r
/
Literate.jl
mirror of https://github.com/fredrikekre/Literate.jl
1
0
Fork 0
Code Releases Activity
Browse Source

Fix cwd and apparent source file when executing markdown. (#195)

pull/203/head
Fredrik Ekre 4 years ago committed by GitHub
parent
d0091536df
commit
53a9d26ff8
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 38 additions and 22 deletions
Whitespace
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Unified View
Diff Options
Show Stats Download Patch File Download Diff File
  1. 5
      CHANGELOG.md
  2. 47
      src/Literate.jl
  3. 8
      test/runtests.jl

5
CHANGELOG.md
Unescape View File

@ -6,6 +6,11 @@ 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). and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased] ## [Unreleased]
### Fixed
- Set current working directory for markdown execution to the output directory, just like
notebook execution. ([#195][github-195])
- Set the apparent source file to the output file for markdown and notebook execution.
([#195][github-195])
## [2.13.1] - 2022-04-12 ## [2.13.1] - 2022-04-12
### Fixed ### Fixed

47
src/Literate.jl
Unescape View File

@ -405,6 +405,12 @@ function preprocessor(inputfile, outputdir; user_config, user_kwargs, type)
inputfile = realpath(abspath(inputfile)) inputfile = realpath(abspath(inputfile))
mkpath(outputdir) mkpath(outputdir)
outputdir = realpath(abspath(outputdir)) outputdir = realpath(abspath(outputdir))
isdir(outputdir) || error("not a directory: $(outputdir)")
ext = type === (:nb) ? ".ipynb" : ".$(type)"
outputfile = joinpath(outputdir, config["name"]::String * ext)
if inputfile == outputfile
throw(ArgumentError("outputfile (`$outputfile`) is identical to inputfile (`$inputfile`)"))
end
output_thing = type === (:md) ? "markdown page" : output_thing = type === (:md) ? "markdown page" :
type === (:nb) ? "notebook" : type === (:nb) ? "notebook" :
@ -414,7 +420,8 @@ function preprocessor(inputfile, outputdir; user_config, user_kwargs, type)
# Add some information for passing around Literate methods # Add some information for passing around Literate methods
config["literate_inputfile"] = inputfile config["literate_inputfile"] = inputfile
config["literate_outputdir"] = outputdir config["literate_outputdir"] = outputdir
config["literate_ext"] = type === (:nb) ? ".ipynb" : ".$(type)" config["literate_ext"] = ext
config["literate_outputfile"] = outputfile
# read content # read content
content = read(inputfile, String) content = read(inputfile, String)
@ -445,13 +452,7 @@ function preprocessor(inputfile, outputdir; user_config, user_kwargs, type)
end end
function write_result(content, config; print=print) function write_result(content, config; print=print)
inputfile = config["literate_inputfile"] outputfile = config["literate_outputfile"]
outputdir = config["literate_outputdir"]
isdir(outputdir) || error("not a directory: $(outputdir)")
outputfile = joinpath(outputdir, config["name"]::String * config["literate_ext"])
if inputfile == outputfile
throw(ArgumentError("outputfile (`$outputfile`) is identical to inputfile (`$inputfile`)"))
end
@info "writing result to `$(Base.contractuser(outputfile))`" @info "writing result to `$(Base.contractuser(outputfile))`"
open(outputfile, "w") do io open(outputfile, "w") do io
print(io, content) print(io, content)
@ -543,10 +544,13 @@ function markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
write(iocode, codefence.second, '\n') write(iocode, codefence.second, '\n')
any(write_line, chunk.lines) && write(iomd, seekstart(iocode)) any(write_line, chunk.lines) && write(iomd, seekstart(iocode))
if execute if execute
execute_markdown!(iomd, sb, join(chunk.lines, '\n'), outputdir; cd(config["literate_outputdir"]) do
inputfile=config["literate_inputfile"], execute_markdown!(iomd, sb, join(chunk.lines, '\n'), outputdir;
flavor=config["flavor"], inputfile=config["literate_inputfile"],
image_formats=config["image_formats"]) fake_source=config["literate_outputfile"],
flavor=config["flavor"],
image_formats=config["image_formats"])
end
end end
end end
write(iomd, '\n') # add a newline between each chunk write(iomd, '\n') # add a newline between each chunk
@ -561,10 +565,10 @@ function markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
end end
function execute_markdown!(io::IO, sb::Module, block::String, outputdir; function execute_markdown!(io::IO, sb::Module, block::String, outputdir;
inputfile::String="<unknown>", flavor::AbstractFlavor, inputfile::String, fake_source::String,
image_formats::Vector) flavor::AbstractFlavor, image_formats::Vector)
# TODO: Deal with explicit display(...) calls # TODO: Deal with explicit display(...) calls
r, str, _ = execute_block(sb, block; inputfile=inputfile) r, str, _ = execute_block(sb, block; inputfile=inputfile, fake_source=fake_source)
# issue #101: consecutive codefenced blocks need newline # issue #101: consecutive codefenced blocks need newline
# issue #144: quadruple backticks allow for triple backticks in the output # issue #144: quadruple backticks allow for triple backticks in the output
plain_fence = "\n````\n" => "\n````" plain_fence = "\n````\n" => "\n````"
@ -698,7 +702,8 @@ function jupyter_notebook(chunks, config)
@info "executing notebook `$(config["name"] * ".ipynb")`" @info "executing notebook `$(config["name"] * ".ipynb")`"
try try
cd(config["literate_outputdir"]) do cd(config["literate_outputdir"]) do
nb = execute_notebook(nb; inputfile=config["literate_inputfile"]) nb = execute_notebook(nb; inputfile=config["literate_inputfile"],
fake_source=config["literate_outputfile"])
end end
catch err catch err
@error "error when executing notebook based on input file: " * @error "error when executing notebook based on input file: " *
@ -709,7 +714,7 @@ function jupyter_notebook(chunks, config)
return nb return nb
end end
function execute_notebook(nb; inputfile::String="<unknown>") function execute_notebook(nb; inputfile::String, fake_source::String)
sb = sandbox() sb = sandbox()
execution_count = 0 execution_count = 0
for cell in nb["cells"] for cell in nb["cells"]
@ -717,7 +722,7 @@ function execute_notebook(nb; inputfile::String="<unknown>")
execution_count += 1 execution_count += 1
cell["execution_count"] = execution_count cell["execution_count"] = execution_count
block = join(cell["source"]) block = join(cell["source"])
r, str, display_dicts = execute_block(sb, block; inputfile=inputfile) r, str, display_dicts = execute_block(sb, block; inputfile=inputfile, fake_source=fake_source)
# str should go into stream # str should go into stream
if !isempty(str) if !isempty(str)
@ -799,7 +804,7 @@ function Base.display(ld::LiterateDisplay, mime::MIME, x)
end end
# Execute a code-block in a module and capture stdout/stderr and the result # Execute a code-block in a module and capture stdout/stderr and the result
function execute_block(sb::Module, block::String; inputfile::String="<unknown>") function execute_block(sb::Module, block::String; inputfile::String, fake_source::String)
@debug """execute_block($sb, block) @debug """execute_block($sb, block)
``` ```
$(block) $(block)
@ -815,13 +820,13 @@ function execute_block(sb::Module, block::String; inputfile::String="<unknown>")
# `rethrow = Union{}` means that we try-catch all the exceptions thrown in the do-block # `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). # and return them via the return value (they get handled below).
c = IOCapture.capture(rethrow = Union{}) do c = IOCapture.capture(rethrow = Union{}) do
include_string(sb, block) include_string(sb, block, fake_source)
end end
popdisplay(disp) # IOCapture.capture has a try-catch so should always end up here popdisplay(disp) # IOCapture.capture has a try-catch so should always end up here
if c.error if c.error
error(""" error("""
$(sprint(showerror, c.value)) $(sprint(showerror, c.value))
when executing the following code block in file `$(Base.contractuser(inputfile))` when executing the following code block from inputfile `$(Base.contractuser(inputfile))`
```julia ```julia
$block $block

8
test/runtests.jl
Unescape View File

@ -824,6 +824,10 @@ end end
print("a: ", a); nothing #hide print("a: ", a); nothing #hide
#- #-
47 #hide 47 #hide
#-
(@__DIR__) == pwd() ? "cwd correct" : "cwd incorrect"
#-
basename(@__FILE__)
""") """)
Literate.markdown(inputfile, outdir; execute=true) Literate.markdown(inputfile, outdir; execute=true)
markdown = read(joinpath(outdir, "inputfile.md"), String) markdown = read(joinpath(outdir, "inputfile.md"), String)
@ -846,6 +850,8 @@ end end
@test !occursin("```julia\n47 #hide\n```", markdown) # line with `#hide` removed @test !occursin("```julia\n47 #hide\n```", markdown) # line with `#hide` removed
@test !occursin("```julia\n```", markdown) # no empty code block @test !occursin("```julia\n```", markdown) # no empty code block
@test occursin("```\n47\n```", markdown) # return value (even though line/block removed) @test occursin("```\n47\n```", markdown) # return value (even though line/block removed)
@test occursin("```\n\"cwd correct\"\n```", markdown) # Correct cwd (@__DIR__)
@test occursin("```\n\"inputfile.md\"\n```", markdown) # Correct source file (@__FILE__)
# FranklinFlavor # FranklinFlavor
Literate.markdown(inputfile, outdir; execute=true, flavor=Literate.FranklinFlavor()) Literate.markdown(inputfile, outdir; execute=true, flavor=Literate.FranklinFlavor())
@ -1179,7 +1185,7 @@ end end
err err
end) end)
@test isa(r, ErrorException) @test isa(r, ErrorException)
@test occursin("when executing the following code block in file ", r.msg) @test occursin("when executing the following code block from inputfile ", r.msg)
@test occursin(inputfile, r.msg) @test occursin(inputfile, r.msg)
# verify that inputfile exists # verify that inputfile exists

Write Preview
Loading…
Cancel
Save