morphit-rs 0.2.0__tar.gz → 0.2.1__tar.gz

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/Cargo.lock

@@ -4178,7 +4178,7 @@ dependencies = [
 
 [[package]]
 name = "morphit"
-version = "0.2.0"
+version = "0.2.1"
 dependencies = [
  "bytemuck",
  "futures-channel",
@@ -4204,7 +4204,7 @@ dependencies = [
 
 [[package]]
 name = "morphit-capi"
-version = "0.2.0"
+version = "0.2.1"
 dependencies = [
  "cbindgen",
  "morphit",
@@ -4218,7 +4218,7 @@ dependencies = [
 
 [[package]]
 name = "morphit-cli"
-version = "0.2.0"
+version = "0.2.1"
 dependencies = [
  "assert_cmd",
  "clap",
@@ -4233,7 +4233,7 @@ dependencies = [
 
 [[package]]
 name = "morphit-py"
-version = "0.2.0"
+version = "0.2.1"
 dependencies = [
  "morphit",
  "morphit-robot",
@@ -4249,7 +4249,7 @@ dependencies = [
 
 [[package]]
 name = "morphit-robot"
-version = "0.2.0"
+version = "0.2.1"
 dependencies = [
  "morphit",
  "rand 0.9.5",
@@ -4265,7 +4265,7 @@ dependencies = [
 
 [[package]]
 name = "morphit-server"
-version = "0.2.0"
+version = "0.2.1"
 dependencies = [
  "axum",
  "clap",
@@ -4287,7 +4287,7 @@ dependencies = [
 
 [[package]]
 name = "morphit-studio"
-version = "0.2.0"
+version = "0.2.1"
 dependencies = [
  "bevy",
  "bevy_editor_cam",
@@ -4312,7 +4312,7 @@ dependencies = [
 
 [[package]]
 name = "morphit-wasm"
-version = "0.2.0"
+version = "0.2.1"
 dependencies = [
  "console_error_panic_hook",
  "js-sys",

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/Cargo.toml

@@ -3,7 +3,7 @@ members = ["crates/morphit", "crates/morphit-robot", "crates/morphit-py"]
 resolver = "3"
 
 [workspace.package]
-version = "0.2.0"
+version = "0.2.1"
 edition = "2024"
 license = "MIT"
 rust-version = "1.85"

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: morphit-rs
-Version: 0.2.0
+Version: 0.2.1
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: Microsoft :: Windows

{morphit_rs-0.2.0/crates/morphit-robot → morphit_rs-0.2.1/crates/morphit}/README.md

@@ -217,7 +217,7 @@ result.save("bunny.json")?;
 ([details](#using-the-release-package-from-cmake)):
 
 ```cmake
-find_package(morphit 0.1 CONFIG REQUIRED)
+find_package(morphit 0.2 CONFIG REQUIRED)
 target_link_libraries(app PRIVATE morphit::morphit_cpp)   # C: morphit::morphit
 ```
 
@@ -626,7 +626,7 @@ lib/cmake/morphit/morphit-config.cmake      (+ version file, system libraries of
 Unpack it anywhere and point `CMAKE_PREFIX_PATH` at the folder:
 
 ```cmake
-find_package(morphit 0.1 CONFIG REQUIRED)
+find_package(morphit 0.2 CONFIG REQUIRED)
 target_link_libraries(app PRIVATE morphit::morphit)           # shared library
 # target_link_libraries(app PRIVATE morphit::morphit_static)  # static, with its system libraries
 # target_link_libraries(app PRIVATE morphit::morphit_cpp)     # C++17 wrapper (also _cpp_static)
@@ -638,7 +638,7 @@ cmake -S . -B build -DCMAKE_PREFIX_PATH=/path/to/morphit-capi-0.2.0-x86_64-unkno
 
 On Windows copy `morphit_capi.dll` next to the executable
 (`$<TARGET_RUNTIME_DLLS:app>` lists it); the static library there is built
-against the DLL runtime (`/MD`). A `0.1` request accepts any `0.1.x`. The
+against the DLL runtime (`/MD`). A `0.2` request accepts any `0.2.x`. The
 examples in `crates/morphit-capi/examples/c` use the package when
 `CMAKE_PREFIX_PATH` points at one (`-DMORPHIT_STATIC=ON` for the static
 library), and `tools/ci/test_capi_package.sh <archive>` builds and runs them
@@ -831,6 +831,9 @@ exits 0 when it answers, which is what the Docker health check runs.
 packs the mesh exactly as loaded (the `X-Morphit-Mesh-Prep` report then says
 `disabled`), and `convex_hull=true` packs the convex hull of each body. The
 web UI has both under Advanced settings, Mesh preparation.
+`advanced` also accepts `prune_contained_spheres` (default `true`; see
+[Differences from the Python code](#differences-from-the-python-code)), under
+Advanced settings, Final prune.
 
 Robot sessions live in the server's memory and in the session directory, and
 expire after the TTL. Run a single instance. Uploads are capped at 100 MB per
@@ -1133,6 +1136,12 @@ one-time device setup per process; ¹ optimizer loop only.
 - Mesh preparation can be switched off (`model.union_overlapping_bodies`) and
   extended with convex hulls (`model.convex_hull`); Python always merges and
   never builds hulls. Both keys are stored in the result's config.
+- The final prune also removes spheres that lie entirely inside another
+  sphere (`training.prune_contained_spheres`, on by default; `false` keeps
+  them as Python does). They add nothing to the covered volume, so coverage
+  and surface distance are unchanged, but they no longer count twice in the
+  per-sphere masses. The key is stored in the result's config, and the HTTP
+  API accepts it in `advanced`.
 - Float64 throughout. GPU support is a search accelerator with CPU-identical
   results rather than a float32 port; `model.device` therefore never changes
   the output.
@@ -1206,7 +1215,7 @@ token. For PyPI, add a *pending trusted publisher* on pypi.org (project
 and create an environment named `pypi`; no token is needed. npm publishes
 only through trusted publishing (2FA-bypass tokens are being deprecated), and
 a trusted publisher can only be added to an existing package: publish the
-first version by hand (`npm publish morphit-rs-<version>.tgz --access public`
+first version by hand (`npm publish ./morphit-rs-<version>.tgz --access public`
 with the tarball from the GitHub Release; the release's `npm-publish` job
 fails until then and can be re-run afterwards), then add a trusted publisher
 for `morphit-rs` on npmjs.com (workflow `release.yml`, environment `npm`,

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/crates/morphit/src/config.rs

@@ -257,6 +257,10 @@ pub struct TrainingConfig {
     pub density_control_warmup_steps: usize,
     pub density_control_cooling_factor: f64,
     pub density_control_min_radius_fraction: f64,
+    /// The final prune also removes spheres lying entirely inside another
+    /// sphere; they add nothing to the covered volume. Not in Python; on by
+    /// default.
+    pub prune_contained_spheres: bool,
 }
 
 impl Default for TrainingConfig {
@@ -291,6 +295,7 @@ impl Default for TrainingConfig {
             density_control_warmup_steps: 10,
             density_control_cooling_factor: 0.85,
             density_control_min_radius_fraction: 0.001,
+            prune_contained_spheres: true,
         }
     }
 }
@@ -668,6 +673,9 @@ mod tests {
         assert_eq!(c.random_seed, None);
         c.set("model.per_sphere_mass", json!(true)).unwrap();
         assert!(c.model.per_sphere_mass);
+        assert_eq!(c.get("training.prune_contained_spheres").unwrap(), json!(true));
+        c.set("training.prune_contained_spheres", json!(false)).unwrap();
+        assert!(!c.training.prune_contained_spheres);
         assert_eq!(c.get("training.iterations").unwrap(), json!(120));
     }
 

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/crates/morphit/src/mesh_prep.rs

@@ -267,7 +267,7 @@ fn prepare(
     }
 
     let n = kept.len();
-    let (uv, uf) = match union(&kept) {
+    let (uv, uf) = match union(&kept, !hulled) {
         Ok(u) => u,
         Err(UnionError::Unavailable(why)) => {
             report.skip(
@@ -631,9 +631,12 @@ enum UnionError {
 
 /// Boolean union of closed bodies, each converted to a Manifold from f32
 /// positions (as Python's manifold3d `Mesh`), combined left to right. The
-/// result's duplicate positions are merged like trimesh's `process=True`.
+/// result's duplicate positions are merged like trimesh's `process=True` when
+/// `weld` is set. Without it, Manifold's own indexing is kept: where two
+/// inputs only touch, Manifold leaves separate vertices at one position, and
+/// welding them would make the result non-manifold there.
 #[cfg(feature = "union")]
-fn union(bodies: &[Body]) -> Result<(Vec<DVec3>, Vec<[u32; 3]>), UnionError> {
+fn union(bodies: &[Body], weld: bool) -> Result<(Vec<DVec3>, Vec<[u32; 3]>), UnionError> {
     use manifold_rust::manifold::Manifold;
     use manifold_rust::types::{Error as MfError, MeshGL};
 
@@ -675,11 +678,11 @@ fn union(bodies: &[Body]) -> Result<(Vec<DVec3>, Vec<[u32; 3]>), UnionError> {
         .map(|p| DVec3::new(p[0] as f64, p[1] as f64, p[2] as f64))
         .collect();
     let faces: Vec<[u32; 3]> = out.tri_verts.chunks_exact(3).map(|t| [t[0], t[1], t[2]]).collect();
-    Ok(merge_positions(&vertices, &faces))
+    Ok(if weld { merge_positions(&vertices, &faces) } else { (vertices, faces) })
 }
 
 #[cfg(not(feature = "union"))]
-fn union(_bodies: &[Body]) -> Result<(Vec<DVec3>, Vec<[u32; 3]>), UnionError> {
+fn union(_bodies: &[Body], _weld: bool) -> Result<(Vec<DVec3>, Vec<[u32; 3]>), UnionError> {
     Err(UnionError::Unavailable("mesh union support is not built in (feature `union`)".into()))
 }
 

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/crates/morphit/src/state.rs

@@ -70,10 +70,48 @@ impl Spheres {
     }
 }
 
+/// Spheres lying entirely inside another one (`|c_i - c_j| + r_j <= r_i`;
+/// touching from inside counts). Of spheres that contain each other
+/// (identical ones) the first is kept, so the largest always survives and the
+/// union of the kept spheres equals the union of all.
+pub fn contained_in_another(centers: &[DVec3], radii: &[f64]) -> Vec<bool> {
+    assert_eq!(centers.len(), radii.len());
+    let n = centers.len();
+    (0..n)
+        .map(|j| {
+            (0..n).any(|i| {
+                if i == j {
+                    return false;
+                }
+                // Same argument order for (i,j) and (j,i), as in `distances::pairwise`.
+                let d = crate::distances::dist(centers[i.min(j)], centers[i.max(j)]);
+                d + radii[j] <= radii[i] && (i < j || d + radii[i] > radii[j])
+            })
+        })
+        .collect()
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
 
+    #[test]
+    fn contained_spheres_are_found() {
+        let x = |v: f64| DVec3::new(v, 0.0, 0.0);
+        // Nested chain: all but the outermost go.
+        assert_eq!(contained_in_another(&[x(0.0), x(0.1), x(0.15)], &[1.0, 0.5, 0.2]), [false, true, true]);
+        // Partial overlap: both stay.
+        assert_eq!(contained_in_another(&[x(0.0), x(0.8)], &[0.5, 0.5]), [false, false]);
+        // Touching from inside counts as contained.
+        assert_eq!(contained_in_another(&[x(0.0), x(0.5)], &[1.0, 0.5]), [false, true]);
+        // Identical spheres: the first is kept.
+        assert_eq!(contained_in_another(&[x(1.0); 3], &[0.3; 3]), [false, true, true]);
+        // Order does not matter: the largest is kept.
+        assert_eq!(contained_in_another(&[x(0.15), x(0.1), x(0.0)], &[0.2, 0.5, 1.0]), [true, true, false]);
+        assert!(contained_in_another(&[], &[]).is_empty());
+        assert_eq!(contained_in_another(&[x(0.0)], &[0.1]), [false]);
+    }
+
     #[test]
     fn real_round_trip() {
         let s = Spheres::from_real(vec![DVec3::ZERO, DVec3::ONE], &[0.1, 0.25], Some(&[2.0, 3.0]));

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/crates/morphit/src/trainer.rs

@@ -21,7 +21,7 @@ use crate::metrics::{DensityEvent, History, IterationRecord};
 use crate::optim::{Optimizer, clip_grad_norm, clip_grad_norm_vec3};
 use crate::result::PackResult;
 use crate::sampling::{MorphRng, lognormal_radii, sample_inside, sample_surface, voxel_grid_centers};
-use crate::state::Spheres;
+use crate::state::{Spheres, contained_in_another};
 
 /// Lifecycle of a session.
 #[derive(Clone, Copy, Debug, PartialEq, Eq)]
@@ -32,7 +32,7 @@ pub enum SessionState {
     Converged,
     /// All configured iterations ran.
     Completed,
-    /// The final escaped-sphere prune ran; no more steps.
+    /// The final prune (escaped and nested spheres) ran; no more steps.
     Finalized,
 }
 
@@ -400,8 +400,10 @@ impl Session {
     }
 
     /// Remove spheres whose centers ended outside the mesh
-    /// (`_finalize_training`) and end the session. Idempotent; returns the
-    /// number of spheres removed. At least one sphere is always kept.
+    /// (`_finalize_training`), then, with `training.prune_contained_spheres`
+    /// (not in Python), spheres lying entirely inside another one, and end the
+    /// session. Idempotent; returns the number of spheres removed. At least
+    /// one sphere is always kept.
     pub fn finalize(&mut self) -> usize {
         if self.state == SessionState::Finalized {
             return self.pruned;
@@ -412,10 +414,26 @@ impl Session {
             tracing::warn!("every sphere center is outside the mesh; keeping the first sphere");
             keep.push(0);
         }
+        let escaped = self.spheres.len() - keep.len();
+        if escaped > 0 {
+            tracing::info!(removed = escaped, "final prune removed spheres whose centers escaped the mesh");
+        }
+        if self.config.training.prune_contained_spheres {
+            // Only among the survivors: an escaped container does not take its contents along.
+            let radii = self.spheres.radii();
+            let centers: Vec<_> = keep.iter().map(|&i| self.spheres.centers[i]).collect();
+            let r: Vec<f64> = keep.iter().map(|&i| radii[i]).collect();
+            let nested = contained_in_another(&centers, &r);
+            let before = keep.len();
+            keep = keep.into_iter().zip(nested).filter_map(|(i, n)| (!n).then_some(i)).collect();
+            let contained = before - keep.len();
+            if contained > 0 {
+                tracing::info!(removed = contained, "final prune removed spheres inside another sphere");
+            }
+        }
         let removed = self.spheres.len() - keep.len();
         if removed > 0 {
             self.spheres = self.spheres.select(&keep);
-            tracing::info!(removed, "final prune removed spheres whose centers escaped the mesh");
         }
         self.pruned = removed;
         self.state = SessionState::Finalized;
@@ -745,6 +763,46 @@ mod tests {
         assert_eq!(s.spheres().len(), 1);
     }
 
+    /// A session on `cube()` whose spheres are replaced by `spheres`.
+    fn with_spheres(prune_contained: bool, spheres: &[([f64; 3], f64)]) -> Session {
+        let mut cfg = small_config(Preset::B, 5, spheres.len());
+        cfg.training.prune_contained_spheres = prune_contained;
+        let mut s = Session::new(cfg, cube()).unwrap();
+        let centers = spheres.iter().map(|(c, _)| DVec3::from_array(*c)).collect();
+        let radii: Vec<f64> = spheres.iter().map(|(_, r)| *r).collect();
+        s.spheres = Spheres::from_real(centers, &radii, None);
+        s
+    }
+
+    #[test]
+    fn finalize_prunes_spheres_inside_another() {
+        let spheres = [
+            ([0.3, 0.4, 0.3], 0.25), // big
+            ([0.35, 0.4, 0.3], 0.1), // inside the big one
+            ([0.7, 0.4, 0.3], 0.2),  // overlaps the big one partly
+            ([0.3, 0.4, 0.3], 0.25), // duplicate of the big one
+        ];
+        let mut s = with_spheres(true, &spheres);
+        let radii = s.spheres.radii();
+        assert_eq!(s.finalize(), 2);
+        assert_eq!(s.spheres().centers, vec![DVec3::new(0.3, 0.4, 0.3), DVec3::new(0.7, 0.4, 0.3)]);
+        assert_eq!(s.spheres().radii(), vec![radii[0], radii[2]]);
+        assert_eq!(s.finalize(), 2);
+        assert_eq!(s.result().num_spheres, 2);
+
+        let mut s = with_spheres(false, &spheres);
+        assert_eq!(s.finalize(), 0);
+        assert_eq!(s.spheres().len(), 4);
+    }
+
+    #[test]
+    fn escaped_container_keeps_its_contents() {
+        // The container's center is outside the box; the nested sphere's is inside.
+        let mut s = with_spheres(true, &[([1.1, 0.4, 0.3], 0.5), ([0.9, 0.4, 0.3], 0.1)]);
+        assert_eq!(s.finalize(), 1);
+        assert_eq!(s.spheres().centers, vec![DVec3::new(0.9, 0.4, 0.3)]);
+    }
+
     #[test]
     fn projection_moves_escaped_centers_inside() {
         let mut s = Session::new(small_config(Preset::B, 5, 4), cube()).unwrap();

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/crates/morphit-py/src/session.rs

@@ -351,8 +351,9 @@ impl PySession {
         self.core.cancel.store(true, Ordering::Release);
     }
 
-    /// Remove spheres whose centers ended outside the mesh and end the
-    /// session; returns how many were removed. Idempotent.
+    /// Remove spheres whose centers ended outside the mesh and spheres inside
+    /// another sphere (unless `training.prune_contained_spheres` is false),
+    /// and end the session; returns how many were removed. Idempotent.
     fn finalize(&self, py: Python<'_>) -> PyResult<usize> {
         let _running = self.core.claim()?;
         let core = Arc::clone(&self.core);

{morphit_rs-0.2.0/crates/morphit → morphit_rs-0.2.1/crates/morphit-robot}/README.md

@@ -217,7 +217,7 @@ result.save("bunny.json")?;
 ([details](#using-the-release-package-from-cmake)):
 
 ```cmake
-find_package(morphit 0.1 CONFIG REQUIRED)
+find_package(morphit 0.2 CONFIG REQUIRED)
 target_link_libraries(app PRIVATE morphit::morphit_cpp)   # C: morphit::morphit
 ```
 
@@ -626,7 +626,7 @@ lib/cmake/morphit/morphit-config.cmake      (+ version file, system libraries of
 Unpack it anywhere and point `CMAKE_PREFIX_PATH` at the folder:
 
 ```cmake
-find_package(morphit 0.1 CONFIG REQUIRED)
+find_package(morphit 0.2 CONFIG REQUIRED)
 target_link_libraries(app PRIVATE morphit::morphit)           # shared library
 # target_link_libraries(app PRIVATE morphit::morphit_static)  # static, with its system libraries
 # target_link_libraries(app PRIVATE morphit::morphit_cpp)     # C++17 wrapper (also _cpp_static)
@@ -638,7 +638,7 @@ cmake -S . -B build -DCMAKE_PREFIX_PATH=/path/to/morphit-capi-0.2.0-x86_64-unkno
 
 On Windows copy `morphit_capi.dll` next to the executable
 (`$<TARGET_RUNTIME_DLLS:app>` lists it); the static library there is built
-against the DLL runtime (`/MD`). A `0.1` request accepts any `0.1.x`. The
+against the DLL runtime (`/MD`). A `0.2` request accepts any `0.2.x`. The
 examples in `crates/morphit-capi/examples/c` use the package when
 `CMAKE_PREFIX_PATH` points at one (`-DMORPHIT_STATIC=ON` for the static
 library), and `tools/ci/test_capi_package.sh <archive>` builds and runs them
@@ -831,6 +831,9 @@ exits 0 when it answers, which is what the Docker health check runs.
 packs the mesh exactly as loaded (the `X-Morphit-Mesh-Prep` report then says
 `disabled`), and `convex_hull=true` packs the convex hull of each body. The
 web UI has both under Advanced settings, Mesh preparation.
+`advanced` also accepts `prune_contained_spheres` (default `true`; see
+[Differences from the Python code](#differences-from-the-python-code)), under
+Advanced settings, Final prune.
 
 Robot sessions live in the server's memory and in the session directory, and
 expire after the TTL. Run a single instance. Uploads are capped at 100 MB per
@@ -1133,6 +1136,12 @@ one-time device setup per process; ¹ optimizer loop only.
 - Mesh preparation can be switched off (`model.union_overlapping_bodies`) and
   extended with convex hulls (`model.convex_hull`); Python always merges and
   never builds hulls. Both keys are stored in the result's config.
+- The final prune also removes spheres that lie entirely inside another
+  sphere (`training.prune_contained_spheres`, on by default; `false` keeps
+  them as Python does). They add nothing to the covered volume, so coverage
+  and surface distance are unchanged, but they no longer count twice in the
+  per-sphere masses. The key is stored in the result's config, and the HTTP
+  API accepts it in `advanced`.
 - Float64 throughout. GPU support is a search accelerator with CPU-identical
   results rather than a float32 port; `model.device` therefore never changes
   the output.
@@ -1206,7 +1215,7 @@ token. For PyPI, add a *pending trusted publisher* on pypi.org (project
 and create an environment named `pypi`; no token is needed. npm publishes
 only through trusted publishing (2FA-bypass tokens are being deprecated), and
 a trusted publisher can only be added to an existing package: publish the
-first version by hand (`npm publish morphit-rs-<version>.tgz --access public`
+first version by hand (`npm publish ./morphit-rs-<version>.tgz --access public`
 with the tarball from the GitHub Release; the release's `npm-publish` job
 fails until then and can be re-run afterwards), then add a trusted publisher
 for `morphit-rs` on npmjs.com (workflow `release.yml`, environment `npm`,

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/crates/morphit-robot/src/config.rs

@@ -10,8 +10,9 @@ use crate::{Error, Result};
 pub const ALLOWED_VARIANTS: [&str; 3] = ["MorphIt-V", "MorphIt-S", "MorphIt-B"];
 
 /// Flat `advanced` keys the UI sends, and the dotted config keys they set.
-/// Anything else is dropped silently, as in the Python API.
-pub const ADVANCED_OVERRIDE_MAP: [(&str, &str); 13] = [
+/// Anything else is dropped silently, as in the Python API
+/// (`prune_contained_spheres` is not in Python).
+pub const ADVANCED_OVERRIDE_MAP: [(&str, &str); 14] = [
     ("num_inside_samples", "model.num_inside_samples"),
     ("num_surface_samples", "model.num_surface_samples"),
     ("density_control_enabled", "training.density_control_enabled"),
@@ -25,6 +26,7 @@ pub const ADVANCED_OVERRIDE_MAP: [(&str, &str); 13] = [
     ("sqem_weight", "training.sqem_weight"),
     ("hausdorff_weight", "training.hausdorff_weight"),
     ("mesh_containment_weight", "training.mesh_containment_weight"),
+    ("prune_contained_spheres", "training.prune_contained_spheres"),
 ];
 
 /// `variant must be one of ('MorphIt-V', 'MorphIt-S', 'MorphIt-B')`.
@@ -135,7 +137,7 @@ mod tests {
     #[test]
     fn advanced_is_filtered_and_mapped() {
         let a = parse_advanced(
-            r#"{"coverage_weight": 2.5, "bogus": 1, "sqem_weight": null, "num_inside_samples": 100}"#,
+            r#"{"coverage_weight": 2.5, "bogus": 1, "sqem_weight": null, "num_inside_samples": 100, "prune_contained_spheres": false}"#,
         )
         .unwrap();
         assert_eq!(
@@ -143,6 +145,7 @@ mod tests {
             vec![
                 ("training.coverage_weight".to_string(), Value::from(2.5)),
                 ("model.num_inside_samples".to_string(), Value::from(100)),
+                ("training.prune_contained_spheres".to_string(), Value::from(false)),
             ]
         );
         assert!(parse_advanced("").unwrap().is_empty());
@@ -183,7 +186,10 @@ mod tests {
     fn config_applies_everything() {
         let mut p = params();
         p.seed = Some(7);
-        p.advanced = parse_advanced(r#"{"coverage_weight": 3, "density_control_enabled": false}"#).unwrap();
+        p.advanced = parse_advanced(
+            r#"{"coverage_weight": 3, "density_control_enabled": false, "prune_contained_spheres": false}"#,
+        )
+        .unwrap();
         let c = p.config("cpu", "/tmp/x", "a.json").unwrap();
         assert_eq!(c.model.num_spheres, 20);
         assert_eq!(c.training.iterations, 200);
@@ -191,6 +197,7 @@ mod tests {
         assert_eq!(c.model.device, "cpu");
         assert_eq!(c.training.coverage_weight, 3.0);
         assert!(!c.training.density_control_enabled);
+        assert!(!c.training.prune_contained_spheres);
         assert_eq!(c.output_filename, "a.json");
         p.advanced = vec![("model.num_inside_samples".into(), Value::from("many"))];
         assert!(matches!(p.config("cpu", "", ""), Err(Error::Invalid(_))));

{morphit_rs-0.2.0 → morphit_rs-0.2.1}/python/morphit_rs/compat.py

@@ -435,7 +435,8 @@ def train_morphit(
             print(f"Stopping at iteration {step.iteration}")
     removed = session.finalize()
     if removed:
-        print(f"\n[final prune] removed {removed} sphere(s) whose centers escaped the mesh")
+        print(f"\n[final prune] removed {removed} sphere(s) whose centers escaped the mesh "
+              f"or that lay inside another sphere")
     model.num_spheres = session.num_spheres
     print("\n=== Training Complete ===")
     print(f"Density control operations: {len(tracker.metrics['density_control_events'])}")