[MISC] automatic linting

seqan · Aug 13, 2024 · 1983ec4 · 1983ec4
1 parent d533f56
commit 1983ec4
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Showing 4 changed files with 65 additions and 15 deletions.
diff --git a/src/chopper.cpp b/src/chopper.cpp
@@ -19,8 +19,8 @@
 #include <chopper/layout/execute.hpp>
 #include <chopper/set_up_parser.hpp>
 #include <chopper/sketch/check_filenames.hpp>
-#include <chopper/sketch/read_data_file.hpp>
 #include <chopper/sketch/output.hpp>
+#include <chopper/sketch/read_data_file.hpp>
 
 #include <hibf/sketch/compute_sketches.hpp>
 
@@ -79,7 +79,12 @@ int main(int argc, char const * argv[])
         seqan::hibf::sketch::compute_sketches(config.hibf_config, sketches);
         compute_sketches_timer.stop();
 
-        exit_code |= chopper::layout::execute(config, filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+        exit_code |= chopper::layout::execute(config,
+                                              filenames,
+                                              sketches,
+                                              union_estimation_timer,
+                                              rearrangement_timer,
+                                              dp_algorithm_timer);
     }
     catch (std::exception const & ext)
     {

diff --git a/test/api/layout/execute_layout_test.cpp b/test/api/layout/execute_layout_test.cpp
@@ -15,10 +15,10 @@
 #include <string>
 #include <vector>
 
-#include <hibf/sketch/compute_sketches.hpp>
-
 #include <chopper/layout/execute.hpp>
 
+#include <hibf/sketch/compute_sketches.hpp>
+
 #include "../api_test.hpp"
 #include "print_debug_file.hpp"
 
@@ -52,7 +52,12 @@ TEST(execute_test, few_ubs)
     seqan::hibf::concurrent_timer rearrangement_timer{};
     seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
-    chopper::layout::execute(config, filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
 
     std::string const expected_file{"@CHOPPER_USER_BINS\n"
                                     "@0 seq0a seq0b\n"
@@ -151,7 +156,12 @@ TEST(execute_test, set_default_tmax)
     seqan::hibf::concurrent_timer rearrangement_timer{};
     seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
-    chopper::layout::execute(config, filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
 
     EXPECT_EQ(config.hibf_config.tmax, 64u);
 }
@@ -189,7 +199,12 @@ TEST(execute_test, many_ubs)
     seqan::hibf::concurrent_timer rearrangement_timer{};
     seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
-    chopper::layout::execute(config, many_filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             many_filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
 
     std::string const expected_file{"@CHOPPER_USER_BINS\n"
                                     "@0 seq0\n"

diff --git a/test/api/layout/execute_with_estimation_test.cpp b/test/api/layout/execute_with_estimation_test.cpp
@@ -60,7 +60,12 @@ TEST(execute_estimation_test, few_ubs)
     seqan::hibf::concurrent_timer rearrangement_timer{};
     seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
-    chopper::layout::execute(config, filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
 
     ASSERT_TRUE(std::filesystem::exists(stats_file));
 
@@ -123,7 +128,12 @@ TEST(execute_estimation_test, many_ubs)
     seqan::hibf::concurrent_timer rearrangement_timer{};
     seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
-    chopper::layout::execute(config, many_filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             many_filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
 
     ASSERT_TRUE(std::filesystem::exists(stats_file));
 
@@ -532,7 +542,12 @@ TEST(execute_estimation_test, many_ubs_force_all)
     seqan::hibf::concurrent_timer rearrangement_timer{};
     seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
-    chopper::layout::execute(config, many_filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             many_filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
 
     ASSERT_TRUE(std::filesystem::exists(stats_file));
 
@@ -638,7 +653,12 @@ TEST(execute_estimation_test, with_rearrangement)
     seqan::hibf::concurrent_timer rearrangement_timer{};
     seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
-    chopper::layout::execute(config, filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
 
     ASSERT_TRUE(std::filesystem::exists(stats_file));
 

diff --git a/test/api/layout/hibf_statistics_test.cpp b/test/api/layout/hibf_statistics_test.cpp
@@ -16,12 +16,12 @@
 #include <string>
 #include <vector>
 
-#include <hibf/sketch/compute_sketches.hpp>
-
 #include <chopper/configuration.hpp>
 #include <chopper/layout/execute.hpp>
 #include <chopper/layout/hibf_statistics.hpp>
 
+#include <hibf/sketch/compute_sketches.hpp>
+
 #include "../api_test.hpp"
 
 TEST(byte_size_to_formatted_str, storage_unit)
@@ -139,7 +139,12 @@ TEST(execute_test, chopper_layout_statistics)
 
     testing::internal::CaptureStdout();
     testing::internal::CaptureStderr();
-    chopper::layout::execute(config, many_filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             many_filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
     std::string layout_result_stdout = testing::internal::GetCapturedStdout();
     std::string layout_result_stderr = testing::internal::GetCapturedStderr();
 
@@ -198,7 +203,12 @@ TEST(execute_test, chopper_layout_statistics_determine_best_bins)
     seqan::hibf::concurrent_timer rearrangement_timer{};
     seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
-    chopper::layout::execute(config, filenames, sketches, union_estimation_timer, rearrangement_timer, dp_algorithm_timer);
+    chopper::layout::execute(config,
+                             filenames,
+                             sketches,
+                             union_estimation_timer,
+                             rearrangement_timer,
+                             dp_algorithm_timer);
 
     std::string expected_cout =
         R"expected_cout(## ### Parameters ###