Merge 6e82c33 into 2b97849

.coveragerc

@@ -0,0 +1,11 @@
+[report]
+omit = 
+    */python?.?/*
+    */*/tests/*
+    */mdtraj/*
+    */setup.py
+    */version.py
+exclude_lines = 
+    pragma: no cover
+    def __repr__
+    raise NotImplementedError

.travis.yml

@@ -0,0 +1,32 @@
+language: python
+
+python:
+    - "2.7"
+    - "3.4"
+    - "3.5"
+    - "3.6"
+    #- "3.7-dev"  # need to do custom requirements install for this
+
+env:
+    - MDTRAJ="release"
+    - MDTRAJ="dev"
+
+matrix:
+    exclude:  # don't run MDTRAJ dev for everything
+        - env: MDTRAJ="dev"
+          python: "3.4"
+        - env: MDTRAJ="dev"
+          python: "3.5"
+
+install:
+    - source ci/pip-install/install.sh
+    - pip install -r ci/pip-install/testing_requirements.txt
+    - if [ "$MDTRAJ" = "dev" ]; then pip install --upgrade --force-reinstall -r ci/pip-install/mdtraj_dev.txt; fi
+    - pip list
+
+script:
+    - py.test -vv --cov=contact_map
+
+after_success:
+    - coveralls
+

MANIFEST.in

@@ -0,0 +1 @@
+include contact_map/tests/trajectory.pdb

appveyor.yml

@@ -0,0 +1,43 @@
+# See also:
+# https://github.com/ogrisel/python-appveyor-demo/blob/master/appveyor.yml
+
+branches:
+  only:
+    - master
+
+max_jobs: 4
+
+environment:
+  global:
+    CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\ci\\appveyor\\run_with_env.cmd"
+    PYTHONUNBUFFERED: 1
+
+  matrix:
+    - PYTHON: "C:\\Miniconda"
+      CONDA_PY: "27"
+      ARCH: "32"
+    - PYTHON: "C:\\Miniconda-x64"
+      CONDA_PY: "27"
+      ARCH: "64"
+    - PYTHON: "C:\\Miniconda36"
+      CONDA_PY: "36"
+      ARCH: "32"
+    - PYTHON: "C:\\Miniconda36-x64"
+      CONDA_PY: "36"
+      ARCH: "64"
+
+build: false
+
+install:
+  # install python
+  - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%
+  # test python version
+  - "%CMD_IN_ENV% conda config --add channels omnia"  # TODO: switch to conda-forge?
+  - "%CMD_IN_ENV% conda update -yq --all"
+  - "%CMD_IN_ENV% conda install -yq conda-build"
+  - "%CMD_IN_ENV% python --version"
+  - "%CMD_IN_ENV% python -c \"import struct; print(struct.calcsize('P') * 8)\""
+  # now we do our own install
+
+test_script:
+  - "%CMD_IN_ENV% conda build --quiet ci\\conda-recipe"

ci/appveyor/run_with_env.cmd

@@ -0,0 +1,51 @@
+:: To build extensions for 64 bit Python 3, we need to configure environment
+:: variables to use the MSVC 2010 C++ compilers from GRMSDKX_EN_DVD.iso of:
+:: MS Windows SDK for Windows 7 and .NET Framework 4 (SDK v7.1)
+::
+:: To build extensions for 64 bit Python 2, we need to configure environment
+:: variables to use the MSVC 2008 C++ compilers from GRMSDKX_EN_DVD.iso of:
+:: MS Windows SDK for Windows 7 and .NET Framework 3.5 (SDK v7.0)
+::
+:: 32 bit builds do not require specific environment configurations.
+::
+:: Note: this script needs to be run with the /E:ON and /V:ON flags for the
+:: cmd interpreter, at least for (SDK v7.0)
+::
+:: More details at:
+:: https://github.com/cython/cython/wiki/64BitCythonExtensionsOnWindows
+:: http://stackoverflow.com/a/13751649/163740
+::
+:: Author: Olivier Grisel
+:: License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+
+:: Modified for use with conda environment variables
+:: Taken from mdtraj
+
+@ECHO OFF
+
+SET COMMAND_TO_RUN=%*
+SET WIN_SDK_ROOT=C:\Program Files\Microsoft SDKs\Windows
+
+SET MAJOR_PYTHON_VERSION="%CONDA_PY:~0,1%"
+IF %MAJOR_PYTHON_VERSION% == "2" (
+    SET WINDOWS_SDK_VERSION="v7.0"
+) ELSE IF %MAJOR_PYTHON_VERSION% == "3" (
+    SET WINDOWS_SDK_VERSION="v7.1"
+) ELSE (
+    ECHO Unsupported Python version: "%MAJOR_PYTHON_VERSION%"
+    EXIT 1
+)
+
+IF "%ARCH%"=="64" (
+    ECHO Configuring Windows SDK %WINDOWS_SDK_VERSION% for Python %MAJOR_PYTHON_VERSION% on a 64 bit architecture
+    SET DISTUTILS_USE_SDK=1
+    SET MSSdk=1
+    "%WIN_SDK_ROOT%\%WINDOWS_SDK_VERSION%\Setup\WindowsSdkVer.exe" -q -version:%WINDOWS_SDK_VERSION%
+    "%WIN_SDK_ROOT%\%WINDOWS_SDK_VERSION%\Bin\SetEnv.cmd" /x64 /release
+    ECHO Executing: %COMMAND_TO_RUN%
+    call %COMMAND_TO_RUN% || EXIT 1
+) ELSE (
+    ECHO Using default MSVC build environment for 32 bit architecture
+    ECHO Executing: %COMMAND_TO_RUN%
+    call %COMMAND_TO_RUN% || EXIT 1
+)

ci/conda-recipe/meta.yaml

@@ -0,0 +1,47 @@
+package:
+  name: contact_map
+  version: "0.1.0"
+
+source:
+  path: ../../
+
+build:
+  preserve_egg_dir: True
+  number: 0
+  script: python setup.py install --single-version-externally-managed --record record.txt
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - mdtraj
+    - numpy
+    - scipy
+    - pandas
+
+  run:
+    - python
+    - mdtraj
+    - numpy
+    - scipy
+    - pandas
+
+test:
+  requires:
+    - pytest
+    #- pytest-cov
+    #- python-coveralls
+
+  source_files:
+    - contact_map/tests/*
+
+  imports:
+    - contact_map
+
+  commands:
+    - py.test -vv
+
+about:
+  home: https://github.com/dwhswenson/contact_map
+  license: LGPL-2.1 or later
+  summary: "Contact maps based on MDTraj"

ci/pip-install/install.sh

@@ -0,0 +1,5 @@
+pip install --upgrade pip
+pip install cython  # may be required for numpy override?
+pip install --upgrade --force-reinstall numpy  # override Travis numpy
+pip install -r requirements.txt
+pip install .

ci/pip-install/mdtraj_dev.txt

@@ -0,0 +1 @@
+git+https://github.com/mdtraj/mdtraj.git

ci/pip-install/testing_requirements.txt

@@ -0,0 +1,3 @@
+pytest
+pytest-cov
+python-coveralls

contact_map/__init__.py

@@ -1,7 +1,7 @@
-from contact_map import (
+from .contact_map import (
     ContactMap, ContactFrequency, ContactDifference
 )
 
-from min_dist import NearestAtoms, MinimumDistanceCounter
+from .min_dist import NearestAtoms, MinimumDistanceCounter
 
 # import concurrence

contact_map/contact_map.py

@@ -115,16 +115,17 @@ def save_to_file(self, filename, mode="w"):
         filename : string
             the file to write to
         mode : 'w' or 'a'
-            file writing mode. Use 'w' to overwrite, 'a' to append.
+            file writing mode. Use 'w' to overwrite, 'a' to append. Note
+            that writing by bytes ('b' flag) is automatically added.
         """
-        f = open(filename, mode)
-        pickle.dump(self, f)
-        f.close()
+        with open(filename, mode+"b") as f:
+            pickle.dump(self, f)
 
     @classmethod
     def from_file(cls, filename):
-        f = open(filename, "r")
-        return pickle.load(f)
+        with open(filename, "rb") as f:
+            reloaded = pickle.load(f)
+        return reloaded
 
     def __sub__(self, other):
         return ContactDifference(positive=self, negative=other)

contact_map/tests/test_contact_map.py

@@ -5,11 +5,12 @@
 import numpy as np
 from numpy.testing import assert_array_equal
 import mdtraj as md
+from .utils import *
 
 # stuff to be testing in this file
 from contact_map.contact_map import *
 
-traj = md.load("./trajectory.pdb")
+traj = md.load(test_file("trajectory.pdb"))
 
 traj_atom_contact_count = {
     frozenset([0, 8]): 1,

contact_map/tests/utils.py

@@ -0,0 +1,6 @@
+import os
+from pkg_resources import resource_filename
+
+def test_file(fname):
+    return resource_filename('contact_map', os.path.join('tests', fname))
+

requirements.txt

@@ -0,0 +1,5 @@
+future
+numpy
+scipy
+pandas
+mdtraj

setup.py

@@ -11,10 +11,20 @@
 
 ##########################
 VERSION = "0.1.0"
-ISRELEASED = True
+ISRELEASED = False
 __version__ = VERSION
+PACKAGE_VERSION = VERSION
+REQUIREMENTS=['future', 'numpy', 'mdtraj', 'scipy', 'pandas']
 ##########################
 
+DESCRIPTION="""
+Contact maps based on MDTraj; useful for studying for intramolecular and
+intermolecular contacts from simulations of biomolecular systems. For a
+more detailed description, see package's documentation.
+"""
+if os.path.isfile('README.rst'):
+    DESCRIPTION = open('README.rst').read()
+
 ################################################################################
 # Writing version control information to the module
 ################################################################################
@@ -84,46 +94,37 @@ def write_version_py(filename='contact_map/version.py'):
 
 write_version_py()
 
-def buildKeywordDictionary():
-    # from distutils.core import Extension
-    setupKeywords = {}
-    setupKeywords["name"]              = "contact_map"
-    setupKeywords["version"]           = "0.1.0"
-    setupKeywords["author"]            = "David W.H. Swenson"
-    setupKeywords["author_email"]      = "dwhs@hyperblazer.net"
-    setupKeywords["license"]           = "LGPL 2.1 of greater"
-    setupKeywords["download_url"]      = "http://github.com/dwhswenson/contact_map"
-    setupKeywords["packages"]          = ['contact_map',
-                                          'contact_map.tests']
-    setupKeywords["package_dir"]       = {
-        'contact_map' : 'contact_map',
-        'contact_map.tests' : 'contact_map/tests'
-    }
-    setupKeywords["data_files"]        = []
-    setupKeywords["ext_modules"]       = []
-    setupKeywords["platforms"]         = ["Linux", "Mac OS X", "Windows"]
-    setupKeywords["description"]       = "MDTraj-based contact maps"
-    setupKeywords["requires"]          = ["mdtraj", "nose"]
-    setupKeywords["long_description"]  = """Blah
-    """
-    outputString=""
-    firstTab     = 40
-    secondTab    = 60
-    for key in sorted( setupKeywords.iterkeys() ):
-         value         = setupKeywords[key]
-         outputString += (key.rjust(firstTab)
-                          + str(value).rjust(secondTab) + "\n")
-
-    print("%s" % outputString)
-
-    return setupKeywords
-
-
-def main():
-    setupKeywords = buildKeywordDictionary()
-    setup(**setupKeywords)
-
-if __name__ == '__main__':
-    main()
+setup(
+    name="contact_map",
+    author="David W.H. Swenson",
+    author_email="dwhs@hyperblazer.net",
+    version=PACKAGE_VERSION,
+    license="LGPL",
+    url="http//github.com/dwhswenson/contact_map",
+    packages=['contact_map', 'contact_map.tests'],
+    package_dir= {
+        'contact_map': 'contact_map',
+        'contact_map.tests': 'contact_map/tests'
+    },
+    package_data={'contact_map.tests': ['contact_map/tests/*pdb']},
+    ext_modules=[],
+    scripts=[],
+    long_description=DESCRIPTION,
+    platforms=['Linux', 'Mac OS X', 'Unix', 'Windows'],
+    install_requires=REQUIREMENTS,
+    requires=REQUIREMENTS,
+    tests_require=["pytest", "pytest-cov", "python-coveralls"],
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)',
+        'Operating System :: POSIX',
+        'Operating System :: Microsoft :: Windows',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Chemistry'
+    ]
+)