chore: Add sedona-geo-traits-ext and sedona-geo-generic-alg to the workspace, eliminating geo, wkt and wkb forks (#203)

This is the final step of the forked dependency elimination plan: https://github.com/apache/sedona-db/pull/165/files. sedona-geo-generic-alg will go live and replace the original wherobots/geo dependency. We also replace forked wkb and wkt dependencies with the latest release versions.

This patch depends on wherobots/geo-index#7 to resolve a geo version conflict.

Remaining tasks:

* geo-index will be the only forked dependency, and we are [submitting patches](kylebarron/geo-index#141) to put the nearest neighbour search APIs needed by sedona-db to the upstream.
* We need a released version of [georust/wkb](https://github.com/georust/wkb) before releasing 0.2.0.

Author: Kontinuation

Cargo.lock

@@ -22,6 +22,8 @@ members = [
     "c/sedona-s2geography",
     "c/sedona-tg",
     "r/sedonadb/src/rust",
+    "rust/sedona-geo-traits-ext",
+    "rust/sedona-geo-generic-alg",
     "rust/sedona-adbc",
     "rust/sedona-expr",
     "rust/sedona-functions",
@@ -65,6 +67,7 @@ arrow-json = { version = "55.1.0" }
 arrow-schema = { version = "55.1.0" }
 async-trait = { version = "0.1.87" }
 bytes = "1.10"
+byteorder = "1"
 chrono = { version = "0.4.38", default-features = false }
 comfy-table = { version = "7.0" }
 criterion = { version = "0.5", features = ["html_reports"] }
@@ -82,23 +85,21 @@ env_logger = "0.11"
 futures = { version = "0.3" }
 object_store = { version = "0.12.0", default-features = false }
 float_next_after = "1"
+num-traits = { version = "0.2", default-features = false, features = ["libm"] }
 mimalloc = { version = "0.1", default-features = false }
 libmimalloc-sys = { version = "0.1", default-features = false }
 once_cell = "1.20"
 
-geos = { version = "10.0.0", features = ["geo"] }
+geos = { version = "10.0.0", features = ["geo", "v3_10_0"] }
 
-# Use our own fork of georust/geo, which implements generic computational geometry algorithms for geo-traits
-geo-generic-alg = { git = "https://github.com/wherobots/geo.git", branch = "generic-alg", package = "geo-generic-alg" }
-geo-types = "0.7.16"
-geo-traits = "0.2.0"
-geo-traits-ext = "0.1.0"
-geo = { version = "0.30.0" }
+geo-types = "0.7.17"
+geo-traits = "0.3.0"
+geo = "0.31.0"
 
 geo-index = { version = "0.3.1" }
 
-wkb = { version = "0.8.0", features = ["geos"] }
-wkt = "0.13.0"
+wkb = "0.9.1"
+wkt = "0.14.0"
 
 parking_lot = "0.12"
 parquet = { version = "55.1.0", default-features = false, features = [
@@ -129,9 +130,6 @@ datafusion-ffi = { git = "https://github.com/paleolimbot/datafusion.git", branch
 datafusion-physical-expr = { git = "https://github.com/paleolimbot/datafusion.git", branch = "local-49-with-patch", package = "datafusion-physical-expr" }
 datafusion-physical-plan = { git = "https://github.com/paleolimbot/datafusion.git", branch = "local-49-with-patch", package = "datafusion-physical-plan" }
 
-geo-types = { git = "https://github.com/wherobots/geo.git", branch = "generic-alg", package = "geo-types" }
-geo-traits = { git = "https://github.com/wherobots/geo.git", branch = "generic-alg", package = "geo-traits" }
-geo-traits-ext = { git = "https://github.com/wherobots/geo.git", branch = "generic-alg", package = "geo-traits-ext" }
+# TODO: remove them once changes we made to geo-index and wkb crates are merged to upstream and released
 geo-index = { git = "https://github.com/wherobots/geo-index.git", branch = "main" }
-wkb = { git = "https://github.com/wherobots/wkb.git", branch = "generic-alg" }
-wkt = { git = "https://github.com/wherobots/wkt.git", branch = "generic-alg" }
+wkb = { git = "https://github.com/georust/wkb.git", rev = "130eb0c2b343bc9299aeafba6d34c2a6e53f3b6a" }

Cargo.toml

@@ -31,6 +31,7 @@ criterion = { workspace = true }
 sedona = { path = "../../rust/sedona" }
 sedona-testing = { path = "../../rust/sedona-testing", features = ["criterion"] }
 rstest = { workspace = true }
+geo-types = { workspace = true }
 
 [dependencies]
 arrow-schema = { workspace = true }
@@ -42,8 +43,14 @@ sedona-expr = { path = "../../rust/sedona-expr" }
 sedona-functions = { path = "../../rust/sedona-functions" }
 sedona-geometry = { path = "../../rust/sedona-geometry" }
 sedona-schema = { path = "../../rust/sedona-schema" }
-wkb = { workspace = true, features = ["geos"] }
+geo-traits = { workspace = true }
+wkb = { workspace = true }
+byteorder = { workspace = true }
 
 [[bench]]
 harness = false
 name = "geos-functions"
+
+[[bench]]
+harness = false
+name = "wkb_to_geos"

c/sedona-geos/Cargo.toml

@@ -0,0 +1,77 @@
+// Licensed to the Apache Software Foundation (ASF) under one
+// or more contributor license agreements.  See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership.  The ASF licenses this file
+// to you under the Apache License, Version 2.0 (the
+// "License"); you may not use this file except in compliance
+// with the License.  You may obtain a copy of the License at
+//
+//   http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing,
+// software distributed under the License is distributed on an
+// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+// KIND, either express or implied.  See the License for the
+// specific language governing permissions and limitations
+// under the License.
+use criterion::{criterion_group, criterion_main};
+use geo_types::{LineString, Point};
+use sedona_geos::wkb_to_geos::GEOSWkbFactory;
+use wkb::Endianness;
+
+fn generate_wkb_linestring(num_points: usize, endianness: Endianness) -> Vec<u8> {
+    let mut points = Vec::new();
+    for i in 0..num_points {
+        points.push(Point::new(i as f64, i as f64));
+    }
+    let linestring = LineString::from(points);
+    let mut buffer = Vec::new();
+    wkb::writer::write_geometry(
+        &mut buffer,
+        &linestring,
+        &wkb::writer::WriteOptions { endianness },
+    )
+    .unwrap();
+    buffer
+}
+
+fn bench_parse(c: &mut criterion::Criterion) {
+    for num_points in [4, 10, 100, 500, 1000] {
+        for endianness in [Endianness::BigEndian, Endianness::LittleEndian] {
+            let wkb_buf = generate_wkb_linestring(num_points, endianness);
+            let wkb = wkb::reader::read_wkb(&wkb_buf).unwrap();
+            let endianness_name: &str = match endianness {
+                Endianness::BigEndian => "big endian",
+                Endianness::LittleEndian => "little endian",
+            };
+
+            c.bench_function(
+                &format!(
+                    "convert linestring containing {num_points} points using to_geos ({endianness_name})"
+                ),
+                |b| {
+                    let factory = GEOSWkbFactory::new();
+                    b.iter(|| {
+                        let g = factory.create(&wkb).unwrap();
+                        criterion::black_box(g);
+                    });
+                },
+            );
+
+            c.bench_function(
+                &format!(
+                    "convert linestring containing {num_points} points using geos wkb parser ({endianness_name})"
+                ),
+                |b| {
+                    b.iter(|| {
+                        let g = geos::Geometry::new_from_wkb(wkb.buf()).unwrap();
+                        criterion::black_box(g);
+                    });
+                },
+            );
+        }
+    }
+}
+
+criterion_group!(benches, bench_parse);
+criterion_main!(benches);

c/sedona-geos/benches/wkb_to_geos.rs

@@ -17,13 +17,15 @@
 use datafusion_common::{DataFusionError, Result};
 use sedona_functions::executor::{GenericExecutor, GeometryFactory};
 
+use crate::wkb_to_geos::GEOSWkbFactory;
+
 /// A [GenericExecutor] that iterates over [geos::Geometry]
 pub type GeosExecutor<'a, 'b> = GenericExecutor<'a, 'b, GeosGeometryFactory, GeosGeometryFactory>;
 
 /// [GeometryFactory] implementation for iterating over [geos::Geometry]
 #[derive(Default)]
 pub struct GeosGeometryFactory {
-    inner: wkb::reader::to_geos::GEOSWkbFactory,
+    inner: GEOSWkbFactory,
 }
 
 impl GeometryFactory for GeosGeometryFactory {

c/sedona-geos/src/executor.rs

@@ -27,3 +27,4 @@ mod st_convexhull;
 mod st_dwithin;
 mod st_length;
 mod st_perimeter;
+pub mod wkb_to_geos;