removed support for Python <= 3.7

.github/workflows/ci.yaml

@@ -25,27 +25,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macOS-latest]
-        python-version: ["2.7", "3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
-        gromacs-version: ["2021.1"]
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        gromacs-version: ["2023.1"]
         # Test other GROMACS versions selectively on a recent Python.
         # On macOS only test one GROMACS version and two Python versions
         # to keep the testing matrix manageable.
-        exclude:
-          - os: macOS-latest
-            python-version: "3.6"
-          - os: macOS-latest
-            python-version: "3.7"
-          - os: macOS-latest
-            python-version: "3.8"
-          - os: macOS-latest
-            python-version: "3.9"
-          - os: macOS-latest
-            python-version: "3.10"
         include:
-          - os: ubuntu-latest
-            python-version: "2.7"
-            gromacs-version: "4.6.5"    
           - os: ubuntu-latest
             python-version: "3.11"
             gromacs-version: "4.6.5"
@@ -60,10 +46,18 @@ jobs:
             gromacs-version: "2020.6"
           - os: ubuntu-latest
             python-version: "3.11"
-            gromacs-version: "2022.4"
+            gromacs-version: "2021.1"       
           - os: ubuntu-latest
             python-version: "3.11"
-            gromacs-version: "2023.1"
+            gromacs-version: "2022.4"
+          # explicitly include a few macOS runners
+          # (conda-forge GROMACS >= 2021 is compiled to use rdtscp CPU instruction but these
+          # are not available in the macOS GitHub runner so we need to use a different GROMACS
+          # version. Try 2018.5 from bioconda. (2021.5 worked previously but not anymore.)
+          # Locally 2023.1 was successfully tested on Intel macOS 13.5.)
+          - os: macOS-latest
+            python-version: "3.11"
+            gromacs-version: "2018.6"
 
 
     env:
@@ -95,6 +89,7 @@ jobs:
       run: |
          micromamba info
          micromamba list
+         cat /proc/cpuinfo || (/usr/sbin/system_profiler SPHardwareDataType; /usr/sbin/sysctl -a | grep machdep.cpu)
 
     - name: Install pytest and plugins
       run: |
@@ -103,7 +98,6 @@ jobs:
     - name: Install GROMACS (${{ matrix.gromacs-version }})
       # UGLY HACK/FIX (probably to issues with bioconda packages)
       # - For 3.9, micromamba insists on using pypy 3.9 (and --py-pin does not help).
-      # - For 2.7 macOS, numkit would get uninstalled.
       # We can't freeze because then it's not possible to install older GROMACS versions from bioconda. 
       run: |
          micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl numkit python=${{ matrix.python-version }}.*=*_cpython

CHANGES

@@ -2,6 +2,12 @@
  CHANGELOG for GromacsWrapper
 ==============================
 
+2023-xx-xx      0.9.0
+orbeckst
+
+* removed support for legacy Python (<= 3.7) (#259)
+
+
 2023-09-16      0.8.5
 orbeckst
 

README.rst

@@ -11,8 +11,8 @@
 
 A primitive Python wrapper around the Gromacs_ tools. The library is
 tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, 2021.x, 2022.x,
-2023.x (and 5.x and 2016.x should also work). It supports Python 2.7
-and 3.6--3.11 on Linux and macOS.
+2023.x (and 5.x and 2016.x should also work). It supports Python
+3.8--3.11 on Linux and macOS.
 
 GromacsWrapper also provides a small library (cook book) of often-used
 recipes and helper functions to set up MD simulations.

doc/sphinx/source/installation.txt

@@ -6,7 +6,6 @@
  Installation
 ==============
 
-
 This document should help you to install the **GromacsWrapper**
 package. Please raise and issue in the `Issue Tracker`_ if problems
 occur or if you have suggestions on how to improve the package or
@@ -103,19 +102,17 @@ formatting so please install black_ and run it on your code.
 Requirements
 ============
 
-Python_ 2.7.x or Python >= 3.6 and GROMACS_ (4.6.x, 2016, 2018, 2019,
-2020, 2021, 2022) must be installed. ipython_ is very much
-recommended.
+Python_ >= 3.8 and GROMACS_ (4.6.x, 2016, 2018, 2019, 2020, 2021,
+2022, 2023) must be installed.
 
 .. _Python: http://www.python.org
-.. _ipython: http://ipython.scipy.org
 
 
 System requirements
 -------------------
 
-Tested with Python 2.7.x and Python 3.6--3.11 on Linux and Mac
-OS X. Earlier Python versions are not supported.
+Tested with Python 3.8--3.11 on Linux and Mac OS X. Earlier Python
+versions were only supported until release 0.8.5.
 
 
 Required Python modules

gromacs/__init__.py

@@ -169,8 +169,6 @@
 .. autodata:: __version__
 
 """
-from __future__ import absolute_import
-
 __docformat__ = "restructuredtext en"
 
 import os

gromacs/cbook.py

@@ -125,8 +125,6 @@
 # new class and set arguments explicitly in init (using kwargs['flag'] =
 # default) ... or I can write some meta(??) class to do this nicely
 
-from __future__ import absolute_import, with_statement
-
 __docformat__ = "restructuredtext en"
 
 import sys
@@ -136,7 +134,6 @@
 import tempfile
 import shutil
 import glob
-import six
 
 import logging
 

gromacs/collections.py

@@ -15,7 +15,7 @@
 """
 
 import os.path
-from six.moves import cPickle
+import pickle
 from numpy import all, any
 
 
@@ -50,10 +50,10 @@ def save(self, filename):
 
         If no extension is provided, ".collection" is appended.
         """
-        cPickle.dump(
+        pickle.dump(
             self,
             open(self._canonicalize(filename), "wb"),
-            protocol=cPickle.HIGHEST_PROTOCOL,
+            protocol=pickle.HIGHEST_PROTOCOL,
         )
 
     def load(self, filename, append=False):
@@ -64,7 +64,7 @@ def load(self, filename, append=False):
 
         If no extension is provided, ".collection" is appended.
         """
-        tmp = cPickle.load(open(self._canonicalize(filename), "rb"))
+        tmp = pickle.load(open(self._canonicalize(filename), "rb"))
         if append:
             self.extend(tmp)
         else:

gromacs/config.py

@@ -225,43 +225,13 @@
 .. autodata:: qscript_template
 
 """
-from __future__ import absolute_import, with_statement, print_function
-
 import os
 import logging
 import re
 import subprocess
 import sys
 
-if sys.version_info[0] < 3:  # several differences for Python 2
-    from ConfigParser import SafeConfigParser as ConfigParser
-    from ConfigParser import NoSectionError, NoOptionError
-
-    # Define read_file to point to the (deprecated in Python 3) readfp
-    # in order to have consistent, non-deprecated syntax
-    ConfigParser.read_file = ConfigParser.readfp
-
-    # Implement the new `fallback` kwarg based on the Python 3.7 implementation
-    # https://github.com/python/cpython/blob/3.7/Lib/configparser.py#L804
-    # This should ensure backwards compatibility.
-    _cf_getbool = ConfigParser.getboolean
-    _UNSET = object()
-
-    def _getboolean(self, section, option, fallback=_UNSET, **kwargs):
-        """Return a boolean for the specified config option
-
-        If *fallback* is used, it will be returned if there if the
-        option is not specified anywhere (defaults, config file)."""
-        try:  # Try using the Python 2 function
-            return _cf_getbool(self, section, option, **kwargs)
-        except (NoSectionError, NoOptionError):
-            if fallback is _UNSET:
-                raise
-        return fallback  # If fallback is given, use that value
-
-    ConfigParser.getboolean = _getboolean
-else:
-    from configparser import ConfigParser
+from configparser import ConfigParser
 
 from pkg_resources import resource_filename, resource_listdir
 

gromacs/core.py

@@ -98,9 +98,6 @@
 .. autoclass:: PopenWithInput
    :members:
 """
-from __future__ import absolute_import, with_statement, print_function
-import six
-
 __docformat__ = "restructuredtext en"
 
 import sys
@@ -277,13 +274,13 @@ def Popen(self, *args, **kwargs):
         use_shell = kwargs.pop("use_shell", False)
         if input:
             stdin = PIPE
-            if isinstance(input, six.string_types) and not input.endswith("\n"):
+            if isinstance(input, str) and not input.endswith("\n"):
                 # make sure that input is a simple string with \n line endings
-                input = six.text_type(input) + "\n"
+                input = str(input) + "\n"
             else:
                 try:
                     # make sure that input is a simple string with \n line endings
-                    input = "\n".join(map(six.text_type, input)) + "\n"
+                    input = "\n".join(map(str, input)) + "\n"
                 except TypeError:
                     # so maybe we are a file or something ... and hope for the best
                     pass
@@ -733,9 +730,6 @@ def __init__(self, *args, **kwargs):
         """
         kwargs.setdefault("close_fds", True)  # fixes 'Too many open fds' with 2.6
         self.input = kwargs.pop("input", None)
-        if six.PY2 and self.input is not None:
-            # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding
-            self.input = self.input.encode("utf-8")
         self.command = args[0]
         try:
             input_string = (

gromacs/environment.py

@@ -36,7 +36,6 @@
    :members:
 
 """
-import six
 
 
 # set up flags for core routines (more convoluted than strictly necessary but should
@@ -87,7 +86,7 @@ def __setitem__(self, name, value):
         self.get_flag(name).set(value)
 
     def _itervalues(self):
-        return six.itervalues(super(Flags, self))
+        return super(Flags, self).values()
 
     def _items(self):
         return super(Flags, self).items()

gromacs/fileformats/__init__.py

@@ -4,7 +4,6 @@
 # See the file COPYING for details.
 
 # file formats
-from __future__ import absolute_import
 
 __all__ = ["XVG", "MDP", "NDX", "uniqueNDX", "XPM", "TOP"]
 

gromacs/fileformats/convert.py

@@ -38,7 +38,6 @@
 .. autofunction:: to_unicode
 
 """
-import six
 
 import re
 
@@ -47,17 +46,17 @@ def to_unicode(obj):
     """Convert obj to unicode (if it can be be converted).
 
     Conversion is only attempted if `obj` is a string type (as
-    determined by :data:`six.string_types`).
+    determined by :class:`str`).
 
     .. versionchanged:: 0.7.0
        removed *encoding* keyword argument
 
     """
-    if not isinstance(obj, six.string_types):
+    if not isinstance(obj, str):
         return obj
 
     try:
-        obj = six.text_type(obj)
+        obj = str(obj)
     except TypeError:
         pass
     return obj

gromacs/fileformats/mdp.py

@@ -18,12 +18,9 @@
 """
 
 
-from __future__ import absolute_import, with_statement
-
 import os, errno
 import re
 import warnings
-import six
 import numpy
 
 
@@ -163,7 +160,7 @@ def write(self, filename=None, skipempty=False):
                 else:  # parameter = value
                     if skipempty and (v == "" or v is None):
                         continue
-                    if isinstance(v, six.string_types) or not hasattr(v, "__iter__"):
+                    if isinstance(v, str) or not hasattr(v, "__iter__"):
                         mdp.write("{k!s} = {v!s}\n".format(**vars()))
                     else:
                         mdp.write("{} = {}\n".format(k, " ".join(map(str, v))))

gromacs/fileformats/ndx.py

@@ -23,10 +23,6 @@
 .. autoclass:: IndexSet
 """
 
-from __future__ import absolute_import, with_statement
-
-from six.moves import range
-
 import os, errno
 import re
 import warnings

gromacs/fileformats/top.py

@@ -51,7 +51,6 @@
    Exchange (HREX) simulations. See ``scripts/gw-partial_tempering.py`` for an example.
 
 """
-from __future__ import absolute_import
 
 import textwrap
 import logging

gromacs/fileformats/xpm.py

@@ -69,10 +69,6 @@
 
 """
 
-from __future__ import absolute_import, with_statement
-
-from six.moves import range
-
 import os, errno
 import re
 import warnings

gromacs/fileformats/xvg.py

@@ -187,9 +187,6 @@
 .. autofunction:: break_array
 
 """
-from __future__ import with_statement, absolute_import
-
-from six.moves import zip, range
 
 import os
 import errno

gromacs/formats.py

@@ -45,8 +45,6 @@
    :members:
 
 """
-from __future__ import absolute_import
-
 __docformat__ = "restructuredtext en"
 
 __all__ = ["XVG", "MDP", "NDX", "uniqueNDX", "XPM", "TOP"]

gromacs/log.py

@@ -60,7 +60,6 @@
 .. autogenerated, see Online Docs
 
 """
-from __future__ import absolute_import
 
 import logging