{"id":15348419,"url":"https://github.com/stain/ro-crate-paper","last_synced_at":"2025-08-02T16:31:21.130Z","repository":{"id":52094550,"uuid":"294050113","full_name":"stain/ro-crate-paper","owner":"stain","description":"Manuscript sources for RO-Crate paper","archived":false,"fork":false,"pushed_at":"2022-01-10T12:33:39.000Z","size":141528,"stargazers_count":1,"open_issues_count":1,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-10-16T01:21:12.869Z","etag":null,"topics":["latex","manubot","packaging","paper","researchobject"],"latest_commit_sha":null,"homepage":"https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/stain.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE-CC0.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-09-09T08:26:28.000Z","updated_at":"2022-01-10T12:27:18.000Z","dependencies_parsed_at":"2022-08-24T01:10:25.403Z","dependency_job_id":null,"html_url":"https://github.com/stain/ro-crate-paper","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stain%2Fro-crate-paper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stain%2Fro-crate-paper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stain%2Fro-crate-paper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stain%2Fro-crate-paper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stain","download_url":"https://codeload.github.com/stain/ro-crate-paper/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":228491851,"owners_count":17928720,"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":["latex","manubot","packaging","paper","researchobject"],"created_at":"2024-10-01T11:47:52.774Z","updated_at":"2024-12-06T16:21:01.760Z","avatar_url":"https://github.com/stain.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Manuscript: Packaging research artefacts with RO-Crate\n\n[![doi:10.3233/DS-210053](https://img.shields.io/badge/doi-10.3233%2FDS--210053-blue)](https://doi.org/10.3233/DS-210053)\n[![RO-Crate](https://img.shields.io/badge/Research%20Object-Crate-darkcyan.svg)](https://w3id.org/ro/doi/10.5281/zenodo.5146227)\n[![HTML from Manubot](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/manuscript.html)\n[![PDF from LaTeX](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/manuscript.pdf)\n[![GitHub Actions Status Manubot](https://github.com/stain/ro-crate-paper/workflows/Manubot/badge.svg)](https://github.com/stain/ro-crate-paper/actions)\n[![GitHub Actions Status LaTeX](https://github.com/stain/ro-crate-paper/workflows/LaTeX/badge.svg)](https://github.com/stain/ro-crate-paper/actions)\n\n## Manuscript description\n\nThis is the manuscript source for the paper _Packaging research artifacts with RO-Crate_, published in the journal [Data Science](https://www.iospress.nl/journal/data-science/) as \u003chttps://doi.org/10.3233/DS-210053\u003e\n\nThe manuscript was edited as a hybrid of [Manubot](https://github.com/manubot/manubot) and [Overleaf](https://www.overleaf.com/) using Markdown in the [content](content)/ folder. \n\nThe manuscript was created in a kind of hybrid mode:\n\n1. Overleaf uses Luatex to render PDF according to the Data Science template, see \u003chttps://www.overleaf.com/read/gbmzkwyhjnzc\u003e\n2. Manubot runs automatically from Git commit and publishes HTML to https://stain.github.io/ro-crate-paper/\n3. Overleaf is triggered manually to sync with GitHub\n \nThe text is all in \u003chttps://github.com/stain/ro-crate-paper/tree/master/content\u003e as Markdown files. Note that some of them used some inline LaTeX that may not render well in the HTML. Figures are also only shown in PDF.\n \nWhy still the HTML? Well, https://www.iospress.nl/journal/data-science/ encourages submission in HTML, and I have been a proponent for that as well, even the cited paper on RASH I was a reviewer on. But the challenge still is how to do collaborative editing and references. So in this hybrid approach I can choose to submit either the PDF or the HTML – or both. I would focus on the Overleaf approach for now.\n \n\n\n### LaTeX requirements\n\n* [LuaLatex](http://www.luatex.org/) (for Unicode support) from TeX Live 2020\n* [fontspec](https://ctan.org/pkg/fontspec)\n* [markdown](https://ctan.org/pkg/markdown) (for embedding `content/*.md`)\n\nIf you have Docker, then `make` will build the manuscript PDF.\n\n### Repository directories \u0026 files\n\nThe directories are as follows:\n\n+ [`content`](content) contains the manuscript source, which includes markdown files as well as inputs for citations and references.\n  See [`USAGE.md`](USAGE.md) for more information.\n+ [`latex`](latex) LaTeX files used by Overleaf, including fonts and bibliography\n+ [`output`](output) contains the outputs (generated files) from Manubot including the resulting manuscripts.\n  You should not edit these files manually, because they will get overwritten.\n+ [`webpage`](webpage) is a directory meant to be rendered as a static webpage for viewing the HTML manuscript.\n+ [`build`](build) contains commands and tools for building the manuscript.\n+ [`ci`](ci) contains files necessary for deployment via continuous integration.\n\n### Local execution\n\nThe easiest way to run Manubot is to use [continuous integration](#continuous-integration) to rebuild the manuscript when the content changes.\nIf you want to build a Manubot manuscript locally, install the [conda](https://conda.io) environment as described in [`build`](build).\nThen, you can build the manuscript on POSIX systems by running the following commands from this root directory.\n\n```sh\n# Activate the manubot conda environment (assumes conda version \u003e= 4.4)\nconda activate manubot\n\n# Build the manuscript, saving outputs to the output directory\nbash build/build.sh\n\n# At this point, the HTML \u0026 PDF outputs will have been created. The remaining\n# commands are for serving the webpage to view the HTML manuscript locally.\n# This is required to view local images in the HTML output.\n\n# Configure the webpage directory\nmanubot webpage\n\n# You can now open the manuscript webpage/index.html in a web browser.\n# Alternatively, open a local webserver at http://localhost:8000/ with the\n# following commands.\ncd webpage\npython -m http.server\n```\n\nSometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected.\nThe following command, while running, will trigger both the `build.sh` script and `manubot webpage` command upon content changes:\n\n```sh\nbash build/autobuild.sh\n```\n\n### Continuous Integration\n\nWhenever a pull request is opened, CI (continuous integration) will test whether the changes break the build process to generate a formatted manuscript.\nThe build process aims to detect common errors, such as invalid citations.\nIf your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly.\n\nWhen a commit to the `master` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/stain/ro-crate-paper/tree/gh-pages) and [`output`](https://github.com/stain/ro-crate-paper/tree/output) branches.\nThe `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs:\n\n+ **HTML manuscript** at https://stain.github.io/ro-crate-paper/\n+ **PDF manuscript** at https://stain.github.io/ro-crate-paper/manuscript.pdf\n\nFor continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml) if using GitHub Actions or [`.travis.yml`](.travis.yml) if using Travis CI.\n\n## License\n\n[![License: CC BY 4.0](https://img.shields.io/badge/License%20All-CC%20BY%204.0-lightgrey.svg)](http://creativecommons.org/licenses/by/4.0/)\n[![License: CC0 1.0](https://img.shields.io/badge/License%20Parts-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/)\n\nExcept when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License ([`LICENSE.md`](LICENSE.md)), which allows reuse with attribution.\nPlease attribute by linking to https://github.com/stain/ro-crate-paper or the DOI of the final paper.\n\nSince CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication ([`LICENSE-CC0.md`](LICENSE-CC0.md)).\nAll files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:\n\n+ `*.sh`\n+ `*.py`\n+ `*.yml` / `*.yaml`\n+ `*.json`\n+ `*.bib`\n+ `*.tsv`\n+ `.gitignore`\n\nThese files are licensed by the [SIL Open Font License](https://opensource.org/licenses/OFL-1.1), see [`LICENSE-SIL.md`](LICENSE-SIL.md):\n+ `*.ttf`\n+ `*.otf`\n\nAll other files are only available under CC BY 4.0, including:\n\n+ `*.md`\n+ `*.html`\n+ `*.pdf`\n+ `*.docx`\n\nPlease open [an issue](https://github.com/stain/ro-crate-paper/issues) for any question related to licensing.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstain%2Fro-crate-paper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstain%2Fro-crate-paper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstain%2Fro-crate-paper/lists"}