Merge pull request #23 from wesbarnett/setup

Merging #23 which adds setup script for standard installation.

.gitignore

@@ -1 +1,4 @@
+*.egg-info
 *.pyc
+build
+dist

DESCRIPTION.rst

@@ -0,0 +1,9 @@
+Alchemical Analysis
+=======================
+
+Analyze alchemical free energy calculations conducted in GROMACS, AMBER or SIRE
+using recommended best practices from Klimovich et al., JCAMD 29:397-411
+(2015). This tool handles analysis via a slate of free energy methods, including BAR,
+MBAR, TI, and the Zwanzig relationship (exponential averaging) among others,
+and provides a good deal of analysis of computed free energies and convergence
+in order to help you assess the quality of your results.

MANIFEST.in

@@ -0,0 +1,3 @@
+include DESCRIPTION.rst
+include README.md
+recursive-include samples *

alchemical_analysis.py → alchemical_analysis/alchemical_analysis.py

@@ -116,8 +116,8 @@ def checkUnitsAndMore(units):
 
    # If using Gromacs we can read in the temperature directly from dhdl.xvg
    if P.software.title() == 'Gromacs':
-      import parsers.parser_gromacs
-      P.temperature = parsers.parser_gromacs.readTempGromacs(P)
+      import parser_gromacs
+      P.temperature = parser_gromacs.readTempGromacs(P)
 
    kB = 1.3806488*6.02214129/1000.0 # Boltzmann's constant (kJ/mol/K).
    beta = 1./(kB*P.temperature)
@@ -1084,7 +1084,32 @@ def stripZeros(a, aa, b, bb):
 # MAIN
 #===================================================================================================
 
-if __name__ == "__main__":
+def main():
+
+   global dhdlt
+   global u_klt
+   global P
+   global K
+   global n_components
+   global pymbar
+   global dhdl
+   global N_k
+   global lv
+   global dlam
+   global ave_dhdl
+   global std_dhdl
+   global lchange
+   global cubspl
+   global mapl
+   global u_kln
+   global Deltaf_ij
+   global dDeltaf_ij
+   global df_allk
+   global ddf_allk
+   global nsnapshots
+   global pl
+   global FP
+   global matplotlib
 
    # Timing.
    stime = ttt_time.time()
@@ -1105,21 +1130,21 @@ def stripZeros(a, aa, b, bb):
       from matplotlib.font_manager import FontProperties as FP
 
    if P.software.title() == 'Gromacs':
-      import parsers.parser_gromacs
-      nsnapshots, lv, dhdlt, u_klt = parsers.parser_gromacs.readDataGromacs(P)
+      import parser_gromacs
+      nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P)
    elif P.software.title() == 'Sire':
-      import parsers.parser_sire
-      nsnapshots, lv, dhdlt, u_klt = parsers.parser_sire.readDataSire(P)
+      import parser_sire
+      nsnapshots, lv, dhdlt, u_klt = parser_sire.readDataSire(P)
    elif P.software.title() == 'Amber':
-      import parsers.parser_amber
-      lv, ave_dhdl, std_dhdl = parsers.parser_amber.readDataAmber(P)
+      import parser_amber
+      lv, ave_dhdl, std_dhdl = parser_amber.readDataAmber(P)
    else:
       from inspect import currentframe, getframeinfo
       lineno = getframeinfo(currentframe()).lineno
       print "\n\n%s\n Looks like there is no yet proper parser to process your files. \n Please modify lines %d and %d of this script.\n%s\n\n" % (78*"*", lineno+3, lineno+4, 78*"*")
       #### LINES TO BE MODIFIED
-      import parsers.YOUR_OWN_FILE_PARSER
-      nsnapshots, lv, dhdlt, u_klt = parsers.YOUR_OWN_FILE_PARSER.yourDataParser(*args, **kwargs)
+      import YOUR_OWN_FILE_PARSER
+      nsnapshots, lv, dhdlt, u_klt = YOUR_OWN_FILE_PARSER.yourDataParser(*args, **kwargs)
       #### All the four are numpy arrays.
       #### lv           is the array of lambda vectors.
       #### nsnapshots   is the number of equilibrated snapshots per each state.
@@ -1154,6 +1179,10 @@ def stripZeros(a, aa, b, bb):
          plotCFM(u_kln, N_k, 50)
 
    print "\nTime spent: %s hours, %s minutes, and %s seconds.\nFinished on %s" % timeStatistics(stime)
+
+if __name__ == "__main__":
+   main()
+
 #===================================================================================================
 #                                   End of the script 
 #===================================================================================================

setup.py

@@ -0,0 +1,107 @@
+"""Alchemical Analysis
+
+See:
+https://github.com/MobleyLab/alchemical-analysis
+"""
+
+# Always prefer setuptools over distutils
+from setuptools import setup, find_packages
+# To use a consistent encoding
+from codecs import open
+from os import path
+
+here = path.abspath(path.dirname(__file__))
+
+# Get the long description from the relevant file
+with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
+    long_description = f.read()
+
+setup(
+    name='alchemical_analysis',
+
+    # Versions should comply with PEP440.  For a discussion on single-sourcing
+    # the version across setup.py and the project code, see
+    # https://packaging.python.org/en/latest/single_source_version.html
+    version='0.1.0',
+
+    description='Alchemical Analysis',
+    long_description=long_description,
+
+    # The project's main homepage.
+    url='https://github.com/MobleyLab/alchemical-analysis',
+
+    # Author details
+    author='Pavel Klimovich, Michael Shirts, and David Mobley',
+    author_email='[email protected]',
+
+    # Choose your license
+    license='LGPL',
+
+    # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
+    classifiers=[
+        # How mature is this project? Common values are
+        #   3 - Alpha
+        #   4 - Beta
+        #   5 - Production/Stable
+        'Development Status :: 5 - Production/Stable',
+
+        # Indicate who your project is intended for
+        'Intended Audience :: Science/Research',
+        'Topic :: Scientific/Engineering :: Chemistry',
+        'Topic :: Scientific/Engineering :: Physics',
+
+        # Pick your license as you wish (should match "license" above)
+        'License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)',
+
+        # Specify the Python versions you support here. In particular, ensure
+        # that you indicate whether you support Python 2, Python 3 or both.
+        'Programming Language :: Python :: 2.7',
+    ],
+
+    # What does your project relate to?
+    keywords='pymbar',
+
+    # You can just specify the packages manually here if your project is
+    # simple. Or you can use find_packages().
+    #packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
+    packages=find_packages(),
+    py_modules=['parser_gromacs','parser_amber','parser_sire','unixlike'],
+
+    # List run-time dependencies here.  These will be installed by pip when
+    # your project is installed. For an analysis of "install_requires" vs pip's
+    # requirements files see:
+    # https://packaging.python.org/en/latest/requirements.html
+    install_requires=["pymbar"],
+
+    # List additional groups of dependencies here (e.g. development
+    # dependencies). You can install these using the following syntax,
+    # for example:
+    # $ pip install -e .[dev,test]
+    # extras_require={
+    #    'dev': ['check-manifest'],
+    #    'test': ['coverage'],
+    #},
+
+    # If there are data files included in your packages that need to be
+    # installed, specify them here.  If using Python 2.6 or less, then these
+    # have to be included in MANIFEST.in as well.
+    #package_data={
+    #    'sample': ['package_data.dat'],
+    #},
+
+    # Although 'package_data' is the preferred approach, in some case you may
+    # need to place data files outside of your packages. See:
+    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa
+    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
+    #data_files=[('my_data', ['data/data_file'])],
+
+    # To provide executable scripts, use entry points in preference to the
+    # "scripts" keyword. Entry points provide cross-platform support and allow
+    # pip to create the appropriate form of executable for the target platform.
+    scripts={"alchemical_analysis/alchemical_analysis.py","alchemical_analysis/parser_gromacs.py","alchemical_analysis/unixlike.py"},
+    entry_points={
+        'console_scripts': [
+            'alchemical_analysis=alchemical_analysis:main',
+        ],
+    },
+)