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WIP: Establish docs infrastructure #183

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17 changes: 11 additions & 6 deletions docs/conf.py
Original file line number Diff line number Diff line change
@@ -31,13 +31,13 @@
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.viewcode',
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
'sphinx.ext.napoleon'
]

# Removes the module name space in front of classes and functions
# i.e. porepy.ad.Scalar() -> Scalar()
add_module_names = False

# Add any paths that contain templates here, relative to this directory.
@@ -62,6 +62,10 @@
html_show_sourcelink = False
html_show_sphinx = False

html_theme_options = {
"show_toc_level": 4 # TODO
}

# -- Autodoc Settings -------------------------------------------------------------------------

# autoclass concatenates docs strings from init and class.
@@ -73,7 +77,7 @@
# orders the members of an object group wise, e.g. private, special or public methods
autodoc_member_order = "groupwise" # alphabetical-groupwise-bysource

# type hints will be shortened: porepy.grids.grid.Grid -> Grid
# type hints will be shortened:
autodoc_typehints_format = "short"

# default configurations for all autodoc directives
@@ -82,12 +86,12 @@
"special-members": False,
"private-members": False,
"show-inheritance": True,
"inherited-members": False,
"inherited-members": True,
"no-value": False
}

# uses type hints in signatures for e.g. linking (default)
autodoc_typehints = "signature"
autodoc_typehints = "none" #TODO "description"

# Avoid double appearance of documentation if child member has no docs
autodoc_inherit_docstrings = False
@@ -102,6 +106,7 @@
'numpy': ('https://numpy.org/doc/stable', None),
'scipy': ('https://docs.scipy.org/doc/scipy', None),
'matplotlib': ('https://matplotlib.org/stable', None),
'skimage': ('https://scikit-image.org/docs/stabe', None)
'skimage': ('https://scikit-image.org/docs/stabe', None),
"sklearn": ("https://scikit-learn.org/stable/", None),
}

30 changes: 0 additions & 30 deletions docs/darsia.corrections.rst

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61 changes: 0 additions & 61 deletions docs/darsia.corrections.shape.rst

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77 changes: 0 additions & 77 deletions docs/darsia.image.rst

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28 changes: 0 additions & 28 deletions docs/darsia.rst

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15 changes: 10 additions & 5 deletions docs/index.rst
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@@ -1,20 +1,25 @@
DarSIA
======

DarSIA, short for Darcy Scale Image Analysis Toolbox, is a research code aiming at quantitative image analysis for images of porous media applications. The Darcy scale is of particular interest, and thus physics upscaling lies at the heart of DarSIA.
DarSIA, short for Darcy Scale Image Analysis, is a research code aiming at quantitative image analysis for images of porous media applications. It provides a collection of algorithms and basic workflows for phyisical image processing. The Darcy scale is of particular interest, and thus physics upscaling lies at the heart of DarSIA.

The supported image data types include optical images (png, jpg, tif, ...), DICOM images, and simulation data (vtk, ... - anything that meshio can read). Preprocessing routines to transform and align images as well as routines for extracting physical information from images (e.g., concentrations) are provided.
Various image data types are supported, including optical images (png, jpg, tif, ...), DICOM images, and simulation data (vtk, and essentially any format readable by meshio). Preprocessing routines to transform and align images as well as routines for extracting physical information from images (e.g., concentrations) are provided.

News
====

The newest release is v.1.0

The DarSIA package
==================

DarSIA is divided into the following modules
DarSIA is divided into subpackages and modules. To navigate through its components follow the link:

.. toctree::
:maxdepth: 1
:titlesonly:

#darsia.corrections

source/darsia

Indices and tables
==================
7 changes: 0 additions & 7 deletions docs/modules.rst

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10 changes: 10 additions & 0 deletions docs/source/corrections/darsia.corrections.basecorrection.rst
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@@ -0,0 +1,10 @@
Base correction (:mod:`darsia.corrections.basecorrection`)
==========================================================

.. automodule:: darsia.corrections.basecorrection

.. rubric:: Classes

.. autosummary::

BaseCorrection
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@@ -1,8 +1,22 @@
darsia.corrections.color package
================================
Color corrections (:mod:`darsia.corrections.color`)
===================================================

Submodules
----------
.. currentmodule:: darsia.corrections.color

.. automodule:: darsia.corrections.color
:members:
:undoc-members:
:show-inheritance:

Color correction implementations
--------------------------------

.. autosummary::
:toctree: generated/

colorcorrection
experimentalcolorcorrection


darsia.corrections.color.colorcorrection module
-----------------------------------------------
@@ -19,11 +33,3 @@ darsia.corrections.color.experimentalcolorcorrection module
:members:
:undoc-members:
:show-inheritance:

Module contents
---------------

.. automodule:: darsia.corrections.color
:members:
:undoc-members:
:show-inheritance:
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