Fix #8 build

.coveragerc

@@ -0,0 +1,11 @@
+[report]
+exclude_lines =
+    def __repr__
+    pass
+    def __str__
+    if __name__ == .__main__.:
+[run]
+omit =
+        *__init__*
+        *future*
+#data_file = /tmp/.coverage

.gitignore

@@ -1,14 +1,39 @@
+# Python build
 *.pyc
+
+# Tensorflow files
 *.json
+
+# Pycharm Project
 .idea/*
+.idea
+
+# Virtualenv
 .venv/*
-boltzmann_machines/test_rbm_1/*
-boltzmann_machines/test_rbm_2/*
+
+models/*
+!models/fetch_models.sh
 data/*.npy
 data/mnist/
 data/cifar-10-batches-py/
+
+# Notebooks
 notebooks/.ipynb_checkpoints/*
-models/*
-!models/fetch_models.sh
+
+# TeX files
 tex/*.swp
-.idea
+
+# python setup.py develop
+# python setup_cpu.py develop
+boltzmann_machines.egg-info/
+
+# Coverage
+.coverage
+.coverage*
+!.coveragerc
+coverage.xml
+
+# Research projects
+.tests/
+boltzmann_machines/test_rbm_1/*
+boltzmann_machines/test_rbm_2/*

.noserc

@@ -2,4 +2,4 @@
 all-modules=True
 exe=True
 with-doctest=True
-exclude-dir=examples
+exclude-dir=examples

.travis.yml

@@ -0,0 +1,28 @@
+language: python
+
+python:
+  - "2.7"
+  - "3.5"
+  - "3.6"
+
+sudo: required
+
+#jobs:
+#  include:
+#    - stage: doc
+#      script:
+#        - make install-docs-requirements
+#        - make docs
+
+install:
+  - pip install -U setuptools
+  - pip list
+  - pip uninstall --yes pytest numpy
+  - python setup_cpu.py develop
+
+script:
+  - make test
+  - codecov
+
+after_success:
+  - bash <(curl -s https://codecov.io/bash)

README.md

@@ -1,3 +1,7 @@
+[![Build Status](https://travis-ci.org/monsta-hd/boltzmann-machines.svg?branch=master)](https://travis-ci.org/monsta-hd/boltzmann-machines)
+[![Documentation Status](https://readthedocs.org/projects/srmourasilva-rbm/badge/?version=latest)](http://boltzmann-machine.readthedocs.io/?badge=latest)
+[![Code coverage](https://codecov.io/gh/monsta-hd/boltzmann-machines/branch/master/graph/badge.svg)](https://codecov.io/gh/monsta-hd/boltzmann-machine)
+
 <p float="left">
   <img src="img/dbm_mnist/rbm1.png" width="140" />
   <img src="img/dbm_mnist/samples.png" width="143" />
@@ -424,12 +428,19 @@ Also, you can download additional data (fine-tuned models' predictions, fine-tun
 Check also my supplementary [notes](tex/notes.pdf) (or [dropbox](https://www.dropbox.com/s/7pk4yeixkxogcem/bm_notes.pdf?dl=0)) with some historical outlines, theory, derivations, observations etc.
 
 ## How to install
-By default, the following commands install (among others) **tensorflow-gpu~=1.3.0**. If you want to install tensorflow without GPU support, replace corresponding line in [requirements.txt](requirements.txt). If you have already tensorflow installed, comment that line.
+By default, the following commands install (among others) **tensorflow-gpu~=1.3.0**.  If you have already tensorflow installed, comment that line.
 ```bash
 git clone https://github.com/monsta-hd/boltzmann-machines.git
 cd boltzmann-machines
 pip install -r requirements.txt
 ```
+If you want to install tensorflow without GPU support, use [setup_cpu.py](setup_cpu.py) instead.
+```bash
+git clone https://github.com/monsta-hd/boltzmann-machines.git
+cd boltzmann-machines
+python setup_cpu.py develop
+```
+
 See [here](docs/virtualenv.md) how to run from a ***virtual environment***.
 </br>
 See [here](docs/docker.md) how to run from a ***docker container***.

boltzmann_machines/__init__.py

@@ -1,12 +1,10 @@
 __author__ = 'Yelysei Bondarenko'
 __email__ = 'yell.bondarenko@gmail.com'
 
-from .dbm import *
-from . import dbm
-from . import ebm
-from . import layers
-
-from . import base
-from . import rbm
-from . import utils
+from boltzmann_machines.dbm import *
+from boltzmann_machines.ebm import *
+#from boltzmann_machines.layers import *
 
+#from boltzmann_machines import base
+#from boltzmann_machines import rbm
+#from boltzmann_machines import utils

boltzmann_machines/base/base.py

@@ -1,5 +1,6 @@
 def is_param_name(name):
     return not name.startswith('_') and not name.endswith('_')
 
+
 def is_attribute_name(name):
     return not name.startswith('_') and name.endswith('_')

boltzmann_machines/base/base_model.py

@@ -1,8 +1,8 @@
 import numpy as np
 from copy import deepcopy
-from ..base.base import is_param_name, is_attribute_name
-from .mixin import SeedMixin
-from ..utils.utils import write_during_training
+from boltzmann_machines.base.base import is_param_name, is_attribute_name
+from boltzmann_machines.base.mixin import SeedMixin
+from boltzmann_machines.utils.utils import write_during_training
 
 
 class BaseModel(SeedMixin):

boltzmann_machines/base/mixin.py

@@ -1,7 +1,7 @@
 import numpy as np
 import tensorflow as tf
 
-from ..utils import RNG
+from boltzmann_machines.utils import RNG
 
 
 class BaseMixin(object):

boltzmann_machines/base/tests/test_tf_model.py

@@ -4,8 +4,6 @@
 
 
 class TestWorkingPaths(object):
-    def __init__(self):
-        pass
 
     def test_filename_only(self):
         tf_model = TFM(model_path='model')

boltzmann_machines/base/tf_model.py

@@ -3,8 +3,7 @@
 import tensorflow as tf
 from functools import wraps
 
-from ..base import (BaseModel, DtypeMixin,
-                                     is_param_name)
+from boltzmann_machines.base import (BaseModel, DtypeMixin, is_param_name)
 
 
 def run_in_tf_session(check_initialized=True, update_seed=False):

boltzmann_machines/dbm.py

@@ -3,10 +3,10 @@
 from tensorflow.core.framework import summary_pb2
 from tensorflow.contrib.distributions import Bernoulli
 
-from .base import run_in_tf_session
-from .ebm import EnergyBasedModel
-from .layers import BernoulliLayer
-from .utils import (make_list_from, write_during_training,
+from boltzmann_machines.base import run_in_tf_session
+from boltzmann_machines.ebm import EnergyBasedModel
+from boltzmann_machines.layers import BernoulliLayer
+from boltzmann_machines.utils import (make_list_from, write_during_training,
                    batch_iter, epoch_iter,
                    log_sum_exp, log_diff_exp, log_mean_exp, log_std_exp)
 

boltzmann_machines/ebm.py

@@ -1,4 +1,4 @@
-from .base import TensorFlowModel
+from boltzmann_machines.base import TensorFlowModel
 
 
 class EnergyBasedModel(TensorFlowModel):

boltzmann_machines/rbm/base_rbm.py

@@ -2,9 +2,9 @@
 import tensorflow as tf
 from tensorflow.core.framework import summary_pb2
 
-from ..ebm import EnergyBasedModel
-from ..base import run_in_tf_session, is_attribute_name
-from ..utils import (make_list_from, batch_iter, epoch_iter,
+from boltzmann_machines.ebm import EnergyBasedModel
+from boltzmann_machines.base import run_in_tf_session, is_attribute_name
+from boltzmann_machines.utils import (make_list_from, batch_iter, epoch_iter,
                                       write_during_training)
 from ..utils.testing import assert_len, assert_shape
 

boltzmann_machines/rbm/rbm.py

@@ -2,9 +2,9 @@
 import tensorflow as tf
 from tensorflow.contrib.distributions import Multinomial
 
-from .env import *
-from .base_rbm import BaseRBM
-from layers import BernoulliLayer, MultinomialLayer, GaussianLayer
+from boltzmann_machines.rbm.env import *
+from boltzmann_machines.rbm.base_rbm import BaseRBM
+from boltzmann_machines.layers import BernoulliLayer, MultinomialLayer, GaussianLayer
 
 
 class BernoulliRBM(BaseRBM):
@@ -125,6 +125,6 @@ def logit_mean(X):
 
 if __name__ == '__main__':
     # run corresponding tests
-    from utils.testing import run_tests
-    from tests import test_rbm as t
+    from boltzmann_machines.utils.testing import run_tests
+    from boltzmann_machines.rbm.tests import test_rbm as t
     run_tests(__file__, t)

boltzmann_machines/rbm/tests/test_rbm.py

@@ -5,12 +5,13 @@
                            assert_almost_equal,
                            assert_raises)
 
-from rbm import BernoulliRBM, MultinomialRBM, GaussianRBM
-from utils import RNG
+from boltzmann_machines.rbm import BernoulliRBM, MultinomialRBM, GaussianRBM
+from boltzmann_machines.utils import RNG
 
 
 class TestRBM(object):
-    def __init__(self):
+
+    def setup_method(self, method):
         self.n_visible = 12
         self.n_hidden = 8
         self.X = RNG(seed=1337).rand(16, self.n_visible)
@@ -130,5 +131,5 @@ def test_consistency_val(self):
         # cleanup
         self.cleanup()
 
-    def tearDown(self):
+    def teardown_method(self, method):
         self.cleanup()

boltzmann_machines/utils/augmentation.py

@@ -11,6 +11,7 @@ def shift(x, offset=(0, 0)):
     y = nd.interpolation.shift(x, shift=offset, mode='nearest')
     return y
 
+
 def horizontal_mirror(x):
-    y = np.fliplr(x[:,:,...])
+    y = np.fliplr(x[:, :, ...])
     return y

boltzmann_machines/utils/dataset.py

@@ -4,7 +4,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-from .rng import RNG
+from boltzmann_machines.utils.rng import RNG
 
 
 def load_mnist(mode='train', path='.'):

boltzmann_machines/utils/testing.py

@@ -14,12 +14,14 @@ def run_tests(script_path, test_module=None):
     params.append('--with-doctest')
     nose.run(argv=params)
 
+
 def assert_shape(obj, name, desired_shape):
     actual_shape = getattr(obj, name).shape
     if actual_shape != desired_shape:
         raise ValueError('`{0}` has invalid shape {1} != {2}'.\
                          format(name, actual_shape, desired_shape))
 
+
 def assert_len(obj, name, desired_len):
     actual_len = len(getattr(obj, name))
     if actual_len != desired_len: