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https://github.com/junolab/weave.jl
Scientific reports/literate programming for Julia
https://github.com/junolab/weave.jl
julia literate-programming reproducible-research scientific-reports scientific-workflows
Last synced: about 1 month ago
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Scientific reports/literate programming for Julia
- Host: GitHub
- URL: https://github.com/junolab/weave.jl
- Owner: JunoLab
- License: mit
- Created: 2014-11-24T23:13:19.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2024-08-04T13:56:51.000Z (4 months ago)
- Last Synced: 2024-10-12T19:20:56.881Z (about 1 month ago)
- Topics: julia, literate-programming, reproducible-research, scientific-reports, scientific-workflows
- Language: Julia
- Homepage: http://weavejl.mpastell.com
- Size: 10.3 MB
- Stars: 828
- Watchers: 17
- Forks: 95
- Open Issues: 152
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: LICENSE.md
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README
# Weave
[](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 the [Julia programming language](https://julialang.org/).
It resembles
[Pweave](http://mpastell.com/pweave),
[knitr](https://yihui.org/knitr/),
[R Markdown](https://rmarkdown.rstudio.com/),
and [Sweave](https://stat.ethz.ch/R-manual/R-patched/library/utils/doc/Sweave.pdf).
You can write your documentation and code in input document using Markdown, Noweb or ordinal Julia script syntax,
and then use `weave` function to execute code and generate an output document while capturing results and figures.
**Current features**
- Publish markdown directly to HTML and PDF using Julia or [Pandoc](https://pandoc.org/MANUAL.html)
- Execute code as in terminal or in a unit of code chunk
- Capture [Plots.jl](https://github.com/JuliaPlots/Plots.jl) or [Gadfly.jl](https://github.com/GiovineItalia/Gadfly.jl) figures
- Supports various input format: Markdown, [Noweb](https://www.cs.tufts.edu/~nr/noweb/), [Jupyter Notebook](https://jupyter.org/), 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
**Citing Weave:** *Pastell, Matti. 2017. Weave.jl: Scientific Reports Using Julia. The Journal of Open Source Software. http://dx.doi.org/10.21105/joss.00204*
## Installation
You can install the latest release using Julia package manager:
```julia
using Pkg
Pkg.add("Weave")
```
## Usage
```julia
using Weave
# add depencies for the example
using Pkg; Pkg.add(["Plots", "DSP"])
filename = normpath(Weave.EXAMPLE_FOLDER, "FIR_design.jmd")
weave(filename, out_path = :pwd)
```
If you have LaTeX installed you can also weave directly to pdf.
```julia
filename = normpath(Weave.EXAMPLE_FOLDER, "FIR_design.jmd")
weave(filename, out_path = :pwd, doctype = "md2pdf")
```
NOTE: `Weave.EXAMPLE_FOLDER` just points to [`examples` directory](./examples).
## Documentation
Documenter.jl with MKDocs generated documentation:
[](http://weavejl.mpastell.com/stable/)
[](http://weavejl.mpastell.com/dev/)
## Editor support
Install [language-weave](https://atom.io/packages/language-weave) to add Weave support to Juno.
It allows running code from Weave documents with usual keybindings and allows preview of
html and pdf output.
The [Julia extension for Visual Studio Code](https://www.julia-vscode.org/)
adds Weave support to [Visual Studio Code](https://code.visualstudio.com/).
## Contributing
You can contribute to this package by opening issues on GitHub or implementing things yourself and making a pull request.
We'd also appreciate more example documents written using Weave.
## Contributors
You can see the list of contributors on GitHub: https://github.com/JunoLab/Weave.jl/graphs/contributors .
Thanks for the important additions, fixes and comments.
## Example projects using Weave
- [DiffEqTutorials.jl](https://github.com/JuliaDiffEq/DiffEqTutorials.jl) uses Weave to output tutorials (`.jmd` documents) to html, pdf and Jupyter notebooks.
- [TuringTutorials](https://github.com/TuringLang/TuringTutorials) uses Weave to convert notebooks to html.
## Related packages
- [Literate.jl](https://github.com/fredrikekre/Literate.jl) can be used to generate Markdown and Jupyter notebooks directly from Julia source files with markdown in comments.
- [Quarto](https://quarto.org) can generate Jupyter notebooks, HTML, or PDF directly from a Markdown format containing Julia code blocks, and also works with R and Python.