change cache to work with figures (#158)

* Changed read/write cache to use serialize/deserialize instead of
JLD2. JLD2 fails to save strings longer than 2^16 characters, which
can occur in the stringmime() of large figures.

* Added test for cache with figures and html output.
Updated REQUIRE & Project.toml to include Serialization instead of
FileIO and JLD2

* Added "Import Pkg;" to expected output of errors, so that tests pass.

Project.toml

@@ -9,8 +9,7 @@ Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
-JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Highlights = "eafb193a-b7ab-5a9e-9068-77385905fa72"
 Mustache = "ffc61752-8dc7-55ee-8c37-f3e9cdd09e70"

REQUIRE

@@ -1,6 +1,5 @@
 julia 0.7
-JLD2
-FileIO
+Serialization
 JSON
 Highlights 0.3.0
 Mustache

src/cache.jl

@@ -1,16 +1,21 @@
-#FileIO and JLD2 are imported only if cache is used
+#Serialization is imported only if cache is used
 
 function write_cache(doc::WeaveDoc, cache_path)
     cache_dir = joinpath(doc.cwd, cache_path)
     isdir(cache_dir) || mkpath(cache_dir)
-    Base.invokelatest(FileIO.save, joinpath(cache_dir, doc.basename * ".jld2"), Dict("doc" => doc))
+    open(joinpath(cache_dir, doc.basename * ".cache"),"w") do io
+        Serialization.serialize(io, doc)
+    end
     return nothing
 end
 
 function read_cache(doc::WeaveDoc, cache_path)
-    name = joinpath(doc.cwd, cache_path, doc.basename * ".jld2")
+    name = joinpath(doc.cwd, cache_path, doc.basename * ".cache")
     isfile(name) || return nothing
-    return Base.invokelatest(FileIO.load, name, "doc")
+    open(name,"r") do io
+        doc = Serialization.deserialize(io)
+    end
+    return doc
 end
 
 function restore_chunk(chunk::CodeChunk, cached)
@@ -35,7 +40,7 @@ end
 #Restore inline code
 function restore_chunk(chunk::DocChunk, cached::WeaveDoc)
     #Get chunk from cached doc
-    c_chunk = filter(x -> x.number == chunk.number && 
+    c_chunk = filter(x -> x.number == chunk.number &&
                     isa(x,  DocChunk), cached.chunks)
     isempty(c_chunk) && return chunk
     c_chunk = c_chunk[1]
@@ -45,7 +50,7 @@ function restore_chunk(chunk::DocChunk, cached::WeaveDoc)
     isempty(c_inline) && return chunk
 
     #Restore cached results for Inline code
-    n = length(chunk.content)    
+    n = length(chunk.content)
     for i in 1:n
         if isa(chunk.content[i], InlineCode)
             ci = filter(x -> x.number == chunk.content[i].number, c_inline)

src/run.jl

@@ -41,7 +41,7 @@ function Base.run(doc::WeaveDoc; doctype = :auto,
         fig_path = mktempdir(abspath(doc.cwd))
     end
 
-    cache == :off || @eval import FileIO, JLD2
+    cache == :off || @eval import Serialization
 
     #This is needed for latex and should work on all output formats
     Sys.iswindows() && (fig_path = replace(fig_path, "\\" => "/"))

test/errors_test.jl

@@ -26,8 +26,7 @@ doc1 = Weave.run(doc, doctype = "pandoc")
 
 doc1.chunks[1].output
 
-@test doc1.chunks[1].output == "Error: ArgumentError: Package NonExisting not found in current path:\n- Run `Pkg.add(\"NonExisting\")` to install the NonExisting package.\n\n"
-
+@test doc1.chunks[1].output == "Error: ArgumentError: Package NonExisting not found in current path:\n- Run `import Pkg; Pkg.add(\"NonExisting\")` to install the NonExisting package.\n\n"
 @test doc1.chunks[2].output == "Error: syntax: incomplete: premature end of input\n"
 @test doc1.chunks[3].output == "\njulia> plot(x)\nError: UndefVarError: plot not defined\n\njulia> y = 10\n10\n\njulia> print(y\nError: syntax: incomplete: premature end of input\n"
 
@@ -35,7 +34,7 @@ doc1.chunks[1].output
 
 doc = Weave.WeaveDoc("dummy1.jmd", p1, Dict())
 doc3 = Weave.run(doc, doctype = "md2html")
-@test doc3.chunks[1].rich_output == "<pre class=\"julia-error\">\nERROR: ArgumentError: Package NonExisting not found in current path:\n- Run &#96;Pkg.add&#40;&quot;NonExisting&quot;&#41;&#96; to install the NonExisting package.\n\n</pre>\n"
+@test doc3.chunks[1].rich_output == "<pre class=\"julia-error\">\nERROR: ArgumentError: Package NonExisting not found in current path:\n- Run &#96;import Pkg; Pkg.add&#40;&quot;NonExisting&quot;&#41;&#96; to install the NonExisting package.\n\n</pre>\n"
 @test doc3.chunks[2].rich_output == "<pre class=\"julia-error\">\nERROR: syntax: incomplete: premature end of input\n</pre>\n"
 @test doc3.chunks[3].output == "\njulia> plot(x)\nError: UndefVarError: plot not defined\n\njulia> y = 10\n10\n\njulia> print(y\nError: syntax: incomplete: premature end of input\n"
 @test doc3.chunks[3].rich_output == ""

test/plotsjl_test.jl

@@ -11,3 +11,12 @@ end
 
 pljtest("plotsjl_test_gr.jmd", "plotsjl_test_gr.md", "pandoc")
 pljtest("plotsjl_test_gr.jmd", "plotsjl_test_gr.tex", "tex")
+
+# test cache with plots
+isdir("documents/cache") && rm("documents/cache", recursive = true)
+weave("documents/plotsjl_test_gr.jmd", cache=:all)
+result =  read("documents/plotsjl_test_gr.html", String)
+rm("documents/plotsjl_test_gr.html")
+weave("documents/plotsjl_test_gr.jmd", cache=:all)
+cached_result =  read("documents/plotsjl_test_gr.html", String)
+@test result == cached_result