{"id":29303560,"url":"https://github.com/scverse/shadows","last_synced_at":"2025-07-07T01:09:07.964Z","repository":{"id":204723628,"uuid":"712510888","full_name":"scverse/shadows","owner":"scverse","description":"Shadow objects for AnnData and MuData (experimental)","archived":false,"fork":false,"pushed_at":"2025-02-28T16:09:51.000Z","size":2282,"stargazers_count":12,"open_issues_count":7,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-05-03T09:05:55.779Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://scverse.org/shadows/","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/scverse.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":"2023-10-31T15:59:35.000Z","updated_at":"2025-03-19T16:23:22.000Z","dependencies_parsed_at":null,"dependency_job_id":"f323346e-7ea6-4c09-960a-5f0e76d073e0","html_url":"https://github.com/scverse/shadows","commit_stats":null,"previous_names":["scverse/shadows"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/shadows","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fshadows","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fshadows/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fshadows/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fshadows/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/shadows/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fshadows/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996091,"owners_count":23541402,"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":"2025-07-07T01:09:02.068Z","updated_at":"2025-07-07T01:09:07.958Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"./docs/img/shadows_header.jpg\" data-canonical-src=\"./docs/img/shadows_header.svg\" width=\"100%\"/\u003e\n\n# Shadows\n\nShadows are on-disk interfaces for scverse data standards such as [AnnData](https://github.com/scverse/anndata) and [MuData](https://github.com/scverse/mudata).\n\nIt is an experimental project.\n\n[![PyPi version](https://img.shields.io/pypi/v/shadows)](https://pypi.org/project/shadows)\n\n## Installation\n\n```\npip install shadows\n# or\npip install git+https://github.com/scverse/shadows\n```\n\n## Features\n\nThe shadows library aims to implement the following features:\n\n- [x] **Shadow objects**: Read-only AnnDataShadow and MuDataShadow for HDF5 files.\n\n- [x] AnnDataShadow and MuDataShadow for Zarr files.\n\n- [x] AnnDataShadow and MuDataShadow for Parquet-based serialization ([pqdata](https://github.com/gtca/pqdata)).\n\n- [x] Data shadows for `.pqdata` and `.zarr` files on S3 storage.\n\n\n### Shadow objects\n\nBriefly, shadow objects simply work like this:\n\n```py\nfrom shadows import *\nash = AnnDataShadow(\"pbmc3k.h5ad\")\nmsh = MuDataShadow(\"pbmc5k_citeseq.h5mu\")\n```\n\nAll the various features are showcased in the following tutorials:\n\n- [Getting started with shadow objects](/docs/examples/shadow-objects.ipynb)\n\n- [Advanced features of shadow objects](/docs/examples/shadows-features.ipynb)\n\n[//]: # (numfocus-fiscal-sponsor-attribution)\n\nshadows is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\nIf you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\n\u003cdiv align=\"center\"\u003e\n\u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  \u003e\n\u003c/a\u003e\n\u003c/div\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fshadows","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fshadows","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fshadows/lists"}