--- a
+++ b/Docs/conf.py
@@ -0,0 +1,387 @@
+# -- Project information -----------------------------------------------------
+import os
+import re
+import subprocess
+import sys
+from datetime import datetime
+from pathlib import Path
+
+sys.path.insert(0, os.path.abspath("exts"))
+sys.path.insert(0, os.path.abspath("tools"))
+
+
+current_year = os.environ.get("YEAR", datetime.now().year)
+
+
+project = "AMMR"
+copyright = f"{current_year}, AnyBody Technology"
+author = "AnyBody Technology"
+# language = "fr"  # For testing language translations
+
+
+def tagged_commit():
+    """Check if we are on a tagged commit"""
+    try:
+        subprocess.check_call(
+            ["git", "describe", "--tags", "--exact-match", "HEAD"],
+            stdout=subprocess.DEVNULL,
+            stderr=subprocess.DEVNULL,
+        )
+    except subprocess.CalledProcessError:
+        return False
+    else:
+        return True
+
+
+if tags.has("offline"):
+    # building offline version
+    pass
+
+
+if not tagged_commit() and not tags.has("offline"):
+    tags.add("draft")
+
+# `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = tags.has("draft")
+
+
+master_doc = "index"
+
+# -- 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.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.githubpages",
+    "myst_parser",
+    "ammr_directives",
+    "sphinxext.opengraph",
+    "sphinx_design",
+    "sphinx_togglebutton",
+    "sphinx_copybutton",
+
+    # "sphinxcontrib.youtube",
+    # "sphinx_copybutton",
+    # "sphinx_design",
+    # "sphinx_examples",
+    # "sphinx_tabs.tabs",
+    # "sphinx_togglebutton",
+    # "sphinxcontrib.bibtex",
+    # "sphinxext.opengraph",
+    # For the kitchen sink
+    # "sphinx.ext.todo",
+]
+
+
+myst_enable_extensions = [
+    "colon_fence",
+    "deflist",
+    "fieldlist",
+    "dollarmath",
+    "amsmath",
+    "html_image",
+    "substitution",
+    "attrs_inline",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+# templates_path = ["_templates"]
+
+
+source_suffix = [".rst", ".md"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [
+    "_build",
+    "README.md",
+    "Thumbs.db",
+    ".DS_Store",
+    "exts",
+    "auto_examples",
+    ".pixi",
+]
+
+# The name of the Pygments (syntax highlighting) style to use.
+highlight_language = "AnyScriptDoc"
+pygments_style = "AnyScript"
+
+ams_version = os.environ.get("AMS_VERSION", "8.1.0")
+if not re.match(r"^\d\.\d\.\d", ams_version):
+    raise ValueError("Wrong format for AMS version, environment variable")
+ams_version_short = ams_version.rpartition(".")[0]
+ams_version_x = ams_version_short + ".x"
+
+
+ammr_version = os.environ.get("AMMR_VERSION", None)
+if ammr_version is None:
+    AMMR_VERSION_RE = re.compile(r'.*AMMR_VERSION\s"(?P<version>.*)"')
+    with open("../AMMR.version.any") as fh:
+        match = AMMR_VERSION_RE.search(fh.read())
+        if match:
+            ammr_version = match.groupdict()["version"]
+        else:
+            raise Exception("Could not parse AMMR version")
+
+
+if not re.match(r"^\d\.\d\.\d", ammr_version):
+    raise ValueError("Wrong format for AMMR version, environment variable")
+
+ammr_version_short = ammr_version.rpartition(".")[0]
+
+rst_epilog = f"""
+
+.. |AMS| replace:: AnyBody Modeling System™
+.. |AMS_VERSION_X| replace:: {ams_version_x}
+.. |AMS_VERSION| replace:: {ams_version}
+.. |AMS_VERSION_SHORT| replace:: {ams_version_short}
+.. |AMMR_VERSION_SHORT| replace:: {ammr_version_short}
+.. |AMMR_VERSION| replace:: {ammr_version}
+.. |AMMR_DEMO_INST_DIR| replace:: :literal:`~/Documents/{ams_version_x}/AMMR.v{ammr_version}-Demo`
+.. |CURRENT_YEAR| replace:: {current_year}
+.. |WHAT_IS_NEW| replace:: :ref:`What's new in AMMR {ammr_version} <whats-new>`
+.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10527958.svg
+                 :target: https://doi.org/10.5281/zenodo.10527958
+"""
+
+myst_substitutions = {
+    "AMS": "AnyBody Modeling System™",
+    "AMS_VERSION_X": ams_version_x,
+    "AMS_VERSION": ams_version_x,
+    "AMS_VERSION_SHORT": ams_version_short,
+    "AMMR_VERSION_SHORT": ams_version_short,
+    "AMMR_VERSION": ammr_version,
+    "CURRENT_YEAR": current_year,
+    "AMMR_DEMO_INST_DIR": f"`~/Documents/{ams_version_x}/AMMR.v{ammr_version}-Demo`",
+    "DOI": "[![DOI image](https://zenodo.org/badge/DOI/10.5281/zenodo.10527958.svg)](https://doi.org/10.5281/zenodo.10527958)",
+    "WHAT_IS_NEW": f"{{ref}}`What's new in AMMR {ammr_version} <whats-new>`",
+    "WHAT_IS_NEW2": f"{{material-outlined}}`update;1em` New in AMMR {ammr_version}",
+}
+
+
+no_index = """
+.. meta::
+   :robots: noindex
+"""
+myst_html_meta = {}
+
+if tags.has("draft"):
+    rst_epilog = rst_epilog + no_index
+    myst_html_meta["robots"] = "noindex"
+
+github_doc_root = "https://github.com/AnyBody/ammr/tree/master/Docs"
+
+version = f"{ammr_version_short}"
+# The full version, including alpha/beta/rc tags.
+release = f"{ammr_version}"
+
+if tags.has("draft") and not release.endswith("beta"):
+    release = release + "-beta"
+
+
+
+
+
+# suppress_warnings = ["myst.domains", "ref.ref"]
+
+numfig = True
+
+
+
+# -- 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 = "sphinx_book_theme"
+# html_logo = "_static/logo-wide.svg"
+html_title = f"{project} v{release} Documentation"
+html_copy_source = False
+# html_favicon = "_static/logo-square.svg"
+html_last_updated_fmt = ""
+
+# html_sidebars = {
+#     "reference/blog/*": [
+#         "navbar-logo.html",
+#         "search-field.html",
+#         "ablog/postcard.html",
+#         "ablog/recentposts.html",
+#         "ablog/tagcloud.html",
+#         "ablog/categories.html",
+#         "ablog/archives.html",
+#         "sbt-sidebar-nav.html",
+#     ]
+# }
+# 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", "body/_static"]
+html_css_files = ["_static/custom.css"]
+
+
+html_logo = "_static/AMMR.svg"
+html_favicon = "_static/favicon.ico"
+
+
+html_theme_options = {
+    "path_to_docs": "Docs",
+    "repository_url": "https://github.com/anybody/ammr",
+    "repository_branch": "master",
+    "use_edit_page_button": True,
+    "use_source_button": True,
+    "use_issues_button": False,
+    "use_repository_button": True,
+    "use_download_button": False,
+
+    "home_page_in_toc": False,
+    "show_toc_level": 1,
+
+    "pygment_light_style": "AnyScript",
+    "pygment_dark_style": "stata-dark",
+
+
+    # "use_sidenotes": True,
+    # "announcement": (
+    #     "⚠️The latest release refactored our HTML, "
+    #     "so double-check your custom CSS rules!⚠️"
+    # ),
+    "logo": {
+        "image_dark": "_static/AMMR.svg",
+        # "text": html_title,  # Uncomment to try text with logo
+    },
+    "icon_links": [
+        # {
+        #     "name": "AnyBody Technology",
+        #     "url": "https://anybodytech.com/",
+        #     # "icon": "_static/ebp-logo.png",
+        #     "type": "local",
+        # },
+        # {
+        #     "name": "GitHub",
+        #     "url": "https://github.com/anybody/ammr",
+        #     "icon": "fa-brands fa-github",
+        # },
+    ],
+    # For testing
+    # "use_fullscreen_button": False,
+    # "home_page_in_toc": True,
+    # "extra_footer": "<a href='https://google.com'>Test</a>",  # DEPRECATED KEY
+    # "show_navbar_depth": 2,
+    # Testing layout areas
+    # "navbar_start": ["test.html"],
+    # "navbar_center": ["test.html"],
+    # "navbar_end": ["test.html"],
+    # "navbar_persistent": ["test.html"],
+    # "footer_start": ["test.html"],
+    # "footer_end": ["test.html"]
+}
+
+bibtex_bibfiles = ["references.bib"]
+# To test that style looks good with common bibtex config
+bibtex_reference_style = "author_year"
+bibtex_default_style = "plain"
+numpydoc_show_class_members = False  # for automodule:: urllib.parse stub file issue
+linkcheck_ignore = [
+    "http://someurl/release",  # This is a fake link
+    "https://doi.org",  # These don't resolve properly and cause SSL issues
+]
+
+
+
+intersphinx_mapping = {}
+if tags.has("offline"):
+    # Todo. Find a way to link to offline html versions.
+    intersphinx_mapping["tutorials"] = ("https://anyscript.org/tutorials/", None)
+else:
+    if tags.has("draft"):
+        intersphinx_mapping["tutorials"] = (
+            "https://anyscript.org/tutorials/beta/",
+            None,
+        )
+    else:
+        intersphinx_mapping["tutorials"] = ("https://anyscript.org/tutorials/", None)
+
+
+
+# sphinxext.opengraph
+# ogp_social_cards = {
+#     "image": "_static/logo-square.png",
+# }
+
+ogp_site_url = "https://anyscript.org/"
+ogp_site_name = "AMMR Documentation"
+ogp_image = "https://anyscript.org/ammr/_static/AMMR_Logo.png"
+ogp_use_first_image = True  # if not found defaults to 'ogp_image'
+
+
+# Generate gallery files
+import frontmatter
+import jinja2
+
+gallery = {}
+galleryfolders = [x for x in Path("Applications").iterdir() if x.is_dir()]
+for folder in galleryfolders:
+    gallery[folder] = []
+    for file in sorted(folder.glob("*.md"), key=lambda x: x.name.upper()):
+        post = frontmatter.load(file)
+        if "gallery_title" in post:
+            gallery[folder].append(
+                {
+                    "doc": file.with_suffix("").as_posix(),
+                    "title": post["gallery_title"],
+                    "image": post["gallery_image"],
+                }
+            )
+
+
+with open("Applications/gallery.txt.jinja2") as fh:
+    gallery_template = jinja2.Template(fh.read())
+
+for folder, section in gallery.items():
+    gallery_txt = folder / "gallery.txt"
+    content = gallery_template.render(examples=section)
+    with open(gallery_txt, encoding="utf8") as fh:
+        previous_content = fh.read()
+    if content != previous_content:
+        with open(gallery_txt, "w", encoding="utf8") as fh:
+            fh.write(content)
+
+# Run the python file "tools/generate_class_template_docs.py"
+# to generate the class template documentation
+
+import generate_class_template_docs
+
+generate_class_template_docs.run_all()
+
+
+user_agent = "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/120.0.0.0 Safari/537.36"
+
+linkcheck_ignore = [
+    r".*linkcheck_ignore",
+    "https://doi.org/10.1115/1.4037100",  # asme.org prevents the linkcheck
+    "https://doi.org/10.1115/1.4052115",  # asme.org prevents the linkcheck
+    "https://dx.doi.org/10.1115/1.4001678",  # asme.org prevents the linkcheck
+    "https://dx.doi.org/10.1115/1.4029258",  # asme.org prevents the linkcheck
+    "https://doi.org/10.1080/10255842.2020.1851367",  # tandfonline.com prevents the linkcheck
+    "https://dx.doi.org/10.1002/jor.20255",  # wiley.com prevents the linkcheck
+    "https://doi.org/10.1016/j.clinbiomech.2006.10.003",  # clinbiomech.com prevents the linkcheck
+    "https://doi.org/10.1002/jor.25267",  # wiley.com prevents the linkcheck
+    "https://web.archive.org*",  # web.archive.org is currently down due to hacking atacks
+    "https://doi.org/10.5281/zenodo.15094590", # version not released yet
+]
+
+linkcheck_allowed_redirects = {
+    "https://doi.org.*": ".*",
+    "https://dx.doi.org.*": ".*",
+    "https://www.anybodytech.com/download/anybodysetup.*": ".*",
+}
+
+def setup(app):
+   ...
\ No newline at end of file