Bump actions/checkout from 5 to 6

.github/workflows/ci_coverage.yml

@@ -39,7 +39,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 

.github/workflows/ci_documentation.yml

@@ -35,12 +35,12 @@ jobs:
     steps:
       - name: Checkout
         if: github.event_name != 'pull_request_target'
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       # pull_request_target does not checkout the merge commit by default
       - name: Checkout
         if: github.event_name == 'pull_request_target'
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           ref: "refs/pull/${{ github.event.number }}/merge"
 

.github/workflows/ci_install.yml

@@ -40,7 +40,7 @@ jobs:
       options: --privileged
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           path: needle
 

.github/workflows/ci_license.yml

@@ -28,7 +28,7 @@ jobs:
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: REUSE Compliance Check
         uses: fsfe/reuse-action@v6

.github/workflows/ci_linux.yml

@@ -49,7 +49,7 @@ jobs:
           fi
 
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup cache
         uses: seqan/actions/setup-actions-cache@main

.github/workflows/ci_macos.yml

@@ -37,7 +37,7 @@ jobs:
         compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main

.github/workflows/cron_codeql.yml

@@ -32,7 +32,7 @@ jobs:
       image: ghcr.io/seqan/gcc-second-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
 
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v4

.github/workflows/cron_sanitizer.yml

@@ -74,7 +74,7 @@ jobs:
       image: ${{ matrix.image || '' }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup compiler
         if: contains(matrix.os, 'macos')

cmake/test/config.cmake

@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: CC0-1.0
 
 include (test/coverage)
+include (CMakeDependentOption)
 
 CPMGetPackage (googletest)
 
@@ -25,6 +26,9 @@ else ()
 endif ()
 add_definitions (-DBINDIR=\"${NEEDLE_TEST_BINARY_DIR}/\")
 
+option (NEEDLE_DO_NOT_KEEP_TEST_OUTPUT "Delete test output." OFF)
+cmake_dependent_option (NEEDLE_DO_NOT_KEEP_TEST_OUTPUT_CI "Delete test output." ON "DEFINED ENV{CI}" OFF)
+
 # Add the test interface library.
 if (NOT TARGET ${PROJECT_NAME}_test)
     add_library (${PROJECT_NAME}_test INTERFACE)
@@ -42,6 +46,11 @@ if (NOT TARGET ${PROJECT_NAME}_test)
         endif ()
     endif ()
 
+    if (NEEDLE_DO_NOT_KEEP_TEST_OUTPUT OR NEEDLE_DO_NOT_KEEP_TEST_OUTPUT_CI)
+        message (STATUS "Deleting test output.")
+        target_compile_definitions (${PROJECT_NAME}_test INTERFACE "NEEDLE_DO_NOT_KEEP_TEST_OUTPUT")
+    endif ()
+
     target_link_libraries (${PROJECT_NAME}_test INTERFACE "${PROJECT_NAME}_lib" "GTest::gtest_main")
 
     # !Workaround: Get seqan3 test include dir from seqan3 target

test/app_test.hpp

@@ -114,6 +114,9 @@ struct app_test : public ::testing::Test
     {
         try
         {
+#ifdef NEEDLE_DO_NOT_KEEP_TEST_OUTPUT
+            std::filesystem::remove_all(current_workdir);
+#endif
             std::filesystem::current_path(original_workdir); // restore the original work dir
         }
         catch (std::exception const & exc)

test/cli/insert_options_test.cpp

@@ -34,17 +34,16 @@ TEST_F(insert_options_test, insert_fail_no_argument)
 
 TEST_F(insert_options_test, with_argument)
 {
-    std::filesystem::path tmp_dir = std::filesystem::temp_directory_path();
     estimate_ibf_arguments ibf_args{};
     minimiser_file_input_arguments minimiser_args{};
     ibf_args.expression_thresholds = {1, 2};
     std::vector<double> fpr = {0.05};
     std::vector<std::filesystem::path> sequence_files = {data("exp_01.fasta")};
-    ibf_args.path_out = tmp_dir / "Test_";
+    ibf_args.path_out = "Test_";
     std::vector<uint8_t> cutoffs{1};
     ibf(sequence_files, ibf_args, minimiser_args, fpr, cutoffs);
 
-    app_test_result result = execute_app("insert -i ", tmp_dir / "Test_", data("exp_01.fasta"));
+    app_test_result result = execute_app("insert -i ", "Test_", data("exp_01.fasta"));
     EXPECT_SUCCESS(result);
     EXPECT_EQ(result.out, "");
     EXPECT_EQ(result.err, std::string{});