Changed to cmayes and modified test files to read from a base dir bas…

…ed on the test file's location.

AUTHORS.rst

@@ -5,9 +5,9 @@ Credits
 Development Lead
 ----------------
 
-* Heather Mayes <hmayes@hmayes.com>
+* Chris Mayes <cmayes@cmayes.com>
 
 Contributors
 ------------
 
-* Chris Mayes <cmayes@cmayes.com>
+* Heather Mayes <hmayes@hmayes.com>

CONTRIBUTING.rst

@@ -13,7 +13,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/hmayes/md_utils/issues.
+Report bugs at https://github.com/cmayes/md_utils/issues.
 
 If you are reporting a bug, please include:
 
@@ -43,7 +43,7 @@ articles, and such.
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/hmayes/md_utils/issues.
+The best way to send feedback is to file an issue at https://github.com/cmayes/md_utils/issues.
 
 If you are proposing a feature:
 
@@ -100,7 +100,7 @@ Before you submit a pull request, check that it meets these guidelines:
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
 3. The pull request should work for Python 2.6, 2.7, 3.3, and 3.4, and for PyPy. Check
-   https://travis-ci.org/hmayes/md_utils/pull_requests
+   https://travis-ci.org/cmayes/md_utils/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
 Tips
@@ -109,3 +109,4 @@ Tips
 To run a subset of tests::
 
     $ python -m unittest tests.test_md_utils
+

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015, Heather Mayes
+Copyright (c) 2015, Chris Mayes
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

README.rst

@@ -2,8 +2,8 @@
 MD Utilities
 ============
 
-.. image:: https://img.shields.io/travis/hmayes/md_utils.svg
-        :target: https://travis-ci.org/hmayes/md_utils
+.. image:: https://img.shields.io/travis/cmayes/md_utils.svg
+        :target: https://travis-ci.org/cmayes/md_utils
 
 .. image:: https://img.shields.io/pypi/v/md_utils.svg
         :target: https://pypi.python.org/pypi/md_utils

docs/conf.py

@@ -56,7 +56,7 @@
 
 # General information about the project.
 project = u'MD Utilities'
-copyright = u'2015, Heather Mayes'
+copyright = u'2015, Chris Mayes'
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -210,7 +210,7 @@
 latex_documents = [
     ('index', 'md_utils.tex',
      u'MD Utilities Documentation',
-     u'Heather Mayes', 'manual'),
+     u'Chris Mayes', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at
@@ -241,7 +241,7 @@
 man_pages = [
     ('index', 'md_utils',
      u'MD Utilities Documentation',
-     [u'Heather Mayes'], 1)
+     [u'Chris Mayes'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -256,7 +256,7 @@
 texinfo_documents = [
     ('index', 'md_utils',
      u'MD Utilities Documentation',
-     u'Heather Mayes',
+     u'Chris Mayes',
      'md_utils',
      'One line description of project.',
      'Miscellaneous'),

md_utils/__init__.py

@@ -3,6 +3,6 @@
 Molecular dynamics utilities.
 """
 
-__author__ = 'Heather Mayes'
-__email__ = '[email protected]'
+__author__ = 'Chris Mayes'
+__email__ = '[email protected]'
 __version__ = '0.3.0'

setup.py

@@ -27,9 +27,9 @@
     version=md_utils.__version__,
     description="Utility scripts for MD data",
     long_description=readme + '\n\n' + history,
-    author="Heather Mayes",
-    author_email='hmayes@hmayes.com',
-    url='https://github.com/hmayes/md_utils',
+    author="Chris Mayes",
+    author_email='cmayes@cmayes.com',
+    url='https://github.com/cmayes/md_utils',
     packages=[
         'md_utils',
     ],

tests/test_calc_pka.py

@@ -22,7 +22,7 @@
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger('test_calc_pka')
 
-DATA_DIR = 'test_data'
+DATA_DIR = os.path.join(os.path.dirname(__file__), 'test_data')
 PKA_DATA_DIR = os.path.join(DATA_DIR, 'calc_pka')
 GOOD_RAD_PATH = os.path.join(PKA_DATA_DIR, 'rad_PMFlast2ns3_1.txt')
 NO_MAX_RAD_PATH = os.path.join(PKA_DATA_DIR, 'rad_no_max.txt')

tests/test_calc_split_avg.py

@@ -15,7 +15,7 @@
 
 BINNED_FILES = {'02': ['rad_PMF.02_01', 'rad_PMF.02_02', 'rad_PMF.02_03'], '01': ['rad_PMF.01_02', 'rad_PMF.01_01']}
 
-DATA_DIR = os.path.join('test_data', 'post_rad_wham')
+DATA_DIR = os.path.join(os.path.dirname(__file__), 'test_data', 'post_rad_wham')
 
 INFILES = [os.path.join(DATA_DIR, radf) for radf in ['rad_PMF.02_01', 'rad_PMF.02_02', 'rad_PMF.02_03']]
 

tests/test_common.py

@@ -22,7 +22,7 @@
 
 
 # Constants #
-DATA_DIR = 'test_data'
+DATA_DIR = os.path.join(os.path.dirname(__file__), 'test_data')
 FES_OUT_DIR = 'fes_out'
 CALC_PKA_DIR = 'calc_pka'
 CSV_FILE = os.path.join(DATA_DIR, CALC_PKA_DIR, 'rad_PMFlast2ns3_1.txt')

tests/test_fes_combo.py

@@ -1,3 +1,5 @@
+# coding=utf-8
+
 import logging
 import os
 import unittest
@@ -12,7 +14,7 @@
 logger = logging.getLogger('test_fes_combo')
 logger.setLevel(logging.INFO)
 
-DATA_DIR = 'test_data'
+DATA_DIR = os.path.join(os.path.dirname(__file__), 'test_data')
 FES_OUT_DIR = 'fes_out'
 FES_ALL_DIR = 'fes_all'
 FES_MULTI_DIR = 'multi'
@@ -33,6 +35,7 @@
 # Target writers #
 FES_ALL_MULTI_FILE = os.path.join(FES_OUT_BASE, FES_MULTI_DIR, DEF_TGT)
 
+
 def header_lines(tgt_file):
     """
     Extracts and returns a list of the header lines from the given file location.
@@ -53,11 +56,13 @@ def header_lines(tgt_file):
                 hlines.append(tline)
         return hlines
 
+
 # Tests #
 class TestFesCombo(unittest.TestCase):
     """
     Tests for the functions in fes_combo.
     """
+
     def test_single(self):
         test_dict = find_files_by_dir(FES_OUT_SINGLE, DEF_FILE_PAT)
         self.assertEqual(1, len(test_dict))

tests/test_wham.py

@@ -31,7 +31,7 @@
 SUB_WHAM_BASE_TPL = os.path.join(TPL_LOC, DEF_BASE_SUBMIT_TPL)
 SUB_WHAM_LINE_TPL = os.path.join(TPL_LOC, DEF_LINE_SUBMIT_TPL)
 
-DATA_DIR = os.path.join('test_data', 'wham_test_data')
+DATA_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), 'test_data', 'wham_test_data'))
 META_00_FNAME = 'meta.00'
 META_PATH = os.path.join(DATA_DIR, META_00_FNAME)
 SUBMIT_05_PATH = os.path.join(DATA_DIR, 'submit_wham_05.sh')

tests/test_wham_rad.py

@@ -25,7 +25,7 @@
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger('test_wham_rad')
 
-DATA_DIR = 'test_data'
+DATA_DIR = os.path.join(os.path.dirname(__file__), 'test_data')
 
 ORIG_WHAM_FNAME = "PMFlast2ns3_1.txt"
 ORIG_WHAM_PATH = os.path.join(DATA_DIR, ORIG_WHAM_FNAME)