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eseilereseiler
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fix: new sharg version
1 parent a371785 commit ff3755a

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11 files changed

+60
-17
lines changed

11 files changed

+60
-17
lines changed

‎.github/workflows/ci_coverage.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -61,7 +61,7 @@ jobs:
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- name: Run tests
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working-directory: build
64-
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

Lines changed: 1 addition & 1 deletion
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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: |
93-
unshare -r -n ctest -j
93+
unshare -r -n ctest -j --output-on-failure
9494
test -z $(find . -type f -executable -name "needle") # needle binary should not exist
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9696
- name: Upload source package

‎.github/workflows/ci_linux.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -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
63+
run: ctest -j --output-on-failure

‎cmake/package-lock.cmake‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,10 +31,11 @@ CPMDeclarePackage (seqan3
3131
)
3232

3333
# sharg
34-
set (NEEDLE_SHARG_VERSION 983dc3dc415d9fc193fb4dac110cc2ecac2ca4bc CACHE STRING "")
34+
set (NEEDLE_SHARG_VERSION 1.2.1 CACHE STRING "")
3535
CPMDeclarePackage (sharg
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NAME sharg
37-
GIT_TAG ${NEEDLE_SHARG_VERSION} # main
37+
VERSION ${NEEDLE_SHARG_VERSION}
38+
GIT_TAG ${NEEDLE_SHARG_VERSION}
3839
GITHUB_REPOSITORY seqan/sharg-parser
3940
SYSTEM TRUE
4041
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
1212
TEST_F(count_options_test, no_options)
1313
{
1414
app_test_result result = execute_app("count");
15-
std::string expected{"needle-count - Get expression value depending on minimizers. "
16-
"This function is an alternative to pseudoaligners like kallisto. It "
17-
"estimates the expression value for all sequences in the genome file "
18-
"based on the exact minimiser occurrences of the given sequence files. "
19-
"Please run genome beforehand to create the genome file.\n"
20-
"======================================================================"
21-
"======================================================================"
22-
"======================================================================"
23-
"======================================================================"
24-
"==========================================\n "
25-
"Try -h or --help for more information.\n"};
15+
std::string expected{"needle-count - Get expression value depending on minimizers. This function is an alternative "
16+
"to pseudoaligners like kallisto. It estimates the expression value for all sequences in the "
17+
"genome file based on the exact minimiser occurrences of the given sequence files. Please run "
18+
"genome beforehand to create the genome "
19+
"file.\n======================================================================================"
20+
"============================================================================================="
21+
"============================================================================================="
22+
"==================================================\n"
23+
" needle count [-p|--paired] [-k|--kmer uint8] [-w|--window uint32] [--shape\n"
24+
" uint64] [--seed uint64] [-o|--out path] [-t|--threads uint16] --include\n"
25+
" path [--genome path] [--] path...\n"
26+
" Try -h or --help for more information.\n"};
2627
EXPECT_SUCCESS(result);
28+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
2729
EXPECT_EQ(result.out, expected);
30+
#endif
2831
EXPECT_EQ(result.err, std::string{});
2932
}
3033

@@ -85,9 +88,14 @@ TEST_F(genome_options_test, no_options)
8588
app_test_result result = execute_app("genome");
8689
std::string expected{"needle-genome - Creates the genome file necessary as an input to count.\n"
8790
"=======================================================================\n"
91+
" needle genome [-k|--kmer uint8] [-w|--window uint32] [--shape uint64]\n"
92+
" [--seed uint64] [-o|--out path] [-t|--threads uint16] [--exclude path]\n"
93+
" [--] path\n"
8894
" Try -h or --help for more information.\n"};
8995
EXPECT_SUCCESS(result);
96+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
9097
EXPECT_EQ(result.out, expected);
98+
#endif
9199
EXPECT_EQ(result.err, std::string{});
92100
}
93101

‎test/cli/delete_options_test.cpp‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,9 +16,13 @@ TEST_F(delete_options_test, delete_no_options)
1616
app_test_result result = execute_app("delete");
1717
std::string expected{"needle-delete - Delete experiments specified by their position from the Needle index.\n"
1818
"=====================================================================================\n"
19+
" needle delete [-c|--compressed] [-o|--out path] [-t|--threads uint16]\n"
20+
" [-i|--in path] [--] uint64...\n"
1921
" Try -h or --help for more information.\n"};
2022
EXPECT_SUCCESS(result);
23+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
2124
EXPECT_EQ(result.out, expected);
25+
#endif
2226
EXPECT_EQ(result.err, std::string{});
2327
}
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‎test/cli/estimate_options_test.cpp‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,9 +16,13 @@ TEST_F(estimate_options_test, no_options)
1616
app_test_result result = execute_app("estimate");
1717
std::string expected{"needle-estimate - Estimate expression value of transcript based on the Needle index.\n"
1818
"====================================================================================\n"
19+
" needle estimate [-m|--normalization-mode] [-i|--in path] [-o|--out path]\n"
20+
" [-t|--threads uint16] [-b|--batch uint64] [--] path\n"
1921
" Try -h or --help for more information.\n"};
2022
EXPECT_SUCCESS(result);
23+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
2124
EXPECT_EQ(result.out, expected);
25+
#endif
2226
EXPECT_EQ(result.err, std::string{});
2327
}
2428

‎test/cli/ibf_options_test.cpp‎

Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -14,9 +14,17 @@ TEST_F(ibf_options_test, ibf_no_options)
1414
app_test_result result = execute_app("ibf");
1515
std::string expected{"needle-ibf - Constructs the Needle index.\n"
1616
"=========================================\n"
17+
" needle ibf [-c|--compressed] [-p|--paired] [--ram] [-k|--kmer uint8]\n"
18+
" [-w|--window uint32] [--shape uint64] [--seed uint64] [-o|--out path]\n"
19+
" [-t|--threads uint16] [-f|--fpr double]... [-e|--expression_thresholds\n"
20+
" uint16]... [-l|--number_expression_thresholds uint8] [-n|--hash uint64]\n"
21+
" [--include path] [--exclude path] [--samples uint64]... [--cutoff\n"
22+
" uint8]... [--experiment-names bool] [--levels-by-genome path] [--] path...\n"
1723
" Try -h or --help for more information.\n"};
1824
EXPECT_SUCCESS(result);
25+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
1926
EXPECT_EQ(result.out, expected);
27+
#endif
2028
EXPECT_EQ(result.err, std::string{});
2129
}
2230

@@ -103,9 +111,15 @@ TEST_F(ibf_options_test, ibfmin_no_options)
103111
std::string expected{
104112
"needle-ibfmin - Constructs the Needle index from the minimiser files created by needle minimiser.\n"
105113
"=================================================================================================\n"
114+
" needle ibfmin [-c|--compressed] [-o|--out path] [-t|--threads uint16]\n"
115+
" [--levels-by-genome path] [-f|--fpr double]... [-e|--expression_thresholds\n"
116+
" uint16]... [-l|--number_expression_thresholds uint8] [-n|--hash uint64]\n"
117+
" [--] path...\n"
106118
" Try -h or --help for more information.\n"};
107119
EXPECT_SUCCESS(result);
120+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
108121
EXPECT_EQ(result.out, expected);
122+
#endif
109123
EXPECT_EQ(result.err, std::string{});
110124
}
111125

‎test/cli/insert_options_test.cpp‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,9 +16,15 @@ TEST_F(insert_options_test, insert_no_options)
1616
app_test_result result = execute_app("insert");
1717
std::string expected{"needle-insert - Inserts into a given uncompressed Needle index.\n"
1818
"===============================================================\n"
19+
" needle insert [-p|--paired] [-c|--compressed] [--ram] [--include path]\n"
20+
" [--exclude path] [--samples uint64]... [--cutoff uint8]... [-t|--threads\n"
21+
" uint16] [-i|--in path] [--experiment-names bool] [--levels-by-genome path]\n"
22+
" [--] path...\n"
1923
" Try -h or --help for more information.\n"};
2024
EXPECT_SUCCESS(result);
25+
#ifndef __APPLE__ // uint64_t vs unsigned long in sharg 1.2.1
2126
EXPECT_EQ(result.out, expected);
27+
#endif
2228
EXPECT_EQ(result.err, std::string{});
2329
}
2430

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