{"id":21426985,"url":"https://github.com/j535d165/scitree","last_synced_at":"2025-07-14T10:31:13.843Z","repository":{"id":65046518,"uuid":"541578065","full_name":"J535D165/scitree","owner":"J535D165","description":"Scitree is a recursive directory listing tool optimized for science","archived":false,"fork":false,"pushed_at":"2023-03-30T11:47:25.000Z","size":53,"stargazers_count":7,"open_issues_count":3,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-12T10:12:59.636Z","etag":null,"topics":["cli","directory-lister","directory-listing","file-sorting","python","research","research-data-management","science","sorting","tree","utrecht-university"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/J535D165.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-09-26T12:36:00.000Z","updated_at":"2024-06-28T08:47:52.000Z","dependencies_parsed_at":"2025-04-12T10:13:10.055Z","dependency_job_id":"08664730-f3f1-4ade-8f87-0f41fa75dc71","html_url":"https://github.com/J535D165/scitree","commit_stats":{"total_commits":34,"total_committers":2,"mean_commits":17.0,"dds":0.02941176470588236,"last_synced_commit":"bf65dbb1447d837fab95bcd349953ce02077e169"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/J535D165/scitree","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/J535D165%2Fscitree","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/J535D165%2Fscitree/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/J535D165%2Fscitree/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/J535D165%2Fscitree/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/J535D165","download_url":"https://codeload.github.com/J535D165/scitree/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/J535D165%2Fscitree/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265280501,"owners_count":23739850,"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":["cli","directory-lister","directory-listing","file-sorting","python","research","research-data-management","science","sorting","tree","utrecht-university"],"created_at":"2024-11-22T21:43:31.936Z","updated_at":"2025-07-14T10:31:13.331Z","avatar_url":"https://github.com/J535D165.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n  \u003cimg alt=\"Scitree - Like tree, but optimized for science\" src=\"https://github.com/J535D165/scitree/raw/main/scitree_repocard.svg\"\u003e\n\u003c/p\u003e\n\n# Scitree - Like `tree`, but optimized for science\n\n![PyPI](https://img.shields.io/pypi/v/scitree) [![DOI](https://zenodo.org/badge/541578065.svg)](https://zenodo.org/badge/latestdoi/541578065)\n\n\u003e In computing, tree is a recursive directory listing command or program that\n\u003e produces a depth-indented listing of files. [Wikipedia, 2022](https://en.wikipedia.org/wiki/Tree_(command)).\n\nScitree is like tree, but different. Instead of sorting content on its name,\nscitree sorts and highlights given opiniated scientific principles. In this\nway, you can inspect directory listings more easily.\n\nScitree is based on [scisort](https://github.com/j535d165/scisort), a Python\npackage to sort file paths based on scientific principles.\n\n## Philosophy\n\nPhilosophy of [scisort](https://github.com/j535d165/scisort) and scitree:\n\n- Read the README first, therefore I'm on top\n- Before I install or use the content, I open the [LICENSE](https://choosealicense.com/).\n- Files first, folders second\n- Numbered files are [naturally sorted](https://en.wikipedia.org/wiki/Natural_sort_order)\n- I love [intuitive and reproducible project structures](https://doi.org/10.1371/journal.pcbi.1005510)\n- Follow the order of execution where possible\n- I ignore, what git ignores\\*\n\n*\\* Only for [`scitree`](https://github.com/J535D165/scitree).*\n\nFor more information about the structure, see [scisort/scisort/keygen.py](https://github.com/J535D165/scisort/blob/main/scisort/keygen.py). \n\n## Installation\n\nScitree requires Python 3.6 or later.\n\n```sh\npip install scitree\n```\n\n## Getting started\n\n### `scitree` command\n\nScittree command on the command line outputs a tree.\n```sh\nscitree\n```\n\n\u003c!--\ncd example/example_makita\nscitree\n\nscitree example/example_makita\n --\u003e\n\n```sh\n./\n├── README.md\n├── LICENSE.txt\n├── jobs.sh\n├── data/\n│   └── Bos_2018.csv\n├── scripts/\n│   ├── get_plot.py\n│   ├── merge_descriptives.py\n│   └── merge_metrics.py\n└── output/\n    ├── simulation/\n    │   └── Bos_2018/\n    │       ├── metrics_sim_Bos_2018_0.json\n    │       ├── metrics_sim_Bos_2018_6.json\n    │       ├── metrics_sim_Bos_2018_559.json\n    │       ├── metrics_sim_Bos_2018_1640.json\n    │       ├── metrics_sim_Bos_2018_3154.json\n    │       ├── metrics_sim_Bos_2018_3518.json\n    │       ├── metrics_sim_Bos_2018_3519.json\n    │       ├── metrics_sim_Bos_2018_3721.json\n    │       ├── metrics_sim_Bos_2018_4612.json\n    │       ├── metrics_sim_Bos_2018_4699.json\n    │       ├── metrics_sim_Bos_2018_5673.json\n    │       ├── plot_recall_sim_Bos_2018.png\n    │       ├── descriptives/\n    │       │   ├── wordcloud_Bos_2018.png\n    │       │   ├── wordcloud_irrelevant_Bos_2018.png\n    │       │   ├── wordcloud_relevant_Bos_2018.png\n    │       │   └── data_stats_Bos_2018.json\n    │       └── state_files/\n    │           ├── sim_Bos_2018_0.asreview\n    │           ├── sim_Bos_2018_6.asreview\n    │           ├── sim_Bos_2018_559.asreview\n    │           ├── sim_Bos_2018_1640.asreview\n    │           ├── sim_Bos_2018_3154.asreview\n    │           ├── sim_Bos_2018_3518.asreview\n    │           ├── sim_Bos_2018_3519.asreview\n    │           ├── sim_Bos_2018_3721.asreview\n    │           ├── sim_Bos_2018_4612.asreview\n    │           ├── sim_Bos_2018_4699.asreview\n    │           └── sim_Bos_2018_5673.asreview\n    └── tables/\n        ├── data_descriptives.csv\n        ├── data_descriptives.xlsx\n        ├── data_metrics.csv\n        └── data_metrics.xlsx\n\n8 directories, 38 files\n```\n\n\n### `scitree` function for Python\n\nThe `scitree` function in Python prints the tree for the current folder (`\".\"`).\n\n```python\nfrom scitree import scitree\n\nscitree()\n```\n\n\n## License\n\n[MIT](/LICENSE)\n\n## Contact\n\nFeel free to reach out with questions, remarks, and suggestions. The\n[issue tracker](/issues) is a good starting point. You can also email me at\n[jonathandebruinos@gmail.com](mailto:jonathandebruinos@gmail.com).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fj535d165%2Fscitree","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fj535d165%2Fscitree","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fj535d165%2Fscitree/lists"}