Merge branch 'main' into hibf

eseiler · eseiler · commit 2aa71e714ffb · 2026-01-27T20:38:47.000+01:00
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
@@ -39,7 +39,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -61,7 +61,7 @@ jobs:
 
       - name: Run tests
         working-directory: build
-        run: ctest -j
+        run: ctest -j --output-on-failure
 
       - name: Generate coverage report
         run: |
@@ -79,7 +79,7 @@ jobs:
                 --output ${GITHUB_WORKSPACE}/build/coverage_report.xml
 
       - name: Submit coverage build
-        uses: codecov/codecov-action@v5.4.2
+        uses: codecov/codecov-action@v5.5.2
         with:
           disable_search: true
           fail_ci_if_error: false
diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
@@ -35,12 +35,12 @@ jobs:
     steps:
       - name: Checkout
         if: github.event_name != 'pull_request_target'
-        uses: actions/checkout@v4
+        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@v4
+        uses: actions/checkout@v6
         with:
           ref: "refs/pull/${{ github.event.number }}/merge"
 
diff --git a/.github/workflows/ci_install.yml b/.github/workflows/ci_install.yml
@@ -40,7 +40,7 @@ jobs:
       options: --privileged
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           path: needle
 
@@ -90,12 +90,12 @@ jobs:
         if: contains(matrix.compiler, 'gcc')
         working-directory: build
         run: |
-          unshare -r -n ctest -j
+          unshare -r -n ctest -j --output-on-failure
           test -z $(find . -type f -executable -name "needle") # needle binary should not exist
 
       - name: Upload source package
         if: contains(matrix.compiler, 'gcc')
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: needle-source-package
           path: create_source_package/needle-*.tar.xz*
diff --git a/.github/workflows/ci_license.yml b/.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@v4
+        uses: actions/checkout@v6
 
       - name: REUSE Compliance Check
-        uses: fsfe/reuse-action@v5
+        uses: fsfe/reuse-action@v6
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
@@ -38,8 +38,18 @@ jobs:
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
+      - name: Free Up Space
+        if: matrix.compiler == 'intel'
+        run: |
+          df -h
+          du -hSd 1 "/__t"
+          if [[ -d "/__t" ]]; then
+            rm -fdr "/__t" || true
+            df -h
+          fi
+
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup cache
         uses: seqan/actions/setup-actions-cache@main
@@ -59,5 +69,5 @@ jobs:
 
       - name: Run tests
         working-directory: build
-        run: ctest -j
+        run: ctest -j --output-on-failure
 
diff --git a/.github/workflows/ci_macos.yml b/.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@v4
+        uses: actions/checkout@v6
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main
@@ -60,4 +60,4 @@ jobs:
 
       - name: Run tests
         working-directory: build
-        run: ctest -j
+        run: ctest -j --output-on-failure
diff --git a/.github/workflows/cron_codeql.yml b/.github/workflows/cron_codeql.yml
@@ -32,17 +32,17 @@ jobs:
       image: ghcr.io/seqan/gcc-second-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: cpp
 
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v3
+      uses: github/codeql-action/autobuild@v4
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4
       with:
         category: "/language:cpp"
diff --git a/.github/workflows/cron_sanitizer.yml b/.github/workflows/cron_sanitizer.yml
@@ -74,7 +74,7 @@ jobs:
       image: ${{ matrix.image || '' }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup compiler
         if: contains(matrix.os, 'macos')
diff --git a/cmake/CPM.cmake b/cmake/CPM.cmake
@@ -2,8 +2,8 @@
 #
 # SPDX-FileCopyrightText: Copyright (c) 2019-2023 Lars Melchior and contributors
 
-set (CPM_DOWNLOAD_VERSION 0.42.0)
-set (CPM_HASH_SUM "2020b4fc42dba44817983e06342e682ecfc3d2f484a581f11cc5731fbe4dce8a")
+set (CPM_DOWNLOAD_VERSION 0.42.1)
+set (CPM_HASH_SUM "f3a6dcc6a04ce9e7f51a127307fa4f699fb2bade357a8eb4c5b45df76e1dc6a5")
 
 if (CPM_SOURCE_CACHE)
     set (CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake
@@ -8,7 +8,7 @@
 # cmake-format: off
 
 # hibf
-set (NEEDLE_HIBF_VERSION e49afc1172ebd183730ca070dd1081458225ef3b CACHE STRING "")
+set (NEEDLE_HIBF_VERSION fc4e40d8672f496a32df73c608915d45e715f6a8 CACHE STRING "")
 CPMDeclarePackage (hibf
                    NAME hibf
                    GIT_TAG ${NEEDLE_HIBF_VERSION} # main
@@ -19,21 +19,23 @@ CPMDeclarePackage (hibf
 )
 
 # seqan3
-set (NEEDLE_SEQAN3_VERSION a63abbb4b01bf6dedf14f2a61eeca28ca6e4994a CACHE STRING "")
+set (NEEDLE_SEQAN3_VERSION 3.4.0 CACHE STRING "")
 CPMDeclarePackage (seqan3
                    NAME seqan3
-                   GIT_TAG ${NEEDLE_SEQAN3_VERSION} # main
+                   VERSION ${NEEDLE_SEQAN3_VERSION}
+                   GIT_TAG ${NEEDLE_SEQAN3_VERSION}
                    GITHUB_REPOSITORY seqan/seqan3
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 
 # sharg
-set (NEEDLE_SHARG_VERSION be113bcffe49c0d62cbd65a191820f05386aa8da CACHE STRING "")
+set (NEEDLE_SHARG_VERSION 1.2.1 CACHE STRING "")
 CPMDeclarePackage (sharg
                    NAME sharg
-                   GIT_TAG ${NEEDLE_SHARG_VERSION} # main
+                   VERSION ${NEEDLE_SHARG_VERSION}
+                   GIT_TAG ${NEEDLE_SHARG_VERSION}
                    GITHUB_REPOSITORY seqan/sharg-parser
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
diff --git a/cmake/test/config.cmake b/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
diff --git a/test/app_test.hpp b/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)
diff --git a/test/cli/count_options_test.cpp b/test/cli/count_options_test.cpp
@@ -12,19 +12,22 @@ struct count_options_test : public app_test
 TEST_F(count_options_test, no_options)
 {
     app_test_result result = execute_app("count");
-    std::string expected{"needle-count - Get expression value depending on minimizers. "
-                         "This function is an alternative to pseudoaligners like kallisto. It "
-                         "estimates the expression value for all sequences in the genome file "
-                         "based on the exact minimiser occurrences of the given sequence files. "
-                         "Please run genome beforehand to create the genome file.\n"
-                         "======================================================================"
-                         "======================================================================"
-                         "======================================================================"
-                         "======================================================================"
-                         "==========================================\n    "
-                         "Try -h or --help for more information.\n"};
+    std::string expected{"needle-count - Get expression value depending on minimizers. This function is an alternative "
+                         "to pseudoaligners like kallisto. It estimates the expression value for all sequences in the "
+                         "genome file based on the exact minimiser occurrences of the given sequence files. Please run "
+                         "genome beforehand to create the genome "
+                         "file.\n======================================================================================"
+                         "============================================================================================="
+                         "============================================================================================="
+                         "==================================================\n"
+                         "    needle count [-p|--paired] [-k|--kmer uint8] [-w|--window uint32] [--shape\n"
+                         "    uint64] [--seed uint64] [-o|--out path] [-t|--threads uint16] --include\n"
+                         "    path [--genome path] [--] path...\n"
+                         "    Try -h or --help for more information.\n"};
     EXPECT_SUCCESS(result);
+#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
     EXPECT_EQ(result.out, expected);
+#endif
     EXPECT_EQ(result.err, std::string{});
 }
 
@@ -85,9 +88,14 @@ TEST_F(genome_options_test, no_options)
     app_test_result result = execute_app("genome");
     std::string expected{"needle-genome - Creates the genome file necessary as an input to count.\n"
                          "=======================================================================\n"
+                         "    needle genome [-k|--kmer uint8] [-w|--window uint32] [--shape uint64]\n"
+                         "    [--seed uint64] [-o|--out path] [-t|--threads uint16] [--exclude path]\n"
+                         "    [--] path\n"
                          "    Try -h or --help for more information.\n"};
     EXPECT_SUCCESS(result);
+#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
     EXPECT_EQ(result.out, expected);
+#endif
     EXPECT_EQ(result.err, std::string{});
 }
 
diff --git a/test/cli/delete_options_test.cpp b/test/cli/delete_options_test.cpp
@@ -16,9 +16,13 @@ TEST_F(delete_options_test, delete_no_options)
     app_test_result result = execute_app("delete");
     std::string expected{"needle-delete - Delete experiments specified by their position from the Needle index.\n"
                          "=====================================================================================\n"
+                         "    needle delete [-c|--compressed] [-o|--out path] [-t|--threads uint16]\n"
+                         "    [-i|--in path] [--] uint64...\n"
                          "    Try -h or --help for more information.\n"};
     EXPECT_SUCCESS(result);
+#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
     EXPECT_EQ(result.out, expected);
+#endif
     EXPECT_EQ(result.err, std::string{});
 }
 
diff --git a/test/cli/estimate_options_test.cpp b/test/cli/estimate_options_test.cpp
@@ -16,9 +16,13 @@ TEST_F(estimate_options_test, no_options)
     app_test_result result = execute_app("estimate");
     std::string expected{"needle-estimate - Estimate expression value of transcript based on the Needle index.\n"
                          "====================================================================================\n"
+                         "    needle estimate [-m|--normalization-mode] [-i|--in path] [-o|--out path]\n"
+                         "    [-t|--threads uint16] [-b|--batch uint64] [--] path\n"
                          "    Try -h or --help for more information.\n"};
     EXPECT_SUCCESS(result);
+#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
     EXPECT_EQ(result.out, expected);
+#endif
     EXPECT_EQ(result.err, std::string{});
 }
 
diff --git a/test/cli/ibf_options_test.cpp b/test/cli/ibf_options_test.cpp
@@ -14,9 +14,17 @@ TEST_F(ibf_options_test, ibf_no_options)
     app_test_result result = execute_app("ibf");
     std::string expected{"needle-ibf - Constructs the Needle index.\n"
                          "=========================================\n"
+                         "    needle ibf [-p|--paired] [--ram] [-k|--kmer uint8] [-w|--window uint32]\n"
+                         "    [--shape uint64] [--seed uint64] [-o|--out path] [-t|--threads uint16]\n"
+                         "    [-f|--fpr double]... [-e|--expression_thresholds uint16]...\n"
+                         "    [-l|--number_expression_thresholds uint8] [-n|--hash uint64] [--include\n"
+                         "    path] [--exclude path] [--samples uint64]... [--cutoff uint8]...\n"
+                         "    [--experiment-names bool] [--levels-by-genome path] [--] path...\n"
                          "    Try -h or --help for more information.\n"};
     EXPECT_SUCCESS(result);
+#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
     EXPECT_EQ(result.out, expected);
+#endif
     EXPECT_EQ(result.err, std::string{});
 }
 
@@ -103,9 +111,14 @@ TEST_F(ibf_options_test, ibfmin_no_options)
     std::string expected{
         "needle-ibfmin - Constructs the Needle index from the minimiser files created by needle minimiser.\n"
         "=================================================================================================\n"
+        "    needle ibfmin [-o|--out path] [-t|--threads uint16] [--levels-by-genome\n"
+        "    path] [-f|--fpr double]... [-e|--expression_thresholds uint16]...\n"
+        "    [-l|--number_expression_thresholds uint8] [-n|--hash uint64] [--] path...\n"
         "    Try -h or --help for more information.\n"};
     EXPECT_SUCCESS(result);
+#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
     EXPECT_EQ(result.out, expected);
+#endif
     EXPECT_EQ(result.err, std::string{});
 }
 
diff --git a/test/cli/insert_options_test.cpp b/test/cli/insert_options_test.cpp
@@ -14,11 +14,17 @@ struct insert_options_test : public app_test
 TEST_F(insert_options_test, insert_no_options)
 {
     app_test_result result = execute_app("insert");
-    std::string expected{"needle-insert - Inserts into a given Needle index.\n"
-                         "==================================================\n"
+    std::string expected{"needle-insert - Inserts into a given uncompressed Needle index.\n"
+                         "===============================================================\n"
+                         "    needle insert [-p|--paired] [-c|--compressed] [--ram] [--include path]\n"
+                         "    [--exclude path] [--samples uint64]... [--cutoff uint8]... [-t|--threads\n"
+                         "    uint16] [-i|--in path] [--experiment-names bool] [--levels-by-genome path]\n"
+                         "    [--] path...\n"
                          "    Try -h or --help for more information.\n"};
     EXPECT_SUCCESS(result);
+#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
     EXPECT_EQ(result.out, expected);
+#endif
     EXPECT_EQ(result.err, std::string{});
 }
 
diff --git a/test/cli/minimiser_options_test.cpp b/test/cli/minimiser_options_test.cpp
@@ -14,9 +14,15 @@ TEST_F(minimiser_options_test, no_options)
     app_test_result result = execute_app("minimiser");
     std::string expected{"needle-minimiser - Calculates minimiser for given experiments.\n"
                          "==============================================================\n"
+                         "    needle minimiser [-p|--paired] [--ram] [-k|--kmer uint8] [-w|--window\n"
+                         "    uint32] [--shape uint64] [--seed uint64] [-o|--out path] [-t|--threads\n"
+                         "    uint16] [--include path] [--exclude path] [--samples uint64]... [--cutoff\n"
+                         "    uint8]... [--] path...\n"
                          "    Try -h or --help for more information.\n"};
     EXPECT_SUCCESS(result);
+#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
     EXPECT_EQ(result.out, expected);
+#endif
     EXPECT_EQ(result.err, std::string{});
 }
 

Original file line number	Diff line number	Diff line change
`@@ -2,8 +2,8 @@`
`2`	`2`	`#`
`3`	`3`	`# SPDX-FileCopyrightText: Copyright (c) 2019-2023 Lars Melchior and contributors`
`4`	`4`
`5`		`-set (CPM_DOWNLOAD_VERSION 0.42.0)`
`6`		`-set (CPM_HASH_SUM "2020b4fc42dba44817983e06342e682ecfc3d2f484a581f11cc5731fbe4dce8a")`
	`5`	`+set (CPM_DOWNLOAD_VERSION 0.42.1)`
	`6`	`+set (CPM_HASH_SUM "f3a6dcc6a04ce9e7f51a127307fa4f699fb2bade357a8eb4c5b45df76e1dc6a5")`
`7`	`7`
`8`	`8`	`if (CPM_SOURCE_CACHE)`
`9`	`9`	`set (CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")`