Remove python 2 Support in MDPOW (#178)

remove python 2 * fix #177 * update setup.py and CHANGES Co-authored-by: ALescoulie <[email protected]> Co-authored-by: Oliver Beckstein <[email protected]>
Becksteinlab · Aug 17, 2021 · fcff52a · fcff52a
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -27,7 +27,7 @@ jobs:
         # macos runners (latest GROMACS, oldes and latest Python)
 
         os: [ubuntu-latest]
-        python-version: [2.7, 3.9]
+        python-version: [3.9]
         gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1"]
         include:
           - os: ubuntu-latest
@@ -39,9 +39,6 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.8
             gromacs-version: 2021.1
-          - os: macos-latest
-            python-version: 2.7
-            gromacs-version: 2021.1
           - os: macos-latest
             python-version: 3.9
             gromacs-version: 2021.1

diff --git a/CHANGES b/CHANGES
@@ -5,6 +5,14 @@ CHANGES for MDPOW
 Add summary of changes for each release. Use ISO dates. Reference
 GitHub issues numbers and PR numbers.
 
+2021-??-??    0.8.0
+ALescoulie
+
+Changes
+
+* dropped support for Python 2 and <3.6: only Python 3.7--3.9
+  are supported (#177)
+
 
 2021-08-04    0.7.1
 orbeckst, iorga
@@ -18,7 +26,7 @@ Fixes
 * fix fep.p_transfer() only analyzing the second input Gsolv (would lead to an
   error like "results.DeltaA does not contain 'Gibbs'") (PR #185)
 * ensure that pickle files created under Python 2 are also readable under
-  Python 3  
+  Python 3
 * documentation fixes (PR #176)
 
 

diff --git a/doc/sphinx/source/scripts.txt b/doc/sphinx/source/scripts.txt
@@ -136,7 +136,7 @@ Usage of the command:
    .. option:: RUNFILE
 
       The runfile :file:`runinput.yml` with all configuration parameters.
-   
+
 
    Options:
 
@@ -242,7 +242,7 @@ Usage of the command:
    "auto" option (or "none").
 
    The total solvation free energy is calculated as
-   
+
    .. math::
 
 	\Delta G^{*} = -(\Delta G_{\text{coul}} + \Delta G_{\text{vdw}})
@@ -275,14 +275,14 @@ Usage of the command:
 
 
    positional arguments:
-   
+
    .. option::  DIRECTORY [DIRECTORY ...]
 
 		directory or directories which contain all the files
 		resulting from running :meth:`mdpow.fep.Ghyd.setup`
 
    optional arguments:
-   
+
    .. option::  -h, --help
 
 		show this help message and exit
@@ -294,80 +294,80 @@ Usage of the command:
 		*none* disables it The plot function is only
 		available for mdpow estimator,and is disabled when
 		using alchemlyb estimators. (default: none)
-		
+
    .. option::  --solvent NAME, -S NAME
 
 		solvent `NAME` for compound, 'water', 'octanol', or
 		'cyclohexane' (default: water)
-		
+
    .. option::  -o FILE, --outfile FILE
 
 		append one-line results summary to `FILE` (default:
 		:file:`gsolv.txt`)
-		
+
    .. option::  -e FILE, --energies FILE
 
 		append solvation free energies to FILE (default:
 		:file:`energies.txt`)
-		
+
    .. option:: --estimator {mdpow,alchemlyb}
-		
+
 		choose the estimator to be used, *alchemlyb* or *mdpow*
 		estimators (default: *alchemlyb*)
-		
+
    .. option:: --method {TI,MBAR,BAR}
-		
+
 		choose the method to calculate free energy (default:
 		*MBAR*)
-		
+
    .. option:: --force
 
 		 force rereading all data (default: False)
-		 
+
    .. option:: --SI
 
 		 enable statistical inefficiency (SI) analysis.
 		 Statistical inefficiency analysis is performed by
 		 default when usingalchemlyb estimators and is always
 		 disabled when using mdpow estimator. (default: True)
-		 
+
    .. option:: --no-SI
 
 		 disable statistical inefficiency
                  analysis. Statistical inefficiency analysis is
                  performed by default when usingalchemlyb estimators
                  and is disabled when using mdpow estimator. (default:
                  False)
-		 
+
    .. option:: -s N, --stride N
 
 		 use every `N`-th datapoint from the original dV/dlambda
 		 data. (default: 1)
-		 
+
    .. option:: --start START
-		
+
 		 start point for the data used from the original
 		 dV/dlambda data. (default: 0)
-		 
+
    .. option:: --stop STOP
 
 		stop point for the data used from the original
 		dV/dlambda data. (default: None)
-		
+
    .. option:: --ignore-corrupted
 
 		skip lines in the md.xvg files that cannot be parsed.
 		(default: False)
-		
+
 		.. warning::
-		   
+
 		   Other lines in the file might have been corrupted
 		   in such a way that they appear correct but are in
 		   fact wrong. WRONG RESULTS CAN OCCUR! USE AT YOUR
-		   OWN RISK 
+		   OWN RISK
 
                 It is recommended to simply rerun the affected simulation(s).
-       
+
 
 
 
@@ -409,7 +409,7 @@ Usage of the command:
 
 
    positional arguments:
-   
+
    .. option::  DIRECTORY [DIRECTORY ...]
 
 		One or more directories that contain the state pickle
@@ -420,13 +420,13 @@ Usage of the command:
                 resulting from running :meth:`mdpow.fep.Ghyd.setup` and
                 :meth:`mdpow.fep.Goct.setup` and the results of the MD FEP
                 simulations.
-		
+
    optional arguments:
-   
+
    .. option::  -h, --help
 
 		show this help message and exit
-		
+
    .. option::  --plotfile FILE
 
 		plot dV/dlambda to FILE; use png or pdf suffix to
@@ -435,75 +435,75 @@ Usage of the command:
 		*none* disables it The plot function is only
 		available for mdpow estimator,and is disabled when
 		using alchemlyb estimators. (default: none)
-		
+
    .. option::  -o FILE, --outfile FILE
 
 		append one-line results summary to `FILE` (default:
 		:file:`pow.txt`)
-		
+
    .. option::  -e FILE, --energies FILE
 
 		append solvation free energies to FILE (default:
 		:file:`energies.txt`)
-		
+
    .. option:: --estimator {mdpow,alchemlyb}
-		
+
 		choose the estimator to be used, *alchemlyb* or *mdpow*
 		estimators (default: *alchemlyb*)
-		
+
    .. option:: --method {TI,MBAR,BAR}
-		
+
 		choose the method to calculate free energy (default:
 		*MBAR*)
-		
+
    .. option:: --force
 
 		 force rereading all data (default: False)
-		 
+
    .. option:: --SI
 
 		 enable statistical inefficiency (SI) analysis.
 		 Statistical inefficiency analysis is performed by
 		 default when usingalchemlyb estimators and is always
 		 disabled when using mdpow estimator. (default: True)
-		 
+
    .. option:: --no-SI
 
 		 disable statistical inefficiency
                  analysis. Statistical inefficiency analysis is
                  performed by default when usingalchemlyb estimators
                  and is disabled when using mdpow estimator. (default:
                  False)
-		 
+
    .. option:: -s N, --stride N
 
 		 use every `N`-th datapoint from the original dV/dlambda
 		 data. (default: 1)
-		 
+
    .. option:: --start START
-		
+
 		 start point for the data used from the original
 		 dV/dlambda data. (default: 0)
-		 
+
    .. option:: --stop STOP
 
 		stop point for the data used from the original
 		dV/dlambda data. (default: None)
-		
+
    .. option:: --ignore-corrupted
 
 		skip lines in the md.xvg files that cannot be parsed.
 		(default: False)
-		
+
 		.. warning::
-		   
+
 		   Other lines in the file might have been corrupted
 		   in such a way that they appear correct but are in
 		   fact wrong. WRONG RESULTS CAN OCCUR! USE AT YOUR
-		   OWN RISK 
+		   OWN RISK
 
                 It is recommended to simply rerun the affected simulation(s).
-       
+
 
 
 .. _mdpow-pow-outputformat-label:

diff --git a/mdpow/__init__.py b/mdpow/__init__.py
@@ -2,10 +2,6 @@
 # Copyright (c) 2010 Oliver Beckstein <[email protected]>
 # Released under the GNU Public License 3 (or higher, your choice)
 # See the file COPYING for details.
-
-
-from __future__ import absolute_import
-
 from . import log
 
 from ._version import get_versions

diff --git a/mdpow/_version.py b/mdpow/_version.py
@@ -9,8 +9,6 @@
 # versioneer-0.18 (https://github.com/warner/python-versioneer)
 
 """Git implementation of _version.py."""
-from __future__ import absolute_import, print_function
-
 import errno
 import os
 import re

diff --git a/mdpow/config.py b/mdpow/config.py
@@ -89,11 +89,6 @@
 .. autofunction:: _generate_template_dict
 
 """
-
-from __future__ import absolute_import, division
-
-import six
-
 import os, errno
 from pkg_resources import resource_filename, resource_listdir
 import yaml
@@ -346,7 +341,7 @@ def _get_template(t):
 
 def iterable(obj):
     """Returns ``True`` if *obj* can be iterated over and is *not* a  string."""
-    if isinstance(obj, six.string_types):
+    if isinstance(obj, str):
         return False  # avoid iterating over characters of a string
 
     if hasattr(obj, 'next'):

diff --git a/mdpow/equil.py b/mdpow/equil.py
@@ -28,10 +28,7 @@
 
 .. autodata:: DIST
 """
-
-from __future__ import absolute_import, division
-
-from six.moves import cPickle as pickle
+import pickle
 
 import os, errno
 import shutil
@@ -229,7 +226,7 @@ def save(self, filename=None):
         else:
             self.filename = filename
         with open(filename, 'wb') as f:
-            pickle.dump(self, f, protocol=pickle.HIGHEST_PROTOCOL)
+            pickle.dump(self, f)
         logger.debug("Instance pickled to %(filename)r" % vars())
 
     def load(self, filename=None):