Merge pull request #245 from paulsengroup/maintenance/refactor

Refactor
paulsengroup · Sep 11, 2024 · 784477d · 784477d
2 parents 1001623 + 53cc3ae
commit 784477d
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Showing 20 changed files with 116 additions and 103 deletions.
diff --git a/.clang-tidy b/.clang-tidy
@@ -28,7 +28,7 @@ HeaderFilterRegex: ""
 FormatStyle: none
 CheckOptions:
   - key: cppcoreguidelines-macro-usage.AllowedRegexp
-    value: "DISABLE_WARNING_.*"
+    value: "HICTK_DISABLE_WARNING_.*"
   - key: misc-include-cleaner.IgnoreHeaders
     value: "fmt/.*"
   - key: misc-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic

diff --git a/src/hictk/metadata/common.hpp b/src/hictk/metadata/common.hpp
@@ -55,14 +55,14 @@ inline void emplace_if_valid(std::string_view key, const T& value, toml::table&
   if (key.empty()) {
     return;
   }
-  DISABLE_WARNING_PUSH
-  DISABLE_WARNING_BOOL_COMPARE
+  HICTK_DISABLE_WARNING_PUSH
+  HICTK_DISABLE_WARNING_BOOL_COMPARE
   if (value <= std::numeric_limits<std::int64_t>::max()) {
     buff.insert(key, static_cast<std::int64_t>(value));
   } else {
     emplace_if_valid(key, fmt::to_string(value), buff);
   }
-  DISABLE_WARNING_POP
+  HICTK_DISABLE_WARNING_POP
 }
 
 template <typename T, typename std::enable_if_t<std::is_floating_point_v<T>>* = nullptr>

diff --git a/src/libhictk/bin_table/include/hictk/impl/bin_table_fixed_impl.hpp b/src/libhictk/bin_table/include/hictk/impl/bin_table_fixed_impl.hpp
@@ -204,11 +204,11 @@ inline std::vector<std::uint64_t> BinTableFixed::compute_num_bins_prefix_sum(
     const Reference &chroms, std::uint32_t bin_size, std::size_t bin_offset) {
   assert(bin_size != 0);
 
-  DISABLE_WARNING_PUSH
-  DISABLE_WARNING_NULL_DEREF
+  HICTK_DISABLE_WARNING_PUSH
+  HICTK_DISABLE_WARNING_NULL_DEREF
   std::vector<std::uint64_t> prefix_sum(chroms.size() + 1);
   prefix_sum.front() = bin_offset;
-  DISABLE_WARNING_POP
+  HICTK_DISABLE_WARNING_POP
 
   // I am using transform instead of inclusive_scan because the latter is not always available
   std::transform(chroms.begin(), chroms.end(), prefix_sum.begin() + 1,

diff --git a/src/libhictk/bin_table/include/hictk/impl/bin_table_impl.hpp b/src/libhictk/bin_table/include/hictk/impl/bin_table_impl.hpp
@@ -103,10 +103,10 @@ inline auto BinTable::find_overlap(const GenomicInterval &query) const
   return std::visit(
       [&](const auto &t) {
         auto its = t.find_overlap(query);
-        DISABLE_WARNING_PUSH
-        DISABLE_WARNING_MAYBE_UNINITIALIZED
+        HICTK_DISABLE_WARNING_PUSH
+        HICTK_DISABLE_WARNING_MAYBE_UNINITIALIZED
         return std::make_pair(iterator{its.first}, iterator{its.second});
-        DISABLE_WARNING_POP
+        HICTK_DISABLE_WARNING_POP
       },
       _table);
 }

diff --git a/src/libhictk/common/include/hictk/suppress_warnings.hpp b/src/libhictk/common/include/hictk/suppress_warnings.hpp
@@ -13,59 +13,62 @@
 
 // Defines for MSVC
 #ifdef _MSC_VER
-    #define DISABLE_WARNING_PUSH                      __pragma(warning(push))
-    #define DISABLE_WARNING_POP                       __pragma(warning(pop))
+    #define HICTK_DISABLE_WARNING_PUSH                      __pragma(warning(push))
+    #define HICTK_DISABLE_WARNING_POP                       __pragma(warning(pop))
     #define DISABLE_WARNING(warningNumber)            __pragma(warning(disable : warningNumber))
 
-    #define DISABLE_WARNING_BOOL_COMPARE              DISABLE_WARNING(4806)
-    #define DISABLE_WARNING_DEPRECATED_DECLARATIONS   DISABLE_WARNING(4996)
-    #define DISABLE_WARNING_MAYBE_UNINITIALIZED
-    #define DISABLE_WARNING_NULL_DEREF
-    #define DISABLE_WARNING_USELESS_CAST
-    #define DISABLE_WARNING_SIGN_COMPARE
-    #define DISABLE_WARNING_UNREACHABLE_CODE          DISABLE_WARNING(4702)
+    #define HICTK_DISABLE_WARNING_BOOL_COMPARE              DISABLE_WARNING(4806)
+    #define HICTK_DISABLE_WARNING_CONVERSION                DISABLE_WARNING(C4244)
+    #define HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS   DISABLE_WARNING(4996)
+    #define HICTK_DISABLE_WARNING_MAYBE_UNINITIALIZED
+    #define HICTK_DISABLE_WARNING_NULL_DEREF
+    #define HICTK_DISABLE_WARNING_USELESS_CAST
+    #define HICTK_DISABLE_WARNING_SIGN_COMPARE
+    #define HICTK_DISABLE_WARNING_UNREACHABLE_CODE          DISABLE_WARNING(4702)
 #endif
 
 // Defines for GCC and Clang
 #if defined(__GNUC__) || defined(__clang__)
     #define DO_PRAGMA(X)                              _Pragma(#X)
-    #define DISABLE_WARNING_PUSH                      DO_PRAGMA(GCC diagnostic push)
-    #define DISABLE_WARNING_POP                       DO_PRAGMA(GCC diagnostic pop)
+    #define HICTK_DISABLE_WARNING_PUSH                      DO_PRAGMA(GCC diagnostic push)
+    #define HICTK_DISABLE_WARNING_POP                       DO_PRAGMA(GCC diagnostic pop)
     #define DISABLE_WARNING(warningName)              DO_PRAGMA(GCC diagnostic ignored warningName)
 
-    #define DISABLE_WARNING_DEPRECATED_DECLARATIONS   DISABLE_WARNING("-Wdeprecated-declarations")
-    #define DISABLE_WARNING_NULL_DEREF                DISABLE_WARNING("-Wnull-dereference")
-    #define DISABLE_WARNING_SIGN_COMPARE              DISABLE_WARNING("-Wsign-compare")
-    #define DISABLE_WARNING_UNREACHABLE_CODE
+    #define HICTK_DISABLE_WARNING_CONVERSION                DISABLE_WARNING("-Wconversion")
+    #define HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS   DISABLE_WARNING("-Wdeprecated-declarations")
+    #define HICTK_DISABLE_WARNING_NULL_DEREF                DISABLE_WARNING("-Wnull-dereference")
+    #define HICTK_DISABLE_WARNING_SIGN_COMPARE              DISABLE_WARNING("-Wsign-compare")
+    #define HICTK_DISABLE_WARNING_UNREACHABLE_CODE
 #endif
 
 // Defines for GCC only
 #if defined(__GNUC__) && !defined(__clang__)
-    #define DISABLE_WARNING_BOOL_COMPARE              DISABLE_WARNING("-Wbool-compare")
-    #define DISABLE_WARNING_MAYBE_UNINITIALIZED       DISABLE_WARNING("-Wmaybe-uninitialized")
-    #define DISABLE_WARNING_USELESS_CAST              DISABLE_WARNING("-Wuseless-cast")
+    #define HICTK_DISABLE_WARNING_BOOL_COMPARE              DISABLE_WARNING("-Wbool-compare")
+    #define HICTK_DISABLE_WARNING_MAYBE_UNINITIALIZED       DISABLE_WARNING("-Wmaybe-uninitialized")
+    #define HICTK_DISABLE_WARNING_USELESS_CAST              DISABLE_WARNING("-Wuseless-cast")
 #endif
 
 // Defines for Clang only
 #ifdef __clang__
-    #define DISABLE_WARNING_BOOL_COMPARE              DISABLE_WARNING("-Wtautological-constant-out-of-range-compare")
-    #define DISABLE_WARNING_MAYBE_UNINITIALIZED
-    #define DISABLE_WARNING_USELESS_CAST
+    #define HICTK_DISABLE_WARNING_BOOL_COMPARE              DISABLE_WARNING("-Wtautological-constant-out-of-range-compare")
+    #define HICTK_DISABLE_WARNING_MAYBE_UNINITIALIZED
+    #define HICTK_DISABLE_WARNING_USELESS_CAST
 #endif
 
 // Defines for unknown/unsupported compilers
 #if !defined(_MSC_VER) && !defined(__GNUC__) && !defined(__clang__)
   #define DISABLE_WARNING
-  #define DISABLE_WARNING_PUSH
-  #define DISABLE_WARNING_POP
+  #define HICTK_DISABLE_WARNING_PUSH
+  #define HICTK_DISABLE_WARNING_POP
 
-  #define DISABLE_WARNING_BOOL_COMPARE
-  #define DISABLE_WARNING_DEPRECATED_DECLARATIONS
-  #define DISABLE_WARNING_MAYBE_UNINITIALIZED
-  #define DISABLE_WARNING_NULL_DEREF
-  #define DISABLE_WARNING_USELESS_CAST
-  #define DISABLE_WARNING_SIGN_COMPARE
-  #define DISABLE_WARNING_UNREACHABLE_CODE
+  #define HICTK_DISABLE_WARNING_BOOL_COMPARE
+  #define HICTK_DISABLE_WARNING_CONVERSION
+  #define HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
+  #define HICTK_DISABLE_WARNING_MAYBE_UNINITIALIZED
+  #define HICTK_DISABLE_WARNING_NULL_DEREF
+  #define HICTK_DISABLE_WARNING_USELESS_CAST
+  #define HICTK_DISABLE_WARNING_SIGN_COMPARE
+  #define HICTK_DISABLE_WARNING_UNREACHABLE_CODE
 #endif
 
 // NOLINTEND(cppcoreguidelines-macro-usage)

diff --git a/src/libhictk/cooler/include/hictk/cooler/cooler.hpp b/src/libhictk/cooler/include/hictk/cooler/cooler.hpp
@@ -9,11 +9,11 @@
 // clang-format off
 #include "hictk/suppress_warnings.hpp"
 // clang-format on
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_NULL_DEREF
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_NULL_DEREF
 #include <highfive/H5File.hpp>
 #include <highfive/H5Group.hpp>
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
 #include <initializer_list>
 #include <memory>

diff --git a/src/libhictk/cooler/include/hictk/cooler/dataset.hpp b/src/libhictk/cooler/include/hictk/cooler/dataset.hpp
@@ -14,10 +14,10 @@
 
 #include <cstddef>
 #include <cstdint>
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_NULL_DEREF
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_NULL_DEREF
 #include <highfive/H5DataSet.hpp>
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 #include <highfive/H5DataSpace.hpp>
 #include <highfive/H5DataType.hpp>
 #include <highfive/H5PropertyList.hpp>
@@ -53,8 +53,8 @@ template <typename T>
 inline constexpr bool is_atomic_buffer_v = is_atomic_buffer<T>::value;
 }  // namespace internal
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_DEPRECATED_DECLARATIONS
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 class Dataset {
   using VariantBuffer = hictk::internal::VariantBuffer;
   using GenericVariant = hictk::internal::GenericVariant;
@@ -308,7 +308,7 @@ class Dataset {
                                                 std::size_t chunk_size) -> iterator;
   };
 };
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
 using DatasetMap = phmap::flat_hash_map<std::string, Dataset>;
 

diff --git a/src/libhictk/cooler/include/hictk/cooler/group.hpp b/src/libhictk/cooler/include/hictk/cooler/group.hpp
@@ -13,17 +13,17 @@
 #include <fmt/format.h>
 #include <parallel_hashmap/phmap.h>
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_NULL_DEREF
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_NULL_DEREF
 #include <highfive/H5File.hpp>
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 #include <highfive/H5Group.hpp>
 #include <string>
 
 namespace hictk::cooler {
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_DEPRECATED_DECLARATIONS
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 struct RootGroup {
   HighFive::Group group{};
 
@@ -44,7 +44,7 @@ struct Group {
   [[nodiscard]] constexpr HighFive::Group &operator()() noexcept { return group; };
   [[nodiscard]] constexpr const HighFive::Group &operator()() const noexcept { return group; };
 };
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
 using GroupMap = phmap::flat_hash_map<std::string, Group>;
 

diff --git a/src/libhictk/cooler/include/hictk/cooler/impl/attribute_impl.hpp b/src/libhictk/cooler/include/hictk/cooler/impl/attribute_impl.hpp
@@ -112,8 +112,8 @@ inline void Attribute::read_vector(const ParentObj& h5obj, std::string_view key,
   }
 }
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_UNREACHABLE_CODE
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_UNREACHABLE_CODE
 template <std::size_t i>
 inline auto Attribute::read_variant(const HighFive::Attribute& attr) -> AttributeVar {
   if constexpr (i < std::variant_size_v<AttributeVar>) {
@@ -135,10 +135,10 @@ inline auto Attribute::read_variant(const HighFive::Attribute& attr) -> Attribut
   }
   return std::monostate();
 }
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_UNREACHABLE_CODE
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_UNREACHABLE_CODE
 template <typename T1, typename Tout, typename Tin>
 // NOLINTNEXTLINE(readability-function-cognitive-complexity)
 inline Tout Attribute::numeric_converter(T1& buff) {
@@ -221,6 +221,6 @@ inline Tout Attribute::numeric_converter(T1& buff) {
           "Expected type {}, found {}. Unable to safely convert value {} of type {} to type {}"),
       type_name<Tout>(), type_name<Tin>(), buff, type_name<Tin>(), type_name<Tout>()));
 }
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
 }  // namespace hictk::cooler
diff --git a/src/libhictk/cooler/include/hictk/cooler/impl/dataset_read_impl.hpp b/src/libhictk/cooler/include/hictk/cooler/impl/dataset_read_impl.hpp
@@ -56,8 +56,8 @@ inline std::size_t Dataset::read(std::vector<std::string> &buff, std::size_t num
   return offset + buff.size();
 }
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_UNREACHABLE_CODE
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_UNREACHABLE_CODE
 template <std::size_t i>
 inline std::size_t Dataset::read(VariantBuffer &vbuff, std::size_t num, std::size_t offset) const {
   if constexpr (i == 0) {
@@ -93,7 +93,7 @@ inline std::size_t Dataset::read(VariantBuffer &vbuff, std::size_t num, std::siz
 
   unreachable_code();
 }
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
 template <typename BuffT, typename T, typename>
 inline BuffT Dataset::read_n(std::size_t num, std::size_t offset) const {
@@ -146,8 +146,8 @@ inline std::size_t Dataset::read(std::string &buff, std::size_t offset) const {
   return offset + 1;
 }
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_UNREACHABLE_CODE
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_UNREACHABLE_CODE
 template <std::size_t i>
 inline std::size_t Dataset::read(GenericVariant &vbuff, std::size_t offset) const {
   if constexpr (i == 0) {
@@ -182,7 +182,7 @@ inline std::size_t Dataset::read(GenericVariant &vbuff, std::size_t offset) cons
 
   unreachable_code();
 }
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
 template <typename BuffT, typename T, typename>
 inline BuffT Dataset::read(std::size_t offset) const {

diff --git a/src/libhictk/cooler/include/hictk/cooler/impl/file_impl.hpp b/src/libhictk/cooler/include/hictk/cooler/impl/file_impl.hpp
@@ -306,8 +306,8 @@ inline auto File::open_or_create_root_group(HighFive::File f, std::string_view u
   return create_root_group(f, uri);
 }
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_UNREACHABLE_CODE
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_UNREACHABLE_CODE
 namespace internal {
 template <typename Variant, std::size_t i = 0>
 [[nodiscard]] inline Variant read_pixel_variant(const HighFive::DataSet &dset) {
@@ -328,7 +328,7 @@ template <typename Variant, std::size_t i = 0>
         fmt::format(FMT_STRING("Unsupported type for dataset \"{}\""), dset.getPath()));
   }
 }
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 }  // namespace internal
 
 inline hictk::internal::NumericVariant File::detect_pixel_type(const RootGroup &root_grp,

diff --git a/src/libhictk/cooler/include/hictk/cooler/impl/file_read_impl.hpp b/src/libhictk/cooler/include/hictk/cooler/impl/file_read_impl.hpp
@@ -440,8 +440,8 @@ bool read_sum_optional(const RootGroup &root_grp, std::string_view key, N &buff,
 
 }  // namespace internal
 
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_UNREACHABLE_CODE
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_UNREACHABLE_CODE
 inline auto File::read_standard_attributes(const RootGroup &root_grp,
                                            bool initialize_missing) -> Attributes {
   auto attrs = initialize_missing ? Attributes::init(0) : Attributes::init_empty();
@@ -496,7 +496,7 @@ inline auto File::read_standard_attributes(const RootGroup &root_grp,
 
   return attrs;
 }
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
 inline auto File::import_chroms(const Dataset &chrom_names, const Dataset &chrom_sizes,
                                 bool missing_ok) -> Reference {

diff --git a/src/libhictk/cooler/include/hictk/cooler/impl/singlecell_cooler_impl.hpp b/src/libhictk/cooler/include/hictk/cooler/impl/singlecell_cooler_impl.hpp
@@ -228,7 +228,7 @@ inline File SingleCellFile::aggregate(std::string_view uri, bool overwrite_if_ex
   return File(uri);
 }
 
-DISABLE_WARNING_PUSH DISABLE_WARNING_UNREACHABLE_CODE inline SingleCellAttributes
+HICTK_DISABLE_WARNING_PUSH HICTK_DISABLE_WARNING_UNREACHABLE_CODE inline SingleCellAttributes
 SingleCellFile::read_standard_attributes(const HighFive::File& f, bool initialize_missing) {
   const RootGroup root_grp{f.getGroup("/")};
   auto attrs =
@@ -274,7 +274,7 @@ SingleCellFile::read_standard_attributes(const HighFive::File& f, bool initializ
 
   return attrs;
 }  // NOLINT(clang-analyzer-cplusplus.NewDeleteLeaks)
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 
 inline BinTable SingleCellFile::init_bin_table(const HighFive::File& f) {
   [[maybe_unused]] HighFive::SilenceHDF5 silencer{};  // NOLINT

diff --git a/src/libhictk/cooler/include/hictk/cooler/validation.hpp b/src/libhictk/cooler/include/hictk/cooler/validation.hpp
@@ -11,10 +11,10 @@
 #include <parallel_hashmap/btree.h>
 
 #include <cstdint>
-DISABLE_WARNING_PUSH
-DISABLE_WARNING_NULL_DEREF
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_NULL_DEREF
 #include <highfive/H5File.hpp>
-DISABLE_WARNING_POP
+HICTK_DISABLE_WARNING_POP
 #include <highfive/H5Group.hpp>
 #include <string>
 #include <string_view>

diff --git a/src/libhictk/hic/include/hictk/hic/impl/file_writer_impl.hpp b/src/libhictk/hic/include/hictk/hic/impl/file_writer_impl.hpp
@@ -672,10 +672,10 @@ inline void HiCFileWriter::write_empty_normalized_expected_values() {
                offset);
   try {
     _fs.seekp(offset);
-    DISABLE_WARNING_PUSH
-    DISABLE_WARNING_USELESS_CAST
+    HICTK_DISABLE_WARNING_PUSH
+    HICTK_DISABLE_WARNING_USELESS_CAST
     _fs.write(std::int32_t(0));
-    DISABLE_WARNING_POP
+    HICTK_DISABLE_WARNING_POP
   } catch (const std::exception &e) {
     throw std::runtime_error(
         fmt::format(FMT_STRING("an error occurred while writing an empty normalized expected "