[INFRA] Update doxygen

seqan · Jun 28, 2024 · 2ce462e · 2ce462e
1 parent 6982ec6
commit 2ce462e
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diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
@@ -47,7 +47,7 @@ jobs:
       - name: Install Doxygen
         uses: seqan/actions/setup-doxygen@main
         with:
-          doxygen: 1.9.6
+          doxygen: 1.10.0
 
       - name: Configure tests
         run: |

diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake
@@ -76,3 +76,10 @@ CPMDeclarePackage (use_ccache
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
 )
+# doxygen-awesome
+set (RAPTOR_DOXYGEN_AWESOME_VERSION 2.3.3)
+CPMDeclarePackage (doxygen_awesome
+                   NAME doxygen_awesome
+                   VERSION ${RAPTOR_DOXYGEN_AWESOME_VERSION}
+                   GITHUB_REPOSITORY jothepro/doxygen-awesome-css
+                   DOWNLOAD_ONLY TRUE)
diff --git a/doc/methods/01_introduction/index.md b/doc/methods/01_introduction/index.md
@@ -1,11 +1,11 @@
+# First steps with Raptor {#tutorial_first_steps}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# First steps with Raptor {#tutorial_first_steps}
-
 ***Learning Objective:***
 
 This tutorial walks you through small Raptor applications. It is intended to give you a short overview of what to expect

diff --git a/doc/methods/02_layout/index.md b/doc/methods/02_layout/index.md
@@ -1,11 +1,11 @@
+# Create a layout with Raptor {#tutorial_layout}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Create a layout with Raptor {#tutorial_layout}
-
 You will learn how to construct a Raptor layout of large collections of nucleotide sequences.
 
 \attention

diff --git a/doc/methods/03_index/index.md b/doc/methods/03_index/index.md
@@ -1,11 +1,11 @@
+# Indexing with Raptor {#tutorial_index}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Indexing with Raptor {#tutorial_index}
-
 You will learn how to construct a Raptor index of large collections of nucleotide sequences.
 
 \tutorial_head{Easy, 30 min, \ref tutorial_first_steps \, for using HIBF: \ref tutorial_layout,

diff --git a/doc/methods/04_search/index.md b/doc/methods/04_search/index.md
@@ -1,11 +1,11 @@
+# Search with Raptor {#tutorial_search}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Search with Raptor {#tutorial_search}
-
 You will learn how to search a Raptor index using one or more sequences queries.
 
 \tutorial_head{Easy, 30 min, \ref tutorial_index, }

diff --git a/doc/setup/index.md b/doc/setup/index.md
@@ -1,11 +1,11 @@
+# Setup {#setup}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Setup {#setup}
-
 [TOC]
 
 # Download and Installation

diff --git a/doc/usage/01_quickstart/index.md b/doc/usage/01_quickstart/index.md
@@ -1,11 +1,11 @@
+# Quickstart {#usage_quickstart}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# Quickstart {#usage_quickstart}
-
 [TOC]
 
 <!-- * reference usage sections

diff --git a/doc/usage/02_prepare/index.md b/doc/usage/02_prepare/index.md
@@ -1,11 +1,11 @@
+# raptor prepare {#usage_prepare}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# raptor prepare {#usage_prepare}
-
 [TOC]
 
 Optionally preprocesses files for the use with `raptor layout` and `raptor build`.

diff --git a/doc/usage/03_layout/index.md b/doc/usage/03_layout/index.md
@@ -1,11 +1,11 @@
+# raptor layout {#usage_layout}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# raptor layout {#usage_layout}
-
 [TOC]
 
 \attention

diff --git a/doc/usage/04_build/index.md b/doc/usage/04_build/index.md
@@ -1,11 +1,11 @@
+# raptor build {#usage_build}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# raptor build {#usage_build}
-
 [TOC]
 
 # Main Parameters

diff --git a/doc/usage/05_search/index.md b/doc/usage/05_search/index.md
@@ -1,11 +1,11 @@
+# raptor search {#usage_search}
+
 <!--
 SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
 SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-# raptor search {#usage_search}
-
 [TOC]
 
 ## Main Parameters

diff --git a/test/documentation/.vercel/0_setup.sh b/test/documentation/.vercel/0_setup.sh
@@ -6,7 +6,7 @@
 
 set -euxo pipefail
 
-DOXYGEN_VERSION=1.9.6
+DOXYGEN_VERSION=1.10.0
 WORK_DIR=`pwd`
 CACHE_DIR="${WORK_DIR}/node_modules" # The node_modules directory is always cached.
 

diff --git a/test/documentation/CMakeLists.txt b/test/documentation/CMakeLists.txt
@@ -10,6 +10,11 @@ get_filename_component (RAPTOR_CLONE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/../.." ABS
 
 include (${RAPTOR_CLONE_DIR}/cmake/version.cmake)
 
+set (CPM_INDENT "CMake Package Manager CPM: ")
+include (${RAPTOR_CLONE_DIR}/cmake/CPM.cmake)
+CPMUsePackageLock (${RAPTOR_CLONE_DIR}/cmake/package-lock.cmake)
+CPMGetPackage (doxygen_awesome)
+
 project (docs
          LANGUAGES NONE
          VERSION "${RAPTOR_PROJECT_VERSION}"

diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js b/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js