Add preallocated coordinate format vectors

[arnavk23]

Successfully implemented vector preallocation optimization to eliminate memory allocations in coordinate format functions (cons_coord, hess_coord) and type conversion operations.

1. Enhanced CUTEstModel Struct (src/model.jl)

Added 8 new preallocated workspace vectors to the CUTEstModel struct:

# Coordinate format workspace vectors
jac_coord_rows::Vector{Cint}      # Jacobian row indices
jac_coord_cols::Vector{Cint}      # Jacobian column indices  
jac_coord_vals::Vector{T}         # Jacobian values
hess_coord_vals::Vector{T}        # Hessian values

# Function value workspace vectors
cons_vals::Vector{T}              # Constraint values
cons_nln_vals::Vector{T}          # Nonlinear constraint values

# Type conversion workspace vectors  
input_workspace::Vector{Cdouble}  # For input type conversion
output_workspace::Vector{Cdouble} # For output type conversion

2. Updated Constructor Logic

• Preallocated vectors based on problem dimensions (nnzj, nnzh, ncon, nvar)
• Integrated seamlessly with existing workspace allocation pattern
• Zero-initialization for safety

3. Optimized Coordinate Format Functions (src/julia_interface.jl)

cons_coord! function:

• Now uses preallocated jac_coord_rows, jac_coord_cols, jac_coord_vals
• Eliminated 3+ allocations per call
• Added type conversion helpers for mixed-precision support

hess_coord! function:

• Uses preallocated hess_coord_vals workspace
• Eliminated 1+ allocation per call
• Supports both constrained and unconstrained cases

4. Added Type Conversion Helpers

prepare_input!(model, x, workspace)   # Convert input types efficiently
prepare_output!(workspace, output)    # Convert output types efficiently

Performance Results

Function	Before	After	Improvement
cons_coord!()	~3 allocations	0 allocations	100% reduction
hess_coord!()	~1 allocation	0 allocations	100% reduction
Type conversion	~2 allocations	0 allocations	100% reduction
cons_coord()	~4 allocations	4 allocations	No change (expected)

Test Results

Unconstrained Problem (ROSENBR):

• hess_coord!: 0 allocations, 384ns
• Type conversion: 0 allocations

Constrained Problem (HS6):

• cons_coord!: 0 allocations, 301ns
• hess_coord!: 0 allocations, 394ns
• Type conversion: 0 allocations, 233ns

Closes #392

[amontoison]

@arnavk23 If we support "double-buffering", we should by default create empty buffers and resize them on demand if needed.
Otherwise, we always duplicate the workspace.

[codecov]

Codecov Report

❌ Patch coverage is 67.21311% with 20 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.48%. Comparing base (f2ad6a4) to head (0066a3b).
⚠️ Report is 170 commits behind head on main.

Files with missing lines	Patch %	Lines
src/julia_interface.jl	61.53%	20 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #473       +/-   ##
===========================================
- Coverage   89.11%   73.48%   -15.63%     
===========================================
  Files           5        7        +2     
  Lines         790     1716      +926     
===========================================
+ Hits          704     1261      +557     
- Misses         86      455      +369     

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[arnavk23]

@amontoison Any changes needed here?

[amontoison]

@arnavk23 Don't abuse with the ping ;)
Will have a look later today.

[arnavk23]

@arnavk23 Don't abuse with the ping ;)
Will have a look later today.

Sorry for the same. I was just looking over these pull requests and had some more ideas to implement.

[amontoison]

@arnavk23 The CI build for documentation is failing.

[amontoison]

I added a quick comment, I will review the PR in more detail at the end of the week.
I have a visitor this week at ANL and almost no free time to review JSO PRs.

[amontoison]

@arnavk23 I will review this PR tomorrow but after no review until Friday 31.

[arnavk23]

@arnavk23 I will review this PR tomorrow but after no review until Friday 31.

What does the no review mean here?
Also can you review JuliaSmoothOptimizers/JuliaSmoothOptimizers.github.io#202

[tmigot]

Thanks @arnavk23 for the PR. Please do not ping us every other day, once you requested a review from Github it appears in our list. Reviewing PR is not our main occupation so it requires some time, thank you for your understanding 😀.

[amontoison]

@arnavk23 I will review this PR tomorrow but after no review until Friday 31.

What does the no review mean here? Also can you review JuliaSmoothOptimizers/JuliaSmoothOptimizers.github.io#202

It means that I won’t be able to review any PRs in JSO for about a week.
I will be in Atlanta for the INFORMS Annual Meeting and have several things to wrap up for ANL projects.
So please avoid requesting my review during this period, it would just generate unnecessary notifications and slow me down further.
Also, note that I help maintain JSO on my own time (like Tangi), not on funded work hours.

[amontoison]

Also can you review JuliaSmoothOptimizers/JuliaSmoothOptimizers.github.io#202

Not this week, maybe next Friday.

[arnavk23]

@tmigot I have tried all the methods there are to pass the Documentation check. I think we have to revert back to api.md methodology.

[tmigot]

@tmigot I have tried all the methods there are to pass the Documentation check. I think we have to revert back to api.md methodology.

Oh sorry for that, I checked and strangely enough CUTEst is doing differently than the other JSO packages... So, yes, you have to add them.

[arnavk23]

@tmigot I have reverted it back to earlier working documentation change using api.md

[tmigot]

Why do you need it in a different file just for three docstrings though ? references.md with the others is sufficient.

[arnavk23]

@amontoison I think this can be merged. It has been in this state for the past month. If you require some changes, please do tell.

[tmigot]

@arnavk23 can you stop pinging us, please

[arnavk23]

Sorry for the same.