Dependency update

Cargo.toml

@@ -11,21 +11,21 @@ readme = "README.md"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-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"
+bevy = {version="0.14.0", 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 = "0.29.0"
+bevy_pancam = { version = "0.13.0", features = ["bevy_egui"] }
+bevy_prototype_lyon = "0.12.0"
 colorgrad = "0.6.2"
-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"
+itertools = "0.13.0"
+fastrand = "2.1.0"
+serde = "1.0.208"
+serde_json = "1.0.125"
+proc-macro2 = "1.0.86"
+chrono = "0.4.38"
 roarsvg = "0.4.1"
-anyhow = "1.0.80"
-image = "0.24.9"
-
+anyhow = "1.0.86"
+image = "0.25.2"
+thiserror="1.0"
 # dependencies exclusive for wasm32
 [target.'cfg(target_arch = "wasm32")'.dependencies]
 wasm-bindgen = { version = "0.2.92", features = ["serde", "serde-serialize"] }

src/aesthetics.rs

@@ -1,13 +1,15 @@
-use crate::escher::{ArrowTag, CircleTag, Hover, Tag};
-use crate::funcplot::{
-    build_grad, from_grad_clamped, lerp, max_f32, min_f32, path_to_vec, plot_box_point, plot_hist,
-    plot_kde, plot_line, plot_scales, zero_lerp, IgnoreSave,
+use crate::{
+    escher::{ArrowTag, CircleTag, Hover, Tag},
+    funcplot::{
+        build_grad, from_grad_clamped, lerp, max_f32, min_f32, path_to_vec, plot_box_point,
+        plot_hist, plot_kde, plot_line, plot_scales, zero_lerp, IgnoreSave,
+    },
+    geom::{
+        AesFilter, AnyTag, Drag, GeomArrow, GeomHist, GeomMetabolite, HistPlot, HistTag, PopUp,
+        Side, VisCondition, Xaxis,
+    },
+    gui::{or_color, ActiveData, UiState},
 };
-use crate::geom::{
-    AesFilter, AnyTag, Drag, GeomArrow, GeomHist, GeomMetabolite, HistPlot, HistTag, PopUp, Side,
-    VisCondition, Xaxis,
-};
-use crate::gui::{or_color, ActiveData, UiState};
 use itertools::Itertools;
 use std::collections::HashMap;
 
@@ -137,7 +139,7 @@ pub fn plot_arrow_color(
             if let Some(index) = aes.identifiers.iter().position(|r| r == tag.id()) {
                 stroke.color = from_grad_clamped(&grad, colors.0[index], min_val, max_val);
             } else {
-                stroke.color = Color::rgb(0.85, 0.85, 0.85);
+                stroke.color = Color::srgb(0.85, 0.85, 0.85);
             }
         }
     }
@@ -168,7 +170,7 @@ pub fn plot_metabolite_color(
             if let Some(index) = aes.identifiers.iter().position(|r| r == tag.id()) {
                 fill.color = from_grad_clamped(&grad, colors.0[index], min_val, max_val);
             } else {
-                fill.color = Color::rgb(0.85, 0.85, 0.85);
+                fill.color = Color::srgb(0.85, 0.85, 0.85);
             }
         }
     }
@@ -503,7 +505,7 @@ fn plot_side_hist(
                         },
                         ..default()
                     },
-                    Fill::color(Color::hex(hex).unwrap()),
+                    Fill::color(Srgba::hex(hex).unwrap()),
                     VisCondition {
                         condition: aes.condition.clone(),
                     },
@@ -686,7 +688,7 @@ fn plot_hover_hist(
                     },
                     ..default()
                 };
-                let fill = Fill::color(Color::hex("ffb73388").unwrap());
+                let fill = Fill::color(Srgba::hex("ffb73388").unwrap());
                 let scales = plot_scales(this_dist, 600., font.clone(), 12.);
                 commands
                     .spawn((
@@ -756,7 +758,7 @@ fn normalize_histogram_height(
                 Some(cond) => or_color(cond, color_ref, true),
                 None => or_color(&ui_condition, color_ref, false),
             };
-            Color::rgba_linear(color.r(), color.g(), color.b(), color.a())
+            Color::linear_rgba(color.r(), color.g(), color.b(), color.a())
         }
     }
 }

src/data.rs

@@ -1,21 +1,21 @@
 //! Input data logic.
 
-use std::collections::HashSet;
-
-use crate::aesthetics;
-use crate::escher::EscherMap;
-use crate::geom::{self, HistTag, Xaxis};
-use crate::geom::{AesFilter, GeomHist, HistPlot};
-use crate::info::Info;
-use bevy::asset::io::Reader;
-use bevy::asset::{AssetLoader, AsyncReadExt, LoadContext};
-use bevy::prelude::*;
-use bevy::reflect::TypePath;
-use bevy::utils::thiserror;
-use bevy::utils::BoxedFuture;
+use crate::{
+    aesthetics,
+    escher::EscherMap,
+    geom::{self, AesFilter, GeomHist, HistPlot, HistTag, Xaxis},
+    info::Info,
+};
+use bevy::{
+    asset::{io::Reader, AssetLoader, AsyncReadExt, LoadContext},
+    prelude::*,
+    reflect::TypePath,
+    utils::BoxedFuture,
+};
 use itertools::Itertools;
 use serde::Deserialize;
-
+use std::collections::HashSet;
+use thiserror::Error as ThisError;
 pub struct DataPlugin;
 
 impl Plugin for DataPlugin {
@@ -36,7 +36,7 @@ pub struct CustomAssetLoader<A> {
 
 /// Possible errors that can be produced by [`CustomAssetLoader`]
 #[non_exhaustive]
-#[derive(Debug, thiserror::Error)]
+#[derive(Debug, ThisError)]
 pub enum CustomJsonLoaderError {
     /// An [IO](std::io) Error
     #[error("Could not load asset: {0}")]
@@ -61,8 +61,8 @@ where
     ) -> BoxedFuture<'a, Result<Self::Asset, Self::Error>> {
         Box::pin(async move {
             let mut bytes = Vec::new();
-            reader.read_to_end(&mut bytes).await?;
-            let custom_asset = serde_json::from_slice::<A>(&bytes)?;
+            reader.read_to_end(&mut bytes).await.unwrap();
+            let custom_asset = serde_json::from_slice::<A>(&bytes).unwrap();
             Ok(custom_asset)
         })
     }
@@ -207,7 +207,7 @@ fn load_data(
     to_remove: Query<Entity, Or<(With<aesthetics::Aesthetics>, With<HistTag>, With<Xaxis>)>>,
 ) {
     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) {
+        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;

src/escher.rs

@@ -1,19 +1,20 @@
 //! Data model of escher JSON maps
 //! TODO: borrow strings
-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 crate::{
+    funcplot::draw_arrow,
+    geom::{GeomHist, HistTag, Side, Xaxis},
+    info::Info,
+    scale::DefaultFontSize,
+};
+use bevy::{prelude::*, reflect::TypePath};
 use bevy_prototype_lyon::prelude::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 use std::{cmp::Ordering, collections::HashMap};
 
-pub const ARROW_COLOR: Color = Color::rgba(95. / 255., 94. / 255., 95. / 255., 1.0);
-pub const MET_COLOR: Color = Color::rgb(190. / 255., 185. / 255., 185. / 255.);
-pub const MET_STROK: Color = Color::rgb(95. / 255., 94. / 255., 95. / 255.);
+pub const ARROW_COLOR: Color = Color::srgba(95. / 255., 94. / 255., 95. / 255., 1.0);
+pub const MET_COLOR: Color = Color::srgb(190. / 255., 185. / 255., 185. / 255.);
+pub const MET_STROK: Color = Color::srgb(95. / 255., 94. / 255., 95. / 255.);
 
 pub struct EscherPlugin;
 
@@ -373,7 +374,7 @@ pub fn load_map(
     mut existing_geom_hist: Query<&mut GeomHist>,
 ) {
     let custom_asset = custom_assets.get_mut(&state.escher_map);
-    if let (Some(bevy::asset::LoadState::Failed), false) =
+    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.");

src/funcplot.rs

@@ -274,7 +274,7 @@ pub fn plot_scales(samples: &[f32], size: f32, font: Handle<Font>, font_size: f3
         size,
         font,
         font_size,
-        Color::rgb(51. / 255., 78. / 255., 107. / 255.),
+        Color::srgb(51. / 255., 78. / 255., 107. / 255.),
     )
 }
 
@@ -346,7 +346,7 @@ fn to_grad(col: &bevy_egui::egui::Rgba) -> GradColor {
 pub fn from_grad_clamped(grad: &Gradient, t: f32, min_val: f32, max_val: f32) -> Color {
     let t = f32::clamp(t, min_val, max_val) as f64;
     let rgba = grad.at(t).to_linear_rgba();
-    Color::rgba(rgba.0 as f32, rgba.1 as f32, rgba.2 as f32, rgba.3 as f32)
+    Color::srgba(rgba.0 as f32, rgba.1 as f32, rgba.2 as f32, rgba.3 as f32)
 }
 
 /// Build a `Gradient` for color interpolation between two colors from

src/gui.rs

@@ -1,16 +1,22 @@
 //! Gui (windows and panels) to upload data and hover.
 
-use crate::data::{Data, ReactionState};
-use crate::escher::{ArrowTag, EscherMap, Hover, MapState, NodeToText, ARROW_COLOR};
-use crate::extra_egui::NewTabHyperlink;
-use crate::geom::{AnyTag, Drag, HistTag, VisCondition, Xaxis};
-use crate::info::Info;
-use crate::screenshot::ScreenshotEvent;
-use bevy::prelude::*;
-use bevy::window::PrimaryWindow;
-use bevy_egui::egui::color_picker::{color_edit_button_rgba, Alpha};
-use bevy_egui::egui::epaint::Rgba;
-use bevy_egui::{egui, EguiContexts, EguiPlugin, EguiSettings};
+use crate::{
+    data::{Data, ReactionState},
+    escher::{ArrowTag, EscherMap, Hover, MapState, NodeToText, ARROW_COLOR},
+    extra_egui::NewTabHyperlink,
+    geom::{AnyTag, Drag, HistTag, VisCondition, Xaxis},
+    info::Info,
+    screenshot::ScreenshotEvent,
+};
+use bevy::{prelude::*, window::PrimaryWindow};
+use bevy_egui::{
+    egui,
+    egui::{
+        color_picker::{color_edit_button_rgba, Alpha},
+        epaint::Rgba,
+    },
+    EguiContexts, EguiPlugin, EguiSettings,
+};
 use bevy_prototype_lyon::prelude::Path;
 use chrono::offset::Utc;
 use itertools::Itertools;
@@ -44,7 +50,7 @@ impl Plugin for GuiPlugin {
         building.add_systems(Update, (listen_js_escher, listen_js_data, listen_js_info));
     }
 }
-const HIGH_COLOR: Color = Color::rgb(183. / 255., 210. / 255., 255.);
+const HIGH_COLOR: Color = Color::srgb(183. / 255., 210. / 255., 255.);
 
 /// Retrieve a mutable reference to the color or insert
 /// * a random color with the alpha that is already in the map at the empty string; or
@@ -507,11 +513,11 @@ fn mouse_click_ui_system(
             Interaction::Hovered | Interaction::Pressed => {
                 drag.dragged = mouse_button_input.pressed(MouseButton::Middle);
                 drag.rotating = mouse_button_input.pressed(MouseButton::Right);
-                *background_color = BackgroundColor(Color::rgba(0.9, 0.9, 0.9, 0.2));
+                *background_color = BackgroundColor(Color::srgba(0.9, 0.9, 0.9, 0.2));
             }
             _ => {
                 drag.dragged &= mouse_button_input.pressed(MouseButton::Middle);
-                *background_color = BackgroundColor(Color::rgba(1.0, 1.0, 1.0, 0.0));
+                *background_color = BackgroundColor(Color::srgba(1.0, 1.0, 1.0, 0.0));
             }
         }
     }

src/info.rs

@@ -2,7 +2,7 @@
 use crate::funcplot::{lerp, IgnoreSave};
 use std::time::Duration;
 
-use bevy::prelude::*;
+use bevy::{color::palettes::css, prelude::*};
 
 pub struct InfoPlugin;
 impl Plugin for InfoPlugin {
@@ -72,7 +72,7 @@ fn spawn_info_box(mut commands: Commands, top: f32, right: f32) {
             },
             focus_policy: bevy::ui::FocusPolicy::Block,
             z_index: ZIndex::Global(10),
-            background_color: BackgroundColor(Color::DARK_GRAY),
+            background_color: BackgroundColor(css::DARK_GRAY.into()),
             ..Default::default()
         })
         .insert(InfoBox)
@@ -105,7 +105,7 @@ fn display_information(
                 TextStyle {
                     font: font.clone(),
                     font_size: 20.,
-                    color: Color::hex("F49596").unwrap(),
+                    color: Srgba::hex("F49596").unwrap().into(),
                 },
             );
         }
@@ -138,12 +138,15 @@ fn pop_infobox(
             }
         }
         // fade out
-        color.0.set_a(lerp(
-            info_state.timer.elapsed_secs(),
-            0.,
-            info_state.timer.duration().as_secs_f32(),
-            1.,
-            0.,
-        ));
+        color
+            .0
+            .set(Box::new(lerp(
+                info_state.timer.elapsed_secs(),
+                0.,
+                info_state.timer.duration().as_secs_f32(),
+                1.,
+                0.,
+            )))
+            .unwrap();
     }
 }

src/legend/mod.rs

@@ -235,7 +235,7 @@ fn color_legend_histograms(
                             let image = images.get_mut(&img_legend.texture).unwrap();
                             if condition == "ALL" {
                                 // show all conditions laminating the legend
-                                background_color.0 = Color::rgba_linear(1., 1., 1., 1.);
+                                background_color.0 = Color::linear_rgba(1., 1., 1., 1.);
                                 let conditions = ui_state.conditions.clone();
                                 let color_ref = match side {
                                     Side::Left => &mut ui_state.color_left,
@@ -251,13 +251,17 @@ fn color_legend_histograms(
                                         // depending on the order of execution, the colors
                                         // might have not been initialized by the histogram plotter
                                         let cl = or_color(k, color_ref, true);
-                                        let c = Color::rgba_linear(cl.r(), cl.g(), cl.b(), cl.a())
-                                            .as_rgba();
+                                        let c = Srgba::from(Color::linear_rgba(
+                                            cl.r(),
+                                            cl.g(),
+                                            cl.b(),
+                                            cl.a(),
+                                        ));
                                         [
-                                            (c.r() * 255.) as u8,
-                                            (c.g() * 255.) as u8,
-                                            (c.b() * 255.) as u8,
-                                            (c.a() * 255.) as u8,
+                                            (c.red * 255.) as u8,
+                                            (c.green * 255.) as u8,
+                                            (c.blue * 255.) as u8,
+                                            (c.alpha * 255.) as u8,
                                         ]
                                     })
                                     .collect();
@@ -276,7 +280,7 @@ fn color_legend_histograms(
                                     });
                                 image.data = data.collect::<Vec<u8>>();
                             } else {
-                                if background_color.0 == Color::rgba_linear(1., 1., 1., 1.) {
+                                if background_color.0 == Color::linear_rgba(1., 1., 1., 1.) {
                                     // previous condition was ALL (or never changed)
                                     // reset the image data that was painted with colors
                                     let data = image.data.chunks(4).flat_map(|pixel| {
@@ -295,7 +299,7 @@ fn color_legend_histograms(
                                         _ => panic!("unexpected side"),
                                     };
                                     let color = or_color(&condition, ref_col, true);
-                                    Color::rgba_linear(color.r(), color.g(), color.b(), color.a())
+                                    Color::linear_rgba(color.r(), color.g(), color.b(), color.a())
                                 };
                             }
                         }
@@ -412,7 +416,7 @@ fn display_conditions(
                             TextStyle {
                                 font: font.clone(),
                                 font_size: 12.,
-                                color: Color::hex("504d50").unwrap(),
+                                color: Srgba::hex("504d50").unwrap().into(),
                             },
                         ),
                         ..Default::default()