seqan · smehringer · Jan 3, 2023 · Jan 2, 2023 · Jan 2, 2023
diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
@@ -130,7 +130,7 @@ jobs:
             build_threads: 2
             test_threads: 2
             cmake: 3.16.9
-            doxygen: 1.9.4
+            doxygen: 1.9.6
             requires_toolchain: false
             requires_ccache: false
             skip_build_tests: true

diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -13,7 +13,7 @@ concurrency:
 
 env:
   CMAKE_VERSION: 3.16.9
-  DOXYGEN_VERSION: 1.9.4
+  DOXYGEN_VERSION: 1.9.6
   TZ: Europe/Berlin
 
 defaults:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -57,6 +57,7 @@ If possible, provide tooling that performs the changes, e.g. a shell-script.
 #### Dependencies
   * We require at least CMake 3.16 for our test suite. Note that the minimum requirement for using SeqAn3 is unchanged
     ([\#3050](https://github.com/seqan/seqan3/pull/3050)).
+  * We now use Doxygen version 1.9.6 to build our documentation ([\#3116](https://github.com/seqan/seqan3/pull/3116)).
 
 # 3.2.0
 

diff --git a/build_system/seqan3-package.cmake b/build_system/seqan3-package.cmake
@@ -16,7 +16,7 @@ set (CPACK_PACKAGE_VENDOR "seqan")
 # A description of the project, used in places such as the introduction screen of CPack-generated Windows installers.
 # set (CPACK_PACKAGE_DESCRIPTION_FILE "") # TODO
 set (CPACK_PACKAGE_CHECKSUM "SHA256")
-set (CPACK_PACKAGE_ICON "${SEQAN3_CLONE_DIR}/test/documentation/seqan_logo.png")
+set (CPACK_PACKAGE_ICON "${SEQAN3_CLONE_DIR}/test/documentation/seqan_logo.svg")
 set (CPACK_RESOURCE_FILE_LICENSE "${SEQAN3_CLONE_DIR}/LICENSE.md")
 set (CPACK_RESOURCE_FILE_README "${SEQAN3_CLONE_DIR}/README.md")
 

diff --git a/test/documentation/.vercel/build.sh b/test/documentation/.vercel/build.sh
@@ -25,3 +25,4 @@ mkdir -p "${EXPORT_DIR}/usr/" "${EXPORT_DIR}/dev/"
 DESTDIR="${EXPORT_DIR}/usr/" cmake3 -DCOMPONENT=doc -P cmake_install.cmake 1>/dev/null
 DESTDIR="${EXPORT_DIR}/dev/" cmake3 -DCOMPONENT=doc-dev -P cmake_install.cmake 1>/dev/null
 cp "${SOURCE_DIR}/test/documentation/.vercel/index.html" "${EXPORT_DIR}/index.html"
+cp "${SOURCE_DIR}/test/documentation/.vercel/vercel.css" "${EXPORT_DIR}/vercel.css"
diff --git a/test/documentation/.vercel/index.html b/test/documentation/.vercel/index.html
@@ -1,27 +1,7 @@
 <html>
   <head>
     <title>SeqAn Documentation Preview</title>
-    <style>
-    body {text-align: center}
-    h1 {color: gray}
-    a.selection {
-      height: 2em;
-      display: inline-block;
-      border-radius: 4px;
-      background: black;
-      color: white;
-      line-height: 2em;
-      padding: 5px;
-      width: 50%;
-      font-size: 1.5em;
-      text-decoration: none;
-      margin: 5px;
-    }
-    a.selection:hover {
-        background-color: #fede09;
-        text-decoration: underline;
-    }
-    </style>
+    <link href="vercel.css" rel="stylesheet" type="text/css">
   </head>
 
   <body>

diff --git a/test/documentation/.vercel/install.sh b/test/documentation/.vercel/install.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 set -exo pipefail
 
-DOXYGEN_VERSION=1.9.4
+DOXYGEN_VERSION=1.9.6
 SOURCE_DIR=`pwd`
 CACHE_DIR="${SOURCE_DIR}/node_modules"
 

diff --git a/test/documentation/.vercel/vercel.css b/test/documentation/.vercel/vercel.css
@@ -0,0 +1,39 @@
+@media (prefers-color-scheme: dark) {
+    :root {
+        --background-color: black;
+    }
+}
+
+@media (prefers-color-scheme: light) {
+    :root {
+        --background-color: rgb(230, 230, 230);
+    }
+}
+
+body {
+    background-color: var(--background-color);
+    text-align: center;
+}
+
+h1 {
+    color: rgb(135,135,135);
+}
+
+a.selection {
+    height: 2em;
+    display: inline-block;
+    border-radius: 4px;
+    background: #090D16;
+    color: #C9D1D9;
+    line-height: 2em;
+    padding: 5px;
+    width: 50%;
+    font-size: 1.5em;
+    text-decoration: none;
+    margin: 5px;
+}
+
+a.selection:hover {
+    background-color: #776700;
+    text-decoration: underline;
+}
diff --git a/test/documentation/DoxygenLayout.xml b/test/documentation/DoxygenLayout.xml
@@ -1,5 +1,5 @@
 <doxygenlayout version="1.0">
-  <!-- Generated by doxygen 1.9.4 -->
+  <!-- Generated by doxygen 1.9.6 -->
   <!-- Navigation index tabs for HTML output -->
   <navindex>
     <tab type="mainpage" visible="yes" title=""/>

diff --git a/test/documentation/seqan3-doxygen.cmake b/test/documentation/seqan3-doxygen.cmake
@@ -52,7 +52,7 @@ if (SEQAN3_VERCEL_PREVIEW_DOC)
     set (SEQAN3_DOXYFILE_OPTION_POWERED_BY_VERCEL
          "HTML_EXTRA_FILES       += ${SEQAN3_DOXYGEN_SOURCE_DIR}/test/documentation/.vercel/powered-by-vercel.svg")
     set (SEQAN3_FOOTER_HTML_OPTION_POWERED_BY_VERCEL
-         "<li class='footer'><a href='https://vercel.com/?utm_source=seqan&utm_campaign=oss'><img class='footer' src='$relpath^powered-by-vercel.svg' width='104' height='31' alt='Powered by Vercel'/></a></li>"
+         "<li class='footer'><a href='https://vercel.com/?utm_source=seqan&utm_campaign=oss'><img class='footer' src='$relpath^powered-by-vercel.svg' height='31' alt='Powered by Vercel' style='width:unset;'/></a></li>"
     )
 endif ()
 

diff --git a/test/documentation/seqan3.css b/test/documentation/seqan3.css
@@ -77,6 +77,7 @@ div.contents {
 #projectlogo {
     padding: 10px;
     width: 150px;
+    filter: drop-shadow(0 0 0.1rem rgb(251,227,0));
 }
 
 hr.footer {
@@ -263,6 +264,7 @@ div.solution {
 #nav-tree .label a[class="hierarchy.html"],
 #nav-tree .label a[class="index.html"],
 #nav-tree .label a[class="files.html"],
+#nav-tree .label a[class="concepts.html"],
 #nav-tree .label a[class="cookbook.html"] {
     color: #3D578C;
     font-weight: bolder;
@@ -283,6 +285,17 @@ div.solution {
     color: grey;
 }
 
+#nav-tree .label a[class^="concept"][class$="html"]::after {
+    content: " Concept";
+    color: grey;
+}
+
+/* Remove suffix from Concept List */
+#nav-tree .label a[class^="concepts.html"]::after {
+    content: "" !important;
+    color: grey;
+}
+
 #nav-tree .label a[class^="class"][class$="html"]::after,
 #nav-tree .label a[class^="struct"][class$="html"]::after {
     content: " Class";

diff --git a/test/documentation/seqan3_dark.css b/test/documentation/seqan3_dark.css
@@ -0,0 +1,209 @@
+@media (prefers-color-scheme: dark) {
+    body {
+        background-color: black;
+        color: #C9D1D9;
+    }
+
+    h1, h2, h3, h4, h5, h6, summary.seqan {
+        color: #7f9edc;
+    }
+
+    details.seqan[open] {
+        background-color: #0e0e0e;
+        box-shadow: 3px 3px 4px #161616;
+    }
+
+    h1 {
+        border-bottom: 2px solid #DADADA;
+    }
+
+    div.contents {
+        background-color: #212121;
+    }
+
+    #titlearea {
+        background-color: #090D16;
+    }
+
+    .footer {
+        background-color: transparent;
+    }
+
+    /* code snippets */
+    div.fragment {
+        background-color: black;
+        border: 1px solid #30363D;
+    }
+
+    /* inline code */
+    code {
+        background-color: black;
+        border: 1px solid #30363D;
+    }
+
+    dl.attention {
+        background-color: #292525;
+    }
+
+    dl.warning {
+        border-color: #311f04;
+        background-color: #FBF0E0;
+    }
+
+    dl.note {
+        border-color: #E9DF24;
+        background-color: #161614;
+    }
+
+    hr {
+        border-top: 2px solid #E4E4E4;
+    }
+
+    /* markdown tables */
+    table.markdownTable {
+        border: 1px solid #283A5D;
+    }
+
+    table.markdownTable caption {
+        color: #000;
+    }
+
+    table.markdownTable thead {
+        background-color: #283A5D;
+        color: #C4CFE5;
+    }
+
+    table.markdownTable td {
+        border-bottom: 2px solid #283A5D;
+    }
+
+    table.markdownTable th {
+        border-bottom: 2px solid #283A5D;
+        background-color: #283A5D;
+        color: #C4CFE5;
+    }
+
+    /* assignment box */
+    div.assignment {
+        background-color: #232527;
+        border-left: 6px solid #2f436a;
+    }
+
+    /* solution box */
+    div.solution {
+        background-color: #819c79;
+        border-left: 6px solid #408000;
+        color: #354C7B;
+    }
+
+    /* Side nav bar styles: */
+    #nav-tree .label a { /*default*/
+        color: #90A5CE;
+    }
+
+    /* make all important pages bold */
+    #nav-tree .label a[class^="modules"][class$="html"],
+    #nav-tree .label a[class^="group"][class$="html"],
+    #nav-tree .label a[class^="usergroup"][class$="html"],
+    #nav-tree .label a[class^="namespace"][class$="html"],
+    #nav-tree .label a[class="nolink"],
+    #nav-tree .label a[class="annotated.html"],
+    #nav-tree .label a[class="hierarchy.html"],
+    #nav-tree .label a[class="index.html"],
+    #nav-tree .label a[class="files.html"],
+    #nav-tree .label a[class="concepts.html"],
+    #nav-tree .label a[class="cookbook.html"] {
+        color: #90A5CE;
+    }
+
+    #nav-tree .selected .label a,
+    #nav-tree .selected .label a[class^="modules"][class$="html"],
+    #nav-tree .selected .label a[class^="group"][class$="html"],
+    #nav-tree .selected .label a[class^="usergroup"][class$="html"],
+    #nav-tree .selected .label a[class^="namespace"][class$="html"],
+    #nav-tree .selected .label a[class="nolink"],
+    #nav-tree .selected .label a[class="annotated.html"],
+    #nav-tree .selected .label a[class="hierarchy.html"],
+    #nav-tree .selected .label a[class="index.html"],
+    #nav-tree .selected .label a[class="files.html"],
+    #nav-tree .selected .label a[class="concepts.html"],
+    #nav-tree .selected .label a[class="cookbook.html"] {
+        color: #DCE2EF;
+    }
+
+    #nav-tree .selected{
+        color: #DCE2EF;
+        background-color: transparent;
+    }
+
+    /* add Concept and Class suffix */
+    #nav-tree .label a[class^="interface"][class$="html"]::after {
+        color: grey;
+    }
+
+    #nav-tree .label a[class^="concept"][class$="html"]::after {
+        color: grey;
+    }
+
+    /* Remove suffix from Concept List */
+    #nav-tree .label a[class^="concepts.html"]::after {
+        color: grey;
+    }
+
+    #nav-tree .label a[class^="class"][class$="html"]::after,
+    #nav-tree .label a[class^="struct"][class$="html"]::after {
+        color: grey;
+    }
+
+    .mlabel.experimental-api
+    {
+        background-color: #826740;
+        border-top: 1px solid #da8d00; /* darken(orange, 14.5) */
+        border-left: 1px solid #da8d00; /* same as above */
+        border-right: 1px solid #ffc965; /* lighten(orange, 40) */
+        border-bottom: 1px solid #ffc965; /* same as above */
+    }
+
+    .mlabel.stable-api
+    {
+        background-color: #214a21;
+        border-top: 1px solid #006d00; /* darken(green, 14.5) */
+        border-left: 1px solid #006d00; /* same as above */
+        border-right: 1px solid #00cc00; /* lighten(green, 20) */
+        border-bottom: 1px solid #00cc00; /* same as above */
+    }
+
+    .mlabel.no-api
+    {
+        background-color: #692b2b;
+        border-top: 1px solid #da0000; /* darken(red, 14.5) */
+        border-left: 1px solid #da0000; /* same as above */
+        border-right: 1px solid #ff9999; /* lighten(red, 60) */
+        border-bottom: 1px solid #ff9999; /* same as above */
+    }
+
+    dl.stable-api {
+        background-color: #214a21;
+        border-color: #00D000;
+    }
+
+    dl.experimental-api {
+        border-color: #E08D12;
+        background-color: #826740;
+    }
+
+    dl.no-api {
+        border-color: #FF0000;
+        background-color: #692b2b;
+    }
+
+    .memtitle.no-api
+    {
+        background-color: #692b2b;
+    }
+
+    .memtitle.experimental-api
+    {
+        background-color: #826740;
+    }
+}