{"id":16878900,"url":"https://github.com/mpharrigan/gitbib","last_synced_at":"2025-04-11T11:36:25.868Z","repository":{"id":71729945,"uuid":"94377606","full_name":"mpharrigan/gitbib","owner":"mpharrigan","description":"Version controled, crossreferenced bibliomanager with automatic metadata fetching","archived":false,"fork":false,"pushed_at":"2021-04-08T18:55:38.000Z","size":457,"stargazers_count":16,"open_issues_count":1,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-25T08:01:35.356Z","etag":null,"topics":["arxiv","bibliographic-database","bibliographic-identifiers","bibliographic-references","bibliography","bibliography-generator","metadata","paper","references","yaml"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mpharrigan.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-06-14T22:21:03.000Z","updated_at":"2024-04-26T04:59:37.000Z","dependencies_parsed_at":"2023-08-01T05:16:41.399Z","dependency_job_id":null,"html_url":"https://github.com/mpharrigan/gitbib","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mpharrigan%2Fgitbib","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mpharrigan%2Fgitbib/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mpharrigan%2Fgitbib/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mpharrigan%2Fgitbib/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mpharrigan","download_url":"https://codeload.github.com/mpharrigan/gitbib/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248384688,"owners_count":21094757,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["arxiv","bibliographic-database","bibliographic-identifiers","bibliographic-references","bibliography","bibliography-generator","metadata","paper","references","yaml"],"created_at":"2024-10-13T15:52:00.772Z","updated_at":"2025-04-11T11:36:25.856Z","avatar_url":"https://github.com/mpharrigan.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Gitbib\n======\n\n - Version control your references\n - Auto-fetch relevant bibliographic data\n - Render as pretty html or `.bib`\n \n[Example](https://htmlpreview.github.io/?https://raw.githubusercontent.com/mpharrigan/gitbib/master/example/gitbib/all.html)\noutput.\n\n![Example](https://github.com/mpharrigan/gitbib/raw/master/example/screenshot.png)\n \nVersion control\n---------------\n  \nPick a paper, come up with a meaningful identifier, attach\na doi or arxiv id, and save in a yaml file:\n\n```yaml\n2015-mdtraj:\n  doi: 10.1016/j.bpj.2015.08.015\n  \n2009-theobald-rmsd:\n  doi: 10.1002/jcc.21439\n```\n\nYou can easily version control this file.\n\n\nDescription and tags\n--------------------\n\nYou might want to add some tags:\n\n```yaml\n2015-mdtraj:\n  doi: 10.1016/j.bpj.2015.08.015\n  tags: [molecular-dynamics, analysis, python]\n\n2009-theobald-rmsd:\n  doi: 10.1002/jcc.21439\n  tags: [molecular-dynamics, analysis, algorithm]\n```\n\nAnd descriptions:\n\n```yaml\n2015-mdtraj:\n  doi: 10.1016/j.bpj.2015.08.015\n  description: \"MDTraj loads every trajectory format!\"\n\n2009-theobald-rmsd:\n  doi: 10.1002/jcc.21439\n  description: \"Fast method for computing RMSD!\"\n```\n\nCross-references are a powerful tool to give context to papers.\n\n```yaml\n2015-mdtraj:\n  doi: 10.1016/j.bpj.2015.08.015\n  description: |+\n    MDTraj loads every trajectory format! It computes\n    RMSD pretty fast using [2009-theobald-rmsd].\n\n2009-theobald-rmsd:\n  doi: 10.1002/jcc.21439\n```\n\nContextualize the work by noting important references\nfrom the paper (with their reference number)\n\n```yaml\n2015-mdtraj:\n  doi: 10.1016/j.bpj.2015.08.015\n  description: |+\n    MDTraj loads every trajectory format!     \n    The authors justify their work by noting that\n    [2013-milliseconds-folding=2] claims analysis \n    is becoming the bottleneck for MD.\n    \n2013-milliseconds-folding:\n  doi: 10.1016/j.sbi.2012.11.002\n```\n\nBibliography data fetching\n--------------------------\n\nRelevant bibliographic data is automatically\nfetched using crossref or arxiv. There is no\nneed for you to manually fill in authors, title,\netc. Gitbib will cache this metadata to avoid\nflooding these services with requests.\n\n\nInstallation\n------------\n\nClone this repository. Install the program's runtime\nand installation requirements, resp.\n\n    pip install -r requirements.txt\n    pip install flit\n    \nInstall the package with flit\n\n    flit install\n\n\nUsage\n-----\n\nGitbib expects a directory full of YAML files containing\nreferences as well as a file named `gitbib.yaml`, which specifies\nconfiguration options. See `example/gitbib.yaml` for a commented\ntemplate of what to put in this file.\n\nPass the directory containing references and `gitbib.yaml` to the\ncommand-line program `gitbib`.\nYou can build the example references by going\nto the `example/` folder in this repository and running gitbib.\n\n    cd example/\n    gitbib ./\n    \nThis will generate html pages and `bib` files for each output\nspecified in `gitbib.yaml` as well as an `index.html` file to\nbrowse through the outputs.\n\nDetails\n-------\n\n### Description syntax\n\nThe description field uses some markdown-style formatting.\nParagraph breaks are indicated with blank lines. Otherwise,\nduplicated whitespace is trimmed.\n\nYou can include `[links](github.com)` like that.\n\nI'm very-much interested in crossreferencing entries.\nIf the entry cites another entry as reference e.g. 23, \nlink it like\n\n    They cite the [2011-prinz=23] review\n    \nOtherwise, crossreference like\n\n    This is cited by the [2011-prinz] review\n    \nSee how important good identifiers are!\n    \n\n### Misc\n\n - identifier: The key (identifier) must be unique across all input `yaml` files.\n   I like all-lowercase, hyphen-spaced identifiers starting\n   with the year, optionally middling with the first author's\n   last name (if necessary to distinguish), and ending with\n   a short description of what the paper is about.\n - identifier: Right now, we support `doi` and `arxiv`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmpharrigan%2Fgitbib","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmpharrigan%2Fgitbib","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmpharrigan%2Fgitbib/lists"}