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[pull] master from SciML:master #31

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codecov bot commented Feb 18, 2024

Codecov Report

Attention: Patch coverage is 82.11533% with 673 lines in your changes missing coverage. Please review.

Project coverage is 82.60%. Comparing base (c50c21a) to head (873aae4).

Files with missing lines Patch % Lines
lib/NonlinearSolveBase/src/utils.jl 56.85% 85 Missing ⚠️
lib/NonlinearSolveBase/src/tracing.jl 24.46% 71 Missing ⚠️
lib/NonlinearSolveQuasiNewton/src/solve.jl 71.52% 41 Missing ⚠️
lib/NonlinearSolveBase/src/abstract_types.jl 72.03% 33 Missing ⚠️
lib/NonlinearSolveBase/src/polyalg.jl 61.03% 30 Missing ⚠️
lib/NonlinearSolveBase/src/jacobian.jl 74.07% 28 Missing ⚠️
...ib/NonlinearSolveBase/src/descent/damped_newton.jl 82.83% 23 Missing ⚠️
lib/NonlinearSolveFirstOrder/src/trust_region.jl 85.80% 23 Missing ⚠️
...rSolveBase/ext/NonlinearSolveBaseLinearSolveExt.jl 67.74% 20 Missing ⚠️
lib/NonlinearSolveBase/src/solve.jl 84.49% 20 Missing ⚠️
... and 43 more
Additional details and impacted files
@@            Coverage Diff             @@
##           master      #31      +/-   ##
==========================================
- Coverage   87.50%   82.60%   -4.90%     
==========================================
  Files          44       87      +43     
  Lines        2625     4214    +1589     
==========================================
+ Hits         2297     3481    +1184     
- Misses        328      733     +405     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

avik-pal and others added 30 commits November 1, 2024 09:58
fix: restore the history of SimpleNonlinearSolve
* fix: hessian through nonlinear solvers

* feat: extend gradient support for cached nlls
* ci: run windows tests with a single worker

* test: try fixing more mac tests

* test: div by zero

* test: add retries to guard against segfaults
* refactor: Move NonlinearSolvePolyAlgorithm to Base

* test: Make NonlinearSolve use 1.3 Base

* refactor: Remove unnecessary snippet

* refactor: Don't use duplicate solve

* refactor: Test Base export NonlinearSolvePolyAlgorithm
…#498)

* Fix ambiguity in `__solve` with polyalgorithm due to dispatch on `Val{N}`

Noticed downstream

```
  Candidates:
    kwcall(::NamedTuple, ::typeof(SciMLBase.__solve), prob::SciMLBase.AbstractNonlinearProblem, alg::NonlinearSolveBase.NonlinearSolvePolyAlgorithm{Val{N}}, args...) where N
      @ NonlinearSolveBase ~/.julia/packages/NonlinearSolveBase/54f3T/src/solve.jl:106
    kwcall(::NamedTuple, ::typeof(SciMLBase.__solve), prob::Union{SciMLBase.NonlinearLeastSquaresProblem{<:Union{Number, var"#s15"} where var"#s15"<:AbstractArray, iip, <:Union{var"#s14", var"#s13"} where {var"#s14"<:ForwardDiff.Dual{T, V, P}, var"#s13"<:(AbstractArray{<:ForwardDiff.Dual{T, V, P}})}} where {iip, T, V, P}, SciMLBase.NonlinearProblem{<:Union{Number, var"#s15"} where var"#s15"<:AbstractArray, iip, <:Union{var"#s14", var"#s13"} where {var"#s14"<:ForwardDiff.Dual{T, V, P}, var"#s13"<:(AbstractArray{<:ForwardDiff.Dual{T, V, P}})}} where {iip, T, V, P}}, alg::NonlinearSolveBase.AbstractNonlinearSolveAlgorithm, args...)
      @ NonlinearSolve ~/.julia/packages/NonlinearSolve/LuVnf/src/forward_diff.jl:14
    kwcall(::NamedTuple, ::typeof(SciMLBase.__solve), prob::Union{SciMLBase.NonlinearLeastSquaresProblem{<:Union{Number, var"#s15"} where var"#s15"<:AbstractArray, iip, <:Union{var"#s14", var"#s13"} where {var"#s14"<:ForwardDiff.Dual{T, V, P}, var"#s13"<:(AbstractArray{<:ForwardDiff.Dual{T, V, P}})}} where {iip, T, V, P}, SciMLBase.NonlinearProblem{<:Union{Number, var"#s15"} where var"#s15"<:AbstractArray, iip, <:Union{var"#s14", var"#s13"} where {var"#s14"<:ForwardDiff.Dual{T, V, P}, var"#s13"<:(AbstractArray{<:ForwardDiff.Dual{T, V, P}})}} where {iip, T, V, P}}, alg::NonlinearSolveBase.NonlinearSolvePolyAlgorithm, args...)
      @ NonlinearSolve ~/.julia/packages/NonlinearSolve/LuVnf/src/forward_diff.jl:14
  
  Possible fix, define
    kwcall(::NamedTuple, ::typeof(SciMLBase.__solve), ::Union{SciMLBase.NonlinearLeastSquaresProblem{<:Union{Number, var"#s15"} where var"#s15"<:AbstractArray, iip, <:Union{var"#s14", var"#s13"} where {var"#s14"<:ForwardDiff.Dual{T, V, P}, var"#s13"<:(AbstractArray{<:ForwardDiff.Dual{T, V, P}})}} where {iip, T, V, P}, SciMLBase.NonlinearProblem{<:Union{Number, var"#s15"} where var"#s15"<:AbstractArray, iip, <:Union{var"#s14", var"#s13"} where {var"#s14"<:ForwardDiff.Dual{T, V, P}, var"#s13"<:(AbstractArray{<:ForwardDiff.Dual{T, V, P}})}} where {iip, T, V, P}}, ::NonlinearSolveBase.NonlinearSolvePolyAlgorithm{Val{N}}, ::Vararg{Any}) where N
```

https://github.com/SciML/OrdinaryDiffEq.jl/actions/runs/11786040241/job/32828542508?pr=2522

The issue is that the polyalgorithm code is dispatching on more details of the polyalgorithm than https://github.com/SciML/NonlinearSolve.jl/blob/master/src/forward_diff.jl#L13-L25 which leads to an ambiguity. But it only needs that information since it's a generated function. The easy fix is to just make the generated function be one step lower.

* Update forward_ad_tests.jl

* Update lib/NonlinearSolveBase/src/solve.jl
* fix: fix SII implementation for caches

* test: fix SII tests

* ci: don't fail CI jobs if code coverage reporting fails

---------

Co-authored-by: Anant Thazhemadam <[email protected]>
* Create SCCNonlinearSolve

* Update lib/SCCNonlinearSolve/src/SCCNonlinearSolve.jl

Co-authored-by: Aayush Sabharwal <[email protected]>

* Update lib/SCCNonlinearSolve/src/SCCNonlinearSolve.jl

Co-authored-by: Aayush Sabharwal <[email protected]>

* Update lib/SCCNonlinearSolve/src/SCCNonlinearSolve.jl

Co-authored-by: Aayush Sabharwal <[email protected]>

* Update lib/SCCNonlinearSolve/test/core_tests.jl

Co-authored-by: Aayush Sabharwal <[email protected]>

* format scc

* just use params

* re format

* SII

* fix CI

* Update lib/SCCNonlinearSolve/src/SCCNonlinearSolve.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* fix up test setup

* Update Project.toml

* Update core_tests.jl

* Update lib/SCCNonlinearSolve/test/core_tests.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Update lib/SCCNonlinearSolve/test/core_tests.jl

* Update core_tests.jl

* Update lib/SCCNonlinearSolve/test/core_tests.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Update core_tests.jl

* Update Project.toml

* Update lib/SCCNonlinearSolve/test/qa_tests.jl

* Update lib/SCCNonlinearSolve/test/qa_tests.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Update Project.toml

* Update qa_tests.jl

* Update lib/SCCNonlinearSolve/test/qa_tests.jl

* Update lib/SCCNonlinearSolve/test/qa_tests.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

---------

Co-authored-by: Aayush Sabharwal <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v4...v5)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* refactor: Move RobustMultiNewton to NonlinearSolveFirstOrder

* refactor: Implicit import NonlinearSolvePolyAlgorithm
* Update release_notes.md

* Update docs/src/release_notes.md
* fix: remove compiled reversediff from default options

* fix: enzyme is now properly supported in 1.11
* feat: add `get_abstol` and `get_reltol` interface methods

* feat: add `initialize_cache!`

* feat: implement initialization for polyalg cache

* feat: implement initialization for no-init cache

* feat: implement initialization for first order cache

* feat: implement initialization for `QuasiNewtonCache`

* feat: implement initialization for `GeneralizedDFSaneCache`

* fix: fix `SII.parameter_values`

* feat: implement initialization for `SimpleNonlinearSolve`

* fix: fix `InternalAPI.reinit_self!` for `GeneralizedDFSaneCache`

* fix: fix `SII.state_values` for `NoInitCache`

* feat: run initialiation on `solve!`

* build: bump SciMLBase compat in NonlinearSolveBase
* build: bump versions of `NonlinearSolve` and sub-packages

* build: bump compats between sub-packages
* Fix incorrect Base version and bump

* Update Project.toml

---------

Co-authored-by: Christopher Rackauckas <[email protected]>
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