Merge pull request #235 from eseiler/infra/update_tdl

[INFRA] Update TDL

.github/workflows/ci_cmake.yml

@@ -27,10 +27,15 @@ defaults:
 
 jobs:
   build:
-    name: "External project"
+    name: "External project ${{ contains(matrix.SHARG_NO_TDL, 'OFF') && 'with TDL' || 'without TDL' }}"
     runs-on: ubuntu-22.04
     timeout-minutes: 120
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
+    strategy:
+      fail-fast: false
+      matrix:
+        SHARG_NO_TDL: [ON, OFF]
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -48,13 +53,30 @@ jobs:
         uses: seqan/actions/setup-toolchain@main
         with:
           compiler: gcc-13
-          use_actions_cache: false
+
+      - name: Install dependencies
+        if: matrix.SHARG_NO_TDL == 'OFF'
+        run: |
+          git clone --depth 1 --single-branch --branch 0.8.0 https://github.com/jbeder/yaml-cpp.git
+          cd yaml-cpp
+          mkdir build
+          cd build
+          cmake ../ -DCMAKE_BUILD_TYPE=Debug \
+                    -DYAML_CPP_BUILD_CONTRIB=OFF \
+                    -DYAML_CPP_BUILD_TOOLS=OFF \
+                    -DYAML_BUILD_SHARED_LIBS=OFF \
+                    -DYAML_CPP_INSTALL=ON \
+                    -DYAML_CPP_BUILD_TESTS=OFF \
+                    -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+          make -j2
+          sudo make install
 
       - name: Configure tests
         run: |
           mkdir sharg-build
           cd sharg-build
-          cmake ../sharg-parser/test/external_project -DCMAKE_BUILD_TYPE=Debug
+          cmake ../sharg-parser/test/external_project -DCMAKE_BUILD_TYPE=Debug \
+                                                      -DSHARG_NO_TDL=${{ matrix.SHARG_NO_TDL }}
           make -j2 sharg_test_prerequisite
 
       - name: Build tests

build_system/sharg-config.cmake

@@ -206,7 +206,20 @@ endif ()
 set (SHARG_USE_TDL FALSE)
 
 if (NOT SHARG_NO_TDL)
-    find_package (TDL QUIET HINTS ${SHARG_SUBMODULES_DIR}/submodules/tool_description_lib ${SHARG_HINT_TDL})
+    find_package (TDL QUIET HINTS ${SHARG_HINT_TDL})
+
+    if (NOT TDL_FOUND)
+        if (EXISTS ${SHARG_SUBMODULES_DIR}/submodules/tool_description_lib)
+            include (FetchContent)
+            FetchContent_Declare (tdl SOURCE_DIR ${SHARG_SUBMODULES_DIR}/submodules/tool_description_lib)
+            set (SHARG_LOG_LEVEL ${CMAKE_MESSAGE_LOG_LEVEL})
+            set (CMAKE_MESSAGE_LOG_LEVEL "ERROR")
+            option (INSTALL_TDL "Enable installation of TDL." ${INSTALL_SHARG})
+            FetchContent_MakeAvailable (tdl)
+            set (CMAKE_MESSAGE_LOG_LEVEL ${SHARG_LOG_LEVEL})
+            set (TDL_FOUND TRUE)
+        endif ()
+    endif ()
 
     if (TDL_FOUND)
         sharg_config_print ("Optional dependency:        TDL found.")

test/api_stability/1.1.1/0001-API-Update-TDL.patch

@@ -1,7 +1,7 @@
-From 27bc700234a23ea6c6c7337a427c4a3c6f2bbe55 Mon Sep 17 00:00:00 2001
+From ace25c7fffccdac9ccaf81329ada87f60021b5f9 Mon Sep 17 00:00:00 2001
 From: Simon Gene Gottlieb <[email protected]>
 Date: Thu, 5 Oct 2023 13:43:30 +0200
-Subject: [PATCH 1/3] [API] Update TDL
+Subject: [PATCH 1/5] [API] Update TDL
 
 ---
  test/unit/detail/format_ctd_test.cpp |  2 +-

test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch

@@ -1,7 +1,7 @@
-From 09a51343b1ee29f245eeae8210d50cd74ac9b1b4 Mon Sep 17 00:00:00 2001
+From 7bf847b4991636a59f26ca89977e94f51edfbf11 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Mon, 5 Feb 2024 16:02:03 +0100
-Subject: [PATCH 2/3] [API] Quoted strings and paths
+Subject: [PATCH 2/5] [API] Quoted strings and paths
 
 ---
  test/snippet/readme_sneak_peek.out            |  6 ++---

test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch

@@ -1,7 +1,7 @@
-From 859b9d015379e0d708700225fa55dd31f7d2e2f5 Mon Sep 17 00:00:00 2001
+From f02ddb2f31a47da16742dbf612d780b328e7602b Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Wed, 7 Feb 2024 13:31:22 +0100
-Subject: [PATCH 3/3] [NOAPI] Update copyright
+Subject: [PATCH 3/5] [NOAPI] Update copyright
 
 ---
  test/unit/detail/format_help_test.cpp | 10 +++++-----

test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch

@@ -0,0 +1,73 @@
+From 9f040f8ccb8d304841d24d8ac4d67db0d06c370f Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <[email protected]>
+Date: Fri, 9 Feb 2024 16:17:21 +0100
+Subject: [PATCH 4/5] [INFRA] Update TDL
+
+---
+ test/unit/detail/format_cwl_test.cpp | 28 +++++++++++++++++++++++++++-
+ 1 file changed, 27 insertions(+), 1 deletion(-)
+
+diff --git a/test/unit/detail/format_cwl_test.cpp b/test/unit/detail/format_cwl_test.cpp
+index 1d27cc3..eaf0cad 100644
+--- a/test/unit/detail/format_cwl_test.cpp
++++ b/test/unit/detail/format_cwl_test.cpp
+@@ -76,8 +76,16 @@ TEST(format_cwl_test, full_information)
+     parser.info.examples.push_back("example2");
+
+     std::string expected_short = "label: default\n"
+-                                 "doc: \"description\\ndescription2\\n\"\n"
++                                 "doc: \"description\\n"
++                                 "description2\\n"
++                                 "\"\n"
+                                  "inputs:\n"
++                                 "  positional_0:\n"
++                                 "    doc: this is a positional option.\n"
++                                 "    type: string?\n"
++                                 "  positional_1:\n"
++                                 "    doc: \"this is a positional option. Default: []\"\n"
++                                 "    type: string?\n"
+                                  "  int:\n"
+                                  "    doc: \"this is a int option. Default: 5\"\n"
+                                  "    type: long?\n"
+@@ -88,6 +96,12 @@ TEST(format_cwl_test, full_information)
+                                  "    type: long\n"
+                                  "    inputBinding:\n"
+                                  "      prefix: --jint\n"
++                                 "  flag:\n"
++                                 "    doc: this is a flag.\n"
++                                 "    type: boolean?\n"
++                                 "  kflag:\n"
++                                 "    doc: this is a flag.\n"
++                                 "    type: boolean?\n"
+                                  "outputs:\n"
+                                  "  []\n"
+                                  "cwlVersion: v1.2\n"
+@@ -196,6 +210,12 @@ TEST(format_cwl_test, subparser)
+         "label: default-index\n"
+         "doc: \"\"\n"
+         "inputs:\n"
++        "  positional_0:\n"
++        "    doc: this is a positional option.\n"
++        "    type: string?\n"
++        "  positional_1:\n"
++        "    doc: \"this is a positional option. Default: []\"\n"
++        "    type: string?\n"
+         "  int:\n"
+         "    doc: \"this is a int option. Default: 5\"\n"
+         "    type: long?\n"
+@@ -244,6 +264,12 @@ TEST(format_cwl_test, subparser)
+         "    type: string?\n"
+         "    inputBinding:\n"
+         "      prefix: --path05\n"
++        "  flag:\n"
++        "    doc: this is a flag.\n"
++        "    type: boolean?\n"
++        "  kflag:\n"
++        "    doc: this is a flag.\n"
++        "    type: boolean?\n"
+         "outputs:\n"
+         "  path04:\n"
+         "    type: File?\n"
+-- 
+2.43.0
+

test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-License-Identifier: BSD-3-Clause

test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch

@@ -0,0 +1,25 @@
+From 3a7dfd8103806e97af6376e9173d686b67fb5b52 Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <[email protected]>
+Date: Fri, 9 Feb 2024 18:13:36 +0100
+Subject: [PATCH 5/5] [INFRA] Use seqan3 main branch
+
+---
+ test/unit/detail/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/test/unit/detail/CMakeLists.txt b/test/unit/detail/CMakeLists.txt
+index 392f878..1f9a8e0 100644
+--- a/test/unit/detail/CMakeLists.txt
++++ b/test/unit/detail/CMakeLists.txt
+@@ -23,7 +23,7 @@ sharg_test (type_name_as_string_test.cpp)
+ sharg_test (version_check_debug_test.cpp)
+ sharg_test (version_check_release_test.cpp)
+
+-file (DOWNLOAD https://raw.githubusercontent.com/seqan/seqan3/master/include/seqan3/version.hpp
++file (DOWNLOAD https://raw.githubusercontent.com/seqan/seqan3/main/include/seqan3/version.hpp
+       ${CMAKE_BINARY_DIR}/include/seqan3/version.hpp)
+ sharg_test (seqan3_test.cpp)
+ target_include_directories (seqan3_test SYSTEM PUBLIC ${CMAKE_BINARY_DIR}/include)
+-- 
+2.43.0
+

test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-License-Identifier: BSD-3-Clause

test/external_project/CMakeLists.txt

@@ -24,9 +24,10 @@ ExternalProject_Add (
     sharg_submodule_add_subdirectory
     PREFIX sharg_submodule_add_subdirectory
     SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_submodule_add_subdirectory"
-    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS}
+    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} #
                "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}" #
-               "-DSHARG_ROOT=${SHARG_ROOT}")
+               "-DSHARG_ROOT=${SHARG_ROOT}" #
+               "-DSHARG_NO_TDL=${SHARG_NO_TDL}")
 
 # 2) This tests test/external_project/sharg_submodule_find_package/CMakeLists.txt
 #    We have a sharg checkout somewhere and we point CMAKE_PREFIX_PATH to <checkout>/sharg/build_system
@@ -37,8 +38,10 @@ ExternalProject_Add (
     sharg_submodule_find_package
     PREFIX sharg_submodule_find_package
     SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_submodule_find_package"
-    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}"
-               "-DCMAKE_PREFIX_PATH=${SHARG_ROOT}/build_system")
+    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} #
+               "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}" #
+               "-DCMAKE_PREFIX_PATH=${SHARG_ROOT}/build_system" #
+               "-DSHARG_NO_TDL=${SHARG_NO_TDL}")
 
 # 3) This tests test/external_project/sharg_installed/CMakeLists.txt
 #    This test assumes that sharg was installed by make install (e.g. system-wide).
@@ -53,8 +56,10 @@ ExternalProject_Add (
     sharg_installed
     PREFIX sharg_installed
     SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_installed"
-    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}"
-               "-DCMAKE_SYSTEM_PREFIX_PATH=${SHARG_SYSTEM_PREFIX}")
+    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} #
+               "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}" #
+               "-DCMAKE_SYSTEM_PREFIX_PATH=${SHARG_SYSTEM_PREFIX}" #
+               "-DSHARG_NO_TDL=${SHARG_NO_TDL}")
 add_dependencies (sharg_installed sharg_test_prerequisite)
 
 # 4) This tests test/external_project/sharg_fetch_content_zip/CMakeLists.txt
@@ -68,8 +73,10 @@ ExternalProject_Add (
     sharg_fetch_content_zip
     PREFIX sharg_fetch_content_zip
     SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_fetch_content_zip"
-    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}"
-               "-DSHARG_PACKAGE_ZIP_URL=${SHARG_PACKAGE_ZIP_URL}")
+    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} #
+               "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}" #
+               "-DSHARG_PACKAGE_ZIP_URL=${SHARG_PACKAGE_ZIP_URL}" #
+               "-DSHARG_NO_TDL=${SHARG_NO_TDL}")
 add_dependencies (sharg_fetch_content_zip sharg_test_prerequisite)
 
 # 5) This test is the same as 2) but emulates the settings within the setup tutorial.
@@ -78,4 +85,6 @@ ExternalProject_Add (
     sharg_setup_tutorial
     PREFIX sharg_setup_tutorial
     SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/sharg_setup_tutorial"
-    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}")
+    CMAKE_ARGS ${SHARG_EXTERNAL_PROJECT_CMAKE_ARGS} #
+               "-DCMAKE_FIND_DEBUG_MODE=${SHARG_EXTERNAL_PROJECT_FIND_DEBUG_MODE}" #
+               "-DSHARG_NO_TDL=${SHARG_NO_TDL}")

test/snippet/CMakeLists.txt

@@ -48,7 +48,6 @@ endmacro ()
 macro (sharg_snippets test_name_prefix snippet_base_path_)
     get_filename_component (snippet_base_path "${snippet_base_path_}" ABSOLUTE BASE_DIR
                             "${CMAKE_CURRENT_SOURCE_DIR}/../..")
-    message (STATUS "${snippet_base_path}")
     sharg_test_files (snippet_files "${snippet_base_path}" "*.cpp")
     foreach (snippet ${snippet_files})
         sharg_snippet ("${test_name_prefix}" "${snippet}" "${snippet_base_path}")

test/unit/detail/CMakeLists.txt

@@ -20,7 +20,7 @@ sharg_test (type_name_as_string_test.cpp)
 sharg_test (version_check_debug_test.cpp)
 sharg_test (version_check_release_test.cpp)
 
-file (DOWNLOAD https://raw.githubusercontent.com/seqan/seqan3/master/include/seqan3/version.hpp
+file (DOWNLOAD https://raw.githubusercontent.com/seqan/seqan3/main/include/seqan3/version.hpp
       ${CMAKE_BINARY_DIR}/include/seqan3/version.hpp)
 sharg_test (seqan3_test.cpp)
 target_include_directories (seqan3_test SYSTEM PUBLIC ${CMAKE_BINARY_DIR}/include)

test/unit/detail/format_cwl_test.cpp

@@ -79,8 +79,16 @@ TEST(format_cwl_test, full_information)
     parser.info.examples.push_back("example2");
 
     std::string expected_short = "label: default\n"
-                                 "doc: \"description\\ndescription2\\n\"\n"
+                                 "doc: \"description\\n"
+                                 "description2\\n"
+                                 "\"\n"
                                  "inputs:\n"
+                                 "  positional_0:\n"
+                                 "    doc: this is a positional option.\n"
+                                 "    type: string?\n"
+                                 "  positional_1:\n"
+                                 "    doc: \"this is a positional option. Default: []\"\n"
+                                 "    type: string?\n"
                                  "  int:\n"
                                  "    doc: \"this is a int option. Default: 5\"\n"
                                  "    type: long?\n"
@@ -91,6 +99,12 @@ TEST(format_cwl_test, full_information)
                                  "    type: long\n"
                                  "    inputBinding:\n"
                                  "      prefix: --jint\n"
+                                 "  flag:\n"
+                                 "    doc: this is a flag.\n"
+                                 "    type: boolean?\n"
+                                 "  kflag:\n"
+                                 "    doc: this is a flag.\n"
+                                 "    type: boolean?\n"
                                  "outputs:\n"
                                  "  []\n"
                                  "cwlVersion: v1.2\n"
@@ -199,6 +213,12 @@ TEST(format_cwl_test, subparser)
         "label: default-index\n"
         "doc: \"\"\n"
         "inputs:\n"
+        "  positional_0:\n"
+        "    doc: this is a positional option.\n"
+        "    type: string?\n"
+        "  positional_1:\n"
+        "    doc: \"this is a positional option. Default: []\"\n"
+        "    type: string?\n"
         "  int:\n"
         "    doc: \"this is a int option. Default: 5\"\n"
         "    type: long?\n"
@@ -247,6 +267,12 @@ TEST(format_cwl_test, subparser)
         "    type: string?\n"
         "    inputBinding:\n"
         "      prefix: --path05\n"
+        "  flag:\n"
+        "    doc: this is a flag.\n"
+        "    type: boolean?\n"
+        "  kflag:\n"
+        "    doc: this is a flag.\n"
+        "    type: boolean?\n"
         "outputs:\n"
         "  path04:\n"
         "    type: File?\n"

test/unit/detail/seqan3_test.cpp

@@ -6,6 +6,10 @@
 
 #include <sharg/parser.hpp>
 
+#if !__has_include(<seqan3/version.hpp>)
+#    error "seqan3/version.hpp is not available"
+#endif
+
 std::string const basic_options_str = "  Common options\n"
                                       "    -h, --help\n"
                                       "          Prints the help page.\n"