added coveralls to travisci

Author: ljchang

.coverage

@@ -0,0 +1 @@
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.gitignore

@@ -7,6 +7,7 @@ nltools.egg-info
 build/
 dist/
 .cache/
+htmlcov
 
 # Logs and databases #
 ######################

.travis.yml

@@ -17,6 +17,11 @@ install:
   - conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION pip pytest numpy pandas scipy matplotlib scikit-learn
   - source activate testenv
   - pip install -r requirements.txt
+  - pip install git+https://github.com/neurolearn/pyneurovault_upload
+  - pip install python-coveralls
   - python setup.py install
 
-script: py.test
+script: coverage run --source nltools -m py.test
+
+after_success:
+  - coveralls

examples/Analysis/README.txt

@@ -0,0 +1,2 @@
+Neuroimaging Analysis Examples
+------------------------------

examples/Analysis/univariate_regression.py

@@ -0,0 +1,92 @@
+"""
+============================================================
+Example of two level univariate regression on simulated data
+============================================================
+This example simulates data according to a very simple sketch of brain
+imaging data and applies a standard two-level univariate GLM to identify
+significant voxels.
+"""
+
+__author__ = ["Luke Chang"]
+__license__ = "MIT"
+
+print(__doc__)
+
+from time import time
+
+import glob
+import numpy as np
+import pandas as pd
+import seaborn as sns
+import os
+import sys
+from nltools.simulator import Simulator
+from nltools.utils import get_resource_path, get_anatomical
+from nltools.analysis import Predict, Roc
+from nltools.data import Brain_Data
+from nltools.stats import threshold
+from nltools.mask import create_sphere
+import matplotlib.pyplot as plt
+import shutil
+import tempfile
+
+tmp_dir = os.path.join(tempfile.gettempdir(), str(os.times()[-1]))
+
+###############################################################################
+# Create data
+
+tic = time() #Start Timer
+
+sim = Simulator()
+r=10
+sigma = .5
+cor = .8
+cov = .6
+n_trials = 10
+n_subs = 5
+s1 = create_sphere([41, 64, 55], radius=r)
+sim.create_cov_data(cor, cov, sigma, mask=s1, reps = n_trials, n_sub = n_subs, output_dir = tmp_dir)
+print 'Simulate Data: Elapsed: %.2f seconds' % (time() - tic) #Stop timer
+
+###############################################################################
+# Load data
+
+tic = time() #Start Timer
+
+y=pd.read_csv(os.path.join(tmp_dir,'y.csv'),header=None,index_col=None).T
+dat = Brain_Data(data=os.path.join(tmp_dir,'maskdata_cor0.8_cov0.6_sigma0.5.nii.gz'),Y=y)
+dat.X = pd.DataFrame({'Intercept':np.ones(len(dat.Y)),'X1':np.array(dat.Y).flatten()},index=None)
+holdout = pd.read_csv(os.path.join(tmp_dir,'rep_id.csv'),header=None,index_col=None).T
+
+print 'Load Data: Elapsed: %.2f seconds' % (time() - tic) #Stop timer
+
+
+###############################################################################
+# Run Regression separately for each subject
+
+tic = time() #Start Timer
+
+start = 0
+stop = n_trials
+dat.X = pd.DataFrame({'Intercept':np.ones(len(dat.Y)),'X1':np.array(dat.Y).flatten()},index=None)
+all = dat.empty()
+for i in xrange(n_subs):
+    sub_out = dat[start:stop].regress()
+    start = start + n_trials
+    stop = stop + n_trials
+    tmp = sub_out['beta'].empty(data=False)[1]
+    all = all.append(tmp)
+print 'Regression: Elapsed: %.2f seconds' % (time() - tic) # Stop timer
+
+###############################################################################
+# Run One sample t-test
+
+tic = time() #Start Timer
+
+l2 = all.ttest(threshold_dict={'fdr':.05})
+l2['thr_t'].plot()
+print 'T-Test: Elapsed: %.2f seconds' % (time() - tic) # Stop timer
+
+shutil.rmtree(tmp_dir, ignore_errors=True) # Delete Data
+
+plt.show()

examples/README.txt

@@ -0,0 +1,19 @@
+nltools usage examples
+======================
+
+.. warning::
+
+    If you want to run the examples, make sure you execute them in a directory
+    where you have write permissions, or you copy the examples into such a
+    directory. If you install nltools manually, make sure you have followed
+    :ref:`the instructions <installation>`.
+
+
+.. contents:: **Contents**
+    :local:
+    :depth: 1
+
+General examples
+----------------
+
+General-purpose and introductory examples for nltools.

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+norecursedirs = env