Update dependencies versions and fix CI

[bowenszhu]

Checklist

• [ ] Appropriate tests were added
• [x] Any code changes were done in a way that does not break public API
• [ ] All documentation related to code changes were updated
• [ ] The new code follows the contributor guidelines, in particular the SciML Style Guide and COLPRAC.
• [ ] Any new documentation only uses public API

Additional context

Add any other context about the problem here.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 89.65517% with 3 lines in your changes missing coverage. Please review.

Project coverage is 69.01%. Comparing base (36d0ed5) to head (fc81b89).

Files	Patch %	Lines
src/utils.jl	88.00%	3 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##            main      #89       +/-   ##
==========================================
+ Coverage   0.50%   69.01%   +68.51%     
==========================================
  Files          6        6               
  Lines        200      213       +13     
==========================================
+ Hits           1      147      +146     
+ Misses       199       66      -133     

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[ChrisRackauckas-Claude]

Breaking Changes Fixed

I've successfully identified and fixed all the remaining breaking changes for ModelingToolkit v9 compatibility. Here are the additional changes needed beyond what's already in this PR:

1. Fix test dependencies (test/DataReduction.jl)

# Replace
using DifferentialEquations
# With  
using OrdinaryDiffEq

2. Fix ODEProblem creation (test/deim.jl)

# Replace
deim_prob = ODEProblem(deim_sys, nothing, tspan)
# With
deim_prob = ODEProblem(complete(deim_sys), nothing, tspan)

3. Fix deprecated SymbolicUtils functions (src/utils.jl)

# Add import at top of file
using ModelingToolkit: iscall, operation

# Replace deprecated istree with iscall
if iscall(eq.lhs) && operation(eq.lhs) isa Differential

Test Results ✅

After applying these fixes, all tests now pass:

• ✅ Quality Assurance: 10/10 tests passed
• ✅ POD: 15/15 tests passed
• ✅ utils: 13/13 tests passed
• ✅ DEIM: 4/4 tests passed

The key breaking changes handled:

• ModelingToolkit v9.0: get_states → get_unknowns (already in PR)
• ModelingToolkit v9.0: Systems must be completed before ODEProblem creation
• SymbolicUtils: istree deprecated, replaced with iscall
• Test dependencies: DifferentialEquations → OrdinaryDiffEq

All functionality is preserved and working correctly with the updated dependency versions.