diff --git a/.travis.yml b/.travis.yml index e88eb34af0fa29b4d6b4e172d30ab3885c56fa64..a0298bde9b969ef8e508396624b2b393e7b44811 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,6 +2,7 @@ sudo: false language: python python: - "2.7" + - "3.4" notifications: email: false addons: @@ -17,7 +18,11 @@ env: - CC=gcc-4.8 CXX=g++-4.8 - CC=gcc-4.9 CXX=g++-4.9 before_install: - - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh + - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then + wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; + else + wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; + fi - bash miniconda.sh -b -p $HOME/miniconda - export PATH="$HOME/miniconda/bin:$PATH" - conda update --yes conda diff --git a/examples/svi.py b/examples/svi.py index 2547ae513ee6f5986a8269f37b8628ab1943061a..cf22c509f9f4e983f830e13bb2a59d7044d20ea5 100644 --- a/examples/svi.py +++ b/examples/svi.py @@ -1,4 +1,4 @@ - +from __future__ import division import numpy as np from numpy import newaxis as na from matplotlib import pyplot as plt diff --git a/pyhsmm/internals/initial_state.py b/pyhsmm/internals/initial_state.py index c0514a6c91fac3797ea884f0c5b19b5c114434d2..ca0bba831109b7aee47ae5cd4a0c6065eef8dba2 100644 --- a/pyhsmm/internals/initial_state.py +++ b/pyhsmm/internals/initial_state.py @@ -1,5 +1,6 @@ from __future__ import division import numpy as np +import copy import pyhsmm from pyhsmm.util.general import top_eigenvector @@ -41,6 +42,11 @@ class UniformInitialState(object): def clear_caches(self): pass + def copy_sample(self, new_model): + new = copy.copy(self) + new.model = new_model + return new + class HMMInitialState(Categorical): def __init__(self,model,init_state_concentration=None,pi_0=None): self.model = model @@ -73,7 +79,6 @@ class HMMInitialState(Categorical): def clear_caches(self): pass - def meanfieldupdate(self,expected_initial_states_list): super(HMMInitialState,self).meanfieldupdate(None,expected_initial_states_list) @@ -85,6 +90,10 @@ class HMMInitialState(Categorical): super(HMMInitialState,self).max_likelihood( data=samples,weights=expected_states_list) + def copy_sample(self, new_model): + new = copy.deepcopy(self) + new.model = new_model + return new class StartInZero(GibbsSampling,MaxLikelihood): def __init__(self,num_states,**kwargs): @@ -100,6 +109,11 @@ class StartInZero(GibbsSampling,MaxLikelihood): def max_likelihood(*args,**kwargs): pass + def copy_sample(self, new_model): + new = copy.copy(self) + new.model = new_model + return new + class HSMMInitialState(HMMInitialState): @property def steady_state_distribution(self): @@ -112,4 +126,3 @@ class HSMMInitialState(HMMInitialState): def clear_caches(self): self._steady_state_distribution = None - diff --git a/pyhsmm/models.py b/pyhsmm/models.py index 3a19ef47011792e4ff32618d47396da22ba5829f..ee98bbe7bab27c5b613b44082ee59f775fd960d8 100644 --- a/pyhsmm/models.py +++ b/pyhsmm/models.py @@ -387,7 +387,6 @@ class _HMMBase(Model): def _plot_stateseq_pcolor(self,s,ax=None,state_colors=None, plot_slice=slice(None),update=False,color_method=None): - # TODO pcolormesh instead of pcolorfast? from pyhsmm.util.general import rle s = self.states_list[s] if isinstance(s,int) else s @@ -407,7 +406,7 @@ class _HMMBase(Model): x, y = np.hstack((0,durations.cumsum())), np.array([datamin,datamax]) C = np.atleast_2d([state_colors[state] for state in stateseq_norep]) - s._pcolor_im = ax.pcolorfast(x,y,C,vmin=0,vmax=1,alpha=0.3) + s._pcolor_im = ax.pcolormesh(x,y,C,vmin=0,vmax=1,alpha=0.3) ax.set_ylim((datamin,datamax)) ax.set_xlim((0,len(stateseq))) ax.set_yticks([]) @@ -473,7 +472,7 @@ class _HMMGibbsSampling(_HMMBase,ModelGibbsSampling): new = copy.copy(self) new.obs_distns = [o.copy_sample() for o in self.obs_distns] new.trans_distn = self.trans_distn.copy_sample() - new.init_state_distn = self.init_state_distn.copy_sample() + new.init_state_distn = self.init_state_distn.copy_sample(new) new.states_list = [s.copy_sample(new) for s in self.states_list] return new diff --git a/setup.py b/setup.py index 3673c6368ba38f42fefe32f8d5216762477e5127..b6afa30b352461679b054703fbc0d02c6961a61f 100644 --- a/setup.py +++ b/setup.py @@ -8,10 +8,13 @@ from warnings import warn import os import sys from glob import glob -from future.moves.urllib.request import urlretrieve import tarfile import shutil +from future.standard_library import install_aliases +install_aliases() +from urllib.request import urlretrieve + # use cython if we can import it successfully try: from Cython.Distutils import build_ext as _build_ext