Merge pull request #249 from GenSpectrum/202-check-linter-in-ci

build: make linter throw errors again and fix them

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
       - name: Run clang-format style check
         uses: jidicula/clang-format-action@v4.11.0
         with:
-          clang-format-version: '16'
+          clang-format-version: '17'
           check-path: ${{ matrix.path['check'] }}
           exclude-regex: ${{ matrix.path['exclude'] }}
 

CMakeLists.txt

@@ -62,9 +62,9 @@ list(REMOVE_ITEM SRC_SILO_API ${SRC_TEST})
 
 option(BUILD_WITH_CLANG_TIDY "Build process clang-tidy" ON)
 if (NOT CMAKE_BUILD_TYPE STREQUAL Release AND BUILD_WITH_CLANG_TIDY)
-    find_program(CLANG_TIDY_EXE NAMES clang-tidy-17)
+    find_program(CLANG_TIDY_EXE NAMES clang-tidy-18)
     if (NOT CLANG_TIDY_EXE)
-        message(STATUS "clang-tidy-17 not found.")
+        message(SEND_ERROR "clang-tidy not found, aborting. You can run the build with '-D BUILD_WITH_CLANG_TIDY=OFF' to disable clang-tidy.")
     else ()
         message(STATUS "clang-tidy found: ${CLANG_TIDY_EXE}")
         message(STATUS "run clang tidy with: ${CLANG_TIDY_EXE}")

Dockerfile

@@ -7,7 +7,7 @@ RUN apk update && apk add --no-cache py3-pip \
     boost-build=1.82.0-r0 \
     libtbb=2021.9.0-r0
 
-RUN pip install conan==2.0.14
+RUN pip install conan==2.0.17
 
 WORKDIR /src
 COPY conanfile.py conanprofile.docker ./

Dockerfile_linter

@@ -6,15 +6,15 @@ RUN apt update \
     && apt install -y \
     cmake=3.22.1-1ubuntu1.22.04.1 \
     python3-pip=22.0.2+dfsg-1ubuntu0.4 \
-    software-properties-common=0.99.22.7 \
+    software-properties-common=0.99.22.9 \
     wget=1.21.2-2ubuntu1 \
     gnupg=2.2.27-3ubuntu2.1 \
     lsb-release=11.1.0ubuntu4 \
     && wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc \
     && add-apt-repository 'deb http://apt.llvm.org/jammy/  llvm-toolchain-jammy main' \
-    && apt install -y clang-tidy
+    && apt install -y clang-tidy-18
 
-RUN pip install conan==2.0.11
+RUN pip install conan==2.0.17
 
 COPY conanfile.py conanprofile.docker ./
 RUN mv conanprofile.docker conanprofile

include/silo/database_info.h

@@ -4,6 +4,8 @@
 #include <map>
 #include <vector>
 
+#include "fmt/format.h"
+
 #include "silo/common/format_number.h"
 #include "silo/common/nucleotide_symbols.h"
 

include/silo/preprocessing/partition.h

@@ -68,8 +68,6 @@ class Partitions {
    static Partitions load(std::istream& input_file);
 
    [[nodiscard]] const std::vector<Partition>& getPartitions() const;
-
-   [[nodiscard]] const std::vector<PartitionChunk>& getAllPartitionChunks() const;
 };
 
 }  // namespace silo::preprocessing

include/silo/storage/database_partition.h

@@ -69,6 +69,12 @@ class DatabasePartition {
 
    DatabasePartition() = default;
 
+   void validateNucleotideSequences() const;
+
+   void validateAminoAcidSequences() const;
+
+   void validateMetadataColumns() const;
+
   public:
    storage::ColumnPartitionGroup columns;
    std::map<std::string, SequenceStorePartition<Nucleotide>&> nuc_sequences;

include/silo/storage/sequence_store.h

@@ -73,7 +73,8 @@ class SequenceStorePartition {
    void fillNBitmaps(const std::vector<std::string>& genomes);
 
   public:
-   explicit SequenceStorePartition(const std::vector<typename SymbolType::Symbol>& reference_genome
+   explicit SequenceStorePartition(
+      const std::vector<typename SymbolType::Symbol>& reference_sequence
    );
 
    const std::vector<typename SymbolType::Symbol>& reference_sequence;

include/silo/zstdfasta/zstd_compressor.h

@@ -28,8 +28,8 @@ class ZstdCompressor {
    ZstdCompressor(const ZstdCompressor& other);
    ZstdCompressor& operator=(const ZstdCompressor& other);
 
-   ZstdCompressor(ZstdCompressor&& other);
-   ZstdCompressor& operator=(ZstdCompressor&& other);
+   ZstdCompressor(ZstdCompressor&& other) noexcept;
+   ZstdCompressor& operator=(ZstdCompressor&& other) noexcept;
 
    virtual ~ZstdCompressor();
 

include/silo/zstdfasta/zstd_decompressor.h

@@ -12,8 +12,8 @@ class ZstdDecompressor {
    ZSTD_DCtx* zstd_context;
 
   public:
-   ZstdDecompressor(ZstdDecompressor&& other);
-   ZstdDecompressor& operator=(ZstdDecompressor&& other);
+   ZstdDecompressor(ZstdDecompressor&& other) noexcept;
+   ZstdDecompressor& operator=(ZstdDecompressor&& other) noexcept;
 
    ZstdDecompressor(const ZstdDecompressor& other) = delete;
    ZstdDecompressor& operator=(const ZstdDecompressor& other) = delete;

src/silo/common/aa_symbols.cpp

@@ -1,7 +1,6 @@
 #include "silo/common/aa_symbols.h"
 
 #include <cassert>
-#include <cstddef>
 
 char silo::AminoAcid::symbolToChar(silo::AminoAcid::Symbol symbol) {
    switch (symbol) {
@@ -118,12 +117,12 @@ std::optional<silo::AminoAcid::Symbol> silo::AminoAcid::charToSymbol(char charac
 }
 
 std::optional<std::vector<silo::AminoAcid::Symbol>> silo::AminoAcid::stringToSymbolVector(
-   const std::string& nucleotides
+   const std::string& sequence
 ) {
-   const size_t size = nucleotides.size();
+   const size_t size = sequence.size();
    std::vector<silo::AminoAcid::Symbol> result(size);
    for (size_t i = 0; i < size; ++i) {
-      auto symbol = silo::AminoAcid::charToSymbol(nucleotides[i]);
+      auto symbol = silo::AminoAcid::charToSymbol(sequence[i]);
       if (symbol == std::nullopt) {
          return std::nullopt;
       }

src/silo/common/bidirectional_map.cpp

@@ -4,7 +4,6 @@
 #include <string>
 
 #include "silo/common/pango_lineage.h"
-#include "silo/common/types.h"
 
 namespace silo::common {
 

src/silo/common/data_version.cpp

@@ -2,7 +2,6 @@
 
 #include <algorithm>
 #include <chrono>
-#include <compare>
 #include <utility>
 
 namespace silo {

src/silo/common/format_number.cpp

@@ -8,7 +8,9 @@
 namespace silo {
 
 struct ThousandSeparator : std::numpunct<char> {
+   // NOLINTNEXTLINE(readability-convert-member-functions-to-static)
    [[nodiscard]] char_type do_thousands_sep() const override { return '\''; }
+   // NOLINTNEXTLINE(readability-convert-member-functions-to-static)
    [[nodiscard]] string_type do_grouping() const override { return "\3"; }
 };
 

src/silo/common/input_stream_wrapper.cpp

@@ -3,12 +3,10 @@
 #include <string>
 
 #include <spdlog/spdlog.h>
-#include <boost/iostreams/categories.hpp>
 #include <boost/iostreams/detail/error.hpp>
 #include <boost/iostreams/filter/lzma.hpp>
 #include <boost/iostreams/filter/zstd.hpp>
 #include <boost/iostreams/filtering_stream.hpp>
-#include <boost/iostreams/read.hpp>
 
 #include "silo/preprocessing/preprocessing_exception.h"
 

src/silo/common/nucleotide_symbols.cpp

@@ -1,7 +1,6 @@
 #include "silo/common/nucleotide_symbols.h"
 
 #include <cassert>
-#include <cstddef>
 
 namespace silo {
 

src/silo/common/pango_lineage.cpp

@@ -1,7 +1,5 @@
 #include "silo/common/pango_lineage.h"
 
-#include <compare>
-
 std::size_t std::hash<silo::common::UnaliasedPangoLineage>::operator()(
    const silo::common::UnaliasedPangoLineage& pango_lineage
 ) const {

src/silo/common/pango_lineage.test.cpp

@@ -3,7 +3,7 @@
 #include <gtest/gtest.h>
 
 TEST(UnaliasedPangoLineage, isSublineageOf) {
-   silo::common::UnaliasedPangoLineage const under_test{"A.1.2"};
+   const silo::common::UnaliasedPangoLineage under_test{"A.1.2"};
 
    EXPECT_TRUE(under_test.isSublineageOf(silo::common::UnaliasedPangoLineage{"A.1"}));
    EXPECT_TRUE(under_test.isSublineageOf(silo::common::UnaliasedPangoLineage{"A"}));
@@ -18,7 +18,7 @@ TEST(UnaliasedPangoLineage, isSublineageOf) {
 }
 
 TEST(PangoLineage, getParentLineages) {
-   silo::common::UnaliasedPangoLineage const under_test{"A.1.23.4.513"};
+   const silo::common::UnaliasedPangoLineage under_test{"A.1.23.4.513"};
 
    const std::vector<silo::common::UnaliasedPangoLineage> expected = {
       silo::common::UnaliasedPangoLineage{"A"},

src/silo/common/string.cpp

@@ -4,7 +4,6 @@
 #include <string_view>
 
 #include "silo/common/bidirectional_map.h"
-#include "silo/common/types.h"
 
 namespace silo::common {
 

src/silo/common/string.test.cpp

@@ -72,6 +72,7 @@ TEST(String, comparesCorrectlyIfPrefixesMatchUpTo32Positions) {
    }
 }
 
+// NOLINTNEXTLINE(readability-function-cognitive-complexity)
 TEST(String, fastComparesCorrectlyIfPrefixesMatchUpTo32Positions) {
    BidirectionalMap<std::string> dict;
    const std::string value = "1234567890abcdefghijklmnopqrstuv";

src/silo/common/string_utils.cpp

@@ -1,6 +1,7 @@
-#include "silo/common/string_utils.h"
 #include <algorithm>
 
+#include "silo/common/string_utils.h"
+
 namespace silo {
 
 std::vector<std::string> splitBy(const std::string& value, const std::string_view delimiter) {

src/silo/common/string_utils.test.cpp

@@ -2,72 +2,74 @@
 
 #include <gtest/gtest.h>
 
-using silo::removeSymbol;
 using silo::splitBy;
+using std::string;
+using std::string_view;
+using std::vector;
 
 TEST(splitBy, correctSplit) {
-   const std::string input("ABC,DEF,ADS,");
-   const std::string delimiter(",");
+   const string input("ABC,DEF,ADS,");
+   const string delimiter(",");
 
    const auto result = splitBy(input, delimiter);
-   EXPECT_EQ(result, std::vector<std::string>({"ABC", "DEF", "ADS", ""}));
+   EXPECT_EQ(result, vector<string>({"ABC", "DEF", "ADS", ""}));
 }
 
 TEST(splitBy, correctSplit2) {
-   const std::string input("ABC");
-   const std::string delimiter(",");
+   const string input("ABC");
+   const string delimiter(",");
 
    const auto result = splitBy(input, delimiter);
-   EXPECT_EQ(result, std::vector<std::string>({"ABC"}));
+   EXPECT_EQ(result, vector<string>({"ABC"}));
 }
 
 TEST(splitBy, correctSplit3) {
-   const std::string input("ABC.*");
-   const std::string delimiter(".*");
+   const string input("ABC.*");
+   const string delimiter(".*");
 
    const auto result = splitBy(input, delimiter);
-   EXPECT_EQ(result, std::vector<std::string>({"ABC", ""}));
+   EXPECT_EQ(result, vector<string>({"ABC", ""}));
 }
 
 TEST(splitBy, correctWithEmptyString) {
-   const std::string input;
-   const std::string_view delimiter(",");
+   const string input;
+   const string_view delimiter(",");
 
    const auto result = splitBy(input, delimiter);
-   EXPECT_EQ(result, std::vector<std::string>{""});
+   EXPECT_EQ(result, vector<string>{""});
 }
 
 TEST(removeSymbol, removesAllOccurences) {
-   const std::string input(R"(ABC"DEF"ADS")");
+   const string input(R"(ABC"DEF"ADS")");
 
    const auto result = silo::removeSymbol(input, '\"');
-   EXPECT_EQ(result, std::string("ABCDEFADS"));
+   EXPECT_EQ(result, string("ABCDEFADS"));
 }
 
 TEST(removeSymbol, removesAtBeginning) {
-   const std::string input(R"("ABC)");
+   const string input(R"("ABC)");
 
    const auto result = silo::removeSymbol(input, '\"');
-   EXPECT_EQ(result, std::string("ABC"));
+   EXPECT_EQ(result, string("ABC"));
 }
 
 TEST(removeSymbol, removesAtEnd) {
-   const std::string input(R"(ABC")");
+   const string input(R"(ABC")");
 
    const auto result = silo::removeSymbol(input, '\"');
-   EXPECT_EQ(result, std::string("ABC"));
+   EXPECT_EQ(result, string("ABC"));
 }
 
 TEST(removeSymbol, removesAtBeginningAndEnd) {
-   const std::string input(R"("ABC")");
+   const string input(R"("ABC")");
 
    const auto result = silo::removeSymbol(input, '\"');
-   EXPECT_EQ(result, std::string("ABC"));
+   EXPECT_EQ(result, string("ABC"));
 }
 
 TEST(removeSymbol, doesNotRemoveIfNotContained) {
-   const std::string input("ABCDEFADS");
+   const string input("ABCDEFADS");
 
    const auto result = silo::removeSymbol(input, '\"');
-   EXPECT_EQ(result, std::string("ABCDEFADS"));
+   EXPECT_EQ(result, string("ABCDEFADS"));
 }

src/silo/config/config_repository.cpp

@@ -3,7 +3,6 @@
 #include <map>
 #include <optional>
 #include <string>
-#include <vector>
 
 #include "silo/config/config_exception.h"
 #include "silo/config/database_config.h"

src/silo/config/database_config.cpp

@@ -1,8 +1,6 @@
 #include "silo/config/database_config.h"
 
-#include <algorithm>
 #include <filesystem>
-#include <iterator>
 #include <stdexcept>
 #include <string_view>
 
@@ -193,11 +191,10 @@ std::string DatabaseSchema::getStrictOrderByClause() const {
    if (date_to_sort_by.has_value()) {
       SPDLOG_INFO("preprocessing - produce order by clause with a date to sort by");
       return fmt::format("ORDER BY {}, {}", date_to_sort_by.value(), primary_key);
-   } else {
-      SPDLOG_INFO("preprocessing - produce order by clause without a date to sort by");
-
-      return fmt::format("ORDER BY {}", primary_key);
    }
+
+   SPDLOG_INFO("preprocessing - produce order by clause without a date to sort by");
+   return fmt::format("ORDER BY {}", primary_key);
 }
 
 std::optional<DatabaseMetadata> DatabaseConfig::getMetadata(const std::string& name) const {

src/silo/database.cpp

@@ -81,6 +81,7 @@ std::optional<std::string> Database::getDefaultSequenceName<AminoAcid>() const {
 template <>
 std::vector<std::string> Database::getSequenceNames<Nucleotide>() const {
    std::vector<std::string> sequence_names;
+   sequence_names.reserve(nuc_sequences.size());
    for (const auto& [name, _] : nuc_sequences) {
       sequence_names.emplace_back(name);
    }
@@ -90,6 +91,7 @@ std::vector<std::string> Database::getSequenceNames<Nucleotide>() const {
 template <>
 std::vector<std::string> Database::getSequenceNames<AminoAcid>() const {
    std::vector<std::string> sequence_names;
+   sequence_names.reserve(aa_sequences.size());
    for (const auto& [name, _] : aa_sequences) {
       sequence_names.emplace_back(name);
    }