authorship 0.1.0

Format author lists for academic texts and journal submissions.

🚢 Authorship 🚢

Format author lists for academic texts and journal submissions.

🕵️ Why does this exist?

Maintaining author lists on collaborative academic work is a bit of a pain. A lot of us have started collecting author information on Google Sheets since it allows people to input their own information, like their ORCID and affiliations. I wanted to automate turning those sheets into some useful forms for copy/pasting into my manuscripts (e.g., in Google Docs or LaTeX) as well submission forms (e.g., bulk author TSV file import on bioRxiv).

💪 Getting Started

This example shows loading a standardized spreadsheet from Google Sheets that is subsequently printed in a nice text format, in a bioRxiv bulk import format, and in LaTeX for a submission to Nature Scientific Data.

from authorship.readers import GoogleSheetReader
from authorship.writers import BiorxivWriter, ScientificDataWriter, TextWriter

# Standard google sheet
reader = GoogleSheetReader("1Fo1YH3ZzOVrQ4wzKnBm6sPha5hZG66-u-uSMDGUvguI")
TextWriter().print(reader)
BiorxivWriter().print(reader)
ScientificDataWriter().print(reader)

The class-resolver package can be used as a shortcut to access the writers based on their names. It's smart and figures out casing/spacing/ punctuation, so you don't have to worry about so many imports. The following example does the same as the previous example:

from authorship.readers import GoogleSheetReader

reader = GoogleSheetReader("1Fo1YH3ZzOVrQ4wzKnBm6sPha5hZG66-u-uSMDGUvguI")
reader.print("text")
reader.print("biorxiv", file="~/Desktop/bioregistry_authors_biorxiv.tsv")
reader.print("scientific data")
reader.print("citation cff")

The next example shows loading an OBO community-flavored spreadsheet from Google Sheets. This has been used for the SSSOM, ODK, Cell Ontology, and several other papers.

from authorship.readers import OboGoogleSheetReader

# OBO community-flavored google sheet
reader = OboGoogleSheetReader(
   "1NfhibWHOKgV2glmgRdKMzHEzTCw2_dUq_t0Zq64cgeQ",
   skiprows=1,
)
reader.print("text")
reader.print("biorxiv", file="~/Desktop/sssom_authors_biorxiv.tsv")
reader.print("scientific data")

🐇 Extending

You can implement your own reader subclassing the authorship.readers.Reader class and implementing the get_authorship() function.

Similarly, you can implement your own writer by subclassing the authorship.writers.Writer class and implementing the iter_lines() function.

We'd be happy to accept new plugins, especially to help auto-generate LaTeX for various journal-specific LaTeX templates.

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install authorship

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/cthoyt/authorship.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

$ git clone git+https://github.com/cthoyt/authorship.git
$ cd authorship
$ pip install -e .

🥼 Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

$ git clone git+https://github.com/cthoyt/authorship.git
$ cd authorship
$ tox -e docs
$ open docs/build/html/index.html

The documentation automatically installs the package as well as the docs extra specified in the setup.cfg. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

$ tox -e finish

This script does the following:

1. Uses Bump2Version to switch the version number in the setup.cfg, src/authorship/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using build
3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion minor after.