Finish fluctmatch-3.3.3

tclick · May 16, 2018 · 498cb95 · 498cb95
2 parents 5b5de5c + 229e6a4
commit 498cb95
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Showing 9 changed files with 21 additions and 11 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.3.2
+current_version = 3.3.3
 commit = True
 tag = True
 

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,10 +2,21 @@
 Changelog
 =========
 
+3.3.3 (2018-05-16)
+------------------
+
+* Removed in_memory keyword argument
+
 3.3.2 (2018-05-16)
 ------------------
 
-* Fixed bug for setting up universe
+* Fixed bug for setting up unive
+
+3.3.1 (2018-05-16)
+------------------
+
+* Fixes bug in writing average coordinate file
+* Added log file command-line option
 
 3.3.0 (2018-05-15)
 ------------------

diff --git a/README.rst b/README.rst
@@ -44,9 +44,9 @@ Overview
     :alt: PyPI Package latest release
     :target: https://pypi.python.org/pypi/fluctmatch
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/tclick/python-fluctmatch/v3.3.2.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/tclick/python-fluctmatch/v3.3.3.svg
     :alt: Commits since latest release
-    :target: https://github.com/tclick/python-fluctmatch/compare/v3.3.2...master
+    :target: https://github.com/tclick/python-fluctmatch/compare/v3.3.3...master
 
 .. |wheel| image:: https://img.shields.io/pypi/wheel/fluctmatch.svg
     :alt: PyPI Wheel

diff --git a/docs/conf.py b/docs/conf.py
@@ -26,7 +26,7 @@
 year = u'2014-2017'
 author = u'Timothy Click'
 copyright = '{0}, {1}'.format(year, author)
-version = release = u'3.3.2'
+version = release = u'3.3.3'
 
 pygments_style = 'trac'
 templates_path = ['.']

diff --git a/setup.py b/setup.py
@@ -45,7 +45,7 @@ def read(*names, **kwargs):
 
 setup(
     name="fluctmatch",
-    version="3.3.2",
+    version="3.3.3",
     license="BSD license",
     description="Elastic network model using fluctuation matching.",
     long_description="%s\n%s" % (

diff --git a/src/fluctmatch/__init__.py b/src/fluctmatch/__init__.py
@@ -24,7 +24,7 @@
 
 import logging
 
-__version__ = "3.3.2"
+__version__ = "3.3.3"
 
 _MODELS = dict()
 _DESCRIBE = dict()

diff --git a/src/fluctmatch/commands/cmd_convert.py b/src/fluctmatch/commands/cmd_convert.py
@@ -229,7 +229,7 @@ def cli(
             print("{:20}{}".format(k, v))
         return
 
-    kwargs = dict(in_memory=False)
+    kwargs = dict()
     universe = modeller(topology, trajectory, com=com, model=model, **kwargs)
 
     kwargs.update(

diff --git a/src/fluctmatch/commands/cmd_write_charmm.py b/src/fluctmatch/commands/cmd_write_charmm.py
@@ -176,5 +176,5 @@ def cli(
         nonbonded=not nonbonded,
         write_traj=write_traj,
     )
-    universe = mda.Universe(topology, trajectory, in_memory=False)
+    universe = mda.Universe(topology, trajectory)
     fmutils.write_charmm_files(universe, **kwargs)
diff --git a/src/fluctmatch/fluctmatch/charmmfluctmatch.py b/src/fluctmatch/fluctmatch/charmmfluctmatch.py
@@ -214,8 +214,7 @@ def initialize(self, restart=False):
             calculations.
         """
         if not restart:
-            in_memory = self.kwargs.get("in_memory", False)
-            universe = mda.Universe(*self.args, in_memory=in_memory)
+            universe = mda.Universe(*self.args)
 
             # Create and write initial internal coordinate files.
             logger.info("Determining the average bond distances...")