Bump clang-format to v18 and enable auto format (#3222)

* Bump clang-format to v18 and enable auto format

* Add repository and ref to actions/checkout step

* Update source, test, and extension format checks

* Run clang-format

---------

Co-authored-by: CI Bot <mewim@users.noreply.github.com>

.github/workflows/ci-workflow.yml

@@ -25,7 +25,7 @@ concurrency:
 jobs:
   gcc-build-test:
     name: gcc build & test
-    needs: [clang-formatting-check, sanity-checks, python-lint-check]
+    needs: [clang-format, sanity-checks, python-lint-check]
     runs-on: kuzu-self-hosted-testing
     env:
       NUM_THREADS: 32
@@ -83,7 +83,7 @@ jobs:
 
   gcc-build-test-x86:
     name: gcc build & test 32-bit
-    needs: [clang-formatting-check, sanity-checks]
+    needs: [clang-format, sanity-checks]
     runs-on: ubuntu-latest
 
     steps:
@@ -157,7 +157,7 @@ jobs:
 
   clang-build-test:
     name: clang build and test
-    needs: [clang-formatting-check, sanity-checks, python-lint-check]
+    needs: [clang-format, sanity-checks, python-lint-check]
     runs-on: kuzu-self-hosted-testing
     env:
       NUM_THREADS: 32
@@ -214,7 +214,7 @@ jobs:
 
   msvc-build-test:
     name: msvc build & test
-    needs: [clang-formatting-check, sanity-checks, python-lint-check]
+    needs: [clang-format, sanity-checks, python-lint-check]
     runs-on: self-hosted-windows
     env:
       # Shorten build path as much as possible
@@ -285,7 +285,7 @@ jobs:
 
   tidy-and-diagnostics:
     name: clang tidy & clangd diagnostics check
-    needs: [clang-formatting-check, sanity-checks]
+    needs: [clang-format, sanity-checks]
     runs-on: kuzu-self-hosted-testing
     env:
       NUM_THREADS: 32
@@ -322,25 +322,37 @@ jobs:
       - name: Ensure generated grammar files are up to date
         run: cmp src/antlr4/Cypher.g4 scripts/antlr4/Cypher.g4.copy
 
-  clang-formatting-check:
-    name: clang-format check
+  clang-format:
+    name: clang format
     runs-on: ubuntu-22.04
     steps:
       - name: Install clang-format
         run: |
-          sudo apt-get update
-          sudo apt-get install -y clang-format-11
+          sudo apt-get install -y lsb-release wget software-properties-common gnupg
+          wget https://apt.llvm.org/llvm.sh
+          chmod +x llvm.sh
+          yes | sudo ./llvm.sh 18 all
 
       - uses: actions/checkout@v3
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - name: Check and fix source format
+        run: python3 scripts/run-clang-format.py --in-place --clang-format-executable /usr/bin/clang-format-18 -r src/
 
-      - name: Check source format
-        run: python3 scripts/run-clang-format.py --clang-format-executable /usr/bin/clang-format-11 -r src/
+      - name: Check and fix test format
+        run: python3 scripts/run-clang-format.py --in-place --clang-format-executable /usr/bin/clang-format-18 -r test/
 
-      - name: Check test format
-        run: python3 scripts/run-clang-format.py --clang-format-executable /usr/bin/clang-format-11 -r test/
+      - name: Check and fix extension format
+        run: python3 scripts/run-clang-format.py --in-place --clang-format-executable /usr/bin/clang-format-18 -r extension/
 
-      - name: Check extension format
-        run: python3 scripts/run-clang-format.py --clang-format-executable /usr/bin/clang-format-11 -r extension/
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        if: github.ref != 'refs/heads/master'
+        with:
+          author_name: "CI Bot"
+          message: "Run clang-format"
 
   python-lint-check:
     name: python lint check
@@ -379,7 +391,7 @@ jobs:
 
   macos-clang-tidy:
     name: macos clang tidy & clangd diagnostics check
-    needs: [clang-formatting-check, sanity-checks]
+    needs: [clang-format, sanity-checks]
     runs-on: self-hosted-mac-x64
     env:
       NUM_THREADS: 32
@@ -404,8 +416,7 @@ jobs:
 
   macos-build-test:
     name: apple clang build & test
-    needs:
-      [clang-formatting-check, sanity-checks, rustfmt-check, python-lint-check]
+    needs: [clang-format, sanity-checks, rustfmt-check, python-lint-check]
     runs-on: self-hosted-mac-x64
     env:
       NUM_THREADS: 32
@@ -475,7 +486,7 @@ jobs:
   shell-test:
     name: shell test
     runs-on: ubuntu-latest
-    needs: [clang-formatting-check, sanity-checks]
+    needs: [clang-format, sanity-checks]
     env:
       WERROR: 0
     steps:

extension/duckdb_scanner/src/duckdb_catalog.cpp

@@ -7,8 +7,8 @@
 namespace kuzu {
 namespace duckdb_scanner {
 
-void DuckDBCatalogContent::init(
-    const std::string& dbPath, const std::string& catalogName, main::ClientContext* context) {
+void DuckDBCatalogContent::init(const std::string& dbPath, const std::string& catalogName,
+    main::ClientContext* context) {
     auto [db, con] = getConnection(dbPath);
     auto query = common::stringFormat(
         "select table_name from information_schema.tables where table_catalog = '{}' and "
@@ -18,12 +18,14 @@ void DuckDBCatalogContent::init(
     std::unique_ptr<duckdb::DataChunk> resultChunk;
     try {
         resultChunk = result->Fetch();
-    } catch (std::exception& e) { throw common::BinderException(e.what()); }
+    } catch (std::exception& e) {
+        throw common::BinderException(e.what());
+    }
     if (resultChunk->size() == 0) {
         return;
     }
-    common::ValueVector tableNamesVector{
-        *common::LogicalType::STRING(), context->getMemoryManager()};
+    common::ValueVector tableNamesVector{*common::LogicalType::STRING(),
+        context->getMemoryManager()};
     duckdb_scanner::duckdb_conversion_func_t conversionFunc;
     duckdb_scanner::getDuckDBVectorConversionFunc(common::PhysicalTypeID::STRING, conversionFunc);
     conversionFunc(resultChunk->data[0], tableNamesVector, resultChunk->size());
@@ -36,8 +38,8 @@ void DuckDBCatalogContent::init(
 static std::string getQuery(const binder::BoundCreateTableInfo& info) {
     auto extraInfo = common::ku_dynamic_cast<binder::BoundExtraCreateCatalogEntryInfo*,
         BoundExtraCreateDuckDBTableInfo*>(info.extraInfo.get());
-    return common::stringFormat(
-        "SELECT * FROM {}.{}.{}", extraInfo->catalogName, extraInfo->schemaName, info.tableName);
+    return common::stringFormat("SELECT * FROM {}.{}.{}", extraInfo->catalogName,
+        extraInfo->schemaName, info.tableName);
 }
 
 void DuckDBCatalogContent::createForeignTable(duckdb::Connection& con, const std::string& tableName,
@@ -57,8 +59,8 @@ void DuckDBCatalogContent::createForeignTable(duckdb::Connection& con, const std
     }
     DuckDBScanBindData bindData(getQuery(*info), std::move(columnTypes), std::move(columnNames),
         std::bind(&DuckDBCatalogContent::getConnection, this, dbPath));
-    auto tableEntry = std::make_unique<catalog::DuckDBTableCatalogEntry>(
-        info->tableName, tableID, getScanFunction(std::move(bindData)));
+    auto tableEntry = std::make_unique<catalog::DuckDBTableCatalogEntry>(info->tableName, tableID,
+        getScanFunction(std::move(bindData)));
     for (auto& propertyInfo : extraInfo->propertyInfos) {
         tableEntry->addProperty(propertyInfo.name, propertyInfo.type.copy());
     }
@@ -82,7 +84,9 @@ static bool getTableInfo(duckdb::Connection& con, const std::string& tableName,
         try {
             columnTypes.push_back(DuckDBTypeConverter::convertDuckDBType(
                 result->GetValue(0, i).GetValue<std::string>()));
-        } catch (common::BinderException& e) { return false; }
+        } catch (common::BinderException& e) {
+            return false;
+        }
         columnNames.push_back(result->GetValue(1, i).GetValue<std::string>());
     }
     return true;
@@ -92,8 +96,8 @@ bool DuckDBCatalogContent::bindPropertyInfos(duckdb::Connection& con, const std:
     const std::string& catalogName, std::vector<binder::PropertyInfo>& propertyInfos) {
     std::vector<common::LogicalType> columnTypes;
     std::vector<std::string> columnNames;
-    if (!getTableInfo(
-            con, tableName, getDefaultSchemaName(), catalogName, columnTypes, columnNames)) {
+    if (!getTableInfo(con, tableName, getDefaultSchemaName(), catalogName, columnTypes,
+            columnNames)) {
         return false;
     }
     for (auto i = 0u; i < columnNames.size(); i++) {
@@ -111,8 +115,8 @@ std::unique_ptr<binder::BoundCreateTableInfo> DuckDBCatalogContent::bindCreateTa
         return nullptr;
     }
     return std::make_unique<binder::BoundCreateTableInfo>(common::TableType::FOREIGN, tableName,
-        std::make_unique<duckdb_scanner::BoundExtraCreateDuckDBTableInfo>(
-            dbPath, catalogName, getDefaultSchemaName(), std::move(propertyInfos)));
+        std::make_unique<duckdb_scanner::BoundExtraCreateDuckDBTableInfo>(dbPath, catalogName,
+            getDefaultSchemaName(), std::move(propertyInfos)));
 }
 
 std::string DuckDBCatalogContent::getDefaultSchemaName() const {

extension/duckdb_scanner/src/duckdb_scan.cpp

@@ -9,8 +9,8 @@ using namespace kuzu::common;
 namespace kuzu {
 namespace duckdb_scanner {
 
-void getDuckDBVectorConversionFunc(
-    PhysicalTypeID physicalTypeID, duckdb_conversion_func_t& conversion_func);
+void getDuckDBVectorConversionFunc(PhysicalTypeID physicalTypeID,
+    duckdb_conversion_func_t& conversion_func);
 
 DuckDBScanBindData::DuckDBScanBindData(std::string query,
     std::vector<common::LogicalType> columnTypes, std::vector<std::string> columnNames,
@@ -19,8 +19,8 @@ DuckDBScanBindData::DuckDBScanBindData(std::string query,
       initDuckDBConn{std::move(initDuckDBConn)} {
     conversionFunctions.resize(this->columnTypes.size());
     for (auto i = 0u; i < this->columnTypes.size(); i++) {
-        getDuckDBVectorConversionFunc(
-            this->columnTypes[i].getPhysicalType(), conversionFunctions[i]);
+        getDuckDBVectorConversionFunc(this->columnTypes[i].getPhysicalType(),
+            conversionFunctions[i]);
     }
 }
 
@@ -34,8 +34,8 @@ DuckDBScanSharedState::DuckDBScanSharedState(std::unique_ptr<duckdb::QueryResult
 struct DuckDBScanFunction {
     static constexpr char DUCKDB_SCAN_FUNC_NAME[] = "duckdb_scan";
 
-    static common::offset_t tableFunc(
-        function::TableFuncInput& input, function::TableFuncOutput& output);
+    static common::offset_t tableFunc(function::TableFuncInput& input,
+        function::TableFuncOutput& output);
 
     static std::unique_ptr<function::TableFuncBindData> bindFunc(DuckDBScanBindData bindData,
         main::ClientContext* /*context*/, function::TableFuncBindInput* input);
@@ -68,8 +68,8 @@ std::unique_ptr<function::TableFuncLocalState> DuckDBScanFunction::initLocalStat
 }
 
 template<typename T>
-void convertDuckDBVectorToVector(
-    duckdb::Vector& duckDBVector, ValueVector& result, uint64_t numValuesToCopy) {
+void convertDuckDBVectorToVector(duckdb::Vector& duckDBVector, ValueVector& result,
+    uint64_t numValuesToCopy) {
     auto duckDBData = (T*)duckDBVector.GetData();
     auto validityMasks = duckdb::FlatVector::Validity(duckDBVector);
     memcpy(result.getData(), duckDBData, numValuesToCopy * result.getNumBytesPerValue());
@@ -79,15 +79,15 @@ void convertDuckDBVectorToVector(
 }
 
 template<>
-void convertDuckDBVectorToVector<struct_entry_t>(
-    duckdb::Vector& duckDBVector, ValueVector& result, uint64_t numValuesToCopy);
+void convertDuckDBVectorToVector<struct_entry_t>(duckdb::Vector& duckDBVector, ValueVector& result,
+    uint64_t numValuesToCopy);
 template<>
-void convertDuckDBVectorToVector<list_entry_t>(
-    duckdb::Vector& duckDBVector, ValueVector& result, uint64_t numValuesToCopy);
+void convertDuckDBVectorToVector<list_entry_t>(duckdb::Vector& duckDBVector, ValueVector& result,
+    uint64_t numValuesToCopy);
 
 template<>
-void convertDuckDBVectorToVector<ku_string_t>(
-    duckdb::Vector& duckDBVector, ValueVector& result, uint64_t numValuesToCopy) {
+void convertDuckDBVectorToVector<ku_string_t>(duckdb::Vector& duckDBVector, ValueVector& result,
+    uint64_t numValuesToCopy) {
     auto strs = reinterpret_cast<duckdb::string_t*>(duckDBVector.GetData());
     auto validityMasks = duckdb::FlatVector::Validity(duckDBVector);
     for (auto i = 0u; i < numValuesToCopy; i++) {
@@ -98,8 +98,8 @@ void convertDuckDBVectorToVector<ku_string_t>(
     }
 }
 
-void getDuckDBVectorConversionFunc(
-    PhysicalTypeID physicalTypeID, duckdb_conversion_func_t& conversion_func) {
+void getDuckDBVectorConversionFunc(PhysicalTypeID physicalTypeID,
+    duckdb_conversion_func_t& conversion_func) {
     switch (physicalTypeID) {
     case PhysicalTypeID::BOOL: {
         conversion_func = convertDuckDBVectorToVector<bool>;
@@ -155,10 +155,10 @@ void getDuckDBVectorConversionFunc(
 }
 
 template<>
-void convertDuckDBVectorToVector<list_entry_t>(
-    duckdb::Vector& duckDBVector, ValueVector& result, uint64_t numValuesToCopy) {
-    memcpy(
-        result.getData(), duckDBVector.GetData(), numValuesToCopy * result.getNumBytesPerValue());
+void convertDuckDBVectorToVector<list_entry_t>(duckdb::Vector& duckDBVector, ValueVector& result,
+    uint64_t numValuesToCopy) {
+    memcpy(result.getData(), duckDBVector.GetData(),
+        numValuesToCopy * result.getNumBytesPerValue());
     auto numValuesInDataVec = 0;
     auto listEntries = reinterpret_cast<duckdb::list_entry_t*>(duckDBVector.GetData());
     auto validityMasks = duckdb::FlatVector::Validity(duckDBVector);
@@ -176,8 +176,8 @@ void convertDuckDBVectorToVector<list_entry_t>(
 }
 
 template<>
-void convertDuckDBVectorToVector<struct_entry_t>(
-    duckdb::Vector& duckDBVector, ValueVector& result, uint64_t numValuesToCopy) {
+void convertDuckDBVectorToVector<struct_entry_t>(duckdb::Vector& duckDBVector, ValueVector& result,
+    uint64_t numValuesToCopy) {
     auto& duckdbChildrenVectors = duckdb::StructVector::GetEntries(duckDBVector);
     for (auto i = 0u; i < duckdbChildrenVectors.size(); i++) {
         duckdb_conversion_func_t conversionFunc;
@@ -193,19 +193,21 @@ static void convertDuckDBResultToVector(duckdb::DataChunk& duckDBResult, DataChu
     for (auto i = 0u; i < conversionFuncs.size(); i++) {
         result.state->selVector->selectedSize = duckDBResult.size();
         assert(duckDBResult.data[i].GetVectorType() == duckdb::VectorType::FLAT_VECTOR);
-        conversionFuncs[i](
-            duckDBResult.data[i], *result.getValueVector(i), result.state->selVector->selectedSize);
+        conversionFuncs[i](duckDBResult.data[i], *result.getValueVector(i),
+            result.state->selVector->selectedSize);
     }
 }
 
-common::offset_t DuckDBScanFunction::tableFunc(
-    function::TableFuncInput& input, function::TableFuncOutput& output) {
+common::offset_t DuckDBScanFunction::tableFunc(function::TableFuncInput& input,
+    function::TableFuncOutput& output) {
     auto duckdbScanSharedState = reinterpret_cast<DuckDBScanSharedState*>(input.sharedState);
     auto duckdbScanBindData = reinterpret_cast<DuckDBScanBindData*>(input.bindData);
     std::unique_ptr<duckdb::DataChunk> result;
     try {
         result = duckdbScanSharedState->queryResult->Fetch();
-    } catch (std::exception& e) { return 0; }
+    } catch (std::exception& e) {
+        return 0;
+    }
     if (result == nullptr) {
         return 0;
     }

extension/duckdb_scanner/src/duckdb_storage.cpp

@@ -7,8 +7,8 @@
 namespace kuzu {
 namespace duckdb_scanner {
 
-std::unique_ptr<main::AttachedDatabase> attachDuckDB(
-    std::string dbName, std::string dbPath, main::ClientContext* clientContext) {
+std::unique_ptr<main::AttachedDatabase> attachDuckDB(std::string dbName, std::string dbPath,
+    main::ClientContext* clientContext) {
     if (dbName == "") {
         if (dbPath.find('.') != std::string::npos) {
             auto fileNamePos = dbPath.find_last_of('/') + 1;

extension/duckdb_scanner/src/duckdb_table_catalog_entry.cpp

@@ -3,8 +3,8 @@
 namespace kuzu {
 namespace catalog {
 
-DuckDBTableCatalogEntry::DuckDBTableCatalogEntry(
-    std::string name, common::table_id_t tableID, function::TableFunction scanFunction)
+DuckDBTableCatalogEntry::DuckDBTableCatalogEntry(std::string name, common::table_id_t tableID,
+    function::TableFunction scanFunction)
     : TableCatalogEntry{CatalogEntryType::FOREIGN_TABLE_ENTRY, std::move(name), tableID},
       scanFunction{std::move(scanFunction)} {}
 

extension/duckdb_scanner/src/duckdb_type_converter.cpp

@@ -65,17 +65,17 @@ common::LogicalType DuckDBTypeConverter::convertDuckDBType(std::string typeStr)
         return *LogicalType::STRUCT(parseStructTypeInfo(typeStr));
     } else if (typeStr.starts_with("UNION")) {
         auto unionFields = parseStructTypeInfo(typeStr);
-        auto unionTagField = StructField(
-            UnionType::TAG_FIELD_NAME, std::make_unique<LogicalType>(UnionType::TAG_FIELD_TYPE));
+        auto unionTagField = StructField(UnionType::TAG_FIELD_NAME,
+            std::make_unique<LogicalType>(UnionType::TAG_FIELD_TYPE));
         unionFields.insert(unionFields.begin(), std::move(unionTagField));
         return *LogicalType::UNION(std::move(unionFields));
     } else if (typeStr.starts_with("MAP")) {
         auto leftBracketPos = typeStr.find('(');
         auto rightBracketPos = typeStr.find_last_of(')');
         auto mapTypeStr = typeStr.substr(leftBracketPos + 1, rightBracketPos - leftBracketPos - 1);
         auto keyValueTypes = StringUtils::splitComma(mapTypeStr);
-        return *LogicalType::MAP(
-            convertDuckDBType(keyValueTypes[0]), convertDuckDBType(keyValueTypes[1]));
+        return *LogicalType::MAP(convertDuckDBType(keyValueTypes[0]),
+            convertDuckDBType(keyValueTypes[1]));
     }
     throw BinderException{stringFormat("Unsupported duckdb type: {}.", typeStr)};
 }

extension/duckdb_scanner/src/include/duckdb_catalog.h

@@ -29,8 +29,8 @@ class DuckDBCatalogContent : public catalog::CatalogContent {
 public:
     DuckDBCatalogContent() : catalog::CatalogContent{nullptr /* vfs */} {}
 
-    virtual void init(
-        const std::string& dbPath, const std::string& catalogName, main::ClientContext* context);
+    virtual void init(const std::string& dbPath, const std::string& catalogName,
+        main::ClientContext* context);
 
 protected:
     bool bindPropertyInfos(duckdb::Connection& con, const std::string& tableName,