Remove all deprecated APIs. (#5146)

[SC-50038](https://app.shortcut.com/tiledb-inc/story/50038/remove-deprecated-apis)

Consistent with [the announcement made in 2.23.0's release
notes](https://github.com/TileDB-Inc/TileDB/releases/tag/2.23.0), this
PR removes all deprecated C and C++ APIs. The infrastructure supporting
the `TILEDB_REMOVE_DEPRECATIONS` CMake option was kept, in case we want
to deprecate another API in the future.

---
TYPE: BREAKING_API
DESC: All deprecated C and C++ APIs were removed.

Author: teo-tsirpanis

test/src/cpp-integration-query-condition.cc

@@ -1566,7 +1566,7 @@ TEST_CASE(
   subarray_w.add_range("d", range[0], range[1]);
   query_w.set_subarray(subarray_w);
   query_w.set_layout(TILEDB_ROW_MAJOR);
-  query_w.set_buffer("a", vals);
+  query_w.set_data_buffer("a", vals);
   REQUIRE(query_w.submit() == Query::Status::COMPLETE);
 
   // Write values from 3-6 as 7 in the array.
@@ -1577,7 +1577,7 @@ TEST_CASE(
   subarray_w2.add_range("d", range2[0], range2[1]);
   query_w2.set_subarray(subarray_w2);
   query_w2.set_layout(TILEDB_ROW_MAJOR);
-  query_w2.set_buffer("a", vals2);
+  query_w2.set_data_buffer("a", vals2);
   REQUIRE(query_w2.submit() == Query::Status::COMPLETE);
 
   array.close();
@@ -1596,7 +1596,7 @@ TEST_CASE(
   subarray_r.add_range("d", range[0], range[1]);
   query_r.set_subarray(subarray_r);
   query_r.set_layout(TILEDB_ROW_MAJOR);
-  query_r.set_buffer("a", vals_read);
+  query_r.set_data_buffer("a", vals_read);
   query_r.set_condition(qc);
   REQUIRE(query_r.submit() == Query::Status::COMPLETE);
 
@@ -1645,17 +1645,17 @@ TEST_CASE(
   // Write all values as 3 in the array.
   std::vector<int> vals = {3, 3, 3, 3, 3, 3, 3, 3, 3, 3};
   Query query_w(ctx, array, TILEDB_WRITE);
-  query_w.set_buffer("d", dim_vals);
-  query_w.set_buffer("a", vals);
-  query_w.set_buffer("a2", vals);
+  query_w.set_data_buffer("d", dim_vals);
+  query_w.set_data_buffer("a", vals);
+  query_w.set_data_buffer("a2", vals);
   REQUIRE(query_w.submit() == Query::Status::COMPLETE);
 
   // Write values from 1-10 as 7 in the array.
   std::vector<int> vals2 = {7, 7, 7, 7, 7, 7, 7, 7, 7, 6};
   Query query_w2(ctx, array, TILEDB_WRITE);
-  query_w2.set_buffer("d", dim_vals);
-  query_w2.set_buffer("a", vals2);
-  query_w2.set_buffer("a2", vals);
+  query_w2.set_data_buffer("d", dim_vals);
+  query_w2.set_data_buffer("a", vals2);
+  query_w2.set_data_buffer("a2", vals);
   REQUIRE(query_w2.submit() == Query::Status::COMPLETE);
 
   array.close();
@@ -1673,9 +1673,9 @@ TEST_CASE(
   std::vector<int> dim_vals_read(10);
   Query query_r(ctx, array_r, TILEDB_READ);
   query_r.set_layout(TILEDB_GLOBAL_ORDER);
-  query_r.set_buffer("a", vals_read);
-  query_r.set_buffer("a2", vals_read2);
-  query_r.set_buffer("d", dim_vals_read);
+  query_r.set_data_buffer("a", vals_read);
+  query_r.set_data_buffer("a2", vals_read2);
+  query_r.set_data_buffer("d", dim_vals_read);
   query_r.set_condition(qc);
   REQUIRE(query_r.submit() == Query::Status::COMPLETE);
 

test/src/unit-arrow.cc

@@ -166,7 +166,9 @@ void allocate_query_buffers(tiledb::Query* const query) {
 
   bool has_ranges = false;
   for (uint64_t dim_idx = 0; dim_idx < schema.domain().ndim(); dim_idx++) {
-    if (query->range_num(dim_idx) > 0) {
+    Subarray subarray(query->ctx(), query->array());
+    query->update_subarray_from_query(&subarray);
+    if (subarray.range_num(dim_idx) > 0) {
       has_ranges = true;
       break;
     }

test/src/unit-backwards_compat.cc

@@ -83,7 +83,7 @@ void set_query_coords(
   Subarray sub(ctx, *array);
   sub.set_subarray<T>(static_cast<T*>(subarray), 2 * ndim);
 
-  query->set_coordinates<T>(static_cast<T*>(*coordinates), ndim);
+  query->set_data_buffer<T>("__coords", static_cast<T*>(*coordinates), ndim);
   query->set_subarray(sub);
 
   std::free(subarray);
@@ -136,8 +136,9 @@ void set_query_var_dimension_buffer(
 
   memset(*offsets, 0, sizeof(uint64_t));
   memset(*buffer, 0, buffer_size);
-  query->set_buffer<T>(
-      dimension.name(), *offsets, 1, static_cast<T*>(*buffer), buffer_size);
+  query->set_data_buffer<T>(
+      dimension.name(), static_cast<T*>(*buffer), buffer_size);
+  query->set_offsets_buffer(dimension.name(), *offsets, 1);
   subarray->add_range(dim_idx, std::string("1"), std::string("1"));
 }
 
@@ -208,7 +209,7 @@ TEST_CASE(
   query_r.set_subarray(sub)
       .set_layout(TILEDB_ROW_MAJOR)
       .set_data_buffer("a", a_read)
-      .set_coordinates(coords_read);
+      .set_data_buffer("__coords", coords_read);
   query_r.submit();
 
   // Note: If you encounter a failure here, in particular with a_read[0] == 100
@@ -720,7 +721,7 @@ TEST_CASE(
     Query query_w(ctx, old_array);
     query_w.set_layout(TILEDB_UNORDERED)
         .set_data_buffer("a", a_write)
-        .set_coordinates(coords_write);
+        .set_data_buffer("__coords", coords_write);
     query_w.submit();
     old_array.close();
 
@@ -736,7 +737,7 @@ TEST_CASE(
     query_r.set_subarray(subarray_r)
         .set_layout(TILEDB_ROW_MAJOR)
         .set_data_buffer("a", a_read)
-        .set_coordinates(coords_read);
+        .set_data_buffer("__coords", coords_read);
     query_r.submit();
     array.close();
 

test/src/unit-capi-serialized_queries.cc

@@ -704,7 +704,7 @@ TEST_CASE_METHOD(
     Subarray cppapi_subarray(ctx, array);
     cppapi_subarray.set_subarray(subarray);
     query.set_subarray(cppapi_subarray);
-    query.set_coordinates(coords);
+    query.set_data_buffer("__coords", coords);
     query.set_data_buffer("a1", a1);
     query.set_data_buffer("a2", a2);
     query.set_validity_buffer("a2", a2_nullable);

test/src/unit-cppapi-checksum.cc

@@ -94,7 +94,7 @@ static void run_checksum_test(tiledb_filter_type_t filter_type) {
   query.set_data_buffer("a1", a1_data)
       .set_data_buffer("a2", a2buf.second)
       .set_offsets_buffer("a2", a2buf.first)
-      .set_coordinates(coords)
+      .set_data_buffer("__coords", coords)
       .set_layout(TILEDB_UNORDERED);
   REQUIRE(query.submit() == Query::Status::COMPLETE);
 

test/src/unit-cppapi-consolidation-with-timestamps.cc

@@ -167,7 +167,11 @@ void ConsolidationWithTimestampsFx::write_sparse(
     std::vector<uint64_t> dim2,
     uint64_t timestamp) {
   // Open array.
-  Array array(ctx_, SPARSE_ARRAY_NAME, TILEDB_WRITE, timestamp);
+  Array array(
+      ctx_,
+      SPARSE_ARRAY_NAME,
+      TILEDB_WRITE,
+      tiledb::TemporalPolicy(tiledb::TimeTravel, timestamp));
 
   // Create query.
   Query query(ctx_, array, TILEDB_WRITE);
@@ -193,7 +197,11 @@ void ConsolidationWithTimestampsFx::write_sparse_v11(uint64_t timestamp) {
   std::vector<uint64_t> buffer_coords_dim2{1, 2, 4, 3};
 
   // Open array.
-  Array array(ctx_, SPARSE_ARRAY_NAME, TILEDB_WRITE, timestamp);
+  Array array(
+      ctx_,
+      SPARSE_ARRAY_NAME,
+      TILEDB_WRITE,
+      tiledb::TemporalPolicy(tiledb::TimeTravel, timestamp));
 
   // Create query.
   Query query(ctx_, array, TILEDB_WRITE);
@@ -290,7 +298,11 @@ void ConsolidationWithTimestampsFx::read_sparse(
     uint64_t timestamp,
     std::vector<uint64_t>* timestamps_ptr) {
   // Open array.
-  Array array(ctx_, SPARSE_ARRAY_NAME, TILEDB_READ, timestamp);
+  Array array(
+      ctx_,
+      SPARSE_ARRAY_NAME,
+      TILEDB_READ,
+      tiledb::TemporalPolicy(tiledb::TimeTravel, timestamp));
 
   // Create query.
   Query query(ctx_, array, TILEDB_READ);

test/src/unit-cppapi-datetimes.cc

@@ -64,7 +64,7 @@ TEST_CASE("C++ API: Datetime attribute", "[cppapi][datetime]") {
   Query query_w(ctx, array_w);
   query_w.set_layout(TILEDB_UNORDERED)
       .set_data_buffer("a", data_w)
-      .set_coordinates(coords_w)
+      .set_data_buffer("__coords", coords_w)
       .submit();
   query_w.finalize();
   array_w.close();
@@ -76,7 +76,7 @@ TEST_CASE("C++ API: Datetime attribute", "[cppapi][datetime]") {
   Query query_r(ctx, array_r);
   query_r.set_layout(TILEDB_ROW_MAJOR)
       .set_data_buffer("a", data_r)
-      .set_coordinates(coords_r);
+      .set_data_buffer("__coords", coords_r);
   REQUIRE(query_r.submit() == Query::Status::COMPLETE);
 
   auto result_num = query_r.result_buffer_elements()["a"].second;
@@ -118,7 +118,7 @@ TEST_CASE("C++ API: Datetime dimension", "[cppapi][datetime]") {
   Query query_w(ctx, array_w);
   query_w.set_layout(TILEDB_UNORDERED)
       .set_data_buffer("a", data_w)
-      .set_coordinates(coords_w)
+      .set_data_buffer("__coords", coords_w)
       .submit();
   query_w.finalize();
   array_w.close();

test/src/unit-cppapi-deletes.cc

@@ -271,7 +271,11 @@ void DeletesFx::write_sparse_v11(uint64_t timestamp) {
   std::vector<uint64_t> buffer_coords_dim2{1, 2, 4, 3};
 
   // Open array.
-  Array array(ctx_, array_name_.c_str(), TILEDB_WRITE, timestamp);
+  Array array(
+      ctx_,
+      array_name_.c_str(),
+      TILEDB_WRITE,
+      tiledb::TemporalPolicy(tiledb::TimeTravel, timestamp));
 
   // Create query.
   Query query(ctx_, array, TILEDB_WRITE);

test/src/unit-cppapi-filter.cc

@@ -195,7 +195,7 @@ TEST_CASE(
   query.set_data_buffer("a1", a1_data)
       .set_data_buffer("a2", a2buf.second)
       .set_offsets_buffer("a2", a2buf.first)
-      .set_coordinates(coords)
+      .set_data_buffer("__coords", coords)
       .set_layout(TILEDB_UNORDERED);
   REQUIRE(query.submit() == Query::Status::COMPLETE);
   array.close();

test/src/unit-cppapi-metadata.cc

@@ -313,7 +313,11 @@ TEST_CASE_METHOD(
 
   // Create and open array in write mode
   tiledb::Context ctx;
-  tiledb::Array array(ctx, std::string(array_name_), TILEDB_WRITE, 1);
+  tiledb::Array array(
+      ctx,
+      std::string(array_name_),
+      TILEDB_WRITE,
+      tiledb::TemporalPolicy(tiledb::TimeTravel, 1));
 
   // Write items
   int32_t v = 5;