MAINT: lint, test setup

.coveragerc

@@ -0,0 +1,10 @@
+[run]
+branch = True
+omit =
+    */tests*
+    */__init__.py
+
+[report]
+omit =
+    */tests*
+    */__init__.py

.travis.yml

@@ -1,20 +1,24 @@
+dist: trusty
 sudo: false
 language: python
-env:
-  - PYTHON_VERSION=3.5
 before_install:
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=/home/travis/miniconda3/bin:$PATH
+  - export MPLBACKEND='Agg'
+  - wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - export MINICONDA_PREFIX="$HOME/miniconda"
+  - bash miniconda.sh -b -p $MINICONDA_PREFIX
+  - export PATH="$MINICONDA_PREFIX/bin:$PATH"
+  - conda config --set always_yes yes
+  - conda update -q conda
+  - conda info -a
 install:
-  # q2-dummy-types is only required for the dummy methods and
-  # visualizers provided as examples. Remove this dependency when you're
-  # ready to develop your plugin, and add your own dependencies (if there are
-  # any).
-  - conda create --yes -n test-env -c qiime2 python=$PYTHON_VERSION qiime nose flake8
+  - conda create -q -n test-env --file https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-conda-linux-64.txt
   - source activate test-env
-  - pip install .
+  - conda install -q pytest-cov
+  - pip install -q flake8 coveralls
+  - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
+  - make install
 script:
-  - nosetests
-  - flake8 q2_vsearch setup.py
+  - make lint
+  - make test-cov
+after_success:
+  - coveralls

LICENSE

@@ -1,4 +1,6 @@
-Copyright (c) 2016, QIIME 2 Development Team
+BSD 3-Clause License
+
+Copyright (c) 2016-2017, QIIME 2 development team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -11,7 +13,7 @@ modification, are permitted provided that the following conditions are met:
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 
-* Neither the name of qiime2 nor the names of its
+* Neither the name of the copyright holder nor the names of its
   contributors may be used to endorse or promote products derived from
   this software without specific prior written permission.
 

Makefile

@@ -0,0 +1,23 @@
+.PHONY: all lint test test-cov install dev clean distclean
+
+all: ;
+
+lint:
+	q2lint
+	flake8
+
+test: all
+	py.test
+
+test-cov: all
+	py.test --cov=q2_vsearch
+
+install: all
+	python setup.py install
+
+dev: all
+	pip install -e .
+
+clean: distclean
+
+distclean: ;

q2_vsearch/__init__.py

@@ -1 +1,9 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2017, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
 __version__ = "0.0.7.dev0"

q2_vsearch/_cluster_features.py

@@ -1,3 +1,10 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2017, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
 
 import tempfile
 import subprocess
@@ -6,6 +13,7 @@
 import skbio
 from q2_types.feature_data import DNAFASTAFormat
 
+
 def run_command(cmd, verbose=True):
     print("Running external command line application. This may print "
           "messages to stdout and/or stderr.")
@@ -16,6 +24,7 @@ def run_command(cmd, verbose=True):
     print(" ".join(cmd), end='\n\n')
     subprocess.run(cmd, check=True)
 
+
 def _collapse_f_from_uc(uc):
     id_to_centroid = {}
     for line in uc:
@@ -44,6 +53,7 @@ def collapse_f(id_, x):
 
     return collapse_f
 
+
 def cluster_features_denovo(sequences: DNAFASTAFormat, table: biom.Table,
                             id: float) -> (biom.Table, DNAFASTAFormat):
     sequences_fp = str(sequences)

q2_vsearch/plugin_setup.py

@@ -1,8 +1,16 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2017, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
 import qiime2.plugin
 
 import q2_vsearch
 import q2_vsearch._cluster_features
-from q2_types.feature_data import DNAFASTAFormat, FeatureData, Sequence
+from q2_types.feature_data import FeatureData, Sequence
 from q2_types.feature_table import FeatureTable, Frequency
 
 plugin = qiime2.plugin.Plugin(
@@ -28,14 +36,14 @@
         ('clustered_table', FeatureTable[Frequency]),
         ('clustered_sequences', FeatureData[Sequence]),
     ],
-    input_descriptions = {
+    input_descriptions={
         'table': 'The feature table to be clustered.',
         'sequences': 'The sequences corresponding to the features in table.',
     },
-    parameter_descriptions = {
+    parameter_descriptions={
         'id': 'The percent identity at which clustering should be performed.',
     },
-    output_descriptions = {
+    output_descriptions={
         'clustered_table': 'The table following clustering of features.',
         'clustered_sequences': 'Sequences representing clustered features.',
     },
@@ -54,6 +62,5 @@
                  'were clustered in that sample. Feature identifiers and '
                  'sequences will be inherited from the centroid feature '
                  'of each cluster. See the vsearch documentation for details '
-                 'on how sequence clustering is performed.'
-                )
+                 'on how sequence clustering is performed.')
 )

q2_vsearch/tests/test_cluster_features.py

@@ -7,12 +7,9 @@
 # ----------------------------------------------------------------------------
 
 import os
-import unittest
 import skbio
-import subprocess
 import biom
 import numpy as np
-import pandas as pd
 
 from qiime2.plugin.testing import TestPluginBase
 from qiime2.util import redirected_stdio
@@ -41,13 +38,13 @@ def test_no_clustering(self):
         # order of identifiers is important for biom.Table equality
         obs_table = \
             obs_table.sort_order(input_table.ids(axis='observation'),
-                                       axis='observation')
+                                 axis='observation')
         self.assertEqual(obs_table, input_table)
 
         obs_seqs = list(skbio.io.read(str(obs_sequences),
-                        constructor=skbio.DNA, format='fasta'))
+                                      constructor=skbio.DNA, format='fasta'))
         exp_seqs = list(skbio.io.read(str(input_sequences),
-                        constructor=skbio.DNA, format='fasta'))
+                                      constructor=skbio.DNA, format='fasta'))
         print(obs_seqs)
         print(exp_seqs)
         self.assertEqual(obs_seqs, exp_seqs)

q2_vsearch/tests/test_plugin_setup.py

@@ -0,0 +1,17 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2017, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import unittest
+
+from q2_vsearch.plugin_setup import plugin as vsearch_plugin
+
+
+class PluginSetupTests(unittest.TestCase):
+
+    def test_plugin_setup(self):
+        self.assertEqual(vsearch_plugin.name, 'vsearch')

setup.py

@@ -1,3 +1,11 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2017, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
 from setuptools import setup, find_packages
 import re
 import ast