Merge pull request #54 from smehringer/direcotory_structure

[MISC] Change direcotory structure of the repository

include/hibf/detail/build/build_data.hpp → include/hibf/build/build_data.hpp

@@ -13,9 +13,9 @@
 #include <cstddef> // for size_t
 #include <vector>  // for vector
 
-#include <hibf/config.hpp>                 // for config
-#include <hibf/detail/build/node_data.hpp> // for node_data
-#include <hibf/detail/timer.hpp>           // for concurrent, timer
+#include <hibf/build/node_data.hpp> // for node_data
+#include <hibf/config.hpp>          // for config
+#include <hibf/detail/timer.hpp>    // for concurrent, timer
 
 namespace seqan::hibf
 {

include/hibf/detail/build/compute_kmers.hpp → include/hibf/build/compute_kmers.hpp

@@ -14,9 +14,9 @@
 
 #include <cinttypes> // for uint64_t
 
-#include <hibf/contrib/robin_hood.hpp>      // for unordered_flat_set
-#include <hibf/detail/build/build_data.hpp> // for build_data
-#include <hibf/detail/layout/layout.hpp>    // for layout
+#include <hibf/build/build_data.hpp>   // for build_data
+#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set
+#include <hibf/layout/layout.hpp>      // for layout
 
 namespace seqan::hibf
 {

include/hibf/detail/build/construct_ibf.hpp → include/hibf/build/construct_ibf.hpp

@@ -12,8 +12,8 @@
 #include <cinttypes> // for uint64_t
 #include <cstddef>   // for size_t
 
+#include <hibf/build/build_data.hpp>         // for build_data
 #include <hibf/contrib/robin_hood.hpp>       // for unordered_flat_set
-#include <hibf/detail/build/build_data.hpp>  // for build_data
 #include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
 
 namespace seqan::hibf

include/hibf/detail/build/initialise_build_tree.hpp → include/hibf/build/initialise_build_tree.hpp

@@ -14,8 +14,8 @@
 
 #include <lemon/list_graph.h> // for ListDigraph
 
-#include <hibf/detail/build/node_data.hpp> // for node_data
-#include <hibf/detail/layout/layout.hpp>   // for layout
+#include <hibf/build/node_data.hpp> // for node_data
+#include <hibf/layout/layout.hpp>   // for layout
 
 namespace seqan::hibf
 {

include/hibf/detail/build/insert_into_ibf.hpp → include/hibf/build/insert_into_ibf.hpp

@@ -10,11 +10,11 @@
 #include <cinttypes> // for uint64_t
 #include <cstddef>   // for size_t
 
+#include <hibf/build/build_data.hpp>         // for build_data
 #include <hibf/contrib/robin_hood.hpp>       // for unordered_flat_set
-#include <hibf/detail/build/build_data.hpp>  // for build_data
-#include <hibf/detail/layout/layout.hpp>     // for layout
 #include <hibf/detail/timer.hpp>             // for concurrent, timer
 #include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
+#include <hibf/layout/layout.hpp>            // for layout
 
 namespace seqan::hibf
 {

include/hibf/detail/build/node_data.hpp → include/hibf/build/node_data.hpp

@@ -14,7 +14,7 @@
 #include <tuple>   // for tie, operator==, tuple
 #include <vector>  // for vector
 
-#include <hibf/detail/layout/layout.hpp> // for operator==, layout
+#include <hibf/layout/layout.hpp> // for operator==, layout
 
 namespace seqan::hibf
 {

include/hibf/detail/build/update_content_node_data.hpp → include/hibf/build/update_content_node_data.hpp

@@ -16,8 +16,8 @@
 
 #include <vector> // for vector
 
-#include <hibf/detail/build/node_data.hpp> // for node_data
-#include <hibf/detail/layout/layout.hpp>   // for layout
+#include <hibf/build/node_data.hpp> // for node_data
+#include <hibf/layout/layout.hpp>   // for layout
 
 namespace seqan::hibf
 {

include/hibf/detail/build/update_header_node_data.hpp → include/hibf/build/update_header_node_data.hpp

@@ -16,8 +16,8 @@
 
 #include <vector> // for vector
 
-#include <hibf/detail/build/node_data.hpp> // for node_data
-#include <hibf/detail/layout/layout.hpp>   // for layout
+#include <hibf/build/node_data.hpp> // for node_data
+#include <hibf/layout/layout.hpp>   // for layout
 
 namespace seqan::hibf
 {

include/hibf/detail/build/update_user_bins.hpp → include/hibf/build/update_user_bins.hpp

@@ -11,7 +11,7 @@
 #include <cinttypes> // for int64_t
 #include <vector>    // for vector
 
-#include <hibf/detail/layout/layout.hpp> // for layout
+#include <hibf/layout/layout.hpp> // for layout
 
 namespace seqan::hibf
 {

include/hibf/config.hpp

@@ -14,8 +14,8 @@
 #include <iosfwd>     // for ostream
 #include <iterator>   // for insert_iterator
 
+#include <hibf/cereal/path.hpp>        // IWYU pragma: keep
 #include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set
-#include <hibf/detail/cereal/path.hpp> // IWYU pragma: keep
 #include <hibf/platform.hpp>
 
 #include <cereal/access.hpp> // for access

include/hibf/hierarchical_interleaved_bloom_filter.hpp

@@ -17,8 +17,8 @@
 #include <utility>    // for addressof
 #include <vector>     // for vector
 
+#include <hibf/cereal/concepts.hpp>          // for cereal_archive
 #include <hibf/config.hpp>                   // for config
-#include <hibf/detail/cereal/concepts.hpp>   // for cereal_archive
 #include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
 #include <hibf/user_bins_type.hpp>           // for user_bins_type
 

include/hibf/interleaved_bloom_filter.hpp

@@ -27,7 +27,7 @@
 #include <utility>     // for addressof
 #include <vector>      // for vector
 
-#include <hibf/detail/cereal/concepts.hpp> // for cereal_archive
+#include <hibf/cereal/concepts.hpp> // for cereal_archive
 
 #include <cereal/macros.hpp>   // for CEREAL_SERIALIZE_FUNCTION_NAME
 #include <sdsl/int_vector.hpp> // for bit_vector

include/hibf/detail/layout/compute_layout.hpp → include/hibf/layout/compute_layout.hpp

@@ -3,9 +3,9 @@
 #include <cstddef> // for size_t
 #include <vector>  // for vector
 
-#include <hibf/config.hpp>                    // for config
-#include <hibf/detail/layout/layout.hpp>      // for layout
-#include <hibf/detail/sketch/hyperloglog.hpp> // for hyperloglog
+#include <hibf/config.hpp>             // for config
+#include <hibf/layout/layout.hpp>      // for layout
+#include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
 
 namespace seqan::hibf::layout
 {

include/hibf/detail/data_store.hpp → include/hibf/layout/data_store.hpp

@@ -8,8 +8,8 @@
 #include <string>    // for string
 #include <vector>    // for vector
 
-#include <hibf/detail/layout/layout.hpp>      // for layout
-#include <hibf/detail/sketch/hyperloglog.hpp> // for hyperloglog
+#include <hibf/layout/layout.hpp>      // for layout
+#include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
 
 namespace seqan::hibf
 {

include/hibf/detail/layout/execute.hpp → include/hibf/layout/execute.hpp

@@ -3,7 +3,7 @@
 #include <cstddef> // for size_t
 
 #include <hibf/config.hpp>            // for config
-#include <hibf/detail/data_store.hpp> // for data_store
+#include <hibf/layout/data_store.hpp> // for data_store
 
 namespace seqan::hibf
 {

include/hibf/detail/layout/hierarchical_binning.hpp → include/hibf/layout/hierarchical_binning.hpp

@@ -7,7 +7,7 @@
 #include <vector>  // for vector
 
 #include <hibf/config.hpp>            // for config
-#include <hibf/detail/data_store.hpp> // for data_store
+#include <hibf/layout/data_store.hpp> // for data_store
 #include <hibf/platform.hpp>          // for HIBF_WORKAROUND_GCC_BOGUS_MEMCPY
 
 namespace seqan::hibf::layout

include/hibf/detail/layout/layout.hpp → include/hibf/layout/layout.hpp

@@ -6,7 +6,7 @@
 #include <iosfwd>    // for ostream
 #include <vector>    // for vector, operator==
 
-#include <hibf/detail/prefixes.hpp> // for header, merged_bin
+#include <hibf/layout/prefixes.hpp> // for header, merged_bin
 #include <hibf/platform.hpp>
 
 namespace seqan::hibf::layout

include/hibf/detail/layout/simple_binning.hpp → include/hibf/layout/simple_binning.hpp

@@ -6,7 +6,7 @@
 #include <utility>   // for addressof
 #include <vector>    // for vector
 
-#include <hibf/detail/data_store.hpp>   // for data_store
+#include <hibf/layout/data_store.hpp>   // for data_store
 #include <hibf/next_multiple_of_64.hpp> // for next_multiple_of_64
 
 namespace seqan::hibf::layout

include/hibf/detail/sketch/estimate_kmer_counts.hpp → include/hibf/sketch/estimate_kmer_counts.hpp

@@ -3,7 +3,7 @@
 #include <cstddef> // for size_t
 #include <vector>  // for vector
 
-#include <hibf/detail/sketch/hyperloglog.hpp> // for hyperloglog
+#include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
 
 namespace seqan::hibf::sketch
 {

include/hibf/detail/sketch/toolbox.hpp → include/hibf/sketch/toolbox.hpp

@@ -7,8 +7,8 @@
 #include <queue>      // for priority_queue
 #include <vector>     // for vector
 
-#include <hibf/contrib/robin_hood.hpp>        // for unordered_flat_map
-#include <hibf/detail/sketch/hyperloglog.hpp> // for hyperloglog
+#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_map
+#include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
 
 namespace seqan::hibf::sketch::toolbox
 {

src/CMakeLists.txt

@@ -1,20 +1,20 @@
 set (HIBF_SOURCE_FILES
      hierarchical_interleaved_bloom_filter.cpp
      config.cpp
-     detail/layout/simple_binning.cpp
-     detail/layout/layout.cpp
-     detail/layout/execute.cpp
-     detail/layout/compute_fpr_correction.cpp
-     detail/layout/compute_layout.cpp
-     detail/layout/hierarchical_binning.cpp
-     detail/sketch/toolbox.cpp
-     detail/sketch/hyperloglog.cpp
-     detail/build/initialise_build_tree.cpp
-     detail/build/insert_into_ibf.cpp
-     detail/build/compute_kmers.cpp
-     detail/build/update_header_node_data.cpp
-     detail/build/construct_ibf.cpp
-     detail/build/update_content_node_data.cpp)
+     layout/simple_binning.cpp
+     layout/layout.cpp
+     layout/execute.cpp
+     layout/compute_fpr_correction.cpp
+     layout/compute_layout.cpp
+     layout/hierarchical_binning.cpp
+     sketch/toolbox.cpp
+     sketch/hyperloglog.cpp
+     build/initialise_build_tree.cpp
+     build/insert_into_ibf.cpp
+     build/compute_kmers.cpp
+     build/update_header_node_data.cpp
+     build/construct_ibf.cpp
+     build/update_content_node_data.cpp)
 
 add_library (hibf STATIC ${HIBF_SOURCE_FILES})
 add_library (seqan::hibf ALIAS hibf)

src/detail/build/compute_kmers.cpp → src/build/compute_kmers.cpp

@@ -14,12 +14,12 @@
 #include <functional> // for function
 #include <iterator>   // for inserter
 
-#include <hibf/config.hpp>                     // for config
-#include <hibf/contrib/robin_hood.hpp>         // for unordered_flat_set
-#include <hibf/detail/build/build_data.hpp>    // for build_data
-#include <hibf/detail/build/compute_kmers.hpp> // for compute_kmers
-#include <hibf/detail/layout/layout.hpp>       // for layout
-#include <hibf/detail/timer.hpp>               // for concurrent, timer
+#include <hibf/build/build_data.hpp>    // for build_data
+#include <hibf/build/compute_kmers.hpp> // for compute_kmers
+#include <hibf/config.hpp>              // for config
+#include <hibf/contrib/robin_hood.hpp>  // for unordered_flat_set
+#include <hibf/detail/timer.hpp>        // for concurrent, timer
+#include <hibf/layout/layout.hpp>       // for layout
 
 namespace seqan::hibf
 {

src/detail/build/construct_ibf.cpp → src/build/construct_ibf.cpp

@@ -13,16 +13,16 @@
 #include <cstddef>   // for size_t
 #include <vector>    // for vector
 
-#include <hibf/config.hpp>                           // for config
-#include <hibf/contrib/robin_hood.hpp>               // for unordered_flat_set
-#include <hibf/detail/build/bin_size_in_bits.hpp>    // for bin_size_in_bits
-#include <hibf/detail/build/build_data.hpp>          // for build_data
-#include <hibf/detail/build/construct_ibf.hpp>       // for construct_ibf
-#include <hibf/detail/build/insert_into_ibf.hpp>     // for insert_into_ibf
-#include <hibf/detail/build/node_data.hpp>           // for node_data
-#include <hibf/detail/build/update_parent_kmers.hpp> // for update_parent_kmers
-#include <hibf/detail/timer.hpp>                     // for concurrent, timer
-#include <hibf/interleaved_bloom_filter.hpp>         // for interleaved_bloom_filter, bin_count, bin_size, hash_fun...
+#include <hibf/build/bin_size_in_bits.hpp>    // for bin_size_in_bits
+#include <hibf/build/build_data.hpp>          // for build_data
+#include <hibf/build/construct_ibf.hpp>       // for construct_ibf
+#include <hibf/build/insert_into_ibf.hpp>     // for insert_into_ibf
+#include <hibf/build/node_data.hpp>           // for node_data
+#include <hibf/build/update_parent_kmers.hpp> // for update_parent_kmers
+#include <hibf/config.hpp>                    // for config
+#include <hibf/contrib/robin_hood.hpp>        // for unordered_flat_set
+#include <hibf/detail/timer.hpp>              // for concurrent, timer
+#include <hibf/interleaved_bloom_filter.hpp>  // for interleaved_bloom_filter, bin_count, bin_size, hash_fun...
 
 namespace seqan::hibf
 {

src/detail/build/initialise_build_tree.cpp → src/build/initialise_build_tree.cpp

@@ -15,11 +15,11 @@
 
 #include <utility> // for move
 
-#include <hibf/detail/build/initialise_build_tree.hpp>    // for initialise_build_tree
-#include <hibf/detail/build/node_data.hpp>                // for node_data
-#include <hibf/detail/build/update_content_node_data.hpp> // for update_content_node_data
-#include <hibf/detail/build/update_header_node_data.hpp>  // for update_header_node_data
-#include <hibf/detail/layout/layout.hpp>                  // for layout
+#include <hibf/build/initialise_build_tree.hpp>    // for initialise_build_tree
+#include <hibf/build/node_data.hpp>                // for node_data
+#include <hibf/build/update_content_node_data.hpp> // for update_content_node_data
+#include <hibf/build/update_header_node_data.hpp>  // for update_header_node_data
+#include <hibf/layout/layout.hpp>                  // for layout
 
 namespace seqan::hibf
 {

src/detail/build/insert_into_ibf.cpp → src/build/insert_into_ibf.cpp

@@ -12,15 +12,15 @@
 #include <iterator>   // for inserter, counted_iterator
 #include <ranges>     // for all_t, operator==
 
+#include <hibf/build/build_data.hpp>                // for build_data
+#include <hibf/build/insert_into_ibf.hpp>           // for insert_into_ibf
 #include <hibf/config.hpp>                          // for config
 #include <hibf/contrib/robin_hood.hpp>              // for unordered_flat_set
 #include <hibf/contrib/std/chunk_view.hpp>          // for chunk_view, operator==, chunk, chunk_fn
 #include <hibf/contrib/std/detail/adaptor_base.hpp> // for operator|
-#include <hibf/detail/build/build_data.hpp>         // for build_data
-#include <hibf/detail/build/insert_into_ibf.hpp>    // for insert_into_ibf
-#include <hibf/detail/layout/layout.hpp>            // for layout
 #include <hibf/detail/timer.hpp>                    // for concurrent, timer
 #include <hibf/interleaved_bloom_filter.hpp>        // for interleaved_bloom_filter, bin_index
+#include <hibf/layout/layout.hpp>                   // for layout
 
 namespace seqan::hibf
 {

src/detail/build/update_content_node_data.cpp → src/build/update_content_node_data.cpp

@@ -20,9 +20,9 @@
 #include <utility>   // for move
 #include <vector>    // for vector
 
-#include <hibf/detail/build/node_data.hpp>                // for node_data
-#include <hibf/detail/build/update_content_node_data.hpp> // for update_content_node_data
-#include <hibf/detail/layout/layout.hpp>                  // for layout
+#include <hibf/build/node_data.hpp>                // for node_data
+#include <hibf/build/update_content_node_data.hpp> // for update_content_node_data
+#include <hibf/layout/layout.hpp>                  // for layout
 
 namespace seqan::hibf
 {

src/detail/build/update_header_node_data.cpp → src/build/update_header_node_data.cpp

@@ -21,9 +21,9 @@
 #include <utility>    // for move
 #include <vector>     // for vector
 
-#include <hibf/detail/build/node_data.hpp>               // for node_data
-#include <hibf/detail/build/update_header_node_data.hpp> // for update_header_node_data
-#include <hibf/detail/layout/layout.hpp>                 // for layout
+#include <hibf/build/node_data.hpp>               // for node_data
+#include <hibf/build/update_header_node_data.hpp> // for update_header_node_data
+#include <hibf/layout/layout.hpp>                 // for layout
 
 namespace seqan::hibf
 {

src/config.cpp

@@ -10,7 +10,7 @@
 #include <iostream>
 
 #include <hibf/config.hpp>
-#include <hibf/detail/prefixes.hpp>
+#include <hibf/layout/prefixes.hpp>
 
 #include <cereal/archives/json.hpp>
 

src/hierarchical_interleaved_bloom_filter.cpp

@@ -18,21 +18,21 @@
 #include <utility>   // for move
 #include <vector>    // for vector
 
+#include <hibf/build/build_data.hpp>                      // for build_data
+#include <hibf/build/compute_kmers.hpp>                   // for compute_kmers
+#include <hibf/build/construct_ibf.hpp>                   // for construct_ibf
+#include <hibf/build/initialise_build_tree.hpp>           // for initialise_build_tree
+#include <hibf/build/insert_into_ibf.hpp>                 // for insert_into_ibf
+#include <hibf/build/node_data.hpp>                       // for node_data
+#include <hibf/build/update_parent_kmers.hpp>             // for update_parent_kmers
+#include <hibf/build/update_user_bins.hpp>                // for update_user_bins
 #include <hibf/config.hpp>                                // for config
 #include <hibf/contrib/robin_hood.hpp>                    // for unordered_flat_set
-#include <hibf/detail/build/build_data.hpp>               // for build_data
-#include <hibf/detail/build/compute_kmers.hpp>            // for compute_kmers
-#include <hibf/detail/build/construct_ibf.hpp>            // for construct_ibf
-#include <hibf/detail/build/initialise_build_tree.hpp>    // for initialise_build_tree
-#include <hibf/detail/build/insert_into_ibf.hpp>          // for insert_into_ibf
-#include <hibf/detail/build/node_data.hpp>                // for node_data
-#include <hibf/detail/build/update_parent_kmers.hpp>      // for update_parent_kmers
-#include <hibf/detail/build/update_user_bins.hpp>         // for update_user_bins
-#include <hibf/detail/layout/compute_fpr_correction.hpp>  // for compute_fpr_correction
-#include <hibf/detail/layout/compute_layout.hpp>          // for compute_layout
-#include <hibf/detail/layout/layout.hpp>                  // for layout
 #include <hibf/hierarchical_interleaved_bloom_filter.hpp> // for hierarchical_interleaved_bloom_filter
 #include <hibf/interleaved_bloom_filter.hpp>              // for interleaved_bloom_filter
+#include <hibf/layout/compute_fpr_correction.hpp>         // for compute_fpr_correction
+#include <hibf/layout/compute_layout.hpp>                 // for compute_layout
+#include <hibf/layout/layout.hpp>                         // for layout
 #include <hibf/user_bins_type.hpp>                        // for user_bins_type
 
 namespace seqan::hibf