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[INFRA] Update CPM Packages #319

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Merged
eseiler merged 2 commits into from
Mar 1, 2026
Merged

[INFRA] Update CPM Packages #319

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b26c0fe
[INFRA] Update CPM Packages
seqan-actions Mar 1, 2026
03ab2d4
fix: hibf config version
eseiler Mar 1, 2026
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6 changes: 3 additions & 3 deletions cmake/package-lock.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
# cmake-format: off

# hibf
set (CHOPPER_HIBF_VERSION fc4e40d8672f496a32df73c608915d45e715f6a8 CACHE STRING "")
set (CHOPPER_HIBF_VERSION bbca76409f5445f1404c206021fcfa37f1fd7054 CACHE STRING "")
CPMDeclarePackage (hibf
NAME hibf
GIT_TAG ${CHOPPER_HIBF_VERSION} # main
Expand All @@ -18,7 +18,7 @@ CPMDeclarePackage (hibf
OPTIONS "INSTALL_HIBF OFF"
)
# sharg
set (CHOPPER_SHARG_VERSION 1.2.1 CACHE STRING "")
set (CHOPPER_SHARG_VERSION 1.2.2 CACHE STRING "")
CPMDeclarePackage (sharg
NAME sharg
VERSION ${CHOPPER_SHARG_VERSION}
Expand All @@ -29,7 +29,7 @@ CPMDeclarePackage (sharg
OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING" "BUILD_TESTING OFF"
)
# seqan3
set (CHOPPER_SEQAN3_VERSION 3.4.0 CACHE STRING "")
set (CHOPPER_SEQAN3_VERSION 3.4.1 CACHE STRING "")
CPMDeclarePackage (seqan3
NAME seqan3
VERSION ${CHOPPER_SEQAN3_VERSION}
Expand Down
3 changes: 2 additions & 1 deletion test/api/config_test.cpp
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Expand Up @@ -95,7 +95,7 @@ static constexpr std::string_view config_string_view{"@CHOPPER_CONFIG\n"
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 123456789,\n"
"@ \"number_of_hash_functions\": 4,\n"
"@ \"maximum_fpr\": 0.0001,\n"
Expand All @@ -104,6 +104,7 @@ static constexpr std::string_view config_string_view{"@CHOPPER_CONFIG\n"
"@ \"sketch_bits\": 8,\n"
"@ \"tmax\": 128,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.0,\n"
"@ \"max_rearrangement_ratio\": 0.333,\n"
"@ \"disable_estimate_union\": true,\n"
Expand Down
6 changes: 4 additions & 2 deletions test/api/layout/execute_layout_test.cpp
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Expand Up @@ -88,7 +88,7 @@ TEST(execute_test, few_ubs)
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 8,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
Expand All @@ -97,6 +97,7 @@ TEST(execute_test, few_ubs)
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 64,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": true,\n"
Expand Down Expand Up @@ -308,7 +309,7 @@ TEST(execute_test, many_ubs)
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 96,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
Expand All @@ -317,6 +318,7 @@ TEST(execute_test, many_ubs)
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 64,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": true,\n"
Expand Down
3 changes: 2 additions & 1 deletion test/api/layout/execute_with_estimation_test.cpp
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Expand Up @@ -270,7 +270,7 @@ TEST(execute_estimation_test, many_ubs)
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 96,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
Expand All @@ -279,6 +279,7 @@ TEST(execute_estimation_test, many_ubs)
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 64,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": true,\n"
Expand Down
3 changes: 2 additions & 1 deletion test/api/layout/input_test.cpp
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Expand Up @@ -42,7 +42,7 @@ std::string const layout_header{"@CHOPPER_USER_BINS\n"
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 3,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
Expand All @@ -51,6 +51,7 @@ std::string const layout_header{"@CHOPPER_USER_BINS\n"
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 64,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": false,\n"
Expand Down
3 changes: 2 additions & 1 deletion test/cli/cli_chopper_layout_from_sketch_file.cpp
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Expand Up @@ -108,7 +108,7 @@ TEST_F(cli_test, chopper_layout_from_sketch_file)
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 4,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
Expand All @@ -117,6 +117,7 @@ TEST_F(cli_test, chopper_layout_from_sketch_file)
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 64,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": false,\n"
Expand Down
6 changes: 4 additions & 2 deletions test/cli/cli_chopper_pipeline_test.cpp
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Expand Up @@ -91,7 +91,7 @@ TEST_F(cli_test, chopper_layout)
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 3,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
Expand All @@ -100,6 +100,7 @@ TEST_F(cli_test, chopper_layout)
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 64,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": false,\n"
Expand Down Expand Up @@ -194,7 +195,7 @@ TEST_F(cli_test, chopper_layout2)
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 4,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
Expand All @@ -203,6 +204,7 @@ TEST_F(cli_test, chopper_layout2)
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 64,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": false,\n"
Expand Down
3 changes: 2 additions & 1 deletion test/cli/util_display_layout_test.cpp
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Expand Up @@ -62,7 +62,7 @@ std::string get_layout_with_correct_filenames(std::string_view const seq1_filena
"@HIBF_CONFIG\n"
"@{\n"
"@ \"hibf_config\": {\n"
"@ \"version\": 2,\n"
"@ \"version\": 3,\n"
"@ \"number_of_user_bins\": 4,\n"
"@ \"number_of_hash_functions\": 2,\n"
"@ \"maximum_fpr\": 0.05,\n"
Expand All @@ -71,6 +71,7 @@ std::string get_layout_with_correct_filenames(std::string_view const seq1_filena
"@ \"sketch_bits\": 12,\n"
"@ \"tmax\": 4,\n"
"@ \"empty_bin_fraction\": 0.0,\n"
"@ \"track_occupancy\": false,\n"
"@ \"alpha\": 1.2,\n"
"@ \"max_rearrangement_ratio\": 0.5,\n"
"@ \"disable_estimate_union\": false,\n"
Expand Down