Merge remote-tracking branch 'origin/master' into s/fix-rebase

Author: shashi

.github/workflows/CompatHelper.yml

@@ -0,0 +1,26 @@
+name: CompatHelper
+
+on:
+  schedule:
+    - cron: '00 * * * *'
+  issues:
+    types: [opened, reopened]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.2.0]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -0,0 +1,11 @@
+name: TagBot
+on:
+  schedule:
+    - cron: 0 * * * *
+jobs:
+  TagBot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.travis.yml

@@ -4,7 +4,7 @@ os:
   - linux
   - osx
 julia:
-  - 1.2
+  - 1.3
   - nightly
 matrix:
   allow_failures:

Project.toml

@@ -1,7 +1,7 @@
 name = "SparsityDetection"
 uuid = "684fba80-ace3-11e9-3d08-3bc7ed6f96df"
 authors = ["Shashi Gowda", "Chris Rackauckas <contact@chrisrackauckas.com>"]
-version = "0.1.1"
+version = "0.2.0"
 
 [deps]
 Cassette = "7057c7e9-c182-5462-911a-8362d720325c"
@@ -10,11 +10,14 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 
 [compat]
+Cassette = "0.2, 0.3"
+SpecialFunctions = "0.8, 0.9, 0.10"
 julia = "1"
 
 [extras]
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "FiniteDiff"]
+test = ["FiniteDiff", "SafeTestsets", "Test"]

README.md

@@ -1,6 +1,6 @@
 # SparsityDetection.jl
 
-[![Build Status](https://travis-ci.org/JuliaDiffEq/SparsityDetection.jl.svg?branch=master)](https://travis-ci.org/JuliaDiffEq/SparsityDetection.jl)
+[![Build Status](https://travis-ci.org/SciML/SparsityDetection.jl.svg?branch=master)](https://travis-ci.org/SciML/SparsityDetection.jl)
 [![Build status](https://ci.appveyor.com/api/projects/status/iruuqu4hxq00vo3s?svg=true)](https://ci.appveyor.com/project/ChrisRackauckas/sparsitydetection-jl)
 
 This is a package for automatic Jacobian and Hessian sparsity pattern detection
@@ -10,6 +10,16 @@ numerically, and instead works by non-standard interpretation in order to
 check every branch for connectivity in order to determine an accurate sparsity
 pattern.
 
+If you use this package, please cite the following:
+
+```
+@article{gowda2019sparsity,
+  title={Sparsity Programming: Automated Sparsity-Aware Optimizations in Differentiable Programming},
+  author={Gowda, Shashi and Ma, Yingbo and Churavy, Valentin and Edelman, Alan and Rackauckas, Christopher},
+  year={2019}
+}
+```
+
 ## Example
 
 Suppose we had the function
@@ -36,9 +46,12 @@ vector of length 30 and takes in a vector of length 30, and `sparsity!` spits
 out a `Sparsity` object which we can turn into a `SparseMatrixCSC`:
 
 ```julia
-using SparsityDetection
+using SparsityDetection, SparseArrays
+input = rand(10)
+output = similar(input)
 sparsity_pattern = sparsity!(f,output,input)
 jac = Float64.(sparse(sparsity_pattern))
+
 ```
 
 ## API

appveyor.yml

@@ -1,7 +1,7 @@
 environment:
   matrix:
-  - julia_version: 1.1
-  - julia_version: nightly
+  - julia_version: 1.3
+#  - julia_version: nightly
 
 platform:
   - x86 # 32-bit

src/index.jl

@@ -1,17 +1,32 @@
 ### Rules
 using Test
-using Cassette
-import Cassette: tag, untag, Tagged, metadata, hasmetadata, istagged
-using SparseArrays
-using SparsityDetection
-import SparsityDetection: abstract_run, HessianSparsityContext,
-                          JacobianSparsityContext, TermCombination, HessInput
-using Test
+using Cassette, SparsityDetection
+using SparseArrays, Test
+
+using Cassette: tag, untag, Tagged, metadata, hasmetadata, istagged
+using SparsityDetection: Path, BranchesPass, SparsityContext, Fixed,
+    Input, Output, pset, Tainted, istainted,
+    alldone, reset!, HessianSparsityContext
+using SparsityDetection: TermCombination
 
 Term(i...) = TermCombination(Set([Dict(j=>1 for j in i)]))
 
 function jactester(f, Y, X, args...)
     ctx, val = jacobian_sparsity(f, Y, X, args...; raw=true)
+    val = nothing
+    while true
+        val = Cassette.overdub(ctx,
+                            f,
+                            tag(Y, ctx, Output()),
+                            tag(X, ctx, Input()),
+                            map(arg -> arg isa Fixed ?
+                                arg.value :
+                                tag(arg, ctx, pset()), args)...)
+        println("Explored path: ", path)
+        alldone(path) && break
+        reset!(path)
+    end
+    return ctx, val
 end
 
 jactestmeta(args...) = jactester(args...)[1].metadata

test/common.jl

@@ -1,3 +1,4 @@
+using SafeTestsets
 include("common.jl")
 
 @testset "Jacobian Sparsity" begin include("jacobian.jl") end