# manubot/rootstock

Clone me to create your manuscript
vincerubinetti and dhimmel images: specify explicit size for icon SVGs
Merges #195

Sometimes you can see a 'flash' of a very large svg image while the page is loading.
This is because the svg has loaded before the css specifying its size has.
To fix, specify a reasonable size explicitly in the svg (so it will load at that size by default
and then been overridden by whatever size the css tells it to be).
Latest commit 4d27314 Mar 20, 2019
Type Name Latest commit message Commit time
Failed to load latest commit information.
build Mar 15, 2019
ci Feb 13, 2019
content Mar 20, 2019
output Aug 9, 2017
webpage Jan 28, 2019
.gitignore Nov 9, 2018
.travis.yml
SETUP.md Feb 28, 2019
USAGE.md

# Automated scholarly manuscripts on GitHub

## Manuscript description

This repository is a template manuscript (a.k.a. rootstock). Actual manuscript instances will clone this repository (see SETUP.md) and replace this paragraph with a description of their manuscript.

## Manubot

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. 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.

### Repository directories & files

The directories are as follows:

### Local execution

To run the Manubot locally, install the conda environment as described in build. Then, you can build the manuscript on POSIX systems by running the following commands.

# Activate the manubot conda environment (assumes conda version >= 4.4)
conda activate manubot

# Build the manuscript, saving outputs to the output directory
sh 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.

# Configure the webpage directory
python build/webpage.py

# View the manuscript locally at http://localhost:8000/
cd webpage
python -m http.server

Sometimes 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 and webpage.py scripts upon content changes:

sh build/autobuild.sh

### Continuous Integration

Whenever a pull request is opened, Travis CI 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 Travis CI logs for the cause of failure and revise your pull request accordingly.

When a commit to the master branch occurs (for example, when a pull request is merged), Travis 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:

For continuous integration configuration details, see .travis.yml.

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/manubot/rootstock.

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.

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