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        "author": "FASTGenomics Team",
        "author_email": "contact@fastgenomics.org",
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        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 3",
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            "Topic :: Scientific/Engineering :: Bio-Informatics",
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        "description": "[![pypi-shield]][pypi]\n[![travis-shield]][travis]\n[![docs-shield]][docs]\n\n[pypi-shield]: https://img.shields.io/pypi/v/fastgenomics.svg\n[pypi]: https://pypi.org/project/fastgenomics\n[travis-shield]: https://travis-ci.org/FASTGenomics/fastgenomics-py.svg?branch=master\n[travis]: https://travis-ci.org/FASTGenomics/fastgenomics-py\n[docs-shield]: https://readthedocs.org/projects/fastgenomics/badge/?version=latest\n[docs]: http://fastgenomics.readthedocs.io\n\n# About\n\nThis python module handles all common interfaces\nof your application to the FASTGenomics runtime:\n\n-  Input/Output of files\n-  Parameters\n\nand provides some convenience functions.\n\n## Examples\n\nA basic interaction through the `fastgenomics` module looks looks this\n\n``` python\nfrom fastgenomics.process import FGProcess\n\napp_dir = \"app_directory/\"\ndata_dir = \"data_directory/\"\nfg = FGProcess(app_dir, data_dir)\n\n# access a parameter\nfg.parameters[\"some_parameter\"]\n\n# access an input/ouput file\nfg.input[\"some_input_file.txt\"].path\nfg.output[\"some_output_file.txt\"].path\n```\n\n### Consistency checks\n\nThe constructor of `FGProcess` will check if all the necessary files\nexist and validate if their content is according to the FASTGenomics\nstandard.  For example, if you make a mistake in the `manifest.json`\nyou will get a relevant error when calling `FGProcess`.\n\n### Reading & Writing AnnData\nYou can also easily load an AnnData object with\n\n``` python\nfrom fastgenomics.external import anndata\n\n# read AnnData\nadata = anndata.read_data(fg)\n\n# Note: this methods works only if the app has exactly a single input of type 'anndata'.\n# If your app has more than one input of type 'anndata' then you can use the following method:\n\nadata_1 = anndata.read_anndata(fg.input['some_anndata_input'])\nadata_2 = anndata.read_anndata(fg.input['another_anndata_input'])\n\n# To write the AnnData object to output:\n\nanndata.write_data(fg, adata)\n\n# Note: this methods works only if the app has exactly a single output of type 'anndata'.\n# Otherwise use the following:\n\nanndata.write_anndata(adata_1, fg.output['some_anndata_output'])\nanndata.write_anndata(adata_2, fg.output['another_anndata_output'])\n\n# To read in the expression matrix, the gene metadata and the cell meta data as an AnnData object use:\nadata = anndata.read(\n            expr=fg.input[\"expression_matrix\"],\n            gene_meta=fg.input[\"genes\"],\n            cell_meta=fg.input[\"cells\"],\n        )\n\n# write AnnData to output files\nanndata.write(\n        adata,\n        expr=fg.output[\"expression_matrix\"],\n        gene_meta=fg.output[\"genes_output\"],\n        cell_meta=fg.output[\"cells_output\"],\n    )\n```\n\nIn the `read` the `cell_metadata` and `gene_metadata` are optional, in\nthe `write` all the outputs are optional.\n\n_note_ This functionality is kept in a separate submodule, to keep the\ndependency on scanpy optional.\n\n### Parameter checks\n\nAside from accessing the parameters you can also use the following\nfunction to validate if a parameter fulfills some arbitrary\nconstraints.  The code below raises a `ValueError` when\n`some_parameter` is not larger then zero.\n\n``` python\nfg.parametres.check(\n    \"some_parameter\",\n    lambda x: x > 0,\n    'Parameter \"some_parameter\" must be larger then 0.')\n```\n\n### Writing the summary with a jinja2 template\nFASTGenomics requires an app to output a `summary.md` file, this file\nis typically generated using a [jinja2\ntemplate](http://jinja.pocoo.org/).  This module provides the\nfollowing utility function for generating a summary file.\n\n``` python\nfg.summary.template = \"path_to_the_tempalte/summary.md.j2\"\nfg.summary.write(some_value=1, some_other_value=2)\n```\n\nThis generates a `summary.md` file in\n`\"[data_dir]/summary/summary.md\"` based on the template in\n`fg.summary.template` passing `some_value=1` and `some_other_value=2`\nto the template engine.\n\n*Note:* The `fg.summary.write` function appends a `###`-level section\nwith the parameter values, with which the app was run.\n\n## Internals\n\nThe module encapsulates most of its functionality in a single class\n`FGProcess(app_dir, data_dir)` that is constructed from two paths:\n`app_dir`, where all the necessary app-related files are (most\nimportantly, the `manifest.json`) and `data_dir`, which points to the\ndirectory structure provided by FASTGenomics.  The class `FGProcess`\nhas the following attributes\n\n- `app`: contains the interpreted `manifest.json` and the locations of\n  app-related files.\n- `parameters`: facilitates the access to parameters provided by the\n  FASTGenomics runtime.\n- `input`, `output`: represents the input and output files provide by\n  the FASTGenomics runtime.\n- `summary`: handles the `summary.md` rendering.\n",
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