Clean includes and remove dead code

paulsengroup · Nov 13, 2024 · 4f2a87e · 4f2a87e
1 parent e4d5536
commit 4f2a87e
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Showing 10 changed files with 18 additions and 77 deletions.
diff --git a/src/io/include/nchg/k_merger.hpp b/src/io/include/nchg/k_merger.hpp
@@ -30,18 +30,16 @@
 #include <utility>
 #include <vector>
 
-#include "hictk/pixel.hpp"
-
 namespace nchg {
 
 /// This class is basically a wrapper around a priority queue of objects of type Node, and can be
 /// used to merge two or more sorted sequences of objects.
-/// Node consist of an object and an index.
+/// Nodes consist of an object and an index.
 /// The object should be comparable with objects of the same type to determine which comes first in
 /// a sorted sequence.
 /// The index represents from which iterator the object was read.
 /// This allows us to know from which iterator we should read the next object (i.e. the same
-/// iterator from which the top pixel originated)
+/// iterator from which the top node originated)
 template <typename It>
 class KMerger {
   using ItInternal = std::remove_cvref_t<It>;

diff --git a/src/io/include/nchg/parquet_stats_file.hpp b/src/io/include/nchg/parquet_stats_file.hpp
@@ -22,12 +22,8 @@
 #include "nchg/suppress_warnings.hpp"
 NCHG_DISABLE_WARNING_PUSH
 NCHG_DISABLE_WARNING_DEPRECATED_DECLARATIONS
-#include <arrow/array/array_base.h>
-#include <arrow/builder.h>
-#include <arrow/record_batch.h>
-#include <arrow/type_fwd.h>
+#include <arrow/io/file.h>
 #include <parquet/stream_reader.h>
-#include <parallel_hashmap/phmap.h>
 NCHG_DISABLE_WARNING_POP
 // clang-format on
 
@@ -105,18 +101,6 @@ class ParquetStatsFile {
   };
 };
 
-template <std::size_t NTOKS>
-[[nodiscard]] std::string_view truncate_record(std::string_view record, char sep = '\t');
-
-namespace internal {
-
-[[nodiscard]] std::shared_ptr<arrow::Schema> get_schema(const hictk::Reference &chroms);
-[[nodiscard]] std::shared_ptr<arrow::Schema> get_schema_padj(const hictk::Reference &chroms);
-
-[[nodiscard]] parquet::Compression::type parse_parquet_compression(std::string_view method);
-
-}  // namespace internal
-
 }  // namespace nchg
 
 #include "../../parquet_stats_file_impl.hpp"
diff --git a/src/io/include/nchg/record_batch_builder.hpp b/src/io/include/nchg/record_batch_builder.hpp
@@ -24,19 +24,18 @@ NCHG_DISABLE_WARNING_PUSH
 NCHG_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <arrow/builder.h>
 #include <arrow/record_batch.h>
-#include <arrow/type_fwd.h>
 #include <parquet/arrow/writer.h>
-#include <parallel_hashmap/phmap.h>
 NCHG_DISABLE_WARNING_POP
 // clang-format on
 
 #include <cstddef>
 #include <cstdint>
 #include <filesystem>
+#include <hictk/chromosome.hpp>
 #include <hictk/reference.hpp>
 #include <memory>
 #include <string_view>
-#include <type_traits>
+#include <vector>
 
 namespace nchg {
 
@@ -93,9 +92,6 @@ template <typename Record>
     const hictk::Reference &chroms, const std::filesystem::path &path, bool force,
     std::string_view compression_method, std::uint8_t compression_lvl, std::size_t threads);
 
-[[nodiscard]] phmap::flat_hash_map<hictk::Chromosome, std::vector<bool>> parse_bin_mask(
-    const hictk::Reference &chroms, std::uint32_t bin_size, const std::filesystem::path &path);
-
 }  // namespace nchg
 
 #include "../../record_batch_builder_impl.hpp"
diff --git a/src/io/k_merger_impl.hpp b/src/io/k_merger_impl.hpp
@@ -18,12 +18,12 @@
 
 #pragma once
 
+#include <algorithm>
 #include <cassert>
+#include <optional>
 #include <utility>
 #include <vector>
 
-#include "hictk/pixel.hpp"
-
 namespace nchg {
 
 template <typename It>

diff --git a/src/io/parquet_helpers.cpp b/src/io/parquet_helpers.cpp
@@ -23,7 +23,6 @@ NCHG_DISABLE_WARNING_PUSH
 NCHG_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <arrow/type.h>
 #include <arrow/util/key_value_metadata.h>
-#include <parallel_hashmap/phmap.h>
 #include <parquet/platform.h>
 NCHG_DISABLE_WARNING_POP
 // clang-format on

diff --git a/src/io/parquet_stats_file.cpp b/src/io/parquet_stats_file.cpp
@@ -22,13 +22,12 @@
 #include "nchg/suppress_warnings.hpp"
 NCHG_DISABLE_WARNING_PUSH
 NCHG_DISABLE_WARNING_DEPRECATED_DECLARATIONS
-#include <arrow/array.h>
-#include <arrow/builder.h>
+#include <arrow/record_batch.h>
 #include <arrow/type.h>
 #include <arrow/io/file.h>
 #include <arrow/util/key_value_metadata.h>
 #include <parquet/arrow/reader.h>
-#include <parquet/properties.h>
+#include <parquet/file_reader.h>
 #include <parquet/stream_reader.h>
 NCHG_DISABLE_WARNING_POP
 // clang-format on
@@ -46,7 +45,6 @@ NCHG_DISABLE_WARNING_POP
 #include <hictk/reference.hpp>
 #include <memory>
 #include <stdexcept>
-#include <string>
 #include <string_view>
 #include <utility>
 #include <vector>

diff --git a/src/io/parquet_stats_file_impl.hpp b/src/io/parquet_stats_file_impl.hpp
@@ -22,24 +22,16 @@
 #include "nchg/suppress_warnings.hpp"
 NCHG_DISABLE_WARNING_PUSH
 NCHG_DISABLE_WARNING_DEPRECATED_DECLARATIONS
-#include <arrow/array.h>
-#include <arrow/io/file.h>
-#include <arrow/util/thread_pool.h>
-#include <parquet/arrow/reader.h>
-#include <parquet/arrow/writer.h>
+#include <parquet/stream_reader.h>
 NCHG_DISABLE_WARNING_POP
 // clang-format on
 
-#include <cstddef>
+#include <cassert>
 #include <cstdint>
-#include <filesystem>
 #include <hictk/chromosome.hpp>
 #include <hictk/pixel.hpp>
 #include <hictk/reference.hpp>
 #include <memory>
-#include <stdexcept>
-#include <string>
-#include <string_view>
 #include <utility>
 
 #include "nchg/parquet_helpers.hpp"

diff --git a/src/io/record_batch_builder.cpp b/src/io/record_batch_builder.cpp
@@ -22,45 +22,21 @@
 #include "nchg/suppress_warnings.hpp"
 NCHG_DISABLE_WARNING_PUSH
 NCHG_DISABLE_WARNING_DEPRECATED_DECLARATIONS
-#include <arrow/array.h>
+#include <arrow/array/array_base.h>
 #include <arrow/builder.h>
 #include <arrow/record_batch.h>
-#include <arrow/type.h>
-#include <arrow/io/file.h>
-#include <arrow/util/key_value_metadata.h>
-#include <parquet/arrow/reader.h>
-#include <parquet/arrow/writer.h>
-#include <parquet/encoding.h>
-#include <parquet/properties.h>
-#include <parquet/stream_reader.h>
-#include <parallel_hashmap/phmap.h>
 NCHG_DISABLE_WARNING_POP
 // clang-format on
 
-#include <fmt/format.h>
-#include <spdlog/spdlog.h>
-
-#include <algorithm>
-#include <array>
-#include <cassert>
 #include <cstddef>
 #include <cstdint>
-#include <exception>
-#include <filesystem>
-#include <fstream>
-#include <hictk/genomic_interval.hpp>
-#include <hictk/numeric_utils.hpp>
 #include <hictk/reference.hpp>
-#include <iosfwd>
 #include <memory>
-#include <numeric>
 #include <stdexcept>
 #include <string>
-#include <string_view>
 #include <utility>
 #include <vector>
 
-#include "nchg/common.hpp"
 #include "nchg/parquet_stats_file.hpp"
 
 namespace nchg {

diff --git a/src/io/record_batch_builder_impl.hpp b/src/io/record_batch_builder_impl.hpp
@@ -22,27 +22,24 @@
 #include "nchg/suppress_warnings.hpp"
 NCHG_DISABLE_WARNING_PUSH
 NCHG_DISABLE_WARNING_DEPRECATED_DECLARATIONS
-#include <arrow/array.h>
+#include <arrow/array/array_base.h>
 #include <arrow/io/file.h>
 #include <arrow/util/thread_pool.h>
-#include <parquet/arrow/reader.h>
+#include <parquet/properties.h>
 #include <parquet/arrow/writer.h>
 NCHG_DISABLE_WARNING_POP
 // clang-format on
 
+#include <fmt/format.h>
 #include <spdlog/spdlog.h>
 
 #include <cstddef>
 #include <cstdint>
 #include <filesystem>
-#include <hictk/chromosome.hpp>
-#include <hictk/pixel.hpp>
-#include <hictk/reference.hpp>
 #include <memory>
 #include <stdexcept>
 #include <string>
 #include <string_view>
-#include <utility>
 
 #include "nchg/parquet_helpers.hpp"
 

diff --git a/src/io/text.cpp b/src/io/text.cpp
@@ -17,15 +17,16 @@
 // <https://www.gnu.org/licenses/>.
 
 // clang-format off
+
+#include "nchg/text.hpp"
+
 #include "nchg/suppress_warnings.hpp"
 NCHG_DISABLE_WARNING_PUSH
 NCHG_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
 NCHG_DISABLE_WARNING_POP
 // clang-format on
 
-#include "nchg/text.hpp"
-
 #include <fmt/format.h>
 #include <spdlog/spdlog.h>