Merge pull request #78 from cesaraustralia/improvements

Improvements

.github/workflows/ci.yml

@@ -0,0 +1,53 @@
+name: CI
+on:
+  - push
+  - pull_request
+defaults:
+  run:
+    shell: bash
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        version:
+          - '1.3'
+          - '1.5'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+          fail_ci_if_error: true
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.5'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -1,7 +1,7 @@
 name = "DynamicGrids"
 uuid = "a5dba43e-3abc-5203-bfc5-584ca68d3f5b"
 authors = ["Rafael Schouten <[email protected]>"]
-version = "0.10.9"
+version = "0.11.0"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
@@ -10,14 +10,14 @@ Crayons = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-FieldDefaults = "49426c49-986f-5969-8844-d5cc96441cfc"
-FieldDocTables = "a5d692f0-33f0-11e9-293e-eb83c8d6177d"
-FieldMetadata = "bf96fef3-21d2-5d20-8afa-0e7d4c32a885"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 FreeTypeAbstraction = "663a7486-cb36-511b-a19d-713bb74d65c9"
-Mixers = "2a8e4939-dab8-5edc-8f64-72a8776f13de"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+ModelParameters = "4744a3fa-6c31-4707-899e-a3298e4618ad"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 UnicodeGraphics = "ebadf6b4-db70-5817-83da-4a19ad584e34"
@@ -28,13 +28,11 @@ ConstructionBase = "1"
 Crayons = "4"
 DimensionalData = "0.11, 0.12, 0.13"
 DocStringExtensions = "0.8"
-FieldDefaults = "0.3.1"
-FieldDocTables = "0.1"
-FieldMetadata = "0.3"
 FileIO = "1"
 FreeTypeAbstraction = "^0.6.5, 0.8"
-Mixers = "0.1"
+ModelParameters = "0.2"
 OffsetArrays = "0.11, 1.0"
+Reexport = "0.2"
 Setfield = "0.6, 0.7"
 UnicodeGraphics = "0.1"
 julia = "1.2, 1.3, 1.4, 1.5"

docs/Project.toml

@@ -1,3 +1,4 @@
 [deps]
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicGrids = "a5dba43e-3abc-5203-bfc5-584ca68d3f5b"

docs/src/index.md

@@ -25,10 +25,14 @@ CellRule
 Cell
 NeighborhoodRule
 Neighbors
+Convolution
 Life
 ManualRule
 Manual
 ManualNeighborhoodRule
+SetNeighbors
+GridRule
+Grid
 Chain
 ```
 
@@ -37,15 +41,17 @@ Chain
 ```@docs
 DynamicGrids.applyrule
 DynamicGrids.applyrule!
-DynamicGrids.precalcrules
+DynamicGrids.precalcrule
 isinferred 
 ```
 
 ### Data objects and methods for use in `applyrule`
 
 ```@docs
 SimData
+DynamicGrids.init
 DynamicGrids.aux
+DynamicGrids.mask
 DynamicGrids.tspan
 DynamicGrids.timestep
 DynamicGrids.currenttimestep
@@ -63,7 +69,9 @@ and how they are combined to update the value of the current cell.
 
 ```@docs
 Neighborhood
-AbstractRadialNeighborhood
+RadialNeighborhood
+AbstractKernel
+Kernel
 Moore
 VonNeumann
 AbstractPositional
@@ -76,13 +84,25 @@ LayeredPositional
 ```@docs
 DynamicGrids.radius
 DynamicGrids.neighbors
+DynamicGrids.positions
+DynamicGrids.offsets
 DynamicGrids.sumneighbors
 DynamicGrids.mapsetneighbor!
 DynamicGrids.setneighbor!
 DynamicGrids.allocbuffers
 DynamicGrids.hoodsize
 ```
 
+## Manual Rules
+
+```@docs
+add!
+sub!
+and!
+or!
+xor!
+```
+
 
 ## Output
 

src/DynamicGrids.jl

@@ -13,43 +13,40 @@ using Colors,
       Crayons,
       DimensionalData,
       DocStringExtensions,
-      FieldDefaults,
-      FieldMetadata,
-      FieldDocTables,
       FreeTypeAbstraction,
       FileIO,
-      Mixers,
+      LinearAlgebra,
       OffsetArrays,
       REPL,
+      Reexport,
       Setfield,
       Test,
       UnicodeGraphics
 
+@reexport using ModelParameters
+
 const DG = DynamicGrids
 
-using Base: tail
+using Base: tail, @propagate_inbounds
 
 import Base: show, getindex, setindex!, lastindex, size, length, push!, append!,
              broadcast, broadcast!, similar, eltype, iterate
 
-import FieldMetadata: @description, description, 
-                      @bounds, bounds,
-                      @flattenable, flattenable,
-                      @default, default
+export sim!, resume!, savegif, isinferred, isinferred
 
+export rules, neighbors, offsets, positions, radius, inbounds, isinbounds 
 
-export sim!, resume!, savegif, isinferred, isinferred
+export gridsize, currenttime, currenttimestep, timestep
 
-export rules, neighbors, inbounds, isinbounds, radius, gridsize, 
-       currenttime, currenttimestep, timestep
+export add!, sub!, and!, or!, xor!
 
-export Rule, NeighborhoodRule, CellRule, ManualRule, ManualNeighborhoodRule
+export Rule, NeighborhoodRule, CellRule, ManualRule, ManualNeighborhoodRule, GridRule
 
-export Chain, Cell, Neighbors, Manual, Life
+export Cell, Neighbors, SetNeighbors, Convolution, Manual, Chain, Life, Grid 
 
 export AbstractRuleset, Ruleset
 
-export Neighborhood, AbstractRadialNeighborhood, Moore,
+export Neighborhood, RadialNeighborhood, AbstractKernel, Kernel, Moore,
        AbstractPositional, Positional, VonNeumann, LayeredPositional
 
 export PerformanceOpt, NoOpt, SparseOpt
@@ -67,11 +64,6 @@ export Greyscale, Grayscale
 
 export CharStyle, Block, Braile
 
-
-const FIELDDOCTABLE = FieldDocTable((:Description, :Default, :Bounds),
-                                    (description, default, bounds);
-                                    truncation=(100,40,100))
-
 # Documentation templates
 @template TYPES =
     """

src/chain.jl

@@ -29,17 +29,17 @@ radius(chain::Chain) = radius(chain[1])
 neighborhoodkey(chain::Chain) = neighborhoodkey(chain[1])
 neighborhood(chain::Chain) = neighborhood(chain[1])
 
-Base.tail(chain::Chain{R,W}) where {R,W} = begin
-    ch = tail(rules(chain))
-    Chain{R,W,typeof(ch)}(ch)
+function Base.tail(chain::Chain{R,W}) where {R,W}
+    chaintail = tail(rules(chain))
+    Chain{R,W,typeof(chaintail)}(chaintail)
 end
 Base.getindex(chain::Chain, i) = getindex(rules(chain), i)
 Base.iterate(chain::Chain) = iterate(rules(chain))
 Base.length(chain::Chain) = length(rules(chain))
 Base.firstindex(chain::Chain) = firstindex(rules(chain))
 Base.lastindex(chain::Chain) = lastindex(rules(chain))
 
-@generated applyrule(data::SimData, chain::Chain{R,W,T}, state, index) where {R,W,T} = begin
+@generated function applyrule(data::SimData, chain::Chain{R,W,T}, state, index) where {R,W,T}
     expr = Expr(:block)
     for i in 1:length(T.parameters)
         rule_expr = quote
@@ -62,7 +62,7 @@ end
 
 Get the state to pass to the specific rule as a `NamedTuple` or single value
 """
-@generated filter_readstate(::Rule{R,W}, state::NamedTuple) where {R<:Tuple,W} = begin 
+@generated function filter_readstate(::Rule{R,W}, state::NamedTuple) where {R<:Tuple,W}
     expr = Expr(:tuple)
     keys = Tuple(R.parameters)
     for k in keys
@@ -77,7 +77,7 @@ end
 
 Get the state to write for the specific rule
 """
-@generated filter_writestate(::Rule{R,W}, state::NamedTuple) where {R<:Tuple,W} = begin 
+@generated function filter_writestate(::Rule{R,W}, state::NamedTuple) where {R<:Tuple,W}
     expr = Expr(:tuple)
     keys = Tuple(W.parameters)
     for k in keys

src/extent.jl

@@ -1,6 +1,9 @@
 
 """
-    Extent(init, mask, aux, tspan, tstopped)
+    Extent(init::Union{AbstractArray,NamedTuple}, 
+           mask::Union{AbstractArray,Nothing}, 
+           aux::Union{NamedTuple,Nothing}, 
+           tspan::AbstractRange)
     Extent(; init, mask=nothing, aux=nothing, tspan, kwargs...)
 
 Container for extensive variables: spatial and timeseries data.
@@ -9,8 +12,16 @@ of rules to alternate spatial and temporal contexts.
 
 Extent is not usually constructed directly by users, but it can be passed
 to `Output` constructors instead of `init`, `mask`, `aux` and `tspan`.
+
+- `init`: initialisation `Array`/`NamedTuple` for grid/s.
+- `mask`: `BitArray` for defining cells that will/will not be run.
+- `aux`: NamedTuple of arbitrary input data. Use `aux(data, Vale{:key})` to access from 
+  a `Rule` in a type-stable way.
+- `tspan`: Time span range. Never type-stable, only access this in `precalc` methods
 """
-mutable struct Extent{I,M,A}
+mutable struct Extent{I<:Union{AbstractArray,NamedTuple},
+                      M<:Union{AbstractArray,Nothing},
+                      A<:Union{NamedTuple,Nothing}}
     init::I
     mask::M
     aux::A
@@ -20,11 +31,15 @@ Extent(init::I, mask::M, aux::A, tspan::T) where {I,M,A,T} = begin
     # Check grid sizes match
     gridsize = if init isa NamedTuple
         size_ = size(first(init_))
-        all(map(i -> size(i) == size_, init)) || throw(ArgumentError("`init` grid sizes do not match"))
+        if !all(map(i -> size(i) == size_, init))
+            throw(ArgumentError("`init` grid sizes do not match"))
+        end
     else
         size_ = size(init_)
     end
-    (mask !== nothing) && (size(mask) != size_) && throw(ArgumentError("`mask` size do not match `init`"))
+    if (mask !== nothing) && (size(mask) != size_) 
+        throw(ArgumentError("`mask` size do not match `init`"))
+    end
     Extent{I,M,A,T}(init, mask, aux, tspan)
 end
 Extent(; init, mask=nothing, aux=nothing, tspan, kwargs...) =
@@ -33,7 +48,9 @@ Extent(; init, mask=nothing, aux=nothing, tspan, kwargs...) =
 init(e::Extent) = e.init
 mask(e::Extent) = e.mask
 aux(e::Extent) = e.aux
-tspan(e::Extent) = e.tspan
+@inline aux(e::Extent, key::Symbol) = aux(e)[key] # Should not be used in rules
+@inline aux(e::Extent, ::Val{Key}) where Key = aux(e)[Key] # Fast compile-time version
+tspan(e::Extent) = e.tspan # Never type-stable, only access in `precalc` methods
 
 settspan!(e::Extent, tspan) = e.tspan = tspan