Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata
Manubot is a system for writing scholarly manuscripts via GitHub. Manubot automates citations and references, versions
manuscripts using git, and enables collaborative writing via GitHub.
An overview manuscript presents
the benefits of collaborative writing with Manubot and its unique features.
The rootstock repository is a general purpose template for creating new Manubot instances, as
detailed in SETUP.md. See USAGE.md for documentation how to write a manuscript.
Please open an issue for questions related to Manubot usage, bug reports, or general inquiries.
The directories are as follows:
contentcontains the manuscript source, which includes markdown files as well as inputs for citations and references. SeeUSAGE.mdfor more information.outputcontains the outputs (generated files) from Manubot including the resulting manuscripts. You should not edit these files manually, because they will get overwritten.webpageis a directory meant to be rendered as a static webpage for viewing the HTML manuscript.buildcontains commands and tools for building the manuscript.cicontains files necessary for deployment via continuous integration.
The easiest way to run Manubot is to use continuous integration to rebuild the manuscript
when the content changes. If you want to build a Manubot manuscript locally, install the conda
environment as described in build. Then, you can build the manuscript on POSIX systems by running the
following commands from this root directory.
# Activate the manubot conda environment (assumes conda version >= 4.4)
conda activate manubot
# Build the manuscript, saving outputs to the output directory
bash build/build.sh
# At this point, the HTML & PDF outputs will have been created. The remaining
# commands are for serving the webpage to view the HTML manuscript locally.
# This is required to view local images in the HTML output.
# Configure the webpage directory
manubot webpage
# You can now open the manuscript webpage/index.html in a web browser.
# Alternatively, open a local webserver at http://localhost:8000/ with the
# following commands.
cd webpage
python -m http.serverSometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is
detected. The following command, while running, will trigger both the build.sh script and manubot webpage command
upon content changes:
bash build/autobuild.shWhenever a pull request is opened, CI (continuous integration) will test whether the changes break the build process to generate a formatted manuscript. The build process aims to detect common errors, such as invalid citations. If your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly.
When a commit to the main branch occurs (for example, when a pull request is merged), CI builds the manuscript and
writes the results to the gh-pages
and output branches. The gh-pages branch
uses GitHub Pages to host the following URLs:
- HTML manuscript at https://lotusnprod.github.io/lotus-manuscript/
- PDF manuscript at https://lotusnprod.github.io/lotus-manuscript/manuscript.pdf
For continuous integration configuration details, see .github/workflows/manubot.yaml
if using GitHub Actions or .travis.yml if using Travis CI.
Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0
License (LICENSE.md), which allows reuse with attribution. Please attribute by linking
to https://github.com/lotusnprod/lotus-manuscript.
Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public
domain dedication (LICENSE-CC0.md). All files matched by the following glob patterns are dual
licensed under CC BY 4.0 and CC0 1.0:
*.sh*.py*.yml/*.yaml*.json*.bib*.tsv.gitignore
All other files are only available under CC BY 4.0, including:
*.md*.html*.pdf*.docx
Please open an issue for any question related to licensing.