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https://github.com/cthoyt/authorship
🚢 Generate publication-ready authorship lists via Google Sheets and more
https://github.com/cthoyt/authorship
academia automation bibliometrics publishing scientometrics writing
Last synced: 2 months ago
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🚢 Generate publication-ready authorship lists via Google Sheets and more
- Host: GitHub
- URL: https://github.com/cthoyt/authorship
- Owner: cthoyt
- License: mit
- Created: 2022-07-08T20:50:21.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2022-07-25T15:44:35.000Z (over 2 years ago)
- Last Synced: 2024-09-18T01:38:05.710Z (3 months ago)
- Topics: academia, automation, bibliometrics, publishing, scientometrics, writing
- Language: Python
- Homepage: https://authorship.readthedocs.io
- Size: 119 KB
- Stars: 4
- Watchers: 2
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
🚢 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](https://docs.google.com/spreadsheets/d/1Fo1YH3ZzOVrQ4wzKnBm6sPha5hZG66-u-uSMDGUvguI/edit#gid=0)
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*.
```python
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`](https://github.com/cthoyt/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:
```python
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](https://docs.google.com/spreadsheets/d/1NfhibWHOKgV2glmgRdKMzHEzTCw2_dUq_t0Zq64cgeQ)
from Google Sheets. This has been used for the SSSOM, ODK, Cell Ontology,
and several other papers.
```python
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](https://pypi.org/project/authorship/) with:
```bash
$ pip install authorship
```
The most recent code and data can be installed directly from GitHub with:
```bash
$ 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](https://github.com/cthoyt/authorship/blob/master/.github/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](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/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:
```bash
$ 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:
```shell
$ tox
```
Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/cthoyt/authorship/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```shell
$ 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`](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`](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:
```shell
$ tox -e finish
```
This script does the following:
1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`,
`src/authorship/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build)
3. Uploads to PyPI using [`twine`](https://github.com/pypa/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.