removed support for Python <= 3.7 (#265)

* close #259 
* removed support for Python <= 3.7
  - removed six and replaced with Python 3.x constructs
  - updated package meta data
  - update installation docs (sphinx and README)
  - updated CHANGES
* switch to testing GROMACS 2023.1 for all Python
  Only use other GROMACS versions for spot testing at highest supported Python.
  Note that we now have failures of GROMACS 2021.1 with macOS Python 3.11.
* changed macOS CI runner
  - only explicitly include one macOS runner at the latest supported Python
  - downgrade GROMACS to 2018.6 bioconda to avoid failing tests because later
    GROMACS releases were compiled to use  rdtscp CPU instruction but these
    are not available on GitHub runners and lead to failing tests)
    (2021.3-bioconda, 2020.6 conda-forge, 2021.1 from bioconda (which worked
    previously!),  2020.5 bioconda, 2019.5 bioconda all failed with the same error
    that RDTSCP information was not available in the macOS runner)
  - also output CPU information: /proc/cpuinfo or sysctl -a

.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