{"id":23473137,"url":"https://github.com/caltechlibrary/cell-atlas","last_synced_at":"2025-06-30T06:03:31.542Z","repository":{"id":51934885,"uuid":"214291002","full_name":"caltechlibrary/cell-atlas","owner":"caltechlibrary","description":"Cell atlas","archived":false,"fork":false,"pushed_at":"2023-02-14T22:32:13.000Z","size":2868546,"stargazers_count":5,"open_issues_count":8,"forks_count":2,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-04-13T08:55:42.148Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://cellstructureatlas.org","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/caltechlibrary.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null}},"created_at":"2019-10-10T21:43:47.000Z","updated_at":"2023-11-28T23:06:44.000Z","dependencies_parsed_at":"2023-02-18T11:48:42.179Z","dependency_job_id":null,"html_url":"https://github.com/caltechlibrary/cell-atlas","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":"caltechlibrary/template","purl":"pkg:github/caltechlibrary/cell-atlas","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/caltechlibrary%2Fcell-atlas","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/caltechlibrary%2Fcell-atlas/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/caltechlibrary%2Fcell-atlas/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/caltechlibrary%2Fcell-atlas/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/caltechlibrary","download_url":"https://codeload.github.com/caltechlibrary/cell-atlas/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/caltechlibrary%2Fcell-atlas/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262720640,"owners_count":23353447,"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":[],"created_at":"2024-12-24T17:15:29.663Z","updated_at":"2025-06-30T06:03:31.521Z","avatar_url":"https://github.com/caltechlibrary.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"Cell atlas\n=====================================================\n\nSource for the \"Atlas of Bacterial and Archaeal Cell Structure\" by Catherine M.\nOikonomou and Grant J. Jensen.\n\nTable of contents\n-----------------\n\n* [Installation](#installation)\n* [Usage](#usage)\n* [Getting help](#getting-help)\n* [Contributing](#contributing)\n* [License](#license)\n* [Authors and history](#authors-and-acknowledgments)\n\n\nInstallation\n------------\n\nInstall [Pandoc](https://pandoc.org/index.html) Version \u003e= 2.11 and [Python](https://www.python.org/) Version \u003e=3.\n\nUsage\n-----\n\nRun the build script using:\n\n```\npython3 _build.py\n# or (depending on python configuration)\npython _build.py\n```\n\n\u003cu\u003eThis will delete the `site/` directory in the this script's working directory\u003c/u\u003e. \nVideos are will not be included in the site build and need to be moved to a `videos` directory \nin 'site' directory.\nSupplemental files (video preview images, narration, and pdb files) are required for the\nsite to function completely and are available to\n[download from CaltechDATA](https://doi.org/10.22002/n91mg-zc832)\n\nOffline versions of the cell atlas are automatically generated in the\n`cell_atlas_offline` and `cell_atlas_offline_lite` directories, assuming you\nhave \"video\", \"videos-480p\", \"narration\", and \"stillimages\" directories present. \nIn order to zip up the offline version, navigate to `cell_atlas_offline` and `cell_atlas_offline_lite` directories \nand use the command `zip -rX cell_atlas_offline_lite.zip *`\n\nYou can optionally create .webp version of image files by installing\n[cwebp](https://developers.google.com/speed/webp/download) and running `python\n_webp.py stillimages`. The site will always fall back to the .jpg images if the\n.webp versions are not available or not suported.\n\nGetting help\n------------\n\nPlease submit an issue using the issue tracker in this repo\n\nContributing\n------------\n\nYou can submit change requests by submitting a pull request through GitHub.\n\n\nLicense\n-------\n\nSoftware produced by the Caltech Library is Copyright (C) 2023, Caltech.  This software is freely distributed under a BSD/MIT type license.  Please see the [LICENSE](LICENSE) file for more information.\n\nThe book text is (C) 2023, Caltech.\n\nAuthors and Acknowledgments\n---------------------------\n\nCatherine M. Oikonomou and Grant J. Jensen wrote \"Atlas of Bacterial and\nArchaeal Cell Structure\". See the [full list of\nAcknowledgments in the book text](https://cellatlas.library.caltech.edu/introduction.html#acknowledgements).\n\nKian Badie, Tom Morrell, and Robert Doiel developed the software in this repository that automates book\nformatting and integrates videos from CaltechDATA.\n\nSoftware Development was funded by the California Institute of Technology\nLibrary and the Jensen Lab.\n\n\"[File](https://thenounproject.com/search/?q=file\u0026i=3723131)\" icon by Vectorstall from [the Noun Project](https://thenounproject.com/).\n\n\"[Video](https://thenounproject.com/search/?q=video\u0026i=2567858)\" icon by i cons from [the Noun Project](https://thenounproject.com/).\n\n\"[Image](https://thenounproject.com/search/?q=image\u0026i=3776456)\" by Dooder from [the Noun Project](https://thenounproject.com/).\n\n\"[cycle](https://thenounproject.com/term/cycle/406578/)\" by ImageCatalog from [the Noun Project](https://thenounproject.com/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcaltechlibrary%2Fcell-atlas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcaltechlibrary%2Fcell-atlas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcaltechlibrary%2Fcell-atlas/lists"}