From 95d1a2708c2bec0ebca03d9b01bc15b7d570c362 Mon Sep 17 00:00:00 2001
From: Simon Gene Gottlieb <simon@gottliebtfreitag.de>
Date: Fri, 19 Nov 2021 12:55:34 +0100
Subject: [PATCH] [MISC] Update seqan3 submodule to 3.1.0 (#55)
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* [MISC] Update seqan3 submodule to 3.1.0

* [INFRA] update doxygen version from 1.9.1 → 1.9.2

* [INFRA] remove obsolete options from doxygen
---
 .github/workflows/ci_misc.yml            | 2 +-
 doc/doxygen_cfg                          | 8 --------
 lib/seqan3                               | 2 +-
 test/api/convert_fastq_test.cpp          | 2 +-
 test/cli/fastq_to_fasta_options_test.cpp | 5 ++---
 5 files changed, 5 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
index ddda2b8f..89983557 100644
--- a/.github/workflows/ci_misc.yml
+++ b/.github/workflows/ci_misc.yml
@@ -29,7 +29,7 @@ jobs:
             build_threads: 2
             test_threads: 2
             cmake: 3.8.2
-            doxygen: 1.9.1
+            doxygen: 1.9.2
             requires_toolchain: false
             requires_ccache: false
             skip_build_tests: true
diff --git a/doc/doxygen_cfg b/doc/doxygen_cfg
index 6914cdca..dfec7074 100644
--- a/doc/doxygen_cfg
+++ b/doc/doxygen_cfg
@@ -12,7 +12,6 @@ OUTPUT_DIRECTORY       = ${APP_TEMPLATE_DOXYGEN_OUTPUT_DIR}
 CREATE_SUBDIRS         = NO
 ALLOW_UNICODE_NAMES    = NO
 OUTPUT_LANGUAGE        = English
-OUTPUT_TEXT_DIRECTION  = None
 BRIEF_MEMBER_DESC      = YES
 REPEAT_BRIEF           = YES
 ABBREVIATE_BRIEF       = "The $name class" \
@@ -195,10 +194,6 @@ REFERENCES_LINK_SOURCE = YES
 SOURCE_TOOLTIPS        = YES
 USE_HTAGS              = NO
 VERBATIM_HEADERS       = YES
-CLANG_ASSISTED_PARSING = NO
-CLANG_ADD_INC_PATHS    = YES
-CLANG_OPTIONS          =
-CLANG_DATABASE_PATH    =
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -284,7 +279,6 @@ PDF_HYPERLINKS         = YES
 USE_PDFLATEX           = YES
 LATEX_BATCHMODE        = NO
 LATEX_HIDE_INDICES     = NO
-LATEX_SOURCE_CODE      = NO
 LATEX_BIB_STYLE        = plain
 LATEX_TIMESTAMP        = NO
 LATEX_EMOJI_DIRECTORY  =
@@ -297,7 +291,6 @@ COMPACT_RTF            = NO
 RTF_HYPERLINKS         = NO
 RTF_STYLESHEET_FILE    =
 RTF_EXTENSIONS_FILE    =
-RTF_SOURCE_CODE        = NO
 #---------------------------------------------------------------------------
 # Configuration options related to the man page output
 #---------------------------------------------------------------------------
@@ -318,7 +311,6 @@ XML_NS_MEMB_FILE_SCOPE = NO
 #---------------------------------------------------------------------------
 GENERATE_DOCBOOK       = NO
 DOCBOOK_OUTPUT         = docbook
-DOCBOOK_PROGRAMLISTING = NO
 #---------------------------------------------------------------------------
 # Configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
diff --git a/lib/seqan3 b/lib/seqan3
index 52f201a5..4668203e 160000
--- a/lib/seqan3
+++ b/lib/seqan3
@@ -1 +1 @@
-Subproject commit 52f201a5ef3d806b7348b67afd80374f160451c7
+Subproject commit 4668203ee1526b4ac3dbdc47869bee72253f684c
diff --git a/test/api/convert_fastq_test.cpp b/test/api/convert_fastq_test.cpp
index 7b9c5fa0..5ed2c14d 100644
--- a/test/api/convert_fastq_test.cpp
+++ b/test/api/convert_fastq_test.cpp
@@ -1,7 +1,7 @@
 #include <gtest/gtest.h>
 
+#include <seqan3/alphabet/detail/debug_stream_alphabet.hpp>
 #include <seqan3/alphabet/nucleotide/dna5.hpp>
-#include <seqan3/core/detail/debug_stream_alphabet.hpp>
 #include <seqan3/io/sequence_file/input.hpp>
 #include <seqan3/test/expect_range_eq.hpp>
 
diff --git a/test/cli/fastq_to_fasta_options_test.cpp b/test/cli/fastq_to_fasta_options_test.cpp
index 75c81f9d..0cd1259f 100644
--- a/test/cli/fastq_to_fasta_options_test.cpp
+++ b/test/cli/fastq_to_fasta_options_test.cpp
@@ -2,10 +2,9 @@
 #include <string>                // strings
 #include <vector>                // vectors
 
+#include <seqan3/alphabet/detail/debug_stream_alphabet.hpp>
 #include <seqan3/alphabet/nucleotide/dna5.hpp>
-#include <seqan3/core/detail/debug_stream_alphabet.hpp>
-#include <seqan3/core/detail/debug_stream_tuple.hpp>
-#include <seqan3/core/detail/debug_stream_type.hpp>
+#include <seqan3/core/debug_stream/tuple.hpp>
 #include <seqan3/io/sequence_file/input.hpp>
 
 // Include the EXPECT_RANGE_EQ macro for better information if range elements differ.