# -*- coding: utf-8 -*- # # Veros documentation build configuration file, created by # sphinx-quickstart on Tue Mar 7 23:56:46 2017. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # 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 sys sys.path.insert(0, os.path.abspath('..')) sys.path.insert(0, os.path.abspath('_3rdparty')) # -- 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. import sphinx_fontawesome extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.viewcode', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.intersphinx', 'sphinx_fontawesome', 'IPython.sphinxext.ipython_console_highlighting', 'IPython.sphinxext.ipython_directive', ] # 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_suffix = ['.rst', '.md'] source_suffix = '.rst' # The master toctree document. master_doc = 'index' # General information about the project. project = u'Veros' copyright = u'2017-2023, The Veros Team, NBI Copenhagen' author = u'The Veros Team, NBI Copenhagen' # 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. # from veros import __version__ as veros_version if "0+untagged" in veros_version: veros_version = "main" # The short X.Y version. version = veros_version # The full version, including alpha/beta/rc tags. release = veros_version # 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 = ['_build', 'Thumbs.db', '.DS_Store', '_generated'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # Redefine the default output path of ipython directive @savefig ipython_savefig_dir = '_generated' # -- 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 = "furo" # 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 = { "light_logo": "veros-logo-400px.png", "dark_logo": "veros-logo-bright-400px.png", "sidebar_hide_name": True, } html_css_files = [ "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.1.1/css/all.min.css" ] # 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 = 'veros_doc' # -- 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 = [ (master_doc, 'veros.tex', u'Veros Documentation', u'The Veros Team', 'manual'), ] # -- 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, 'Veros', u'Veros Documentation', [author], 1) ] # -- 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, 'Veros', u'Veros Documentation', author, 'Veros', 'The versatile ocean simulator in pure Python', 'Miscellaneous'), ] # -- Options for autodoc -------------------------------------------------- autodoc_member_order = "bysource" autodoc_default_options = {"show-inheritance": None} autodoc_mock_imports = ["loguru", "numpy", "h5netcdf", "scipy"] # -- Options for intersphinx ---------------------------------------------- intersphinx_mapping = {'python': ('https://docs.python.org/3', None)} # -- Custom directives ---------------------------------------------------- from os.path import basename try: from StringIO import StringIO except ImportError: from io import StringIO from docutils import nodes, statemachine from docutils.parsers.rst import Directive, directives class ExecDirective(Directive): """Execute the specified python code and insert the output into the document""" has_content = True def run(self): old_stdout, sys.stdout = sys.stdout, StringIO() tab_width = self.options.get('tab-width', self.state.document.settings.tab_width) source = self.state_machine.input_lines.source(self.lineno - self.state_machine.input_offset - 1) try: exec('\n'.join(self.content)) text = sys.stdout.getvalue() lines = statemachine.string2lines(text, tab_width, convert_whitespace=True) self.state_machine.insert_input(lines, source) return [] except Exception: warn_text = "Unable to execute python code at %s:%d" % (basename(source), self.lineno) warning = self.state_machine.reporter.warning(warn_text) return [warning, nodes.error(None, nodes.paragraph(text=warn_text), nodes.paragraph(text=str(sys.exc_info()[1])))] finally: sys.stdout = old_stdout class ClickDirective(Directive): """Execute the specified click command and insert the output into the document""" required_arguments = 1 optional_arguments = 0 option_spec = { 'args': directives.unchanged } has_content = False def run(self): import importlib import shlex from click.testing import CliRunner arg = self.arguments[0] options = shlex.split(self.options.get('args', '')) try: modname, funcname = arg.split(':') except ValueError: raise self.error('run-click argument must be "module:function"') try: mod = importlib.import_module(modname) func = getattr(mod, funcname) runner = CliRunner() with runner.isolated_filesystem(): result = runner.invoke(func, options) text = result.output if result.exit_code != 0: raise RuntimeError('Command exited with non-zero exit code; output: "%s"' % text) node = nodes.literal_block(text=text) node['language'] = 'text' return [node] except Exception: warn_text = "Error while running command %s %s" % (arg, ' '.join(map(shlex.quote, options))) warning = self.state_machine.reporter.warning(warn_text) return [warning, nodes.error(None, nodes.paragraph(text=warn_text), nodes.paragraph(text=str(sys.exc_info()[1])))] def setup(app): app.add_directive('exec', ExecDirective) app.add_directive('run-click', ClickDirective)