{"id":21702418,"url":"https://github.com/aphp/eds-scikit","last_synced_at":"2025-04-12T14:51:14.554Z","repository":{"id":64269156,"uuid":"571584236","full_name":"aphp/eds-scikit","owner":"aphp","description":"eds-scikit is a Python library providing tools to process and analyse OMOP data","archived":false,"fork":false,"pushed_at":"2024-04-12T14:14:13.000Z","size":14440,"stargazers_count":31,"open_issues_count":14,"forks_count":5,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-04-12T22:13:26.347Z","etag":null,"topics":["clinical-data-warehouse","data-science","medical","omop","python"],"latest_commit_sha":null,"homepage":"https://aphp.github.io/eds-scikit","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aphp.png","metadata":{"files":{"readme":"README.md","changelog":"changelog.md","contributing":"contributing.md","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}},"created_at":"2022-11-28T12:57:23.000Z","updated_at":"2024-04-15T09:28:08.691Z","dependencies_parsed_at":"2023-12-21T11:06:01.465Z","dependency_job_id":"71c436e6-664d-4191-b13e-729b4c764cb0","html_url":"https://github.com/aphp/eds-scikit","commit_stats":{"total_commits":94,"total_committers":6,"mean_commits":"15.666666666666666","dds":0.5638297872340425,"last_synced_commit":"d3f817c237adce1752e5e474a376ec52e29ba355"},"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aphp%2Feds-scikit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aphp%2Feds-scikit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aphp%2Feds-scikit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aphp%2Feds-scikit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aphp","download_url":"https://codeload.github.com/aphp/eds-scikit/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225825871,"owners_count":17530145,"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":["clinical-data-warehouse","data-science","medical","omop","python"],"created_at":"2024-11-25T21:15:32.083Z","updated_at":"2024-11-25T21:15:32.810Z","avatar_url":"https://github.com/aphp.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cdiv align=\"center\"\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://aphp.github.io/eds-scikit/\"\u003e\n    \u003cimg src=\"https://github.com/aphp/eds-scikit/raw/main/docs/_static/scikit_logo_text.png\" width=\"30%\" onerror=\"this.style.display='none'\"\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n#\n\n\u003cp align=\"center\"\u003e\n\n![Tests](https://img.shields.io/github/actions/workflow/status/aphp/eds-scikit/testing.yml?branch=main\u0026label=tests\u0026style=flat-square)\n[![Documentation](https://img.shields.io/github/actions/workflow/status/aphp/eds-scikit/publish_doc.yml?branch=main\u0026label=docs\u0026style=flat-square)](https://aphp.github.io/eds-scikit/latest/)\n[![PyPI](https://img.shields.io/pypi/v/eds-scikit?color=blue\u0026style=flat-square)](https://pypi.org/project/eds-scikit/)\n[![Supported Python](https://img.shields.io/badge/python-%3E%3D%203.7.1%20%7C%20%3C%203.8-brightgreen?style=flat-square)](https://www.python.org/)\n[![Black](https://img.shields.io/badge/code%20style-black-black?style=flat-square)]([https://www.python.org/](https://github.com/psf/black))\n[![Coverage](https://raw.githubusercontent.com/aphp/eds-scikit/coverage/coverage.svg)](https://raw.githubusercontent.com/aphp/eds-scikit/coverage/coverage.txt)\n[![DOI](https://zenodo.org/badge/571584236.svg)](https://zenodo.org/badge/latestdoi/571584236\u0026style=flat-square)\n\n\u003c/p\u003e\n\u003c/div\u003e\n\n\neds-scikit is a tool to assist data scientists working on the AP-HP's Clinical Data Warehouse. It is specifically targeted for OMOP-standardized data. It main goals are to:\n\n- Ease access and analysis of data\n- Allow a better transfer of knowledge between projects\n- Improve research reproducibility\n\n## Development\n\nThis library is developed and maintained by the core team of AP-HP’s Clinical Data Warehouse (EDS) with the strong support of [Inria's SODA team](https://team.inria.fr/soda/).\n\n## How to use\n\nPlease check the [online documentation](https://aphp.github.io/eds-scikit/) for more informations. You will find\n- Detailed explanation of the project goal and working principles\n- A complete API documentation\n- Various Jupyter Notebooks describing how to use various functionnalities of eds-scikit\n- And more !\n## Requirements\neds-scikit stands on the shoulders of [Spark 2.4](https://spark.apache.org/docs/2.4.8/index.html) which requires:\n\n- Python ~3.7.1\n- Java 8\n## Installation\n\nYou can install eds-scikit via `pip`:\n\n```bash\npip install \"eds-scikit[aphp]\"\n```\n\n:warning: If you get an an error during installation, please try downgrading pip via `pip install -U \"pip\u003c23\" before install `eds-scikit`\n\n:warning: If you don't work in AP-HP's ecosystem (EDS), please install via:\n\n```bash\npip install eds-scikit\n```\n\nYou can now import the library via\n\n```python\nimport eds_scikit\n```\n### Contributing\n\n- You want to help on the project ?\n- You developped an interesting feature and you think it could benefit other by being integrated in the library ?\n- You found a bug ?\n- You have a question about the library ?\n- ...\n\nPlease check our [contributing guidelines](https://aphp.github.io/eds-scikit/contributing/).\n\n### Citation\n\nIf you use `eds-scikit`, please cite us as below.\n\n```bibtex\n@misc{eds-scikit,\n    author = {Petit-Jean, Thomas and Remaki, Adam and Maladière, Vincent and Varoquaux, Gaël and Bey, Romain},\n    doi = {10.5281/zenodo.7401549},\n    title = {eds-scikit: data analysis on OMOP databases},\n    url = {https://github.com/aphp/eds-scikit}\n}\n```\n\n### Acknowledgment\n\nWe would like to thank the following funders:\n- [Assistance Publique – Hôpitaux de Paris](https://www.aphp.fr/)\n- [AP-HP Foundation](https://fondationrechercheaphp.fr/)\n- [Inria](https://www.inria.fr)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faphp%2Feds-scikit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faphp%2Feds-scikit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faphp%2Feds-scikit/lists"}