test: roundtrip bincode metadata into Python (#750)

Author: molpopgen

.github/workflows/python.yml

@@ -38,10 +38,14 @@ jobs:
       - name: run JSON metadata example
         run: |
           cargo run --example json_metadata --features derive
+      - name: run bincode metadata example
+        run: |
+          cargo run --example bincode_metadata --features derive
       - name: setup Python and run tests
         run: |
           uv venv -p ${{ matrix.python }}
           source .venv/bin/activate
           uv pip install -r python/requirements_locked_3_13.txt
+          uv pip install python/tskit_glue
           python -m pytest python
 

Cargo.toml

@@ -60,3 +60,7 @@ name = "tree_traversals"
 [[example]]
 name = "json_metadata"
 required-features = ["derive"]
+
+[[example]]
+name = "bincode_metadata"
+required-features = ["derive"]

examples/bincode_metadata.rs

@@ -0,0 +1,51 @@
+#[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)]
+#[serializer("bincode")]
+struct MutationMetadata {
+    effect_size: f64,
+    dominance: f64,
+}
+
+#[derive(serde::Serialize, serde::Deserialize, tskit::metadata::IndividualMetadata)]
+#[serializer("bincode")]
+struct IndividualMetadata {
+    name: String,
+    phenotypes: Vec<i32>,
+}
+
+fn main() {
+    let ts = make_treeseq().unwrap();
+    ts.dump("with_bincode_metadata.trees", 0).unwrap();
+}
+
+fn make_tables() -> anyhow::Result<tskit::TableCollection> {
+    let mut tables = tskit::TableCollection::new(100.0)?;
+    let pop0 = tables.add_population()?;
+    let ind0 = tables.add_individual_with_metadata(
+        0,
+        None,
+        None,
+        &IndividualMetadata {
+            name: "Jerome".to_string(),
+            phenotypes: vec![0, 1, 2, 0],
+        },
+    )?;
+    let node0 = tables.add_node(tskit::NodeFlags::new_sample(), 0.0, pop0, ind0)?;
+    let site0 = tables.add_site(50.0, Some("A".as_bytes()))?;
+    let _ = tables.add_mutation_with_metadata(
+        site0,
+        node0,
+        tskit::MutationId::NULL,
+        1.0,
+        Some("G".as_bytes()),
+        &MutationMetadata {
+            effect_size: -1e-3,
+            dominance: 0.1,
+        },
+    )?;
+    tables.build_index()?;
+    Ok(tables)
+}
+
+fn make_treeseq() -> anyhow::Result<tskit::TreeSequence> {
+    Ok(make_tables()?.tree_sequence(0)?)
+}

python/requirements.txt

@@ -1,2 +1,3 @@
 tskit>=0.6.3
 pytest
+maturin

python/requirements_locked_3_13.txt

@@ -10,6 +10,8 @@ jsonschema==4.23.0
     # via tskit
 jsonschema-specifications==2025.4.1
     # via jsonschema
+maturin==1.8.6
+    # via -r requirements.txt
 numpy==2.2.5
     # via tskit
 packaging==25.0

python/test_bincode_metadata.py

@@ -0,0 +1,28 @@
+import tskit
+import tskit_glue
+import numpy as np
+
+
+def setup_ts_without_schema():
+    ts = tskit.TreeSequence.load("with_bincode_metadata.trees")
+    return ts
+
+
+def test_individual_metadata():
+    # NOTE: the assertions here rely on knowing
+    # what examples/json_metadata.rs put into the
+    # metadata!
+    ts = setup_ts_without_schema()
+    md = tskit_glue.decode_bincode_individual_metadata(ts.individual(0).metadata)
+    assert md.name() == "Jerome"
+    assert md.phenotypes() == [0, 1, 2, 0]
+
+
+def test_mutation_metadata():
+    # NOTE: the assertions here rely on knowing
+    # what examples/json_metadata.rs put into the
+    # metadata!
+    ts = setup_ts_without_schema()
+    md = tskit_glue.decode_bincode_mutation_metadata(ts.mutation(0).metadata)
+    assert np.isclose(md.effect_size(), -1e-3)
+    assert np.isclose(md.dominance(), 0.1)

python/tskit_glue/Cargo.lock

@@ -0,0 +1,14 @@
+[package]
+name = "tskit_glue"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "tskit_glue"
+crate-type = ["cdylib"]
+
+[dependencies]
+pyo3 = "0.24.0"
+serde = {version = "1.0.203", features = ["derive"]}
+bincode = {version = "1.3.1"}

python/tskit_glue/Cargo.toml

@@ -0,0 +1,15 @@
+[build-system]
+requires = ["maturin>=1.8,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "tskit_glue"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Rust",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+dynamic = ["version"]
+[tool.maturin]
+features = ["pyo3/extension-module"]