https://github.com/mpharrigan/gitbib
Version controled, crossreferenced bibliomanager with automatic metadata fetching
https://github.com/mpharrigan/gitbib
arxiv bibliographic-database bibliographic-identifiers bibliographic-references bibliography bibliography-generator metadata paper references yaml
Last synced: about 1 year ago
JSON representation
Version controled, crossreferenced bibliomanager with automatic metadata fetching
- Host: GitHub
- URL: https://github.com/mpharrigan/gitbib
- Owner: mpharrigan
- License: mpl-2.0
- Created: 2017-06-14T22:21:03.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2021-04-08T18:55:38.000Z (about 5 years ago)
- Last Synced: 2025-03-25T08:01:35.356Z (about 1 year ago)
- Topics: arxiv, bibliographic-database, bibliographic-identifiers, bibliographic-references, bibliography, bibliography-generator, metadata, paper, references, yaml
- Language: Python
- Homepage:
- Size: 446 KB
- Stars: 16
- Watchers: 3
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Gitbib
======
- Version control your references
- Auto-fetch relevant bibliographic data
- Render as pretty html or `.bib`
[Example](https://htmlpreview.github.io/?https://raw.githubusercontent.com/mpharrigan/gitbib/master/example/gitbib/all.html)
output.
Version control
---------------
Pick a paper, come up with a meaningful identifier, attach
a doi or arxiv id, and save in a yaml file:
```yaml
2015-mdtraj:
doi: 10.1016/j.bpj.2015.08.015
2009-theobald-rmsd:
doi: 10.1002/jcc.21439
```
You can easily version control this file.
Description and tags
--------------------
You might want to add some tags:
```yaml
2015-mdtraj:
doi: 10.1016/j.bpj.2015.08.015
tags: [molecular-dynamics, analysis, python]
2009-theobald-rmsd:
doi: 10.1002/jcc.21439
tags: [molecular-dynamics, analysis, algorithm]
```
And descriptions:
```yaml
2015-mdtraj:
doi: 10.1016/j.bpj.2015.08.015
description: "MDTraj loads every trajectory format!"
2009-theobald-rmsd:
doi: 10.1002/jcc.21439
description: "Fast method for computing RMSD!"
```
Cross-references are a powerful tool to give context to papers.
```yaml
2015-mdtraj:
doi: 10.1016/j.bpj.2015.08.015
description: |+
MDTraj loads every trajectory format! It computes
RMSD pretty fast using [2009-theobald-rmsd].
2009-theobald-rmsd:
doi: 10.1002/jcc.21439
```
Contextualize the work by noting important references
from the paper (with their reference number)
```yaml
2015-mdtraj:
doi: 10.1016/j.bpj.2015.08.015
description: |+
MDTraj loads every trajectory format!
The authors justify their work by noting that
[2013-milliseconds-folding=2] claims analysis
is becoming the bottleneck for MD.
2013-milliseconds-folding:
doi: 10.1016/j.sbi.2012.11.002
```
Bibliography data fetching
--------------------------
Relevant bibliographic data is automatically
fetched using crossref or arxiv. There is no
need for you to manually fill in authors, title,
etc. Gitbib will cache this metadata to avoid
flooding these services with requests.
Installation
------------
Clone this repository. Install the program's runtime
and installation requirements, resp.
pip install -r requirements.txt
pip install flit
Install the package with flit
flit install
Usage
-----
Gitbib expects a directory full of YAML files containing
references as well as a file named `gitbib.yaml`, which specifies
configuration options. See `example/gitbib.yaml` for a commented
template of what to put in this file.
Pass the directory containing references and `gitbib.yaml` to the
command-line program `gitbib`.
You can build the example references by going
to the `example/` folder in this repository and running gitbib.
cd example/
gitbib ./
This will generate html pages and `bib` files for each output
specified in `gitbib.yaml` as well as an `index.html` file to
browse through the outputs.
Details
-------
### Description syntax
The description field uses some markdown-style formatting.
Paragraph breaks are indicated with blank lines. Otherwise,
duplicated whitespace is trimmed.
You can include `[links](github.com)` like that.
I'm very-much interested in crossreferencing entries.
If the entry cites another entry as reference e.g. 23,
link it like
They cite the [2011-prinz=23] review
Otherwise, crossreference like
This is cited by the [2011-prinz] review
See how important good identifiers are!
### Misc
- identifier: The key (identifier) must be unique across all input `yaml` files.
I like all-lowercase, hyphen-spaced identifiers starting
with the year, optionally middling with the first author's
last name (if necessary to distinguish), and ending with
a short description of what the paper is about.
- identifier: Right now, we support `doi` and `arxiv`.