Merge pull request #371 from JunoLab/avi/error

follow RMarkdown more: make `throw_error` option into chunk option

doc/src/chunk_options.md

@@ -33,6 +33,7 @@ we've mostly followed [RMarkdown's namings](http://yihui.name/knitr/options), bu
 ### Evaluation
 
 - `eval = true`: Evaluate the code chunk. If `false` the chunk won’t be executed.
+- `error = true`: If `true` [`weave`](@ref) won't stop on errors and rather they will be included in output document. If `false`, [`weave`](@ref) will halt on any of un-caught errors.
 - `cache = false`: Cache results, depending on `cache` parameter on [`weave`](@ref) function.
 - `tangle = true`: Set tangle to `false` to exclude chunk from tangled code.
 

src/Weave.jl

@@ -96,7 +96,6 @@ Weave an input document to output file.
   * `:all` caches everything
   * `:user` caches based on chunk options
   * `:refresh` runs all code chunks and save new cache
-- `throw_errors::Bool = false`: If `false` errors are included in output document and the whole document is executed. If `true` errors are thrown when they occur
 - `template::Union{Nothing,AbstractString,Mustache.MustacheTokens} = nothing`: Template (file path) or `Mustache.MustacheTokens`s for `md2html` or `md2tex` formats
 - `css::Union{Nothing,AbstractString} = nothing`: Path of a CSS file used for md2html format
 - `highlight_theme::Union{Nothing,Type{<:Highlights.AbstractTheme}} = nothing`: Theme used for syntax highlighting (defaults to `Highlights.Themes.DefaultTheme`)
@@ -118,7 +117,6 @@ function weave(
     fig_ext::Union{Nothing,AbstractString} = nothing,
     cache_path::AbstractString = "cache",
     cache::Symbol = :off,
-    throw_errors::Bool = false,
     template::Union{Nothing,AbstractString,Mustache.MustacheTokens} = nothing,
     css::Union{Nothing,AbstractString} = nothing, # TODO: rename to `stylesheet`
     highlight_theme::Union{Nothing,Type{<:Highlights.AbstractTheme}} = nothing,
@@ -158,7 +156,6 @@ function weave(
         fig_ext = get(weave_options, "fig_ext", fig_ext)
         cache_path = get(weave_options, "cache_path", cache_path)
         cache = Symbol(get(weave_options, "cache", cache))
-        throw_errors = get(weave_options, "throw_errors", throw_errors)
     end
 
     doc = run_doc(
@@ -171,7 +168,6 @@ function weave(
         fig_ext = fig_ext,
         cache_path = cache_path,
         cache = cache,
-        throw_errors = throw_errors,
     )
 
     # render document

src/config.jl

@@ -5,6 +5,7 @@ const _DEFAULT_PARAMS = Dict{Symbol,Any}(
     :hold => false,
     :fig => true,
     :eval => true,
+    :error => true,
     :tangle => true,
     :cache => false,
     :fig_cap => nothing,

src/display_methods.jl

@@ -12,24 +12,10 @@ mutable struct Report <: AbstractDisplay
     mimetypes::Vector{String}
     first_plot::Bool
     header_script::String
-    throw_errors::Bool
 end
 
-function Report(cwd, basename, format, mimetypes, throw_errors)
-    Report(
-        cwd,
-        basename,
-        format,
-        "",
-        1,
-        String[],
-        nothing,
-        mimetypes,
-        true,
-        "",
-        throw_errors,
-    )
-end
+Report(cwd, basename, format, mimetypes) =
+    Report(cwd, basename, format, "", 1, String[], nothing, mimetypes, true, "")
 
 # Default mimetypes in order, can be overridden for some inside `run method` formats
 const default_mime_types = ["image/svg+xml", "image/png", "text/html", "text/plain"]

src/run.jl

@@ -13,7 +13,6 @@ function run_doc(
     fig_ext::Union{Nothing,AbstractString} = nothing,
     cache_path::AbstractString = "cache",
     cache::Symbol = :off,
-    throw_errors::Bool = false,
 )
     # cache :all, :user, :off, :refresh
 
@@ -43,7 +42,7 @@ function run_doc(
 
     mimetypes = doc.format.mimetypes
 
-    report = Report(cwd, doc.basename, doc.format, mimetypes, throw_errors)
+    report = Report(cwd, doc.basename, doc.format, mimetypes)
     cd_back = let d = pwd(); () -> cd(d); end
     cd(cwd)
     pushdisplay(report)
@@ -207,7 +206,7 @@ function run_code(doc::WeaveDoc, chunk::CodeChunk, report::Report, mod::Module)
             doc.path,
             chunk.options[:term],
             i == n,
-            report.throw_errors,
+            chunk.options[:error],
         )
         figures = report.figures # Captured figures
         result = ChunkOutput(s, out, report.rich_output, figures)
@@ -230,7 +229,7 @@ function parse_input(s)
     return res
 end
 
-function capture_output(mod, s, path, term, lastline, throw_errors = false)
+function capture_output(mod, s, path, term, lastline, error)
     local out = nothing
     local obj = nothing
 
@@ -244,7 +243,7 @@ function capture_output(mod, s, path, term, lastline, throw_errors = false)
             !isnothing(obj) && (term || lastline) && display(obj)
         catch _err
             err = unwrap_load_err(_err)
-            throw_errors && throw(err)
+            error || throw(err)
             display(err)
             @warn "ERROR: $(typeof(err)) occurred, including output in Weaved document"
         finally

test/test_error_rendering.jl

@@ -27,7 +27,7 @@ $err_stmt1
 $err_stmt2
 ```
 
-```julia; term=true
+```julia; term = true
 $err_stmt3
 ```
 """
@@ -47,6 +47,17 @@ let doc = mock_run(str; doctype = "github")
     @test occursin(err_str3_2, get_output(3))
 end
 
-@test_throws ArgumentError mock_run(str; doctype = "github", throw_errors = true)
+# TODO: move this into chunk option tests
+str = """
+```julia; error = true
+using  # won't be thrown
+```
+
+```julia; error = false
+using NonExisting # will be thrown
+```
+"""
+
+@test_throws ArgumentError mock_run(str; doctype = "github")
 
 # TODO: test error rendering in `rich_output`