v2; make StateSpaceSet subtype Vector{<:AbstractVector} (#32)

* bump to 2.0

* add back the .github repo

* fix the main test file for state space sets

* rename files

* restore the bejavior of using SVectors by default, and fix distance tests

* all tests passing

* also test broadcasting

* oops typo

* enforce T real; allow MVector

* add tests for MVector

* add test of no reals

* final changelog

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,30 @@
+---
+name: Problem/bug report
+about: Create a report for incorrect/unexpected/erroring behavior
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the problem**
+
+A clear and concise description of what the problem is, and what you were expecting to happen instead.
+
+**Minimal Working Example**
+
+Please provide a piece of code that leads to the bug you encounter.
+
+This code should be **runnable**, **self-contained**, and minimal. Remove all irrelevant dependencies
+and actively try to reduce the code to its smallest possible version.
+This will help us identify and fix the problem faster.
+
+**Package versions**
+
+Please provide the versions you use. To do this, run the code:
+```julia
+import Pkg
+Pkg.status(["Package1", "Package2"]; # etc.
+    mode = PKGMODE_MANIFEST
+)
+```

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,14 @@
+---
+name: Feature request
+about: Suggest a new feature for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the feature you'd like to have**
+
+**Cite scientific papers related to the feature/algorithm**
+
+**If possible, sketch out an implementation strategy**

.github/workflows/CompatHelper.yml

@@ -0,0 +1,44 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+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 }}

.github/workflows/doccleanup.yml

@@ -0,0 +1,26 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.github/workflows/documentation.yml

@@ -0,0 +1,26 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key for using TagBot
+        run: julia --project=docs/ docs/make.jl

.github/workflows/test_coverage.yml

@@ -0,0 +1,53 @@
+name: CI - test & coverage
+on:
+  pull_request:
+    branches:
+      - main
+      - '**' # matches every branch
+  push:
+    branches:
+      - main
+    tags: '*'
+jobs:
+  test:
+    name: Tests, Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1'
+        os:  [ubuntu-latest] # adjust according to need, e.g. os: [ubuntu-latest] if testing only on linux
+        arch:
+          - x64
+    steps:
+      # Cancel ongoing CI test runs if pushing to branch again before the previous tests
+      # have finished
+      - name: Cancel ongoing test runs for previous commits
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      # Do tests
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        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/julia-buildpkg@v1
+
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

CHANGELOG.md

@@ -2,11 +2,12 @@ Changelog for StateSpaceSets.jl is kept w.r.t. version 1.3
 
 # 2.0
 
-- `StateSpaceSet` now subtypes `AbstractVector`, in particular `StateSpaceSet{V<:AbstractVector} <: AbstractVector{X}`. This lead to the breaking change that `size(ssset) = (length(ssset), )` while before `size` was `length(ssset), dimension(ssset)`. Now you have to use `dimension(ssset)` exclusively to get the "number of columns" in the state space set.
-- The keyword `container` can be given to all functions that make state space sets
+- `StateSpaceSet` now subtypes `AbstractVector`, in particular `StateSpaceSet{V<:AbstractVector} <: AbstractVector{V}`. This leads to the breaking change that `size(ssset) = (length(ssset), )` while before `size` was `length(ssset), dimension(ssset)`. Now you have to use `dimension(ssset)` exclusively to get the "number of columns" in the state space set.
+- `StateSpaceSet` now supports arbitrary inner vectors as state space points.
+  The keyword `container` can be given to all functions that make state space sets
   and sets the type of the container of the inner vectors. This is the abstract type
   and is typically `SVector` or `Vector`.
-- All deprecations of v1 have been removed. Primarily this includes `Dataset` and an old version of `statespace_sampler`.
+- All deprecations of v1 have been removed. Primarily this includes the `Dataset` name and an old version of `statespace_sampler`.
 
 
 # 1.5

Project.toml

@@ -2,7 +2,7 @@ name = "StateSpaceSets"
 uuid = "40b095a5-5852-4c12-98c7-d43bf788e795"
 authors = ["George Datseris <[email protected]>"]
 repo = "https://github.com/JuliaDynamics/StateSpaceSets.jl.git"
-version = "1.5.0"
+version = "2.0.0"
 
 [deps]
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"

src/neighborhoods.jl

@@ -6,13 +6,10 @@ using Neighborhood, Distances
 export WithinRange, NeighborNumber
 export Euclidean, Chebyshev, Cityblock
 
-Neighborhood.KDTree(D::AbstractStateSpaceSet, metric::Metric = Euclidean(); kwargs...) =
-KDTree(vec(D), metric; kwargs...)
-
 # Convenience extensions for ::StateSpaceSet in bulksearches
 for f ∈ (:bulkisearch, :bulksearch)
     for nt ∈ (:NeighborNumber, :WithinRange)
         @eval Neighborhood.$(f)(ss::KDTree, D::AbstractStateSpaceSet, st::$nt, args...; kwargs...) =
-        $(f)(ss, D.data, st, args...; kwargs...)
+        $(f)(ss, vec(D), st, args...; kwargs...)
     end
 end

src/set_distance.jl

@@ -49,6 +49,8 @@ The distance is calculated with the metric given to `Hausdorff` which defaults t
 
 `Hausdorff` is 2x slower than [`StrictlyMinimumDistance`](@ref), however it is
 a proper metric in the space of sets of state space sets.
+
+This metric only works for `StateSpaceSet`s whose elements are `SVector`s.
 """
 struct Hausdorff{M<:Metric}
     metric::M
@@ -79,6 +81,8 @@ Brute force performs better for datasets that are either large dimensional or
 have a small amount of points. Deciding a cutting point is not trivial,
 and is recommended to simply benchmark the [`set_distance`](@ref) function to
 make a decision.
+
+If `brute = false` this metric only works for `StateSpaceSet`s whose elements are `SVector`s.
 """
 struct StrictlyMinimumDistance{M<:Metric}
     brute::Bool