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    "info": {
        "author": "Per Unneberg",
        "author_email": "per.unneberg@scilifelab.se",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Framework :: Pytest",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Natural Language :: English",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Utilities"
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        "description": "pytest-ngsfixtures\n==================\n\n.. image:: https://anaconda.org/percyfal/pytest-ngsfixtures/badges/version.svg\n\t   :target: https://anaconda.org/percyfal/pytest-ngsfixtures\n.. image:: https://badge.fury.io/py/pytest-ngsfixtures.svg\n\t   :target: https://badge.fury.io/py/pytest-ngsfixtures\n.. image:: https://travis-ci.org/percyfal/pytest-ngsfixtures.svg?branch=master\n\t   :target: https://travis-ci.org/percyfal/pytest-ngsfixtures\n\n\nAbout\n=====\n\nThis is a `pytest plugin\n<http://doc.pytest.org/en/latest/plugins.html>`_ that provides\nfunctionality for next generation sequencing `pytest fixtures\n<http://doc.pytest.org/en/latest/fixture.html>`_. There are some\npredefined fixtures, but the main functionality depends on configuring\nfixtures via the `pytest.mark` helper function.\n\nSee the `pytest-ngsfixtures documentation`_ for more information and\nusage.\n\n* Free software: GNU General Public License v3\n\nFeatures\n--------\n\n- a small test ngs data set\n- predefined sample layouts\n- wrappers for quickly setting up workflow tests\n\n\nInstallation\n============\n\n.. code-block:: bash\n\n   $ conda install -c percyfal pytest-ngsfixtures\n   $ pip install pytest-ngsfixtures\n\n\nUsage\n=========\n\nYou can easily setup a test requiring the predefined `samples` and\n`ref` fixtures:\n\n.. code-block:: python\n\n   def test_data(samples, ref):\n    shell(\"bwa index {}\".format(ref.join(\"scaffolds.fa\")))\n    shell(\"bwa mem {} {} {} | samtools view -b > {}\".format(\n        ref.join(\"scaffolds.fa\"),\n        samples.join(\"s1_1.fastq.gz\"),\n        samples.join(\"s1_2.fastq.gz\"),\n        samples.join(\"s1.bam\")\n    ))\n    assert samples.join(\"s1.bam\").exists()\n\nThe samples and ref fixtures can also be configured to use local\nfiles:\n\n.. code-block:: python\n\n   import pytest\n\n   @pytest.mark.samples(layout={'s1_1.fastq.gz': \"/path/to/read1.fastq.gz\",\n\t\t                's1_2.fastq.gz': \"/path/to/read2.fastq.gz\"})\n   @pytest.mark.ref(data={'ref.fa': \"/path/to/reference.fa\"})\n   def test_data(samples, ref):\n       # Do something with data\n\nIn addition, there are wrapper functions and fixtures for workflow\nmanagers, including Snakemake.\n\n.. code-block:: python\n\n   import pytest\n   from pytest_ngsfixtures.wm.snakemake import snakefile, run as snakemake_run\n\n   # By default, the snakefile fixture assumes there is a Snakefile in\n   # the test file directory\n   def test_workflow(samples, snakefile):\n       snakemake_run(snakefile, options=[\"-d\", str(samples)])\n       assert samples.join(\"results.txt\").exists()\n\n\nSee the `pytest-ngsfixtures documentation`_ for more examples.\n\n\n\nCredits\n=======\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _`pytest-ngsfixtures documentation`: https://percyfal.github.io/pytest-ngsfixtures/\n\n\nHistory\n=======\n\n0.8.1 (2019-09-06)\n-------------------\n\nHotfix: fix failing conda builds\n\n\n0.8.0 (2019-09-05)\n-------------------\n\nFeatures\n++++++++\n\n* Add support for python 3.7\n* Pin pytest >= 5.0\n* PEP-8 formatting\n* Check for correct snakemake repo tag\n\n\n0.7.6 (2018-05-25)\n------------------\n\nFeatures\n++++++++\n\n* Add path option to override tmpdir_factory invocation\n* Pass ignore_errors to copy/link function\n\n\n0.7.5 (2018-05-25)\n-------------------\n\nFeatures\n+++++++++\n\n* Add Fixture class to setup fixtures (#63)\n\n\n0.7.4 (2018-05-24)\n------------------\n\nBugfixes\n++++++++\n\n* Make pytest.mark.fixture have precedence over pytest.mark.parametrize when updating functions\n\n0.7.3 (2018-05-24)\n------------------\n\nFeatures\n+++++++++\n\n* Add testdir parameter and allow configuration of all fixture options via parametrization (#62)\n\n0.7.2 (2018-05-24)\n------------------\n\nBugfixes\n++++++++\n\n* Fix layout for multi-run samples (#61)\n\n0.7.1 (2018-05-23)\n------------------\n\nBugfixes\n++++++++\n\n* Update busybox images for tests (#59)\n* Fix failing test (#58)\n\n\n0.7.0 (2018-05-23)\n------------------\n\nBreaking changes\n+++++++++++++++++\n\nThis is a major update in which the API has changed considerably.\nNotably, most of the code for generating fixtures has been removed and\nrefactored completely. Most importantly, the factory functions have\nbeen replaced by a small number of fixtures that can be configured via\nthe `pytest.mark` helper.\n\nIn addition, most data files have been removed\nin an attempt to make the package as small as possible. As the\nlocation of test data has been decoupled from package functionality,\nit makes more sense to distribute package data separately.\n\nSee the API documentation for more information.\n\n\nFeatures\n++++++++\n\n* Remove application data (#30)\n* Simplify config.runfmt_alias function (#56)\n* Only package tiny sequence data (#55)\n* Simplify sample layout configuration (#57)\n\n0.6.4 (2018-01-31)\n------------------\n\n* Add docker-py as a dependency (#52)\n\n\n0.6.3 (2018-01-02)\n------------------\n\n* Remove obsolete working directory argument - requires snakemake >=\n  4.4.0\n* Install correct docker API (#50)\n* Allow modifying path in shell wrapper (#51)\n\n0.6.2 (2017-12-19)\n------------------\n\nAdd shell wrappers and wrappers for easily setting up workflow tests.\n\nAdd tutorial.\n\nBugfixes.\n\n* Update pypi badge\n* Remove tox.ini\n* Defer setting alias to FixtureFile (#42)\n* ReadFixtureFile.SM now returns id (#39)\n* Options ngs_layout and ngs_runfmt are now lists (#41)\n* Update project layout configuration (#40)\n* Add function to return runfmt and alias as tuple (#43)\n* Read 1 and 2 have same id when alias required (#45)\n* Census is not increased for read 2 (#44)\n* Add option to only setup sampleinfo (#47)\n* Add tutorial (#46)\n* Add working snakemake tests (#8)\n\n0.6.1 (2017-11-22)\n------------------\n\nAdded some fixes that turned out to be necessary for optional performance.\n\n* Add fixture that parametrizes over input parameters (#37)\n* Fix bug that returned wrong number of snakemake targets in application output generation (#36)\n* Add travis builds (#35)\n* Fix reference layout error for python 3.5 (#34)\n* Update option defaults (#32)\n* Expose fewer predefined fixtures via plugin (#31)\n* Unify parameter names (#33)\n\n\n0.6.0 (2017-11-21)\n------------------\n\nThis is a major revision of the code. Several new abstraction classes\nhave been introduced to ease interaction with local test files, along\nwith new factory functions. For backwards compatibility, most factory\nfunctions should work as previously. Documentation has been much\nimproved.\n\n* Clarify fixture function naming convention (#29)\n* Expose bulk of factory inner functions (#24)\n* Create separate module for os-related functions (#27)\n* Use separate conda build statements to build for different python versions (#23)\n\n0.5.2 (2017-11-16)\n------------------\n\n* Add pool fixtures (#22)\n* Add safe_copy function (#21)\n\n0.5.1 (2017-10-25)\n------------------\n\n* Change name to pytest-ngsfixtures (#20)\n* Add bcftools versions 1.4, 1.4.1, 1.5, 1.6\n* Add bowtie 1.2.1.1\n\n0.5.0 (2017-09-25)\n------------------\n\n* Add star application\n* Add vsearch application\n* Add rseqc application\n* Add snakemake dependency\n* Update docs\n\n* Separate qualimap pe and se output (#12)\n* Add mapdamage2 (#11)\n* Fix mapdamage2 missing output (#18)\n* Use realpath to determine download url (#17)\n* Rename download_ngsfixtures_data.py to pytest_ngsfixtures_download_data.py\n* Update versions for samtools\n\n0.4.0 (2017-03-28)\n------------------\n\n* Add picard output data\n* Add functions for dealing with application fixtures\n* Move docs to gh-pages\n* Add pytest_ngsfixtures_add_application.py for templating new\n  applications\n* Application outputs now implemented as dictionaries for\n  multiple-output applications\n\n\n0.3.1 (2017-03-03)\n------------------\n\nDefer download to script, minor bug fixes\n\n* Add application_fixtures to config module\n* Fix sample_alias bug (#4)\n* Add script download_ngsfixtures_data.py for manual download of data (#5)\n\n\n0.3.0 (2017-03-02)\n------------------\n\nAdd application data, pool data, and functions for downloading data\n\n* Add application data for cutadapt, fastqc, qualimap and samtools\n* Add pooled sequencing data\n* Add functionality for downloading large data sets\n* Improve make targets for easier releases\n* Minor bug fixes\n\n\n0.2.0 (2017-02-24)\n------------------\n\nAdd new reference files, test files, and factory functions.\n\n* Use snakemake instead of make to generate data files\n* Add separate test file for factory functions\n* Add scaffold file with randomly inserted N's\n* Improve safe_symlink\n* Add threads options for running tests\n* Add Snakefile and rules for generating application files\n* Add fileset, filetype factory functions\n\n\n0.1.0 (2017-01-24)\n------------------\n\n* First release on PyPI.\n\n\n",
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