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gavinmdouglasgavinmdouglas
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Merge pull request #169 from picrust/v2.4.1
v2.4.1
2 parents 0d3150c + 3d68bb3 commit aebf71e

24 files changed

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-25
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‎picrust2/__init__.py

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__copyright__ = "Copyright 2018-2021, PICRUSt Project"
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__license__ = "GPL"
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__url__ = "https://github.com/picrust/picrust2"
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__version__ = "2.4.0"
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__version__ = "2.4.1"

‎picrust2/default.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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from os import path
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‎picrust2/metagenome_pipeline.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import sys
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import pandas as pd

‎picrust2/pathway_pipeline.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import sys
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from collections import defaultdict

‎picrust2/pipeline.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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from os import path
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import sys

‎picrust2/place_seqs.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import sys
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from os import path, chdir, getcwd

‎picrust2/util.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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from os import makedirs, chmod
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from os.path import abspath, dirname, isdir, join, exists, splitext

‎picrust2/wrap_hsp.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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from os import path
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import sys

‎scripts/add_descriptions.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import argparse
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from picrust2.default import default_map

‎scripts/convert_table.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import argparse
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from picrust2.util import (check_files_exist, contrib_to_legacy,

‎scripts/hsp.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import argparse
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from picrust2.wrap_hsp import castor_hsp_workflow

‎scripts/metagenome_pipeline.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import argparse
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from os import path

‎scripts/pathway_pipeline.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import argparse
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from picrust2.pathway_pipeline import pathway_pipeline

‎scripts/picrust2_pipeline.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import argparse
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from os import path

‎scripts/place_seqs.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import argparse
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from picrust2.place_seqs import place_seqs_pipeline

‎scripts/print_picrust2_config.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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from sys import platform, version as python_version, executable
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‎scripts/shuffle_predictions.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import argparse
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from picrust2.util import check_files_exist, shuffle_predictions
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parser.add_argument('-s', '--seed', default=None, metavar='INT',
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required=False, type=int,
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help="Random seed: set this if you want reproducible "
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"shufflings (default: %(default)d).")
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"shufflings (default: None).")
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parser.add_argument('-v', '--version', default=False, action='version',
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version='%(prog)s ' + __version__)

‎setup.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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__maintainer__ = "Gavin Douglas"
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long_description = ("Please visit the google group here if you have questions: "

‎tests/test_hsp.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import unittest
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from os import path

‎tests/test_metagenome_pipeline.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import unittest
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from os import path

‎tests/test_pathway_pipeline.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import unittest
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import pandas as pd

‎tests/test_place_seqs.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import unittest
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import gzip

‎tests/test_util.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import unittest
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from os import path

‎tests/test_workflow.py

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__copyright__ = "Copyright 2018-2021, The PICRUSt Project"
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__license__ = "GPL"
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__version__ = "2.4.0"
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__version__ = "2.4.1"
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import unittest
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from os import path
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catch incompatabilities between the different scripts that the other tests
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might not catch.'''
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def test_help_calls(self):
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'''Quick test that help commands can be run for all scripts, which
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is a check that there are no obvious argparse syntax errors.'''
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system_call_check("add_descriptions.py -h")
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system_call_check("convert_table.py -h")
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system_call_check("hsp.py -h")
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system_call_check("metagenome_pipeline.py -h")
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system_call_check("picrust2_pipeline.py -h")
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system_call_check("place_seqs.py -h")
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system_call_check("print_picrust2_config.py -h")
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system_call_check("pathway_pipeline.py -h")
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system_call_check("shuffle_predictions.py -h")
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def test_full_pipeline_tsv(self):
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'''Test that full pipeline can be run without error with
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TSV sequence abundance table.'''

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