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README.md

Building the manuscript

build.sh builds the repository. sh build/build.sh should be executed from the root directory of the repository. By default, build.sh creates HTML and PDF outputs. However, setting the BUILD_PDF environment variable to false will suppress PDF output. For example, run local builds using the command BUILD_PDF=false sh build/build.sh.

To build a DOCX file of the manuscript, set the BUILD_DOCX environment variable to true. For example, use the command BUILD_DOCX=true sh build/build.sh. To export DOCX for all Travis builds, set a Travis environment variable. Currently, equation numbers via pandoc-eqnos are not supported for DOCX output. There is varying support for embedding images in DOCX output. Please reference Pull Request #40 for possible solutions and continued discussion.

Environment

Note: currently, Windows is not supported.

Install or update the conda environment specified in environment.yml by running:

# If the manubot environment already exists, remove it first
conda env remove --name manubot

# Install the environment
conda env create --file environment.yml

Activate with conda activate manubot (assumes conda version of at least 4.4). The environment should successfully install on both Linux and macOS. However, it will fail on Windows due to the pango dependency.