add boilerplate read the docs

.github/workflows/docs_pages.yml

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+name: BiRD-documentation
+
+on:
+  push:
+    branches: [ sphinx ]
+    paths:
+      - 'docs/**'
+      - '.github/workflows/docs_pages.yml'
+
+jobs:
+
+  build_docs:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.10
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install sphinx sphinx_rtd_theme sphinx-autoapi
+
+      - name: Build documentation
+        run: |
+          cd docs
+          make html
+
+      - name: deploy
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html
+          force_orphan: true
+          full_commit_message: ${{ github.event.head_commit.message }}
+
+

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+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 $(SPHINXOPTS).
+%: Makefile
+	rm -rf _build
+	rm -rf source/_autosummary
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+github: html
+	-git branch -D gh-pages
+	-git push origin --delete gh-pages
+	ghp-import -n -b gh-pages -m "Update documentation" ./_build/html
+	git checkout gh-pages
+	git push --set-upstream origin gh-pages
+	git checkout ${BRANCH}

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=source
+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%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/_templates/layout.html

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+{% extends "!layout.html" %}
+
+{% block menu %}
+    {{ super() }}
+        <p class="caption">
+            <span class="caption-text">Indices</span>
+        </p>
+        <ul>
+    <li class="toctree-l1"><a href= "{{pathto('genindex.html', 1)}}">Everything</a></li>
+    <li class="toctree-l1"><a href= "{{pathto('py-modindex.html', 1)}}">Module Index</a></li>
+    </ul>
+
+    {% if menu_links %}
+        <p class="caption">
+            <span class="caption-text">External links</span>
+        </p>
+        <ul>
+            {% for text, link in menu_links %}
+                <li class="toctree-l1"><a href="{{ link }}">{{ text }}</a></li>
+            {% endfor %}
+        </ul>
+    {% endif %}
+{% endblock %}
+
+{% block htmltitle %}
+    {% if title == '' or title == 'Home' %}
+        <title>{{ docstitle|e }}</title>
+    {% else %}
+        <title>{{ title|striptags|e }}{{ titlesuffix }}</title>
+    {% endif %}
+{% endblock %}

docs/source/_templates/notused_packages.rst_t

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+{%- macro automodule(modname, options) -%}
+.. automodule:: {{ modname }}
+{%- for option in options %}
+   :{{ option }}:
+{%- endfor %}
+{%- endmacro %}
+
+{%- macro toctree(docnames) -%}
+.. toctree::
+   :maxdepth: {{ maxdepth }}
+{% for docname in docnames %}
+   {{ docname }}
+{%- endfor %}
+{%- endmacro %}
+
+{%- if is_namespace %}
+{{- [pkgname, "namespace"] | join(" ") | e | heading }}
+{% else %}
+{{- [pkgname, "package"] | join(" ") | e | heading }}
+{% endif %}
+
+{%- if is_namespace %}
+.. py:module:: {{ pkgname }}
+{% endif %}
+
+{%- if modulefirst and not is_namespace %}
+{{ automodule(pkgname, automodule_options) }}
+{% endif %}
+
+{%- if subpackages %}
+Subpackages
+-----------
+
+{{ toctree(subpackages) }}
+{% endif %}
+
+{%- if submodules %}
+Submodules
+----------
+{% if separatemodules %}
+{{ toctree(submodules) }}
+{% else %}
+{%- for submodule in submodules %}
+{% if show_headings %}
+{{- [submodule, "module"] | join(" ") | e | heading(2) }}
+{% endif %}
+{{ automodule(submodule, automodule_options) }}
+{% endfor %}
+{%- endif %}
+{%- endif %}
+
+# https://github.com/sphinx-doc/sphinx/blob/master/sphinx/templates/apidoc

docs/source/acknowledgments.rst

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+Quick start
+=====
+
+
+.. _installation:
+
+Installation
+------------
+
+To use the functions include this import:
+
+.. code-block:: console
+
+   import bird
+
+Examples
+----------------
+
+For example:
+
+>>> import bird
+

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+import os
+import sys
+# Need this so sphinx can find lumache.py. Change is .py files are elsewhere than root.
+sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath('../../bird'))
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+with open(os.path.join(here, '..', '..',  "bird", "version.py"), encoding="utf-8") as f:
+    version = f.read()
+version = version.split("=")[-1].strip().strip('"').strip("'")
+
+# -- Project information
+
+project = "Bio Reactor Design (BiRD)"
+copyright = '2024'
+author = 'NREL'
+
+release = version
+version = version
+
+# -- General configuration
+
+extensions = [
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+#    'autoapi.extension',
+#    'sphinxcontrib.apidoc',
+]
+
+#autoapi_type = 'python'
+#autoapi_dirs = ['../../bird']
+
+#apidoc_module_dir = '../../src'
+#apidoc_output_dir = '.'
+#apidoc_excluded_paths = ['tests']
+#apidoc_separate_modules = True
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+}
+intersphinx_disabled_domains = ['std']
+
+templates_path = ['_templates']
+
+# -- Options for HTML output
+
+html_theme = 'sphinx_rtd_theme'
+
+# -- Options for EPUB output
+epub_show_urls = 'footnote'
+
+html_context = {
+    "display_github": True, # Integrate GitHub
+    "github_repo": "NREL/BioReactorDesign", # Repo name
+    "github_version": "main", # Version
+    "conf_py_path": "docs/source/", # Path in the checkout to the docs root
+}
+
+# -- Options for HTML output -------------------------------------------------
+
+html_short_title = "bird-doc"
+html_show_sourcelink = False
+html_show_sphinx = True
+html_show_copyright = True
+
+# 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']
+repository_url = f"https://github.com/NREL/BioReactorDesign"
+html_context = {
+    "menu_links": [
+        (
+            '<i class="fa fa-github fa-fw"></i> Source Code',
+            repository_url,
+        ),
+        (
+            '<i class="fa fa-book fa-fw"></i> License',
+            f"{repository_url}/blob/main/LICENSE",
+        ),
+    ],
+}

docs/source/contribute.rst

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+Quick start
+=====
+
+
+.. _installation:
+
+Installation
+------------
+
+To use the functions include this import:
+
+.. code-block:: console
+
+   import bird
+
+Examples
+----------------
+
+For example:
+
+>>> import bird
+

docs/source/index.rst

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+Bio Reactor Design (BiRD)
+===================================
+
+`BiRD` is ...
+
+.. note::
+
+   This project is under active development.
+
+
+.. toctree::
+   :hidden:
+
+   quickstart
+   meshing
+   preprocess
+   postprocess
+   contribute
+   references
+   acknowledgments

docs/source/meshing.rst

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+Quick start
+=====
+
+
+.. _installation:
+
+Installation
+------------
+
+To use the functions include this import:
+
+.. code-block:: console
+
+   import bird
+
+Examples
+----------------
+
+For example:
+
+>>> import bird
+

docs/source/postprocess.rst

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+Quick start
+=====
+
+
+.. _installation:
+
+Installation
+------------
+
+To use the functions include this import:
+
+.. code-block:: console
+
+   import bird
+
+Examples
+----------------
+
+For example:
+
+>>> import bird
+