update to catalyst 16, removed mtk dep, --update-manifests option in dev.sh

Author: nifets

VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

backend/Manifest-v1.11.toml

@@ -1,6 +1,6 @@
 name = "GRSServer"
 uuid = "86ab0978-0466-42e7-a2ae-38e617ed6ea3"
-version = "0.1.1"
+version = "0.1.2"
 authors = ["nifets <stefanmanol@gmail.com>", "lmshk "]
 
 [deps]
@@ -13,7 +13,6 @@ HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
-ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 Oxygen = "df9a0d86-3283-4920-82dc-4555fc0d1d8b"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
@@ -24,14 +23,13 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [compat]
 Arrow = "2.8.0"
-Catalyst = "15.0.11"
+Catalyst = "16"
 Colors = "0.13.1"
 Dates = "1.11.0"
 GeneRegulatorySystems = "0.4.0"
 JSON = "1.3.0"
 Logging = "1.11.0"
 LoggingExtras = "1.2.0"
-ModelingToolkit = "9.84.0"
 MultivariateStats = "0.10.4"
 Oxygen = "1.10.0"
 Setfield = "1.1.2"

backend/Manifest-v1.12.toml

@@ -1,7 +1,6 @@
 module NetworkRepresentation
 
 using Catalyst
-using ModelingToolkit
 
 using GeneRegulatorySystems.Models
 using GeneRegulatorySystems.Models: Wrapped, Instant
@@ -58,7 +57,7 @@ struct SpeciesId
 end
 
 function SpeciesId(s::SymbolicUtils.BasicSymbolic)
-    SpeciesId(normalize_name(strip_time(Symbol(s))))
+    SpeciesId(strip_time(normalize_name(s)))
 end
 
 function species_components(name::Symbol)

backend/Project.toml

@@ -4,9 +4,10 @@ set -euo pipefail
 # Development launcher for the GRS app.
 #
 # Usage:
-#   ./dev.sh              Start Vite frontend + Julia backend (browser mode)
-#   ./dev.sh --tauri      Start via Tauri (desktop window, Julia spawned by Rust)
-#   ./dev.sh --sync-version   Update all package files from VERSION
+#   ./dev.sh                    Start Vite frontend + Julia backend (browser mode)
+#   ./dev.sh --tauri            Start via Tauri (desktop window, Julia spawned by Rust)
+#   ./dev.sh --sync-version     Update all package files from VERSION
+#   ./dev.sh --update-manifests Regenerate Manifest-v1.11.toml and Manifest-v1.12.toml
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
 FRONTEND_DIR="$SCRIPT_DIR/frontend"
@@ -61,6 +62,26 @@ if [ "${1:-}" = "--sync-version" ]; then
     exit 0
 fi
 
+if [ "${1:-}" = "--update-manifests" ]; then
+    CHANNELS=$(juliaup status 2>/dev/null | awk 'NR>2 && $0 !~ /^-/ { for(i=1;i<=NF;i++) if ($i ~ /^[0-9]+\.[0-9]+$/ || $i == "release" || $i == "lts") { print $i; break } }')
+    if [ -z "$CHANNELS" ]; then
+        echo "[dev.sh] Could not detect juliaup channels. Is juliaup installed?"
+        exit 1
+    fi
+    for CHANNEL in $CHANNELS; do
+        MINOR=$(julia +${CHANNEL} --version 2>/dev/null | sed 's/julia version \([0-9]*\.[0-9]*\).*/\1/')
+        if [ -z "$MINOR" ]; then
+            echo "[dev.sh] Could not determine version for channel ${CHANNEL}, skipping."
+            continue
+        fi
+        echo "[dev.sh] Updating Manifest-v${MINOR}.toml (channel: ${CHANNEL})..."
+        rm -f "$BACKEND_DIR/Manifest-v${MINOR}.toml"
+        touch "$BACKEND_DIR/Manifest-v${MINOR}.toml"
+        (cd "$BACKEND_DIR" && julia +${CHANNEL} --project=. -e 'using Pkg; Pkg.resolve(); Pkg.instantiate()')
+    done
+    exit 0
+fi
+
 # ============================================================================
 # Prerequisite checks
 # ============================================================================
@@ -102,11 +123,16 @@ if [ ! -d "$FRONTEND_DIR/node_modules" ]; then
     (cd "$FRONTEND_DIR" && npm install)
 fi
 
-# --- Backend: Julia Pkg.instantiate ---
+# --- Backend: Julia Pkg setup ---
+
+JULIA_MINOR=$(echo "$JULIA_VERSION" | sed 's/\([0-9]*\.[0-9]*\).*/\1/')
+VERSIONED_MANIFEST="$BACKEND_DIR/Manifest-v${JULIA_MINOR}.toml"
 
-if [ ! -f "$BACKEND_DIR/Manifest.toml" ]; then
-    echo "[dev.sh] Instantiating Julia backend dependencies..."
-    (cd "$BACKEND_DIR" && julia --project=. -e 'using Pkg; Pkg.instantiate()')
+if [ ! -f "$VERSIONED_MANIFEST" ] || [ "$BACKEND_DIR/Project.toml" -nt "$VERSIONED_MANIFEST" ]; then
+    echo "[dev.sh] Resolving Julia backend dependencies for v${JULIA_MINOR}..."
+    rm -f "$VERSIONED_MANIFEST"
+    touch "$VERSIONED_MANIFEST"
+    (cd "$BACKEND_DIR" && julia --project=. -e 'using Pkg; Pkg.resolve(); Pkg.instantiate()')
 fi
 
 # ============================================================================

backend/src/network_representation.jl

@@ -1,7 +1,7 @@
 {
   "name": "grs-frontend",
   "private": true,
-  "version": "0.1.1",
+  "version": "0.1.2",
   "type": "module",
   "scripts": {
     "dev": "vite",

dev.sh

@@ -1,6 +1,6 @@
 [package]
 name = "GRS-App"
-version = "0.1.1"
+version = "0.1.2"
 description = "Gene Regulatory Systems"
 authors = ["nifets", "lmshk"]
 license = ""