Update dependencies manually

[YigitElma]

Updating the dependencies manually before the new release. The Dependabot issue persists.

jax.tree_util.tree_broadcast was added with jax 0.6.2. Bumped min jax version to 0.6.2 and removed 0.5.0, 0.5.3 and 0.6.1 (they were a year old).

New jax versions introduce small numerical differences and cause some tests to fail. Sticking with jax<0.10.0 for now. Bounce stuff will be fixed in a different PR.

[github-actions]

Memory benchmark result

|               Test Name                |      %Δ      |    Master (MB)     |      PR (MB)       |    Δ (MB)    |    Time PR (s)     |  Time Master (s)   |
| -------------------------------------- | ------------ | ------------------ | ------------------ | ------------ | ------------------ | ------------------ |
  test_objective_jac_w7x                 |    3.54 %    |     3.995e+03      |     4.137e+03      |    141.26    |       31.14        |       29.84        |
  test_proximal_jac_w7x_with_eq_update   |   -1.73 %    |     6.610e+03      |     6.496e+03      |   -114.11    |       153.40       |       152.25       |
  test_proximal_freeb_jac                |   -0.25 %    |     1.336e+04      |     1.333e+04      |    -33.24    |       84.14        |       82.15        |
  test_proximal_freeb_jac_blocked        |    0.57 %    |     7.601e+03      |     7.644e+03      |    43.02     |       71.21        |       69.30        |
  test_proximal_freeb_jac_batched        |    0.83 %    |     7.579e+03      |     7.641e+03      |    62.82     |       70.30        |       67.56        |
  test_proximal_jac_ripple               |    3.02 %    |     3.498e+03      |     3.604e+03      |    105.64    |       55.58        |       53.05        |
  test_proximal_jac_ripple_bounce1d      |   -0.39 %    |     3.839e+03      |     3.824e+03      |    -14.93    |       68.09        |       68.01        |
  test_eq_solve                          |    0.78 %    |     2.049e+03      |     2.065e+03      |    15.96     |       86.84        |       87.12        |

For the memory plots, go to the summary of Memory Benchmarks workflow and download the artifact.

[YigitElma]

@f0uriest what do you think about bumping the minimum jax version to 0.6.2? It is almost a year old now (June 17, 2025).

[YigitElma]

• Try test_solve_bounds with svd
• Bump the min version of jax

[YigitElma]

I had to add this eps because with newer versions of jax, some stuff that were rounded to 0 now has slight difference which caused the test_z1_first test to fail (first 2 roots were not found).

[unalmis]

Blocking as the modification to the bounce integrals breaks invariants and leads to errors. If you need to edit bounce integral code your options are to either merge #2226 or merge #2199 which requires the spare pullback pr . Either will take 5 minutes of time.

Out of scope

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.33%. Comparing base (e80e4bb) to head (e550ef3).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2222      +/-   ##
==========================================
- Coverage   94.35%   94.33%   -0.02%     
==========================================
  Files         101      101              
  Lines       28856    28855       -1     
==========================================
- Hits        27226    27221       -5     
- Misses       1630     1634       +4     

Files with missing lines	Coverage Δ
desc/coils.py	97.96% <100.00%> (ø)
desc/particles.py	92.90% <100.00%> (-0.03%)	⬇️
desc/profiles.py	95.53% <100.00%> (ø)

... and 3 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[YigitElma]

I realized this would also have the same problem as #2228