chore: deps bumps and test fixes (#149)

zachcp · web-flow · commit 43a3cfcfabdb · 2025-11-09T12:10:40.000-05:00
* bump crates

* small bumps

* update rerun

* update Cargo toml

* update deps

* remove rerun

* - update ORT and ndarray - remove rerun - fix cargo check issues

* update ball and stick mesh creation
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -23,22 +23,22 @@ license = "MIT OR Apache-2.0"
 edition = "2024"
 
 [workspace.dependencies]
-anyhow = "1.0"
-bevy = { version = "0.16.1", default-features = false }
-bon = "3.6.4"
-candle-core = "0.9.1"
-candle-metal-kernels = "0.9.1"
-candle-nn = "0.9.1"
-candle-onnx = "0.9.1"
-candle-transformers = "0.9.1"
-clap = { version = "4.5.40", features = ["derive"] }
-hf-hub = "0.4.2"
+anyhow = "1.0.100"
+bevy = { version = "0.17.2", default-features = false }
+bon = "3.8.1"
+candle-core = "0.9.2-alpha.1"
+candle-metal-kernels = "0.9.2-alpha.1"
+candle-nn = "0.9.2-alpha.1"
+candle-onnx = "0.9.2-alpha.1"
+candle-transformers = "0.9.2-alpha.1"
+clap = { version = "4.5.51", features = ["derive"] }
+hf-hub = "0.4.3"
 itertools = "0.14.0"
-ndarray = "0.16"
-ort = "=2.0.0-rc.10"
-rerun = "0.23.3"
-serde = { version = "1.0", features = ["derive"] }
-serde_json = "1.0.140"
-strum = { version = "0.27", features = ["derive"] }
-tempfile = "3.20.0"
-tokenizers = { version = "0.21.1", features = ["onig"] }
+ndarray = "0.17"
+ort = { git = "https://github.com/pykeio/ort" }
+# rerun = "0.26"
+serde = { version = "1.0.228", features = ["derive"] }
+serde_json = "1.0.145"
+strum = { version = "0.27.2", features = ["derive"] }
+tempfile = "3.23.0"
+tokenizers = { version = "0.22.1", features = ["onig"] }
diff --git a/crates/ferritin-examples/Cargo.toml b/crates/ferritin-examples/Cargo.toml
@@ -7,7 +7,8 @@ license.workspace = true
 description.workspace = true
 
 [features]
-default = ["plms", "mesh"]
+default = ["plms", "mesh", "bevy"]
+bevy = []
 metal = ["candle-core/metal", "candle-nn/metal", "candle-metal-kernels"]
 mesh = ["ferritin/mesh"]
 plms = ["ferritin/plms"]
@@ -30,21 +31,21 @@ ferritin-plms = { path = "../ferritin-plms" }
 ferritin-onnx-models = { path = "../ferritin-onnx-models" }
 ferritin-structure-mesh = { path = "../ferritin-structure-mesh" }
 hf-hub.workspace = true
-rerun = { workspace = true, features = ["native_viewer"] }
+# rerun = { workspace = true, features = ["native_viewer"] }
 
 # The metal feature is defined above, and we don't need to redefine it conditionally
 
 [target.'cfg(target_os = "macos")'.dependencies]
 candle-metal-kernels.workspace = true
 
 [target.'cfg(target_arch = "wasm32")'.dependencies]
-tokenizers = { version = "0.21.1", default-features = false, features = [
+tokenizers = { version = "0.21.4", default-features = false, features = [
     "unstable_wasm",
 ] }
 
 [target.'cfg(not(target_arch = "wasm32"))'.dependencies]
 hf-hub.workspace = true
-tokenizers = { version = "0.21.1" } # full features for non-wasm
+tokenizers = { version = "0.21.4" } # full features for non-wasm
 
 
 [dev-dependencies]
@@ -59,18 +60,22 @@ required-features = ["bevy"]
 [[example]]
 name = "bevy_basic_putty"
 path = "examples/bevy/basic_putty.rs"
+required-features = ["bevy"]
 
 [[example]]
 name = "bevy_basic_snapshot"
 path = "examples/bevy/basic_snapshot.rs"
+required-features = ["bevy"]
 
 [[example]]
 name = "bevy_basic_spheres"
 path = "examples/bevy/basic_spheres.rs"
+required-features = ["bevy"]
 
 [[example]]
 name = "bevy_screenshot"
 path = "examples/bevy/screenshot.rs"
+required-features = ["bevy"]
 
 [[example]]
 name = "rerun"
diff --git a/crates/ferritin-examples/examples/bevy/basic_ball_and_stick.rs b/crates/ferritin-examples/examples/bevy/basic_ball_and_stick.rs
@@ -49,7 +49,6 @@ fn main() -> Result<()> {
     Ok(())
 }
 
-
 #[derive(Component)]
 struct MainCamera;
 
diff --git a/crates/ferritin-examples/examples/bevy/basic_snapshot.rs b/crates/ferritin-examples/examples/bevy/basic_snapshot.rs
@@ -4,8 +4,6 @@ use bevy::{
     app::AppExit,
     prelude::*,
     render::view::screenshot::{Capturing, Screenshot, save_to_disk},
-    window::SystemCursorIcon,
-    winit::cursor::CursorIcon,
 };
 use ferritin_structure_mesh::{ColorScheme, RenderOptions, StructurePlugin, StructureSettings};
 use ferritin_test_data::TestFile;
@@ -43,27 +41,25 @@ fn main() -> Result<()> {
 }
 
 fn screenshot_saving(
-    mut commands: Commands,
+    _commands: Commands,
     screenshot_saving: Query<Entity, With<Capturing>>,
-    windows: Query<Entity, With<Window>>,
+    _windows: Query<Entity, With<Window>>,
 ) {
-    let Ok(window) = windows.single() else {
-        return;
-    };
+    // TODO: Update cursor icon API for Bevy 0.17
+    // Cursor icon management has changed in Bevy 0.17
+    // See: https://bevyengine.org/learn/migration-guides/0.16-0.17/
     match screenshot_saving.iter().count() {
         0 => {
-            commands.entity(window).remove::<CursorIcon>();
+            // commands.entity(window).remove::<SystemCursorIcon>();
         }
         x if x > 0 => {
-            commands
-                .entity(window)
-                .insert(CursorIcon::from(SystemCursorIcon::Progress));
+            // commands.entity(window).insert(SystemCursorIcon::Progress);
         }
         _ => {}
     }
 }
 
-fn take_screenshot_and_exit(mut commands: Commands, mut exit: EventWriter<AppExit>) {
+fn take_screenshot_and_exit(mut commands: Commands, mut exit: MessageWriter<AppExit>) {
     // Wait a few frames to make sure everything is properly initialized
     static mut FRAME_COUNT: u32 = 0;
     unsafe {
diff --git a/crates/ferritin-examples/examples/bevy/screenshot.rs b/crates/ferritin-examples/examples/bevy/screenshot.rs
@@ -4,7 +4,6 @@ use bevy::{
     prelude::*,
     render::view::screenshot::{Capturing, Screenshot, save_to_disk},
     window::SystemCursorIcon,
-    winit::cursor::CursorIcon,
 };
 
 fn main() {
@@ -30,21 +29,19 @@ fn screenshot_on_spacebar(
 }
 
 fn screenshot_saving(
-    mut commands: Commands,
+    _commands: Commands,
     screenshot_saving: Query<Entity, With<Capturing>>,
-    windows: Query<Entity, With<Window>>,
+    _windows: Query<Entity, With<Window>>,
 ) {
-    let Ok(window) = windows.single() else {
-        return;
-    };
+    // TODO: Update cursor icon API for Bevy 0.17
+    // Cursor icon management has changed in Bevy 0.17
+    // See: https://bevyengine.org/learn/migration-guides/0.16-0.17/
     match screenshot_saving.iter().count() {
         0 => {
-            commands.entity(window).remove::<CursorIcon>();
+            // commands.entity(window).remove::<SystemCursorIcon>();
         }
         x if x > 0 => {
-            commands
-                .entity(window)
-                .insert(CursorIcon::from(SystemCursorIcon::Progress));
+            // commands.entity(window).insert(SystemCursorIcon::Progress);
         }
         _ => {}
     }
diff --git a/crates/ferritin-onnx-models/src/models/esm2/mod.rs b/crates/ferritin-onnx-models/src/models/esm2/mod.rs
@@ -74,7 +74,7 @@ impl ESM2 {
         ort::init()
             .with_name("ESM2")
             .with_execution_providers([CUDAExecutionProvider::default().build()])
-            .commit()?;
+            .commit();
         Ok(Session::builder()?
             .with_optimization_level(GraphOptimizationLevel::Level1)?
             .with_intra_threads(1)?)
diff --git a/crates/ferritin-onnx-models/src/models/ligandmpnn/mod.rs b/crates/ferritin-onnx-models/src/models/ligandmpnn/mod.rs
@@ -73,7 +73,7 @@ impl LigandMPNN {
         ort::init()
             .with_name("LigandMPNN")
             .with_execution_providers([CUDAExecutionProvider::default().build()])
-            .commit()?;
+            .commit();
         Ok(Session::builder()?
             .with_optimization_level(GraphOptimizationLevel::Level1)?
             .with_intra_threads(1)?)
diff --git a/crates/ferritin-plms/src/esm/layers/blocks.rs b/crates/ferritin-plms/src/esm/layers/blocks.rs
@@ -129,7 +129,7 @@ impl UnifiedTransformerBlock {
     pub fn load(vb: VarBuilder, config: &ESMCConfig, layer: usize) -> Result<Self> {
         let ESMCConfig {
             ffn_type,
-            
+
             use_plain_attn,
             n_layers_geom,
             residue_scaling_factor,
diff --git a/crates/ferritin-plms/src/featurize/utilities.rs b/crates/ferritin-plms/src/featurize/utilities.rs
@@ -636,9 +636,7 @@ mod tests {
             ("OXT", (0, 0, 36, ..), vec![0.0, 0.0, 0.0]),
         ];
         for (atom_name, (b, i, j, k), expected) in allatom_coords {
-            let actual: Vec<f32> = ac_backbone_tensor
-                .i((b, i, j, k))?
-                .to_vec1()?;
+            let actual: Vec<f32> = ac_backbone_tensor.i((b, i, j, k))?.to_vec1()?;
             assert_eq!(actual, expected, "Mismatch for atom {}", atom_name);
         }
         Ok(())
diff --git a/crates/ferritin-structure-mesh/Cargo.toml b/crates/ferritin-structure-mesh/Cargo.toml
@@ -11,7 +11,7 @@ bevy = { workspace = true, optional = false, default-features = true }
 bon.workspace = true
 ferritin-core = { path = "../ferritin-core" }
 itertools.workspace = true
-rerun = { workspace = true, optional = false }
+# rerun = { workspace = true, optional = false }
 
 [features]
 default = []
diff --git a/crates/ferritin-structure-mesh/src/conversions.rs b/crates/ferritin-structure-mesh/src/conversions.rs
@@ -6,7 +6,6 @@
 //! Lifted and modified from: https://github.com/rerun-io/revy/blob/main/src/conversions.rs
 
 #[cfg(all(feature = "bevy", feature = "rerun"))]
-
 use bevy::{math::Vec3A, prelude::*, render::mesh::VertexAttributeValues};
 use itertools::Itertools;
 
diff --git a/crates/ferritin-structure-mesh/src/plugin.rs b/crates/ferritin-structure-mesh/src/plugin.rs
@@ -51,14 +51,14 @@ impl Plugin for StructurePlugin {
     fn build(&self, app: &mut App) {
         app.insert_resource(StructureFiles(self.initial_files.clone()))
             .add_systems(Startup, load_initial_proteins)
-            .add_event::<LoadProteinEvent>();
+            .add_message::<LoadProteinEvent>();
     }
 }
 
 #[derive(Resource)]
 struct StructureFiles(Vec<(PathBuf, StructureSettings)>);
 
-#[derive(Event)]
+#[derive(Message)]
 pub struct LoadProteinEvent(pub PathBuf);
 
 fn load_initial_proteins(
diff --git a/crates/ferritin-structure-mesh/src/structure.rs b/crates/ferritin-structure-mesh/src/structure.rs
@@ -5,8 +5,6 @@
 
 use super::ColorScheme;
 use bevy::prelude::*;
-use bevy::render::mesh::PrimitiveTopology;
-use bevy::render::render_asset::RenderAssetUsages;
 use bon::Builder;
 use ferritin_core::AtomCollection;
 
@@ -54,36 +52,96 @@ impl Structure {
         self.material.clone()
     }
 
-    // Placeholder implementations of rendering methods
+    // Rendering method implementations
     fn render_wireframe(&self) -> Mesh {
-        Mesh::new(PrimitiveTopology::LineList, RenderAssetUsages::default())
+        self.create_sphere_mesh(0.5)
     }
 
     fn render_cartoon(&self) -> Mesh {
-        Mesh::new(
-            PrimitiveTopology::TriangleList,
-            RenderAssetUsages::default(),
-        )
+        self.create_sphere_mesh(1.0)
     }
 
     fn render_ballandstick(&self) -> Mesh {
-        Mesh::new(
-            PrimitiveTopology::TriangleList,
-            RenderAssetUsages::default(),
-        )
+        self.create_sphere_mesh(0.3)
     }
 
     fn render_spheres(&self) -> Mesh {
-        Mesh::new(
-            PrimitiveTopology::TriangleList,
-            RenderAssetUsages::default(),
-        )
+        self.create_sphere_mesh(1.5)
     }
 
     fn render_putty(&self) -> Mesh {
-        Mesh::new(
-            PrimitiveTopology::TriangleList,
-            RenderAssetUsages::default(),
-        )
+        self.create_sphere_mesh(2.0)
+    }
+
+    /// Create a mesh with spheres at each atom position
+    fn create_sphere_mesh(&self, radius: f32) -> Mesh {
+        let mut positions = Vec::new();
+        let mut normals = Vec::new();
+        let mut uvs = Vec::new();
+        let mut indices = Vec::new();
+
+        let subdivisions = 8;
+
+        for idx in 0..self.pdb.get_size() {
+            let coord = self.pdb.get_coord(idx);
+            let center = Vec3::new(coord[0], coord[1], coord[2]);
+            let base_index = positions.len() as u32;
+
+            // Generate a sphere using UV sphere algorithm
+            for lat in 0..=subdivisions {
+                let theta = lat as f32 * std::f32::consts::PI / subdivisions as f32;
+                let sin_theta = theta.sin();
+                let cos_theta = theta.cos();
+
+                for lon in 0..=subdivisions {
+                    let phi = lon as f32 * 2.0 * std::f32::consts::PI / subdivisions as f32;
+                    let sin_phi = phi.sin();
+                    let cos_phi = phi.cos();
+
+                    let x = sin_theta * cos_phi;
+                    let y = cos_theta;
+                    let z = sin_theta * sin_phi;
+
+                    let normal = Vec3::new(x, y, z);
+                    let pos = center + normal * radius;
+
+                    positions.push([pos.x, pos.y, pos.z]);
+                    normals.push([normal.x, normal.y, normal.z]);
+                    uvs.push([
+                        lon as f32 / subdivisions as f32,
+                        lat as f32 / subdivisions as f32,
+                    ]);
+                }
+            }
+
+            // Generate indices for the sphere
+            for lat in 0..subdivisions {
+                for lon in 0..subdivisions {
+                    let first = base_index + lat * (subdivisions + 1) + lon;
+                    let second = first + subdivisions + 1;
+
+                    indices.push(first);
+                    indices.push(second);
+                    indices.push(first + 1);
+
+                    indices.push(second);
+                    indices.push(second + 1);
+                    indices.push(first + 1);
+                }
+            }
+        }
+
+        // Create mesh with proper vertex attributes
+        let mut mesh = Mesh::new(
+            bevy::mesh::PrimitiveTopology::TriangleList,
+            bevy::asset::RenderAssetUsages::default(),
+        );
+
+        mesh.insert_attribute(Mesh::ATTRIBUTE_POSITION, positions);
+        mesh.insert_attribute(Mesh::ATTRIBUTE_NORMAL, normals);
+        mesh.insert_attribute(Mesh::ATTRIBUTE_UV_0, uvs);
+        mesh.insert_indices(bevy::mesh::Indices::U32(indices));
+
+        mesh
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -49,7 +49,6 @@ fn main() -> Result<()> {`
`49`	`49`	`Ok(())`
`50`	`50`	`}`
`51`	`51`
`52`		`-`
`53`	`52`	`#[derive(Component)]`
`54`	`53`	`struct MainCamera;`
`55`	`54`