pdb-tools 2.4.12__py3-none-any.whl → 2.5.1__py3-none-any.whl

tests/test_pdb_wc.py

@@ -1,161 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Copyright 2018 João Pedro Rodrigues
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-"""
-Unit Tests for `pdb_wc`.
-"""
-
-import os
-import sys
-import unittest
-
-from config import data_dir
-from utils import OutputCapture
-
-
-class TestTool(unittest.TestCase):
-    """
-    Generic class for testing tools.
-    """
-
-    def setUp(self):
-        # Dynamically import the module
-        name = 'pdbtools.pdb_wc'
-        self.module = __import__(name, fromlist=[''])
-
-    def exec_module(self):
-        """
-        Execs module.
-        """
-
-        with OutputCapture() as output:
-            try:
-                self.module.main()
-            except SystemExit as e:
-                self.retcode = e.code
-
-        self.stdout = output.stdout
-        self.stderr = output.stderr
-
-        return
-
-    def test_default(self):
-        """$ pdb_wc data/dummy.pdb"""
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        sys.argv = ['', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 7)
-        self.assertEqual(len(self.stderr), 0)
-
-        self.assertEqual(self.stdout,
-                         ["No. models:\t1",
-                          "No. chains:\t4\t(   4.0/model)",
-                          "No. residues:\t10\t(  10.0/model)",
-                          "No. atoms:\t176\t( 176.0/model)",
-                          "No. HETATM:\t9",
-                          "Multiple Occ.:\tTrue",
-                          "Res. Inserts:\tFalse"])
-
-    def test_single_option_1(self):
-        """$ pdb_wc -m data/ensemble_OK.pdb"""
-
-        fpath = os.path.join(data_dir, 'ensemble_OK.pdb')
-        sys.argv = ['', '-m', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 2)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        self.assertEqual(self.stdout,
-                         ["No. models:\t2", "\t->\t1,2"])
-
-    def test_single_option_2(self):
-        """$ pdb_wc -c data/dummy.pdb"""
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        sys.argv = ['', '-c', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 2)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        self.assertEqual(self.stdout,
-                         ['No. chains:\t4\t(   4.0/model)', '\t->\tA,B,C,D'])
-
-    def test_file_not_found(self):
-        """$ pdb_wc not_existing.pdb"""
-
-        # Error (file not found)
-        afile = os.path.join(data_dir, 'not_existing.pdb')
-        sys.argv = ['', afile]
-
-        # Execute the script
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:22],
-                         "ERROR!! File not found")
-
-    @unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
-    def test_helptext(self):
-        """$ pdb_wc"""
-
-        sys.argv = ['']
-
-        # Execute the script
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr, self.module.__doc__.split("\n")[:-1])
-
-    def test_invalid_option(self):
-        """$ pdb_wc -X data/dummy.pdb"""
-
-        sys.argv = ['', '-X', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:36],
-                         "ERROR!! The following options are no")
-
-
-if __name__ == '__main__':
-    from config import test_dir
-
-    mpath = os.path.abspath(os.path.join(test_dir, '..'))
-    sys.path.insert(0, mpath)  # so we load dev files before  any installation
-
-    unittest.main()

tests/utils.py

@@ -1,56 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Copyright 2018 João Pedro Rodrigues
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-"""
-Utility classes/functions for the Tests.
-"""
-
-try:
-    from cStringIO import StringIO
-except ImportError:  # Py 3.x?
-    from io import StringIO
-
-import sys
-
-
-class OutputCapture(object):
-    """Context manager to capture output usually redirected to stdout.
-
-    Use as:
-    >>> with OutputCapture() as output:
-    >>> ....run_stuff()
-    >>> print(output)  # list with lines
-    """
-
-    def __enter__(self):
-        self.stdout = []
-        self.stderr = []
-
-        self._stdout = sys.stdout
-        self._stderr = sys.stderr
-        sys.stdout = self._stringout = StringIO()
-        sys.stderr = self._stringerr = StringIO()
-        return self
-
-    def __exit__(self, *args):
-
-        self.stdout.extend(self._stringout.getvalue().splitlines())
-        self.stderr.extend(self._stringerr.getvalue().splitlines())
-        del self._stringout    # free up some memory
-        del self._stringerr    # free up some memory
-        sys.stdout = self._stdout
-        sys.stderr = self._stderr