[FIX] API test

eseiler · eseiler · commit be4c84b867fc · 2025-08-11T09:09:55.000+02:00
diff --git a/test/api_stability/1.1.1/0001-API-Update-TDL.patch b/test/api_stability/1.1.1/0001-API-Update-TDL.patch
@@ -1,7 +1,7 @@
-From fbbfddee4e2ced58e61a8b4bc8f0ffb8d091bdc7 Mon Sep 17 00:00:00 2001
+From 56e4f3e1556953805955a69086643797bb241258 Mon Sep 17 00:00:00 2001
 From: Simon Gene Gottlieb <simon@gottliebtfreitag.de>
 Date: Thu, 5 Oct 2023 13:43:30 +0200
-Subject: [PATCH 01/11] [API] Update TDL
+Subject: [PATCH 01/12] [API] Update TDL
 
 ---
  test/unit/detail/format_ctd_test.cpp |  2 +-
diff --git a/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch b/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch
@@ -1,7 +1,7 @@
-From e017d182f0d6ffb1c64d5a079dd9753de7d376a3 Mon Sep 17 00:00:00 2001
+From dd5002d51c50a66b32b1a7eaf2b817181a795d91 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Mon, 5 Feb 2024 16:02:03 +0100
-Subject: [PATCH 02/11] [API] Quoted strings and paths
+Subject: [PATCH 02/12] [API] Quoted strings and paths
 
 ---
  test/snippet/readme_sneak_peek.out            |  6 ++---
diff --git a/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch b/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch
@@ -1,7 +1,7 @@
-From 945b0f37bd687e94f7b3dfd24fac4e158e3c496c Mon Sep 17 00:00:00 2001
+From 7f44461f6cceef680417f63a1b74262caac86770 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Wed, 7 Feb 2024 13:31:22 +0100
-Subject: [PATCH 03/11] [NOAPI] Update copyright
+Subject: [PATCH 03/12] [NOAPI] Update copyright
 
 ---
  test/unit/detail/format_help_test.cpp | 10 +++++-----
diff --git a/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch b/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch
@@ -1,7 +1,7 @@
-From 7d646fd2a88a59270681aeaaac337b4fead10d3e Mon Sep 17 00:00:00 2001
+From 4e54484eb562d9168e46b96e4ef8ac8f027c08e3 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Fri, 9 Feb 2024 16:17:21 +0100
-Subject: [PATCH 04/11] [INFRA] Update TDL
+Subject: [PATCH 04/12] [INFRA] Update TDL
 
 ---
  test/unit/detail/format_cwl_test.cpp | 28 +++++++++++++++++++++++++++-
diff --git a/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch b/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch
@@ -1,7 +1,7 @@
-From 786bf6563f78a9db8a2a418c457b525349196f2a Mon Sep 17 00:00:00 2001
+From fc231c8b28ae2ce7a3902f0f17ced9b359b759ed Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Fri, 9 Feb 2024 18:13:36 +0100
-Subject: [PATCH 05/11] [INFRA] Use seqan3 main branch
+Subject: [PATCH 05/12] [INFRA] Use seqan3 main branch
 
 ---
  test/unit/detail/CMakeLists.txt | 2 +-
diff --git a/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch b/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch
@@ -1,7 +1,7 @@
-From e9090607843b59186ffb2b46c51c98dfeffda2c2 Mon Sep 17 00:00:00 2001
+From d55c37406b97aa736bd52e31969e2448efbdf61d Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Wed, 14 Feb 2024 12:34:40 +0100
-Subject: [PATCH 06/11] [API][FIX] positional options in CWL/CTD
+Subject: [PATCH 06/12] [API][FIX] positional options in CWL/CTD
 
 ---
  test/unit/detail/format_ctd_test.cpp | 4 ++--
diff --git a/test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch b/test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch
@@ -1,7 +1,7 @@
-From 57a727d581ed2d6d0a3949d7d570a863698e2f4f Mon Sep 17 00:00:00 2001
+From 44dc2e1c35ebe408ed99d55b04aff6368346aebd Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Mon, 29 Apr 2024 16:37:15 +0200
-Subject: [PATCH 07/11] [API][MISC] Defer everything to parse()
+Subject: [PATCH 07/12] [API][MISC] Defer everything to parse()
 
 ---
  test/unit/detail/format_help_test.cpp         |  2 +-
diff --git a/test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch b/test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch
@@ -1,7 +1,7 @@
-From a171aa659e28b96f85a18394ccc4b8f2c45bcc1e Mon Sep 17 00:00:00 2001
+From 94acad75ac9c3c75bab270df0525d3ea53839de1 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Mon, 29 Apr 2024 16:37:30 +0200
-Subject: [PATCH 08/11] [API][MISC] Allow options for subcommands
+Subject: [PATCH 08/12] [API][MISC] Allow options for subcommands
 
 ---
  test/unit/parser/format_parse_test.cpp        | 6 +++---
diff --git a/test/api_stability/1.1.1/0009-FIX-is_option_set-match-both-long-and-short-ids.patch b/test/api_stability/1.1.1/0009-FIX-is_option_set-match-both-long-and-short-ids.patch
@@ -1,7 +1,7 @@
-From 4508f7d320f8c772322a93f401049443bbebdd13 Mon Sep 17 00:00:00 2001
+From 86dea37024405c6029f6dbfce9852b66cc64428d Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Wed, 2 Apr 2025 18:02:31 +0200
-Subject: [PATCH 09/11] [FIX] is_option_set: match both long and short ids
+Subject: [PATCH 09/12] [FIX] is_option_set: match both long and short ids
 
 ---
  test/unit/parser/format_parse_test.cpp | 4 ++--
diff --git a/test/api_stability/1.1.1/0010-NOAPI-Update-copyright.patch b/test/api_stability/1.1.1/0010-NOAPI-Update-copyright.patch
@@ -1,7 +1,7 @@
-From fea24d1a1a2b9ad6ac6472b972d060930d15cb6c Mon Sep 17 00:00:00 2001
+From 38bcde0406173d67507cf7e9899f064cefc6c7fb Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Tue, 29 Jul 2025 14:21:32 +0200
-Subject: [PATCH 10/11] [NOAPI] Update copyright
+Subject: [PATCH 10/12] [NOAPI] Update copyright
 
 ---
  test/unit/detail/format_help_test.cpp | 10 +++++-----
diff --git a/test/api_stability/1.1.1/0011-INFRA-Bump-minor-version.patch b/test/api_stability/1.1.1/0011-INFRA-Bump-minor-version.patch
@@ -1,7 +1,7 @@
-From 576592820c278c5ba94739ef956ac5e1a7c72adb Mon Sep 17 00:00:00 2001
+From 79e68c4b56bc02196317cc5f01beb01608e8ba41 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Tue, 29 Jul 2025 14:45:23 +0200
-Subject: [PATCH 11/11] [INFRA] Bump minor version
+Subject: [PATCH 11/12] [INFRA] Bump minor version
 
 ---
  test/snippet/readme_sneak_peek.out   | 2 +-
@@ -10,7 +10,7 @@ Subject: [PATCH 11/11] [INFRA] Bump minor version
  3 files changed, 3 insertions(+), 3 deletions(-)
 
 diff --git a/test/snippet/readme_sneak_peek.out b/test/snippet/readme_sneak_peek.out
-index 8b51ee2..8debcce 100644
+index 8b51ee2..9f8c7e4 100644
 --- a/test/snippet/readme_sneak_peek.out
 +++ b/test/snippet/readme_sneak_peek.out
 @@ -25,4 +25,4 @@ OPTIONS
@@ -20,7 +20,7 @@ index 8b51ee2..8debcce 100644
 -    Sharg version: 1.1.2-rc.1
 +    Sharg version: 1.2.0-rc.2
 diff --git a/test/unit/detail/format_ctd_test.cpp b/test/unit/detail/format_ctd_test.cpp
-index 4e9261a..cfa93e1 100644
+index 4e9261a..b42fd53 100644
 --- a/test/unit/detail/format_ctd_test.cpp
 +++ b/test/unit/detail/format_ctd_test.cpp
 @@ -110,7 +110,7 @@ TEST_F(format_ctd_test, empty_information)
@@ -33,7 +33,7 @@ index 4e9261a..cfa93e1 100644
      parser.info.short_description = "A short description here.";
  
 diff --git a/test/unit/detail/format_cwl_test.cpp b/test/unit/detail/format_cwl_test.cpp
-index 52079db..1e63141 100644
+index 52079db..925d869 100644
 --- a/test/unit/detail/format_cwl_test.cpp
 +++ b/test/unit/detail/format_cwl_test.cpp
 @@ -16,7 +16,7 @@ TEST(format_cwl_test, empty_information)
diff --git a/test/api_stability/1.1.1/0012-API-Handle-multiple-citations.patch b/test/api_stability/1.1.1/0012-API-Handle-multiple-citations.patch
@@ -0,0 +1,70 @@
+From b30b7bd14d8433492e3c969885eb09bab9c4544e Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <enrico.seiler@hotmail.de>
+Date: Wed, 6 Aug 2025 10:29:26 +0200
+Subject: [PATCH 12/12] [API] Handle multiple citations
+
+---
+ test/unit/detail/format_help_test.cpp |  2 ++
+ test/unit/detail/format_html_test.cpp |  3 +-
+ test/unit/detail/format_man_test.cpp  | 10 +++++--
+ 3 files changed, 8 insertions(+), 3 deletions(-)
+
+diff --git a/test/unit/detail/format_help_test.cpp b/test/unit/detail/format_help_test.cpp
+index 54a99b6..ef2e326 100644
+--- a/test/unit/detail/format_help_test.cpp
++++ b/test/unit/detail/format_help_test.cpp
+@@ -176,6 +176,8 @@ TEST(help_page_printing, with_citation)
+                "    3-clause BSDL.\n"
+                "    In your academic works please cite: citation\n";
+     EXPECT_EQ(std_cout, expected);
++               "    In your academic works please cite:\n    [1]   citation\n";
++    EXPECT_EQ(get_parse_cout_on_exit(parser), expected);
+ }
+ 
+ TEST(help_page_printing, with_author)
+diff --git a/test/unit/detail/format_html_test.cpp b/test/unit/detail/format_html_test.cpp
+index 7f2a62d..aa38a45 100644
+--- a/test/unit/detail/format_html_test.cpp
++++ b/test/unit/detail/format_html_test.cpp
+@@ -201,8 +201,9 @@ TEST(html_format, full_information_information)
+           "<br>\n"
+           "<strong>SeqAn Copyright: </strong>2006-2025 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.\n"
+           "<br>\n"
+-          "<strong>In your academic works please cite: </strong>citation\n"
++          "<strong>In your academic works please cite: </strong>\n"
+           "<br>\n"
++          "</p>\n<dl>\n<dt><strong>[1]</strong></dt>\n<dd>citation</dd>\n</dl>\n<p>\n"
+           "For full copyright and/or warranty information see <strong>--copyright</strong>.\n"
+           "<br>\n"
+           "</p>\n"
+diff --git a/test/unit/detail/format_man_test.cpp b/test/unit/detail/format_man_test.cpp
+index df48961..154adfc 100644
+--- a/test/unit/detail/format_man_test.cpp
++++ b/test/unit/detail/format_man_test.cpp
+@@ -310,7 +310,10 @@ TEST_F(format_man_test, full_info_short_and_citation)
+ .br
+ \fBSeqAn Copyright: \fR2006-2025 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
+ .br
+-\fBIn your academic works please cite: \fRcitation
++\fBIn your academic works please cite: \fR
++.TP
++\fB[1]\fP
++citation
+ )";
+     testing::internal::CaptureStdout();
+     EXPECT_EXIT(parser.parse(), ::testing::ExitedWithCode(EXIT_SUCCESS), "");
+@@ -335,7 +338,10 @@ TEST_F(format_man_test, full_info_short_long_and_citation)
+ .br
+ \fBSeqAn Copyright: \fR2006-2025 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
+ .br
+-\fBIn your academic works please cite: \fRcitation
++\fBIn your academic works please cite: \fR
++.TP
++\fB[1]\fP
++citation
+ .br
+ For full copyright and/or warranty information see \fB--copyright\fR.
+ )";
+-- 
+2.47.2
+
