Merge branch 'feature/update_clang_format' into 'master'

Update clang format See merge request minknow/pod5-file-format!143
nanoporetech · Nov 29, 2022 · 62028c7 · 62028c7
2 parents 9135f00 + 3a39371
commit 62028c7
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Showing 92 changed files with 8,858 additions and 4,023 deletions.
diff --git a/.clang-format b/.clang-format
@@ -1,16 +1,42 @@
 ---
+# See https://releases.llvm.org/14.0.0/tools/clang/docs/ClangFormatStyleOptions.html
 BasedOnStyle: Chromium
 AccessModifierOffset: -4
+AlignAfterOpenBracket: AlwaysBreak
+# AlignArrayOfStructures can cause crashes, see https://github.com/llvm/llvm-project/issues/55269
+#AlignArrayOfStructures: Left
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: Empty
 AllowShortFunctionsOnASingleLine: All
-BreakConstructorInitializers: BeforeColon
+BinPackArguments: false
+BinPackParameters: false
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Custom
+BraceWrapping:
+  # NB: due to https://github.com/llvm/llvm-project/issues/55582 the Multiline setting will not
+  # always work (should be fixed in clang-format 15, but that is not available as a python wheel yet
+  # due to https://github.com/ssciwr/clang-format-wheel/issues/49)
+  AfterControlStatement: MultiLine # makes sure multiline ifs don't run into their bodies
+  AfterFunction: true # makes constructors with initialisers much nicer
+BreakBeforeConceptDeclarations: true
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializers: BeforeComma
+BreakStringLiterals: true
 ColumnLimit: 100
-ConstructorInitializerIndentWidth: 8
-ContinuationIndentWidth: 8
+CompactNamespaces: true
+ConstructorInitializerIndentWidth: 0
+ContinuationIndentWidth: 4
 Cpp11BracedListStyle: true
-DerivePointerAlignment: true
+DerivePointerAlignment: false # force use of the PointerAlignment setting
 FixNamespaceComments: true
 IncludeBlocks : Regroup
 IncludeCategories:
+  # Aim is:
+  # 0. the "main" header file (#include "foo.h" in foo.cpp) automatically gets priority 0
+  # 1. internal headers (#include "util/helpers.h"): quotation marks, with a '/'
+  # 2. third-party headers (#include <boost/string_view.hpp>): angle brackets, '/' or .h/.hpp/.h++
+  #    file ext
+  # 3. standard library headers (#include <vector>): angle brackets, no file ext, no '/'
   - Regex:    '^"'
     Priority: 1
   - Regex:    '^<.*/'
@@ -22,12 +48,22 @@ IncludeCategories:
   - Regex:    '\.h\+\+>'
     Priority: 2
 IncludeIsMainRegex: '(_test|_tests|Tests|Test)?$'
+  # foo.h will be considered the "main" header (and sorted to the top) for all of the following:
+  # - foo.cpp
+  # - foo_test.cpp
+  # - foo_tests.cpp
+  # - fooTests.cpp (although this is intended for Foo.h and FooTests.cpp)
+  # - fooTest.cpp (although this is intended for Foo.h and FooTest.cpp)
 IndentCaseLabels: false
 IndentWidth: 4
+PackConstructorInitializers: CurrentLine
 PointerAlignment: Middle
+QualifierAlignment: Right # const east
+# clang 14 *should* know about QualifierOrder (according to its docs) but claims it doesn't
+#QualifierOrder: ['static', 'constexpr', 'inline', 'type', 'const', 'volatile', 'restrict']
 ReflowComments: false
-SortIncludes: true
+SeparateDefinitionBlocks: Always
+SortIncludes: CaseInsensitive
 SortUsingDeclarations: true
-Standard: Cpp11
-
-...
+SpaceAroundPointerQualifiers: Before
+Standard: c++20
diff --git a/c++/examples/find_all_read_ids.cpp b/c++/examples/find_all_read_ids.cpp
@@ -7,7 +7,8 @@
 #include <fstream>
 #include <iostream>
 
-int main(int argc, char** argv) {
+int main(int argc, char ** argv)
+{
     if (argc != 2) {
         std::cerr << "Expected one argument - an pod5 file to search\n";
     }
@@ -16,7 +17,7 @@ int main(int argc, char** argv) {
     pod5_init();
 
     // Open the file ready for walking:
-    Pod5FileReader_t* file = pod5_open_file(argv[1]);
+    Pod5FileReader_t * file = pod5_open_file(argv[1]);
     if (!file) {
         std::cerr << "Failed to open file " << argv[1] << ": " << pod5_get_error_string() << "\n";
         return EXIT_FAILURE;
@@ -35,7 +36,7 @@ int main(int argc, char** argv) {
     std::size_t read_count = 0;
 
     for (std::size_t batch_index = 0; batch_index < batch_count; ++batch_index) {
-        Pod5ReadRecordBatch_t* batch = nullptr;
+        Pod5ReadRecordBatch_t * batch = nullptr;
         if (pod5_get_read_batch(&batch, file, batch_index) != POD5_OK) {
             std::cerr << "Failed to get batch: " << pod5_get_error_string() << "\n";
             return EXIT_FAILURE;
@@ -50,8 +51,10 @@ int main(int argc, char** argv) {
         for (std::size_t row = 0; row < batch_row_count; ++row) {
             uint16_t read_table_version = 0;
             ReadBatchRowInfo_t read_data;
-            if (pod5_get_read_batch_row_info_data(batch, row, READ_BATCH_ROW_INFO_VERSION,
-                                                  &read_data, &read_table_version) != POD5_OK) {
+            if (pod5_get_read_batch_row_info_data(
+                    batch, row, READ_BATCH_ROW_INFO_VERSION, &read_data, &read_table_version)
+                != POD5_OK)
+            {
                 std::cerr << "Failed to get read " << row << "\n";
                 return EXIT_FAILURE;
             }

diff --git a/c++/examples/find_specific_read_ids.cpp b/c++/examples/find_specific_read_ids.cpp
@@ -8,7 +8,8 @@
 #include <iostream>
 #include <vector>
 
-int main(int argc, char** argv) {
+int main(int argc, char ** argv)
+{
     if (argc != 3) {
         std::cerr << "Expected two arguments:\n"
                   << " - an pod5 file to search\n"
@@ -19,7 +20,7 @@ int main(int argc, char** argv) {
     pod5_init();
 
     // Open the file ready for walking:
-    Pod5FileReader_t* file = pod5_open_file(argv[1]);
+    Pod5FileReader_t * file = pod5_open_file(argv[1]);
     if (!file) {
         std::cerr << "Failed to open file " << argv[1] << ": " << pod5_get_error_string() << "\n";
         return EXIT_FAILURE;
@@ -41,7 +42,7 @@ int main(int argc, char** argv) {
             search_uuids.push_back(boost::lexical_cast<boost::uuids::uuid>(line));
         }
         std::cout << "  Read " << search_uuids.size() << " ids from the text file\n";
-    } catch (std::exception const& e) {
+    } catch (std::exception const & e) {
         std::cerr << "Failed to parse UUID values from " << input_path << ": " << e.what() << "\n";
     }
 
@@ -53,9 +54,15 @@ int main(int argc, char** argv) {
     std::vector<std::uint32_t> traversal_batch_counts(batch_count);
     std::vector<std::uint32_t> traversal_row_indices(search_uuids.size());
     std::size_t find_success_count = 0;
-    if (pod5_plan_traversal(file, (uint8_t*)search_uuids.data(), search_uuids.size(),
-                            traversal_batch_counts.data(), traversal_row_indices.data(),
-                            &find_success_count) != POD5_OK) {
+    if (pod5_plan_traversal(
+            file,
+            (uint8_t *)search_uuids.data(),
+            search_uuids.size(),
+            traversal_batch_counts.data(),
+            traversal_row_indices.data(),
+            &find_success_count)
+        != POD5_OK)
+    {
         std::cerr << "Failed to plan traversal of file: " << pod5_get_error_string() << "\n";
         return EXIT_FAILURE;
     }
@@ -70,7 +77,7 @@ int main(int argc, char** argv) {
     // Walk the suggested traversal route, storing read data.
     std::size_t step_index = 0;
     for (std::size_t batch_index = 0; batch_index < batch_count; ++batch_index) {
-        Pod5ReadRecordBatch_t* batch = nullptr;
+        Pod5ReadRecordBatch_t * batch = nullptr;
         if (pod5_get_read_batch(&batch, file, batch_index) != POD5_OK) {
             std::cerr << "Failed to get batch: " << pod5_get_error_string() << "\n";
             return EXIT_FAILURE;
@@ -83,8 +90,10 @@ int main(int argc, char** argv) {
 
             uint16_t read_table_version = 0;
             ReadBatchRowInfo_t read_data;
-            if (pod5_get_read_batch_row_info_data(batch, batch_row, READ_BATCH_ROW_INFO_VERSION,
-                                                  &read_data, &read_table_version) != POD5_OK) {
+            if (pod5_get_read_batch_row_info_data(
+                    batch, batch_row, READ_BATCH_ROW_INFO_VERSION, &read_data, &read_table_version)
+                != POD5_OK)
+            {
                 std::cerr << "Failed to get read " << batch_row << "\n";
                 return EXIT_FAILURE;
             }

diff --git a/c++/examples/find_specific_read_ids_with_signal.cpp b/c++/examples/find_specific_read_ids_with_signal.cpp
@@ -8,7 +8,8 @@
 #include <iostream>
 #include <vector>
 
-int main(int argc, char** argv) {
+int main(int argc, char ** argv)
+{
     if (argc != 3) {
         std::cerr << "Expected two arguments:\n"
                   << " - an pod5 file to search\n"
@@ -19,7 +20,7 @@ int main(int argc, char** argv) {
     pod5_init();
 
     // Open the file ready for walking:
-    Pod5FileReader_t* file = pod5_open_file(argv[1]);
+    Pod5FileReader_t * file = pod5_open_file(argv[1]);
     if (!file) {
         std::cerr << "Failed to open file " << argv[1] << ": " << pod5_get_error_string() << "\n";
         return EXIT_FAILURE;
@@ -41,7 +42,7 @@ int main(int argc, char** argv) {
             search_uuids.push_back(boost::lexical_cast<boost::uuids::uuid>(line));
         }
         std::cout << "  Read " << search_uuids.size() << " ids from the text file\n";
-    } catch (std::exception const& e) {
+    } catch (std::exception const & e) {
         std::cerr << "Failed to parse UUID values from " << input_path << ": " << e.what() << "\n";
     }
 
@@ -53,9 +54,15 @@ int main(int argc, char** argv) {
     std::vector<std::uint32_t> traversal_batch_counts(batch_count);
     std::vector<std::uint32_t> traversal_row_indices(search_uuids.size());
     std::size_t find_success_count = 0;
-    if (pod5_plan_traversal(file, (uint8_t*)search_uuids.data(), search_uuids.size(),
-                            traversal_batch_counts.data(), traversal_row_indices.data(),
-                            &find_success_count) != POD5_OK) {
+    if (pod5_plan_traversal(
+            file,
+            (uint8_t *)search_uuids.data(),
+            search_uuids.size(),
+            traversal_batch_counts.data(),
+            traversal_row_indices.data(),
+            &find_success_count)
+        != POD5_OK)
+    {
         std::cerr << "Failed to plan traversal of file: " << pod5_get_error_string() << "\n";
         return EXIT_FAILURE;
     }
@@ -72,7 +79,7 @@ int main(int argc, char** argv) {
     // Walk the suggested traversal route, storing read data.
     std::size_t step_index = 0;
     for (std::size_t batch_index = 0; batch_index < batch_count; ++batch_index) {
-        Pod5ReadRecordBatch_t* batch = nullptr;
+        Pod5ReadRecordBatch_t * batch = nullptr;
         if (pod5_get_read_batch(&batch, file, batch_index) != POD5_OK) {
             std::cerr << "Failed to get batch: " << pod5_get_error_string() << "\n";
             return EXIT_FAILURE;
@@ -85,8 +92,10 @@ int main(int argc, char** argv) {
 
             uint16_t read_table_version = 0;
             ReadBatchRowInfo_t read_data;
-            if (pod5_get_read_batch_row_info_data(batch, batch_row, READ_BATCH_ROW_INFO_VERSION,
-                                                  &read_data, &read_table_version) != POD5_OK) {
+            if (pod5_get_read_batch_row_info_data(
+                    batch, batch_row, READ_BATCH_ROW_INFO_VERSION, &read_data, &read_table_version)
+                != POD5_OK)
+            {
                 std::cerr << "Failed to get read " << batch_row << "\n";
                 return EXIT_FAILURE;
             }