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@paquiteau
paquiteau committed Feb 16, 2024
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169 changes: 83 additions & 86 deletions docs/source/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,56 +9,56 @@
# 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.
sys.path.insert(0, os.path.abspath('../..'))
sys.path.insert(0, os.path.abspath("../.."))

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

# General information about the project.
project = 'modopt'
project = "modopt"

mdata = metadata(project)
author = mdata['Author']
version = mdata['Version']
copyright = '2020, {}'.format(author)
gh_user = 'sfarrens'
author = mdata["Author"]
version = mdata["Version"]
copyright = "2020, {}".format(author)
gh_user = "sfarrens"

# If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = '3.3'
needs_sphinx = "3.3"

# 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.autodoc',
'sphinx.ext.autosummary',
'sphinx.ext.coverage',
'sphinx.ext.doctest',
'sphinx.ext.ifconfig',
'sphinx.ext.intersphinx',
'sphinx.ext.mathjax',
'sphinx.ext.napoleon',
'sphinx.ext.todo',
'sphinx.ext.viewcode',
'sphinxawesome_theme',
'sphinxcontrib.bibtex',
'myst_parser',
'nbsphinx',
'nbsphinx_link',
'numpydoc',
"sphinx_gallery.gen_gallery"
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"sphinx.ext.coverage",
"sphinx.ext.doctest",
"sphinx.ext.ifconfig",
"sphinx.ext.intersphinx",
"sphinx.ext.mathjax",
"sphinx.ext.napoleon",
"sphinx.ext.todo",
"sphinx.ext.viewcode",
"sphinxawesome_theme",
"sphinxcontrib.bibtex",
"myst_parser",
"nbsphinx",
"nbsphinx_link",
"numpydoc",
"sphinx_gallery.gen_gallery",
]

# Include module names for objects
add_module_names = False

# Set class documentation standard.
autoclass_content = 'class'
autoclass_content = "class"

# Audodoc options
autodoc_default_options = {
'member-order': 'bysource',
'private-members': True,
'show-inheritance': True
"member-order": "bysource",
"private-members": True,
"show-inheritance": True,
}

# Generate summaries
Expand All @@ -69,17 +69,17 @@

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
source_suffix = ['.rst', '.md']
source_suffix = [".rst", ".md"]

# The master toctree document.
master_doc = 'index'
master_doc = "index"

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

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'default'
pygments_style = "default"

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True
Expand All @@ -88,7 +88,7 @@

# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'sphinxawesome_theme'
html_theme = "sphinxawesome_theme"
# html_theme = 'sphinx_book_theme'

# Theme options are theme-specific and customize the look and feel of a theme
Expand All @@ -101,11 +101,10 @@
"breadcrumbs_separator": "/",
"show_prev_next": True,
"show_scrolltop": True,

}
html_collapsible_definitions = True
html_awesome_headerlinks = True
html_logo = 'modopt_logo.jpg'
html_logo = "modopt_logo.jpg"
html_permalinks_icon = (
'<svg xmlns="http://www.w3.org/2000/svg" '
'viewBox="0 0 24 24">'
Expand All @@ -118,7 +117,7 @@
)
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
html_title = '{0} v{1}'.format(project, version)
html_title = "{0} v{1}".format(project, version)

# A shorter title for the navigation bar. Default is the same as html_title.
# html_short_title = None
Expand All @@ -134,7 +133,7 @@

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
html_last_updated_fmt = '%d %b, %Y'
html_last_updated_fmt = "%d %b, %Y"

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
Expand All @@ -147,7 +146,6 @@
html_show_copyright = True



# -- Options for Sphinx Gallery ----------------------------------------------

sphinx_gallery_conf = {
Expand All @@ -157,17 +155,16 @@
}



# -- Options for nbshpinx output ------------------------------------------


# Custom fucntion to find notebooks, create .nblink files and update the
# notebooks.rst file
def add_notebooks(nb_path='../../notebooks'):
def add_notebooks(nb_path="../../notebooks"):

print('Looking for notebooks')
nb_ext = '.ipynb'
nb_rst_file_name = 'notebooks.rst'
print("Looking for notebooks")
nb_ext = ".ipynb"
nb_rst_file_name = "notebooks.rst"
nb_link_format = '{{\n "path": "{0}/{1}"\n}}'

nbs = sorted([nb for nb in os.listdir(nb_path) if nb.endswith(nb_ext)])
Expand All @@ -176,35 +173,35 @@ def add_notebooks(nb_path='../../notebooks'):

nb_name = nb.rstrip(nb_ext)

nb_link_file_name = nb_name + '.nblink'
print('Writing {0}'.format(nb_link_file_name))
with open(nb_link_file_name, 'w') as nb_link_file:
nb_link_file_name = nb_name + ".nblink"
print("Writing {0}".format(nb_link_file_name))
with open(nb_link_file_name, "w") as nb_link_file:
nb_link_file.write(nb_link_format.format(nb_path, nb))

print('Looking for {0} in {1}'.format(nb_name, nb_rst_file_name))
with open(nb_rst_file_name, 'r') as nb_rst_file:
print("Looking for {0} in {1}".format(nb_name, nb_rst_file_name))
with open(nb_rst_file_name, "r") as nb_rst_file:
check_name = nb_name not in nb_rst_file.read()

if check_name:
print('Adding {0} to {1}'.format(nb_name, nb_rst_file_name))
with open(nb_rst_file_name, 'a') as nb_rst_file:
print("Adding {0} to {1}".format(nb_name, nb_rst_file_name))
with open(nb_rst_file_name, "a") as nb_rst_file:
if list_pos == 0:
nb_rst_file.write('\n')
nb_rst_file.write(' {0}\n'.format(nb_name))
nb_rst_file.write("\n")
nb_rst_file.write(" {0}\n".format(nb_name))

return nbs


# Add notebooks
add_notebooks()

binder = 'https://mybinder.org/v2/gh'
binder_badge = 'https://mybinder.org/badge_logo.svg'
github = 'https://github.com/'
github_badge = 'https://badgen.net/badge/icon/github?icon=github&label'
binder = "https://mybinder.org/v2/gh"
binder_badge = "https://mybinder.org/badge_logo.svg"
github = "https://github.com/"
github_badge = "https://badgen.net/badge/icon/github?icon=github&label"

# Remove promts and add binder badge
nb_header_pt1 = r'''
nb_header_pt1 = r"""
{% if env.metadata[env.docname]['nbsphinx-link-target'] %}
{% set docpath = env.metadata[env.docname]['nbsphinx-link-target'] %}
{% else %}
Expand All @@ -220,18 +217,18 @@ def add_notebooks(nb_path='../../notebooks'):
}
</style>
'''
"""
nb_header_pt2 = (
r''' <p><div class="inline-block">'''
r'''<a href="{0}/{1}/{2}/'''.format(binder, gh_user, project) +
r'''master?filepath={{ docpath }}">''' +
r'''<img alt="Binder badge" src="{0}" '''.format(binder_badge) +
r'''style="vertical-align:text-bottom"></a></div>'''
r'''<div class="inline-block"><a href=''' +
r'''"{0}/{1}/{2}/blob/master/'''.format(github, gh_user, project) +
r'''{{ docpath }}"><img alt="GitHub badge" ''' +
r'''src="{0}" style="vertical-align:text-bottom">'''.format(github_badge) +
r'''</a></div></p>'''
r""" <p><div class="inline-block">"""
r"""<a href="{0}/{1}/{2}/""".format(binder, gh_user, project)
+ r"""master?filepath={{ docpath }}">"""
+ r"""<img alt="Binder badge" src="{0}" """.format(binder_badge)
+ r"""style="vertical-align:text-bottom"></a></div>"""
r"""<div class="inline-block"><a href="""
+ r""""{0}/{1}/{2}/blob/master/""".format(github, gh_user, project)
+ r"""{{ docpath }}"><img alt="GitHub badge" """
+ r"""src="{0}" style="vertical-align:text-bottom">""".format(github_badge)
+ r"""</a></div></p>"""
)

nbsphinx_prolog = nb_header_pt1 + nb_header_pt2
Expand All @@ -240,28 +237,28 @@ def add_notebooks(nb_path='../../notebooks'):

# Refer to the package libraries for type definitions
intersphinx_mapping = {
'python': ('http://docs.python.org/3', None),
'numpy': ('https://numpy.org/doc/stable/', None),
'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
'progressbar': ('https://progressbar-2.readthedocs.io/en/latest/', None),
'matplotlib': ('https://matplotlib.org', None),
'astropy': ('http://docs.astropy.org/en/latest/', None),
'cupy': ('https://docs-cupy.chainer.org/en/stable/', None),
'torch': ('https://pytorch.org/docs/stable/', None),
'sklearn': (
'http://scikit-learn.org/stable',
(None, './_intersphinx/sklearn-objects.inv')
"python": ("http://docs.python.org/3", None),
"numpy": ("https://numpy.org/doc/stable/", None),
"scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
"progressbar": ("https://progressbar-2.readthedocs.io/en/latest/", None),
"matplotlib": ("https://matplotlib.org", None),
"astropy": ("http://docs.astropy.org/en/latest/", None),
"cupy": ("https://docs-cupy.chainer.org/en/stable/", None),
"torch": ("https://pytorch.org/docs/stable/", None),
"sklearn": (
"http://scikit-learn.org/stable",
(None, "./_intersphinx/sklearn-objects.inv"),
),
'tensorflow': (
'https://www.tensorflow.org/api_docs/python',
"tensorflow": (
"https://www.tensorflow.org/api_docs/python",
(
'https://github.com/GPflow/tensorflow-intersphinx/'
+ 'raw/master/tf2_py_objects.inv')
)

"https://github.com/GPflow/tensorflow-intersphinx/"
+ "raw/master/tf2_py_objects.inv"
),
),
}

# -- BibTeX Setting ----------------------------------------------

bibtex_bibfiles = ['refs.bib', 'my_ref.bib']
bibtex_default_style = 'alpha'
bibtex_bibfiles = ["refs.bib", "my_ref.bib"]
bibtex_default_style = "alpha"
8 changes: 4 additions & 4 deletions modopt/__init__.py
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Expand Up @@ -13,12 +13,12 @@
from modopt.base import *

try:
_version = version('modopt')
_version = version("modopt")
except Exception: # pragma: no cover
_version = 'Unkown'
_version = "Unkown"
warn(
'Could not extract package metadata. Make sure the package is '
+ 'correctly installed.',
"Could not extract package metadata. Make sure the package is "
+ "correctly installed.",
)

__version__ = _version
2 changes: 1 addition & 1 deletion modopt/base/__init__.py
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Expand Up @@ -9,4 +9,4 @@
"""

__all__ = ['np_adjust', 'transform', 'types', 'wrappers', 'observable']
__all__ = ["np_adjust", "transform", "types", "wrappers", "observable"]
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