Merge tag 'release-0.5.1'

release 0.5.1 (bug fixes)

.coveragerc

@@ -0,0 +1,15 @@
+[run]
+branch = True
+source = gromacs 
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    def _repr_html_
+    def __str__
+    raise NotImplementedError
+    if __name__ == .__main__.:
+
+omit =
+    gromacs/tests/*

.travis.yml

@@ -39,7 +39,7 @@ install:
 
 # run tests
 script: 
-  - py.test --cov gromacs/tests --pep8 gromacs/tests
+  - py.test --cov gromacs
 
 after_success:
   - codecov

CHANGES

@@ -2,7 +2,22 @@
  CHANGELOG for GromacsWrapper
 ==============================
 
-2016-xx-xx      0.4.1
+2016-06-29      0.5.1
+whitead, dotsdl, orbeckst
+
+* fixed: check_mdrun_success() works now for Gromacs 4 and Gromacs 5
+  (issue #64)
+* fixed: MDRunner working for Gromacs 4 and Gromacs 5 (issue #64)  
+* fixed setup.energy_minimize() not falling back to single precision
+  mdrun (issue #63)
+* fixed: added missing alias "gmx solvate" <--> "genbox" (issue #62)
+* added keyword argument use_shell=True to Command() to make Popen use
+  the shell
+* added template for Gromacs 4.6.x gromacswrapper.cfg
+* improved testing
+
+
+2016-05-23      0.5.0
 quantifiedcode-bot, orbeckst, jandom, whitead
 
 * requires Python 2.7

MANIFEST.in

@@ -1,3 +1,3 @@
-include   py setup.py COPYING COPYING.LESSER README.rst CHANGES
+include   setup.py COPYING COPYING.LESSER README.rst CHANGES
 recursive-include scripts *.py
 graft     gromacs/templates/

README.rst

@@ -7,7 +7,7 @@
  README: GromacsWrapper
 ========================
 
-|zenodo| |docs|
+|build| |cov| |docs| |zenodo| 
 
 A primitive wrapper around the Gromacs tools until we have proper
 python bindings. It also provides a small library (cook book) of
@@ -27,6 +27,13 @@ running simulations with sensible parameters.
    http://gromacswrapper.readthedocs.org/en/latest/
 .. _GromacsWrapper git repository:
    http://github.com/Becksteinlab/GromacsWrapper
+.. |build| image:: https://travis-ci.org/Becksteinlab/GromacsWrapper.svg?branch=develop
+   :target: https://travis-ci.org/Becksteinlab/GromacsWrapper
+   :alt: Build Status
+.. |cov| image:: https://codecov.io/gh/Becksteinlab/GromacsWrapper/branch/develop/graph/badge.svg
+   :target: https://codecov.io/gh/Becksteinlab/GromacsWrapper?branch=develop
+   :alt: Code Coverage
+   :scale: 100%
 .. |zenodo| image:: https://zenodo.org/badge/13219/Becksteinlab/GromacsWrapper.svg
    :target: https://zenodo.org/badge/latestdoi/13219/Becksteinlab/GromacsWrapper
    :alt: Latest release on zenodo (with DOI)

environment.yml

@@ -5,5 +5,6 @@ dependencies:
 - gromacs>=5.1
 - numpy>=1.9
 - scipy
+- pandas
 - pip:
   - recsql>=0.7

gromacs/__init__.py

@@ -35,7 +35,7 @@
      Contains classes that wrap the gromacs tools. They are automatically
      generated from the list of tools in :data:`gromacs.tools.gmx_tools`.
 
-:mod:`gromacs.formats`
+:mod:`gromacs.fileformats`
      Classes to represent data files in various formats such as
      xmgrace graphs. The classes allow reading and writing and for
      graphs, also plotting of the data.
@@ -112,7 +112,7 @@
 -----------------------
 
 A number of package-specific exceptions (:exc:`GromacsError`) and
-warnings (:exc:`GromacsFailureWarning`, :exc:`GromacsImportWarning`, 
+warnings (:exc:`GromacsFailureWarning`, :exc:`GromacsImportWarning`,
 :exc:`GromacsValueWarning`, :exc:`AutoCorrectionWarning`,
 :exc:`BadParameterWarning`) can be raised.
 
@@ -230,13 +230,13 @@ def start_logging(logfile="gromacs.log"):
     The default logfile is named ``gromacs.log`` and messages are
     logged with the tag *gromacs*.
     """
-    import log
+    from . import log
     log.create("gromacs", logfile=logfile)
     logging.getLogger("gromacs").info("GromacsWrapper %s STARTED logging to %r", get_version(), logfile)
 
 def stop_logging():
     """Stop logging to logfile and console."""
-    import log
+    from . import log
     logger = logging.getLogger("gromacs")
     logger.info("GromacsWrapper %s STOPPED logging", get_version())
     log.clear_handlers(logger)  # this _should_ do the job...

gromacs/core.py

@@ -248,6 +248,8 @@ def Popen(self, *args,**kwargs):
 
         stdin = kwargs.pop('stdin', None)
         input = kwargs.pop('input', None)
+
+        use_shell = kwargs.pop('use_shell', False)
         if input:
             stdin = PIPE
             if isinstance(input, basestring):
@@ -267,8 +269,8 @@ def Popen(self, *args,**kwargs):
                                                    # (cannot move out of method because filtering of stdin etc)
         try:
             p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout,
-                               universal_newlines=True, input=input)
-        except OSError,err:
+                               universal_newlines=True, input=input, shell=use_shell)
+        except OSError as err:
             logger.error(" ".join(cmd))            # log command line
             if err.errno == errno.ENOENT:
                 errmsg = "Failed to find Gromacs command %r, maybe its not on PATH or GMXRC must be sourced?" % self.command_name
@@ -493,7 +495,7 @@ def __init__(self, *args, **kwargs):
         self.failuremode = kwargs.pop('failure','raise')
         self.extra_doc = kwargs.pop('doc',None)
         self.gmxargs = self._combineargs(*args, **kwargs)
-        self.__doc__ = self.gmxdoc        
+        self.__doc__ = self.gmxdoc
 
     def failuremode():
         doc = """mode determines how the GromacsCommand behaves during failure
@@ -602,7 +604,7 @@ def _get_gmx_docs(self):
 
         .. Note::
 
-           The header is on STDOUT and is ignored. The docs are read from STDERR in GMX 4. 
+           The header is on STDOUT and is ignored. The docs are read from STDERR in GMX 4.
            In GMX 5, the opposite is true (Grrr)
         """
         # Uses the class-wide arguments so that 'canned invocations' in cbook
@@ -612,15 +614,15 @@ def _get_gmx_docs(self):
         # temporarily throttle logger to avoid reading about the help function invocation or not found
         logging.disable(logging.CRITICAL)
         try:
-            rc,header,docs = self.run('h', stdout=PIPE, stderr=PIPE, use_input=False)            
+            rc,header,docs = self.run('h', stdout=PIPE, stderr=PIPE, use_input=False)
         except:
             logging.critical("Invoking command {} failed when determining its doc string. Proceed with caution".format(self.command_name))
-            return "(No Gromacs documentation available)"            
+            return "(No Gromacs documentation available)"
         finally:
             logging.disable(logging.NOTSET)     # ALWAYS restore logging....
         m = re.match(self.doc_pattern, docs, re.DOTALL)    # keep from DESCRIPTION onwards
         if m is None:
-            m = re.match(self.doc_pattern, header, re.DOTALL)    # Try now with GMX 5 approach            
+            m = re.match(self.doc_pattern, header, re.DOTALL)    # Try now with GMX 5 approach
             if m is None:
                 return "(No Gromacs documentation available)"
         return m.group('DOCS')
@@ -675,11 +677,13 @@ def __init__(self,*args,**kwargs):
             input_string = ""
         self.command_string = input_string + " ".join(self.command)
         super(PopenWithInput,self).__init__(*args,**kwargs)
+
     def communicate(self, use_input=True):
         """Run the command, using the input that was set up on __init__ (for *use_input* = ``True``)"""
         if use_input:
             return super(PopenWithInput,self).communicate(self.input)
         else:
             return super(PopenWithInput,self).communicate()
+
     def __str__(self):
         return "<Popen on %r>" % self.command_string

gromacs/formats.py

@@ -3,8 +3,7 @@
 # Released under the GNU Public License 3 (or higher, your choice)
 # See the file COPYING for details.
 
-"""
-:mod:`gromacs.formats` -- Accessing various files
+""":mod:`gromacs.formats` -- Accessing various files
 =================================================
 
 This module contains classes that represent data files on
@@ -23,6 +22,11 @@
 do *not* make use of :mod:`gromacs.tools` or :mod:`gromacs.cbook` and
 can be safely imported at any time.
 
+.. SeeAlso::
+
+   This module gives access to a selection of classes from
+   :mod:`gromacs.fileformats`.
+
 
 Classes
 -------
@@ -39,6 +43,8 @@
    :members:
 .. autoclass:: XPM
    :members:
+.. autoclass:: TOP
+   :members:
 
 """
 from __future__ import absolute_import