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https://github.com/cthoyt/citation-url
Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.
https://github.com/cthoyt/citation-url
Last synced: about 1 month ago
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Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.
- Host: GitHub
- URL: https://github.com/cthoyt/citation-url
- Owner: cthoyt
- License: mit
- Created: 2022-02-11T16:42:39.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2022-02-12T17:38:33.000Z (almost 3 years ago)
- Last Synced: 2024-09-13T23:44:41.683Z (2 months ago)
- Language: Python
- Size: 88.9 KB
- Stars: 2
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
citation-url
Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.
This module has a single `parse()` function that takes in a URL and gives back
a parse status (success, unknown, or irreconcilable), a prefix, and
an identifier. If the status is unknown or irreconcilable, the prefix will
be left as `None` and the identifier will match the input:
```python
>>> from citation_url import parse, Status
>>> parse("https://joss.theoj.org/papers/10.21105/joss.01708")
(Status.success, 'doi', '10.21105/joss.01708')
>>> parse("http://www.ncbi.nlm.nih.gov/pubmed/34739845")
(Status.success, 'pubmed', '34739845')
>>> parse("https://example.com/true-garbage")
(Status.unknown, None, 'https://example.com/true-garbage')
>>> parse("https://example.com/true-garbage")
(Status.unknown, None, 'https://example.com/true-garbage')
>>> parse("http://msb.embopress.org/content/13/11/954.full.pdf")
(Status.irreconcilable, None, 'http://msb.embopress.org/content/13/11/954.full.pdf')
```
## 🕵️ Why?
I wanted to be able to curate a list of papers in
[Zotero](https://www.zotero.org), [Mendeley](https://www.mendeley.com/), or any
other modern citation manager, make an XML export in the EndNote format, extract
and normalize the messy contents in the `electronic-resource-num`, `text-urls`,
and `pdf-urls` fields, then ensure that there are corresponding entries
on [Wikidata](https://www.wikidata.org) using the Su Lab's
[Wikidata Integrator](https://github.com/SuLab/WikidataIntegrator).
Reuse this functionality with:
```shell
$ python -m citation_url.endnote --help
```
## 🚀 Installation
The most recent release can be installed from
[PyPI](https://pypi.org/project/citation_url/) with:
```bash
$ pip install citation_url
```
The most recent code and data can be installed directly from GitHub with:
```bash
$ pip install git+https://github.com/cthoyt/citation-url.git
```
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/cthoyt/citation-url/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 instrutions
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/citation-url.git
$ cd citation-url
$ 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/citation-url/actions?query=workflow%3ATests).
### 📖 Building the Documentation
```shell
$ tox -e docs
```
### 📦 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` and
`src/citation_url/version.py` to not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel
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.