let's see what happens...

Author: molpopgen

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_json_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 = 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/src/lib.rs

@@ -7,22 +7,35 @@ struct MutationMetadata {
     dominance: f64,
 }
 
+#[pymethods]
+impl MutationMetadata {
+    fn effect_size(&self) -> f64 {
+        self.effect_size
+    }
+    fn dominance(&self) -> f64 {
+        self.dominance
+    }
+}
+
 #[derive(serde::Serialize, serde::Deserialize)]
 #[pyclass]
 struct IndividualMetadata {
     name: String,
     phenotypes: Vec<i32>,
 }
 
-/// Formats the sum of two numbers as string.
+/// Decode mutation metadata generated in rust via the `bincode` crate.
 #[pyfunction]
-fn sum_as_string(a: usize, b: usize) -> PyResult<String> {
-    Ok((a + b).to_string())
+fn decode_bincode_mutation_metadata(md: Vec<u8>) -> MutationMetadata {
+    // NOTE: the unwrap here is not correct for production code
+    // and a failure will crash the Python interpreter!
+    let md = bincode::deserialize_from(md.as_slice()).unwrap();
+    md
 }
 
 /// A Python module implemented in Rust.
 #[pymodule]
 fn tskit_glue(m: &Bound<'_, PyModule>) -> PyResult<()> {
-    m.add_function(wrap_pyfunction!(sum_as_string, m)?)?;
+    m.add_function(wrap_pyfunction!(decode_bincode_mutation_metadata, m)?)?;
     Ok(())
 }