Migrated iteration 5 to branch

.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CI.yml

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+name: CI
+on:
+  push:
+    branches:
+      - main
+    tags: ['*']
+  pull_request:
+  workflow_dispatch:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.10'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      contents: write
+      statuses: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - uses: julia-actions/cache@v2
+      - name: Configure doc environment
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Run doctests
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Documenter: DocMeta, doctest
+          using OceanSonar
+          DocMeta.setdocmeta!(OceanSonar, :DocTestSetup, :(using OceanSonar); recursive=true)
+          doctest(OceanSonar)

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

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+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

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+/Manifest.toml
+/docs/Manifest.toml
+/docs/build/
+/readme/Manifest.toml

.vscode/settings.json

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+{
+}

CITATION.bib

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+@misc{OceanSonar.jl,
+    author  = {Aaron Kaw <aaronjkaw@gmail.com> and contributors},
+    title   = {OceanSonar.jl},
+    url     = {https://github.com/kapple19/OceanSonar.jl},
+    version = {v1.0.0-DEV},
+    year    = {2024},
+    month   = {3}
+}

Project.toml

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+name = "OceanSonar"
+uuid = "606d67fd-65b6-4abb-b2f0-1946d248e4dc"
+authors = ["Aaron Kaw <[email protected]> and contributors"]
+version = "1.0.0-DEV"
+
+[deps]
+ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+IntervalArithmetic = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[weakdeps]
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+
+[extensions]
+OceanSonarMakieExt = "Makie"
+OceanSonarPlotsExt = "Plots"
+
+[compat]
+ForwardDiff = "0.10"
+Interpolations = "0.15"
+IntervalArithmetic = "0.22"
+LinearAlgebra = "1.10"
+Makie = "0.21"
+NaNMath = "1.0"
+OrdinaryDiffEq = "6.85"
+Plots = "1.40"
+PrecompileTools = "1.2"
+Statistics = "1.10"
+julia = "1.11"

benchmark/benchmarks.jl

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+using OceanSonar
+using BenchmarkTools
+
+SUITE = BenchmarkGroup()
+SUITE["rand"] = @benchmarkable rand(10)
+
+# Write your benchmarks here.

docs/Project.toml

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+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+OceanSonar = "606d67fd-65b6-4abb-b2f0-1946d248e4dc"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

docs/make.jl

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+using OceanSonar
+using Documenter
+
+DocMeta.setdocmeta!(OceanSonar, :DocTestSetup, :(using OceanSonar); recursive=true)
+
+pages = [
+    "Ocean Sonar" => "index.md"
+    "General" => [
+        "Usage" => "general/usage.md"
+        "Implementation" => "general/implementation.md"
+    ]
+    "Oceanography" => [
+        "Parameters" => [
+            "Celerity" => [
+                "Atmosphere" => "oceanography/parameters/celerity/atmosphere.md"
+                "Ocean" => "oceanography/parameters/celerity/ocean.md"
+                "Seabed" => [
+                    "Compressional" => "oceanography/parameters/celerity/seabed/compressional.md"
+                    "Shear" => "oceanography/parameters/celerity/seabed/shear.md"
+                ]
+            ]
+            "Density" => [
+                "Atmosphere" => "oceanography/parameters/density/atmosphere.md"
+                "Ocean" => "oceanography/parameters/density/ocean.md"
+                "Seabed" => "oceanography/parameters/density/seabed.md"
+            ]
+            "Attenuation" => [
+                "Atmosphere" => "oceanography/parameters/attenuation/atmosphere.md"
+                "Ocean" => "oceanography/parameters/attenuation/ocean.md"
+                "Seabed" => [
+                    "Compressional" => "oceanography/parameters/attenuation/seabed/compressional.md"
+                    "Shear" => "oceanography/parameters/attenuation/seabed/shear.md"
+                ]
+            ]
+        ]
+        "Slice" => [
+            "Introduction" => "oceanography/environment/intro.md"
+            "Boundary" => [
+                "Altimetry" => "oceanography/environment/boundary/altimetry.md"
+                "Bathymetry" => "oceanography/environment/boundary/bathymetry.md"
+            ]
+            "Medium" => [
+                "Introduction" => "oceanography/environment/medium/intro.md"
+                "Atmosphere" => "oceanography/environment/medium/atmosphere.md"
+                "Ocean" => "oceanography/environment/medium/ocean.md"
+                "Seabed" => "oceanography/environment/medium/seabed.md"
+            ]
+        ]
+    ]
+    "Acoustics" => [
+        "Scenario" => "acoustics/scenario.md"
+        "Reflection" => [
+            "Bottom" => "acoustics/reflection/bottom.md"
+        ]
+        "Propagation" => [
+            "Introduction" => "acoustics/propagation/intro.md"
+            "Tracing" => [
+                "Introduction" => "acoustics/propagation/tracing/intro.md"
+                "Rays" => "acoustics/propagation/tracing/rays.md"
+                "Beams" => "acoustics/propagation/tracing/beam.md"
+                "Grid" => "acoustics/propagation/tracing/grid.md"
+            ]
+            "Parabolic" => [
+                "Marchers" => "acoustics/propagation/parabolic/marcher.md"
+            ]
+        ]
+    ]
+]
+
+makedocs(;
+    sitename="OceanSonar.jl",
+    modules=[OceanSonar],
+    authors="Aaron Kaw <[email protected]> and contributors",
+    format = Documenter.HTML(;
+        canonical="https://kapple19.github.io/OceanSonar.jl",
+        edit_link = :commit,
+        collapselevel = 1,
+        assets = String[]
+    ),
+    pages = pages,
+)
+
+deploydocs(;
+    repo="github.com/kapple19/OceanSonar.jl",
+    devbranch="main",
+)

docs/src/acoustics/propagation/intro.md

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+# Acoustic Propagation
+
+```@docs
+Propagation
+PropagationConfig
+```

docs/src/acoustics/propagation/parabolic/marcher.md

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+# Marchers
+
+To be renamed.
+
+```@example
+using OceanSonar
+using Plots
+
+θ_deg = range(0, 90, 301)
+θ = deg2rad.(θ_deg)
+q = -sin.(θ).^2
+
+helmholtz(q) = √(1 + q)
+helmholtz_q = helmholtz.(q)
+
+plot()
+
+for model = list_models(OceanSonar.RationalFunctionApproximation)
+    rfa = OceanSonar.RationalFunctionApproximation(model)
+    errs = helmholtz_q - rfa.(q) .|> abs
+    plot!(θ_deg, errs,
+        label = string(model, " (", length(rfa.a), ")")
+    )
+end
+model = :pade
+rfa = OceanSonar.RationalFunctionApproximation(model, m = 5)
+errs = helmholtz_q - rfa.(q) .|> abs
+plot!(θ_deg, errs,
+    label = string(model, " (", length(rfa.a), ")")
+)
+
+plot!(
+    xlims = (0, 90),
+    ylims = (0, 0.001),
+    legend_position = :best
+)
+
+savefig("phase_errors.svg")
+```
+
+Replication of Figure 6.1b of Jensen, et al (2011).
+
+![phase_errors.svg](phase_errors.svg)

docs/src/acoustics/propagation/tracing/beam.md

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+# Acoustic Beam Tracing
+
+```@docs
+Beam
+```

docs/src/acoustics/propagation/tracing/grid.md

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+# Acoustic Tracing Interpolation to Grid
+
+```@example
+using OceanSonar
+using Plots
+using .Threads
+
+@time "all" begin
+    begin
+        models = list_models(Scenario)
+        for m in eachindex(models)
+            model = models[m]
+            scen = Scenario(model)
+            prop = @time "$model" Propagation(:trace, scen,
+                angles = critical_angles(scen)
+            )
+            fig = visual(prop)
+            savefig(fig, "prop_" * modelsnake(scen.model) * ".svg")
+        end
+    end
+end
+```
+
+![prop_parabolic_bathymetry.svg](prop_parabolic_bathymetry.svg)
+
+![prop_index_squared_profile.svg](prop_index_squared_profile.svg)
+
+![prop_munk_profile.svg](prop_munk_profile.svg)
+
+![prop_lloyd_mirror.svg](prop_lloyd_mirror.svg)

docs/src/acoustics/propagation/tracing/intro.md

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+# Acoustic Tracing Models
+
+```@docs
+TraceConfig
+```