mirror of https://github.com/mpastell/Weave.jl
159 lines
30 KiB
JSON
159 lines
30 KiB
JSON
{
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"docs": [
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{
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"location": "/",
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"text": "Weave.jl - Scientific Reports Using Julia\n\n\nThis is the documentation of \nWeave.jl\n. Weave is a scientific report generator/literate programming tool for Julia. It resembles \nPweave\n, Knitr, rmarkdown and Sweave.\n\n\nCurrent features\n\n\n\n\nNoweb, markdown or script syntax for input documents.\n\n\nExecute code as terminal or \"script\" chunks.\n\n\nCapture Plots, Gadfly, PyPlot and Winston figures.\n\n\nSupports LaTex, Pandoc, Github markdown, MultiMarkdown, Asciidoc and reStructuredText output\n\n\nPublish markdown directly to html and pdf using julia or Pandoc markdown.\n\n\nSimple caching of results\n\n\nConvert to and from IJulia notebooks\n\n\n\n\n\n\n\n\nContents\n\n\n\n\nGetting started\n\n\nUsing Weave\n\n\nWeave\n\n\nWeave from shell\n\n\nTangle\n\n\nSupported formats\n\n\nDocument syntax\n\n\nNoweb format\n\n\nMarkdown format\n\n\nScript format\n\n\n\n\n\n\nPublishing to html and pdf\n\n\nTemplates\n\n\n\n\n\n\nChunk options\n\n\nOptions for code\n\n\nOptions for figures\n\n\nSet default chunk options\n\n\n\n\n\n\nWorking with Jupyter notebooks\n\n\nWeaving\n\n\nConverting between formats\n\n\n\n\n\n\nFunction index",
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"title": "Home"
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},
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{
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"location": "/#weavejl-scientific-reports-using-julia",
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"text": "This is the documentation of Weave.jl . Weave is a scientific report generator/literate programming tool for Julia. It resembles Pweave , Knitr, rmarkdown and Sweave. Current features Noweb, markdown or script syntax for input documents. Execute code as terminal or \"script\" chunks. Capture Plots, Gadfly, PyPlot and Winston figures. Supports LaTex, Pandoc, Github markdown, MultiMarkdown, Asciidoc and reStructuredText output Publish markdown directly to html and pdf using julia or Pandoc markdown. Simple caching of results Convert to and from IJulia notebooks",
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"title": "Weave.jl - Scientific Reports Using Julia"
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},
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{
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"location": "/#contents",
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"text": "Getting started Using Weave Weave Weave from shell Tangle Supported formats Document syntax Noweb format Markdown format Script format Publishing to html and pdf Templates Chunk options Options for code Options for figures Set default chunk options Working with Jupyter notebooks Weaving Converting between formats Function index",
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"title": "Contents"
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},
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{
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"location": "/getting_started/",
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"text": "Getting started\n\n\nThe best way to get started using Weave.jl is to look at the example input and output documents. Examples for different formats are included in the packages \nexamples\n directory.\n\n\nFirst have a look at source document using markdown code chunks and Gadfly for figures: \ngadfly_md_sample.jmd\n and then see the output in different formats:\n\n\n\n\nPandoc markdown: \ngadfly_md_sample.md\n\n\nHTML: \ngadfly_md_sample.html\n\n\npdf: \ngadfly_md_sample.pdf\n\n\n\n\nProducing pdf output requires that you have pdflatex installed.\n\n\nYou can Weave the files to your working directory using:\n\n\nusing\n \nWeave\n\n\n#Markdown\n\n\nweave\n(\nPkg\n.\ndir\n(\n\"Weave\"\n,\n\"examples\"\n,\n\"gadfly_md_sample.jmd\"\n),\n \nout_path\n \n=\n \n:\npwd\n,\n\n \ndoctype\n \n=\n \n\"pandoc\"\n)\n\n\n#HTML\n\n\nweave\n(\nPkg\n.\ndir\n(\n\"Weave\"\n,\n\"examples\"\n,\n\"gadfly_md_sample.jmd\"\n),\n \nout_path\n \n=\n \n:\npwd\n,\n\n \ndoctype\n \n=\n \n\"md2html\"\n)\n\n\n#pdf\n\n\nweave\n(\nPkg\n.\ndir\n(\n\"Weave\"\n,\n\"examples\"\n,\n\"gadfly_md_sample.jmd\"\n),\n \nout_path\n \n=\n \n:\npwd\n,\n\n \ndoctype\n \n=\n \n\"md2pdf\"\n)",
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"title": "Getting started"
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},
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{
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"location": "/getting_started/#getting-started",
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"text": "The best way to get started using Weave.jl is to look at the example input and output documents. Examples for different formats are included in the packages examples directory. First have a look at source document using markdown code chunks and Gadfly for figures: gadfly_md_sample.jmd and then see the output in different formats: Pandoc markdown: gadfly_md_sample.md HTML: gadfly_md_sample.html pdf: gadfly_md_sample.pdf Producing pdf output requires that you have pdflatex installed. You can Weave the files to your working directory using: using Weave #Markdown weave ( Pkg . dir ( \"Weave\" , \"examples\" , \"gadfly_md_sample.jmd\" ), out_path = : pwd , \n doctype = \"pandoc\" ) #HTML weave ( Pkg . dir ( \"Weave\" , \"examples\" , \"gadfly_md_sample.jmd\" ), out_path = : pwd , \n doctype = \"md2html\" ) #pdf weave ( Pkg . dir ( \"Weave\" , \"examples\" , \"gadfly_md_sample.jmd\" ), out_path = : pwd , \n doctype = \"md2pdf\" )",
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"title": "Getting started"
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},
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{
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"location": "/usage/",
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"text": "Using Weave\n\n\nYou can write your documentation and code in input document using Noweb, Markdown or script syntax and use \nweave\n function to execute to document to capture results and figures.\n\n\n\n\nWeave\n\n\nWeave document with markup and julia code using Gadfly for plots, \nout_path = :pwd\n makes the results appear in the current working directory.\n\n\nusing\n \nWeave\n\n\nweave\n(\nPkg\n.\ndir\n(\n\"Weave\"\n,\n\"examples\"\n,\n\"gadfly_sample.mdw\"\n),\n \nout_path\n \n=\n \n:\npwd\n)\n\n\n\n\n\n\nUsing PyPlot:\n\n\nweave\n(\nPkg\n.\ndir\n(\n\"Weave\"\n,\n\"examples\"\n,\n\"julia_sample.mdw\"\n),\n \nplotlib\n=\n\"PyPlot\"\n,\n \nout_path\n \n=\n \n:\npwd\n)\n\n\n\n\n\n\n#\n\n\nWeave.weave\n \u2014 \nMethod\n.\n\n\nweave(source ; doctype = :auto, plotlib=:auto,\n informat=:auto, out_path=:doc, fig_path = \"figures\", fig_ext = nothing,\n cache_path = \"cache\", cache=:off,\n template = nothing, highlight_theme = nothing, css = nothing\n latex_cmd = \"pdflatex\")\n\n\n\n\n\nWeave an input document to output file.\n\n\n\n\ndoctype\n: :auto = set based on file extension or specify one of the supported formats. See \nlist_out_formats()\n\n\nplotlib\n: \n\"PyPlot\"\n, \n\"Gadfly\"\n or \nnothing\n\n\ninformat\n: :auto = set based on file extension or set to \n\"noweb\"\n, \n\"markdown\"\n or \nscript\n\n\nout_path\n: Path where the output is generated. Can be: \n:doc\n: Path of the source document, \n:pwd\n: Julia working directory, \n\"somepath\"\n: output directory as a String e.g \n\"/home/mpastell/weaveout\"\n or filename as string e.g. ~/outpath/outfile.tex.\n\n\nfig_path\n: where figures will be generated, relative to out_path\n\n\nfig_ext\n: Extension for saved figures e.g. \n\".pdf\"\n, \n\".png\"\n. Default setting depends on \ndoctype\n.\n\n\ncache_path\n: where of cached output will be saved.\n\n\ncache\n: controls caching of code: \n:off\n = no caching, \n:all\n = cache everything, \n:user\n = cache based on chunk options, \n:refresh\n, run all code chunks and save new cache.\n\n\ntemplate\n : Template (file path) for md2html or md2tex formats.\n\n\nhighlight_theme\n : Theme (Highlights.AbstractTheme) for used syntax highlighting\n\n\ncss\n : CSS (file path) used for md2html format\n\n\nlatex_cmd\n the command used to make pdf from .tex\n\n\n\n\nNote:\n Run Weave from terminal and not using IJulia, Juno or ESS, they tend to mess with capturing output.\n\n\nsource\n\n\n\n\nWeave from shell\n\n\nYou can also use the \nweave.jl\n script under bin directory to weave documents from the shell:\n\n\n$ ./weave.jl\nusage: weave.jl \n[\n--doctype DOCTYPE\n]\n \n[\n--plotlib PLOTLIB\n]\n\n \n[\n--informat INFORMAT\n]\n \n[\n--out_path OUT_PATH\n]\n\n \n[\n--fig_path FIG_PATH\n]\n \n[\n--fig_ext FIG_EXT\n]\n source...\n\n\n\n\n\n\n\nTangle\n\n\nTangling extracts the code from document:\n\n\n#\n\n\nWeave.tangle\n \u2014 \nMethod\n.\n\n\ntangle(source ; out_path=:doc, informat=\"noweb\")\n\n\nTangle source code from input document to .jl file.\n\n\n\n\ninformat\n: \n\"noweb\"\n of \n\"markdown\"\n\n\nout_path\n: Path where the output is generated. Can be: \n:doc\n: Path of the source document, \n:pwd\n: Julia working directory, \n\"somepath\"\n, directory name as a string e.g \n\"/home/mpastell/weaveout\"\n\n\n\n\nor filename as string e.g. ~/outpath/outfile.jl.\n\n\nsource\n\n\n\n\nSupported formats\n\n\nWeave sets the output format based on the file extension, but you can also set it using \ndoctype\n option. The rules for detecting the format are:\n\n\next\n \n==\n \n\".jl\"\n \n&&\n \nreturn\n \n\"md2html\"\n\n\ncontains\n(\next\n,\n \n\".md\"\n)\n \n&&\n \nreturn\n \n\"md2html\"\n\n\ncontains\n(\next\n,\n \n\".rst\"\n)\n \n&&\n \nreturn\n \n\"rst\"\n\n\ncontains\n(\next\n,\n \n\".tex\"\n)\n \n&&\n \nreturn\n \n\"texminted\"\n\n\ncontains\n(\next\n,\n \n\".txt\"\n)\n \n&&\n \nreturn\n \n\"asciidoc\"\n\n\nreturn\n \n\"pandoc\"\n\n\n\n\n\n\nYou can get a list of supported output formats:\n\n\nlist_out_formats\n()\n\n\n\n\n\n\ngithub\n:\n \nGithub\n \nmarkdown\n\n\nmd2tex\n:\n \nJulia\n \nmarkdown\n \nto\n \nlatex\n\n\npandoc2html\n:\n \nMarkdown\n \nto\n \nHTML\n \n(\nrequires\n \nPandoc\n)\n\n\npandoc\n:\n \nPandoc\n \nmarkdown\n\n\npandoc2pdf\n:\n \nPandoc\n \nmarkdown\n\n\ntex\n:\n \nLatex\n \nwith\n \ncustom\n \ncode\n \nenvironments\n\n\ntexminted\n:\n \nLatex\n \nusing\n \nminted\n \nfor\n \nhighlighting\n\n\nmd2html\n:\n \nJulia\n \nmarkdown\n \nto\n \nhtml\n\n\nrst\n:\n \nreStructuredText\n \nand\n \nSphinx\n\n\nmultimarkdown\n:\n \nMultiMarkdown\n\n\nmd2pdf\n:\n \nJulia\n \nmarkdown\n \nto\n \nlatex\n\n\nasciidoc\n:\n \nAsciiDoc\n\n\n\n\n\n\n#\n\n\nWeave.list_out_formats\n \u2014 \nMethod\n.\n\n\nlist_out_formats()\n\n\nList supported output formats\n\n\nsource\n\n\n\n\nDocument syntax\n\n\nWeave uses noweb, markdown or script syntax for defining the code chunks and documentation chunks. You can also weave Jupyter notebooks. The format is detected based on the file extension, but you can also set it manually using the \ninformat\n parameter.\n\n\nThe rules for autodetection are:\n\n\next\n \n==\n \n\".jl\"\n \n&&\n \nreturn\n \n\"script\"\n\n\next\n \n==\n \n\".jmd\"\n \n&&\n \nreturn\n \n\"markdown\"\n\n\next\n \n==\n \n\".ipynb\"\n \n&&\n \nreturn\n \n\"notebook\"\n\n\nreturn\n \n\"noweb\"\n\n\n\n\n\n\n\n\nNoweb format\n\n\n\n\nCode chunks\n\n\nstart with a line marked with \n<<>>=\n or \n<<options>>=\n and end with line marked with \n@\n. The code between the start and end markers is executed and the output is captured to the output document. See \nchunk options\n.\n\n\n\n\nDocumentation chunks\n\n\nAre the rest of the document (between \n@\n and \n<<>>=\n lines and the first chunk be default) and can be written with several different markup languages.\n\n\nSample document\n\n\n\n\nMarkdown format\n\n\nMarkdown code chunks are defined using fenced code blocks with options following on the same line. e.g. to hide code from output you can use:\n\n\n```julia; echo=false\n\n\nSee sample document:\n\n\n\n\nScript format\n\n\nWeave also support script input format with a markup in comments. These scripts can be executed normally using Julia or published with Weave. Documentation is in lines starting with \n#'\n, \n#%%\n or \n# %%\n, and code is executed and results are included in the weaved document.\n\n\nAll lines that are not documentation are treated as code. You can set chunk options using lines starting with \n#+\n just before code e.g. \n#+ term=true\n.\n\n\nThe format is identical to \nPweave\n and the concept is similar to publishing documents with MATLAB or using Knitr's \nspin\n. Weave will remove the first empty space from each line of documentation.\n\n\nSee sample document:",
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"title": "Using Weave"
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},
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{
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"location": "/usage/#using-weave",
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"text": "You can write your documentation and code in input document using Noweb, Markdown or script syntax and use weave function to execute to document to capture results and figures.",
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"title": "Using Weave"
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},
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{
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"location": "/usage/#weave",
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"text": "Weave document with markup and julia code using Gadfly for plots, out_path = :pwd makes the results appear in the current working directory. using Weave weave ( Pkg . dir ( \"Weave\" , \"examples\" , \"gadfly_sample.mdw\" ), out_path = : pwd ) Using PyPlot: weave ( Pkg . dir ( \"Weave\" , \"examples\" , \"julia_sample.mdw\" ), plotlib = \"PyPlot\" , out_path = : pwd ) # Weave.weave \u2014 Method . weave(source ; doctype = :auto, plotlib=:auto,\n informat=:auto, out_path=:doc, fig_path = \"figures\", fig_ext = nothing,\n cache_path = \"cache\", cache=:off,\n template = nothing, highlight_theme = nothing, css = nothing\n latex_cmd = \"pdflatex\") Weave an input document to output file. doctype : :auto = set based on file extension or specify one of the supported formats. See list_out_formats() plotlib : \"PyPlot\" , \"Gadfly\" or nothing informat : :auto = set based on file extension or set to \"noweb\" , \"markdown\" or script out_path : Path where the output is generated. Can be: :doc : Path of the source document, :pwd : Julia working directory, \"somepath\" : output directory as a String e.g \"/home/mpastell/weaveout\" or filename as string e.g. ~/outpath/outfile.tex. fig_path : where figures will be generated, relative to out_path fig_ext : Extension for saved figures e.g. \".pdf\" , \".png\" . Default setting depends on doctype . cache_path : where of cached output will be saved. cache : controls caching of code: :off = no caching, :all = cache everything, :user = cache based on chunk options, :refresh , run all code chunks and save new cache. template : Template (file path) for md2html or md2tex formats. highlight_theme : Theme (Highlights.AbstractTheme) for used syntax highlighting css : CSS (file path) used for md2html format latex_cmd the command used to make pdf from .tex Note: Run Weave from terminal and not using IJulia, Juno or ESS, they tend to mess with capturing output. source",
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"title": "Weave"
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},
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{
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"location": "/usage/#weave-from-shell",
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"text": "You can also use the weave.jl script under bin directory to weave documents from the shell: $ ./weave.jl\nusage: weave.jl [ --doctype DOCTYPE ] [ --plotlib PLOTLIB ] \n [ --informat INFORMAT ] [ --out_path OUT_PATH ] \n [ --fig_path FIG_PATH ] [ --fig_ext FIG_EXT ] source...",
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"title": "Weave from shell"
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},
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{
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"location": "/usage/#tangle",
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"text": "Tangling extracts the code from document: # Weave.tangle \u2014 Method . tangle(source ; out_path=:doc, informat=\"noweb\") Tangle source code from input document to .jl file. informat : \"noweb\" of \"markdown\" out_path : Path where the output is generated. Can be: :doc : Path of the source document, :pwd : Julia working directory, \"somepath\" , directory name as a string e.g \"/home/mpastell/weaveout\" or filename as string e.g. ~/outpath/outfile.jl. source",
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"title": "Tangle"
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},
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{
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"location": "/usage/#supported-formats",
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"text": "Weave sets the output format based on the file extension, but you can also set it using doctype option. The rules for detecting the format are: ext == \".jl\" && return \"md2html\" contains ( ext , \".md\" ) && return \"md2html\" contains ( ext , \".rst\" ) && return \"rst\" contains ( ext , \".tex\" ) && return \"texminted\" contains ( ext , \".txt\" ) && return \"asciidoc\" return \"pandoc\" You can get a list of supported output formats: list_out_formats () github : Github markdown md2tex : Julia markdown to latex pandoc2html : Markdown to HTML ( requires Pandoc ) pandoc : Pandoc markdown pandoc2pdf : Pandoc markdown tex : Latex with custom code environments texminted : Latex using minted for highlighting md2html : Julia markdown to html rst : reStructuredText and Sphinx multimarkdown : MultiMarkdown md2pdf : Julia markdown to latex asciidoc : AsciiDoc # Weave.list_out_formats \u2014 Method . list_out_formats() List supported output formats source",
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"title": "Supported formats"
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},
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{
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"location": "/usage/#document-syntax",
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"text": "Weave uses noweb, markdown or script syntax for defining the code chunks and documentation chunks. You can also weave Jupyter notebooks. The format is detected based on the file extension, but you can also set it manually using the informat parameter. The rules for autodetection are: ext == \".jl\" && return \"script\" ext == \".jmd\" && return \"markdown\" ext == \".ipynb\" && return \"notebook\" return \"noweb\"",
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"title": "Document syntax"
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},
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{
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"location": "/usage/#noweb-format",
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"text": "",
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"title": "Noweb format"
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},
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{
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"location": "/usage/#code-chunks",
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"text": "start with a line marked with <<>>= or <<options>>= and end with line marked with @ . The code between the start and end markers is executed and the output is captured to the output document. See chunk options .",
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"title": "Code chunks"
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},
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{
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"location": "/usage/#documentation-chunks",
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"text": "Are the rest of the document (between @ and <<>>= lines and the first chunk be default) and can be written with several different markup languages. Sample document",
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"title": "Documentation chunks"
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},
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{
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"location": "/usage/#markdown-format",
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"text": "Markdown code chunks are defined using fenced code blocks with options following on the same line. e.g. to hide code from output you can use: ```julia; echo=false See sample document:",
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"title": "Markdown format"
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},
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{
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"location": "/usage/#script-format",
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"text": "Weave also support script input format with a markup in comments. These scripts can be executed normally using Julia or published with Weave. Documentation is in lines starting with #' , #%% or # %% , and code is executed and results are included in the weaved document. All lines that are not documentation are treated as code. You can set chunk options using lines starting with #+ just before code e.g. #+ term=true . The format is identical to 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. See sample document:",
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"title": "Script format"
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},
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{
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"location": "/publish/",
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"text": "Publishing to html and pdf\n\n\nYou can also publish any supported input format using markdown for doc chunks to html and pdf documents. Producing pdf output requires that you have pdflatex installed and in your path. \nThe markdown variant is \nJulia markdown\n.\n\n\nYou can use a YAML header in the beginning of the input document delimited with \"\u2013-\" to set the document title, author and date e.g.\n\n\n---\ntitle : Weave example\nauthor : Matti Pastell\ndate: 15th December 2016\n---\n\n\n\n\n\nHere is a a sample document and output:\n\n\nFIR_design.jl\n, \nFIR_design.html\n , \nFIR_design.pdf\n.\n\n\nweave\n(\n\"FIR_design.jl\"\n)\n\n\nweave\n(\n\"FIR_design.jl\"\n,\n \ndocformat\n \n=\n \n\"md2pdf\"\n)\n\n\n\n\n\n\nNote:\n docformats \nmd2pdf\n and \nmd2html\n use Julia markdown and \npandoc2pdf\n and \npandoc2html\n use Pandoc.\n\n\n\n\nTemplates\n\n\nYou can use a custom template with \nmd2pdf\n and \nmd2html\n formats with \ntemplate\n argument (e.g) \nweave(\"FIR_design.jl\", template = \"custom.tpl\"\n). You can use the existing templates as starting point.\n\n\nFor HTML: \njulia_html.tpl\n and LaTex: \njulia_tex.tpl\n\n\nTemplates are rendered using \nMustache.jl\n.",
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"title": "Publishing scripts"
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},
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{
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"location": "/publish/#publishing-to-html-and-pdf",
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"text": "You can also publish any supported input format using markdown for doc chunks to html and pdf documents. Producing pdf output requires that you have pdflatex installed and in your path. The markdown variant is Julia markdown . You can use a YAML header in the beginning of the input document delimited with \"\u2013-\" to set the document title, author and date e.g. ---\ntitle : Weave example\nauthor : Matti Pastell\ndate: 15th December 2016\n--- Here is a a sample document and output: FIR_design.jl , FIR_design.html , FIR_design.pdf . weave ( \"FIR_design.jl\" ) weave ( \"FIR_design.jl\" , docformat = \"md2pdf\" ) Note: docformats md2pdf and md2html use Julia markdown and pandoc2pdf and pandoc2html use Pandoc.",
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"title": "Publishing to html and pdf"
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},
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{
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"location": "/publish/#templates",
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"text": "You can use a custom template with md2pdf and md2html formats with template argument (e.g) weave(\"FIR_design.jl\", template = \"custom.tpl\" ). You can use the existing templates as starting point. For HTML: julia_html.tpl and LaTex: julia_tex.tpl Templates are rendered using Mustache.jl .",
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"title": "Templates"
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},
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{
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"location": "/chunk_options/",
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"text": "Chunk options\n\n\nI've mostly followed \nKnitr\n's naming for chunk options, but not all options are implemented.\n\n\nOptions are separated using \";\" and need to be valid Julia expressions. Example: A code chunk that saves and displays a 12 cm wide image and hides the source code:\n\n\n<<\nfig_width\n=\n5\n;\n \necho\n=\nfalse\n \n>>=\n\n\nusing\n \nGadfly\n\n\nx\n \n=\n \nlinspace\n(\n0\n,\n \n2\n\u03c0\n,\n \n200\n)\n\n\nplot\n(\nx\n=\nx\n,\n \ny\n \n=\n \nsin\n(\nx\n),\n \nGeom\n.\nline\n)\n\n\n@\n\n\n\n\n\n\nWeave currently supports the following chunk options with the following defaults:\n\n\n\n\nOptions for code\n\n\n\n\necho = true\n. Echo the code in the output document. If \nfalse\n the source code will be hidden.\n\n\nresults = \"markup\"\n. The output format of the printed results. \"markup\" for literal block, \"hidden\" for hidden results or anything else for raw output (I tend to use \u2018tex\u2019 for Latex and \u2018rst\u2019 for rest. Raw output is useful if you wan\u2019t to e.g. create tables from code chunks.\n\n\neval = true\n. Evaluate the code chunk. If false the chunk won\u2019t be executed.\n\n\nterm=false\n. If true the output emulates a REPL session. Otherwise only stdout and figures will be included in output.\n\n\nlabel\n. Chunk label, will be used for figure labels in Latex as fig:label\n\n\nwrap = true\n. Wrap long lines from output.\n\n\nline_width = 75\n. Line width for wrapped lines.\n\n\ncache = false\n. Cache results, depends on \ncache\n parameter on \nweave\n function.\n\n\nhold = false\n. Hold all results until the end of the chunk.\n\n\ntangle = true\n. Set tangle to false to exclude chunk from tangled code.\n\n\n\n\n\n\nOptions for figures\n\n\n\n\nfig_width\n. Figure width defined in markup, default depends on the output format.\n\n\nout_width\n. Width of saved figure.\n\n\nout_height\n. Height of saved figure.\n\n\ndpi\n=96. Resolution of saved figures.\n\n\nfig_cap\n. Figure caption.\n\n\nlabel\n. Chunk label, will be used for figure labels in Latex as fig:label\n\n\nfig_ext\n. File extension (format) of saved figures.\n\n\nfig_pos=\"htpb\"\n. Figure position in Latex.\n\n\nfig_env=\"figure\"\n. Figure environment in Latex.\n\n\n\n\n\n\nSet default chunk options\n\n\nYou can set or alter the default chunk options for a document either before running weave or inside the weaved document. You can e.g. use a hidden chunk in the beginning of the source document to set the options:\n\n\n<<\necho\n \n=\n \nfalse\n>>=\n\n\nimport\n \nWeave\n\n\nWeave\n.\nset_chunk_defaults\n(\nDict\n{\nSymbol\n,\n \nAny\n}(\n\n \n:\nout_width\n \n=>\n \n\"\n\\\\\n0.5linewidth\"\n,\n\n \n:\nresults\n \n=>\n \n\"tex\"\n\n \n))\n\n\n@\n\n\n\n\n\n\nset_chunk_defaults(opts)\nget_chunk_defaults()\nrestore_chunk_defaults()",
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"title": "Chunk options"
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},
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{
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"location": "/chunk_options/#chunk-options",
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"text": "I've mostly followed Knitr 's naming for chunk options, but not all options are implemented. Options are separated using \";\" and need to be valid Julia expressions. Example: A code chunk that saves and displays a 12 cm wide image and hides the source code: << fig_width = 5 ; echo = false >>= using Gadfly x = linspace ( 0 , 2 \u03c0 , 200 ) plot ( x = x , y = sin ( x ), Geom . line ) @ Weave currently supports the following chunk options with the following defaults:",
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"title": "Chunk options"
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},
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{
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"location": "/chunk_options/#options-for-code",
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"text": "echo = true . Echo the code in the output document. If false the source code will be hidden. results = \"markup\" . The output format of the printed results. \"markup\" for literal block, \"hidden\" for hidden results or anything else for raw output (I tend to use \u2018tex\u2019 for Latex and \u2018rst\u2019 for rest. Raw output is useful if you wan\u2019t to e.g. create tables from code chunks. eval = true . Evaluate the code chunk. If false the chunk won\u2019t be executed. term=false . If true the output emulates a REPL session. Otherwise only stdout and figures will be included in output. label . Chunk label, will be used for figure labels in Latex as fig:label wrap = true . Wrap long lines from output. line_width = 75 . Line width for wrapped lines. cache = false . Cache results, depends on cache parameter on weave function. hold = false . Hold all results until the end of the chunk. tangle = true . Set tangle to false to exclude chunk from tangled code.",
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"title": "Options for code"
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},
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{
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"location": "/chunk_options/#options-for-figures",
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"text": "fig_width . Figure width defined in markup, default depends on the output format. out_width . Width of saved figure. out_height . Height of saved figure. dpi =96. Resolution of saved figures. fig_cap . Figure caption. label . Chunk label, will be used for figure labels in Latex as fig:label fig_ext . File extension (format) of saved figures. fig_pos=\"htpb\" . Figure position in Latex. fig_env=\"figure\" . Figure environment in Latex.",
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"title": "Options for figures"
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},
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{
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"location": "/chunk_options/#set-default-chunk-options",
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"text": "You can set or alter the default chunk options for a document either before running weave or inside the weaved document. You can e.g. use a hidden chunk in the beginning of the source document to set the options: << echo = false >>= import Weave Weave . set_chunk_defaults ( Dict { Symbol , Any }( \n : out_width => \" \\\\ 0.5linewidth\" , \n : results => \"tex\" \n )) @ set_chunk_defaults(opts)\nget_chunk_defaults()\nrestore_chunk_defaults()",
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"title": "Set default chunk options"
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},
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{
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"location": "/notebooks/",
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"text": "Working with Jupyter notebooks\n\n\n\n\nWeaving\n\n\nWeave supports using Jupyter notebooks as input format, this means you can weave notebooks to any supported formats. You can't use chunk options with notebooks.\n\n\nweave\n(\n\"notebook.ipynb\"\n)\n\n\n\n\n\n\nIn order to output notebooks from other formats you need to convert the document to a notebook and run the code using IJulia.\n\n\n\n\nConverting between formats\n\n\nYou can convert between all supported input formats using the \nconvert_doc\n function.\n\n\nTo convert from script to notebook:\n\n\nconvert_doc\n(\n\"examples/FIR_design.jl\"\n,\n \n\"FIR_design.ipynb\"\n)\n\n\n\n\n\n\nand from notebooks to markdown use:\n\n\nconvert_doc\n(\n\"FIR_design.ipynb\"\n,\n \n\"FIR_design.jmd\"\n)\n\n\n\n\n\n\n#\n\n\nWeave.convert_doc\n \u2014 \nMethod\n.\n\n\nconvert_doc(infile::AbstractString, outfile::AbstractString; format = nothing)\n\n\nConvert Weave documents between different formats\n\n\n\n\ninfile\n = Name of the input document\n\n\noutfile\n = Name of the output document\n\n\nformat\n = Output format (optional). Detected from outfile extension, but can be set to \n\"script\"\n, \n\"markdown\"\n, \n\"notebook\"\n or \n\"noweb\"\n.\n\n\n\n\nsource",
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"title": "Working with Jupyter notebooks"
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},
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{
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"location": "/notebooks/#working-with-jupyter-notebooks",
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"text": "",
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"title": "Working with Jupyter notebooks"
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},
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{
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"location": "/notebooks/#weaving",
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"text": "Weave supports using Jupyter notebooks as input format, this means you can weave notebooks to any supported formats. You can't use chunk options with notebooks. weave ( \"notebook.ipynb\" ) In order to output notebooks from other formats you need to convert the document to a notebook and run the code using IJulia.",
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"title": "Weaving"
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},
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{
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"location": "/notebooks/#converting-between-formats",
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"text": "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 notebooks to markdown use: convert_doc ( \"FIR_design.ipynb\" , \"FIR_design.jmd\" ) # Weave.convert_doc \u2014 Method . convert_doc(infile::AbstractString, outfile::AbstractString; format = nothing) Convert Weave documents between different formats infile = Name of the input document outfile = Name of the output document format = Output format (optional). Detected from outfile extension, but can be set to \"script\" , \"markdown\" , \"notebook\" or \"noweb\" . source",
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"title": "Converting between formats"
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},
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{
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"location": "/function_index/",
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"text": "Function index\n\n\n\n\nWeave.convert_doc\n\n\nWeave.get_chunk_defaults\n\n\nWeave.list_out_formats\n\n\nWeave.restore_chunk_defaults\n\n\nWeave.tangle\n\n\nWeave.weave",
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"title": "Function index"
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},
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{
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"location": "/function_index/#function-index",
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"text": "Weave.convert_doc Weave.get_chunk_defaults Weave.list_out_formats Weave.restore_chunk_defaults Weave.tangle Weave.weave",
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"title": "Function index"
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|
}
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|
]
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} |