mirror of https://github.com/mpastell/Weave.jl
Merge branch 'master' into texpipeline
Shuhei Kadowaki
commit
5ae1fd5cf1
|
|
@ -0,0 +1,67 @@
|
|||
# TODO: build docs via github-actions
|
||||
|
||||
name: CI
|
||||
on:
|
||||
push:
|
||||
branches:
|
||||
- master
|
||||
pull_request:
|
||||
jobs:
|
||||
test:
|
||||
name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
|
||||
runs-on: ${{ matrix.os }}
|
||||
continue-on-error: ${{ matrix.allow-failure }}
|
||||
strategy:
|
||||
fail-fast: false # don't stop CI even when one of them fails
|
||||
matrix:
|
||||
version:
|
||||
- '1.4'
|
||||
os:
|
||||
- ubuntu-latest
|
||||
- macOS-latest
|
||||
# - windows-latest # TODO: test on Windows
|
||||
arch:
|
||||
- x64
|
||||
- x86
|
||||
allow-failure: [false]
|
||||
include:
|
||||
# this is so verbose... any other way to simplify this ?
|
||||
- version: 'nightly'
|
||||
os: ubuntu-latest
|
||||
arch: x64
|
||||
allow-failure: true
|
||||
- version: 'nightly'
|
||||
os: ubuntu-latest
|
||||
arch: x86
|
||||
allow-failure: true
|
||||
- version: 'nightly'
|
||||
os: macOS-latest
|
||||
arch: x64
|
||||
allow-failure: true
|
||||
# - version: 'nightly'
|
||||
# os: windows-latest
|
||||
# arch: x64
|
||||
# allow-failure: true
|
||||
# - version: 'nightly'
|
||||
# os: windows-latest
|
||||
# arch: x86
|
||||
# allow-failure: true
|
||||
exclude:
|
||||
- os: macOS-latest
|
||||
arch: x86
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- uses: julia-actions/setup-julia@v1
|
||||
with:
|
||||
version: ${{ matrix.version }}
|
||||
arch: ${{ matrix.arch }}
|
||||
- uses: julia-actions/julia-buildpkg@latest
|
||||
- uses: julia-actions/julia-runtest@latest
|
||||
- uses: julia-actions/julia-processcoverage@v1
|
||||
- uses: codecov/codecov-action@v1
|
||||
with:
|
||||
file: ./lcov.info
|
||||
flags: unittests
|
||||
name: codecov-umbrella
|
||||
fail_ci_if_error: false
|
||||
token: ${{ secrets.CODECOV_TOKEN }}
|
||||
|
|
@ -1,6 +1,5 @@
|
|||
Manifest.toml
|
||||
|
||||
src/*.cov
|
||||
test.jl
|
||||
examples/figures/
|
||||
examples/*.md
|
||||
examples/*.pdf
|
||||
|
|
@ -22,15 +21,9 @@ test/**/*.ipynb
|
|||
|
||||
doc/build
|
||||
doc/site
|
||||
stable/
|
||||
doc/Manifest.toml
|
||||
Manifest.toml
|
||||
|
||||
tmp/
|
||||
.idea
|
||||
*.*~
|
||||
*.aux
|
||||
*.log
|
||||
*.out
|
||||
\#*\#
|
||||
.juliahistory
|
||||
|
|
|
|||
13
.travis.yml
13
.travis.yml
|
|
@ -1,19 +1,6 @@
|
|||
language: julia
|
||||
|
||||
julia:
|
||||
- 1 # current stable
|
||||
- nightly
|
||||
|
||||
script:
|
||||
- if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
|
||||
- julia --check-bounds=yes -e 'using Pkg; Pkg.build()'
|
||||
- xvfb-run julia -e 'using Pkg; Pkg.test("Weave", coverage=true)'
|
||||
after_success:
|
||||
- julia -e 'using Pkg; cd(Pkg.dir("Weave")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
|
||||
|
||||
jobs:
|
||||
allow_failures:
|
||||
- julia: nightly
|
||||
include:
|
||||
- stage: "Documentation"
|
||||
julia: 1
|
||||
|
|
|
|||
|
|
@ -26,13 +26,10 @@ YAML = "0.3, 0.4"
|
|||
julia = "1.2"
|
||||
|
||||
[extras]
|
||||
Cairo = "159f3aea-2a34-519c-b102-8c37f9878175"
|
||||
Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
|
||||
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
|
||||
Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004"
|
||||
IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
|
||||
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
|
||||
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
|
||||
|
||||
[targets]
|
||||
test = ["Cairo", "Conda", "DataFrames", "Gadfly", "IJulia", "Plots", "Test"]
|
||||
test = ["DataFrames", "Test"]
|
||||
|
|
|
|||
|
|
@ -1,12 +1,12 @@
|
|||
# Weave
|
||||
|
||||
[](https://travis-ci.org/JunoLab/Weave.jl)
|
||||
|
||||
[](https://codecov.io/gh/JunoLab/Weave.jl)
|
||||
[](http://weavejl.mpastell.com/stable/)
|
||||
[](http://weavejl.mpastell.com/dev/)
|
||||
[](http://dx.doi.org/10.21105/joss.00204)
|
||||
|
||||
Weave is a scientific report generator/literate programming tool
|
||||
for Julia.
|
||||
Weave is a scientific report generator/literate programming tool for the [Julia programming language](https://julialang.org/).
|
||||
It resembles
|
||||
[Pweave](http://mpastell.com/pweave),
|
||||
[knitr](https://yihui.org/knitr/),
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
|
||||
|
|
|
|||
|
|
@ -41,8 +41,8 @@ e.g.: `weave("FIR_design_plots.jl", template = "custom.tpl"`.
|
|||
|
||||
As starting point, you can use the existing templates:
|
||||
|
||||
- HTML (`md2html`): [`md2html.tpl`](https://github.com/mpastell/Weave.jl/blob/master/templates/md2html.tpl)
|
||||
- LaTex (`md2pdf`): [`md2pdf.tpl`](https://github.com/mpastell/Weave.jl/blob/master/templates/md2pdf.tpl)
|
||||
- HTML (`md2html`): [`md2html.tpl`](https://github.com/JunoLab/Weave.jl/blob/master/templates/md2html.tpl)
|
||||
- LaTex (`md2pdf`): [`md2pdf.tpl`](https://github.com/JunoLab/Weave.jl/blob/master/templates/md2pdf.tpl)
|
||||
|
||||
Templates are rendered using [Mustache.jl](https://github.com/jverzani/Mustache.jl).
|
||||
|
||||
|
|
|
|||
|
|
@ -152,8 +152,8 @@ Weave will remove the first empty space from each line of documentation.
|
|||
|
||||
!!! tip
|
||||
- Here are sample documents:
|
||||
+ [markdown format](https://github.com/mpastell/Weave.jl/blob/master/examples/FIR_design.jmd)
|
||||
+ [script format](https://github.com/mpastell/Weave.jl/blob/master/examples/FIR_design.jl)
|
||||
+ [markdown format](https://github.com/JunoLab/Weave.jl/blob/master/examples/FIR_design.jmd)
|
||||
+ [script format](https://github.com/JunoLab/Weave.jl/blob/master/examples/FIR_design.jl)
|
||||
- [Details about chunk options](@ref chunk-options)
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
#' # Introduction
|
||||
|
||||
#' This an example of a julia script that can be published using
|
||||
#' [Weave](http://mpastell.github.io/Weave.jl/latest/usage/).
|
||||
#' [Weave](http://weavejl.mpastell.com/dev/usage/).
|
||||
#' The script can be executed normally using Julia
|
||||
#' or published to HTML or pdf with Weave.
|
||||
#' Text is written in markdown in lines starting with "`#'` " and code
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ date: 21th April 2016
|
|||
|
||||
|
||||
This an example of a julia script that can be published using
|
||||
[Weave](http://mpastell.github.io/Weave.jl/latest/usage/).
|
||||
[Weave](http://weavejl.mpastell.com/dev/usage/).
|
||||
The script can be executed normally using Julia
|
||||
or published to HTML or pdf with Weave.
|
||||
Text is written in markdown in lines starting with "`#'` " and code
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
#' # Introduction
|
||||
|
||||
#' This an example of a julia script that can be published using
|
||||
#' [Weave](http://mpastell.github.io/Weave.jl/latest/usage/).
|
||||
#' [Weave](http://weavejl.mpastell.com/dev/usage/).
|
||||
#' The script can be executed normally using Julia
|
||||
#' or published to HTML or pdf with Weave.
|
||||
#' Text is written in markdown in lines starting with "`#'` " and code
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ date : 13th December 2016
|
|||
# Intro
|
||||
|
||||
This a sample [Julia](http://julialang.org/) markdown document that can
|
||||
be executed using [Weave.jl](https://github.com/mpastell/Weave.jl).
|
||||
be executed using [Weave.jl](https://github.com/JunoLab/Weave.jl).
|
||||
|
||||
The code is delimited from docs using markdown fenced code blocks
|
||||
markup which can be seen looking at the source document
|
||||
|
|
@ -71,6 +71,6 @@ plot(y = cumsum(randn(1000, 1)), Geom.line)
|
|||
Read the documentation:
|
||||
|
||||
- stable: [http://mpastell.github.io/Weave.jl/stable/](http://mpastell.github.io/Weave.jl/stable/)
|
||||
- latest: [http://mpastell.github.io/Weave.jl/latest/](http://mpastell.github.io/Weave.jl/latest/)
|
||||
- latest: [http://weavejl.mpastell.com/dev/](http://weavejl.mpastell.com/dev/)
|
||||
|
||||
See other examples in the [GitHub repo](https://github.com/mpastell/Weave.jl/tree/master/examples)
|
||||
See other examples in the [GitHub repo](https://github.com/JunoLab/Weave.jl/tree/master/examples)
|
||||
|
|
|
|||
|
|
@ -29,10 +29,10 @@
|
|||
\section{Intro}
|
||||
|
||||
This is a minimal example on using PGF format with Gadfly plots in
|
||||
\href{https://github.com/mpastell/Weave.jl}{Weave.jl} document.
|
||||
\href{https://github.com/JunoLab/Weave.jl}{Weave.jl} document.
|
||||
The source is in github:
|
||||
|
||||
\url{https://github.com/mpastell/Weave.jl/blob/master/examples/gadfly_pgf.texw}.
|
||||
\url{https://github.com/JunoLab/Weave.jl/blob/master/examples/gadfly_pgf.texw}.
|
||||
|
||||
You can run this example with first weaving it from Julia using:
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
# Introduction
|
||||
|
||||
This a sample [Julia](http://julialang.org/) noweb document that can
|
||||
be executed using [Weave.jl](https://github.com/mpastell/Weave.jl).
|
||||
be executed using [Weave.jl](https://github.com/JunoLab/Weave.jl).
|
||||
|
||||
The code is delimited from docs using `<<>>=` and `@` markup which can be seen
|
||||
looking at the source document `gadfly_sample.mdw` in the examples directory
|
||||
|
|
@ -65,6 +65,6 @@ plot(y = cumsum(randn(1000, 1)), Geom.line)
|
|||
Read the documentation:
|
||||
|
||||
- stable: <http://mpastell.github.io/Weave.jl/stable/>
|
||||
- latest: <http://mpastell.github.io/Weave.jl/latest/>
|
||||
- latest: <http://weavejl.mpastell.com/dev/>
|
||||
|
||||
See other examples in: <https://github.com/mpastell/Weave.jl/tree/master/examples>
|
||||
See other examples in: <https://github.com/JunoLab/Weave.jl/tree/master/examples>
|
||||
|
|
|
|||
21
src/Weave.jl
21
src/Weave.jl
|
|
@ -30,6 +30,7 @@ end
|
|||
|
||||
# utilitity functions
|
||||
take2string!(io) = String(take!(io))
|
||||
joinlines(lines) = join(lines, '\n')
|
||||
|
||||
"""
|
||||
list_out_formats()
|
||||
|
|
@ -96,7 +97,6 @@ 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 +118,6 @@ 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 +157,6 @@ 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 +169,6 @@ function weave(
|
|||
fig_ext = fig_ext,
|
||||
cache_path = cache_path,
|
||||
cache = cache,
|
||||
throw_errors = throw_errors,
|
||||
)
|
||||
|
||||
# render document
|
||||
|
|
@ -221,7 +218,7 @@ function weave(
|
|||
rm(intermediate)
|
||||
elseif doctype == "md2pdf"
|
||||
run_latex(doc, out_path, latex_cmd)
|
||||
out_path = get_out_path(doc, out_path, ext = "pdf")
|
||||
out_path = get_out_path(doc, out_path, "pdf")
|
||||
end
|
||||
|
||||
@info "Weaved to $(out_path)"
|
||||
|
|
@ -263,7 +260,7 @@ using [`nbconvert`](https://nbconvert.readthedocs.io/en/latest/).
|
|||
|
||||
!!! warning
|
||||
The code is _**not**_ executed by Weave, but by [`nbconvert`](https://nbconvert.readthedocs.io/en/latest/).
|
||||
This means that the output doesn't necessarily always work properly; see [#116](https://github.com/mpastell/Weave.jl/issues/116).
|
||||
This means that the output doesn't necessarily always work properly; see [#116](https://github.com/JunoLab/Weave.jl/issues/116).
|
||||
|
||||
!!! note
|
||||
In order to _just_ convert Weave document to Jupyter Notebook,
|
||||
|
|
@ -321,18 +318,6 @@ end
|
|||
|
||||
include_weave(source, informat = nothing) = include_weave(Main, source, informat)
|
||||
|
||||
# Hooks to run before and after chunks, this is form IJulia,
|
||||
# but note that Weave hooks take the chunk as input
|
||||
const preexecute_hooks = Function[]
|
||||
push_preexecute_hook(f::Function) = push!(preexecute_hooks, f)
|
||||
pop_preexecute_hook(f::Function) =
|
||||
splice!(preexecute_hooks, findfirst(x -> x == f, preexecute_hooks))
|
||||
|
||||
const postexecute_hooks = Function[]
|
||||
push_postexecute_hook(f::Function) = push!(postexecute_hooks, f)
|
||||
pop_postexecute_hook(f::Function) =
|
||||
splice!(postexecute_hooks, findfirst(x -> x == f, postexecute_hooks))
|
||||
|
||||
include("types.jl")
|
||||
include("config.jl")
|
||||
include("WeaveMarkdown/markdown.jl")
|
||||
|
|
|
|||
|
|
@ -1,10 +1,11 @@
|
|||
# TODO: follow RMarkdown convention more
|
||||
const _DEFAULT_PARAMS = Dict{Symbol,Any}(
|
||||
:echo => true,
|
||||
:results => "markup",
|
||||
:hold => false,
|
||||
:fig => true,
|
||||
:include => true,
|
||||
:eval => true,
|
||||
:error => true,
|
||||
:tangle => true,
|
||||
:cache => false,
|
||||
:fig_cap => nothing,
|
||||
|
|
@ -14,11 +15,10 @@ const _DEFAULT_PARAMS = Dict{Symbol,Any}(
|
|||
:fig_path => DEFAULT_FIG_PATH,
|
||||
:dpi => 96,
|
||||
:term => false,
|
||||
:prompt => "\njulia> ",
|
||||
:prompt => "julia>",
|
||||
:label => nothing,
|
||||
:wrap => true,
|
||||
:line_width => 75,
|
||||
:engine => "julia",
|
||||
:fig_ext => nothing,
|
||||
:fig_pos => nothing,
|
||||
:fig_env => nothing,
|
||||
|
|
|
|||
|
|
@ -2,34 +2,20 @@ using Markdown, .WeaveMarkdown
|
|||
|
||||
# Contains report global properties
|
||||
mutable struct Report <: AbstractDisplay
|
||||
cwd::AbstractString
|
||||
basename::AbstractString
|
||||
cwd::String
|
||||
basename::String
|
||||
format::WeaveFormat
|
||||
rich_output::AbstractString
|
||||
rich_output::String
|
||||
fignum::Int
|
||||
figures::Vector{String}
|
||||
cur_chunk::Any
|
||||
mimetypes::Array{AbstractString}
|
||||
cur_chunk::Union{Nothing,CodeChunk}
|
||||
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"]
|
||||
|
|
|
|||
|
|
@ -4,14 +4,13 @@ using Base64, ..Plots, ..Weave
|
|||
|
||||
|
||||
# Pre-execute hooks to set the plot size for the chunk
|
||||
function plots_set_size(chunk)
|
||||
function plots_set_size!(chunk)
|
||||
w = chunk.options[:fig_width] * chunk.options[:dpi]
|
||||
h = chunk.options[:fig_height] * chunk.options[:dpi]
|
||||
Plots.default(size = (w, h))
|
||||
return chunk
|
||||
end
|
||||
|
||||
Weave.push_preexecute_hook(plots_set_size)
|
||||
Weave.push_preexecution_hook!(plots_set_size!)
|
||||
|
||||
# PNG or SVG is not working, output html
|
||||
function Base.display(
|
||||
|
|
|
|||
|
|
@ -91,9 +91,7 @@ function format_chunk(chunk::CodeChunk, docformat)
|
|||
|
||||
# Handle figures
|
||||
if chunk.options[:fig] && length(chunk.figures) > 0
|
||||
if chunk.options[:include]
|
||||
result *= formatfigures(chunk, docformat)
|
||||
end
|
||||
result *= formatfigures(chunk, docformat)
|
||||
end
|
||||
|
||||
return result
|
||||
|
|
|
|||
113
src/run.jl
113
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)
|
||||
|
|
@ -193,58 +192,43 @@ function run_inline(inline::InlineCode, doc::WeaveDoc, report::Report, mod::Modu
|
|||
return inline
|
||||
end
|
||||
|
||||
reset_report(report::Report) = report.figures = String[]
|
||||
|
||||
function run_code(doc::WeaveDoc, chunk::CodeChunk, report::Report, mod::Module)
|
||||
ss = parse_input(chunk.content)
|
||||
n = length(ss)
|
||||
results = ChunkOutput[]
|
||||
for (i, s) in enumerate(ss)
|
||||
reset_report(report)
|
||||
obj, out = capture_output(
|
||||
mod,
|
||||
s,
|
||||
doc.path,
|
||||
chunk.options[:term],
|
||||
i == n,
|
||||
report.throw_errors,
|
||||
)
|
||||
figures = report.figures # Captured figures
|
||||
result = ChunkOutput(s, out, report.rich_output, figures)
|
||||
report.rich_output = ""
|
||||
push!(results, result)
|
||||
end
|
||||
return results
|
||||
code = chunk.content
|
||||
path = doc.path
|
||||
error = chunk.options[:error]
|
||||
codes = chunk.options[:term] ? split_code(code) : [code]
|
||||
capture = code -> capture_output(code, mod, path, error, report)
|
||||
return capture.(codes)
|
||||
end
|
||||
|
||||
# Parse chunk input to array of expressions
|
||||
function parse_input(s)
|
||||
function split_code(code)
|
||||
res = String[]
|
||||
s = lstrip(s)
|
||||
n = sizeof(s)
|
||||
pos = 1
|
||||
while (oldpos = pos) ≤ n
|
||||
_, pos = Meta.parse(s, pos)
|
||||
push!(res, s[oldpos:pos-1])
|
||||
e = 1
|
||||
ex = :init
|
||||
while true
|
||||
s = e
|
||||
ex, e = Meta.parse(code, s)
|
||||
isnothing(ex) && break
|
||||
push!(res, strip(code[s:e-1]))
|
||||
end
|
||||
return res
|
||||
end
|
||||
|
||||
function capture_output(mod, s, path, term, lastline, throw_errors = false)
|
||||
local out = nothing
|
||||
local obj = nothing
|
||||
function capture_output(code, mod, path, error, report)
|
||||
reset_report!(report)
|
||||
|
||||
old = stdout
|
||||
rw, wr = redirect_stdout()
|
||||
reader = @async read(rw, String)
|
||||
|
||||
local out = nothing
|
||||
task_local_storage(:SOURCE_PATH, path) do
|
||||
try
|
||||
obj = include_string(mod, s, path) # TODO: fix line number
|
||||
!isnothing(obj) && (term || lastline) && display(obj)
|
||||
obj = include_string(mod, code, path) # TODO: fix line number
|
||||
!isnothing(obj) && 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
|
||||
|
|
@ -255,13 +239,20 @@ function capture_output(mod, s, path, term, lastline, throw_errors = false)
|
|||
end
|
||||
end
|
||||
|
||||
out = replace(out, r"\u001b\[.*?m" => "") # remove ANSI color codes
|
||||
return (obj, out)
|
||||
return ChunkOutput(code, remove_ansi_control_chars(out), report.rich_output, report.figures)
|
||||
end
|
||||
|
||||
function reset_report!(report)
|
||||
report.rich_output = ""
|
||||
report.figures = String[]
|
||||
end
|
||||
|
||||
unwrap_load_err(err) = return err
|
||||
unwrap_load_err(err::LoadError) = return err.error
|
||||
|
||||
# https://stackoverflow.com/a/33925425/12113178
|
||||
remove_ansi_control_chars(s) = replace(s, r"(\x9B|\x1B\[)[0-?]*[ -\/]*[@-~]" => "")
|
||||
|
||||
function eval_chunk(doc::WeaveDoc, chunk::CodeChunk, report::Report, mod::Module)
|
||||
if !chunk.options[:eval]
|
||||
chunk.output = ""
|
||||
|
|
@ -269,10 +260,7 @@ function eval_chunk(doc::WeaveDoc, chunk::CodeChunk, report::Report, mod::Module
|
|||
return chunk
|
||||
end
|
||||
|
||||
# Run preexecute_hooks
|
||||
for hook in preexecute_hooks
|
||||
chunk = Base.invokelatest(hook, chunk)
|
||||
end
|
||||
execute_prehooks!(chunk)
|
||||
|
||||
report.fignum = 1
|
||||
report.cur_chunk = chunk
|
||||
|
|
@ -283,10 +271,7 @@ function eval_chunk(doc::WeaveDoc, chunk::CodeChunk, report::Report, mod::Module
|
|||
|
||||
chunk.result = run_code(doc, chunk, report, mod)
|
||||
|
||||
# Run post_execute chunks
|
||||
for hook in postexecute_hooks
|
||||
chunk = Base.invokelatest(hook, chunk)
|
||||
end
|
||||
execute_posthooks!(chunk)
|
||||
|
||||
chunks = if chunk.options[:term]
|
||||
collect_term_results(chunk)
|
||||
|
|
@ -296,13 +281,28 @@ function eval_chunk(doc::WeaveDoc, chunk::CodeChunk, report::Report, mod::Module
|
|||
collect_results(chunk)
|
||||
end
|
||||
|
||||
# else
|
||||
# chunk.options[:fig] && (chunk.figures = copy(report.figures))
|
||||
# end
|
||||
|
||||
return chunks
|
||||
end
|
||||
|
||||
# Hooks to run before and after chunks, this is form IJulia,
|
||||
const preexecution_hooks = Function[]
|
||||
push_preexecution_hook!(f::Function) = push!(preexecution_hooks, f)
|
||||
function pop_preexecution_hook!(f::Function)
|
||||
i = findfirst(x -> x == f, preexecution_hooks)
|
||||
isnothing(i) && error("this function has not been registered in the pre-execution hook yet")
|
||||
return splice!(preexecution_hooks, i)
|
||||
end
|
||||
execute_prehooks!(chunk::CodeChunk) = for prehook in preexecution_hooks; Base.invokelatest(prehook, chunk); end
|
||||
|
||||
const postexecution_hooks = Function[]
|
||||
push_postexecution_hook!(f::Function) = push!(postexecution_hooks, f)
|
||||
function pop_postexecution_hook!(f::Function)
|
||||
i = findfirst(x -> x == f, postexecution_hooks)
|
||||
isnothing(i) && error("this function has not been registered in the post-execution hook yet")
|
||||
return splice!(postexecution_hooks, i)
|
||||
end
|
||||
execute_posthooks!(chunk::CodeChunk) = for posthook in postexecution_hooks; Base.invokelatest(posthook, chunk); end
|
||||
|
||||
"""
|
||||
clear_module!(mod::Module)
|
||||
|
||||
|
|
@ -391,7 +391,7 @@ function collect_term_results(chunk::CodeChunk)
|
|||
prompt = chunk.options[:prompt]
|
||||
result_chunks = CodeChunk[]
|
||||
for r in chunk.result
|
||||
output *= string(prompt, r.code, r.stdout)
|
||||
output *= string('\n', indent_term_code(prompt, r.code), '\n', r.stdout)
|
||||
if !isempty(r.figures)
|
||||
rchunk = CodeChunk(
|
||||
"",
|
||||
|
|
@ -421,6 +421,15 @@ function collect_term_results(chunk::CodeChunk)
|
|||
return result_chunks
|
||||
end
|
||||
|
||||
function indent_term_code(prompt, code)
|
||||
prompt_with_space = string(prompt, ' ')
|
||||
n = length(prompt_with_space)
|
||||
pads = ' ' ^ n
|
||||
return map(enumerate(split(code, '\n'))) do (i,line)
|
||||
isone(i) ? string(prompt_with_space, line) : string(pads, line)
|
||||
end |> joinlines
|
||||
end
|
||||
|
||||
function collect_hold_results(chunk::CodeChunk)
|
||||
for r in chunk.result
|
||||
chunk.output *= r.stdout
|
||||
|
|
|
|||
|
|
@ -1,7 +1,4 @@
|
|||
using Weave
|
||||
using Test
|
||||
|
||||
#Test if running document with and without cache works
|
||||
# Test if running document with and without cache works
|
||||
isdir("documents/cache") && rm("documents/cache", recursive = true)
|
||||
weave("documents/chunk_options.noweb", cache=:all)
|
||||
result = read("documents/chunk_options.md", String)
|
||||
|
|
|
|||
|
|
@ -1,18 +0,0 @@
|
|||
~~~~{.julia}
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
{#fig:sin_fun}
|
||||
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
{width=15cm #fig:cos2_fun}\
|
||||
|
||||
|
|
@ -1,17 +0,0 @@
|
|||
````julia
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
````
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
````julia
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
````
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,17 +0,0 @@
|
|||
````julia
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
````
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
````julia
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
````
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
~~~~{.julia}
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
{#fig:sin_fun}
|
||||
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
{width=15cm #fig:cos2_fun}\
|
||||
|
||||
|
|
@ -1,17 +0,0 @@
|
|||
````julia
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
````
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
````julia
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
````
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
\begin{juliacode}
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
\end{juliacode}
|
||||
\begin{figure}[ht]
|
||||
\center
|
||||
\includegraphics[width=\linewidth]{figures/gadfly_formats_test_sin_fun_1.pdf}
|
||||
\caption{sin(x) function.}
|
||||
\label{fig:sin_fun}
|
||||
\end{figure}
|
||||
|
||||
\begin{figure}[htpb]
|
||||
\center
|
||||
\includegraphics[width=\linewidth]{figures/gadfly_formats_test_2_1.pdf}
|
||||
\caption{cos(x) function.}
|
||||
\end{figure}
|
||||
|
||||
\begin{juliacode}
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
\end{juliacode}
|
||||
\includegraphics[width=15cm]{figures/gadfly_formats_test_cos2_fun_1.pdf}
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
\begin{juliacode}
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
\end{juliacode}
|
||||
\begin{figure}[ht]
|
||||
\center
|
||||
\includegraphics[width=\linewidth]{figures/gadfly_formats_test_sin_fun_1.png}
|
||||
\caption{sin(x) function.}
|
||||
\label{fig:sin_fun}
|
||||
\end{figure}
|
||||
|
||||
\begin{figure}[htpb]
|
||||
\center
|
||||
\includegraphics[width=\linewidth]{figures/gadfly_formats_test_2_1.png}
|
||||
\caption{cos(x) function.}
|
||||
\end{figure}
|
||||
|
||||
\begin{juliacode}
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
\end{juliacode}
|
||||
\includegraphics[width=15cm]{figures/gadfly_formats_test_cos2_fun_1.png}
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
\begin{juliacode}
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
\end{juliacode}
|
||||
\begin{figure}[ht]
|
||||
\center
|
||||
\includegraphics[width=\linewidth]{figures/gadfly_formats_test_sin_fun_1.ps}
|
||||
\caption{sin(x) function.}
|
||||
\label{fig:sin_fun}
|
||||
\end{figure}
|
||||
|
||||
\begin{figure}[htpb]
|
||||
\center
|
||||
\includegraphics[width=\linewidth]{figures/gadfly_formats_test_2_1.ps}
|
||||
\caption{cos(x) function.}
|
||||
\end{figure}
|
||||
|
||||
\begin{juliacode}
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
\end{juliacode}
|
||||
\includegraphics[width=15cm]{figures/gadfly_formats_test_cos2_fun_1.ps}
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
\begin{juliacode}
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
\end{juliacode}
|
||||
\begin{figure}[ht]
|
||||
\center
|
||||
\resizebox{\linewidth}{!}{\input{figures/gadfly_formats_test_sin_fun_1.tex}}
|
||||
\caption{sin(x) function.}
|
||||
\label{fig:sin_fun}
|
||||
\end{figure}
|
||||
|
||||
\begin{figure}[htpb]
|
||||
\center
|
||||
\resizebox{\linewidth}{!}{\input{figures/gadfly_formats_test_2_1.tex}}
|
||||
\caption{cos(x) function.}
|
||||
\end{figure}
|
||||
|
||||
\begin{juliacode}
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
\end{juliacode}
|
||||
\resizebox{15cm}{!}{\input{figures/gadfly_formats_test_cos2_fun_1.tex}}
|
||||
|
|
@ -1,19 +0,0 @@
|
|||
---
|
||||
weave_options:
|
||||
out_path: gadfly
|
||||
---
|
||||
|
||||
<<fig_cap="sin(x) function."; label="sin_fun"; fig_pos="ht">>=
|
||||
using Gadfly
|
||||
x = range(0, stop =2π, step=0.05)
|
||||
plot(x=x, y = sin.(x), Geom.line)
|
||||
@
|
||||
|
||||
|
||||
<<echo=false; fig_cap="cos(x) function."; dpi=200>>=
|
||||
plot(x=x, y = cos.(x), Geom.line)
|
||||
@
|
||||
|
||||
<<label="cos2_fun"; out_width="15cm">>=
|
||||
plot(x=x, y = cos.(2x), Geom.line)
|
||||
@
|
||||
|
|
@ -1,12 +0,0 @@
|
|||
|
||||
# Gadfly
|
||||
|
||||
```{julia;fig_ext=".svg";dpi=300}
|
||||
using Gadfly
|
||||
x = collect(range(0, stop=2π, length=200))
|
||||
plot(
|
||||
layer(x=x, y = sin.(x), Geom.line),
|
||||
layer(x=x, y = cos.(x), Geom.line, Theme(default_color=colorant"red")),
|
||||
Guide.manual_color_key("Legend", ["sin", "cos"], ["deepskyblue", "red"])
|
||||
)
|
||||
```
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
|
||||
|
||||
|
||||
<div class="Random plot">
|
||||
|
||||
<p>Some inline output</p>
|
||||
|
||||
|
||||
<pre class='hljl'>
|
||||
<span class='hljl-nf'>println</span><span class='hljl-p'>(</span><span class='hljl-s'>"Testing output"</span><span class='hljl-p'>)</span>
|
||||
</pre>
|
||||
|
||||
|
||||
<pre class="output">
|
||||
Testing output
|
||||
</pre>
|
||||
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
|
||||
|
||||
|
||||
\begin{frame}[fragile]
|
||||
\frametitle{Random plot}
|
||||
|
||||
Some inline output
|
||||
|
||||
|
||||
\begin{lstlisting}
|
||||
(*@\HLJLnf{println}@*)(*@\HLJLp{(}@*)(*@\HLJLs{"{}Testing}@*) (*@\HLJLs{output"{}}@*)(*@\HLJLp{)}@*)
|
||||
\end{lstlisting}
|
||||
|
||||
\begin{lstlisting}
|
||||
Testing output
|
||||
\end{lstlisting}
|
||||
|
||||
|
||||
|
||||
|
||||
\end{frame}
|
||||
|
||||
|
|
@ -1,17 +0,0 @@
|
|||
Here's some text
|
||||
|
||||
And here's some code
|
||||
|
||||
```julia
|
||||
x = 1
|
||||
y = 2
|
||||
@show x + y
|
||||
```
|
||||
|
||||
Here's some more complicated code
|
||||
|
||||
```julia
|
||||
@code_native +(1.0, π)
|
||||
using Test
|
||||
@test 1 == 1
|
||||
```
|
||||
|
|
@ -1,31 +0,0 @@
|
|||
---
|
||||
title: A minimal beamer example using Weave markdown
|
||||
author: Matti Pastell
|
||||
weave_options:
|
||||
out_path: inline
|
||||
---
|
||||
|
||||
```julia; echo=false
|
||||
struct Begin
|
||||
text
|
||||
title
|
||||
end
|
||||
|
||||
struct End
|
||||
text
|
||||
end
|
||||
Base.show(io::IO, m::MIME"text/latex", b::Begin) = write(io, "\\begin{$(b.text)}[fragile]\n\\frametitle{$(b.title)}\n")
|
||||
Base.show(io::IO, m::MIME"text/latex", e::End) = write(io, "\\end{$(e.text)}")
|
||||
|
||||
Base.show(io::IO, m::MIME"text/html", b::Begin) = write(io, "<div class=\"$(b.title)\">\n")
|
||||
Base.show(io::IO, m::MIME"text/html", e::End) = write(io, "</div>")
|
||||
```
|
||||
|
||||
! Begin("frame", "Random plot")
|
||||
|
||||
Some inline `j print("output")`
|
||||
|
||||
```julia
|
||||
println("Testing output")
|
||||
```
|
||||
! End("frame")
|
||||
|
|
@ -1,31 +0,0 @@
|
|||
|
||||
|
||||
```julia
|
||||
display("text/markdown",
|
||||
"""
|
||||
|
||||
### Small markdown sample
|
||||
|
||||
**Hello** from `code` block.
|
||||
|
||||
""")
|
||||
```
|
||||
|
||||
|
||||
```julia
|
||||
struct Dummy
|
||||
s::String
|
||||
end
|
||||
|
||||
function Base.show(io::IO, m::MIME"text/markdown", d::Dummy)
|
||||
print(io, d.s)
|
||||
end
|
||||
|
||||
Dummy("""
|
||||
|
||||
* one
|
||||
* two
|
||||
* three
|
||||
|
||||
""")
|
||||
```
|
||||
|
|
@ -1,16 +0,0 @@
|
|||
|
||||
using Plots
|
||||
pyplot()
|
||||
x = range(0, stop=2*pi, length=50)
|
||||
println(x)
|
||||
p = plot(x = x, y = sin(x), size =(900,300))
|
||||
|
||||
plot(x = x, y = sin(x))
|
||||
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
|
||||
plot(y = cumsum(randn(1000, 1)))
|
||||
|
|
@ -1,60 +0,0 @@
|
|||
~~~~{.julia}
|
||||
using Plots
|
||||
pyplot()
|
||||
x = linspace(0, 2*pi)
|
||||
println(x)
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
~~~~
|
||||
linspace(0.0,6.283185307179586,50)
|
||||
~~~~
|
||||
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
p = plot(x, sin(x), size =(900,300))
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
julia> plot(x, sin(x))
|
||||
|
||||
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
\
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
\
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
julia> plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
|
||||
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
\
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
julia> scatter!(rand(100),markersize=6,c=:orange)
|
||||
|
||||
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
\
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,47 +0,0 @@
|
|||
\begin{juliacode}
|
||||
using Plots
|
||||
pyplot()
|
||||
x = linspace(0, 2*pi)
|
||||
println(x)
|
||||
\end{juliacode}
|
||||
\begin{juliaout}
|
||||
linspace(0.0,6.283185307179586,50)
|
||||
\end{juliaout}
|
||||
|
||||
\begin{juliacode}
|
||||
p = plot(x, sin(x), size =(900,300))
|
||||
\end{juliacode}
|
||||
|
||||
\begin{juliaterm}
|
||||
julia> plot(x, sin(x))
|
||||
|
||||
|
||||
\end{juliaterm}
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_2_1.pdf}
|
||||
|
||||
\begin{juliacode}
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
\end{juliacode}
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_3_1.pdf}
|
||||
|
||||
\begin{juliaterm}
|
||||
julia> plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
|
||||
|
||||
\end{juliaterm}
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_4_1.pdf}
|
||||
|
||||
\begin{juliaterm}
|
||||
julia> scatter!(rand(100),markersize=6,c=:orange)
|
||||
|
||||
|
||||
\end{juliaterm}
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_4_2.pdf}
|
||||
|
||||
\begin{figure}[htpb]
|
||||
\center
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_random_1.pdf}
|
||||
\caption{A random walk.}
|
||||
\label{fig:random}
|
||||
\end{figure}
|
||||
|
|
@ -1,41 +0,0 @@
|
|||
~~~~{.julia}
|
||||
using Plots
|
||||
gr()
|
||||
x = range(0, stop=2π, length=50)
|
||||
println(x)
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
~~~~
|
||||
0.0:0.1282282715750936:6.283185307179586
|
||||
~~~~
|
||||
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
p = plot(x, sin.(x), size =(900,300))
|
||||
p
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
\
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
plot(x, sin.(x))
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
\
|
||||
|
||||
|
||||
~~~~{.julia}
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
~~~~~~~~~~~~~
|
||||
|
||||
|
||||
\
|
||||
|
||||
|
||||
{#fig:random}
|
||||
|
|
@ -1,33 +0,0 @@
|
|||
\begin{juliacode}
|
||||
using Plots
|
||||
gr()
|
||||
x = range(0, stop=2π, length=50)
|
||||
println(x)
|
||||
\end{juliacode}
|
||||
\begin{juliaout}
|
||||
0.0:0.1282282715750936:6.283185307179586
|
||||
\end{juliaout}
|
||||
|
||||
\begin{juliacode}
|
||||
p = plot(x, sin.(x), size =(900,300))
|
||||
p
|
||||
\end{juliacode}
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_gr_1_1.pdf}
|
||||
|
||||
\begin{juliacode}
|
||||
plot(x, sin.(x))
|
||||
\end{juliacode}
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_gr_2_1.pdf}
|
||||
|
||||
\begin{juliacode}
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
\end{juliacode}
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_gr_3_1.pdf}
|
||||
|
||||
\begin{figure}[htpb]
|
||||
\center
|
||||
\includegraphics[width=\linewidth]{figures/plotsjl_test_gr_random_1.pdf}
|
||||
\caption{A random walk.}
|
||||
\label{fig:random}
|
||||
\end{figure}
|
||||
|
|
@ -1,29 +0,0 @@
|
|||
|
||||
|
||||
```julia
|
||||
using Plots
|
||||
pyplot()
|
||||
x = linspace(0, 2*pi)
|
||||
println(x)
|
||||
p = plot(x, sin(x), size =(900,300))
|
||||
```
|
||||
|
||||
|
||||
```julia; term=true
|
||||
plot(x, sin(x))
|
||||
```
|
||||
|
||||
```julia
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
```
|
||||
|
||||
```julia; term=true
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
```
|
||||
|
||||
|
||||
```{julia;echo=false; fig_cap="A random walk."; label="random"}
|
||||
plot(cumsum(randn(1000, 1)))
|
||||
```
|
||||
|
|
@ -1,25 +0,0 @@
|
|||
|
||||
|
||||
```julia
|
||||
using Plots
|
||||
gr()
|
||||
x = range(0, stop=2π, length=50)
|
||||
println(x)
|
||||
p = plot(x, sin.(x), size =(900,300))
|
||||
p
|
||||
```
|
||||
|
||||
|
||||
```julia
|
||||
plot(x, sin.(x))
|
||||
```
|
||||
|
||||
```julia
|
||||
plot(rand(100) / 3,reg=true,fill=(0,:green))
|
||||
scatter!(rand(100),markersize=6,c=:orange)
|
||||
```
|
||||
|
||||
|
||||
```{julia;echo=false; fig_cap="A random walk."; label="random"}
|
||||
plot(cumsum(randn(1000, 1), dims=1))
|
||||
```
|
||||
|
|
@ -1,37 +0,0 @@
|
|||
|
||||
y= [2, 5, 12]
|
||||
|
||||
|
||||
x = 1:10
|
||||
d = Dict("Weave" => "testing")
|
||||
y = [2, 4 ,8]
|
||||
|
||||
|
||||
x = [12, 10]
|
||||
println(y)
|
||||
println(x)
|
||||
|
||||
|
||||
println("Results without code")
|
||||
println(x)
|
||||
|
||||
|
||||
y = 1:5
|
||||
println(y)
|
||||
|
||||
|
||||
a = "Don't print me"
|
||||
println(a)
|
||||
|
||||
|
||||
println("No markup for results.")
|
||||
|
||||
|
||||
println(collect(0:10:1000))
|
||||
|
||||
|
||||
println(collect(0:10:1000))
|
||||
|
||||
|
||||
println(collect(0:10:1000))
|
||||
|
||||
|
|
@ -1,32 +0,0 @@
|
|||
# NOTE
|
||||
# this file keeps old end2end tests, which are very fragile
|
||||
# - they are being gradually replaced with unit tests, that are much more maintainable and
|
||||
# much more helpful for detecting bugs
|
||||
# - the purpose of this file is to temporarily keep the old end2end tests in a way that
|
||||
# they're allowed to fail
|
||||
|
||||
tpl = mt"""
|
||||
{{{ :body }}}
|
||||
"""
|
||||
|
||||
out = weave(joinpath(@__DIR__, "documents", "markdown_beamer.jmd"), doctype="md2html", template=tpl)
|
||||
@test read(out, String) == read(out*".ref", String)
|
||||
rm(out)
|
||||
|
||||
out = weave(joinpath(@__DIR__, "documents", "markdown_beamer.jmd"), doctype="md2tex", template=tpl)
|
||||
@test read(out, String) == read(out*".ref", String)
|
||||
rm(out)
|
||||
|
||||
|
||||
@testset "chunk options" begin
|
||||
|
||||
result = read("documents/chunk_options.md", String)
|
||||
ref = read("documents/chunk_options_ref.md", String)
|
||||
@test result == ref
|
||||
|
||||
tangle("documents/chunk_options.noweb", out_path = "documents/tangle")
|
||||
result = read("documents/tangle/chunk_options.jl", String)
|
||||
ref = read("documents/tangle/chunk_options.jl.ref", String)
|
||||
@test ref == result
|
||||
|
||||
end
|
||||
|
|
@ -1,85 +1,3 @@
|
|||
# TODO: this test is horrible, refactor
|
||||
|
||||
using Weave: Highlights.Themes.DefaultTheme
|
||||
|
||||
# Test rendering of doc chunks
|
||||
content = """
|
||||
# Test chunk
|
||||
|
||||
Test rendering \$\alpha\$
|
||||
"""
|
||||
|
||||
dchunk = Weave.DocChunk(content, 1, 1)
|
||||
|
||||
pformat = Weave.FORMATS["github"]
|
||||
f = Weave.format_chunk(dchunk, pformat)
|
||||
@test f == content
|
||||
|
||||
docformat = Weave.FORMATS["md2html"]
|
||||
f_check = "<h1>Test chunk</h1>\n<p>Test rendering <span class=\"math\">\$\alpha\$</span></p>\n"
|
||||
f = Weave.format_chunk(dchunk, docformat)
|
||||
@test f_check == f
|
||||
|
||||
# Test with actual doc
|
||||
|
||||
parsed = Weave.WeaveDoc("documents/chunk_options.noweb")
|
||||
doc = run_doc(parsed, doctype = "md2html")
|
||||
|
||||
c_check = "<pre class='hljl'>\n<span class='hljl-n'>x</span><span class='hljl-t'> </span><span class='hljl-oB'>=</span><span class='hljl-t'> </span><span class='hljl-p'>[</span><span class='hljl-ni'>12</span><span class='hljl-p'>,</span><span class='hljl-t'> </span><span class='hljl-ni'>10</span><span class='hljl-p'>]</span><span class='hljl-t'>\n</span><span class='hljl-nf'>println</span><span class='hljl-p'>(</span><span class='hljl-n'>y</span><span class='hljl-p'>)</span>\n</pre>\n"
|
||||
doc.format.highlight_theme = DefaultTheme
|
||||
c = Weave.format_code(doc.chunks[3].content, doc.format)
|
||||
@test c_check == c
|
||||
|
||||
o_check = "\nprintln(x)\n"
|
||||
o = Weave.format_output(doc.chunks[4].content, doc.format)
|
||||
@test o_check == o
|
||||
|
||||
# Tex format
|
||||
parsed = Weave.WeaveDoc("documents/chunk_options.noweb")
|
||||
doc = run_doc(parsed, doctype = "md2tex")
|
||||
|
||||
c_check = "\\begin{lstlisting}\n(*@\\HLJLnf{println}@*)(*@\\HLJLp{(}@*)(*@\\HLJLn{x}@*)(*@\\HLJLp{)}@*)\n\\end{lstlisting}\n"
|
||||
doc.format.highlight_theme = DefaultTheme
|
||||
c = Weave.format_code(doc.chunks[4].content, doc.format)
|
||||
@test c_check == c
|
||||
|
||||
o_check = "\nx = [12, 10]\nprintln(y)\n"
|
||||
o = Weave.format_output(doc.chunks[3].content, doc.format)
|
||||
@test o_check == o
|
||||
|
||||
# Test wrapping
|
||||
|
||||
cows = repeat("🐄", 100)
|
||||
testcows = """
|
||||
🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄
|
||||
🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄🐄"""
|
||||
|
||||
wcows = Weave.wrapline(cows)
|
||||
|
||||
@test wcows == testcows
|
||||
@test length(split(wcows, "\n")[1]) == 75
|
||||
@test length(split(wcows, "\n")[2]) == 25
|
||||
|
||||
|
||||
tfied = "\\ensuremath{\\bm{\\mathrm{L}}} \\ensuremath{\\bm{\\mathfrak{F}}} \\ensuremath{\\bm{\\iota}} \\ensuremath{\\mathfrak{A}} \\ensuremath{\\bm{\\varTheta}}"
|
||||
|
||||
@test Weave.uc2tex("𝐋 𝕱 𝛊 𝔄 𝚹") == tfied
|
||||
|
||||
# Test markdown output from chunks
|
||||
parsed = Weave.WeaveDoc("documents/markdown_output.jmd")
|
||||
doc = run_doc(parsed, doctype = "md2html")
|
||||
@test doc.chunks[1].rich_output == "\n<div class=\"markdown\"><h3>Small markdown sample</h3>\n<p><strong>Hello</strong> from <code>code</code> block.</p>\n</div>"
|
||||
@test doc.chunks[2].rich_output == "\n<div class=\"markdown\"><ul>\n<li><p>one</p>\n</li>\n<li><p>two</p>\n</li>\n<li><p>three</p>\n</li>\n</ul>\n</div>"
|
||||
|
||||
ldoc = run_doc(parsed, doctype = "md2tex")
|
||||
@test ldoc.chunks[1].rich_output == "\n\\subsubsection{Small markdown sample}\n\\textbf{Hello} from \\texttt{code} block.\n\n"
|
||||
@test ldoc.chunks[2].rich_output == "\n\\begin{itemize}\n\\item one\n\n\n\\item two\n\n\n\\item three\n\n\\end{itemize}\n"
|
||||
|
||||
mdoc = run_doc(parsed, doctype = "github")
|
||||
@test mdoc.chunks[1].rich_output == "\n\n### Small markdown sample\n\n**Hello** from `code` block.\n\n"
|
||||
@test mdoc.chunks[2].rich_output == "\n\n* one\n* two\n* three\n\n"
|
||||
|
||||
|
||||
# Test disable escaping of unicode
|
||||
@testset "escape/unescape unicode characters" begin
|
||||
|
||||
|
|
|
|||
|
|
@ -1,31 +0,0 @@
|
|||
# Test for Gadfly with different chunk options and figure formatsusing Weave
|
||||
|
||||
using Gadfly, Cairo
|
||||
|
||||
|
||||
function test_gadfly(doctype, fig_ext)
|
||||
out = weave(
|
||||
joinpath(@__DIR__ , "documents/gadfly_formats_test.jnw"),
|
||||
doctype = doctype,
|
||||
fig_ext = fig_ext
|
||||
)
|
||||
result = read(out, String)
|
||||
# cp(out, out*fig_ext*"."*doctype, force=true) # Used when adding new tests
|
||||
ref = read(out*fig_ext*"."*doctype, String)
|
||||
@test result == ref
|
||||
rm(out)
|
||||
end
|
||||
|
||||
test_gadfly("github", ".png")
|
||||
test_gadfly("github", ".pdf")
|
||||
test_gadfly("github", ".svg")
|
||||
test_gadfly("pandoc", ".png")
|
||||
test_gadfly("pandoc", ".js.svg")
|
||||
test_gadfly("tex", ".pdf")
|
||||
test_gadfly("tex", ".png")
|
||||
test_gadfly("tex", ".ps")
|
||||
test_gadfly("tex", ".tex")
|
||||
|
||||
p = Gadfly.plot(x=1:10, y=1:10)
|
||||
@test showable(MIME"application/pdf"(), p) == true
|
||||
@test showable(MIME"application/png"(), p) == true
|
||||
|
|
@ -1,6 +1,9 @@
|
|||
using Test
|
||||
import Weave: WeaveMarkdown
|
||||
import Markdown
|
||||
# TODO: make this more sensible:
|
||||
# - separate tests for
|
||||
# 1. features that are "copy-and-pasted" from `Markdown` module
|
||||
# 2. features that are extended by Weave
|
||||
|
||||
using Weave: WeaveMarkdown, Markdown
|
||||
|
||||
# Test markdown2html writer
|
||||
|
||||
|
|
|
|||
|
|
@ -1,7 +0,0 @@
|
|||
file = joinpath(@__DIR__, "documents", "jupyter_test.jmd")
|
||||
using IJulia, Conda
|
||||
|
||||
Conda.add("nbconvert") # should be the same as IJulia.JUPYTER, i.e. the miniconda Python
|
||||
|
||||
Weave.notebook(file, jupyter_path = IJulia.JUPYTER)
|
||||
@test "jupyter_test.ipynb" ∈ readdir(@__DIR__) # test if the result was weaved
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
using Plots
|
||||
|
||||
|
||||
function pljtest(source, resfile, doctype)
|
||||
weave("documents/$source", out_path = "documents/plotsjl/$resfile", doctype=doctype)
|
||||
result = read("documents/plotsjl/$resfile", String)
|
||||
ref = read("documents/plotsjl/$resfile.ref", String)
|
||||
@test result == ref
|
||||
rm("documents/plotsjl/$resfile")
|
||||
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
|
||||
|
|
@ -1,3 +1,5 @@
|
|||
@testset "evaluation error handling" begin
|
||||
|
||||
using Weave: unwrap_load_err
|
||||
|
||||
|
||||
|
|
@ -27,7 +29,7 @@ $err_stmt1
|
|||
$err_stmt2
|
||||
```
|
||||
|
||||
```julia; term=true
|
||||
```julia; term = true
|
||||
$err_stmt3
|
||||
```
|
||||
"""
|
||||
|
|
@ -47,6 +49,17 @@ let doc = mock_run(str; doctype = "github")
|
|||
@test occursin(err_str3_2, get_output(3))
|
||||
end
|
||||
|
||||
@test_throws ArgumentError mock_run(str; doctype = "github", throw_errors = true)
|
||||
# TODO: move this into chunk option tests
|
||||
str = """
|
||||
```julia; error = true
|
||||
using # won't be thrown
|
||||
```
|
||||
|
||||
# TODO: test error rendering in `rich_output`
|
||||
```julia; error = false
|
||||
using NonExisting # will be thrown
|
||||
```
|
||||
"""
|
||||
|
||||
@test_throws ArgumentError mock_run(str; doctype = "github")
|
||||
|
||||
end # @testset "evaluation error handling"
|
||||
|
|
@ -1,3 +1,5 @@
|
|||
@testset "meta information for evaluation" begin
|
||||
|
||||
doc_body = """
|
||||
```julia
|
||||
include("test_include.jl")
|
||||
|
|
@ -23,13 +25,13 @@ include("test_include.jl")
|
|||
read("./test_include.jl", String)
|
||||
```
|
||||
"""
|
||||
doc_dir = joinpath(@__DIR__, "mocks")
|
||||
doc_path = joinpath(doc_dir, "test_meta.jmd")
|
||||
doc_dir = normpath(@__DIR__, "..", "mocks")
|
||||
doc_path = normpath(doc_dir, "test_meta.jmd")
|
||||
write(doc_path, doc_body)
|
||||
|
||||
script_line = ":include_me"
|
||||
script_body = "$script_line"
|
||||
script_path = joinpath(@__DIR__, "mocks", "test_include.jl")
|
||||
script_path = normpath(@__DIR__, "..", "mocks", "test_include.jl")
|
||||
write(script_path, script_body)
|
||||
|
||||
|
||||
|
|
@ -43,3 +45,5 @@ check_output(i, s) = occursin(s, mock.chunks[i].output)
|
|||
@test check_output(4, doc_path)
|
||||
@test_broken check_output(5, 18)
|
||||
@test check_output(6, string('"', script_line, '"')) # current working directory
|
||||
|
||||
end # @testset "meta information for evaluation"
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
@testset "module evaluation" begin
|
||||
|
||||
function mock_output(str, mod = nothing)
|
||||
result_doc = mock_run(str; mod = mod)
|
||||
return result_doc.chunks[1].output
|
||||
end
|
||||
|
||||
str = """
|
||||
```julia
|
||||
@__MODULE__
|
||||
```
|
||||
"""
|
||||
|
||||
# in sandbox
|
||||
@test occursin(r"\#+WeaveSandBox[\#\d]+", mock_output(str))
|
||||
|
||||
# in Main
|
||||
@test strip(mock_output(str, Main)) == "Main"
|
||||
|
||||
end # @testset "module evaluation"
|
||||
|
||||
@testset "clear_module!" begin
|
||||
|
||||
ary = rand(1000000)
|
||||
size = Base.summarysize(ary)
|
||||
|
||||
# simple case
|
||||
m = Core.eval(@__MODULE__, :(module $(gensym(:WeaveTestModule)) end))
|
||||
Core.eval(m, :(a = $ary))
|
||||
Weave.clear_module!(m)
|
||||
@test Base.summarysize(m) < size
|
||||
|
||||
# recursive case
|
||||
m = Core.eval(@__MODULE__, :(module $(gensym(:WeaveTestModule)) end))
|
||||
Core.eval(m, :(
|
||||
module $(gensym(:WeaveTestSubModule))
|
||||
a = $ary
|
||||
end
|
||||
))
|
||||
Weave.clear_module!(m)
|
||||
@test Base.summarysize(m) < size
|
||||
|
||||
# doesn't work with constants
|
||||
m = Core.eval(@__MODULE__, :(module $(gensym(:WeaveTestModule)) end))
|
||||
Core.eval(m, :(const a = $ary))
|
||||
Weave.clear_module!(m)
|
||||
@test_broken Base.summarysize(m) < size
|
||||
|
||||
end # @testset "clear_module!"
|
||||
|
|
@ -1,10 +1,15 @@
|
|||
# TODO:
|
||||
# - reorganize this
|
||||
# - test for `include_weave`
|
||||
# - fire horrible tests
|
||||
# - test for ipynb integration
|
||||
# - test for integrations with other libraries, especially for Plots.jl and Gadfly.jl
|
||||
|
||||
# %%
|
||||
using Weave, Test
|
||||
using Weave: WeaveDoc, run_doc
|
||||
|
||||
|
||||
# TODO: add test for header processsing
|
||||
# TODO: add test for `include_weave`
|
||||
|
||||
function mock_doc(str, informat = "markdown")
|
||||
f = tempname()
|
||||
write(f, str)
|
||||
|
|
@ -27,29 +32,21 @@ function test_mock_weave(test_function, str; kwargs...)
|
|||
end
|
||||
|
||||
|
||||
# %%
|
||||
@testset "Weave" begin
|
||||
@testset "module evaluation" begin
|
||||
include("test_module_evaluation.jl")
|
||||
@testset "reader" begin
|
||||
include("reader/test_chunk_options.jl")
|
||||
include("reader/test_inline.jl")
|
||||
end
|
||||
|
||||
@testset "header" begin
|
||||
@testset "header processing" begin
|
||||
include("test_header.jl")
|
||||
end
|
||||
|
||||
@testset "inline" begin
|
||||
include("test_inline.jl")
|
||||
end
|
||||
|
||||
@testset "chunk options" begin
|
||||
include("test_chunk_options.jl")
|
||||
end
|
||||
|
||||
@testset "evaluation's meta info" begin
|
||||
include("test_meta.jl")
|
||||
end
|
||||
|
||||
@testset "error rendering" begin
|
||||
include("test_error_rendering.jl")
|
||||
@testset "run" begin
|
||||
include("run/test_module.jl")
|
||||
include("run/test_meta.jl")
|
||||
include("run/test_error.jl")
|
||||
end
|
||||
|
||||
@testset "conversions" begin
|
||||
|
|
@ -60,39 +57,10 @@ end
|
|||
include("test_display.jl")
|
||||
end
|
||||
|
||||
@testset "Formatters" begin
|
||||
@testset "legacy" begin
|
||||
include("formatter_test.jl")
|
||||
include("markdown_test.jl")
|
||||
include("figureformatter_test.jl")
|
||||
end
|
||||
|
||||
@testset "Cache" begin
|
||||
include("cache_test.jl")
|
||||
end
|
||||
|
||||
# @testset "Notebooks" begin
|
||||
# @info("Testing Jupyter options")
|
||||
# include("notebooks.jl")
|
||||
# end
|
||||
|
||||
# trigger only on CI
|
||||
if get(ENV, "CI", nothing) == "true"
|
||||
@testset "Plots" begin
|
||||
include("plotsjl_test.jl")
|
||||
end
|
||||
|
||||
@testset "Gadfly" begin
|
||||
include("gadfly_formats.jl")
|
||||
end
|
||||
else
|
||||
@info "skipped Plots.jl and Gadfly.jl integration test"
|
||||
end
|
||||
|
||||
try
|
||||
@testset "end2end (maybe fail)" begin
|
||||
include("end2end.jl")
|
||||
end
|
||||
catch err
|
||||
@error err
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -1,2 +0,0 @@
|
|||
|
||||
{{{ :body }}}
|
||||
|
|
@ -1,45 +0,0 @@
|
|||
@testset "evaluation module" begin
|
||||
function mock_output(str, mod = nothing)
|
||||
result_doc = mock_run(str; mod = mod)
|
||||
return result_doc.chunks[1].output
|
||||
end
|
||||
|
||||
str = """
|
||||
```julia
|
||||
@__MODULE__
|
||||
```
|
||||
"""
|
||||
|
||||
# in sandbox
|
||||
@test occursin(r"\#+WeaveSandBox[\#\d]+", mock_output(str))
|
||||
|
||||
# in Main
|
||||
@test strip(mock_output(str, Main)) == "Main"
|
||||
end
|
||||
|
||||
@testset "clear_module!" begin
|
||||
ary = rand(1000000)
|
||||
size = Base.summarysize(ary)
|
||||
|
||||
# simple case
|
||||
m = Core.eval(@__MODULE__, :(module $(gensym(:WeaveTestModule)) end))
|
||||
Core.eval(m, :(a = $ary))
|
||||
Weave.clear_module!(m)
|
||||
@test Base.summarysize(m) < size
|
||||
|
||||
# recursive case
|
||||
m = Core.eval(@__MODULE__, :(module $(gensym(:WeaveTestModule)) end))
|
||||
Core.eval(m, :(
|
||||
module $(gensym(:WeaveTestSubModule))
|
||||
a = $ary
|
||||
end
|
||||
))
|
||||
Weave.clear_module!(m)
|
||||
@test Base.summarysize(m) < size
|
||||
|
||||
# doesn't work with constants
|
||||
m = Core.eval(@__MODULE__, :(module $(gensym(:WeaveTestModule)) end))
|
||||
Core.eval(m, :(const a = $ary))
|
||||
Weave.clear_module!(m)
|
||||
@test_broken Base.summarysize(m) < size
|
||||
end
|
||||
Loading…
Reference in New Issue