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docs: update documentation
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avik-pal committed Oct 22, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/Documentation.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ jobs:
- uses: actions/checkout@v4
- uses: julia-actions/setup-julia@latest
with:
version: '1'
version: '1.10'
- name: Install dependencies
run: |
import Pkg
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35 changes: 31 additions & 4 deletions .github/workflows/Downgrade.yml
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Expand Up @@ -14,15 +14,42 @@ jobs:
test:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
version: ["1.10"]
version:
- "1.10"
group:
- Core
- Downstream
- Misc
- Wrappers
steps:
- uses: actions/checkout@v4
- uses: julia-actions/setup-julia@v2
with:
version: ${{ matrix.version }}
- uses: julia-actions/julia-downgrade-compat@v1
- name: "Install Dependencies and Run Tests"
run: |
import Pkg
Pkg.Registry.update()
# Install packages present in subdirectories
dev_pks = Pkg.PackageSpec[]
for path in ("lib/SciMLJacobianOperators", "lib/BracketingNonlinearSolve", "lib/NonlinearSolveBase", "lib/SimpleNonlinearSolve")
push!(dev_pks, Pkg.PackageSpec(; path))
end
Pkg.develop(dev_pks)
Pkg.instantiate()
Pkg.test(; coverage=true)
shell: julia --color=yes --code-coverage=user --depwarn=yes --project=. {0}
env:
GROUP: ${{ matrix.group }}
- uses: julia-actions/julia-processcoverage@v1
with:
skip: Pkg,TOML
- uses: julia-actions/julia-buildpkg@v1
- uses: julia-actions/julia-runtest@v1
directories: src,ext,lib/SciMLJacobianOperators/src
- uses: codecov/codecov-action@v4
with:
file: lcov.info
token: ${{ secrets.CODECOV_TOKEN }}
verbose: true
fail_ci_if_error: true
2 changes: 1 addition & 1 deletion Project.toml
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Expand Up @@ -68,7 +68,7 @@ BenchmarkTools = "1.4"
CUDA = "5.5"
CommonSolve = "0.2.4"
ConcreteStructs = "0.2.3"
DiffEqBase = "6.158.3"
DiffEqBase = "6.155.3"
DifferentiationInterface = "0.6.1"
Enzyme = "0.13.2"
ExplicitImports = "1.5"
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7 changes: 4 additions & 3 deletions docs/Project.toml
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Expand Up @@ -3,6 +3,7 @@ ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
AlgebraicMultigrid = "2169fc97-5a83-5252-b627-83903c6c433c"
ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
BracketingNonlinearSolve = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e"
DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
Expand All @@ -11,8 +12,8 @@ DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
NonlinearSolveBase = "be0214bd-f91f-a760-ac4e-3421ce2b2da0"
OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Expand All @@ -29,16 +30,16 @@ ADTypes = "1.9.0"
AlgebraicMultigrid = "0.5, 0.6"
ArrayInterface = "6, 7"
BenchmarkTools = "1"
DiffEqBase = "6.136"
BracketingNonlinearSolve = "1"
DifferentiationInterface = "0.6.1"
Documenter = "1"
DocumenterCitations = "1"
DocumenterInterLinks = "1.0.0"
IncompleteLU = "0.2"
InteractiveUtils = "<0.0.1, 1"
LinearSolve = "2"
ModelingToolkit = "9"
NonlinearSolve = "4"
NonlinearSolveBase = "1"
OrdinaryDiffEqTsit5 = "1.1.0"
Plots = "1"
Random = "1.10"
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8 changes: 5 additions & 3 deletions docs/make.jl
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
using Documenter, DocumenterCitations, DocumenterInterLinks
using NonlinearSolve, SimpleNonlinearSolve, Sundials, SteadyStateDiffEq, SciMLBase,
DiffEqBase
BracketingNonlinearSolve, NonlinearSolveBase
using SciMLJacobianOperators
import DiffEqBase

cp(joinpath(@__DIR__, "Manifest.toml"),
joinpath(@__DIR__, "src/assets/Manifest.toml"), force = true)
Expand All @@ -20,8 +21,9 @@ interlinks = InterLinks(
makedocs(;
sitename = "NonlinearSolve.jl",
authors = "Chris Rackauckas",
modules = [NonlinearSolve, SimpleNonlinearSolve, SteadyStateDiffEq,
Sundials, DiffEqBase, SciMLBase, SciMLJacobianOperators],
modules = [NonlinearSolve, SimpleNonlinearSolve, SteadyStateDiffEq, DiffEqBase,
Sundials, NonlinearSolveBase, SciMLBase, SciMLJacobianOperators,
BracketingNonlinearSolve],
clean = true,
doctest = false,
linkcheck = true,
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4 changes: 3 additions & 1 deletion docs/pages.jl
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@@ -1,6 +1,7 @@
# Put in a separate page so it can be used by SciMLDocs.jl

pages = ["index.md",
pages = [
"index.md",
"Getting Started with Nonlinear Rootfinding in Julia" => "tutorials/getting_started.md",
"Tutorials" => Any[
"tutorials/code_optimization.md",
Expand Down Expand Up @@ -31,6 +32,7 @@ pages = ["index.md",
"Native Functionalities" => Any[
"native/solvers.md",
"native/simplenonlinearsolve.md",
"native/bracketingnonlinearsolve.md",
"native/steadystatediffeq.md",
"native/descent.md",
"native/globalization.md",
Expand Down
20 changes: 8 additions & 12 deletions docs/src/basics/diagnostics_api.md
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Expand Up @@ -27,20 +27,16 @@ Note that you will have to restart Julia to disable the timer outputs once enabl
## Example Usage

```@example diagnostics_example
using ModelingToolkit, NonlinearSolve
using NonlinearSolve
@variables x y z
@parameters σ ρ β
function nlfunc(resid, u0, p)
resid[1] = u0[1] * u0[1] - p
resid[2] = u0[2] * u0[2] - p
resid[3] = u0[3] * u0[3] - p
nothing
end
# Define a nonlinear system
eqs = [0 ~ σ * (y - x), 0 ~ x * (ρ - z) - y, 0 ~ x * y - β * z]
@mtkbuild ns = NonlinearSystem(eqs, [x, y, z], [σ, ρ, β])
u0 = [x => 1.0, y => 0.0, z => 0.0]
ps = [σ => 10.0 ρ => 26.0 β => 8 / 3]
prob = NonlinearProblem(ns, u0, ps)
prob = NonlinearProblem(nlfunc, [1.0, 3.0, 5.0], 2.0)
solve(prob)
```
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2 changes: 1 addition & 1 deletion docs/src/basics/solve.md
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@@ -1,7 +1,7 @@
# [Common Solver Options (Solve Keyword Arguments)](@id solver_options)

```@docs
solve(prob::SciMLBase.NonlinearProblem, args...; kwargs...)
solve(::NonlinearProblem, args...; kwargs...)
```

## General Controls
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22 changes: 14 additions & 8 deletions docs/src/basics/termination_condition.md
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Expand Up @@ -23,17 +23,23 @@ terminated = cache(du, u, uprev)
### Absolute Tolerance

```@docs
AbsTerminationMode
AbsNormTerminationMode
AbsNormSafeTerminationMode
AbsNormSafeBestTerminationMode
NonlinearSolveBase.AbsTerminationMode
NonlinearSolveBase.AbsNormTerminationMode
NonlinearSolveBase.AbsNormSafeTerminationMode
NonlinearSolveBase.AbsNormSafeBestTerminationMode
```

### Relative Tolerance

```@docs
RelTerminationMode
RelNormTerminationMode
RelNormSafeTerminationMode
RelNormSafeBestTerminationMode
NonlinearSolveBase.RelTerminationMode
NonlinearSolveBase.RelNormTerminationMode
NonlinearSolveBase.RelNormSafeTerminationMode
NonlinearSolveBase.RelNormSafeBestTerminationMode
```

### Both Tolerances

```@docs
NonlinearSolveBase.NormTerminationMode
```
3 changes: 0 additions & 3 deletions docs/src/devdocs/algorithm_helpers.md
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Expand Up @@ -60,9 +60,6 @@ NonlinearSolve.GenericTrustRegionScheme
## Miscellaneous

```@docs
SimpleNonlinearSolve.__nextfloat_tdir
SimpleNonlinearSolve.__prevfloat_tdir
SimpleNonlinearSolve.__max_tdir
NonlinearSolve.callback_into_cache!
NonlinearSolve.concrete_jac
```
21 changes: 21 additions & 0 deletions docs/src/native/bracketingnonlinearsolve.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
# BracketingNonlinearSolve.jl

These methods can be used independently of the rest of NonlinearSolve.jl

```@index
Pages = ["bracketingnonlinearsolve.md"]
```

## Interval Methods

These methods are suited for interval (scalar) root-finding problems,
i.e. [`IntervalNonlinearProblem`](@ref).

```@docs
ITP
Alefeld
Bisection
Falsi
Ridder
Brent
```
16 changes: 1 addition & 15 deletions docs/src/native/simplenonlinearsolve.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,20 +6,6 @@ These methods can be used independently of the rest of NonlinearSolve.jl
Pages = ["simplenonlinearsolve.md"]
```

## Interval Methods

These methods are suited for interval (scalar) root-finding problems,
i.e. `IntervalNonlinearProblem`.

```@docs
ITP
Alefeld
Bisection
Falsi
Ridder
Brent
```

## General Methods

These methods are suited for any general nonlinear root-finding problem, i.e.
Expand Down Expand Up @@ -54,6 +40,6 @@ Squares problems.
[^1]: Needs [`StaticArrays.jl`](https://github.com/JuliaArrays/StaticArrays.jl) to be
installed and loaded for the non-allocating version.
[^2]: This method is non-allocating if the termination condition is set to either `nothing`
(default) or [`AbsNormTerminationMode`](@ref).
(default) or [`NonlinearSolveBase.AbsNormTerminationMode`](@ref).
[^3]: Only the defaults are guaranteed to work inside kernels. We try to provide warnings
if the used version is not non-allocating.
28 changes: 14 additions & 14 deletions docs/src/tutorials/modelingtoolkit.md
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Expand Up @@ -5,7 +5,7 @@ modeling system for the Julia SciML ecosystem. It adds a high-level interactive
for the numerical solvers which can make it easy to symbolically modify and generate
equations to be solved. The basic form of using ModelingToolkit looks as follows:

```@example mtk
```julia
using ModelingToolkit, NonlinearSolve

@variables x y z
Expand All @@ -30,20 +30,20 @@ sol = solve(prob, NewtonRaphson())
As a symbolic system, ModelingToolkit can be used to represent the equations and derive new
forms. For example, let's look at the equations:

```@example mtk
```julia
equations(ns)
```

We can ask it what the Jacobian of our system is via `calculate_jacobian`:

```@example mtk
```julia
calculate_jacobian(ns)
```

We can tell MTK to generate a computable form of this analytical Jacobian via `jac = true`
to help the solver use efficient forms:

```@example mtk
```julia
prob = NonlinearProblem(ns, u0, ps, jac = true)
sol = solve(prob, NewtonRaphson())
```
Expand All @@ -54,7 +54,7 @@ One of the major reasons for using ModelingToolkit is to allow structural simpli
the systems. It's very easy to write down a mathematical model that, in theory, could be
solved more simply. Let's take a look at a quick system:

```@example mtk
```julia
@variables u1 u2 u3 u4 u5
eqs = [0 ~ u1 - sin(u5), 0 ~ u2 - cos(u1), 0 ~ u3 - hypot(u1, u2),
0 ~ u4 - hypot(u2, u3), 0 ~ u5 - hypot(u4, u1)]
Expand All @@ -63,47 +63,47 @@ eqs = [0 ~ u1 - sin(u5), 0 ~ u2 - cos(u1), 0 ~ u3 - hypot(u1, u2),

If we run structural simplification, we receive the following form:

```@example mtk
```julia
sys = structural_simplify(sys)
```

```@example mtk
```julia
equations(sys)
```

How did it do this? Let's look at the `observed` to see the relationships that it found:

```@example mtk
```julia
observed(sys)
```

Using ModelingToolkit, we can build and solve the simplified system:

```@example mtk
```julia
u0 = [u5 .=> 1.0]
prob = NonlinearProblem(sys, u0)
sol = solve(prob, NewtonRaphson())
```

We can then use symbolic indexing to retrieve any variable:

```@example mtk
```julia
sol[u1]
```

```@example mtk
```julia
sol[u2]
```

```@example mtk
```julia
sol[u3]
```

```@example mtk
```julia
sol[u4]
```

```@example mtk
```julia
sol[u5]
```

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23 changes: 23 additions & 0 deletions lib/BracketingNonlinearSolve/README.md
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@@ -0,0 +1,23 @@
# BracketingNonlinearSolve.jl

Fast implementations of interval root finding algorithms in Julia that satisfy the SciML
common interface. BracketingNonlinearSolve.jl focuses on low-dependency implementations of
very fast methods for very small and simple problems. For the full set of solvers, see
[NonlinearSolve.jl](https://github.com/SciML/NonlinearSolve.jl), of which
BracketingNonlinearSolve.jl is just one solver set.

For information on using the package,
[see the stable documentation](https://docs.sciml.ai/NonlinearSolve/stable/). Use the
[in-development documentation](https://docs.sciml.ai/NonlinearSolve/dev/) for the version of
the documentation which contains the unreleased features.

## High Level Examples

```julia
using BracketingNonlinearSolve

f(u, p) = u .* u .- 2.0
u0 = (1.0, 2.0) # brackets
probB = IntervalNonlinearProblem(f, u0)
sol = solve(probB, ITP())
```
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