Moved to doxygen.

.gitignore

-# Logs
-logs
-*.log
-npm-debug.log*
-yarn-debug.log*
-yarn-error.log*
-
-package-lock.json
-
-# Runtime data
-pids
-*.pid
-*.seed
-*.pid.lock
-
-# Directory for instrumented libs generated by jscoverage/JSCover
-lib-cov
-
-# Coverage directory used by tools like istanbul
-coverage
-
-# nyc test coverage
-.nyc_output
-
-# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
-.grunt
-
-# Bower dependency directory (https://bower.io/)
-bower_components
-
-# node-waf configuration
-.lock-wscript
-
-# Compiled binary addons (http://nodejs.org/api/addons.html)
-build/Release
-
-# Dependency directories
-node_modules/
-jspm_packages/
-
-# Typescript v1 declaration files
-typings/
-
-# Optional npm cache directory
-.npm
-
-# Optional eslint cache
-.eslintcache
-
-# Optional REPL history
-.node_repl_history
-
-# Output of 'npm pack'
-*.tgz
-
-# dotenv environment variable files
-.env*
-
-# gatsby files
-.cache/
-public
-
-# Mac files
-.DS_Store
-
-# Yarn
-yarn-error.log
-.pnp/
-.pnp.js
-# Yarn Integrity file
-.yarn-integrity

.gitlab-ci.yml

-image: eicweb.phy.anl.gov:4567/containers/eic_container/node:15.12
-
-stages:
-  - build
-  - deploy
-
-# http://docs.gitlab.com/ce/ci/yaml/README.html#cache
-cache:
-  paths:
-    - node_modules/
-
-pages:
-  stage: deploy
-  script:
-    #- wget https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/194563/artifacts/raw/doc/detector.md -O src/docs/detector.md
-    - npm install
-    - ./node_modules/.bin/gatsby build --prefix-paths
-  artifacts:
-    paths:
-      - public
-  retry:
-    max: 2

README.md

-# ATHENA Detector Documentation
-
-## Overview
-
-This is primarily used for rendering the `<documentation>` tags in the compact description xml files.
-The result of processing the compact detector description is accessed via a job artifact. 
-
-https://eicweb.phy.anl.gov/EIC/detectors/athena/-/jobs/194563/artifacts/raw/doc/detector.md
-

src/docs/detector.md → detector.md

-
 # Athena Detector 
+
+# Introduction 
   - https://eicweb.phy.anl.gov/EIC/detectors/athena.git 
   - https://eicweb.phy.anl.gov/EIC/detectors/ip6.git
   
-## Detector Subsystems
+# Detector Subsystems
 
-### IP Subsystems
+## IP Subsystems
 
     The interaction point subsystems are included before the central detector subsystems.
     This is becuase the IP subsystems, for exmaple the beampipe, will define paramters
@@ -28,7 +29,7 @@
 
 ### PID Detector Region Parameters
     
-## Main Constant Definitions
+# Main Constant Definitions
 
       The ip6 (or other ip) defines should be included first.
       These files have only a define tags.
@@ -284,11 +285,11 @@ The logic goes like this:
     
 ## Hadronic Calorimeter Parameters
     
-#### Material Thickness 
+### Material Thickness 
      
       - Single Layer Thickness (for both barrel and endcap)
     
       - Hcal Barrel Layers and computed Thickness
     
       - Hcal Endcap Layers and computed Thickness
-    
\ No newline at end of file
+    

LICENSE → doc/doxygen-awesome-sidebar-only-darkmode-toggle.css

+
+/**
+
+Doxygen Awesome
+https://github.com/jothepro/doxygen-awesome-css
+
 MIT License
 
-Copyright (c) 2020 Rocketseat
+Copyright (c) 2021 jothepro
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,3 +25,16 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
+
+*/
+
+@media screen and (min-width: 768px) {
+
+    #MSearchBox {
+        width: calc(var(--side-nav-fixed-width) - calc(2 * var(--spacing-medium)) - var(--searchbar-height) - 1px);
+    }
+
+    #MSearchField {
+        width: calc(var(--side-nav-fixed-width) - calc(2 * var(--spacing-medium)) - 66px - var(--searchbar-height));
+    }
+}

doc/doxygen-awesome-sidebar-only.css

+/**
+
+Doxygen Awesome
+https://github.com/jothepro/doxygen-awesome-css
+
+MIT License
+
+Copyright (c) 2021 jothepro
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+ */
+
+html {
+    /* side nav width. MUST be = `TREEVIEW_WIDTH`.
+     * Make sure it is wide enought to contain the page title (logo + title + version)
+     */
+    --side-nav-fixed-width: 340px;
+    --menu-display: none;
+
+    --top-height: 120px;
+}
+
+
+@media screen and (min-width: 768px) {
+    html {
+        --searchbar-background: var(--page-background-color);
+    }
+
+    #side-nav {
+        min-width: var(--side-nav-fixed-width);
+        max-width: var(--side-nav-fixed-width);
+        top: var(--top-height);
+    }
+
+    #nav-tree, #side-nav {
+        height: calc(100vh - var(--top-height)) !important;
+    }
+
+    #nav-tree {
+        padding: 0;
+    }
+
+    #top {
+        display: block;
+        border-bottom: none;
+        height: var(--top-height);
+        margin-bottom: calc(0px - var(--top-height));
+        max-width: var(--side-nav-fixed-width);
+        background: var(--side-nav-background);
+    }
+    #main-nav {
+        float: left;
+        padding-right: 0;
+    }
+
+    .ui-resizable-handle {
+        cursor: default;
+        width: 1px !important;
+        box-shadow: 0 calc(-2 * var(--top-height)) 0 0 var(--separator-color);
+    }
+
+    #nav-path {
+        position: fixed;
+        right: 0;
+        left: var(--side-nav-fixed-width);
+        bottom: 0;
+        width: auto;
+    }
+
+    #doc-content {
+        height: calc(100vh - 31px) !important;
+        padding-bottom: calc(3 * var(--spacing-large));
+        padding-top: calc(var(--top-height) - 80px);
+        box-sizing: border-box;
+        margin-left: var(--side-nav-fixed-width) !important;
+    }
+
+    #MSearchBox {
+        width: calc(var(--side-nav-fixed-width) - calc(2 * var(--spacing-medium)));
+    }
+
+    #MSearchField {
+        width: calc(var(--side-nav-fixed-width) - calc(2 * var(--spacing-medium)) - 65px);
+    }
+
+    #MSearchResultsWindow {
+        left: var(--spacing-medium) !important;
+        right: auto;
+    }
+}

doc/doxygen-custom/custom.css

+.github-corner svg {
+    fill: var(--primary-light-color);
+    color: var(--page-background-color);
+    width: 72px;
+    height: 72px;
+}
+
+@media screen and (max-width: 767px) {
+    .github-corner svg {
+        width: 55px;
+        height: 55px;
+    }
+    #projectnumber {
+        margin-right: 22px;
+    }
+}

doc/doxygen-custom/footer.html

+<!-- HTML footer for doxygen 1.9.1-->
+<!-- start footer part -->
+<!--BEGIN GENERATE_TREEVIEW-->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    $navpath
+    <li class="footer">$generatedby <a href="https://www.doxygen.org/index.html"><img class="footer" src="$relpath^doxygen.svg" width="104" height="31" alt="doxygen"/></a> $doxygenversion </li>
+  </ul>
+</div>
+<!--END GENERATE_TREEVIEW-->
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small>
+$generatedby&#160;<a href="https://www.doxygen.org/index.html"><img class="footer" src="$relpath^doxygen.svg" width="104" height="31" alt="doxygen"/></a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+<script type="text/javascript">
+  $(document).ready(function(){
+    toggleButton = document.createElement('doxygen-awesome-dark-mode-toggle')
+    toggleButton.title = "Toggle Light/Dark Mode"
+    document.getElementById("MSearchBox").parentNode.appendChild(toggleButton)
+  })
+</script>
+</body>
+</html>

doc/doxygen-custom/header.html

+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
+<meta name="viewport" content="width=device-width, initial-scale=1"/>
+
+<!-- BEGIN opengraph metadata -->
+<meta property="og:title" content="Athena Detector" />
+<meta property="og:image" content="https://repository-images.githubusercontent.com/348492097/4f16df80-88fb-11eb-9d31-4015ff22c452" />
+<meta property="og:description" content="Athenta" />
+<meta property="og:url" content="https://eic.phy.anl.gov/documentation/athena-detector" />
+<!-- END opengraph metadata -->
+
+<!-- BEGIN twitter metadata -->
+<meta name="twitter:image:src" content="https://repository-images.githubusercontent.com/348492097/4f16df80-88fb-11eb-9d31-4015ff22c452" />
+<meta name="twitter:title" content="Doxygen Awesome" />
+<meta name="twitter:description" content="Custom CSS theme for doxygen html-documentation with lots of customization parameters." />
+<!-- END twitter metadata -->
+
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
+<link rel="icon" type="image/svg+xml" href="logo.drawio.svg"/>
+<script type="text/javascript" src="$relpath^jquery.js"></script>
+<script type="text/javascript" src="$relpath^dynsections.js"></script>
+<script type="text/javascript" src="$relpath^doxygen-awesome-darkmode-toggle.js"></script>
+$treeview
+$search
+$mathjax
+<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+$extrastylesheet
+</head>
+<body>
+
+<style>.gitlab-corner-wrapper{overflow:hidden;width:100px;height:100px;position:absolute;top:0;right:0}.gitlab-corner{position:absolute;top:-11px;right:-46px;transform:rotate(45deg);background:#333;border:40px solid #333;border-bottom:none;border-top:#333 solid 14px}.gitlab-corner svg{width:60px;height:60px;margin-bottom:-4px}.cls-1{fill:#fc6d26}.cls-2{fill:#e24329}.cls-3{fill:#fca326}.gitlab-corner:hover .cls-1{animation:cycle .6s}.gitlab-corner:hover .cls-2{animation:cycleMid .6s}.gitlab-corner:hover .cls-3{animation:cycleEnd .6s}@keyframes cycle{100%,15%,60%{fill:#fc6d26}30%,75%{fill:#e24329}45%,90%{fill:#fca326}}@keyframes cycleMid{100%,15%,60%{fill:#e24329}30%,75%{fill:#fca326}45%,90%{fill:#fc6d26}}@keyframes cycleEnd{100%,15%,60%{fill:#fca326}30%,75%{fill:#fc6d26}45%,90%{fill:#e24329}}@media (max-width:500px){.gitlab-corner:hover .cls-1,.gitlab-corner:hover .cls-2,.gitlab-corner:hover .cls-3{animation:none}.gitlab-corner .cls-1{animation:cycle .6s}.gitlab-corner .cls-2{animation:cycleMid .6s}.gitlab-corner .cls-3{animation:cycleEnd .6s}}</style><div class="gitlab-corner-wrapper">
+  <a href="https://eicweb.phy.anl.gov/eic/documentation/athena-detector"
+    class="gitlab-corner" aria-label="View source on eicweb">
+    <svg id="logo_art" data-name="logo art" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 586 559"><g id="g44"><path id="path46" class="cls-1" d="M461.17,301.83l-18.91-58.12L404.84,128.43a6.47,6.47,0,0,0-12.27,0L355.15,243.64H230.82L193.4,128.43a6.46,6.46,0,0,0-12.26,0L143.78,243.64l-18.91,58.19a12.88,12.88,0,0,0,4.66,14.39L293,435,456.44,316.22a12.9,12.9,0,0,0,4.73-14.39"/></g><g id="g48"><path id="path50" class="cls-2" d="M293,434.91h0l62.16-191.28H230.87L293,434.91Z"/></g><g id="g56"><path id="path58" class="cls-1" d="M293,434.91,230.82,243.63h-87L293,434.91Z"/></g><g id="g64"><path id="path66" class="cls-3" d="M143.75,243.69h0l-18.91,58.12a12.88,12.88,0,0,0,4.66,14.39L293,435,143.75,243.69Z"/></g><g id="g72"><path id="path74" class="cls-2" d="M143.78,243.69h87.11L193.4,128.49a6.47,6.47,0,0,0-12.27,0l-37.35,115.2Z"/></g><g id="g76"><path id="path78" class="cls-1" d="M293,434.91l62.16-191.28H442.3L293,434.91Z"/></g><g id="g80"><path id="path82" class="cls-3" d="M442.24,243.69h0l18.91,58.12a12.85,12.85,0,0,1-4.66,14.39L293,434.91l149.2-191.22Z"/></g><g id="g84"><path id="path86" class="cls-2" d="M442.28,243.69h-87.1l37.42-115.2a6.46,6.46,0,0,1,12.26,0l37.42,115.2Z"/></g></svg></a></div>
+
+
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <!--BEGIN PROJECT_LOGO-->
+  <td id="projectlogo"><img alt="Logo" src="$relpath^$projectlogo"/></td>
+  <!--END PROJECT_LOGO-->
+  <!--BEGIN PROJECT_NAME-->
+  <td id="projectalign" style="padding-left: 0.5em;">
+   <div id="projectname">$projectname
+   <!--BEGIN PROJECT_NUMBER-->&#160;<span id="projectnumber">$projectnumber</span><!--END PROJECT_NUMBER-->
+   </div>
+   <!--BEGIN PROJECT_BRIEF--><div id="projectbrief">$projectbrief</div><!--END PROJECT_BRIEF-->
+  </td>
+  <!--END PROJECT_NAME-->
+  <!--BEGIN !PROJECT_NAME-->
+   <!--BEGIN PROJECT_BRIEF-->
+    <td style="padding-left: 0.5em;">
+    <div id="projectbrief">$projectbrief</div>
+    </td>
+   <!--END PROJECT_BRIEF-->
+  <!--END !PROJECT_NAME-->
+  <!--BEGIN DISABLE_INDEX-->
+   <!--BEGIN SEARCHENGINE-->
+   <td>$searchbox</td>
+   <!--END SEARCHENGINE-->
+  <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->

doc/page.dox

+/**
+ * \defgroup detconstruction Detector Constructors
+ * \defgroup subsystems Subsystems
+ */
+
+
+/**
+ *    \addtogroup subsytems 
+ */
+//@{
+/**
+ * \defgroup rich         RICH detectors 
+ * \defgroup trackers     Trackers
+ * \defgroup ecal         Electromagnetic Calorimeters
+ * \defgroup hcal         Hadronic Calorimeters
+ * \defgroup magnets      Magnets
+ */
+//@}
+
+
+
+
+

doc/pages.md

+
+Release notes {#releases}
+=============
+
+@tableofcontents
+
+@section rel_page Release History
+
+Blah blah blah# List of services
+
+asdf
+

gatsby-config.js

-module.exports = {
-  pathPrefix : `/documentation/athena-detector`,
-  siteMetadata : {
-    siteTitle : `ATHENA Detector`,
-    defaultTitle : `ATHENA Detector`,
-    siteTitleShort : `ATHENA Detector`,
-    siteDescription : `ATHENA Detector documentation`,
-    siteUrl : `https://eic.phy.anl.gov/documentation/athena-detector`,
-    siteAuthor : `whit`,
-    siteImage : `/banner.png`,
-    siteLanguage : `en`,
-    themeColor : `#e1a809`,
-    basePath : `/`,
-    footer : `whit`,
-  },
-  plugins : [
-    {
-      resolve : `@rocketseat/gatsby-theme-docs`,
-      options : {
-        configPath : `src/config`,
-        docsPath : `src/docs`,
-        repositoryUrl : `https://eicweb.phy.anl.gov/EIC/documentation/athena-detector/`,
-        baseDir : `/`,
-      },
-    },
-    {
-      resolve : `gatsby-plugin-manifest`,
-      options : {
-        name : `Rocketseat Gatsby Themes`,
-        short_name : `RS Gatsby Themes`,
-        start_url : `/`,
-        background_color : `#ffffff`,
-        display : `standalone`,
-        icon : `static/favicon.png`,
-      },
-    },
-    `gatsby-plugin-sitemap`,
-    //`gatsby-plugin-google-analytics`,
-    {
-      resolve : `gatsby-plugin-canonical-urls`,
-      options : {
-        siteUrl : `https://rocketdocs.netlify.com`,
-      },
-    },
-    `gatsby-plugin-offline`,
-    `gatsby-plugin-emotion`,
-  ],
-};

package.json

-{
-  "name": "gatsby-starter-rocket-docs",
-  "private": true,
-  "version": "1.0.0",
-  "description": "Out of the box Gatsby Starter for creating documentation websites easily and quickly. With support for MDX, code highlight, Analytics, SEO and more",
-  "author": "João Pedro Schmitz <oi@joaopedro.cc> (@joaopedro_cc)",
-  "license": "MIT",
-  "starter-name": "gatsby-starter-rocket-docs",
-  "dependencies": {
-    "@emotion/react": "^11.4.0",
-    "@emotion/styled": "^11.3.0",
-    "@rocketseat/gatsby-theme-docs": "^2.1.0",
-    "gatsby": "^3.11.0",
-    "gatsby-plugin-canonical-urls": "^3.11.0",
-    "gatsby-plugin-emotion": "^6.11.0",
-    "gatsby-plugin-google-analytics": "^3.11.0",
-    "gatsby-plugin-manifest": "^3.11.0",
-    "gatsby-plugin-offline": "^4.11.0",
-    "gatsby-plugin-sitemap": "^4.7.0",
-    "markdown-toc": "^1.2.0",
-    "prop-types": "^15.7.2",
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2"
-  },
-  "devDependencies": {},
-  "keywords": [
-    "gatsby",
-    "rocketseat",
-    "gatsby-starter"
-  ],
-  "scripts": {
-    "build": "gatsby build",
-    "start": "gatsby develop",
-    "serve": "gatsby serve",
-    "clean": "gatsby clean"
-  }
-}

src/@rocketseat/gatsby-theme-docs/.../theme.js

-export default {
-  colors: {
-    primary: '#E1A809',
-    background: '#fff',
-    sidebar: {
-      background: '#ffffff',
-      link: '#999',
-      heading: '#aaa',
-      linkActive: '#13131A',
-      itemActive: '#F5F5FA',
-      footer: '#A8A8B3',
-    },
-  },
-};

src/@rocketseat/gatsby-theme-docs/components/Docs/EditGithub.js

-import React from 'react';
-import PropTypes from 'prop-types';
-import { MdEdit } from 'react-icons/md';
-
-export default function EditGithub({ githubEditUrl }) {
-  if (githubEditUrl) {
-    return (
-      <a
-        href={githubEditUrl}
-        target="_blank"
-        rel="noopener noreferrer"
-        style={{
-          display: 'flex',
-          alignItems: 'center',
-          textDecoration: 'none',
-          marginTop: '48px',
-          color: '#78757a',
-          opacity: '0.8',
-          fontSize: '14px',
-          fontWeight: 'normal',
-        }}
-      >
-        <MdEdit style={{ marginRight: '5px' }} />
-        Edit this page on eicweb 
-      </a>
-    );
-  }
-  return null;
-}
-
-EditGithub.propTypes = {
-  githubEditUrl: PropTypes.string,
-};
-
-EditGithub.defaultProps = {
-  githubEditUrl: null,
-};

src/@rocketseat/gatsby-theme-docs/components/Logo.js

-import styled from '@emotion/styled';
-
-import logo from '../../../docs/eicweb-logo-small.png';
-
-export default styled.div`
-  width: 220px;
-  height: 90px;
-  background-size: contain;
-  background: url(${logo}) center no-repeat;
-`;