Python utilities for Manubot: Manuscripts, open and automated
Manubot is a workflow and set of tools for the next generation of scholarly publishing. This repository contains a Python package with several Manubot-related utilities, as described in the usage section below. Package documentation is available at https://manubot.github.io/manubot (auto-generated from the Python source code).
The manubot cite
command-line interface retrieves and formats bibliographic metadata for user-supplied persistent identifiers like DOIs or PubMed IDs.
The manubot process
command-line interface prepares scholarly manuscripts for Pandoc consumption.
The manubot process
command is used by Manubot manuscripts, which are based off the Rootstock template, to automate several aspects of manuscript generation.
See Rootstock's manuscript usage guide for more information.
Note: If you want to experience Manubot by editing an existing manuscript, see https://github.com/manubot/try-manubot. If you want to create a new manuscript, see https://github.com/manubot/rootstock.
To cite the Manubot project or for more information on its design and history, see:
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology (2019-06-24) https://doi.org/c7np
DOI: 10.1371/journal.pcbi.1007128 · PMID: 31233491 · PMCID: PMC6611653
The Manubot version of this manuscript is available at https://greenelab.github.io/meta-review/.
Installation
If you are using the manubot
Python package as part of a manuscript repository, installation of this package is handled though the Rootstock's environment specification.
For other use cases, this package can be installed via pip
.
Install the latest release version from PyPI:
pip install --upgrade manubot
Or install from the source code on GitHub, using the version specified by a commit hash:
COMMIT=d2160151e52750895571079a6e257beb6e0b1278
pip install --upgrade git+https://github.com/manubot/manubot@$COMMIT
The --upgrade
argument ensures pip
updates an existing manubot
installation if present.
Usage
Installing the python package creates the manubot
command line program.
Here is the usage information as per manubot --help
:
usage: manubot [-h] [--version] {process,cite,webpage} ...
Manubot: the manuscript bot for scholarly writing
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
subcommands:
All operations are done through subcommands:
{process,cite,webpage}
process process manuscript content
cite citekey to CSL JSON command line utility
webpage deploy Manubot outputs to a webpage directory tree
Note that all operations are done through the following sub-commands.
Process
The manubot process
program is the primary interface to using Manubot.
There are two required arguments: --content-directory
and --output-directory
, which specify the respective paths to the content and output directories.
The content directory stores the manuscript source files.
Files generated by Manubot are saved to the output directory.
One common setup is to create a directory for a manuscript that contains both the content
and output
directory.
Under this setup, you can run the Manubot using:
manubot process \
--skip-citations \
--content-directory=content \
--output-directory=output
See manubot process --help
for documentation of all command line arguments:
usage: manubot process [-h] --content-directory CONTENT_DIRECTORY
--output-directory OUTPUT_DIRECTORY
[--template-variables-path TEMPLATE_VARIABLES_PATH]
--skip-citations [--cache-directory CACHE_DIRECTORY]
[--clear-requests-cache]
[--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
Process manuscript content to create outputs for Pandoc consumption. Performs
bibliographic processing and templating.
optional arguments:
-h, --help show this help message and exit
--content-directory CONTENT_DIRECTORY
Directory where manuscript content files are located.
--output-directory OUTPUT_DIRECTORY
Directory to output files generated by this script.
--template-variables-path TEMPLATE_VARIABLES_PATH
Path or URL of a file containing template variables
for jinja2. Serialization format is inferred from the
file extension, with support for JSON, YAML, and TOML.
If the format cannot be detected, the parser assumes
JSON. Specify this argument multiple times to read
multiple files. Variables can be applied to a
namespace (i.e. stored under a dictionary key) like
`--template-variables-path=namespace=path_or_url`.
Namespaces must match the regex `[a-zA-
Z_][a-zA-Z0-9_]*`.
--skip-citations Skip citation and reference processing. Support for
citation and reference processing has been moved from
`manubot process` to the pandoc-manubot-cite filter.
Therefore this argument is now required. If citation-
tags.tsv is found in content, these tags will be
inserted in the markdown output using the reference-
link syntax for citekey aliases. Appends
content/manual-references*.* paths to Pandoc's
metadata.bibliography field.
--cache-directory CACHE_DIRECTORY
Custom cache directory. If not specified, caches to
output-directory.
--clear-requests-cache
--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set the logging level for stderr logging
Manual references
Manubot has the ability to rely on user-provided reference metadata rather than generating it.
manubot process
searches the content directory for files containing manually-provided reference metadata that match the glob manual-references*.*
.
These files are stored in the Pandoc metadata bibliography
field, such that they can be loaded by pandoc-manubot-cite
.
Cite
manubot cite
is a command line utility to produce bibliographic metadata for citation keys.
The utility either outputs metadata as CSL JSON items or produces formatted references if --render
.
Citation keys should be in the format prefix:accession
.
For example, the following example generates Markdown-formatted references for four persistent identifiers:
manubot cite --format=markdown \
doi:10.1098/rsif.2017.0387 pubmed:29424689 pmc:PMC5640425 arxiv:1806.05726
The following terminal recording demonstrates the main features of manubot cite
(for a slightly outdated version):
Additional usage information is available from manubot cite --help
:
usage: manubot cite [-h] [--output OUTPUT] [--render]
[--format {plain,markdown,docx,html,jats}] [--csl CSL]
[--bibliography BIBLIOGRAPHY] [--allow-invalid-csl-data]
[--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
citekeys [citekeys ...]
Generate bibliographic metadata in CSL JSON format for one or more citation
keys. Optionally, render metadata into formatted references using Pandoc. Text
outputs are UTF-8 encoded.
positional arguments:
citekeys One or more (space separated) citation keys to
generate bibliographic metadata for.
optional arguments:
-h, --help show this help message and exit
--output OUTPUT Specify a file to write output, otherwise default to
stdout.
--render Whether to render CSL Data into a formatted reference
list using Pandoc. Pandoc version 2.0 or higher is
required for complete support of available output
formats.
--format {plain,markdown,docx,html,jats}
Format to use for output file. Implies --render. If
not specified, attempt to infer this from the --output
filename extension. Otherwise, default to plain.
--csl CSL Specify an XML CSL definition to style references
(i.e. Pandoc's --csl option). Implies --render.
Defaults to Manubot's style.
--bibliography BIBLIOGRAPHY
File to read manual reference metadata. Specify
multiple times to load multiple files. Similar to
pandoc --bibliography.
--allow-invalid-csl-data
Allow CSL Items that do not conform to the JSON
Schema. Skips CSL pruning.
--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set the logging level for stderr logging
Pandoc filter
This package creates the pandoc-manubot-cite
Pandoc filter,
providing access to Manubot's cite-by-ID functionality from within a Pandoc workflow.
Currently, this filter is experimental and subject to breaking changes at any point.
usage: pandoc-manubot-cite [-h] [--input [INPUT]] [--output [OUTPUT]]
target_format
Pandoc filter for citation by persistent identifier. Filters are command-line
programs that read and write a JSON-encoded abstract syntax tree for Pandoc.
Unless you are debugging, run this filter as part of a pandoc command by
specifying --filter=pandoc-manubot-cite.
positional arguments:
target_format output format of the pandoc command, as per Pandoc's --to
option
optional arguments:
-h, --help show this help message and exit
--input [INPUT] path read JSON input (defaults to stdin)
--output [OUTPUT] path to write JSON output (defaults to stdout)
Other Pandoc filters exist that do something similar:
pandoc-url2cite
, pandoc-url2cite-hs, &
pwcite
.
Currently, pandoc-manubot-cite
supports the most types of persistent identifiers.
We're interested in creating as much compatibility as possible between these filters and their syntaxes.
Manual references
Manual references are loaded from the references
and bibliography
Pandoc metadata fields.
If a manual reference filename ends with .json
or .yaml
, it's assumed to contain CSL Data (i.e. Citation Style Language JSON).
Otherwise, the format is inferred from the extension and converted to CSL JSON using the pandoc-citeproc --bib2json
utility.
The standard citation key for manual references is inferred from the CSL JSON id
or note
field.
When no prefix is provided, such as doi:
, url:
, or raw:
, a raw:
prefix is automatically added.
If multiple manual reference files load metadata for the same standard citation id
, precedence is assigned according to descending filename order.
Webpage
The manubot webpage
command populates a webpage
directory with Manubot output files.
usage: manubot webpage [-h] [--checkout [CHECKOUT]] [--version VERSION]
[--timestamp] [--no-ots-cache | --ots-cache OTS_CACHE]
[--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
Update the webpage directory tree with Manubot output files. This command
should be run from the root directory of a Manubot manuscript that follows the
Rootstock layout, containing `output` and `webpage` directories. HTML and PDF
outputs are copied to the webpage directory, which is structured as static
source files for website hosting.
optional arguments:
-h, --help show this help message and exit
--checkout [CHECKOUT]
branch to checkout /v directory contents from. For
example, --checkout=upstream/gh-pages. --checkout is
equivalent to --checkout=gh-pages. If --checkout is
ommitted, no checkout is performed.
--version VERSION Used to create webpage/v/{version} directory.
Generally a commit hash, tag, or 'local'. When
omitted, version defaults to the commit hash on CI
builds and 'local' elsewhere.
--timestamp timestamp versioned manuscripts in webpage/v using
OpenTimestamps. Specify this flag to create timestamps
for the current HTML and PDF outputs and upgrade any
timestamps from past manuscript versions.
--no-ots-cache disable the timestamp cache.
--ots-cache OTS_CACHE
location for the timestamp cache (default:
ci/cache/ots).
--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set the logging level for stderr logging
Development
Environment
Create a development environment using:
conda create --name manubot-dev --channel conda-forge \
python=3.8 pandoc=2.8
conda activate manubot-dev # assumes conda >= 4.4
pip install --editable ".[all]"
Commands
Below are some common commands used for development. They assume the working directory is set to the repository's root, and the conda environment is activated.
# run the test suite
pytest
# reformat Python files according to the black style rules (required to pass CI)
black .
# detect any flake8 linting violations
flake8
# regenerate the README codeblocks for --help messages
python manubot/tests/test_readme.py
# generate the docs
portray as_html --overwrite --output_dir=docs
# process the example testing manuscript
manubot process \
--content-directory=manubot/process/tests/manuscripts/example/content \
--output-directory=manubot/process/tests/manuscripts/example/output \
--skip-citations \
--log-level=INFO
Release instructions
This section is only relevant for project maintainers. Travis CI deployments are used to upload releases to PyPI.
To create a new release, bump the __version__
in manubot/__init__.py
.
Then, set the TAG
and OLD_TAG
environment variables:
TAG=v$(python setup.py --version)
# fetch tags from the upstream remote
# (assumes upstream is the manubot organization remote)
git fetch --tags upstream master
# get previous release tag, can hardcode like OLD_TAG=v0.3.1
OLD_TAG=$(git describe --tags --abbrev=0)
The following commands can help draft release notes:
# check out a branch for a pull request as needed
git checkout -b "release-$TAG"
# create release notes file if it doesn't exist
touch "release-notes/$TAG.md"
# commit list since previous tag
echo $'\n\nCommits\n-------\n' >> "release-notes/$TAG.md"
git log --oneline --decorate=no $OLD_TAG..HEAD >> "release-notes/$TAG.md"
# commit authors since previous tag
echo $'\n\nCode authors\n------------\n' >> "release-notes/$TAG.md"
git log $OLD_TAG..HEAD --format='%aN <%aE>' | sort --unique >> "release-notes/$TAG.md"
After a commit with the above updates is part of upstream:master
,
for example after a PR is merged,
use the GitHub inteferace to create a release with the new "Tag version".
Monitor GitHub Actions and PyPI for successful deployment of the release.
Goals & Acknowledgments
Our goal is to create scholarly infrastructure that encourages open science and assists reproducibility.
Accordingly, we hope for the Manubot software and philosophy to be adopted widely, by both academic and commercial entities.
As such, Manubot is free/libre and open source software (see LICENSE.md
).
We would like to thank the contributors and funders whose support makes this project possible. Specifically, Manubot development has been financially supported by:
- the Alfred P. Sloan Foundation in Grant G-2018-11163 to @dhimmel.
- the Gordon & Betty Moore Foundation (@DDD-Moore) in Grant GBMF4552 to @cgreene.