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Merge pull request #70 from JuliaGraphs/hw/fix_rng
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fix rng pr
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@hexaeder
hexaeder authored Oct 16, 2024
2 parents 4b085ae + 465d170 commit 224621d
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Showing 7 changed files with 20 additions and 28 deletions.
12 changes: 2 additions & 10 deletions .github/workflows/CI.yml
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Expand Up @@ -26,16 +26,7 @@ jobs:
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/cache@v2
- uses: julia-actions/julia-buildpkg@v1
- uses: julia-actions/julia-runtest@v1
- uses: julia-actions/julia-processcoverage@v1
Expand All @@ -50,6 +41,7 @@ jobs:
- uses: julia-actions/setup-julia@v2
with:
version: '1'
- uses: julia-actions/cache@v2
- uses: julia-actions/julia-buildpkg@v1
- uses: julia-actions/julia-docdeploy@v1
env:
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2 changes: 1 addition & 1 deletion .github/workflows/CompatHelper.yml
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Expand Up @@ -15,7 +15,7 @@ jobs:
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
uses: julia-actions/setup-julia@v2
with:
version: '1'
arch: ${{ runner.arch }}
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4 changes: 3 additions & 1 deletion docs/Project.toml
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Expand Up @@ -5,10 +5,12 @@ GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"

[compat]
CairoMakie = "0.10"
CairoMakie = "0.11"
Documenter = "1"
GraphMakie = "0.5"
Graphs = "1.9"
NetworkLayout = "0.4"
StableRNGs = "1.0.1"
2 changes: 2 additions & 0 deletions docs/make.jl
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Expand Up @@ -3,7 +3,9 @@ using NetworkLayout
using Graphs
using GraphMakie
using CairoMakie
using StableRNGs

NetworkLayout.DEFAULT_RNG[] = StableRNG
DocMeta.setdocmeta!(NetworkLayout, :DocTestSetup, :(using NetworkLayout); recursive=true)

makedocs(; modules=[NetworkLayout],
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8 changes: 4 additions & 4 deletions docs/src/index.md
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Expand Up @@ -10,7 +10,7 @@ All example images on this page are created using [`Makie.jl`](https://github.co
```@example layouts
using CairoMakie
CairoMakie.activate!(type="png") # hide
set_theme!(resolution=(800, 400)) #hide
set_theme!(size=(800, 400)) #hide
using NetworkLayout
using GraphMakie, Graphs
nothing #hide
Expand Down Expand Up @@ -167,7 +167,7 @@ hidedecorations!(ax); hidespines!(ax); f #hide
f #hide
```
```@example layouts
set_theme!(resolution=(800, 800)) #hide
set_theme!(size=(800, 800)) #hide
using Random; Random.seed!(5) # hide
layout = Spectral()
f, ax, p = graphplot(g, layout=layout, node_size=0.0, edge_width=1.0)
Expand Down Expand Up @@ -201,11 +201,11 @@ nothing #hide
```
Example animation on how those keyword arguments effect different iterative layouts:
```@example layouts
springl = Spring(;initialpos, pin, seed=11) #2
springl = Spring(;initialpos, pin, seed=2)
sfdpl = SFDP(;initialpos, pin, tol=0.0)
stressl = Stress(;initialpos, pin, reltols=0.0, abstolx=0.0, iterations=100)
f = Figure(resolution=(1200,500))
f = Figure(size=(1200,500))
ax1 = f[1,1] = Axis(f; title="Spring")
ax2 = f[1,2] = Axis(f; title="SFDP")
ax3 = f[1,3] = Axis(f; title="Stress")
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10 changes: 4 additions & 6 deletions src/sfdp.jl
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Expand Up @@ -76,12 +76,12 @@ function Base.iterate(iter::LayoutIterator{<:SFDP{Dim,Ptype,T}}) where {Dim,Ptyp
pin = [get(algo.pin, i, SVector{Dim,Bool}(false for _ in 1:Dim)) for i in 1:N]

# iteratorstate: (#iter, energy, step, progress, old pos, pin, stopflag)
return startpos, (1, typemax(T), one(T), 0, startpos, pin, false)
return startpos, (1, typemax(T), one(T), 0, startpos, pin, rng, false)
end

function Base.iterate(iter::LayoutIterator{<:SFDP}, state)
algo, adj_matrix = iter.algorithm, iter.adj_matrix
iter, energy0, step, progress, locs0, pin, stopflag = state
iter, energy0, step, progress, locs0, pin, rng, stopflag = state
K, C, tol = algo.K, algo.C, algo.tol

# stop if stopflag (tol reached) or nr of iterations reached
Expand Down Expand Up @@ -109,9 +109,7 @@ function Base.iterate(iter::LayoutIterator{<:SFDP}, state)
end
if any(isnan, force)
# if two points are at the exact same location use random force in any direction
# copy rng from alg struct to not advance the "initial" rng state
# otherwise algo(g)==algo(g) might be broken
force += randn(copy(algo.rng), Ftype)
force = randn(rng, Ftype)
end
mask = (!).(pin[i]) # where pin=true mask will multiply with 0
locs[i] = locs[i] .+ (step .* (force ./ norm(force))) .* mask
Expand All @@ -124,7 +122,7 @@ function Base.iterate(iter::LayoutIterator{<:SFDP}, state)
stopflag = true
end

return locs, (iter + 1, energy, step, progress, locs, pin, stopflag)
return locs, (iter + 1, energy, step, progress, locs, pin, rng, stopflag)
end

# Calculate Attractive force
Expand Down
10 changes: 4 additions & 6 deletions src/spring.jl
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Expand Up @@ -75,12 +75,12 @@ function Base.iterate(iter::LayoutIterator{<:Spring{Dim,Ptype}}) where {Dim,Ptyp
pin = [get(algo.pin, i, SVector{Dim,Bool}(false for _ in 1:Dim)) for i in 1:N]

# iteratorstate: #iter nr, old pos, pin
return (startpos, (1, startpos, pin))
return (startpos, (1, startpos, pin, rng))
end

function Base.iterate(iter::LayoutIterator{<:Spring}, state)
algo, adj_matrix = iter.algorithm, iter.adj_matrix
iteration, old_pos, pin = state
iteration, old_pos, pin, rng = state
iteration >= algo.iterations && return nothing

# The optimal distance bewteen vertices
Expand Down Expand Up @@ -114,9 +114,7 @@ function Base.iterate(iter::LayoutIterator{<:Spring}, state)
else
# if two points are at the exact same location
# use random force in any direction
# copy rng from alg struct to not advance the "initial" rng state
# otherwise algo(g)==algo(g) might be broken
force_vec += randn(copy(algo.rng), Ftype)
force_vec += randn(rng, Ftype)
end

end
Expand All @@ -134,5 +132,5 @@ function Base.iterate(iter::LayoutIterator{<:Spring}, state)
locs[i] += force[i] .* scale .* mask
end

return locs, (iteration + 1, locs, pin)
return locs, (iteration + 1, locs, pin, rng)
end

2 comments on commit 224621d

@hexaeder
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Registration pull request created: JuliaRegistries/General/117382

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.4.8 -m "<description of version>" 224621dbf629f3ca27aee559d58d7bd064092b17
git push origin v0.4.8

Also, note the warning: Version 0.4.8 skips over 0.4.7
This can be safely ignored. However, if you want to fix this you can do so. Call register() again after making the fix. This will update the Pull request.

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