From df333e73fd410712abf68eb84558b1fc30e75a07 Mon Sep 17 00:00:00 2001 From: mohamed82008 Date: Fri, 28 Sep 2018 21:45:40 +1000 Subject: [PATCH 1/6] depend on Bijectors --- src/Turing.jl | 1 + test/transform.jl/transform.jl | 188 --------------------------------- test/utility.jl | 1 - 3 files changed, 1 insertion(+), 189 deletions(-) delete mode 100644 test/transform.jl/transform.jl diff --git a/src/Turing.jl b/src/Turing.jl index 09880f149..3a2894bcd 100644 --- a/src/Turing.jl +++ b/src/Turing.jl @@ -11,6 +11,7 @@ module Turing using Requires using Reexport @reexport using Distributions +using Bijectors @reexport using MCMCChain using ForwardDiff using StatsFuns diff --git a/test/transform.jl/transform.jl b/test/transform.jl/transform.jl deleted file mode 100644 index cfff212be..000000000 --- a/test/transform.jl/transform.jl +++ /dev/null @@ -1,188 +0,0 @@ -using Turing, Test -using Turing: link, invlink, logpdf_with_trans -using ForwardDiff: derivative, jacobian -using LinearAlgebra: logabsdet - -# logabsdet doesn't handle scalars. -_logabsdet(x::AbstractArray) = logabsdet(x)[1] -_logabsdet(x::Real) = log(abs(x)) - -# Generate a (vector / matrix of) random number(s). -_rand_real(::Real) = randn() -_rand_real(x) = randn(size(x)) - -# Standard tests for all distributions involving a single-sample. -function single_sample_tests(dist, jacobian) - - # Do the regular single-sample tests. - single_sample_tests(dist) - - # Check that the implementation of the logpdf agrees with the AD version. - x = rand(dist) - logpdf_ad = logpdf(dist, x) - _logabsdet(jacobian(x->link(dist, x), x)) - @test logpdf_ad ≈ logpdf_with_trans(dist, x, true) -end - -# Standard tests for all distributions involving a single-sample. Doesn't check that the -# logpdf implementation is consistent with the link function for technical reasons. -function single_sample_tests(dist) - - # Check that invlink is inverse of link. - x = rand(dist) - @test invlink(dist, link(dist, copy(x))) ≈ x atol=1e-9 - - # Check that link is inverse of invlink. Hopefully this just holds given the above... - y = link(dist, x) - @test link(dist, invlink(dist, copy(y))) ≈ y atol=1e-9 - - # This should probably be exact. - @test logpdf(dist, x) == logpdf_with_trans(dist, x, false) - - # Check that invlink maps back to the apppropriate constrained domain. - @test all(isfinite, logpdf.(Ref(dist), [invlink(dist, _rand_real(x)) for _ in 1:100])) - - # This is a quirk of the current implementation, of which it would be nice to be rid. - @test typeof(x) == typeof(y) -end - -# Standard tests for all distributions involving multiple samples. xs should be whatever -# the appropriate repeated version of x is for the distribution in question. ie. for -# univariate distributions, just a vector of identical values. For vector-valued -# distributions, a matrix whose columns are identical. -function multi_sample_tests(dist, x, xs, N) - ys = link(dist, copy(xs)) - @test invlink(dist, link(dist, copy(xs))) ≈ xs atol=1e-9 - @test link(dist, invlink(dist, copy(ys))) ≈ ys atol=1e-9 - @test logpdf_with_trans(dist, xs, true) == fill(logpdf_with_trans(dist, x, true), N) - @test logpdf_with_trans(dist, xs, false) == fill(logpdf_with_trans(dist, x, false), N) - - # This is a quirk of the current implementation, of which it would be nice to be rid. - @test typeof(xs) == typeof(ys) -end - -# Scalar tests -@testset "scalar" begin -let - # Tests with scalar-valued distributions. - uni_dists = [ - Arcsine(2, 4), - Beta(2,2), - BetaPrime(), - Biweight(), - Cauchy(), - Chi(3), - Chisq(2), - Cosine(), - Epanechnikov(), - Erlang(), - Exponential(), - FDist(1, 1), - Frechet(), - Gamma(), - InverseGamma(), - InverseGaussian(), - # Kolmogorov(), - Laplace(), - Levy(), - Logistic(), - LogNormal(1.0, 2.5), - Normal(0.1, 2.5), - Pareto(), - Rayleigh(1.0), - TDist(2), - TruncatedNormal(0, 1, -Inf, 2), - ] - for dist in uni_dists - - single_sample_tests(dist, derivative) - - # specialised multi-sample tests. - N = 10 - x = rand(dist) - xs = fill(x, N) - multi_sample_tests(dist, x, xs, N) - end -end -end - -# Tests with vector-valued distributions. -@testset "vector" begin -let - vector_dists = [ - Dirichlet(2, 3), - MvNormal(randn(10), exp.(randn(10))), - MvLogNormal(MvNormal(randn(10), exp.(randn(10)))), - ] - for dist in vector_dists - - if dist isa Dirichlet - single_sample_tests(dist) - - # This should fail at the minute. Not sure what the correct way to test this is. - x = rand(dist) - logpdf_turing = logpdf_with_trans(dist, x, true) - J = jacobian(x->link(dist, x), x) - @test_broken logpdf(dist, x) - _logabsdet(J) ≈ logpdf_turing - else - single_sample_tests(dist, jacobian) - end - - # Multi-sample tests. Columns are observations due to Distributions.jl conventions. - N = 10 - x = rand(dist) - xs = repeat(x, 1, N) - multi_sample_tests(dist, x, xs, N) - end -end -end - -# Tests with matrix-valued distributions. -@testset "matrix" begin -let - matrix_dists = [ - Wishart(7, [1 0.5; 0.5 1]), - InverseWishart(2, [1 0.5; 0.5 1]), - ] - for dist in matrix_dists - - single_sample_tests(dist) - - # This should fail at the minute. Not sure what the correct way to test this is. - x = rand(dist) - logpdf_turing = logpdf_with_trans(dist, x, true) - J = jacobian(x->link(dist, x), x) - @test_broken logpdf(dist, x) - _logabsdet(J) ≈ logpdf_turing - - # Multi-sample tests comprising vectors of matrices. - N = 10 - x = rand(dist) - xs = [x for _ in 1:N] - multi_sample_tests(dist, x, xs, N) - end -end -end - -################################## Miscelaneous old tests ################################## - -# julia> logpdf_with_trans(Dirichlet([1., 1., 1.]), exp.([-1000., -1000., -1000.]), true) -# NaN -# julia> logpdf_with_trans(Dirichlet([1., 1., 1.]), [-1000., -1000., -1000.], true, true) -# -1999.30685281944 -# -# julia> logpdf_with_trans(Dirichlet([1., 1., 1.]), exp.([-1., -2., -3.]), true) -# -3.006450206744678 -# julia> logpdf_with_trans(Dirichlet([1., 1., 1.]), [-1., -2., -3.], true, true) -# -3.006450206744678 -d = Dirichlet([1., 1., 1.]) -r = [-1000., -1000., -1000.] -r2 = [-1., -2., -3.] - -# test link -#link(d, r) - -# test invlink -@test invlink(d, r) ≈ [0., 0., 1.] atol=1e-9 - -# test logpdf_with_trans -#@test logpdf_with_trans(d, invlink(d, r), true) -1999.30685281944 1e-9 ≈ # atol=NaN -@test logpdf_with_trans(d, invlink(d, r2), true) ≈ -3.760398892580863 atol=1e-9 diff --git a/test/utility.jl b/test/utility.jl index cc48257a5..dffe49df4 100644 --- a/test/utility.jl +++ b/test/utility.jl @@ -60,7 +60,6 @@ function runtests(; tests = ["all"]) CORE_TESTS = ["ad.jl", "compiler.jl", "container.jl", "varinfo.jl", # "io.jl", "util.jl"] - DISTR_TESTS = ["transform.jl"] SAMPLER_TESTS = ["resample.jl", "adapt.jl", "vectorisation.jl", "gibbs.jl", "nuts.jl", "hmcda.jl", "hmc_core.jl", "hmc.jl", "sghmc.jl", "sgld.jl", "is.jl", "mh.jl", From 55d53fd9014ad6355cadcc160a8fdbb003f51d91 Mon Sep 17 00:00:00 2001 From: mohamed82008 Date: Fri, 28 Sep 2018 22:04:18 +1000 Subject: [PATCH 2/6] fix tests and missed changes --- REQUIRE | 1 + src/Turing.jl | 1 - src/utilities/transform.jl | 348 ------------------------------------- test/utility.jl | 2 +- 4 files changed, 2 insertions(+), 350 deletions(-) delete mode 100644 src/utilities/transform.jl diff --git a/REQUIRE b/REQUIRE index 0cd5f6ceb..c9802fec9 100644 --- a/REQUIRE +++ b/REQUIRE @@ -9,6 +9,7 @@ Libtask 0.1.1 Flux 0.6.7 MacroTools StatsFuns 0.7.0 +Bijectors ProgressMeter 0.6.0 BinaryProvider 0.4.0 diff --git a/src/Turing.jl b/src/Turing.jl index 3a2894bcd..c317ebaeb 100644 --- a/src/Turing.jl +++ b/src/Turing.jl @@ -121,7 +121,6 @@ include("utilities/resample.jl") include("support/stan-interface.jl") end include("utilities/helper.jl") -include("utilities/transform.jl") include("utilities/robustinit.jl") include("utilities/util.jl") # utility functions include("utilities/io.jl") # I/O diff --git a/src/utilities/transform.jl b/src/utilities/transform.jl deleted file mode 100644 index 98d36e20e..000000000 --- a/src/utilities/transform.jl +++ /dev/null @@ -1,348 +0,0 @@ -#= - NOTE: Codes below are adapted from - https://github.com/brian-j-smith/Mamba.jl/blob/master/src/distributions/transformdistribution.jl - The Mamba.jl package is licensed under the MIT License: - > Copyright (c) 2014: Brian J Smith and other contributors: - > - > https://github.com/brian-j-smith/Mamba.jl/contributors - > - > Permission is hereby granted, free of charge, to any person obtaining - > a copy of this software and associated documentation files (the - > "Software"), to deal in the Software without restriction, including - > without limitation the rights to use, copy, modify, merge, publish, - > distribute, sublicense, and/or sell copies of the Software, and to - > permit persons to whom the Software is furnished to do so, subject to - > the following conditions: - > - > The above copyright notice and this permission notice shall be - > included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - > EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF - > MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. - > IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY - > CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, - > TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE - > SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -=# - -############# -# a ≦ x ≦ b # -############# - -const TransformDistribution{T<:ContinuousUnivariateDistribution} = Union{T, Truncated{T}} - -function link(d::TransformDistribution, x::Real) - a, b = minimum(d), maximum(d) - lowerbounded, upperbounded = isfinite(a), isfinite(b) - if lowerbounded && upperbounded - return StatsFuns.logit((x - a) / (b - a)) - elseif lowerbounded - return log(x - a) - elseif upperbounded - return log(b - x) - else - return x - end -end - -function invlink(d::TransformDistribution, y::Real) - a, b = minimum(d), maximum(d) - lowerbounded, upperbounded = isfinite(a), isfinite(b) - if lowerbounded && upperbounded - return (b - a) * StatsFuns.logistic(y) + a - elseif lowerbounded - return exp(y) + a - elseif upperbounded - return b - exp(y) - else - return y - end -end - -function logpdf_with_trans(d::TransformDistribution, x::Real, transform::Bool) - lp = logpdf(d, x) - if transform - a, b = minimum(d), maximum(d) - lowerbounded, upperbounded = isfinite(a), isfinite(b) - if lowerbounded && upperbounded - lp += log((x - a) * (b - x) / (b - a)) - elseif lowerbounded - lp += log(x - a) - elseif upperbounded - lp += log(b - x) - end - end - return lp -end - - -############### -# -∞ < x < -∞ # -############### - -const RealDistribution = Union{ - Cauchy, Gumbel, Laplace, Logistic, NoncentralT, Normal, NormalCanon, TDist, -} - -link(d::RealDistribution, x::Real) = x -invlink(d::RealDistribution, y::Real) = y -logpdf_with_trans(d::RealDistribution, y::Real, transform::Bool) = logpdf(d, y) - - -######### -# 0 < x # -######### - -const PositiveDistribution = Union{ - BetaPrime, Chi, Chisq, Erlang, Exponential, FDist, Frechet, Gamma, InverseGamma, - InverseGaussian, Kolmogorov, LogNormal, NoncentralChisq, NoncentralF, Rayleigh, Weibull, -} - -link(d::PositiveDistribution, x::Real) = log(x) -invlink(d::PositiveDistribution, y::Real) = exp(y) -function logpdf_with_trans(d::PositiveDistribution, x::Real, transform::Bool) - return logpdf(d, x) + transform * log(x) -end - - -############# -# 0 < x < 1 # -############# - -const UnitDistribution = Union{Beta, KSOneSided, NoncentralBeta} - -link(d::UnitDistribution, x::Real) = StatsFuns.logit(x) -invlink(d::UnitDistribution, y::Real) = StatsFuns.logistic(y) -function logpdf_with_trans(d::UnitDistribution, x::Real, transform::Bool) - return logpdf(d, x) + transform * log(x * (one(x) - x)) -end - - -########### -# ∑xᵢ = 1 # -########### - -const SimplexDistribution = Union{Dirichlet} - -function link(d::SimplexDistribution, x::AbstractVector{T}) where T<:Real - y, K = similar(x), length(x) - - sum_tmp = zero(T) - z = x[1] - y[1] = StatsFuns.logit(z) - log(one(T) / (K - 1)) - @inbounds for k in 2:K - 1 - sum_tmp += x[k - 1] - z = x[k] / (one(T) - sum_tmp) - y[k] = StatsFuns.logit(z) - log(one(T) / (K - k)) - end - y[K] = zero(T) - - return y -end - -# Vectorised implementation of the above. -function link(d::SimplexDistribution, X::AbstractMatrix{T}) where T<:Real - Y, K, N = similar(X), size(X, 1), size(X, 2) - - @inbounds for n in 1:size(X, 2) - sum_tmp, z = zero(T), X[1, n] - Y[1, n] = StatsFuns.logit(z) - log(one(T) / (K - 1)) - for k in 2:K - 1 - sum_tmp += X[k - 1, n] - z = X[k, n] / (one(T) - sum_tmp) - Y[k, n] = StatsFuns.logit(z) - log(one(T) / (K - k)) - end - Y[K, n] = zero(T) - end - - return Y -end - -function invlink(d::SimplexDistribution, y::AbstractVector{T}) where T<:Real - x, K = similar(y), length(y) - - z = StatsFuns.logistic(y[1] + log(one(T) / (K - 1))) - x[1] = z - sum_tmp = zero(T) - @inbounds for k = 2:K - 1 - z = StatsFuns.logistic(y[k] + log(one(T) / (K - k))) - sum_tmp += x[k-1] - x[k] = (one(T) - sum_tmp) * z - end - sum_tmp += x[K-1] - x[K] = one(T) - sum_tmp - - return x -end - -# Vectorised implementation of the above. -function invlink(d::SimplexDistribution, Y::AbstractMatrix{T}) where T<:Real - X, K, N = similar(Y), size(Y, 1), size(Y, 2) - - @inbounds for n in 1:size(X, 2) - sum_tmp, z = zero(T), StatsFuns.logistic(Y[1, n] + log(one(T) / (K - 1))) - X[1, n] = z - for k in 2:K - 1 - z = StatsFuns.logistic(Y[k, n] + log(one(T) / (K - k))) - sum_tmp += X[k - 1] - X[k, n] = (one(T) - sum_tmp) * z - end - sum_tmp += X[K - 1, n] - X[K, n] = one(T) - sum_tmp - end - - return X -end - -function logpdf_with_trans( - d::SimplexDistribution, - x::AbstractVector{<:Real}, - transform::Bool, -) - lp = logpdf(d, x) - if transform - K = length(x) - - sum_tmp = zero(eltype(x)) - z = x[1] - lp += log(z) + log(one(eltype(x)) - z) - @inbounds for k in 2:K-1 - sum_tmp += x[k-1] - z = x[k] / (one(eltype(x)) - sum_tmp) - lp += log(z) + log(one(eltype(x)) - z) + log(one(eltype(x)) - sum_tmp) - end - end - return lp -end - -# REVIEW: why do we put this piece of code here? -function logpdf_with_trans(d::Categorical, x::Int) - return d.p[x] > 0.0 && insupport(d, x) ? log(d.p[x]) : eltype(d.p)(-Inf) -end - - -############### -# MvLogNormal # -############### - -using Distributions: AbstractMvLogNormal - -link(d::AbstractMvLogNormal, x::AbstractVector{<:Real}) = log.(x) -invlink(d::AbstractMvLogNormal, y::AbstractVector{<:Real}) = exp.(y) -function logpdf_with_trans( - d::AbstractMvLogNormal, - x::AbstractVector{<:Real}, - transform::Bool, -) - return logpdf(d, x) + transform * sum(log, x) -end - -##################### -# Positive definite # -##################### - -const PDMatDistribution = Union{InverseWishart, Wishart} - -function link(d::PDMatDistribution, X::AbstractMatrix{T}) where {T<:Real} - Y = cholesky(X).L - for m in 1:size(Y, 1) - Y[m, m] = log(Y[m, m]) - end - return Matrix(Y) -end - -function invlink(d::PDMatDistribution, Y::AbstractMatrix{T}) where {T<:Real} - X, dim = copy(Y), size(Y) - for m in 1:size(X, 1) - X[m, m] = exp(X[m, m]) - end - return LowerTriangular(X) * LowerTriangular(X)' -end - -function logpdf_with_trans(d::PDMatDistribution, X::AbstractMatrix{<:Real}, transform::Bool) - lp = logpdf(d, X) - if transform && isfinite(lp) - U = cholesky(X).U - for i in 1:dim(d) - lp += (dim(d) - i + 2) * log(U[i, i]) - end - lp += dim(d) * log(2.0) - end - return lp -end - - -############################################ -# Defaults (assume identity link function) # -############################################ - -# UnivariateDistributions -using Distributions: UnivariateDistribution - -link(d::UnivariateDistribution, x::Real) = x -link(d::UnivariateDistribution, x::AbstractVector{<:Real}) = link.(Ref(d), x) - -invlink(d::UnivariateDistribution, y::Real) = y -invlink(d::UnivariateDistribution, y::AbstractVector{<:Real}) = invlink.(Ref(d), y) - -logpdf_with_trans(d::UnivariateDistribution, x::Real, ::Bool) = logpdf(d, x) -function logpdf_with_trans( - d::UnivariateDistribution, - x::AbstractVector{<:Real}, - transform::Bool, -) - return logpdf_with_trans.(Ref(d), x, transform) -end - -# MultivariateDistributions -using Distributions: MultivariateDistribution - -link(d::MultivariateDistribution, x::AbstractVector{<:Real}) = copy(x) -function link(d::MultivariateDistribution, X::AbstractMatrix{<:Real}) - Y = similar(X) - for n in 1:size(X, 2) - Y[:, n] = link(d, view(X, :, n)) - end - return Y -end - -invlink(d::MultivariateDistribution, y::AbstractVector{<:Real}) = copy(y) -function invlink(d::MultivariateDistribution, Y::AbstractMatrix{<:Real}) - X = similar(Y) - for n in 1:size(Y, 2) - X[:, n] = invlink(d, view(Y, :, n)) - end - return X -end - -function logpdf_with_trans(d::MultivariateDistribution, x::AbstractVector{<:Real}, ::Bool) - return logpdf(d, x) -end -function logpdf_with_trans( - d::MultivariateDistribution, - X::AbstractMatrix{<:Real}, - transform::Bool, -) - return [logpdf_with_trans(d, view(X, :, n), transform) for n in 1:size(X, 2)] -end - -# MatrixDistributions -using Distributions: MatrixDistribution - -link(d::MatrixDistribution, X::AbstractMatrix{<:Real}) = copy(X) -link(d::MatrixDistribution, X::AbstractVector{<:AbstractMatrix{<:Real}}) = link.(Ref(d), X) - -invlink(d::MatrixDistribution, Y::AbstractMatrix{<:Real}) = copy(Y) -function invlink(d::MatrixDistribution, Y::AbstractVector{<:AbstractMatrix{<:Real}}) - return invlink.(Ref(d), Y) -end - -logpdf_with_trans(d::MatrixDistribution, X::AbstractMatrix{<:Real}, ::Bool) = logpdf(d, X) -function logpdf_with_trans( - d::MatrixDistribution, - X::AbstractVector{<:AbstractMatrix{<:Real}}, - transform::Bool, -) - return logpdf_with_trans.(Ref(d), X, Ref(transform)) -end diff --git a/test/utility.jl b/test/utility.jl index dffe49df4..dd78e75b0 100644 --- a/test/utility.jl +++ b/test/utility.jl @@ -66,7 +66,7 @@ function runtests(; tests = ["all"]) # "pmmh.jl", "ipmcmc.jl", "pgibbs.jl", "smc.jl" ] TRACE_TESTS = ["trace.jl"] - ALL = union(CORE_TESTS, DISTR_TESTS, SAMPLER_TESTS, TRACE_TESTS) + ALL = union(CORE_TESTS, SAMPLER_TESTS, TRACE_TESTS) # test groups that should be executed TEST_GROUPS = "all" ∈ tests ? ALL : tests From 2fbbebce4669fe8a78da2ee00a4ace1b901f47aa Mon Sep 17 00:00:00 2001 From: Cameron Pfiffer Date: Mon, 1 Oct 2018 06:00:28 -0700 Subject: [PATCH 3/6] Removed 'Recent Posts' from homepage. --- docs/homepage/_layouts/home.html | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/homepage/_layouts/home.html b/docs/homepage/_layouts/home.html index d1428ebb0..09f7c011f 100644 --- a/docs/homepage/_layouts/home.html +++ b/docs/homepage/_layouts/home.html @@ -4,8 +4,6 @@ {{ content }} -

{{ site.data.ui-text[site.locale].recent_posts | default: "Recent Posts" }}

- {% for post in paginator.posts %} {% include archive-single.html %} {% endfor %} From 359c6f47ed623ed92c0c72404eeffa158cf1c358 Mon Sep 17 00:00:00 2001 From: Cameron Pfiffer Date: Mon, 1 Oct 2018 06:01:18 -0700 Subject: [PATCH 4/6] Updated documentation badge hyperlink. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index daa21bbb5..0df89b496 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![Coverage Status](https://coveralls.io/repos/github/yebai/Turing.jl/badge.svg?branch=master)](https://coveralls.io/github/yebai/Turing.jl?branch=master) [![Turing](http://pkg.julialang.org/badges/Turing_0.7.svg)](http://pkg.julialang.org/detail/Turing) [![Turing](http://pkg.julialang.org/badges/Turing_0.6.svg)](http://pkg.julialang.org/detail/Turing) -[![Documentation](https://img.shields.io/badge/doc-latest-blue.svg)](http://turing.ml/latest/) +[![Documentation](https://img.shields.io/badge/doc-latest-blue.svg)](http://turing.ml/docs/) News: **Turing.jl is now Julia 1.0 compatible now! Be aware that some things still might fail.** From d59da94a21c3dc29a2a0bb377eb403fa5d5057c1 Mon Sep 17 00:00:00 2001 From: Hong Ge Date: Mon, 1 Oct 2018 19:54:43 +0100 Subject: [PATCH 5/6] Renamed `homepage` ==> `site`. --- .gitignore | 4 ++-- docs/make.jl | 6 +++--- docs/{homepage => site}/Rakefile | 0 docs/{homepage => site}/_config.yml | 0 docs/{homepage => site}/_data/navigation.yml | 0 docs/{homepage => site}/_docs/advanced.md | 0 docs/{homepage => site}/_docs/api.md | 0 docs/{homepage => site}/_docs/assets/Documenter.css | 0 docs/{homepage => site}/_docs/assets/logo-build.jl | 0 docs/{homepage => site}/_docs/assets/logo.png | Bin .../_docs/assets/mathjaxhelper.js | 0 docs/{homepage => site}/_docs/contributing/guide.md | 0 .../_docs/contributing/style_guide.md | 0 docs/{homepage => site}/_docs/get-started.md | 0 docs/{homepage => site}/_docs/guide.md | 0 docs/{homepage => site}/_docs/index.md | 0 docs/{homepage => site}/_docs/quick-start.md | 0 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site}/assets/logo.png (100%) rename docs/{homepage => site}/assets/mathjaxhelper.js (100%) rename docs/{homepage => site}/assets/turing-logo.svg (100%) rename docs/{homepage => site}/banner.js (100%) rename docs/{homepage => site}/favicon.ico (100%) rename docs/{homepage => site}/index.html (100%) rename docs/{homepage => site}/index.md (100%) rename docs/{homepage => site}/package.json (100%) diff --git a/.gitignore b/.gitignore index c174e24ec..6b16e9092 100644 --- a/.gitignore +++ b/.gitignore @@ -15,7 +15,7 @@ deps/build.log docs/build/ docs/site/ -docs/homepage/_site/ -docs/homepage/.sass-cache/ +docs/site/_site/ +docs/site/.sass-cache/ .DS_Store diff --git a/docs/make.jl b/docs/make.jl index ffb05ab97..900d2f58e 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -5,9 +5,9 @@ using LibGit2: clone include("homepage-updater.jl") # Get paths. -examples_path = joinpath(@__DIR__, joinpath("homepage", "_tutorials")) +examples_path = joinpath(@__DIR__, joinpath("site", "_tutorials")) source_path = joinpath(@__DIR__, "src") -build_relative = joinpath("homepage", "_docs") +build_relative = joinpath("site", "_docs") build_path = joinpath(@__DIR__, build_relative) isdir(examples_path) || mkpath(examples_path) @@ -62,7 +62,7 @@ postprocess_markdown(build_path, yaml_dict, original = source_path) page_update = update_homepage( "github.com/TuringLang/Turing.jl.git", "gh-pages", - "homepage" + "site" ) # # Deploy documentation. diff --git a/docs/homepage/Rakefile b/docs/site/Rakefile similarity index 100% rename from docs/homepage/Rakefile rename to docs/site/Rakefile diff --git a/docs/homepage/_config.yml b/docs/site/_config.yml similarity index 100% rename from docs/homepage/_config.yml rename to docs/site/_config.yml diff --git a/docs/homepage/_data/navigation.yml b/docs/site/_data/navigation.yml similarity index 100% rename from docs/homepage/_data/navigation.yml rename to docs/site/_data/navigation.yml diff --git a/docs/homepage/_docs/advanced.md 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ed1a28ab5aca0b4734e627a028aac62d5240ab9a Mon Sep 17 00:00:00 2001 From: Hong Ge Date: Mon, 1 Oct 2018 20:25:11 +0100 Subject: [PATCH 6/6] Added `vec_assume_mat.jl` to skiptests (#570). --- test/vectorisation.jl/skip_tests | 1 + 1 file changed, 1 insertion(+) diff --git a/test/vectorisation.jl/skip_tests b/test/vectorisation.jl/skip_tests index dffb623ce..20d5a1530 100644 --- a/test/vectorisation.jl/skip_tests +++ b/test/vectorisation.jl/skip_tests @@ -1,2 +1,3 @@ # tests to skip vec_assume_mv.jl +vec_assume_mat.jl