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Python utilities for Manubot: Manuscripts, open and automated
https://github.com/manubot/manubot

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Python utilities for Manubot: Manuscripts, open and automated

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# Python utilities for Manubot: Manuscripts, open and automated



[![documentation](https://img.shields.io/badge/-Documentation-purple?logo=read-the-docs&logoColor=white&style=for-the-badge)](https://manubot.github.io/manubot/)

[![PyPI](https://img.shields.io/pypi/v/manubot.svg?logo=PyPI&logoColor=white&style=for-the-badge)](https://pypi.org/project/manubot/)



[![GitHub Actions CI Tests Status](https://img.shields.io/github/actions/workflow/status/manubot/manubot/test.yml?branch=main&label=actions&style=for-the-badge&logo=github&logoColor=white)](https://github.com/manubot/manubot/actions)

[![AppVeyor Windows Build Status](https://img.shields.io/appveyor/build/manubot/manubot/main?style=for-the-badge&logo=appveyor&logoColor=white&label=AppVeyor)](https://ci.appveyor.com/project/manubot/manubot/branch/main)



[Manubot](https://manubot.org/ "Manubot homepage") 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](#usage) below.

Package documentation is available at  (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](https://github.com/manubot/rootstock), to automate several aspects of manuscript generation.

The `manubot ai-revision` command is used to automatically revise a manuscript based on a set of AI-generated suggestions.

See Rootstock's [manuscript usage guide](https://github.com/manubot/rootstock/blob/main/USAGE.md) for more information.



**Note:**

If you want to experience Manubot by editing an existing manuscript, see .

If you want to create a new manuscript, see .



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) 


DOI: [10.1371/journal.pcbi.1007128](https://doi.org/10.1371/journal.pcbi.1007128) · PMID: [31233491](https://www.ncbi.nlm.nih.gov/pubmed/31233491) · PMCID: [PMC6611653](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611653)



The Manubot version of this manuscript is available at .



## 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](https://github.com/manubot/rootstock/blob/main/build/environment.yml).

For other use cases, this package can be installed via `pip`.



Install the latest release version [from PyPI](https://pypi.org/project/manubot/):



```sh

pip install --upgrade manubot

```



Or install from the source code on [GitHub](https://github.com/manubot/manubot), using the version specified by a commit hash:



```sh

COMMIT=d2160151e52750895571079a6e257beb6e0b1278

pip install --upgrade git+https://github.com/manubot/manubot@$COMMIT

```



The `--upgrade` argument ensures `pip` updates an existing `manubot` installation if present.



Some functions in this package require [Pandoc](https://pandoc.org/),

which must be [installed](https://pandoc.org/installing.html) separately on the system.

The pandoc-manubot-cite filter depends on Pandoc as well as panflute (a Python package).

Users must install a [compatible version of panflute](https://github.com/sergiocorreia/panflute#supported-pandoc-versions) based on their Pandoc version.

For example, on a system with Pandoc 2.9,

install the appropriate panflute like `pip install panflute==1.12.5`.



## 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,ai-revision} ...



Manubot: the manuscript bot for scholarly writing



options:

  -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,ai-revision}

    process             process manuscript content

    cite                citekey to CSL JSON command line utility

    webpage             deploy Manubot outputs to a webpage directory tree

    ai-revision         revise manuscript content with language models

```



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:



```sh

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] [--skip-remote]

                       [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]



Process manuscript content to create outputs for Pandoc consumption. Performs

bibliographic processing and templating.



options:

  -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

  --skip-remote         Do not add the rootstock repository to the local git

                        repository remotes.

  --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](http://citeproc-js.readthedocs.io/en/latest/csl-json/markup.html#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:



```shell

manubot cite --format=markdown \

  doi:10.1098/rsif.2017.0387 pubmed:29424689 pmc:PMC5640425 arxiv:1806.05726

```



The following [terminal recording](https://asciinema.org/a/205085?speed=2) demonstrates the main features of `manubot cite` (for a slightly outdated version):



![manubot cite demonstration](media/terminal-recordings/manubot-cite-cast.gif)



Additional usage information is available from `manubot cite --help`:



```

usage: manubot cite [-h] [--output OUTPUT]

                    [--format {csljson,cslyaml,plain,markdown,docx,html,jats} | --yml | --txt | --md]

                    [--csl CSL] [--bibliography BIBLIOGRAPHY]

                    [--no-infer-prefix] [--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.



options:

  -h, --help            show this help message and exit

  --output OUTPUT       Specify a file to write output, otherwise default to

                        stdout.

  --format {csljson,cslyaml,plain,markdown,docx,html,jats}

                        Format to use for output file. csljson and cslyaml

                        output the CSL data. All other choices render the

                        references using Pandoc. If not specified, attempt to

                        infer this from the --output filename extension.

                        Otherwise, default to csljson.

  --yml                 Short for --format=cslyaml.

  --txt                 Short for --format=plain.

  --md                  Short for --format=markdown.

  --csl CSL             URL or path with CSL XML style used to style

                        references (i.e. Pandoc's --csl option). Defaults to

                        Manubot's style.

  --bibliography BIBLIOGRAPHY

                        File to read manual reference metadata. Specify

                        multiple times to load multiple files. Similar to

                        pandoc --bibliography.

  --no-infer-prefix     Do not attempt to infer the prefix for citekeys

                        without a known prefix.

  --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.



Options are set via Pandoc metadata fields [listed in the docs](https://manubot.github.io/manubot/reference/manubot/pandoc/cite_filter).



```

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



options:

  -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`](https://github.com/phiresky/pandoc-url2cite), [pandoc-url2cite-hs](https://github.com/Aver1y/pandoc-url2cite-hs), &

[`pwcite`](https://github.com/wikicite/wcite#filter-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](https://github.com/jgm/pandoc-citeproc/blob/master/man/pandoc-citeproc.1.md#convert-mode).

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.



options:

  -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

```



### AI-assisted academic authoring



The `manubot ai-revision` command uses large language models from [OpenAI](https://openai.com/api/) to automatically revise a manuscript and suggest text improvements.



```

usage: manubot ai-revision [-h] --content-directory CONTENT_DIRECTORY

                           [--config-directory CONFIG_DIRECTORY]

                           [--model-type MODEL_TYPE]

                           [--model-kwargs key=value [key=value ...]]

                           [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]



Revise manuscript content using AI models to suggest text improvements.



options:

  -h, --help            show this help message and exit

  --content-directory CONTENT_DIRECTORY

                        Directory where manuscript content files are located.

  --config-directory CONFIG_DIRECTORY

                        Directory where AI revision configuration files are

                        located. If unspecified, disables custom

                        configuration.

  --model-type MODEL_TYPE

                        Model type used to revise the manuscript. Default is

                        GPT3CompletionModel. It can be any subclass of

                        manubot_ai_editor.models.ManuscriptRevisionModel

  --model-kwargs key=value [key=value ...]

                        Keyword arguments for the revision model (--model-

                        type), with format key=value.

  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}

                        Set the logging level for stderr logging

```



The usual call is:



```

manubot ai-revision --content-directory content/

```



The parameters `--model-type` and `--model-kwargs` are used for debugging purposes.

For example, since the tool splits the text into paragraphs, you might want to see if paragraphs were detected correctly.

The tool incurs a cost when using the OpenAI API, so this could be important to check for text with complicated structure.



```

manubot ai-revision \

  --content-directory content/ \

  --model-type DummyManuscriptRevisionModel \

  --model-kwargs add_paragraph_marks=true

```



## Development



### Environment



Create a development environment using:



```shell

conda create --name manubot-dev --channel conda-forge \

  python=3.11 pandoc=2.11.3.1

conda activate manubot-dev  # assumes conda >= 4.4

pip install --editable ".[webpage,dev]"

```



### 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.



```shell

# run the test suite

pytest



# install pre-commit git hooks (once per local clone).

# The pre-commit checks declared in .pre-commit-config.yaml will now

# run on changed files during git commits.

pre-commit install



# run the pre-commit checks (required to pass CI)

pre-commit run --all-files



# commit despite failing pre-commit checks (will fail CI)

git commit --no-verify



# 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



[![PyPI](https://img.shields.io/pypi/v/manubot.svg?logo=PyPI&style=for-the-badge)](https://pypi.org/project/manubot/)



This section is only relevant for project maintainers.

GitHub Actions [deploys](.github/workflows/release.yml) releases to [PyPI](https://pypi.org/project/manubot).



To create a new release, bump the `__version__` in [`manubot/__init__.py`](manubot/__init__.py).

Then, set the `TAG` and `OLD_TAG` environment variables:



```shell

TAG=v$(python setup.py --version)



# fetch tags from the upstream remote

# (assumes upstream is the manubot organization remote)

git fetch --tags upstream main



# 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:



```shell

# 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 --reverse $OLD_TAG..HEAD >> "release-notes/$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:main`,

for example after a PR is merged,

use the [GitHub interface](https://github.com/manubot/manubot/releases/new) to create a release with the new "Tag version".

Monitor [GitHub Actions](https://github.com/manubot/manubot/actions?query=workflow%3ARelease) and [PyPI](https://pypi.org/project/manubot/#history) 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`](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](https://sloan.org/grant-detail/8501) to [**@dhimmel**](https://github.com/dhimmel).

- the **Gordon & Betty Moore Foundation** ([**@DDD-Moore**](https://github.com/DDD-Moore)) in [Grant GBMF4552](https://www.moore.org/grant-detail?grantId=GBMF4552) to [**@cgreene**](https://github.com/cgreene).