[c++,r] Move nanoarrow to src/external

single-cell-data · Apr 3, 2024 · cb7524b · cb7524b
1 parent aa0adcb
commit cb7524b
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Showing 10 changed files with 21 additions and 26 deletions.
diff --git a/apis/r/inst/include/tiledbsoma_types.h b/apis/r/inst/include/tiledbsoma_types.h
@@ -15,7 +15,7 @@
 #define TILEDB_NO_API_DEPRECATION_WARNINGS
 #endif
 
-#include <tiledbsoma/utils/nanoarrow.h> 	// for C interface to Arrow
+#include <tiledbsoma/nanoarrow/nanoarrow.h> // for C interface to Arrow
 #include <tiledb/tiledb>					// for QueryCondition etc
 #define ARROW_SCHEMA_AND_ARRAY_DEFINED 1
 #include <tiledbsoma/tiledbsoma>

diff --git a/apis/r/src/rinterface.cpp b/apis/r/src/rinterface.cpp
@@ -1,7 +1,7 @@
-#include <Rcpp.h>               			// for R interface to C++
-#include <nanoarrow/r.h>        			// for C interface to Arrow (via R package)
-#include <tiledbsoma/utils/nanoarrow.hpp>   // for C/C++ interface to Arrow
-#include <RcppInt64>            			// for fromInteger64
+#include <Rcpp.h>                               // for R interface to C++
+#include <nanoarrow/r.h>                        // for C interface to Arrow (via R package)
+#include <tiledbsoma/nanoarrow/nanoarrow.hpp>   // for C/C++ interface to Arrow
+#include <RcppInt64>                            // for fromInteger64
 
 // we currently get deprecation warnings by default which are noisy
 #ifndef TILEDB_NO_API_DEPRECATION_WARNINGS

diff --git a/apis/r/src/riterator.cpp b/apis/r/src/riterator.cpp
@@ -5,17 +5,14 @@
 
 //#define RCPP_DEBUG_LEVEL 5
 
-#include <Rcpp.h>          			     // for R interface to C++
-#include <nanoarrow/r.h>				 // for C interface to Arrow (via R package nanoarrow)
-#include <tiledbsoma/utils/nanoarrow.h>
+#include <Rcpp.h>                        // for R interface to C++
+#include <nanoarrow/r.h>                 // for C interface to Arrow (via R package nanoarrow)
+#include <tiledbsoma/nanoarrow/nanoarrow.h>
 
 #include <tiledb/tiledb>
 #if TILEDB_VERSION_MAJOR == 2 && TILEDB_VERSION_MINOR >= 4
 #include <tiledb/tiledb_experimental>
 #endif
-
-// We get these via nanoarrow and must not include carrow.h again
-#define ARROW_SCHEMA_AND_ARRAY_DEFINED 1
 #include <tiledbsoma/tiledbsoma>
 
 #include "rutilities.h"         // local declarations

diff --git a/apis/r/src/rutilities.cpp b/apis/r/src/rutilities.cpp
@@ -4,12 +4,9 @@
 #define TILEDB_NO_API_DEPRECATION_WARNINGS
 #endif
 
-#include <Rcpp.h>               			// for R interface to C++
-#include <tiledbsoma/utils/nanoarrow.h>     // for C interface to Arrow
-#include <RcppInt64>            			// for fromInteger64
-
-// We get these via nanoarrow and must cannot include carrow.h again
-#define ARROW_SCHEMA_AND_ARRAY_DEFINED 1
+#include <Rcpp.h>                           // for R interface to C++
+#include <tiledbsoma/nanoarrow/nanoarrow.h> // for C interface to Arrow
+#include <RcppInt64>                        // for fromInteger64
 #include <tiledbsoma/tiledbsoma>
 
 #include "rutilities.h"         // local declarations

diff --git a/libtiledbsoma/CMakeLists.txt b/libtiledbsoma/CMakeLists.txt
@@ -4,7 +4,7 @@
 #
 # The MIT License
 #
-# Copyright (c) 2022-2023 TileDB, Inc.
+# Copyright (c) 2022-2024 TileDB, Inc.
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/libtiledbsoma/src/CMakeLists.txt b/libtiledbsoma/src/CMakeLists.txt
@@ -69,10 +69,10 @@ add_library(TILEDB_SOMA_OBJECTS OBJECT
   ${CMAKE_CURRENT_SOURCE_DIR}/utils/stats.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/utils/util.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/utils/version.cc
-  ${CMAKE_CURRENT_SOURCE_DIR}/utils/nanoarrow.c
 
   ${CMAKE_CURRENT_SOURCE_DIR}/external/src/thread_pool/thread_pool.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/external/src/thread_pool/status.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/src/nanoarrow/nanoarrow.c
 )
 
 message(STATUS "Building TileDB without deprecation warnings")
@@ -94,6 +94,7 @@ target_include_directories(TILEDB_SOMA_OBJECTS
   ${CMAKE_CURRENT_SOURCE_DIR}/soma
   ${CMAKE_CURRENT_SOURCE_DIR}/external/khash
   ${CMAKE_CURRENT_SOURCE_DIR}/external/include
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/include/nanoarrow
   $<TARGET_PROPERTY:TileDB::tiledb_shared,INTERFACE_INCLUDE_DIRECTORIES>
   $<TARGET_PROPERTY:spdlog::spdlog,INTERFACE_INCLUDE_DIRECTORIES>
   ${pybind11_INCLUDE_DIRS}
@@ -213,12 +214,6 @@ install(FILES
   DESTINATION "include/tiledbsoma/reindexer/"
 )
 
-install(FILES
-  ${CMAKE_CURRENT_SOURCE_DIR}/utils/nanoarrow.h
-  ${CMAKE_CURRENT_SOURCE_DIR}/utils/nanoarrow.hpp
-  DESTINATION "include/tiledbsoma/utils/"
-)
-
 install(FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/tiledbsoma/tiledbsoma
   DESTINATION "include/tiledbsoma"
@@ -239,6 +234,12 @@ install(FILES
   DESTINATION "include/tiledbsoma/soma/span"
 )
 
+install(FILES
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/include/nanoarrow/nanoarrow.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/include/nanoarrow/nanoarrow.hpp
+  DESTINATION "include/tiledbsoma/nanoarrow"
+)
+
 
 # ###########################################################
 # API symbol exports

diff --git a/libtiledbsoma/src/utils/nanoarrow.h → ...rc/external/include/nanoarrow/nanoarrow.h b/libtiledbsoma/src/utils/nanoarrow.h → ...rc/external/include/nanoarrow/nanoarrow.h
diff --git a/libtiledbsoma/src/utils/nanoarrow.hpp → .../external/include/nanoarrow/nanoarrow.hpp b/libtiledbsoma/src/utils/nanoarrow.hpp → .../external/include/nanoarrow/nanoarrow.hpp
diff --git a/libtiledbsoma/src/utils/nanoarrow.c → ...ma/src/external/src/nanoarrow/nanoarrow.c b/libtiledbsoma/src/utils/nanoarrow.c → ...ma/src/external/src/nanoarrow/nanoarrow.c
diff --git a/libtiledbsoma/src/utils/arrow_adapter.h b/libtiledbsoma/src/utils/arrow_adapter.h
@@ -8,7 +8,7 @@
 // https://arrow.apache.org/docs/format/Columnar.html#buffer-listing-for-each-layout
 // https://arrow.apache.org/docs/format/CDataInterface.html#exporting-a-simple-int32-array
 
-#include "nanoarrow.hpp"
+#include "tiledbsoma/nanoarrow/nanoarrow.hpp"
 
 namespace tiledbsoma {