[c++,r,python] Move nanoarrow to src/external (#2383)

* [c++,r] Move `nanoarrow` to `src/external` * Slight tweak to CMakeLists, adjustment for vendoring * Un-clang-format files restoring release 0.4.0 copies * Re-adjust after rebase * Path adjustment for nanoarrow include, pkg-config update * Adjusting Python too * Adjusting Python too, once more * Adjust include path for R for the non pkg-config case too * The Python installation for 'interop' needs another includes case
single-cell-data · Apr 5, 2024 · d2b15c2 · d2b15c2
1 parent c6a6bcc
commit d2b15c2
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Showing 15 changed files with 3,771 additions and 3,977 deletions.
diff --git a/apis/python/setup.py b/apis/python/setup.py
@@ -217,8 +217,10 @@ def run(self):
 INC_DIRS = [
     "dist_links/libtiledbsoma/include",
     "dist_links/libtiledbsoma/external/include",
+    "dist_links/libtiledbsoma/src/external/include",
     "../../build/externals/install/include",
     str(tiledbsoma_dir / "include"),
+    str(tiledbsoma_dir / "include/tiledbsoma"),
     str(tiledbsoma_dir.parent / "build/externals/install/include"),
     str(tiledbsoma_dir / "include"),
     str(tiledb_dir / "include"),

diff --git a/apis/r/configure b/apis/r/configure
@@ -46,7 +46,7 @@ export CXX="`${R_HOME}/bin/R CMD config CXX`"
 export CMAKE_OSX_ARCHITECTURES="`uname -m`"
 tools/build_libtiledbsoma.sh
 
-pkgincl="-I../inst/tiledb/include -I../inst/tiledbsoma/include"
+pkgincl="-I../inst/tiledb/include -I../inst/tiledbsoma/include -I../inst/tiledbsoma/include/tiledbsoma"
 pkglibs="-ltiledb -L../inst/tiledb/lib -ltiledbsoma -L../inst/tiledbsoma/lib"
 rpath="-Wl,-rpath,'\$\$ORIGIN/../tiledb/lib' -Wl,-rpath,'\$\$ORIGIN/../tiledbsoma/lib'"
 macosver=`${R_HOME}/bin/Rscript -e 'if (Sys.info()["sysname"] == "Darwin") cat("-mmacosx-version-min=11.0") else cat("")'`

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 <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 <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
@@ -3,20 +3,15 @@
 #define TILEDB_NO_API_DEPRECATION_WARNINGS
 #endif
 
-//#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 <RcppInt64>            // for fromInteger64
+#include <Rcpp.h>                        // for R interface to C++
+#include <nanoarrow/r.h>                 // for C interface to Arrow (via R package nanoarrow)
+#include <nanoarrow/nanoarrow.h>
+#include <RcppInt64>                    // for fromInteger64
 
 #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 <nanoarrow/nanoarrow.h>            // for C interface to Arrow
+#include <RcppInt64>                        // for fromInteger64
 #include <tiledbsoma/tiledbsoma>
 
 #include "rutilities.h"         // local declarations

diff --git a/apis/r/src/xptr-utils.h b/apis/r/src/xptr-utils.h
@@ -24,9 +24,6 @@ const tiledb_xptr_object tiledb_xptr_vlv_buf_t                   { 180 };
 const tiledb_xptr_object tiledb_xptr_query_buf_t                 { 190 };
 
 // the definitions above are internal to tiledb-r but we need a new value here if we want tag the external pointer
-const tiledb_xptr_object tiledb_arrow_array_t                    { 300 };
-const tiledb_xptr_object tiledb_arrow_schema_t                   { 310 };
-
 const tiledb_xptr_object tiledb_soma_reader_t                    { 500 };
 
 // templated checkers for external pointer tags
@@ -52,10 +49,6 @@ template <> inline const int32_t XPtrTagType<tiledb::VFS>                  = til
 // template <> inline const int32_t XPtrTagType<vlv_buf_t>                    = tiledb_xptr_vlv_buf_t;
 // template <> inline const int32_t XPtrTagType<query_buf_t>                  = tiledb_xptr_query_buf_t;
 
-
-template <> inline const int32_t XPtrTagType<ArrowArray>             	   = tiledb_arrow_array_t;
-template <> inline const int32_t XPtrTagType<ArrowSchema>             	   = tiledb_arrow_schema_t;
-
 template <> inline const int32_t XPtrTagType<tdbs::SOMAArray>             = tiledb_soma_reader_t;
 
 template <typename T> Rcpp::XPtr<T> make_xptr(T* p, bool finalize=true) {
@@ -81,4 +74,3 @@ template<typename T> void check_xptr_tag(Rcpp::XPtr<T> ptr) {
 // in rinterface.cpp
 Rcpp::XPtr<ArrowSchema> schema_owning_xptr(void);
 Rcpp::XPtr<ArrowArray> array_owning_xptr(void);
-
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/cmake/inputs/tiledbsoma.pc.in b/libtiledbsoma/cmake/inputs/tiledbsoma.pc.in
@@ -9,6 +9,6 @@ URL: https://github.com/single-cell-data/TileDB-SOMA
 Version: @VERSION@
 Requires: @PKGCONF_REQ_PUB@
 Requires.private: @PKGCONF_REQ_PRIV@
-Cflags: -I"${includedir}"
+Cflags: -I"${includedir}" -I"${includedir}/tiledbsoma"
 Libs: -L"${libdir}" -ltiledbsoma
-Libs.private: -L"${libdir}" -ltiledbsoma @PKGCONF_LIBS_PRIV@
+Libs.private: -L"${libdir}" -ltiledbsoma @PKGCONF_LIBS_PRIV@
diff --git a/libtiledbsoma/src/CMakeLists.txt b/libtiledbsoma/src/CMakeLists.txt
@@ -50,7 +50,7 @@ message(STATUS "Building with commit hash ${BUILD_COMMIT_HASH}")
 # Common object library
 # ###########################################################
 set_source_files_properties(
-  ${CMAKE_CURRENT_SOURCE_DIR}/utils/nanoarrow.c PROPERTIES LANGUAGE CXX)
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/src/nanoarrow/nanoarrow.c PROPERTIES LANGUAGE CXX)
 
 add_library(TILEDB_SOMA_OBJECTS OBJECT
   ${CMAKE_CURRENT_SOURCE_DIR}/reindexer/reindexer.cc
@@ -72,10 +72,10 @@ 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")
@@ -90,6 +90,11 @@ target_compile_options(
 
 set_property(TARGET TILEDB_SOMA_OBJECTS PROPERTY POSITION_INDEPENDENT_CODE ON)
 
+target_include_directories(TILEDB_SOMA_OBJECTS
+  PUBLIC
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/include/nanoarrow
+)
+
 target_include_directories(TILEDB_SOMA_OBJECTS
   PRIVATE
   ${CMAKE_CURRENT_SOURCE_DIR}
@@ -216,12 +221,6 @@ 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"
@@ -242,6 +241,12 @@ 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