Solve some deprecation warnings

[giordano]

┌ Warning: mpiexec() is deprecated, use the non-do-block form
│   caller = ip:0x0
└ @ Core :-1
┌ Warning: `PDiagMat(dim::Int, diag::AbstractVector{<:Real})` is deprecated, use `PDiagMat(diag)` instead.
│   caller = ip:0x0
└ @ Core :-1

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.46%. Comparing base (46678bf) to head (9c90676).
Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #286      +/-   ##
==========================================
- Coverage   92.48%   92.46%   -0.02%     
==========================================
  Files           7        7              
  Lines         386      385       -1     
==========================================
- Hits          357      356       -1     
  Misses         29       29              

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[giordano]

It appears deprecation warnings massively slow down runtime on Julia v1.12 (Julia Version 1.12.0-DEV.1638 Commit 55bdb54dd2e (2024-11-15 11:14 UTC)), compare TimerOutputs during tests on master (e74ca8c):

────────────────────────────────────────────────────────────────────────────────
                                       Time                    Allocations      
                              ───────────────────────   ────────────────────────
      Tot / % measured:            24.3s / 100.0%           60.3MiB / 100.0%    

Section               ncalls     time    %tot     avg     alloc    %tot      avg
────────────────────────────────────────────────────────────────────────────────
Proposals and weights    100    21.6s   89.1%   216ms   35.8MiB   59.3%   367KiB
Gather weights           100    1.77s    7.3%  17.7ms     0.00B    0.0%    0.00B
Summary statistics         1    573ms    2.4%   573ms   20.0MiB   33.1%  20.0MiB
Unpack statistics          1    151ms    0.6%   151ms   2.72MiB    4.5%  2.72MiB
Filter initialization      1   98.7ms    0.4%  98.7ms    709KiB    1.1%   709KiB
Copy states              100   53.4ms    0.2%   534μs   63.3KiB    0.1%     648B
Model initialization       1   3.82ms    0.0%  3.82ms   0.99MiB    1.6%  0.99MiB
State initialization       1    707μs    0.0%   707μs   53.5KiB    0.1%  53.5KiB
Update statistics          1    366μs    0.0%   366μs      992B    0.0%     992B
Normalize weights        100    183μs    0.0%  1.83μs     0.00B    0.0%    0.00B
Resample                 100    180μs    0.0%  1.80μs   17.2KiB    0.0%     176B
────────────────────────────────────────────────────────────────────────────────
────────────────────────────────────────────────────────────────────────────────
                                       Time                    Allocations      
                              ───────────────────────   ────────────────────────
      Tot / % measured:            27.3s / 100.0%            174MiB / 100.0%    

Section               ncalls     time    %tot     avg     alloc    %tot      avg
────────────────────────────────────────────────────────────────────────────────
Proposals and weights    100    23.6s   86.5%   236ms    122MiB   70.3%  1.22MiB
Gather weights           100    2.50s    9.2%  25.0ms   9.45KiB    0.0%    96.8B
Filter initialization      1    731ms    2.7%   731ms   50.4MiB   29.1%  50.4MiB
Summary statistics         1    416ms    1.5%   416ms      816B    0.0%     816B
Copy states              100   24.0ms    0.1%   240μs   65.0KiB    0.0%     666B
Model initialization       1   2.10ms    0.0%  2.10ms   0.99MiB    0.6%  0.99MiB
State initialization       1    706μs    0.0%   706μs   53.5KiB    0.0%  53.5KiB
Normalize weights        100    298μs    0.0%  2.98μs     0.00B    0.0%    0.00B
Resample                 100    266μs    0.0%  2.66μs   17.2KiB    0.0%     176B
Update statistics          1    184μs    0.0%   184μs      816B    0.0%     816B
Unpack statistics          1   25.3μs    0.0%  25.3μs      832B    0.0%     832B
────────────────────────────────────────────────────────────────────────────────
────────────────────────────────────────────────────────────────────────────────
                                       Time                    Allocations      
                              ───────────────────────   ────────────────────────
      Tot / % measured:            24.5s / 100.0%           50.6MiB / 100.0%    

Section               ncalls     time    %tot     avg     alloc    %tot      avg
────────────────────────────────────────────────────────────────────────────────
Proposals and weights    100    22.4s   91.4%   224ms   45.6MiB   90.1%   467KiB
Gather weights           100    1.90s    7.8%  19.0ms   4.69KiB    0.0%    48.0B
Summary statistics         1    151ms    0.6%   151ms      992B    0.0%     992B
Filter initialization      1   33.6ms    0.1%  33.6ms   3.69MiB    7.3%  3.69MiB
Copy states              100   12.1ms    0.0%   121μs   65.0KiB    0.1%     666B
Model initialization       1   2.10ms    0.0%  2.10ms   0.99MiB    2.0%  0.99MiB
State initialization       1    690μs    0.0%   690μs   53.5KiB    0.1%  53.5KiB
Update statistics          1    348μs    0.0%   348μs      992B    0.0%     992B
Normalize weights        100    314μs    0.0%  3.14μs     0.00B    0.0%    0.00B
Resample                 100    270μs    0.0%  2.70μs   17.2KiB    0.0%     176B
Unpack statistics          1    213μs    0.0%   213μs    208KiB    0.4%   208KiB
────────────────────────────────────────────────────────────────────────────────

vs tests on this PR

────────────────────────────────────────────────────────────────────────────────
                                       Time                    Allocations      
                              ───────────────────────   ────────────────────────
      Tot / % measured:            3.13s / 100.0%           55.0MiB / 100.0%    

Section               ncalls     time    %tot     avg     alloc    %tot      avg
────────────────────────────────────────────────────────────────────────────────
Proposals and weights    100    1.74s   55.6%  17.4ms   30.4MiB   55.3%   311KiB
Summary statistics         1    690ms   22.0%   690ms   20.0MiB   36.4%  20.0MiB
Gather weights           100    475ms   15.1%  4.75ms     0.00B    0.0%    0.00B
Unpack statistics          1   97.3ms    3.1%  97.3ms   2.75MiB    5.0%  2.75MiB
Filter initialization      1   89.6ms    2.9%  89.6ms    709KiB    1.3%   709KiB
Copy states              100   35.0ms    1.1%   350μs   63.3KiB    0.1%     648B
Model initialization       1   3.36ms    0.1%  3.36ms   0.99MiB    1.8%  0.99MiB
State initialization       1    709μs    0.0%   709μs   53.5KiB    0.1%  53.5KiB
Update statistics          1    367μs    0.0%   367μs      992B    0.0%     992B
Resample                 100   82.7μs    0.0%   827ns   17.2KiB    0.0%     176B
Normalize weights        100   80.9μs    0.0%   809ns     0.00B    0.0%    0.00B
────────────────────────────────────────────────────────────────────────────────
────────────────────────────────────────────────────────────────────────────────
                                       Time                    Allocations      
                              ───────────────────────   ────────────────────────
      Tot / % measured:            5.10s /  99.8%            168MiB / 100.0%    

Section               ncalls     time    %tot     avg     alloc    %tot      avg
────────────────────────────────────────────────────────────────────────────────
Proposals and weights    100    2.91s   57.2%  29.1ms    117MiB   69.4%  1.17MiB
Gather weights           100    1.39s   27.4%  13.9ms   9.45KiB    0.0%    96.8B
Filter initialization      1    578ms   11.4%   578ms   50.4MiB   29.9%  50.4MiB
Summary statistics         1    172ms    3.4%   172ms      816B    0.0%     816B
Copy states              100   29.0ms    0.6%   290μs   65.0KiB    0.0%     666B
Model initialization       1   3.34ms    0.1%  3.34ms   0.99MiB    0.6%  0.99MiB
State initialization       1    734μs    0.0%   734μs   53.5KiB    0.0%  53.5KiB
Normalize weights        100    117μs    0.0%  1.17μs     0.00B    0.0%    0.00B
Resample                 100    111μs    0.0%  1.11μs   17.2KiB    0.0%     176B
Update statistics          1   93.6μs    0.0%  93.6μs      816B    0.0%     816B
Unpack statistics          1   18.1μs    0.0%  18.1μs      832B    0.0%     832B
────────────────────────────────────────────────────────────────────────────────
────────────────────────────────────────────────────────────────────────────────
                                       Time                    Allocations      
                              ───────────────────────   ────────────────────────
      Tot / % measured:            3.30s / 100.0%           45.3MiB / 100.0%    

Section               ncalls     time    %tot     avg     alloc    %tot      avg
────────────────────────────────────────────────────────────────────────────────
Proposals and weights    100    2.31s   70.1%  23.1ms   40.2MiB   88.9%   412KiB
Gather weights           100    590ms   17.9%  5.90ms   4.69KiB    0.0%    48.0B
Summary statistics         1    346ms   10.5%   346ms      992B    0.0%     992B
Filter initialization      1   33.1ms    1.0%  33.1ms   3.69MiB    8.2%  3.69MiB
Copy states              100   12.4ms    0.4%   124μs   65.0KiB    0.1%     666B
Model initialization       1   2.07ms    0.1%  2.07ms   0.99MiB    2.2%  0.99MiB
State initialization       1    688μs    0.0%   688μs   53.5KiB    0.1%  53.5KiB
Update statistics          1    280μs    0.0%   280μs      992B    0.0%     992B
Unpack statistics          1    210μs    0.0%   210μs    208KiB    0.4%   208KiB
Normalize weights        100    116μs    0.0%  1.16μs     0.00B    0.0%    0.00B
Resample                 100    102μs    0.0%  1.02μs   17.2KiB    0.0%     176B
────────────────────────────────────────────────────────────────────────────────

There's a slight improvement also for v1.11, but that's of the order of ~10%, not ~10x