diff --git a/previews/PR338/chunk_options/index.html b/previews/PR338/chunk_options/index.html index d4489ce..b71ee48 100644 --- a/previews/PR338/chunk_options/index.html +++ b/previews/PR338/chunk_options/index.html @@ -10,4 +10,4 @@ weave_options: out_width : 50% ---

You can also set or change the default chunk options for a document either before weave using the set_chunk_defaults function.

Weave.set_chunk_defaults! — Function
set_chunk_defaults!(k, v)
 set_chunk_defaults!(kv::Pair...)
-set_chunk_defaults!(opts::AbstractDict)

Set default options for code chunks, use get_chunk_defaults to see the current values.

E.g.: all the three examples below will set default dpi to 200 and fig_width to 8:

  • set_chunk_defaults!(:dpi, 200); set_chunk_defaults!(:fig_width, 8)
  • set_chunk_defaults!(:dpi => 200, :fig_width => 8)
  • set_chunk_defaults!(Dict(:dpi => 200, :fig_width => 8))
source
Weave.get_chunk_defaults — Function
get_chunk_defaults()

Get default options used for code chunks.

source
Weave.restore_chunk_defaults! — Function
restore_chunk_defaults!()

Restore Weave.jl default chunk options.

source
+set_chunk_defaults!(opts::AbstractDict)

Set default options for code chunks, use get_chunk_defaults to see the current values.

E.g.: all the three examples below will set default dpi to 200 and fig_width to 8:

source
Weave.get_chunk_defaults — Function
get_chunk_defaults()

Get default options used for code chunks.

source
Weave.restore_chunk_defaults! — Function
restore_chunk_defaults!()

Restore Weave.jl default chunk options.

source
diff --git a/previews/PR338/examples/FIR_design.html b/previews/PR338/examples/FIR_design.html index e14d2b5..ef10ada 100644 --- a/previews/PR338/examples/FIR_design.html +++ b/previews/PR338/examples/FIR_design.html @@ -654,8 +654,8 @@ div.title {text-align: center;}

FIR filter design with Julia

-

Matti Pastell

-

21th April 2016

+
Matti Pastell
+
21th April 2016

Introduction

diff --git a/previews/PR338/examples/jl_0gFG2O/FIR_design_5_1.png b/previews/PR338/examples/jl_OUMly7/FIR_design_5_1.png similarity index 100% rename from previews/PR338/examples/jl_0gFG2O/FIR_design_5_1.png rename to previews/PR338/examples/jl_OUMly7/FIR_design_5_1.png diff --git a/previews/PR338/examples/jl_0gFG2O/FIR_design_6_1.png b/previews/PR338/examples/jl_OUMly7/FIR_design_6_1.png similarity index 100% rename from previews/PR338/examples/jl_0gFG2O/FIR_design_6_1.png rename to previews/PR338/examples/jl_OUMly7/FIR_design_6_1.png diff --git a/previews/PR338/examples/jl_gLPVV0/FIR_design_plots_4_1.png b/previews/PR338/examples/jl_rjjBKf/FIR_design_plots_4_1.png similarity index 100% rename from previews/PR338/examples/jl_gLPVV0/FIR_design_plots_4_1.png rename to previews/PR338/examples/jl_rjjBKf/FIR_design_plots_4_1.png diff --git a/previews/PR338/function_index/index.html b/previews/PR338/function_index/index.html index 608bcc8..17bee10 100644 --- a/previews/PR338/function_index/index.html +++ b/previews/PR338/function_index/index.html @@ -1,2 +1,2 @@ -Function index · Weave.jl
Edit on GitHub
+Function index · Weave.jl
Edit on GitHub
diff --git a/previews/PR338/getting_started/index.html b/previews/PR338/getting_started/index.html index 656d2bf..2196b2d 100644 --- a/previews/PR338/getting_started/index.html +++ b/previews/PR338/getting_started/index.html @@ -10,4 +10,4 @@ weave(filename; doctype = "md2html", out_path = :pwd) weave(filename; doctype = "md2pdf", out_path = :pwd) # Julia markdown to Pandoc markdown -weave(filename; doctype = "pandoc", out_path = :pwd)
Tips

Weave.EXAMPLE_FOLDER points to the examples directory.

+weave(filename; doctype = "pandoc", out_path = :pwd)
Tips

Weave.EXAMPLE_FOLDER points to the examples directory.

diff --git a/previews/PR338/header/index.html b/previews/PR338/header/index.html index 4d43ee3..8ecade2 100644 --- a/previews/PR338/header/index.html +++ b/previews/PR338/header/index.html @@ -27,4 +27,4 @@ weave_options: md2pdf: out_path : pdf fig_ext : .png ---- +--- diff --git a/previews/PR338/index.html b/previews/PR338/index.html index d5a5393..c63149e 100644 --- a/previews/PR338/index.html +++ b/previews/PR338/index.html @@ -1,2 +1,2 @@ -Weave.jl - Scientific Reports Using Julia · Weave.jl
Edit on GitHub

Weave.jl - Scientific Reports Using Julia

This is the documentation of Weave.jl. Weave is a scientific report generator/literate programming tool for Julia. It resembles Pweave, knitr, R Markdown, and Sweave.

Current features

  • Publish markdown directly to HTML and PDF using Julia or Pandoc
  • Execute code as in terminal or in a unit of code chunk
  • Capture Plots.jl or Gadfly.jl figures
  • Supports various input format: Markdown, Noweb, Jupyter Notebook, and ordinal Julia script
  • Conversions between those input formats
  • Supports various output document formats: HTML, PDF, GitHub markdown, Jupyter Notebook, MultiMarkdown, Asciidoc and reStructuredText
  • Simple caching of results

Weave in Juno demo

Index

+Weave.jl - Scientific Reports Using Julia · Weave.jl
Edit on GitHub

Weave.jl - Scientific Reports Using Julia

This is the documentation of Weave.jl. Weave is a scientific report generator/literate programming tool for Julia. It resembles Pweave, knitr, R Markdown, and Sweave.

Current features

  • Publish markdown directly to HTML and PDF using Julia or Pandoc
  • Execute code as in terminal or in a unit of code chunk
  • Capture Plots.jl or Gadfly.jl figures
  • Supports various input format: Markdown, Noweb, Jupyter Notebook, and ordinal Julia script
  • Conversions between those input formats
  • Supports various output document formats: HTML, PDF, GitHub markdown, Jupyter Notebook, MultiMarkdown, Asciidoc and reStructuredText
  • Simple caching of results

Weave in Juno demo

Index

diff --git a/previews/PR338/notebooks/index.html b/previews/PR338/notebooks/index.html index 00f26b0..0edca68 100644 --- a/previews/PR338/notebooks/index.html +++ b/previews/PR338/notebooks/index.html @@ -1,2 +1,2 @@ -Working with Jupyter notebooks · Weave.jl
Edit on GitHub

Working with Jupyter notebooks

Weaving from Jupyter notebooks

Weave supports using Jupyter Notebooks as input format. This means you can weave notebooks to any supported formats; by default, it will be weaved to HTML.

weave("notebook.ipynb") # will be weaved to HTML
Warning

You can't use chunk options with notebooks.

Output to Jupyter notebooks

As of Weave 0.5.1. there is new notebook method to convert Weave documents to Jupyter notebooks using nbconvert.

Weave.notebook — Function
notebook(source::AbstractString; kwargs...)

Convert Weave document source to Jupyter Notebook and execute the code using nbconvert. Ignores all chunk options.

Keyword options

  • out_path::Union{Symbol,AbstractString} = :pwd: Path where the output is generated can be either of:
    • :doc: Path of the source document
    • :pwd: Julia working directory (default)
    • "somepath": String of output directory e.g. "~/outdir", or of filename e.g. "~/outdir/outfile.tex"
  • timeout = -1: nbconvert cell timeout in seconds. Defaults to -1 (no timeout)
  • nbconvert_options::AbstractString = "": String of additional options to pass to nbconvert, such as "--allow-errors"
  • jupyter_path::AbstractString = "jupyter": Path/command for the Jupyter you want to use. Defaults to "jupyter", which runs whatever is linked/alias to that
Warning

The code is not executed by Weave, but by nbconvert. This means that the output doesn't necessarily always work properly; see #116.

Note

In order to just convert Weave document to Jupyter Notebook, use convert_doc instead.

source

You can specify jupyter used to execute the notebook with the jupyter_path keyword argument (this defaults to the "jupyter", i.e. whatever you have linked to that location).

Instead, you might want to use the convert_doc method below and run the code in Jupyter.

Converting between formats

You can convert between all supported input formats using the convert_doc function.

To convert from script to notebook:

convert_doc("examples/FIR_design.jl", "FIR_design.ipynb")

and from notebook to Markdown use:

convert_doc("FIR_design.ipynb", "FIR_design.jmd")
Weave.convert_doc — Function
convert_doc(infile::AbstractString, outfile::AbstractString; outformat::Union{Nothing,AbstractString} = nothing)

Convert Weave documents between different formats

  • infile: Path of the input document
  • outfile: Path of the output document
  • outformat = nothing: Output document format (optional). By default (i.e. given nothing) Weave will try to automatically detect it from the outfile's extension. You can also specify either of "script", "markdown", "notebook", or "noweb"
source
+Working with Jupyter notebooks · Weave.jl
Edit on GitHub

Working with Jupyter notebooks

Weaving from Jupyter notebooks

Weave supports using Jupyter Notebooks as input format. This means you can weave notebooks to any supported formats; by default, it will be weaved to HTML.

weave("notebook.ipynb") # will be weaved to HTML
Warning

You can't use chunk options with notebooks.

Output to Jupyter notebooks

As of Weave 0.5.1. there is new notebook method to convert Weave documents to Jupyter notebooks using nbconvert.

Weave.notebook — Function
notebook(source::AbstractString; kwargs...)

Convert Weave document source to Jupyter Notebook and execute the code using nbconvert. Ignores all chunk options.

Keyword options

  • out_path::Union{Symbol,AbstractString} = :pwd: Path where the output is generated can be either of:
    • :doc: Path of the source document
    • :pwd: Julia working directory (default)
    • "somepath": String of output directory e.g. "~/outdir", or of filename e.g. "~/outdir/outfile.tex"
  • timeout = -1: nbconvert cell timeout in seconds. Defaults to -1 (no timeout)
  • nbconvert_options::AbstractString = "": String of additional options to pass to nbconvert, such as "--allow-errors"
  • jupyter_path::AbstractString = "jupyter": Path/command for the Jupyter you want to use. Defaults to "jupyter", which runs whatever is linked/alias to that
Warning

The code is not executed by Weave, but by nbconvert. This means that the output doesn't necessarily always work properly; see #116.

Note

In order to just convert Weave document to Jupyter Notebook, use convert_doc instead.

source

You can specify jupyter used to execute the notebook with the jupyter_path keyword argument (this defaults to the "jupyter", i.e. whatever you have linked to that location).

Instead, you might want to use the convert_doc method below and run the code in Jupyter.

Converting between formats

You can convert between all supported input formats using the convert_doc function.

To convert from script to notebook:

convert_doc("examples/FIR_design.jl", "FIR_design.ipynb")

and from notebook to Markdown use:

convert_doc("FIR_design.ipynb", "FIR_design.jmd")
Weave.convert_doc — Function
convert_doc(infile::AbstractString, outfile::AbstractString; outformat::Union{Nothing,AbstractString} = nothing)

Convert Weave documents between different formats

  • infile: Path of the input document
  • outfile: Path of the output document
  • outformat = nothing: Output document format (optional). By default (i.e. given nothing) Weave will try to automatically detect it from the outfile's extension. You can also specify either of "script", "markdown", "notebook", or "noweb"
source
diff --git a/previews/PR338/publish/index.html b/previews/PR338/publish/index.html index 2d84162..3d1109f 100644 --- a/previews/PR338/publish/index.html +++ b/previews/PR338/publish/index.html @@ -6,4 +6,4 @@ date: 15th December 2016 ---

Here are sample input and outputs:

They are generated as follows:

weave(Weave.SAMPLE_JL_DOC)) # default to md2html output format
 weave(Weave.SAMPLE_JL_DOC; doctype = "md2pdf")
Tips

Weave.SAMPLE_JL_DOC is the path of FIR_design.jl.

Note

"md2html" and "md2pdf" assume Julia markdown format as an input, while pandoc2pdf and pandoc2html assume Noweb input format (i.e. Pandoc markdown).

Templates

You can use a custom template with md2html and md2pdf formats with template keyword option, e.g.: weave("FIR_design_plots.jl", template = "custom.tpl".

As starting point, you can use the existing templates:

Templates are rendered using Mustache.jl.

Supported Markdown syntax

The markdown variant used by Weave is Julia markdown. In addition Weave supports few additional Markdown features:

Comments

You can add comments using html syntax: <!-- -->

Multiline equations

You can add multiline equations using:

$$
 x^2 = x*x
-$$
+$$ diff --git a/previews/PR338/search/index.html b/previews/PR338/search/index.html index 33c1359..9bbab35 100644 --- a/previews/PR338/search/index.html +++ b/previews/PR338/search/index.html @@ -1,2 +1,2 @@ -Search · Weave.jl

Loading search...

    +Search · Weave.jl

    Loading search...

      diff --git a/previews/PR338/usage/index.html b/previews/PR338/usage/index.html index 40b756b..f3fe56a 100644 --- a/previews/PR338/usage/index.html +++ b/previews/PR338/usage/index.html @@ -2,7 +2,7 @@ Using Weave · Weave.jl
      Edit on GitHub

      Using Weave

      You can write your documentation and code in input document using Markdown, Noweb or script syntax and use weave function to execute to document to capture results and figures.

      weave

      Weave document with markup and julia code using Plots.jl for plots, out_path = :pwd makes the results appear in the current working directory.

      A prepared example: Weave.SAMPLE_JL_DOC

      # First add depencies for the example
 using Pkg; Pkg.add.(["Plots", "DSP"])
 using Weave
-weave(Weave.SAMPLE_JL_DOC; out_path=:pwd)
      Weave.weave — Function
      weave(source::AbstractString; kwargs...)

      Weave an input document to output file.

      Keyword options

      • doctype::Union{Nothing,AbstractString} = nothing: Output document format. By default (i.e. given nothing), Weave will set it automatically based on file extension. You can also manually specify it; see list_out_formats() for the supported formats
      • informat::Union{Nothing,AbstractString} = nothing: Input document format. By default (i.e. given nothing), Weave will set it automatically based on file extension. You can also specify either of "script", "markdown", "notebook", or "noweb"
      • out_path::Union{Symbol,AbstractString} = :doc: Path where the output is generated can be either of:
        • :doc: Path of the source document (default)
        • :pwd: Julia working directory
        • "somepath": String of output directory e.g. "~/outdir", or of filename e.g. "~/outdir/outfile.tex"
      • args::Dict = Dict(): Arguments to be passed to the weaved document; will be available as WEAVE_ARGS in the document
      • mod::Union{Module,Nothing} = nothing: Module where Weave evals code. You can pass a Module object, otherwise create an new sandbox module.
      • fig_path::Union{Nothing,AbstractString} = nothing: Where figures will be generated, relative to out_path. By default (i.e. given nothing), Weave will automatically create figures directory.
      • fig_ext::Union{Nothing,AbstractString} = nothing: Extension for saved figures e.g. ".pdf", ".png". Default setting depends on doctype
      • cache_path::AbstractString = "cache": Where of cached output will be saved
      • cache::Symbol = :off: Controls caching of code:
        • :off means no caching (default)
        • :all caches everything
        • :user caches based on chunk options
        • :refresh runs all code chunks and save new cache
      • template::Union{Nothing,AbstractString,Mustache.MustacheTokens} = nothing: Template (file path) or Mustache.MustacheTokenss for md2html or md2tex formats
      • css::Union{Nothing,AbstractString} = nothing: Path of a CSS file used for md2html format
      • highlight_theme::Union{Nothing,AbstractString,Symbol,Type{<:Highlights.AbstractTheme}} = nothing: Theme used for syntax highlighting.
        • If given nothing (default), Weave will use Highlights.Themes.DefaultTheme
        • If given an instance of AbstractString or Symbol, Weave will try to search a theme based on string matching, e.g. highlight_theme = "github" will use Highlights.Themes.GitHubTheme
        • If given an instance of Highlights.AbstractTheme, it will be directly used
      • pandoc_options::Vector{<:AbstractString} = String[]: Strings of options to pass to pandoc for pandoc2html and pandoc2pdf formats, e.g. ["--toc", "-N"]
      • latex_cmd::Vector{<:AbstractString} = ["xelatex", "-shell-escape", "-halt-on-error"]: The command used to make PDF file from .tex
      • keep_unicode::Bool = false: If true, do not convert unicode characters to their respective latex representation. This is especially useful if a font and tex-engine with support for unicode characters are used
      Note

      Run Weave from terminal and try to avoid weaving from IJulia or ESS; they tend to mess with capturing output.

      source

      tangle

      Tangling extracts the code from document:

      Weave.tangle — Function
      tangle(source::AbstractString; kwargs...)

      Tangle source code from input document to .jl file.

      Keyword options

      • informat::Union{Nothing,AbstractString} = nothing: Input document format. By default (i.e. given nothing), Weave will set it automatically based on file extension. You can also specify either of "script", "markdown", "notebook", or "noweb"
      • out_path::Union{Symbol,AbstractString} = :doc: Path where the output is generated can be either of:
        • :doc: Path of the source document (default)
        • :pwd: Julia working directory
        • "somepath": String of output directory e.g. "~/outdir", or of filename e.g. "~/outdir/outfile.tex"
      source

      Supported Output Formats

      Weave automatically detects the output format based on the file extension. The auto output format detection is handled by detect_doctype(path::AbstractString):

      function detect_doctype(path::AbstractString)
+weave(Weave.SAMPLE_JL_DOC; out_path=:pwd)
      Weave.weave — Function
      weave(source::AbstractString; kwargs...)

      Weave an input document to output file.

      Keyword options

      • doctype::Union{Nothing,AbstractString} = nothing: Output document format. By default (i.e. given nothing), Weave will set it automatically based on file extension. You can also manually specify it; see list_out_formats() for the supported formats
      • informat::Union{Nothing,AbstractString} = nothing: Input document format. By default (i.e. given nothing), Weave will set it automatically based on file extension. You can also specify either of "script", "markdown", "notebook", or "noweb"
      • out_path::Union{Symbol,AbstractString} = :doc: Path where the output is generated can be either of:
        • :doc: Path of the source document (default)
        • :pwd: Julia working directory
        • "somepath": String of output directory e.g. "~/outdir", or of filename e.g. "~/outdir/outfile.tex"
      • args::Dict = Dict(): Arguments to be passed to the weaved document; will be available as WEAVE_ARGS in the document
      • mod::Union{Module,Nothing} = nothing: Module where Weave evals code. You can pass a Module object, otherwise create an new sandbox module.
      • fig_path::Union{Nothing,AbstractString} = nothing: Where figures will be generated, relative to out_path. By default (i.e. given nothing), Weave will automatically create figures directory.
      • fig_ext::Union{Nothing,AbstractString} = nothing: Extension for saved figures e.g. ".pdf", ".png". Default setting depends on doctype
      • cache_path::AbstractString = "cache": Where of cached output will be saved
      • cache::Symbol = :off: Controls caching of code:
        • :off means no caching (default)
        • :all caches everything
        • :user caches based on chunk options
        • :refresh runs all code chunks and save new cache
      • template::Union{Nothing,AbstractString,Mustache.MustacheTokens} = nothing: Template (file path) or Mustache.MustacheTokenss for md2html or md2tex formats
      • css::Union{Nothing,AbstractString} = nothing: Path of a CSS file used for md2html format
      • highlight_theme::Union{Nothing,AbstractString,Symbol,Type{<:Highlights.AbstractTheme}} = nothing: Theme used for syntax highlighting.
        • If given nothing (default), Weave will use Highlights.Themes.DefaultTheme
        • If given an instance of AbstractString or Symbol, Weave will try to search a theme based on string matching, e.g. highlight_theme = "github" will use Highlights.Themes.GitHubTheme
        • If given an instance of Highlights.AbstractTheme, it will be directly used
      • pandoc_options::Vector{<:AbstractString} = String[]: Strings of options to pass to pandoc for pandoc2html and pandoc2pdf formats, e.g. ["--toc", "-N"]
      • latex_cmd::Vector{<:AbstractString} = ["xelatex", "-shell-escape", "-halt-on-error"]: The command used to make PDF file from .tex
      • keep_unicode::Bool = false: If true, do not convert unicode characters to their respective latex representation. This is especially useful if a font and tex-engine with support for unicode characters are used
      Note

      Run Weave from terminal and try to avoid weaving from IJulia or ESS; they tend to mess with capturing output.

      source

      tangle

      Tangling extracts the code from document:

      Weave.tangle — Function
      tangle(source::AbstractString; kwargs...)

      Tangle source code from input document to .jl file.

      Keyword options

      • informat::Union{Nothing,AbstractString} = nothing: Input document format. By default (i.e. given nothing), Weave will set it automatically based on file extension. You can also specify either of "script", "markdown", "notebook", or "noweb"
      • out_path::Union{Symbol,AbstractString} = :doc: Path where the output is generated can be either of:
        • :doc: Path of the source document (default)
        • :pwd: Julia working directory
        • "somepath": String of output directory e.g. "~/outdir", or of filename e.g. "~/outdir/outfile.tex"
      source

      Supported Output Formats

      Weave automatically detects the output format based on the file extension. The auto output format detection is handled by detect_doctype(path::AbstractString):

      function detect_doctype(path::AbstractString)
     _, ext = lowercase.(splitext(path))
 
     match(r"^\.(jl|.?md|ipynb)", ext) !== nothing && return "md2html"
@@ -11,7 +11,7 @@ weave(Weave.SAMPLE_JL_DOC; out_path=:pwd)

      You can also manually specify it using the doctype keyword option. You can get a list of supported output formats:

      list_out_formats()
      12-element Array{Pair{String,String},1}:
+end

      You can also manually specify it using the doctype keyword option. You can get a list of supported output formats:

      list_out_formats()
      12-element Array{Pair{String,String},1}:
         "github" => "GitHub Markdown"
         "md2tex" => "Weave-styled LaTeX"
    "pandoc2html" => "HTML via intermediate Pandoc Markdown (requires Pandoc 2)"
@@ -36,4 +36,4 @@ return "noweb"

      Pweave and the concept is similar to publishing documents with MATLAB or using Knitr's spin. Weave will remove the first empty space from each line of documentation.

      Tip

      Configuration via YAML Header

      When weaveing markdown files, you can use YAML header to provide additional metadata and configuration options. See Header Configuration section for more details.

      Passing Runtime Arguments to Documents

      You can pass arguments as Dict to the weaved document using the args argument to weave. The arguments will be available as WEAVE_ARGS variable in the document.

      This makes it possible to create the same report easily for e.g. different date ranges of input data from a database or from files with similar format giving the filename as input.

      In order to pass a filename to a document you need call weave using:

      weave("mydoc.jmd", args = Dict("filename" => "somedata.h5"))

      and you can access the filename from document as follows:

          ```julia
     print(WEAVE_ARGS["filename"])
     ```

      You can use the out_path argument to control the name of the output document.

      include_weave

      You can call include_weave on a Weave document and run all code chunks within in the current session.

      Weave.include_weave — Function
      include_weave(source::AbstractString, informat::Union{Nothing,AbstractString} = nothing)
-include_weave(m::Module, source::AbstractString, informat::Union{Nothing,AbstractString} = nothing)

      Include code from Weave document calling include_string on all code from doc. Code is run in the path of the include document.

      source
      +include_weave(m::Module, source::AbstractString, informat::Union{Nothing,AbstractString} = nothing)

      Include code from Weave document calling include_string on all code from doc. Code is run in the path of the include document.

      source