Added documentation.

.readthedocs.yml

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+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  apt_packages:
+    - graphviz
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

docs/.gitignore

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+_autosummary/
+_build/

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_templates/class_custom.rst

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+{{ name | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ fullname }}
+    :members:
+    :show-inheritance:
+    :inherited-members:
+    :undoc-members:
+    :member-order: groupwise
+
+    {% block attributes %}
+    {% if attributes %}
+    .. rubric:: {{ _('Attributes') }}
+
+    .. autosummary::
+    {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block methods %}
+    {% if methods %}
+    .. rubric:: {{ _('Methods') }}
+
+    .. autosummary::
+    {% for item in methods %}
+      ~{{ name }}.{{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block dia %}
+    .. rubric:: {{ _('Inheritance Diagram') }}
+
+    .. inheritance-diagram:: {{ fullname }}
+    {% endblock %}
+

docs/_templates/function_custom.rst

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+{{ name | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ fullname }}

docs/_templates/module_custom.rst

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+{{ name | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+    {% block attributes %}
+    {% if attributes %}
+    .. rubric:: Module Attributes
+
+    .. autosummary::
+      :toctree:
+    {% for item in attributes %}
+      {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block functions %}
+    {% if functions %}
+    .. rubric:: {{ _('Functions') }}
+
+    .. autosummary::
+      :toctree:
+      :template: function_custom.rst
+    {% for item in functions %}
+      {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block classes %}
+    {% if classes %}
+    .. rubric:: {{ _('Classes') }}
+
+    .. autosummary::
+      :toctree:
+      :template: class_custom.rst
+    {% for item in classes %}
+      {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block exceptions %}
+    {% if exceptions %}
+    .. rubric:: {{ _('Exceptions') }}
+
+    .. autosummary::
+      :toctree:
+    {% for item in exceptions %}
+      {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block modules %}
+    {% if modules %}
+    .. rubric:: Modules
+
+    .. autosummary::
+       :toctree:
+       :template: module_custom.rst
+       :recursive:
+    {% for item in modules %}
+       {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+

docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# 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
+
+package_path = os.path.abspath('../')
+sys.path.insert(0, package_path)
+os.environ['PYTHONPATH'] = ';'.join((package_path, os.environ.get('PYTHONPATH', '')))
+
+# -- Project information -----------------------------------------------------
+
+project = 'fano'
+copyright = '2024, Roy T. Smart'
+author = 'Roy T. Smart'
+
+# -- General configuration ---------------------------------------------------
+
+# 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.napoleon',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.inheritance_diagram',
+    'sphinx.ext.viewcode',
+    'sphinxcontrib.bibtex',
+    'jupyter_sphinx',
+]
+autosummary_generate = True  # Turn on sphinx.ext.autosummary
+autosummary_imported_members = True
+autosummary_ignore_module_all = False
+# autoclass_content = 'both'
+autodoc_typehints = "description"
+
+graphviz_output_format = 'png'
+inheritance_graph_attrs = dict(rankdir='TB')
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# This pattern also affects html_static_path and html_extra_path.
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# -- 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 = 'pydata_sphinx_theme'
+
+# 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']
+
+html_theme_options = {
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/sun-data/fano",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        },
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/fano/",
+            "icon": "fa-brands fa-python",
+        },
+    ],
+}
+
+# https://github.com/readthedocs/readthedocs.org/issues/2569
+master_doc = 'index'
+
+bibtex_bibfiles = ['refs.bib']
+bibtex_default_style = 'plain'
+bibtex_reference_style = 'author_year'
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'matplotlib': ('https://matplotlib.org/stable', None),
+    'astropy': ('https://docs.astropy.org/en/stable/', None),
+}

docs/index.rst

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+Introduction
+============
+
+This package aims to compute the Fano factor and electron-hole pair creation
+energy for a silicon detector using a method similar to the one described in
+:cite:t:`Fraser1994`.
+
+API Reference
+=============
+
+.. autosummary::
+    :toctree: _autosummary
+    :template: module_custom.rst
+    :recursive:
+
+    fano
+
+
+References
+==========
+
+.. bibliography::
+
+|
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/refs.bib

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+@article{Fraser1994,
+title = {The X-ray energy response of silicon Part A. Theory},
+journal = {Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment},
+volume = {350},
+number = {1},
+pages = {368-378},
+year = {1994},
+issn = {0168-9002},
+doi = {https://doi.org/10.1016/0168-9002(94)91185-1},
+url = {https://www.sciencedirect.com/science/article/pii/0168900294911851},
+author = {G.W. Fraser and A.F. Abbey and A. Holland and K. McCarthy and A. Owens and A. Wells},
+abstract = {In this, the first part of a two-part study of the interaction of soft X-rays with silicon, motivated by the calibration requirements of CCD imaging spectrometers in astronomy, we describe a Monte Carlo model of X-ray energy loss whose products are the energy- and temperature-dependences of (i) W, the average energy required to create an electron-hole pair, and (ii) the Fano factor F, W and F have invariably been treated as material constants in previous analyses of Si X-ray detector performance. We show that in fact, at constant detector temperature T, W is an increasing function of X-ray energy for E < 0.5 keV while F is predicted to increase slowly with E. The temperature coefficient dW/dT has a calculated value ∼ 1 × 10−4 K−1 at a typical CCD operating temperature of 170 K. We discuss the practical implications of these results. Finally, we describe our separate calculations of the near-edge variation of CCD quantum detection efficiency arising from silicon K-shell Extended X-ray Absorption Fine Structure (EXAFS).}
+}