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quilt3distribute\n\n[![Build Status](https://github.com/AllenCellModeling/quilt3distribute/workflows/Build/badge.svg)](https://github.com/AllenCellModeling/quilt3distribute/actions)\n[![Documentation](https://github.com/AllenCellModeling/quilt3distribute/workflows/Documentation/badge.svg)](https://AllenCellModeling.github.io/quilt3distribute)\n[![Code Coverage](https://codecov.io/gh/AllenCellModeling/quilt3distribute/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/quilt3distribute)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3382259.svg)](https://doi.org/10.5281/zenodo.3382259)\n\u003cbr\u003e\n\n![dataset packaging and distribution](http://www.allencell.org/uploads/8/1/9/9/81996008/published/automatingaccess-button-3_2.png?1549322257)\n\nPeople commonly work with tabular datasets, people want to share their data, this makes that easier through Quilt3.\n\n---\n\n## Features\n* Automatically determines which files to upload based off CSV headers. (Explicit override available)\n* Simple interface for attaching metadata to each file based off the manifest contents.\n* Groups metadata for files that are referenced multiple times.\n* Validates and runs basic cleaning operations on your dataset manifest CSV.\n* Optionally add license details and usage instructions to your dataset README.\n* Parses README for any referenced files and packages them up as well.\n* Support for adding extra files not contained in the manifest.\n* Constructs an \"associates\" map that is placed into each files metadata for quick navigation around the package.\n* Enforces that the metadata attached to each file is standardized across the package for each file column.\n\n## Quick Start\nConstruct a csv (or pandas dataframe) dataset manifest ([Example](quilt3distribute/tests/data/example.csv)):\n\n| CellId | Structure | 2dReadPath | 3dReadPath |\n|--------|-----------|------------|------------|\n| 1      | lysosome  | 2d/1.png   | 3d/1.tiff  |\n| 2      | laminb1   | 2d/2.png   | 3d/2.tiff  |\n| 3      | golgi     | 2d/3.png   | 3d/3.tiff  |\n| 4      | myosin    | 2d/4.png   | 3d/4.tiff  |\n\n```python\nfrom quilt3distribute import Dataset\n\n# Create the dataset\nds = Dataset(\n    dataset=\"single_cell_examples.csv\",\n    name=\"single_cell_examples\",\n    package_owner=\"jacksonb\",\n    readme_path=\"single_cell_examples.md\"\n)\n\n# Optionally add common additional requirements\nds.add_usage_doc(\"https://docs.quiltdata.com/walkthrough/reading-from-a-package\")\nds.add_license(\"https://www.allencell.org/terms-of-use.html\")\n\n# Optionally indicate column values to use for file metadata\nds.set_metadata_columns([\"CellId\", \"Structure\"])\n\n# Optionally rename the columns on the package level\nds.set_column_names_map({\n    \"2dReadPath\": \"images_2d\",\n    \"3dReadPath\": \"images_3d\"\n})\n\n# Distribute\npkg = ds.distribute(push_uri=\"s3://quilt-jacksonb\", message=\"Initial dataset example\")\n```\n\n***Returns:***\n```\n(remote Package)\n └─README.md\n └─images_2d\n   └─03cdf019_1.png\n   └─148ddc09_2.png\n   └─2b2cf361_3.png\n   └─312a0367_4.png\n └─images_3d\n   └─a0ce6e01_1.tiff\n   └─c360072c_2.tiff\n   └─d9b55cba_3.tiff\n   └─eb29e6b3_4.tiff\n └─metadata.csv\n └─referenced_files\n   └─some_file_referenced_by_the_readme.png\n```\n\n***Example Metadata:***\n```python\npkg[\"images_2d\"][\"03cdf019_1.png\"].meta\n```\n```json\n{\n    \"CellId\": 1,\n    \"Structure\": \"lysosome\",\n    \"associates\": {\n        \"images_2d\": \"images_2d/03cdf019_1.png\",\n        \"images_3d\": \"images_3d/a0ce6e01_1.tiff\"\n    }\n}\n```\n\n## Installation\n**Stable Release:** `pip install quilt3distribute`\u003cbr\u003e\n**Development Head:** `pip install git+https://github.com/AllenCellModeling/quilt3distribute.git`\n\n\n### Credits\n\nThis package was created with Cookiecutter. [Original repository](https://github.com/audreyr/cookiecutter)\n\n\n***Free software: Allen Institute Software License***\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Fquilt3distribute","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fallencellmodeling%2Fquilt3distribute","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Fquilt3distribute/lists"}