v0.7 upgrade

.JuliaFormatter.toml

@@ -0,0 +1,15 @@
+# Options for the JuliaFormatter auto syntax formatting tool.
+# https://domluna.github.io/JuliaFormatter.jl/stable/
+# https://docs.sciml.ai/SciMLStyle/stable/
+
+# We don't use SciML style since aligning with opening brackets doesn't look good if
+# the opening bracket is near the end of the line. This squeezes the code to the right,
+# and this alignment confuses auto indent.
+# Based on the default style we do pick these non-default options from SciML style:
+whitespace_ops_in_indices = true
+remove_extra_newlines = true
+always_for_in = true
+whitespace_typedefs = true
+
+# And add other options we like:
+separate_kwargs_with_semicolon = true

.github/workflows/CI.yml

@@ -1,6 +1,13 @@
 name: CI
 on:
-  - push
+  push:
+    branches: [master]
+    tags: ["*"]
+  pull_request:
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+  actions: write
+  contents: read
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -9,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - "1.6"
+          - "lts"
           - "1"
           - "nightly"
         os:
@@ -24,15 +31,12 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v4
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v5
+        with:
+          files: lcov.info
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/Docs.yml

@@ -1,24 +1,49 @@
-name: Documentation
+# Sample workflow for building and deploying a VitePress site to GitHub Pages
+#
+name: Documenter
 
 on:
+  # Runs on pushes targeting the `master` branch. Change this to `main` if you're
+  # using the `main` branch as the default branch.
   push:
     branches:
       - main
-    tags: '*'
+    tags: ['*']
   pull_request:
 
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+  statuses: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
 jobs:
+  # Build job
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1.6'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+      - name: Pull Julia cache
+        uses: julia-actions/cache@v2
+      - name: Install documentation dependencies
+        run: julia --project=docs -e 'using Pkg; pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
+      #- name: Creating new mds from src
+      - name: Build and deploy docs
+        uses: julia-actions/julia-docdeploy@v1
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
-        run: julia --project=docs/ docs/make.jl
-
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          JULIA_DEBUG: "Documenter"

.gitignore

@@ -8,3 +8,12 @@ docs/build/
 *.gif
 test/benchmark.jl
 .vscode
+docs/node_modules
+docs/final_site
+_extensions
+
+
+scripts
+.documenter
+docs/src/CHANGELOG.md
+*.png

CHANGELOG.md

@@ -0,0 +1,77 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.7.0] - 2025-03-21
+
+### Added
+- Improved documentation by using VitePress and showcasing all methods on a DEM.
+- Added hydrology operators: `priorityflood`, `streamflow`
+- Added *multiscale* options to some filters using a `window` kwarg for a Stencil from Stencils.jl package. Other methods now take a `radius` kwarg.
+- Added `BPI`
+- Overhauled curvature methods by introducing `plan_curvature`, `profile_curvature` and `contour_curvature`, while deprecating `curvature` for `laplacian`
+- Added direction kwarg to slope and curvature methods.
+- Added this `CHANGELOG.md`
+- Added package extensions on GeoArrays, Rasters to support automatic cellsizes.
+- Added package extension on Eikonal for a faster `spread` method.
+
+### Changed
+- Added Stencils as dependency.
+- Refactored spread to choose from multiple algorithms
+
+### Fixed
+- Relaxed `Array` input to `AbstractArray` for `opening`
+## [0.6.0] - 2023-08-25
+### Changed
+- Renamed package to Geomorphometry
+
+### Added
+- Added `erosion` parameter in `PMF`
+
+## [0.5.2] - 2023-08-14
+### Changed
+- Light maintenance to CI scripts
+- Compat updates
+
+## [0.5.1] - 2023-01-12
+### Added
+- Relaxed input for `PMF`
+
+## [0.5.0] - 2022-11-02
+
+### Added
+- Added `multihillshade`
+
+### Changed
+- Uses LocalFilters for terrain filters, improving performance, but changing the edge behaviour of some filters.
+
+## [0.4.0] - 2022-10-17
+### Added
+- Added `hillshade`, `curvature`
+
+### Changed
+- Used LocalFilters for `PMF`.
+
+## [0.3.2] - 2022-09-07
+### Added
+- Added terrain kernels for different algorithms.
+
+### Fixed
+- Fixed bug in TPI
+
+## [0.3.1] - 2022-06-15
+### 
+- Added `skewness` filter
+
+## [0.3.0] - 2022-02-01
+### Added
+- Added PSF (Progressive Slope Filter) function.
+
+### Changed
+- Improved performance of mapwindow function used in most filters.
+
+## [0.2.0] - 2021-11-22
+### Added
+- Initial release of the GeoArrayOps package.
+- Basic terrain analysis functions.
+

Project.toml

@@ -1,36 +1,55 @@
 name = "Geomorphometry"
 uuid = "714e3e49-7933-471a-9334-4a6a65a92f36"
 authors = ["Maarten Pronk <git@evetion.nl>", "Deltares"]
-version = "0.6.0"
+version = "0.7.0"
 
 [deps]
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
-ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
-ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LocalFilters = "085fde7c-5f94-55e4-8448-8bbb5db6dde9"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 PaddedViews = "5432bcbf-9aad-5242-b902-cca2824c8663"
+QuickHeaps = "30b38841-0f52-47f8-a5f8-18d5d4064379"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+Stencils = "264155e8-78a8-466a-aa59-c9b28c34d21a"
+
+[weakdeps]
+ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+Eikonal = "a6aab1ba-8f88-4217-b671-4d0788596809"
+GeoArrays = "2fb1d81b-e6a0-5fc5-82e6-8e06903437ab"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
+
+[extensions]
+GeomorphometryEikonalExt = "Eikonal"
+GeomorphometryGeoArraysExt = "GeoArrays"
+GeomorphometryRastersExt = ["Rasters", "ArchGDAL"]
 
 [compat]
+ArchGDAL = "0.10"
 DataStructures = "0.18"
 Distances = "0.10"
+Eikonal = "0.1.1"
 FillArrays = "0.12, 0.13, 1"
-ImageCore = "0.9, 0.10"
-ImageFiltering = "0.6, 0.7"
+GeoArrays = "0.9"
 LocalFilters = "1.2"
 OffsetArrays = "1.10"
 PaddedViews = "0.5"
+Rasters = "0.13"
 StaticArrays = "1"
 StatsBase = "0.33, 0.34"
-julia = "1.6, 1.7, 1.8"
+Stencils = "0.3.4"
+julia = "1.10"
 
 [extras]
+ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+Eikonal = "a6aab1ba-8f88-4217-b671-4d0788596809"
+GeoArrays = "2fb1d81b-e6a0-5fc5-82e6-8e06903437ab"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test", "GeoArrays", "Rasters", "ArchGDAL", "Eikonal"]

docs/Project.toml

@@ -1,6 +1,11 @@
 [deps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
+Eikonal = "a6aab1ba-8f88-4217-b671-4d0788596809"
+GeoArrays = "2fb1d81b-e6a0-5fc5-82e6-8e06903437ab"
 Geomorphometry = "714e3e49-7933-471a-9334-4a6a65a92f36"
-
-[compat]
-Documenter = "^0.27"
+LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"

docs/make.jl

@@ -1,17 +1,70 @@
-push!(LOAD_PATH, "../src/")
-using Documenter, Geomorphometry
+using Revise
+using Geomorphometry
+using Documenter
+using DocumenterVitepress
+using CairoMakie
+using DocumenterCitations
+using Downloads
 
-makedocs(
-    sitename="Geomorphometry.jl",
-    pages=[
-        "index.md",
-        "Tutorials" => [],
-        "Topics" => [],
-        "Reference" => "reference.md",
-        "How-To Guides" => [],
-    ]
+Revise.revise()
+dir = @__DIR__
+
+bib = CitationBibliography(joinpath(@__DIR__, "src", "refs.bib"); style = :authoryear)
+cp(joinpath(dir, "../CHANGELOG.md"), joinpath(dir, "src/CHANGELOG.md"); force = true)
+CairoMakie.activate!(; type = "png")
+
+fn = joinpath(dir, "src", "saba.tif")
+isfile(fn) || Downloads.download(
+    "https://github.com/Deltares/Geomorphometry.jl/releases/download/v0.6.0/saba.tif",
+    fn,
+)
+fn = joinpath(dir, "src", "saba_dsm.tif")
+isfile(fn) || Downloads.download(
+    "https://github.com/Deltares/Geomorphometry.jl/releases/download/v0.6.0/saba_dsm.tif",
+    fn,
+)
+
+DocMeta.setdocmeta!(
+    Geomorphometry,
+    :DocTestSetup,
+    :(using Geomorphometry);
+    recursive = true,
+)
+
+makedocs(;
+    modules = [Geomorphometry],
+    authors = "Maarten Pronk <git@evetion.nl> and contributors",
+    repo = "https://github.com/Deltares/Geomorphometry.jl/blob/{commit}{path}#L{line}",
+    sitename = "Geomorphometry.jl",
+    format = MarkdownVitepress(;
+        repo = "github.com/Deltares/Geomorphometry.jl",
+        # md_output_path = ".",
+        # build_vitepress = true,
+        devbranch = "main",
+    ),
+    doctest = true,
+    checkdocs = :all,
+    pages = [
+        "Home" => "index.md",
+        "Getting started" =>
+            Any["Installation" => "installation.md", "Usage" => "usage.md"],
+        "Background" => Any["Concepts" => "concepts.md", "Future plans" => "todo.md"],
+        "Reference" => Any[
+            "Validation" => "validation.md",
+            "API" => "reference.md",
+            "Changelog" => "CHANGELOG.md",
+            "Bibliography" => "bibliography.md",
+        ],
+    ],
+    # clean = false,
+    plugins = [bib],
+    warnonly = [:missing_docs, :cross_references],
 )
 
-deploydocs(
-    repo="github.com/Deltares/Geomorphometry.jl.git",
+deploydocs(;
+    repo = "github.com/Deltares/Geomorphometry.jl.git",
+    target = "build",
+    devbranch = "main",
+    branch = "gh-pages",
+    push_preview = true,
 )