<commit_before>#!/usr/bin/env python

from setuptools import setup

# Explicitly list bin scripts to be installed, seeing as I have a few local
# bin files that are not (yet) part of the distribution.
scripts = [
    'bin/aa-info.py',
    'bin/aa-to-properties.py',
    'bin/adaptor-distances.py',
    'bin/alignments-per-read.py',
    'bin/bit-score-to-e-value.py',
    'bin/cat-json-blast-records.py',
    'bin/check-fasta-json-blast-consistency.py',
    'bin/codon-distance.py',
    'bin/convert-blast-xml-to-json.py',
    'bin/convert-diamond-to-json.py',
    'bin/convert-sam-to-fastq.sh',
    'bin/dna-to-aa.py',
    'bin/e-value-to-bit-score.py',
    'bin/extract-ORFs.py',
    'bin/fasta-base-indices.py',
    'bin/fasta-lengths.py',
    'bin/fasta-subset.py',
    'bin/fasta-subtraction.py',
    'bin/fasta-to-phylip.py'
    'bin/filter-fasta-by-complexity.py',
    'bin/filter-fasta-by-taxonomy.py',
    'bin/filter-fasta.py',
    'bin/filter-hits-to-fasta.py',
    'bin/find-hits.py',
    'bin/get-features.py',
    'bin/get-reads.py',
    'bin/graph-evalues.py',
    'bin/local-align.py',
    'bin/noninteractive-alignment-panel.py',
    'bin/position-summary.py',
    'bin/pre-commit.sh',
    'bin/print-blast-xml-for-derek.py',
    'bin/print-blast-xml.py',
    'bin/print-read-lengths.py',
    'bin/proteins-to-viruses.py',
    'bin/randomize-fasta.py',
    'bin/read-blast-json.py',
    'bin/read-blast-xml.py',
    'bin/sff-to-fastq.py',
    'bin/split-fasta-by-adaptors.py',
    'bin/summarize-fasta-bases.py',
    'bin/summarize-reads.py',
    'bin/trim-primers.py',
    'bin/trim-reads.py',
    'bin/write-htcondor-job-spec.py',
]

setup(name='dark-matter',
      version='1.0.97',
      packages=['dark', 'dark.blast', 'dark.diamond'],
      include_package_data=True,
      url='https://github.com/acorg/dark-matter',
      download_url='https://github.com/acorg/dark-matter',
      author='<NAME>, <NAME>, <NAME>',
      author_email='<EMAIL>',
      keywords=['virus discovery'],
      classifiers=[
          'Programming Language :: Python :: 2.7',
          'Programming Language :: Python :: 3',<commit_msg>Added missing comma in setup.py.<commit_after>#!/usr/bin/env python

from setuptools import setup

# Explicitly list bin scripts to be installed, seeing as I have a few local
# bin files that are not (yet) part of the distribution.
scripts = [
    'bin/aa-info.py',
    'bin/aa-to-properties.py',
    'bin/adaptor-distances.py',
    'bin/alignments-per-read.py',
    'bin/bit-score-to-e-value.py',
    'bin/cat-json-blast-records.py',
    'bin/check-fasta-json-blast-consistency.py',
    'bin/codon-distance.py',
    'bin/convert-blast-xml-to-json.py',
    'bin/convert-diamond-to-json.py',
    'bin/convert-sam-to-fastq.sh',
    'bin/dna-to-aa.py',
    'bin/e-value-to-bit-score.py',
    'bin/extract-ORFs.py',
    'bin/fasta-base-indices.py',
    'bin/fasta-lengths.py',
    'bin/fasta-subset.py',
    'bin/fasta-subtraction.py',
    'bin/fasta-to-phylip.py',
    'bin/filter-fasta-by-complexity.py',
    'bin/filter-fasta-by-taxonomy.py',
    'bin/filter-fasta.py',
    'bin/filter-hits-to-fasta.py',
    'bin/find-hits.py',
    'bin/get-features.py',
    'bin/get-reads.py',
    'bin/graph-evalues.py',
    'bin/local-align.py',
    'bin/noninteractive-alignment-panel.py',
    'bin/position-summary.py',
    'bin/pre-commit.sh',
    'bin/print-blast-xml-for-derek.py',
    'bin/print-blast-xml.py',
    'bin/print-read-lengths.py',
    'bin/proteins-to-viruses.py',
    'bin/randomize-fasta.py',
    'bin/read-blast-json.py',
    'bin/read-blast-xml.py',
    'bin/sff-to-fastq.py',
    'bin/split-fasta-by-adaptors.py',
    'bin/summarize-fasta-bases.py',
    'bin/summarize-reads.py',
    'bin/trim-primers.py',
    'bin/trim-reads.py',
    'bin/write-htcondor-job-spec.py',
]

setup(name='dark-matter',
      version='1.0.98',
      packages=['dark', 'dark.blast', 'dark.diamond'],
      include_package_data=True,
      url='https://github.com/acorg/dark-matter',
      download_url='https://github.com/acorg/dark-matter',
      author='<NAME>, <NAME>, <NAME>',
      author_email='<EMAIL>',
      keywords=['virus discovery'],
      classifiers=[
          'Programming Language :: Python :: 2.7',
          'Programming Language :: Python :: 3',
{'fraction_non_alphanumeric': 0.19696969696969696, 'fraction_numerical': 0.0032634032634032634, 'mean_word_length': 2.773966578715919, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 11, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 8}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6103554', 'n_tokens_mistral': 1746, 'n_tokens_neox': 1686, 'n_words': 201}