DOCS: improved documentation using citet and citep for references, ma…

…kefiles for unix and windows to avoid having to use tox, use pydata theme rather than read the docs and improve docstrings for classes SIES and ES. Add badges for project visibility.

.gitignore

@@ -176,4 +176,7 @@ poetry.toml
 # LSP config files
 pyrightconfig.json
 
+# For the documentation
+_autosummary
+
 # End of https://www.toptal.com/developers/gitignore/api/python

README.md

@@ -1,8 +1,15 @@
 Iterative Ensemble Smoother
 ===========================
 
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/equinor/iterative_ensemble_smoother/blob/main/COPYING)
+[![Stars](https://img.shields.io/github/stars/equinor/iterative_ensemble_smoother.svg?style=social&label=Star&maxAge=2592000)](https://github.com/equinor/iterative_ensemble_smoother/stargazers)
+[![Python](https://img.shields.io/pypi/pyversions/iterative_ensemble_smoother.svg)](https://pypi.org/pypi/iterative_ensemble_smoother)
+[![PyPI](https://img.shields.io/pypi/v/iterative_ensemble_smoother.svg)](https://pypi.org/pypi/iterative_ensemble_smoother)
+[![Downloads](https://static.pepy.tech/badge/iterative_ensemble_smoother)](https://pepy.tech/project/iterative_ensemble_smoother)
+[![Build Status](https://github.com/equinor/iterative_ensemble_smoother/actions/workflows/upload_to_pypi.yml/badge.svg)](https://github.com/equinor/iterative_ensemble_smoother/actions/workflows/main.yml)
 [![Precommit: enabled](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![docs](https://readthedocs.org/projects/iterative_ensemble_smoother/badge/?version=latest&style=plastic)](https://iterative-ensemble-smoother.readthedocs.io/)
 
@@ -21,31 +28,9 @@ pip install iterative_ensemble_smoother
 
 ## Usage
 
-The following illustrates usage but does not actually create the inputs and can not be run.
+**iterative_ensemble_smoother** mainly implements `SIES` and `ESMDA` classes. Check out
+the examples section to see how to use them.
 
-The example below illustrates the usage of the package.
-Note that it does not create the necessary inputs and cannot be run directly.
-For complete information and runnable examples, please refer to [the documentation](http://iterative_ensemble_smoother.rtfd.io).
-
-```python
-import iterative_ensemble_smoother as ies
-
-# `prior` is a matrix of size (num_params, ensemble_size).
-# In geostatistical applications, it typically consists of Gaussian random fields
-# that model rock properties like porosities and permeabilities.
-
-# `response_ensemble` is a matrix of size (num_obs, ensemble_size) and is
-# generated by running a dynamical model, such as a flow simulator.
-# In geostatistical applications, this is typically a porous flow simulator like Eclipse or OPM flow.
-
-# `obs_errors` and `obs_values` are 1D array of size `num_obs` that hold observations from real-life
-# sensors and their uncertainty specifications.
-# In geostatistical applications, the observations are typically pressures, temperatures, production rates etc.
-
-smoother = ies.ES()
-smoother.fit(response_ensemble, obs_errors, obs_values)
-posterior = smoother.update(prior)
-```
 
 ## Building from source
 
@@ -57,7 +42,7 @@ cd iterative_ensemble_smoother
 pip install .
 ```
 
-### Building the documentation
+## Building the documentation
 
 ```bash
 apt install pandoc # Pandoc is required to build the documentation.

docs/source/_templates/autosummary/base.rst

@@ -0,0 +1,8 @@
+..
+   Template for the html base rendering
+
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}

docs/source/_templates/autosummary/class.rst

@@ -0,0 +1,18 @@
+..
+   Template for the html class rendering
+
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :private-members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+   {% endblock %}
+
+   .. rubric:: {{ _('Methods definition') }}

docs/source/_templates/autosummary/module.rst

@@ -0,0 +1,64 @@
+..
+   Template for the html module rendering
+
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Module Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+   {% for item in classes %}
+      :template: class.rst
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/source/api.rst

@@ -1,10 +1,11 @@
-API reference
+.. _api_ref:
+
+=============
+API Reference
 =============
 
-.. currentmodule:: iterative_ensemble_smoother
+.. automodule:: iterative_ensemble_smoother
 
-.. autoclass:: iterative_ensemble_smoother.SIES
-   :members:
+.. raw:: latex
 
-.. autoclass:: iterative_ensemble_smoother.ESMDA
-   :members:
+    \clearpage

docs/source/bibliography.rst

@@ -2,3 +2,5 @@ Bibliography
 ============
 
 .. bibliography::
+   :all:
+   :labelprefix: Bib-

docs/source/conf.py

@@ -1,26 +1,168 @@
+"""
+iterative_ensemble_smoother documentation build configuration file.
+"""
+import datetime
+import os
+import re
+import sys
 from subprocess import check_output
 
+import iterative_ensemble_smoother as ies
+
+package_path = os.path.abspath("..")
+sys.path.insert(0, package_path)
+
 project = "iterative_ensemble_smoother"
-copyright = "2022, Equinor"
 author = "Equinor"
-release = "0.1.1"
-
+copyright = f"2022-{datetime.datetime.today().year}, {author}"
+# The default replacements for |version| and |release|, also used in various
+# other places throughout the built documents.
+version = re.sub(r"\.dev.*$", r".dev", ies.__version__)
+release = version
 
+# convert the python file to a notebook
 check_output(["jupytext", "Polynomial.py", "-o", "Polynomial.ipynb"])
 
+# Do the same for this file
 check_output(["jupytext", "Oscillator.py", "-o", "Oscillator.ipynb"])
 
-
+# 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.doctest",
-    "nbsphinx",
+    "sphinx.ext.napoleon",  # autodoc understands numpy docstrings
+    "sphinx.ext.autodoc",  # Core library for html generation from docstrings
+    "sphinx.ext.autosummary",  # Create neat summary tables
+    "sphinx.ext.doctest",  # Test snippets in the documentation
+    "sphinx.ext.viewcode",  # Add links to highlighted source code
+    "sphinx.ext.intersphinx",  # Link to other projects’ documentation
+    "sphinx.ext.autosectionlabel",  # Allow reference sections using its title
+    # allows BibTeX citations to be inserted into documentation generated by Sphinx
     "sphinxcontrib.bibtex",
+    "jupyter_sphinx",
     "numpydoc",
+    "m2r2",  # compatibility with markdown
+    "myst_nb",  # to include jupyter notebooks
 ]
-bibtex_bibfiles = ["refs.bib"]
+
+# -----------------------------------------------------------------------------
+# Autosummary
+# -----------------------------------------------------------------------------
+
+# autosummaries from source-files
+autosummary_generate = True
+# dont show __init__ docstring
+autoclass_content = "class"
+# sort class members
+autodoc_member_order = "groupwise"
+# autodoc_member_order = 'bysource'
+
+autosummary_generate = True  # Turn on sphinx.ext.autosummary
+# This is because numpydoc screew up with autosummary
+# numpydoc_show_class_members=False
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = True
+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
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# Add any external modules you want to refer to in the docs here.
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+}
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+# source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md", ".ipynb"]
+
+# The encoding of source files.
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = "index"
+
+# 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"
-html_theme = "sphinx_rtd_theme"
 
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ["build", "_templates/*.rst'", "Thumbs.db", ".DS_Store"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# -----------------------------------------------------------------------------
+# 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"
+html_theme = "pydata_sphinx_theme"
+
+# TODO: when ies gets a nice logo
+# html_logo = '_static/logo.svg'
+# html_favicon = '_static/favicon.ico'
+
+# 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 = {
+    # "google_analytics_id": "UA-140243896-1",
+    "show_prev_next": False,
+    "github_url": "https://github.com/equinor/iterative_ensemble_smoother",
+    "icon_links": [
+        {
+            "name": "Support",
+            "url": "https://github.com/equinor/iterative_ensemble_smoother/issues",
+            "icon": "fa fa-comment fa-fw",
+        },
+        # {
+        #     "name": "The Paper",
+        #     "url": "https://doi.org/10.21105/joss.01450",
+        #     "icon": "fa fa-file-text fa-fw",
+        # },
+    ],
+}
+
+# Title displayed on the html page
+html_title = "Iterative Ensemble Smoother"
+
+# -----------------------------------------------------------------------------
+# Bibliography
+# -----------------------------------------------------------------------------
+
+bibtex_bibfiles = ["./refs.bib"]
+bibtex_default_style = "unsrt"
+bibtex_reference_style = "author_year"
+suppress_warnings = ["bibtex.duplicate_citation", "autosectionlabel.*"]
 
 numpydoc_class_members_toctree = False
+
+# -----------------------------------------------------------------------------
+# Myst configuration
+# -----------------------------------------------------------------------------
+
+# see https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#syntax-mathjax
+# for math parsing in jupyter notebooks
+myst_enable_extensions = [
+    "amsmath",
+    "dollarmath",
+]

docs/source/examples.rst

@@ -7,3 +7,5 @@ Example Usage
 
    Polynomial
    Oscillator
+
+* :ref:`genindex`

docs/source/glossary.rst

@@ -17,8 +17,8 @@ Glossary
 
     forward model
          A forward model maps model parameters to predicted measurements
-         (:term:`prediction`). See, for instance, :cite:`evensen2018analysis` and
-         :cite:`evensen2019efficient`.
+         (:term:`prediction`). See, for instance, :cite:t:`evensen2018analysis` and
+         :cite:t:`evensen2019efficient`.
 
     error function
         The error function, or erf_, is a function that for a