Add soft scoping rule capabilities

This patch enables "soft" scoping rules (see e.g.
https://github.com/JuliaLang/SoftGlobalScope.jl) for code execution
(markdown and notebook output). This is enabled by default for Jupyter
notebook output (to mimic how the IJulia kernel works), and disabled
otherwise. Soft scope rules can be enabled/disabled with the `softscope
:: Bool` configuration variable. Fixes #227.

CHANGELOG.md

@@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Added
+- "Soft" scoping rules (see e.g. https://github.com/JuliaLang/SoftGlobalScope.jl) are now
+  available for code execution (markdown and notebook output). This is enabled by default
+  for Jupyter notebook output (to mimic how the IJulia kernel works), and disabled
+  otherwise. Soft scope rules can be enabled/disabled with the `softscope :: Bool`
+  configuration variable. ([#227][github-227], [#230][github-230])
 ### Changed
 - The minimum Julia version requirement for Literate >= 2.16.0 is now 1.6.0 (from 1.0.0).
   ([#230][github-230])
@@ -269,6 +275,7 @@ https://discourse.julialang.org/t/ann-literate-jl/10651 for release announcement
 [github-221]: https://github.com/fredrikekre/Literate.jl/pull/221
 [github-222]: https://github.com/fredrikekre/Literate.jl/issues/222
 [github-223]: https://github.com/fredrikekre/Literate.jl/pull/223
+[github-227]: https://github.com/fredrikekre/Literate.jl/issues/227
 [github-228]: https://github.com/fredrikekre/Literate.jl/issues/228
 [github-229]: https://github.com/fredrikekre/Literate.jl/pull/229
 [github-230]: https://github.com/fredrikekre/Literate.jl/pull/230

src/Literate.jl

@@ -312,6 +312,7 @@ function create_configuration(inputfile; user_config, user_kwargs, type=nothing)
     cfg["flavor"] = type === (:md) ? DocumenterFlavor() : DefaultFlavor()
     cfg["credit"] = true
     cfg["mdstrings"] = false
+    cfg["softscope"] = type === (:nb) ? true : false # on for Jupyter notebooks
     cfg["keep_comments"] = false
     cfg["execute"] = type === :md ? false : true
     cfg["codefence"] = get(user_config, "flavor", cfg["flavor"]) isa DocumenterFlavor &&
@@ -408,6 +409,8 @@ Available options:
 - `devurl` (default: `"dev"`): URL for "in-development" docs, see [Documenter docs]
   (https://juliadocs.github.io/Documenter.jl/). Unused if `repo_root_url`/
   `nbviewer_root_url`/`binder_root_url` are set.
+- `softscope` (default: `true` for Jupyter notebooks, `false` otherwise): enable/disable
+  "soft" scoping rules when executing, see e.g. https://github.com/JuliaLang/SoftGlobalScope.jl.
 - `repo_root_url`: URL to the root of the repository. Determined automatically on Travis CI,
   GitHub Actions and GitLab CI. Used for `@__REPO_ROOT_URL__`.
 - `nbviewer_root_url`: URL to the root of the repository as seen on nbviewer. Determined
@@ -580,6 +583,7 @@ function markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
                                       flavor=config["flavor"],
                                       image_formats=config["image_formats"],
                                       file_prefix="$(config["name"])-$(chunknum)",
+                                      softscope=config["softscope"],
                     )
                 end
             end
@@ -597,9 +601,10 @@ end
 
 function execute_markdown!(io::IO, sb::Module, block::String, outputdir;
                            inputfile::String, fake_source::String,
-                           flavor::AbstractFlavor, image_formats::Vector, file_prefix::String)
+                           flavor::AbstractFlavor, image_formats::Vector, file_prefix::String,
+                           softscope::Bool)
     # TODO: Deal with explicit display(...) calls
-    r, str, _ = execute_block(sb, block; inputfile=inputfile, fake_source=fake_source)
+    r, str, _ = execute_block(sb, block; inputfile=inputfile, fake_source=fake_source, softscope=softscope)
     # issue #101: consecutive codefenced blocks need newline
     # issue #144: quadruple backticks allow for triple backticks in the output
     plain_fence = "\n````\n" =>  "\n````"
@@ -734,7 +739,8 @@ function jupyter_notebook(chunks, config)
         try
             cd(config["literate_outputdir"]) do
                 nb = execute_notebook(nb; inputfile=config["literate_inputfile"],
-                                          fake_source=config["literate_outputfile"])
+                                          fake_source=config["literate_outputfile"],
+                                          softscope=config["softscope"])
             end
         catch err
             @error "error when executing notebook based on input file: " *
@@ -745,7 +751,7 @@ function jupyter_notebook(chunks, config)
     return nb
 end
 
-function execute_notebook(nb; inputfile::String, fake_source::String)
+function execute_notebook(nb; inputfile::String, fake_source::String, softscope::Bool)
     sb = sandbox()
     execution_count = 0
     for cell in nb["cells"]
@@ -753,7 +759,7 @@ function execute_notebook(nb; inputfile::String, fake_source::String)
         execution_count += 1
         cell["execution_count"] = execution_count
         block = join(cell["source"])
-        r, str, display_dicts = execute_block(sb, block; inputfile=inputfile, fake_source=fake_source)
+        r, str, display_dicts = execute_block(sb, block; inputfile=inputfile, fake_source=fake_source, softscope=softscope)
 
         # str should go into stream
         if !isempty(str)
@@ -835,7 +841,7 @@ function Base.display(ld::LiterateDisplay, mime::MIME, x)
 end
 
 # Execute a code-block in a module and capture stdout/stderr and the result
-function execute_block(sb::Module, block::String; inputfile::String, fake_source::String)
+function execute_block(sb::Module, block::String; inputfile::String, fake_source::String, softscope::Bool)
     @debug """execute_block($sb, block)
     ```
     $(block)
@@ -851,7 +857,11 @@ function execute_block(sb::Module, block::String; inputfile::String, fake_source
     # `rethrow = Union{}` means that we try-catch all the exceptions thrown in the do-block
     # and return them via the return value (they get handled below).
     c = IOCapture.capture(rethrow = Union{}) do
-        include_string(sb, block, fake_source)
+        if softscope
+            include_string(REPL.softscope, sb, block, fake_source)
+        else
+            include_string(sb, block, fake_source)
+        end
     end
     popdisplay(disp) # IOCapture.capture has a try-catch so should always end up here
     if c.error

test/runtests.jl

@@ -905,6 +905,27 @@ end end
             Literate.markdown(inputfile, relpath(outdir); execute=true,
                               flavor=Literate.CommonMarkFlavor())
             @test read(joinpath(outdir, "inputfile-1.svg"), String) == "issue228"
+
+            # Softscope
+            write(
+                inputfile,
+                """
+                ret = 0
+                for k = 1:10
+                    ret += k
+                end
+                println("ret = ", ret)
+                """
+            )
+            Literate.markdown(inputfile, outdir; execute=true, softscope=true)
+            @test occursin("ret = 55", read(joinpath(outdir, "inputfile.md"), String))
+            ## Disabled softscope
+            try
+                Literate.markdown(inputfile, outdir; execute=true, softscope=false)
+                error("unreachable")
+            catch err
+                @test occursin(r"`?ret`? not defined", sprint(Base.showerror, err))
+            end
         end # cd(sandbox)
     end # mktemp
 end end
@@ -1319,8 +1340,33 @@ end end
             @test keys(cellout[1]["data"]) == Set(("text/latex",))
             @test cellout[1]["data"]["text/latex"] == "DF(4) as text/latex"
             @test !haskey(cellout[1], "execution_count")
-        end
-    end
+
+            # Softscope
+            # TODO: Windows CI says here, but no longer: The input file that have been used
+            #       above multiple times without problem now gives
+            #       "SystemError: opening file: Invalid argument" for some reason...
+            new_inputfile = "inputfile2.jl"
+            write(
+                new_inputfile,
+                """
+                ret = 0
+                for k = 1:10
+                    ret += k
+                end
+                println("ret = ", ret)
+                """
+            )
+            Literate.notebook(new_inputfile, outdir)
+            @test occursin("ret = 55", read(joinpath(outdir, "inputfile2.ipynb"), String))
+            ## Disabled softscope
+            try
+                Literate.notebook(new_inputfile, outdir; softscope=false)
+                error("unreachable")
+            catch err
+                @test occursin(r"`?ret`? not defined", sprint(Base.showerror, err))
+            end
+        end # cd(sandbox)
+    end # mktempdir
 end end
 
 @testset "Configuration" begin; Base.CoreLogging.with_logger(Base.CoreLogging.NullLogger()) do