath(SPHINXDOC_PATH))
sys.path.append(os.path.abspath(join(SPHINXDOC_PATH, "_sphinx-ext")))

# The following line is necessary for the Tools section
sys.path.append(os.path.abspath(join(TRUNK_PATH, "pygimli")))

# -- General configuration ----------------------------------------------------

# MPL configuration in API docs, tutorials and examples
plot_rcparams = {"savefig.bbox": "tight"}

# If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = "1.8" # due to napoleon

# Check for external sphinx extensions
deps = ["sphinxcontrib-programoutput",
        "sphinxcontrib-bibtex",
        "sphinxcontrib-doxylink",
	    "bibtexparser",
	]

# check for p.version too
modules = [p.project_name for p in pkg_resources.working_set]

req = []
for dep in deps:
    if dep not in modules:
        req.append(dep)
if req:
    msg = "Sorry, there are missing dependencies to build the docs.\n" + \
          "Try: sudo pip install %s.\n" % (" ".join(req)) + \
          "Or install all dependencies with: pip install -r requirements.txt\n" + \
          "You can install them all in userspace by adding the --user flag."
    print((pkg_resources.working_set))
    raise ImportError(msg)

# 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.todo",
              "sphinx.ext.viewcode",
              "sphinx.ext.autosummary",
              "sphinx.ext.mathjax",
              "sphinx.ext.intersphinx",
              "sphinx.ext.imgconverter",
              "sphinx.ext.autosectionlabel",
              "sphinx.ext.napoleon",
              "matplotlib.sphinxext.plot_directive",
              "srclinks",
              "sphinxcontrib.doxylink",
              "sphinx_design",
              # "sphinxcontrib.spelling"
              ]

extensions += [dep.replace("-", ".") for dep in deps]


# Sphinx-gallery settings
try:
    import sphinx_gallery
    from sphinx_gallery.sorting import FileNameSortKey
    extensions += ["sphinx_gallery.gen_gallery"]

    def reset_mpl(gallery_conf, fname):
        import matplotlib
        matplotlib.rcParams.update(plot_rcparams)

    # Setup automatic gallery generation
    sphinx_gallery_conf = {
        "examples_dirs": [join(SPHINXDOC_PATH, "examples"),
                          join(SPHINXDOC_PATH, "tutorials")],
        "gallery_dirs": ["_examples_auto", "_tutorials_auto"],

        # "reference_url": {
        #     "pygimli": "https://pygimli.org",
        #     "python": "https://docs.python.org/dev",
        #     "numpy": "https://numpy.org/doc/stable",
        #     "scipy": "https://docs.scipy.org/doc/scipy/reference",
        #     "matplotlib": "https://matplotlib.org/stable",
        # },

        # Don"t report time of fast scripts (< 10 sec)
        "min_reported_time": 10,

        # path where to store your example linker templates
        "backreferences_dir": "pygimliapi" + os.path.sep + "_generated",

        # Your documented modules. You can use a string or a list of strings
        "doc_module": "pygimli",

        # Sort gallery example by file name instead of number of lines (default)
        "within_subsection_order": FileNameSortKey,

        "remove_config_comments": True,

        # Only parse filenames starting with plot_
        "filename_pattern": "plot_",

        "first_notebook_cell": ("# Checkout www.pygimli.org for more examples"),

        "reset_modules": (reset_mpl),

        # Avoid representation of mpl axis, LineCollections, etc.
        "ignore_repr_types": r"matplotlib[text, axes, collections]",
        }

    pyvista = pygimli.optImport("pyvista", "build the gallery with 3D visualizations")
    if pyvista:
        # necessary when building the sphinx gallery
        os.environ['PYVISTA_BUILDING_GALLERY'] = "true"
        pyvista.BUILDING_GALLERY = True
        os.environ["PYVISTA_OFF_SCREEN"] = "true"
        pyvista.OFF_SCREEN = True
        pyvista.set_plot_theme("document")
        pyvista.global_theme.window_size = [1024, 768]
        pyvista.global_theme.font.size = 22
        pyvista.global_theme.font.label_size = 22
        pyvista.global_theme.font.title_size = 22
        pyvista.global_theme.return_cpos = False
        pyvista.set_jupyter_backend(None) 
        sphinx_gallery_conf["image_scrapers"] = ("pyvista", "matplotlib")

except ImportError:
    err = """
    The sphinx_gallery extension is not installed, so the tutorials
    and examples will not be rendered and additional warnings will occur
    due to missing references.

    Install sphinx_gallery via:

        sudo pip3 install sphinx-gallery
    """
    pygimli.warn(err)


intersphinx_mapping = {
    "python": ("https://docs.python.org/3/", None),
    "numpy": ("https://numpy.org/doc/stable/", None),
    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
    "matplotlib": ("https://matplotlib.org/stable/", None),
}

autosectionlabel_prefix_document = True
autoclass_content = "class"
autosummary_generate = True
autosummary_generate_overwrite = False
autosummary_imported_members = True
autodoc_mock_imports = ["os", "os.path" "sys", "locale", "numpy", "matplotlib",
                        "matplotlib.pyplot", "pyvista", "pyqt5"]

autodoc_default_options = {
    "imported-members": True,
    # "special-members": "__init__",
    "undoc-members": False,
    "show-inheritance": True,
}

# Get mathjax
# Formulas disappear after scrolling
# mathjax_path = "https://www.pygimli.org/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
# Slow, but works
mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js" +\
               "?config=TeX-AMS-MML_HTMLorMML"

# Add any paths that contain templates here, relative to this directory.
templates_path = [join(SPHINXDOC_PATH, "_templates"),
                  join(DOC_BUILD_DIR, "_templates")]

# MPL plot directive settings
plot_formats = [("png", 96)]
if not in_source:
    plot_formats.append(("pdf", 96))
plot_include_source = True
plot_html_show_source_link = False
plot_apply_rcparams = True  # if context option is used

# The suffix of source filenames.
source_suffix = ".rst"

# The encoding of source files.
source_encoding = "utf-8-sig"

# The master toctree document.
master_doc = "documentation"

# General information about the project.
project = "pyGIMLi"
year = datetime.date.today().year
copyright = f"{year} - pyGIMLi Development Team"

# 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 short X.Y version.
version = pygimli.__version__
install_version = pygimli.__version__.split("+")[0]

rst_epilog = """
.. |version| replace:: pyGIMLi {versionnum}
""".format(versionnum = version)

# The full version, including alpha/beta/rc tags.
release = pygimli.__version__

release = release.replace("_", "\\_")

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
# language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
# today = ""
# Else, today_fmt is used as the format for a strftime call.
# today_fmt = "%B %d, %Y"

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ["_build", "_sphinx-ext", "_templates", "tmp", "examples",
                    "tutorials" ]

# The reST default role (used for this markup: `text`) to use for all documents
# default_role = None

# If true, "()" will be appended to :func: etc. cross-reference text.
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
# show_authors = False

# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []

# -- Options for HTML output --------------------------------------------------

# Add any paths that contain custom themes here, relative to this directory.
# html_theme_path = [join(SPHINXDOC_PATH, "_themes")]

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.

html_theme = "pydata_sphinx_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 = {
    "logo": {
      "text": "py<b>GIMLi</b>",
    },
    "secondary_sidebar_items": ["page-toc", "improve-this-page"],
    "footer_items": ["footer"],
    "pygment_light_style": "friendly",
    "pygment_dark_style": "native"
}

html_css_files = [
    'css/custom.css',
]

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
html_title = "pyGIMLi - Geophysical Inversion and Modelling Library"

# A shorter title for the navigation bar.  Default is the same as html_title.
html_short_title = "pyGIMLi"

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = join(SPHINXDOC_PATH, "_static/gimli_logo_simple.svg")

# 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 = join(SPHINXDOC_PATH, "_static/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 = [join(SPHINXDOC_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"  # + " with " + version

# 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 = {
  "index": [],
}

# Additional templates that should be rendered to pages, maps page names to
# template names.
html_additional_pages = {"index": "index.html", "publist": "publications.html"}

# If false, no module index is generated.
html_domain_indices = True

html_index = "index.html"

# If false, no index is generated.
html_use_index = True

html_use_modindex = 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 = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
# does not have any affect. sphinx credit is located in footer.html
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 = "https://pygimli.org"

# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = "gimlidoc"

# -- Options for LaTeX output

# The name of an image file (relative to this directory) to place at the top of
# the title page.
latex_logo = join(SPHINXDOC_PATH, "_static/gimli_logo.pdf")

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
# latex_use_parts = False

# If true, show page references after internal links.
latex_show_pagerefs = True

# 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

extradir = path.abspath(join(SPHINXDOC_PATH, "_static"))  # .replace("\\", "/")

latex_elements = {
    # The paper size ("letterpaper" or "a4paper").
    "papersize": "a4paper",

    # The font size ("10pt", "11pt" or "12pt").
    "pointsize": "11pt",

    # Additional stuff for the LaTeX preamble.
    "preamble":
    "\\usepackage{amsfonts}\n\
    \\usepackage{amssymb}\n\
    \\usepackage{graphicx}\n\
    \\usepackage{amsmath}\n\
    \\usepackage{bm}\n\
    \\usepackage{pslatex}\n\
    \\graphicspath{{" + SPHINXDOC_PATH + "}}"
}

if sphinx.__version__.startswith("1.3"):
    latex_elements["preamble"] += \
        "\\RequirePackage{fixltx2e}\n\
     \\MakeRobust\\DUspan\n"

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual])
latex_documents = [("documentation", "gimli.tex", "GIMLi Documentation",
                    r"Carsten Rücker, Thomas Günther \& Florian Wagner",
                    "manual")]

try:
    pngmath_latex_preamble  # check whether this is already defined
except NameError:
    pngmath_latex_preamble = ""

pngmath_latex_preamble = "\
        \\usepackage{amsfonts}\n\
        \\usepackage{amssymb}\n\
        \\usepackage{amsmath}\n\
        \\usepackage{bm}\n\
        \\usepackage{pslatex}\n"

# latex.add_macro("\\newcommand{\\arr}[1]{\\ensuremath{\\textbf{#1}}}")

_mathpng_tempdir = DOC_BUILD_DIR + "mathtmp"

staticpath = os.path.abspath(join(SPHINXDOC_PATH, "_static"))
latex_additional_macros = open(join(staticpath, "mylatex-commands.sty"))

mathjax_latex_preamble = ""

LatexCommandTranslator = {}
LatexCommandTranslator["mathDictionary"] = {}
LatexCommandTranslator["commandDictionary"] = {}
LatexCommandTranslator["command1Dictionary"] = {}

trans = LatexCommandTranslator

for macro in latex_additional_macros:
    # used when building latex and pdf versions
    latex_elements["preamble"] += macro + "\n"
    # used when building html version
    pngmath_latex_preamble += macro + "\n"

    mathOperator = re.search("\\\\DeclareMathOperator{\\\\([A-Za-z]*)}{(.*)}",
                             macro)
    if mathOperator:
        LatexCommandTranslator["mathDictionary"][mathOperator.group(
            1)] = mathOperator.group(2).replace("\\", "\\\\")

    newCommand = re.search("\\\\newcommand{\\\\([A-Za-z]*)}{(.*)}", macro)
    if newCommand:
        LatexCommandTranslator["commandDictionary"][newCommand.group(
            1)] = newCommand.group(2).replace("\\", "\\\\")
    newCommand = re.search("\\\\renewcommand{\\\\([A-Za-z]*)}{(.*)}", macro)
    if newCommand:
        LatexCommandTranslator["commandDictionary"][newCommand.group(
            1)] = newCommand.group(2).replace("\\", "\\\\")

    newCommand = re.search("\\\\newcommand{\\\\([A-Za-z]*)}\\[1\\]{(.*)}",
                           macro)
    if newCommand:
        LatexCommandTranslator["command1Dictionary"][newCommand.group(
            1)] = newCommand.group(2).replace("\\", "\\\\")
    newCommand = re.search("\\\\renewcommand{\\\\([A-Za-z]*)}\\[1\\]{(.*)}",
                           macro)
    if newCommand:
        LatexCommandTranslator["command1Dictionary"][newCommand.group(
            1)] = newCommand.group(2).replace("\\", "\\\\")

latex_additional_macros.close()

plot2rst_commandTranslator = LatexCommandTranslator

# -- Options for manual page output -------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [("index", "GIMLi", "GIMLi Documentation", ["GIMLi Group"], 1)]

# If true, show URL addresses after external links.
# man_show_urls = 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 = [
    ("index", "GIMLi", "GIMLi Documentation", "GIMLi Group", "GIMLi",
     "Geophysical Inversion and Modelling Library", "Miscellaneous"),
]

# Documents to append as an appendix to all manuals.
# texinfo_appendices = []

# If false, no module index is generated.
# texinfo_domain_indices = True

# How to display URL addresses: "footnote", "no", or "inline".
texinfo_show_urls = "footnote"

# -- Options for pybtex output ------------------------------------------------
# load our plugins for manual bibstyle

# temporary disable due to python3 pybtex quirks
for dist in pkg_resources.find_distributions(SPHINXDOC_PATH +
                                             "/_templates/pybtex_plugins/"):
    pkg_resources.working_set.add(dist)

# End pybtex stuff

# -- Options for doxylink -----------------------------------------------------
doxylink = {"gimliapi": (join(DOXY_BUILD_DIR, "gimli.tag"), "https://www.pygimli.org/gimliapi")}

# Create HTML table
from bib2html import write_html
publications = write_html()

################################################################################################
# Extra call to create small gallery of all already made tutorials and examples in the sidebar.
################################################################################################
make_gallery(os.path.abspath(SPHINXDOC_PATH), os.path.abspath(DOC_BUILD_DIR))

# Add carousel to start page
from paper_carousel import showcase
random.shuffle(showcase) # mix it up
html_context = {
    "showcase": showcase,
    "publications": publications,
    "default_mode": "light"
}

srclink_project = "https://github.com/gimli-org/gimli"
srclink_src_path = "doc/"
srclink_branch = "dev"

# New docstring parsing using Napoleon instead of numpydoc
# The monkeypatch detects draw or show commands
from sphinx.ext.napoleon import NumpyDocstring

def monkeypatch(self, section: str, use_admonition: bool):
    lines = self._strip_empty(self._consume_to_next_section())
    lines = self._dedent(lines)
    all_lines = " ".join(lines)
    if ("show" in all_lines or "draw" in all_lines) and \
        "Example" in section and ".. plot::" not in all_lines:
        header = ".. plot::\n\n"
        lines = self._indent(lines, 3)
    else:
        header = ".. rubric:: %s" % section
    if lines:
        return [header, ""] + lines + [""]
    else:
        return [header, ""]

NumpyDocstring._parse_generic_section = monkeypatch

# Napoleon settings
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = True
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = False
napoleon_use_admonition_for_examples = False
napoleon_use_admonition_for_notes = False
napoleon_use_admonition_for_references = False
napoleon_use_ivar = True
napoleon_use_param = True
napoleon_use_rtype = True

# Bibtex settings
bibtex_bibfiles = ["gimliuses.bib", "libgimli.bib", "references.bib"]
bibtex_reference_style = "author_year"