fixed test

Author: Koushul

.gitignore

@@ -14,6 +14,4 @@ web/spatial_viewer/dist/
 
 results/
 .vscode/
-.cursor/
-
-examples/
+.cursor/

examples/mock_h5ad_roundtrip.rs

@@ -0,0 +1,123 @@
+//! Mock “training finished” path: write a tiny `.h5ad`, patch `var` with `mean_lasso_r2`
+//! (same HDF5 path as real training), then read back with **anndata-rs** and optionally **h5py**.
+//!
+//! Run from repo root:
+//! ```text
+//! cargo run --example mock_h5ad_roundtrip
+//! ```
+//!
+//! If `python3` + `h5py` are available, the script also probes `var/_index` (usually readable)
+//! and `var/mean_lasso_r2` (may fail on some arm64 `h5py` wheels when data use Blosc).
+
+use anndata::data::ArrayData;
+use anndata::{AnnData, AnnDataOp, Backend};
+use anndata_hdf5::H5;
+use ndarray::Array2;
+use polars::prelude::{DataFrame, NamedFrom, Series};
+use spacetravlr::spatial_estimator::{MeanLassoR2Accum, dense_to_csr_f64, patch_adata_var_mean_lasso_r2};
+use std::collections::HashMap;
+use std::path::Path;
+use std::process::Command;
+use std::sync::atomic::AtomicU64;
+use std::sync::Arc;
+
+fn main() -> anyhow::Result<()> {
+    let dir = std::env::temp_dir().join(format!(
+        "spacetravlr_mock_roundtrip_{}",
+        std::process::id()
+    ));
+    let _ = std::fs::remove_dir_all(&dir);
+    std::fs::create_dir_all(&dir)?;
+    let p = dir.join("mock.h5ad");
+
+    println!("→ write {}", p.display());
+    let a = AnnData::<H5>::new(&p)?;
+    a.set_obs_names(vec!["c0".into(), "c1".into()].into())?;
+    a.set_var_names(vec!["G0".into(), "G1".into()].into())?;
+    let obs = DataFrame::new(vec![Series::new(
+        "cell_type".into(),
+        vec!["t".to_string(), "t".to_string()],
+    )
+    .into()])?;
+    a.set_obs(obs)?;
+    let var = DataFrame::new(vec![Series::new("gene_ids".into(), vec!["g0", "g1"]).into()])?;
+    a.set_var(var)?;
+    let dense = Array2::from_elem((2, 2), 0.5f64);
+    let csr = dense_to_csr_f64(&dense)?;
+    a.set_x(ArrayData::from(csr))?;
+    a.close()?;
+
+    println!("→ patch_adata_var_mean_lasso_r2 (adds mean_lasso_r2 column)");
+    let mut m: HashMap<String, usize> = HashMap::new();
+    m.insert("G0".into(), 0);
+    m.insert("G1".into(), 1);
+    let scores = Arc::new(vec![
+        AtomicU64::new(0.25f64.to_bits()),
+        AtomicU64::new(f64::NAN.to_bits()),
+    ]);
+    let accum = MeanLassoR2Accum {
+        gene_to_idx: Arc::new(m),
+        scores,
+    };
+    patch_adata_var_mean_lasso_r2(&p, &accum)?;
+
+    println!("→ read back with anndata-rs");
+    let a2 = AnnData::<H5>::open(H5::open(&p)?)?;
+    let v = a2.read_var()?;
+    let r2 = v.column("mean_lasso_r2")?.f64()?;
+    anyhow::ensure!((r2.get(0).unwrap() - 0.25).abs() < 1e-9);
+    anyhow::ensure!(r2.get(1).unwrap().is_nan());
+    a2.close()?;
+    println!("   OK: anndata-rs read_var + mean_lasso_r2");
+
+    try_h5py_probe(&p);
+
+    let _ = std::fs::remove_dir_all(&dir);
+    println!("→ done (temp dir removed)");
+    Ok(())
+}
+
+fn try_h5py_probe(p: &Path) {
+    let path = p.to_string_lossy().replace('\\', "\\\\");
+    let script = format!(
+        r#"
+import sys
+path = r"{path}"
+try:
+    import h5py
+except ImportError:
+    print("   (skip h5py: not installed)")
+    sys.exit(0)
+f = h5py.File(path, "r")
+vg = f["var"]
+names = list(vg.keys())
+print("   h5py var keys:", names)
+for k in names:
+    obj = vg[k]
+    if not hasattr(obj, "shape"):
+        continue
+    try:
+        sl = obj[:2] if getattr(obj, "shape", (0,))[0] != 0 else obj[()]
+        print(f"   OK: h5py read var/{{k}} (sample {{type(sl).__name__}})")
+    except Exception as e:
+        print(f"   WARN: h5py cannot read var/{{k}}:", type(e).__name__, e)
+f.close()
+"#
+    );
+    let out = Command::new("python3")
+        .args(["-c", &script])
+        .output();
+    match out {
+        Ok(o) => {
+            let s = String::from_utf8_lossy(&o.stdout);
+            let e = String::from_utf8_lossy(&o.stderr);
+            if !s.trim().is_empty() {
+                print!("{s}");
+            }
+            if !e.trim().is_empty() && !o.status.success() {
+                eprint!("{e}");
+            }
+        }
+        Err(e) => println!("   (skip h5py probe: {e})"),
+    }
+}

examples/repack_h5ad_var.rs

@@ -0,0 +1,24 @@
+//! Rewrite `var` in place (read → set_var) so datasets use current anndata write defaults.
+//! After patching anndata to default to gzip, this fixes existing `.h5ad` files that used Blosc.
+//!
+//! ```text
+//! cargo run --example repack_h5ad_var -- /path/to/file.h5ad
+//! ```
+
+use anndata::{AnnData, AnnDataOp, Backend};
+use anndata_hdf5::H5;
+use std::path::PathBuf;
+
+fn main() -> anyhow::Result<()> {
+    let path = PathBuf::from(
+        std::env::args()
+            .nth(1)
+            .ok_or_else(|| anyhow::anyhow!("usage: repack_h5ad_var <file.h5ad>"))?,
+    );
+    let adata = AnnData::<H5>::open(H5::open_rw(&path)?)?;
+    let v = adata.read_var()?;
+    adata.set_var(v)?;
+    adata.close()?;
+    println!("repacked var: {}", path.display());
+    Ok(())
+}