One hot encoder

tests/driver_tests.py

@@ -0,0 +1,172 @@
+# -*- coding: utf-8 -*-
+
+"""Copyright 2015-Present Randal S. Olson.
+
+This file is part of the TPOT library.
+
+TPOT is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as
+published by the Free Software Foundation, either version 3 of
+the License, or (at your option) any later version.
+
+TPOT is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with TPOT. If not, see <http://www.gnu.org/licenses/>.
+
+"""
+
+import subprocess
+import sys
+from contextlib import contextmanager
+try:
+    from StringIO import StringIO
+except ImportError:
+    from io import StringIO
+
+import numpy as np
+
+from tpot.driver import positive_integer, float_range, _get_arg_parser, _print_args, _read_data_file
+from nose.tools import assert_raises
+from unittest import TestCase
+
+
+@contextmanager
+def captured_output():
+    new_out, new_err = StringIO(), StringIO()
+    old_out, old_err = sys.stdout, sys.stderr
+    try:
+        sys.stdout, sys.stderr = new_out, new_err
+        yield sys.stdout, sys.stderr
+    finally:
+        sys.stdout, sys.stderr = old_out, old_err
+
+
+def test_driver():
+    """Assert that the TPOT driver outputs normal result in mode mode."""
+    batcmd = "python -m tpot.driver tests/tests.csv -is , -target class -g 2 -p 2 -os 4 -cv 5 -s 45 -v 1"
+    ret_stdout = subprocess.check_output(batcmd, shell=True)
+    try:
+        ret_val = float(ret_stdout.decode('UTF-8').split('\n')[-2].split(': ')[-1])
+    except Exception:
+        ret_val = -float('inf')
+    assert ret_val > 0.0
+
+
+def test_read_data_file():
+    """Assert that _read_data_file raises ValueError when the targe column is missing."""
+    # Mis-spelled target
+    args_list = [
+        'tests/tests.csv',
+        '-is', ',',
+        '-target', 'clas'   # typo for right target 'class'
+    ]
+    args = _get_arg_parser().parse_args(args_list)
+    assert_raises(ValueError, _read_data_file, args=args)
+
+    # Correctly spelled target
+    args_list = [
+        'tests/tests.csv',
+        '-is', ',',
+        '-target', 'class'
+    ]
+    args = _get_arg_parser().parse_args(args_list)
+    input_data = _read_data_file(args)
+
+    assert isinstance(input_data, np.recarray)
+
+
+class ParserTest(TestCase):
+    def setUp(self):
+        self.parser = _get_arg_parser()
+
+    def test_default_param(self):
+        """Assert that the TPOT driver stores correct default values for all parameters."""
+        args = self.parser.parse_args(['tests/tests.csv'])
+        self.assertEqual(args.CROSSOVER_RATE, 0.1)
+        self.assertEqual(args.DISABLE_UPDATE_CHECK, False)
+        self.assertEqual(args.GENERATIONS, 100)
+        self.assertEqual(args.INPUT_FILE, 'tests/tests.csv')
+        self.assertEqual(args.INPUT_SEPARATOR, '\t')
+        self.assertEqual(args.MAX_EVAL_MINS, 5)
+        self.assertEqual(args.MUTATION_RATE, 0.9)
+        self.assertEqual(args.NUM_CV_FOLDS, 5)
+        self.assertEqual(args.NUM_JOBS, 1)
+        self.assertEqual(args.OFFSPRING_SIZE, None)
+        self.assertEqual(args.OUTPUT_FILE, '')
+        self.assertEqual(args.POPULATION_SIZE, 100)
+        self.assertEqual(args.RANDOM_STATE, None)
+        self.assertEqual(args.SUBSAMPLE, 1.0)
+        self.assertEqual(args.SCORING_FN, None)
+        self.assertEqual(args.TARGET_NAME, 'class')
+        self.assertEqual(args.TPOT_MODE, 'classification')
+        self.assertEqual(args.VERBOSITY, 1)
+
+    def test_print_args(self):
+        """Assert that _print_args prints correct values for all parameters."""
+        args = self.parser.parse_args(['tests/tests.csv'])
+        with captured_output() as (out, err):
+            _print_args(args)
+        output = out.getvalue()
+        expected_output = """
+TPOT settings:
+CONFIG_FILE\t=\tNone
+CROSSOVER_RATE\t=\t0.1
+GENERATIONS\t=\t100
+INPUT_FILE\t=\ttests/tests.csv
+INPUT_SEPARATOR\t=\t\t
+MAX_EVAL_MINS\t=\t5
+MAX_TIME_MINS\t=\tNone
+MUTATION_RATE\t=\t0.9
+NUM_CV_FOLDS\t=\t5
+NUM_JOBS\t=\t1
+OFFSPRING_SIZE\t=\t100
+OUTPUT_FILE\t=\t
+POPULATION_SIZE\t=\t100
+RANDOM_STATE\t=\tNone
+SCORING_FN\t=\taccuracy
+SUBSAMPLE\t=\t1.0
+TARGET_NAME\t=\tclass
+TPOT_MODE\t=\tclassification
+VERBOSITY\t=\t1
+
+"""
+
+        self.assertEqual(_sort_lines(expected_output), _sort_lines(output))
+
+
+def _sort_lines(text):
+    return '\n'.join(sorted(text.split('\n')))
+
+
+def test_positive_integer():
+    """Assert that the TPOT CLI interface's integer parsing throws an exception when n < 0."""
+    assert_raises(Exception, positive_integer, '-1')
+
+
+def test_positive_integer_2():
+    """Assert that the TPOT CLI interface's integer parsing returns the integer value of a string encoded integer when n > 0."""
+    assert 1 == positive_integer('1')
+
+
+def test_positive_integer_3():
+    """Assert that the TPOT CLI interface's integer parsing throws an exception when n is not an integer."""
+    assert_raises(Exception, positive_integer, 'foobar')
+
+
+def test_float_range():
+    """Assert that the TPOT CLI interface's float range returns a float with input is in 0. - 1.0."""
+    assert 0.5 == float_range('0.5')
+
+
+def test_float_range_2():
+    """Assert that the TPOT CLI interface's float range throws an exception when input it out of range."""
+    assert_raises(Exception, float_range, '2.0')
+
+
+def test_float_range_3():
+    """Assert that the TPOT CLI interface's float range throws an exception when input is not a float."""
+    assert_raises(Exception, float_range, 'foobar')