Merge pull request #100 from Juice-jl/compressed-io

Support for `read` and `write` of circuits to *.gz compressed files

Author: guyvdbroeck

.github/workflows/slow_tests.yml

@@ -3,9 +3,10 @@ name: Slow Tests
 # Controls when the action will run. Triggers the workflow on push or pull request
 # events but only for the master branch
 on: 
-  pull_request:
-    branches:
-      master
+  # tests are not being maintained so don't run on pull requests
+  # pull_request:
+  #   branches:
+  #     master
 
   schedule:
     - cron: '0 0 */7 * *'
@@ -26,14 +27,13 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: 1.5
+          version: 1.6
 
       # Runs a single command using the runners shell
       - name: Unit Tests
         run: |
           julia --project=test -e 'using Pkg; Pkg.instantiate(); Pkg.build(); Pkg.precompile();'
           julia --project=test -e 'using Pkg; Pkg.develop("ProbabilisticCircuits");'
-          julia --project=test --check-bounds=yes --depwarn=yes test/_manual_/aqua_test.jl
           julia --project=test --check-bounds=yes --depwarn=yes test/_manual_/strudel_marginal_tests.jl
           julia --project=test --check-bounds=yes --depwarn=yes test/_manual_/strudel_likelihood_tests.jl
           julia --project=test --check-bounds=yes --depwarn=yes test/_manual_/ensembles_tests.jl

Project.toml

@@ -1,7 +1,7 @@
 name = "ProbabilisticCircuits"
 uuid = "2396afbe-23d7-11ea-1e05-f1aa98e17a44"
 authors = ["Guy Van den Broeck <guyvdb@cs.ucla.edu>"]
-version = "0.3.1"
+version = "0.3.2"
 
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
@@ -38,11 +38,11 @@ CUDA = "3"
 Clustering = "0.14"
 DataFrames = "1.2"
 DataStructures = "0.17, 0.18"
+DirectedAcyclicGraphs = "0.1.2"
 Distributions = "0.25"
-DirectedAcyclicGraphs = "0.1.1"
 Graphs = "1.4"
 Lerche = "0.5"
-LogicCircuits = "0.3.1"
+LogicCircuits = "0.3.2"
 LoopVectorization = "0.11, 0.12"
 MetaGraphs = "0.7"
 Metis = "1.0"

src/io/io.jl

@@ -14,7 +14,12 @@ include("plot.jl")
 # if no logic circuit file format is given on read, infer file format from extension
 
 function file2pcformat(file) 
-    if endswith(file,".jpc")
+    if endswith(file,".gz")
+        # duplicate code from `LogicCircuits.file2logicformat` -- not sure how to make this nicer
+        file_inner, _ = splitext(file)
+        format_inner = file2pcformat(file_inner)
+        GzipFormat(format_inner)
+    elseif endswith(file,".jpc")
         JpcFormat()
     elseif endswith(file,".psdd")
         PsddFormat()
@@ -64,6 +69,10 @@ Base.parse(::Type{ProbCircuit}, args...) =
 Base.read(io::IO, ::Type{ProbCircuit},  args...) = 
     read(io, PlainProbCircuit,  args...)
 
+Base.read(io::IO, ::Type{ProbCircuit}, f::GzipFormat) = 
+    # avoid method ambiguity
+    read(io, PlainProbCircuit,  f)
+
 # copy read/write API for tuples of files
 
 function Base.read(files::Tuple{AbstractString, AbstractString}, ::Type{C}, args...) where C <: StructProbCircuit
@@ -81,4 +90,4 @@ function Base.write(files::Tuple{AbstractString,AbstractString},
             write((io1, io2), circuit, args...)
         end
     end
-end
+end

src/io/spn_io.jl

@@ -1,5 +1,5 @@
 export zoo_spn, zoo_spn_file, 
-    SpnFormat, SpnVtreeFormat
+    SpnFormat
 
 struct SpnFormat <: FileFormat end
 

test/_manual_/aqua_test.jl test/aqua_test.jltest/_manual_/aqua_test.jl renamed to test/aqua_test.jl

@@ -60,6 +60,23 @@ include("../helper/pc_equals.jl")
         test_my_circuit(pc3)
         test_pc_equals(pc1, pc3)
         @test vtree(pc1) == vtree(pc3)
+
+        # read/write compressed
+        write("$jpc_path.gz", pc1)
+        pc2 = read("$jpc_path.gz", ProbCircuit)
+        
+        test_my_circuit(pc2)
+        test_pc_equals(pc1, pc2)
+
+        # read/write compressed structured
+        paths = ("$jpc_path.gz", vtree_path)
+        write(paths, pc1)
+        pc3 = read(paths, StructProbCircuit) 
+        
+        @test pc3 isa StructProbCircuit
+        test_my_circuit(pc3)
+        test_pc_equals(pc1, pc3)
+        @test vtree(pc1) == vtree(pc3)
 
     end
 

test/io/jpc_io_test.jl

@@ -70,6 +70,22 @@ include("../helper/pc_equals.jl")
         @test vtree(pc1) == vtree(pc3)
         test_pc_equals(pc0, pc3)
 
+        # read/write compressed
+        write("$psdd_path.gz", pc1)
+        pc2 = read("$psdd_path.gz", ProbCircuit)
+        
+        test_my_circuit(pc2)
+        test_pc_equals(pc1, pc2)
+
+        # read/write compressed structured
+        paths = ("$psdd_path.gz", vtree_path)
+        write(paths, pc1)
+        pc3 = read(paths, StructProbCircuit) 
+        
+        @test pc3 isa StructProbCircuit
+        test_my_circuit(pc3)
+        test_pc_equals(pc1, pc3)
+        @test vtree(pc1) == vtree(pc3)
     end
 
 end

test/io/psdd_io_test.jl

@@ -44,6 +44,13 @@ include("../helper/pc_equals.jl")
         test_my_circuit(pc2)
         test_pc_equals(pc1, pc2)
 
+        # try compressed
+        write("$spn_path.gz", pc1)
+        pc2 = read("$spn_path.gz", ProbCircuit)
+        
+        test_my_circuit(pc2)
+        test_pc_equals(pc1, pc2)
+
     end
 
 end