Chore: Update to bevy 0.13.0

Cargo.toml

@@ -11,19 +11,20 @@ readme = "README.md"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-bevy = {version="0.11", features = ["bevy_render", "bevy_core_pipeline", "bevy_asset", "bevy_sprite", "bevy_winit", "png", "x11", "bevy_ui", "tga", "bmp", "jpeg", "webgl2"], default-features=false }
-bevy_egui = "0.21"
-bevy_pancam = { git = "https://github.com/johanhelsing/bevy_pancam.git", rev="8b6263dcf634dfcc26954c5d712b88a6d7d43e29", features = ["bevy_egui"] }
-bevy_prototype_lyon = "0.9.0"
+bevy = {version="0.13", features = ["multi-threaded", "bevy_render", "bevy_core_pipeline", "bevy_asset", "bevy_sprite", "bevy_winit", "png", "x11", "bevy_ui", "tga", "bmp", "jpeg", "webgl2"], default-features=false }
+bevy_egui = "0.25"
+bevy_pancam = { version = "0.11.0", features = ["bevy_egui"] }
+bevy_prototype_lyon = "0.11.0"
 colorgrad = "0.6.2"
-itertools = "0.10.5"
-fastrand = "1.8.0"
-serde = "1.0.147"
-serde_json = "1.0.88"
-proc-macro2 = "1.0.43"
-chrono = "0.4.31"
+itertools = "0.12.1"
+fastrand = "2.0.1"
+serde = "1.0.197"
+serde_json = "1.0.114"
+proc-macro2 = "1.0.76"
+chrono = "0.4.35"
 roarsvg = "0.4.1"
-image = "0.24.6"
+anyhow = "1.0.80"
+image = "0.24.9"
 
 # dependencies exclusive for wasm32
 [target.'cfg(target_arch = "wasm32")'.dependencies]

README.md

@@ -42,11 +42,11 @@ distinction between color and size, it is simply that they are not independently
 
 ## How to use
 
-Shu is distributed both through a web app (preview build at https://carrascomj.github.io/shu) and as standalone
+Shu is distributed both through a web app (preview build at https://biosustain.github.io/shu) and as standalone
 native application. To use the latter, download the [latest release for your operating system](https://github.com/biosustain/shu/releases/latest), unpack if necessary and run it as executable.
 
 Documentation for the rust crate and the python API will be made available once they are published. In the meantime, a preview
-of the python documentation can be found at https://carrascomj.github.io/shu/docs.
+of the python documentation can be found at https://biosustain.github.io/shu/docs.
 
 ### Building from source (latest master commit)
 

src/aesthetics.rs

@@ -218,7 +218,7 @@ fn restore_geoms<T: Tag>(
         Query<&mut Stroke, (With<T>, Without<Fill>)>,
     )>,
 ) {
-    for _ in restore_event.iter() {
+    for _ in restore_event.read() {
         for (mut fill, mut path) in query.p0().iter_mut() {
             // met colors
             fill.color = T::default_color();
@@ -496,8 +496,11 @@ fn plot_side_hist(
                     ShapeBundle {
                         path: GeometryBuilder::build_as(&line),
                         // increment z to avoid flickering problems
-                        transform: trans
-                            .with_translation(trans.translation + Vec3::new(0., 0., *z_eps)),
+                        spatial: SpatialBundle {
+                            transform: trans
+                                .with_translation(trans.translation + Vec3::new(0., 0., *z_eps)),
+                            ..default()
+                        },
                         ..default()
                     },
                     Fill::color(Color::hex(hex).unwrap()),
@@ -568,7 +571,10 @@ fn plot_side_box(
                     (
                         ShapeBundle {
                             path: GeometryBuilder::build_as(&line_box),
-                            transform: trans.with_scale(Vec3::new(1., 1., 1.)),
+                            spatial: SpatialBundle {
+                                transform: trans.with_scale(Vec3::new(1., 1., 1.)),
+                                ..default()
+                            },
                             ..default()
                         },
                         Fill::color(color),
@@ -594,7 +600,10 @@ fn plot_side_box(
                     (
                         ShapeBundle {
                             path: GeometryBuilder::build_as(&shape),
-                            transform: trans.with_scale(Vec3::new(1., 1., 1.)),
+                            spatial: SpatialBundle {
+                                transform: trans.with_scale(Vec3::new(1., 1., 1.)),
+                                ..default()
+                            },
                             ..default()
                         },
                         Fill::color(color),
@@ -670,8 +679,11 @@ fn plot_hover_hist(
                 );
                 let geometry = ShapeBundle {
                     path: GeometryBuilder::build_as(&line),
-                    transform,
-                    visibility: Visibility::Hidden,
+                    spatial: SpatialBundle {
+                        transform,
+                        visibility: Visibility::Hidden,
+                        ..default()
+                    },
                     ..default()
                 };
                 let fill = Fill::color(Color::hex("ffb73388").unwrap());
@@ -841,8 +853,9 @@ fn follow_the_axes(
     for (axis_trans, axis) in axes.iter() {
         for (mut trans, hist) in hists.iter_mut() {
             if (axis.node_id == hist.node_id) & (hist.side == axis.side) {
-                trans.translation = axis_trans.translation;
-                trans.rotation = axis_trans.rotation;
+                // z has to be maintained per element in the axis to avoid flickering
+                trans.translation.x = axis_trans.translation.x;
+                trans.translation.y = axis_trans.translation.y;
                 if hist.follow_scale {
                     trans.scale.x = axis_trans.scale.x;
                 }

src/data.rs

@@ -7,9 +7,11 @@ use crate::escher::EscherMap;
 use crate::geom::{self, HistTag, Xaxis};
 use crate::geom::{AesFilter, GeomHist, HistPlot};
 use crate::info::Info;
-use bevy::asset::{AssetLoader, LoadContext, LoadedAsset};
+use bevy::asset::io::Reader;
+use bevy::asset::{AssetLoader, AsyncReadExt, LoadContext};
 use bevy::prelude::*;
-use bevy::reflect::{TypePath, TypeUuid};
+use bevy::reflect::TypePath;
+use bevy::utils::thiserror;
 use bevy::utils::BoxedFuture;
 use itertools::Itertools;
 use serde::Deserialize;
@@ -18,10 +20,10 @@ pub struct DataPlugin;
 
 impl Plugin for DataPlugin {
     fn build(&self, app: &mut App) {
-        app.add_asset::<EscherMap>()
-            .add_asset::<Data>()
-            .add_asset_loader(CustomAssetLoader::<EscherMap>::new(vec!["json"]))
-            .add_asset_loader(CustomAssetLoader::<Data>::new(vec!["metabolism.json"]))
+        app.init_asset::<EscherMap>()
+            .init_asset::<Data>()
+            .register_asset_loader(CustomAssetLoader::<EscherMap>::new(vec!["json"]))
+            .register_asset_loader(CustomAssetLoader::<Data>::new(vec!["metabolism.json"]))
             .add_systems(PostUpdate, load_data);
     }
 }
@@ -32,19 +34,36 @@ pub struct CustomAssetLoader<A> {
     _mark: std::marker::PhantomData<A>,
 }
 
+/// Possible errors that can be produced by [`CustomAssetLoader`]
+#[non_exhaustive]
+#[derive(Debug, thiserror::Error)]
+pub enum CustomJsonLoaderError {
+    /// An [IO](std::io) Error
+    #[error("Could not load asset: {0}")]
+    Io(#[from] std::io::Error),
+    /// A [RON](ron) Error
+    #[error("Could not parse JSON: {0}")]
+    JsonSpannedError(#[from] serde_json::Error),
+}
+
 impl<A> AssetLoader for CustomAssetLoader<A>
 where
     for<'de> A: serde::Deserialize<'de> + bevy::asset::Asset,
 {
+    type Asset = A;
+    type Settings = ();
+    type Error = CustomJsonLoaderError;
     fn load<'a>(
         &'a self,
-        bytes: &'a [u8],
-        load_context: &'a mut LoadContext,
-    ) -> BoxedFuture<'a, Result<(), bevy::asset::Error>> {
+        reader: &'a mut Reader,
+        _settings: &'a (),
+        _load_context: &'a mut LoadContext,
+    ) -> BoxedFuture<'a, Result<Self::Asset, Self::Error>> {
         Box::pin(async move {
-            let custom_asset = serde_json::from_slice::<A>(bytes)?;
-            load_context.set_default_asset(LoadedAsset::new(custom_asset));
-            Ok(())
+            let mut bytes = Vec::new();
+            reader.read_to_end(&mut bytes).await?;
+            let custom_asset = serde_json::from_slice::<A>(&bytes)?;
+            Ok(custom_asset)
         })
     }
 
@@ -93,8 +112,7 @@ impl Number {
 }
 
 /// Metabolic data from the user that can be read from a `file.metabolism.json`.
-#[derive(Deserialize, TypeUuid, Default, TypePath)]
-#[uuid = "413be529-bfeb-41a3-8db0-4b8b382a2c46"]
+#[derive(Deserialize, Asset, Default, TypePath)]
 pub struct Data {
     /// Vector of reactions' identifiers
     reactions: Option<Vec<String>>,
@@ -188,14 +206,14 @@ fn load_data(
     // remove data to be plotted, axes and histograms
     to_remove: Query<Entity, Or<(With<aesthetics::Aesthetics>, With<HistTag>, With<Xaxis>)>>,
 ) {
-    let custom_asset = if let Some(reac_handle) = &mut state.reaction_data {
-        if asset_server.get_load_state(&*reac_handle) == bevy::asset::LoadState::Failed {
+    let custom_asset = if let Some(reac_handle) = &state.reaction_data {
+        if let Some(bevy::asset::LoadState::Failed) = asset_server.get_load_state(reac_handle) {
             info_state
                 .notify("Failed loading data! Check if your metabolism.json is in correct format.");
             state.reaction_data = None;
             return;
         }
-        custom_assets.get_mut(reac_handle)
+        custom_assets.get_mut(reac_handle.id())
     } else {
         return;
     };

src/escher.rs

@@ -4,8 +4,8 @@ use crate::funcplot::draw_arrow;
 use crate::geom::{GeomHist, HistTag, Side, Xaxis};
 use crate::info::Info;
 use crate::scale::DefaultFontSize;
+use bevy::prelude::*;
 use bevy::reflect::TypePath;
-use bevy::{prelude::*, reflect::TypeUuid};
 use bevy_prototype_lyon::prelude::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
@@ -37,8 +37,7 @@ pub struct NodeToText {
     pub inner: HashMap<u64, Entity>,
 }
 
-#[derive(Deserialize, TypeUuid, Default, Serialize, TypePath)]
-#[uuid = "413be529-bfeb-41b3-9db0-4b8b380a2c46"]
+#[derive(Deserialize, Asset, Default, Serialize, TypePath)]
 pub struct EscherMap {
     #[allow(dead_code)]
     info: EscherInfo,
@@ -314,7 +313,7 @@ fn build_text_tag(
             color: ARROW_COLOR,
         },
     )
-    .with_alignment(TextAlignment::Center);
+    .with_justify(JustifyText::Center);
     (
         Text2dBundle {
             text,
@@ -374,8 +373,8 @@ pub fn load_map(
     mut existing_geom_hist: Query<&mut GeomHist>,
 ) {
     let custom_asset = custom_assets.get_mut(&state.escher_map);
-    if (asset_server.get_load_state(&state.escher_map) == bevy::asset::LoadState::Failed)
-        & !state.loaded
+    if let (Some(bevy::asset::LoadState::Failed), false) =
+        (asset_server.get_load_state(&state.escher_map), state.loaded)
     {
         info_state.notify("Failed loading map! Check that you JSON is correct.");
         state.loaded = true;
@@ -432,7 +431,10 @@ pub fn load_map(
         commands.spawn((
             ShapeBundle {
                 path: GeometryBuilder::build_as(&shape),
-                transform: Transform::from_xyz(met.x - center_x, -met.y + center_y, 2. + z_eps),
+                spatial: SpatialBundle {
+                    transform: Transform::from_xyz(met.x - center_x, -met.y + center_y, 2. + z_eps),
+                    ..default()
+                },
                 ..Default::default()
             },
             Fill::color(MET_COLOR),
@@ -531,7 +533,10 @@ pub fn load_map(
         commands.spawn((
             ShapeBundle {
                 path: builder.build(),
-                transform: Transform::from_xyz(ori.x - center_x, ori.y + center_y, 1. + z_eps),
+                spatial: SpatialBundle {
+                    transform: Transform::from_xyz(ori.x - center_x, ori.y + center_y, 1. + z_eps),
+                    ..Default::default()
+                },
                 ..Default::default()
             },
             Stroke::new(ARROW_COLOR, 10.0),

src/funcplot.rs

@@ -1,7 +1,7 @@
 //! Functions for plotting data.
 
 use bevy::prelude::{
-    Color, Component, Font, Handle, Text, Text2dBundle, TextStyle, Transform, Vec2,
+    Color, Component, Font, Handle, SpatialBundle, Text, Text2dBundle, TextStyle, Transform, Vec2,
 };
 use bevy_prototype_lyon::{
     entity::ShapeBundle,
@@ -249,8 +249,11 @@ pub fn plot_line(size: f32, transform: Transform) -> (ShapeBundle, Stroke) {
     (
         ShapeBundle {
             path: GeometryBuilder::build_as(&path_builder.build()),
-            visibility: bevy::prelude::Visibility::Hidden,
-            transform,
+            spatial: SpatialBundle {
+                visibility: bevy::prelude::Visibility::Hidden,
+                transform,
+                ..Default::default()
+            },
             ..Default::default()
         },
         Stroke::color(Color::BLACK),