Merge branch 'master' into fix-fasta

Makefile

@@ -5,10 +5,9 @@ clean-test:
 	rm -rf cover/
 
 test: clean-test
-	nosetests --verbosity=2 -w tests
+	nosetests --verbosity=2 --with-coverage -w tests
 
-coverage: clean-test
-	coverage run --source=dataset_creator setup.py test
+coverage: test
 	coverage report -m
 	coverage html
 

README.rst

@@ -3,6 +3,7 @@
     :align: center
     :alt: Dataset-creator
 
+
 =========================================
 Dataset creator for phylogenetic software
 =========================================
@@ -12,7 +13,6 @@ Dataset creator for phylogenetic software
 
     * - tests
       - | |travis| |requires| |coveralls|
-        | |quantified-code|
     * - package
       - |version| |wheel| |supported-versions| |supported-implementations|
 
@@ -44,9 +44,6 @@ Dataset creator for phylogenetic software
     :alt: Supported implementations
     :target: https://pypi.python.org/pypi/dataset-creator
 
-.. |quantified-code| image:: https://www.quantifiedcode.com/api/v1/project/f059ab475f2547758722b80ea528c457/badge.svg
-  :target: https://www.quantifiedcode.com/app/project/f059ab475f2547758722b80ea528c457
-  :alt: Code issues
 
 Dataset-Creator - easy way to creat phylogenetic datasets in many formats
 =========================================================================

setup.py

@@ -4,7 +4,6 @@
 
 import io
 import re
-import sys
 from os.path import dirname
 from os.path import join
 
@@ -24,9 +23,6 @@ def read(*names, **kwargs):
     'six==1.10.0',
 ]
 
-if sys.version_info < (2, 7,):
-    required_libs.append('ordereddict==1.1')
-
 setup(
     name='dataset-creator',
     version='0.3.21',
@@ -45,12 +41,11 @@ def read(*names, **kwargs):
         'Operating System :: Unix',
         'Operating System :: POSIX',
         'Programming Language :: Python',
-        'Programming Language :: Python :: 2.6',
-        'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.3',
         'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: Implementation :: PyPy',
         'Topic :: Utilities',
     ],

tests/test_creator.py

@@ -1,4 +1,5 @@
 import unittest
+from copy import copy
 
 from .data import test_data
 from dataset_creator.dataset import Dataset
@@ -8,9 +9,13 @@
 class TestCreator(unittest.TestCase):
     def setUp(self):
         self.maxDiff = None
+        self.test_data = copy(test_data)
+
+    def tearDown(self):
+        self.test_data = None
 
     def test_nexus_header(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene')
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene')
         creator = Creator(dataset.data, format='NEXUS')
         expected = """
 #NEXUS
@@ -24,7 +29,7 @@ def test_nexus_header(self):
         self.assertEqual(expected.strip(), result)
 
     def test_nexus_dataset_block(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene')
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene')
         creator = Creator(dataset.data, format='NEXUS')
         expected = """
 [ArgKin]

tests/test_dataset.py

@@ -1,6 +1,7 @@
 import json
 import os
 import unittest
+from copy import copy
 
 from seqrecord_expanded import SeqRecordExpanded
 
@@ -15,6 +16,8 @@
 class TestDataset(unittest.TestCase):
     def setUp(self):
         self.maxDiff = None
+        self.test_data = copy(test_data)
+        self.test_data_numbers = get_test_data("sample_data_numbers.txt")
 
     def test_sorting_seq_records(self):
         """Test SeqRecordExpanded objects are sorted by gene_code and then by
@@ -61,113 +64,110 @@ def test_sorting_seq_records(self):
         self.assertEqual(expected, [i.voucher_code for i in result])
 
     def test_extract_genes(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene')
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene')
         expected = ['ArgKin', 'COI-begin', 'COI_end', 'ef1a', 'RpS2', 'RpS5', 'wingless']
         result = dataset.gene_codes
         self.assertEqual(expected, result)
 
     def test_extract_number_of_chars(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene')
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene')
         expected = '4739'
         result = dataset.number_chars
         self.assertEqual(expected, result)
 
     def test_extract_number_of_chars_wrong_argument(self):
         self.assertRaises(AttributeError,
-                          Dataset, test_data, format='NEXUS', partitioning='by gene',
+                          Dataset, self.test_data, format='NEXUS', partitioning='by gene',
                           codon_positions='5th position')
 
     def test_extract_number_of_chars_first_codon_positions(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene',
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene',
                           codon_positions='1st')
         expected = '1578'
         result = dataset.number_chars
         self.assertEqual(expected, result)
 
     def test_extract_number_of_chars_second_codon_positions(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene',
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene',
                           codon_positions='2nd')
         expected = '1577'
         result = dataset.number_chars
         self.assertEqual(expected, result)
 
     def test_extract_number_of_chars_third_codon_positions(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene',
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene',
                           codon_positions='3rd')
         expected = '1573'
         result = dataset.number_chars
         self.assertEqual(expected, result)
 
     def test_extract_number_of_chars_first_and_second_codon_positions(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene',
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene',
                           codon_positions='1st-2nd')
         expected = '3155'
         result = dataset.number_chars
         self.assertEqual(expected, result)
 
     def test_extract_number_of_taxa(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene')
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene')
         expected = '10'
         result = dataset.number_taxa
         self.assertEqual(expected, result)
 
     def test_prepared_data(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene')
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene')
         expected = ['ArgKin', 'COI-begin', 'COI_end', 'ef1a', 'RpS2', 'RpS5', 'wingless']
         result = dataset.data.gene_codes
         self.assertEqual(expected, result)
 
     def test_dataset_nexus(self):
-        dataset = Dataset(test_data, format='NEXUS', partitioning='by gene')
+        dataset = Dataset(self.test_data, format='NEXUS', partitioning='by gene')
         test_data_file = os.path.join(NEXUS_DATA_PATH, 'dataset.nex')
         expected = open(test_data_file, 'r').read()
         result = dataset.dataset_str
         self.assertEqual(expected.strip(), result)
 
     def test_dataset_nexus_using_default_parameters(self):
-        dataset = Dataset(test_data, format='NEXUS')
+        dataset = Dataset(self.test_data, format='NEXUS')
         test_data_file = os.path.join(NEXUS_DATA_PATH, 'dataset.nex')
         expected = open(test_data_file, 'r').read()
         result = dataset.dataset_str
         self.assertEqual(expected.strip(), result)
 
     def test_dataset_nexus_wrong_partitioning_parameter(self):
-        self.assertRaises(AttributeError, Dataset, seq_records=test_data, format='NEXUS',
+        self.assertRaises(AttributeError, Dataset, seq_records=self.test_data, format='NEXUS',
                           codon_positions='1st', partitioning='1st-2nd-3rd')
 
     def test_dataset_nexus_1st_codon_position(self):
-        test_data = get_test_data("sample_data_numbers.txt")
-        dataset = Dataset(test_data, format='NEXUS', codon_positions='1st', partitioning='by gene')
+        dataset = Dataset(self.test_data_numbers, format='NEXUS', codon_positions='1st', partitioning='by gene')
         test_data_file = os.path.join(NEXUS_DATA_PATH, 'dataset_1st_codon_numbers.nex')
         expected = open(test_data_file, 'r').read()
         result = dataset.dataset_str
         self.assertEqual(expected.strip(), result)
 
     def test_dataset_nexus_3rd_codon_position(self):
-        test_data = get_test_data("sample_data_numbers.txt")
-        dataset = Dataset(test_data, format='NEXUS', codon_positions='3rd', partitioning='by codon position')
+        dataset = Dataset(self.test_data_numbers, format='NEXUS', codon_positions='3rd', partitioning='by codon position')
         test_data_file = os.path.join(NEXUS_DATA_PATH, 'dataset_3rd_codon_numbers.nex')
         expected = open(test_data_file, 'r').read()
         result = dataset.dataset_str
         self.assertEqual(expected, result)
 
     def test_dataset_nexus_3rd_codon_position_partitioned_as_1st2nd_3rd(self):
-        test_data = get_test_data("sample_data_numbers.txt")
-        dataset = Dataset(test_data, format='NEXUS', codon_positions='3rd', partitioning='1st-2nd, 3rd')
+        dataset = Dataset(self.test_data_numbers, format='NEXUS', codon_positions='3rd', partitioning='1st-2nd, 3rd')
         test_data_file = os.path.join(NEXUS_DATA_PATH, 'dataset_3rd_codon_numbers.nex')
         expected = open(test_data_file, 'r').read()
         result = dataset.dataset_str
         self.assertEqual(expected.strip(), result)
 
     def test_dataset_nexus_all_codon_positions_partitioned_by_codon_positions(self):
-        dataset = Dataset(test_data, format='NEXUS', codon_positions='ALL', partitioning='by codon position')
+        dataset = Dataset(self.test_data, format='NEXUS', codon_positions='ALL', partitioning='by codon position')
         test_data_file = os.path.join(NEXUS_DATA_PATH, 'dataset_partitioned_as_each.nex')
         expected = open(test_data_file, 'r').read()
         result = dataset.dataset_str
         self.assertEqual(expected.strip(), result)
 
     def test_dataset_nexus_all_codon_positions_partitioned_as_1st2nd_3rd(self):
-        dataset = Dataset(test_data, format='NEXUS', codon_positions='ALL', partitioning='1st-2nd, 3rd')
+        dataset = Dataset(self.test_data, format='NEXUS', codon_positions='ALL', partitioning='1st-2nd, 3rd')
         test_data_file = os.path.join(NEXUS_DATA_PATH, 'dataset_partitioned_as_1st2nd_3rd.nex')
         expected = open(test_data_file, 'r').read()
         result = dataset.dataset_str
@@ -213,7 +213,7 @@ def test_degenerate(self):
         self.assertEqual(expected, result)
 
     def test_using_outgroup(self):
-        dataset = Dataset(test_data, format='NEXUS', codon_positions='ALL',
+        dataset = Dataset(self.test_data, format='NEXUS', codon_positions='ALL',
                           outgroup='CP100-19')
         expected = 'outgroup CP100_19_Aus_jus;'
         result = dataset.dataset_str

tests/test_nexus.py

@@ -1,4 +1,5 @@
 # -*- coding: UTF-8 -*-
+from copy import copy
 import json
 import os
 
@@ -43,7 +44,7 @@ def get_test_data(type_of_data=None, filename="sample_data.txt"):
 class TestNexus(unittest.TestCase):
     def setUp(self):
         self.maxDiff = None
-        self.seq_records = get_test_data('seq_records')
+        self.seq_records = copy(get_test_data('seq_records'))
 
     def tearDown(self):
         del self.seq_records