From 400bd0717554bdcc426cf88d7af008246292436c Mon Sep 17 00:00:00 2001 From: "seqan-actions[bot]" Date: Thu, 30 Jan 2025 14:21:24 +0100 Subject: [PATCH 1/2] [INFRA] Update CPM Packages --- cmake/package-lock.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake index e6a0dcaf..da8e59fd 100644 --- a/cmake/package-lock.cmake +++ b/cmake/package-lock.cmake @@ -6,7 +6,7 @@ # This file should be committed to version control # hibf -set (CHOPPER_HIBF_VERSION 06aaab39a3f5117c35d112e83241074178edab67) +set (CHOPPER_HIBF_VERSION 5853f7a35061632f4c3674fc9fc434f917f230f6) CPMDeclarePackage (hibf NAME hibf GIT_TAG ${CHOPPER_HIBF_VERSION} # main @@ -26,7 +26,7 @@ CPMDeclarePackage (sharg OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING" "BUILD_TESTING OFF" ) # seqan3 -set (CHOPPER_SEQAN3_VERSION 7ee839814e168ab57c4401d46e6114a801cebc28) +set (CHOPPER_SEQAN3_VERSION 666b87694bef9411d995e4678a26e5e9a31ca255) CPMDeclarePackage (seqan3 NAME seqan3 GIT_TAG ${CHOPPER_SEQAN3_VERSION} # main From 926722ef14fd1baa76f3aa985f1ba01c2af4c383 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Thu, 30 Jan 2025 14:41:44 +0100 Subject: [PATCH 2/2] [TEST] Update hibf_config --- test/api/config_test.cpp | 3 ++- test/api/layout/execute_layout_test.cpp | 6 ++++-- test/api/layout/execute_with_estimation_test.cpp | 3 ++- test/api/layout/input_test.cpp | 3 ++- test/cli/cli_chopper_layout_from_sketch_file.cpp | 3 ++- test/cli/cli_chopper_pipeline_test.cpp | 6 ++++-- test/cli/util_display_layout_test.cpp | 3 ++- 7 files changed, 18 insertions(+), 9 deletions(-) diff --git a/test/api/config_test.cpp b/test/api/config_test.cpp index be717ddc..8830da25 100644 --- a/test/api/config_test.cpp +++ b/test/api/config_test.cpp @@ -95,7 +95,7 @@ static constexpr std::string_view config_string_view{"@CHOPPER_CONFIG\n" "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 123456789,\n" "@ \"number_of_hash_functions\": 4,\n" "@ \"maximum_fpr\": 0.0001,\n" @@ -103,6 +103,7 @@ static constexpr std::string_view config_string_view{"@CHOPPER_CONFIG\n" "@ \"threads\": 31,\n" "@ \"sketch_bits\": 8,\n" "@ \"tmax\": 128,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.0,\n" "@ \"max_rearrangement_ratio\": 0.333,\n" "@ \"disable_estimate_union\": true,\n" diff --git a/test/api/layout/execute_layout_test.cpp b/test/api/layout/execute_layout_test.cpp index acede96d..5449ec12 100644 --- a/test/api/layout/execute_layout_test.cpp +++ b/test/api/layout/execute_layout_test.cpp @@ -88,7 +88,7 @@ TEST(execute_test, few_ubs) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 8,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -96,6 +96,7 @@ TEST(execute_test, few_ubs) "@ \"threads\": 1,\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": true,\n" @@ -307,7 +308,7 @@ TEST(execute_test, many_ubs) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 96,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -315,6 +316,7 @@ TEST(execute_test, many_ubs) "@ \"threads\": 1,\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": true,\n" diff --git a/test/api/layout/execute_with_estimation_test.cpp b/test/api/layout/execute_with_estimation_test.cpp index f3f7b2ab..c33d0243 100644 --- a/test/api/layout/execute_with_estimation_test.cpp +++ b/test/api/layout/execute_with_estimation_test.cpp @@ -270,7 +270,7 @@ TEST(execute_estimation_test, many_ubs) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 96,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -278,6 +278,7 @@ TEST(execute_estimation_test, many_ubs) "@ \"threads\": 1,\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": true,\n" diff --git a/test/api/layout/input_test.cpp b/test/api/layout/input_test.cpp index a1b240e2..f35a147c 100644 --- a/test/api/layout/input_test.cpp +++ b/test/api/layout/input_test.cpp @@ -42,7 +42,7 @@ std::string const layout_header{"@CHOPPER_USER_BINS\n" "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 3,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -50,6 +50,7 @@ std::string const layout_header{"@CHOPPER_USER_BINS\n" "@ \"threads\": 2,\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n" diff --git a/test/cli/cli_chopper_layout_from_sketch_file.cpp b/test/cli/cli_chopper_layout_from_sketch_file.cpp index 7c664147..16c5f5c0 100644 --- a/test/cli/cli_chopper_layout_from_sketch_file.cpp +++ b/test/cli/cli_chopper_layout_from_sketch_file.cpp @@ -108,7 +108,7 @@ TEST_F(cli_test, chopper_layout_from_sketch_file) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 4,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -116,6 +116,7 @@ TEST_F(cli_test, chopper_layout_from_sketch_file) "@ \"threads\": 2,\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n" diff --git a/test/cli/cli_chopper_pipeline_test.cpp b/test/cli/cli_chopper_pipeline_test.cpp index 25eaa6f2..98520094 100644 --- a/test/cli/cli_chopper_pipeline_test.cpp +++ b/test/cli/cli_chopper_pipeline_test.cpp @@ -91,7 +91,7 @@ TEST_F(cli_test, chopper_layout) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 3,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -99,6 +99,7 @@ TEST_F(cli_test, chopper_layout) "@ \"threads\": 2,\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n" @@ -193,7 +194,7 @@ TEST_F(cli_test, chopper_layout2) "@HIBF_CONFIG\n" "@{\n" "@ \"hibf_config\": {\n" - "@ \"version\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 4,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -201,6 +202,7 @@ TEST_F(cli_test, chopper_layout2) "@ \"threads\": 2,\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 64,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n" diff --git a/test/cli/util_display_layout_test.cpp b/test/cli/util_display_layout_test.cpp index 9c7c7fe1..945c0c2a 100644 --- a/test/cli/util_display_layout_test.cpp +++ b/test/cli/util_display_layout_test.cpp @@ -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\": 1,\n" + "@ \"version\": 2,\n" "@ \"number_of_user_bins\": 4,\n" "@ \"number_of_hash_functions\": 2,\n" "@ \"maximum_fpr\": 0.05,\n" @@ -70,6 +70,7 @@ std::string get_layout_with_correct_filenames(std::string_view const seq1_filena "@ \"threads\": 2,\n" "@ \"sketch_bits\": 12,\n" "@ \"tmax\": 4,\n" + "@ \"empty_bin_fraction\": 0.0,\n" "@ \"alpha\": 1.2,\n" "@ \"max_rearrangement_ratio\": 0.5,\n" "@ \"disable_estimate_union\": false,\n"