Release epifx 0.4.0

NEWS

+0.4.0 (2016-04-22)
+------------------
+
+* This release requires pypfilt >= 0.4.0.
+
+* Breaking change: models must define default parameter bounds by implementing
+  the `param_bounds` method.
+
+* Breaking change: model expectation functions now receive the previous and
+  current state vectors, in addition to the infection probability vector. This
+  means that expectation functions will need to change from:
+
+      expect(params, unit, period, pr_inf)
+
+  to:
+
+      expect(params, unit, period, pr_inf, prev, curr)
+
+* Enhancement: `epifx.summary.make` now passes additional keyword arguments to
+  the `pypfilt.summary.HDF5` constructor, allowing users to override default
+  settings, such as `first_day=False`.
+
+* Bug fix: ensure that infection probabilities are strictly non-negative.
+
+* Bug fix: ensure that population invariants are enforced correctly.
+
+* Bug fix: correctly scale the daily seeding probability.
+
+* Add instructions for installing epifx in a virtual environment.
+
 0.3.1 (2016-02-25)
 ------------------
 
@@ -58,7 +88,7 @@
 * Default to comparing only the simulation outputs and ignore the metadata;
   this can be overridden by the `--meta-data` (`-m`) option.
 
-* Build a universal wheel via ``python setup.py bdist_wheel``, which supports
+* Build a universal wheel via `python setup.py bdist_wheel`, which supports
   both Python 2 and Python 3.
 
 * This release requires pypfilt >= 0.1.2.

doc/conf.py

@@ -69,16 +69,16 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'epifx'
-copyright = u'2014-15, Rob Moss'
+copyright = u'2014-16, Rob Moss'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.3'
+version = '0.4'
 # The full version, including alpha/beta/rc tags.
-release = '0.3.1'
+release = '0.4.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

epifx/__init__.py

@@ -15,9 +15,9 @@ import epifx.summary
 __package_name__ = u'epifx'
 __author__ = u'Rob Moss'
 __email__ = u'rgmoss@unimelb.edu.au'
-__copyright__ = u'2014-2015, Rob Moss'
+__copyright__ = u'2014-2016, Rob Moss'
 __license__ = u'BSD 3-Clause License'
-__version__ = u'0.3.1'
+__version__ = u'0.4.0'
 
 
 SEIR = epifx.model.SEIR

setup.py

@@ -5,7 +5,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='epifx',
-    version='0.3.1',
+    version='0.4.0',
     url='https://bitbucket.org/robmoss/epidemic-forecasting-for-python/',
     description='Epidemic forecasting with mechanistic infection models',
     license='BSD 3-Clause License',
@@ -21,7 +21,7 @@ setup(
     install_requires=[
         'h5py >= 2.2',
         'numpy >= 1.8',
-        'pypfilt >= 0.3',
+        'pypfilt >= 0.4',
         'scipy >= 0.11',
     ],
     classifiers=[