Build With Serialization Disabled (#924)

CONTRIBUTING.md

@@ -30,8 +30,10 @@ Thanks for your interest in TileDB-Py. The notes below give some pointers for fi
       - `--tiledb=$CONDA_PREFIX`
     - from source: https://docs.tiledb.com/main/how-to/installation/building-from-source/c-cpp
       - use `--tiledb=/path/to/tiledb/dist` option when running ``setup.py`` in the step below
-      - also please note that libtiledb needs to be built with serialization enabled for TileDB-Py build to succeed
-        (pass the ``--enable-serialization`` option to the ``bootstrap`` script before compiling)
+      - if building libtiledb from source,  to enable serialization pass ``--enable-serialization`` 
+        to the ``bootstrap`` script before compiling
+	- serialization is optional. if libtiledb is not build with serialization, then it will not be
+	  enabled in TileDB-Py
             
   - build TileDB-Py
   ```

HISTORY.md

@@ -1,6 +1,7 @@
 # TileDB-Py 0.13.0 Release Notes
 
-## Bug fixes
+## Bug Fixes
+* Enable building with serialization disabled [#924](https://github.com/TileDB-Inc/TileDB-Py/pull/924)
 * Do not print out `FragmentInfo_frags` for `repr` [#925](https://github.com/TileDB-Inc/TileDB-Py/pull/925)
 
 # TileDB-Py 0.12.3 Release Notes

setup.py

@@ -597,6 +597,24 @@ def install_requires():
 MODULAR_SOURCES = ["tiledb/np2buf.pyx", "tiledb/indexing.pyx", "tiledb/libmetadata.pyx"]
 MODULAR_HEADERS = ["tiledb/libtiledb.pxd", "tiledb/indexing.pxd"]
 
+TILEDB_MAIN_SOURCES = [
+    "tiledb/main.cc",
+    "tiledb/core.cc",
+    "tiledb/npbuffer.cc",
+    "tiledb/fragment.cc",
+    "tiledb/schema_evolution.cc",
+    "tiledb/tests/test_metadata.cc",
+    # TODO currently included in core.cc due to dependency.
+    #      need to un-comment after refactor.
+    # "tiledb/query_condition.cc",
+]
+
+if "TILEDB_SERIALIZATION" in os.environ:
+    TILEDB_MAIN_SOURCES += [
+        "tiledb/serialization.cc",
+        "tiledb/tests/test_serialization.cc",
+    ]
+
 __extensions = [
     Extension(
         "tiledb.libtiledb",
@@ -614,19 +632,7 @@ def install_requires():
     ),
     Extension(
         "tiledb.main",
-        [
-            "tiledb/main.cc",
-            "tiledb/core.cc",
-            "tiledb/npbuffer.cc",
-            "tiledb/fragment.cc",
-            "tiledb/serialization.cc",
-            "tiledb/schema_evolution.cc",
-            "tiledb/tests/test_serialization.cc",
-            "tiledb/tests/test_metadata.cc",
-            # TODO currently included in core.cc due to dependency.
-            #      need to un-comment after refactor.
-            # "tiledb/query_condition.cc",
-        ],
+        TILEDB_MAIN_SOURCES,
         include_dirs=INC_DIRS + [get_pybind_include(), get_pybind_include(user=True)],
         language="c++",
         library_dirs=LIB_DIRS,

tiledb/core.cc

@@ -19,10 +19,13 @@
 #define TILEDB_DEPRECATED_EXPORT
 
 #include <tiledb/arrowio>
-#include <tiledb/tiledb.h>               // C
-#include <tiledb/tiledb>                 // C++
-#include <tiledb/tiledb_experimental.h>  // C
+#include <tiledb/tiledb.h>              // C
+#include <tiledb/tiledb>                // C++
+#include <tiledb/tiledb_experimental.h> // C
+
+#if defined(TILEDB_SERIALIZATION)
 #include <tiledb/tiledb_serialization.h> // C
+#endif
 
 #include "../external/string_view.hpp"
 #include "../external/tsl/robin_map.h"
@@ -655,6 +658,7 @@ class PyQuery {
     }
   }
 
+#if defined(TILEDB_SERIALIZATION)
   void set_serialized_query(py::buffer serialized_query) {
     int rc;
     tiledb_query_t *c_query;
@@ -676,6 +680,7 @@ class PyQuery {
     if (rc == TILEDB_ERR)
       TPY_ERROR_LOC("Could not deserialize query.");
   }
+#endif
 
   void set_attr_cond(py::object attr_cond) {
     if (!attr_cond.is(py::none())) {
@@ -1548,7 +1553,9 @@ void init_core(py::module &m) {
 #endif
           .def("set_subarray", &PyQuery::set_subarray)
           .def("set_attr_cond", &PyQuery::set_attr_cond)
+#if defined(TILEDB_SERIALIZATION)
           .def("set_serialized_query", &PyQuery::set_serialized_query)
+#endif
           .def("submit", &PyQuery::submit)
           .def("unpack_buffer", &PyQuery::unpack_buffer)
           .def("estimated_result_sizes", &PyQuery::estimated_result_sizes)

tiledb/fragment.py

@@ -1,7 +1,7 @@
-import pprint
-import warnings
 import numpy as np
 import os
+import pprint
+import warnings
 
 import tiledb
 from tiledb.main import PyFragmentInfo

tiledb/main.cc

@@ -9,8 +9,10 @@ void init_core(py::module &);
 void init_fragment(py::module &);
 // void init_query_condition(py::module &);
 void init_schema_evolution(py::module &);
+#if defined(TILEDB_SERIALIZATION)
 void init_serialization(py::module &);
 void init_test_serialization(py::module &);
+#endif
 void init_test_metadata(py::module &);
 
 PYBIND11_MODULE(main, m) {
@@ -19,8 +21,10 @@ PYBIND11_MODULE(main, m) {
   init_fragment(m);
   //_query_condition(m);
   init_schema_evolution(m);
+#if defined(TILEDB_SERIALIZATION)
   init_serialization(m);
   init_test_serialization(m);
+#endif
   init_test_metadata(m);
 }
 

tiledb/tests/test_serialization.py

@@ -1,16 +1,14 @@
-from contextlib import AbstractContextManager
-import itertools
+import pytest
+
+ser_test = pytest.importorskip(
+    "tiledb.main.test_serialization", reason="Serialzation not enabled."
+)
 
 import numpy as np
 from numpy.testing import assert_array_equal
-import pytest
 
 import tiledb
-from tiledb.main import tiledb_serialization_type_t as ser_type
-from tiledb.main import serialization as ser
-
 from tiledb.tests.common import DiskTestCase
-from tiledb.main import test_serialization as ser_test
 
 
 class SerializationTest(DiskTestCase):