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eseilereseiler
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Merge pull request #233 from seqan/actions/update_cpm_package_lock
[INFRA] Update CPM Packages
2 parents 67b9121 + ff3755a commit 4d567d7

12 files changed

+62
-19
lines changed

‎.github/workflows/ci_coverage.yml‎

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@@ -61,7 +61,7 @@ jobs:
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- name: Run tests
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working-directory: build
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run: ctest -j
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run: ctest -j --output-on-failure
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- name: Generate coverage report
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run: |

‎.github/workflows/ci_install.yml‎

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@@ -90,7 +90,7 @@ jobs:
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if: contains(matrix.compiler, 'gcc')
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working-directory: build
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run: |
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unshare -r -n ctest -j
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unshare -r -n ctest -j --output-on-failure
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test -z $(find . -type f -executable -name "needle") # needle binary should not exist
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- name: Upload source package

‎.github/workflows/ci_linux.yml‎

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@@ -69,5 +69,5 @@ jobs:
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- name: Run tests
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working-directory: build
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run: ctest -j
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run: ctest -j --output-on-failure
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‎.github/workflows/ci_macos.yml‎

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@@ -60,4 +60,4 @@ jobs:
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- name: Run tests
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working-directory: build
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run: ctest -j
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run: ctest -j --output-on-failure

‎cmake/CPM.cmake‎

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

‎cmake/package-lock.cmake‎

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Original file line numberDiff line numberDiff line change
@@ -31,10 +31,11 @@ CPMDeclarePackage (seqan3
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)
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# sharg
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set (NEEDLE_SHARG_VERSION d3b6c025554fc28a6f94d475fc136894b441432e CACHE STRING "")
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set (NEEDLE_SHARG_VERSION 1.2.1 CACHE STRING "")
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CPMDeclarePackage (sharg
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NAME sharg
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GIT_TAG ${NEEDLE_SHARG_VERSION} # main
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VERSION ${NEEDLE_SHARG_VERSION}
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GIT_TAG ${NEEDLE_SHARG_VERSION}
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GITHUB_REPOSITORY seqan/sharg-parser
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SYSTEM TRUE
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EXCLUDE_FROM_ALL TRUE

‎test/cli/count_options_test.cpp‎

Lines changed: 19 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -12,19 +12,22 @@ struct count_options_test : public app_test
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TEST_F(count_options_test, no_options)
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{
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app_test_result result = execute_app("count");
15-
std::string expected{"needle-count - Get expression value depending on minimizers. "
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"This function is an alternative to pseudoaligners like kallisto. It "
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"estimates the expression value for all sequences in the genome file "
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"based on the exact minimiser occurrences of the given sequence files. "
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"Please run genome beforehand to create the genome file.\n"
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"======================================================================"
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"======================================================================"
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"======================================================================"
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"======================================================================"
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"==========================================\n "
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"Try -h or --help for more information.\n"};
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std::string expected{"needle-count - Get expression value depending on minimizers. This function is an alternative "
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"to pseudoaligners like kallisto. It estimates the expression value for all sequences in the "
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"genome file based on the exact minimiser occurrences of the given sequence files. Please run "
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"genome beforehand to create the genome "
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"file.\n======================================================================================"
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"============================================================================================="
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"============================================================================================="
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"==================================================\n"
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" needle count [-p|--paired] [-k|--kmer uint8] [-w|--window uint32] [--shape\n"
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" uint64] [--seed uint64] [-o|--out path] [-t|--threads uint16] --include\n"
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" path [--genome path] [--] path...\n"
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" Try -h or --help for more information.\n"};
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EXPECT_SUCCESS(result);
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#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
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EXPECT_EQ(result.out, expected);
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#endif
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EXPECT_EQ(result.err, std::string{});
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}
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@@ -85,9 +88,14 @@ TEST_F(genome_options_test, no_options)
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app_test_result result = execute_app("genome");
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std::string expected{"needle-genome - Creates the genome file necessary as an input to count.\n"
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"=======================================================================\n"
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" needle genome [-k|--kmer uint8] [-w|--window uint32] [--shape uint64]\n"
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" [--seed uint64] [-o|--out path] [-t|--threads uint16] [--exclude path]\n"
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" [--] path\n"
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" Try -h or --help for more information.\n"};
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EXPECT_SUCCESS(result);
96+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
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EXPECT_EQ(result.out, expected);
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#endif
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EXPECT_EQ(result.err, std::string{});
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}
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‎test/cli/delete_options_test.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -16,9 +16,13 @@ TEST_F(delete_options_test, delete_no_options)
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app_test_result result = execute_app("delete");
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std::string expected{"needle-delete - Delete experiments specified by their position from the Needle index.\n"
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"=====================================================================================\n"
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" needle delete [-c|--compressed] [-o|--out path] [-t|--threads uint16]\n"
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" [-i|--in path] [--] uint64...\n"
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" Try -h or --help for more information.\n"};
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EXPECT_SUCCESS(result);
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#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
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EXPECT_EQ(result.out, expected);
25+
#endif
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EXPECT_EQ(result.err, std::string{});
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}
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‎test/cli/estimate_options_test.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -16,9 +16,13 @@ TEST_F(estimate_options_test, no_options)
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app_test_result result = execute_app("estimate");
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std::string expected{"needle-estimate - Estimate expression value of transcript based on the Needle index.\n"
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"====================================================================================\n"
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" needle estimate [-m|--normalization-mode] [-i|--in path] [-o|--out path]\n"
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" [-t|--threads uint16] [-b|--batch uint64] [--] path\n"
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" Try -h or --help for more information.\n"};
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EXPECT_SUCCESS(result);
23+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
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EXPECT_EQ(result.out, expected);
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#endif
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EXPECT_EQ(result.err, std::string{});
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}
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‎test/cli/ibf_options_test.cpp‎

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@@ -14,9 +14,17 @@ TEST_F(ibf_options_test, ibf_no_options)
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app_test_result result = execute_app("ibf");
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std::string expected{"needle-ibf - Constructs the Needle index.\n"
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"=========================================\n"
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" needle ibf [-c|--compressed] [-p|--paired] [--ram] [-k|--kmer uint8]\n"
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" [-w|--window uint32] [--shape uint64] [--seed uint64] [-o|--out path]\n"
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" [-t|--threads uint16] [-f|--fpr double]... [-e|--expression_thresholds\n"
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" uint16]... [-l|--number_expression_thresholds uint8] [-n|--hash uint64]\n"
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" [--include path] [--exclude path] [--samples uint64]... [--cutoff\n"
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" uint8]... [--experiment-names bool] [--levels-by-genome path] [--] path...\n"
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" Try -h or --help for more information.\n"};
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EXPECT_SUCCESS(result);
25+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
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EXPECT_EQ(result.out, expected);
27+
#endif
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EXPECT_EQ(result.err, std::string{});
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}
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@@ -103,9 +111,15 @@ TEST_F(ibf_options_test, ibfmin_no_options)
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std::string expected{
104112
"needle-ibfmin - Constructs the Needle index from the minimiser files created by needle minimiser.\n"
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"=================================================================================================\n"
114+
" needle ibfmin [-c|--compressed] [-o|--out path] [-t|--threads uint16]\n"
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" [--levels-by-genome path] [-f|--fpr double]... [-e|--expression_thresholds\n"
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" uint16]... [-l|--number_expression_thresholds uint8] [-n|--hash uint64]\n"
117+
" [--] path...\n"
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" Try -h or --help for more information.\n"};
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EXPECT_SUCCESS(result);
120+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
108121
EXPECT_EQ(result.out, expected);
122+
#endif
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EXPECT_EQ(result.err, std::string{});
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}
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