Merge pull request #8 from UDST/tests-ci

Consolidate tests, clean up requirements, add CI and coveralls

.travis.yml

@@ -0,0 +1,32 @@
+language: python
+
+python:
+  - "2.7"
+
+before_install:
+  - pip install --upgrade pip
+  - pip install --upgrade wheel
+  - wget http://bit.ly/miniconda -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set show_channel_urls true
+  - conda update conda
+  - conda config --add channels udst --force
+  - conda config --add channels conda-forge --force
+  - conda create --quiet --name TESTENV python=$TRAVIS_PYTHON_VERSION future numpy pandas patsy scipy statsmodels urbansim coverage coveralls pytest
+  - source activate TESTENV
+  - pip install pylogit
+  - conda info --all
+  - conda list
+
+install:
+  - pip install .
+  - pip show choicemodels
+
+script:
+  - coverage run --source choicemodels -m pytest --verbose
+
+after_success:
+  - coverage report -m
+  - coveralls

README.md

@@ -1,13 +1,16 @@
+[![Build Status](https://travis-ci.org/UDST/choicemodels.svg?branch=master)](https://travis-ci.org/UDST/choicemodels)
+[![Coverage Status](https://coveralls.io/repos/github/UDST/choicemodels/badge.svg?branch=master)](https://coveralls.io/github/UDST/choicemodels?branch=master)
+
 # ChoiceModels
 
-This is a package for discrete choice model estimation and simulation, with an emphasis on large choice sets and behavioral refinements to multinomial models. Most of these models are not available in Statsmodels or Scikit-learn. 
+This is a package for discrete choice model estimation and simulation, with an emphasis on large choice sets and behavioral refinements to multinomial models. Most of these models are not available in Statsmodels or Scikit-learn.
 
 The underlying estimation routines come from two main places: (1) UrbanSim's `urbanchoice` codebase, which is being moved into ChoiceModels, and (2) Timothy Brathwaite's PyLogit package, which handles more flexible model specifications.
 
 
 ## Installation
 
-Clone this repository and run `python setup.py develop`. 
+Clone this repository and run `python setup.py develop`.
 
 Two required packages should also be installed the same way:
 - PyLogit: https://github.com/timothyb0912/pylogit
@@ -30,7 +33,7 @@ UrbanSim won't be a requirement any more after we finish refactoring the estimat
 
 - Stores and reports fitted MNL models.
 
-There's documentation in these classes' docstrings, and a usage demo in a Jupyter notebook. 
+There's documentation in these classes' docstrings, and a usage demo in a Jupyter notebook.
 
 https://github.com/udst/choicemodels/blob/master/choicemodels/tools/interaction.py
 https://github.com/udst/choicemodels/blob/master/choicemodels/mnl.py

notebooks/mnl_refactoring_test.py → notebooks/mnl_refactoring.py

@@ -16,15 +16,15 @@
 
 numalts = 10
 
-merged = MergedChoiceTable(observations = choosers, 
-						   alternatives = tracts, 
-                           chosen_alternatives = choosers.full_tract_id, 
+merged = MergedChoiceTable(observations = choosers,
+						   alternatives = tracts,
+                           chosen_alternatives = choosers.full_tract_id,
                            sample_size = numalts)
 
 model_expression = "home_density + work_density + school_density"
 
-model = MultinomialLogit(merged.to_frame(), 
-						 merged.observation_id_col, 
+model = MultinomialLogit(merged.to_frame(),
+						 merged.observation_id_col,
 						 merged.choice_col,
 						 model_expression)
 
@@ -42,7 +42,7 @@
 						 alternative_id_col = merged.alternative_id_col,
 						 choice_col = merged.choice_col,
 						 model_expression = model_expression)
-						 
+
 results = model.fit()
 print(results.print_summaries())
-"""
+"""

requirements-dev.txt

@@ -0,0 +1,3 @@
+coverage
+coveralls
+pytest

requirements.txt

@@ -0,0 +1,8 @@
+future >= 0.16.0
+numpy >= 1.8.0
+pandas >= 0.17.0
+patsy >= 0.3.0
+pylogit >= 0.1.2
+scipy >= 0.13.3
+statsmodels >= 0.8.0
+urbansim >= 3.1.1

setup.py

@@ -5,34 +5,33 @@
     from ez_setup import use_setuptools
     use_setuptools()
 
-from setuptools import setup, find_packages
+from setuptools import setup
 
 
 # read README as the long description
 with open('README.md', 'r') as f:
     long_description = f.read()
 
+with open('requirements.txt') as f:
+    install_requires = f.readlines()
+install_requires = [item.strip() for item in install_requires]
+
 setup(
     name='choicemodels',
     version='0.1dev',
     description='Tools for discrete choice estimation',
     long_description=long_description,
-    author='Urban Analytics Lab',
-    url='https://github.com/ual/choicemodels',
+    author='UC Berkeley Urban Analytics Lab',
+    url='https://github.com/udst/choicemodels',
     classifiers=[
+        'Intended Audience :: Science/Research',
+        'Topic :: Scientific/Engineering :: Information Analysis',
         'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.6',
         'License :: OSI Approved :: BSD License'
     ],
-    packages=find_packages(exclude=['*.tests']),
-    install_requires=[
-        'future>=0.16.0',
-        'numpy>=1.8.0',
-        'pandas>=0.17.0',
-        'patsy>=0.3.0',
-        'scipy>=0.13.3',
-        'statsmodels>=0.8.0',
-    ]
+    packages=['choicemodels'],
+    install_requires=install_requires
 )

tests/test_choicemodels.py

@@ -0,0 +1,13 @@
+def test_import():
+    import choicemodels
+
+def test_simple_estimation():
+    import choicemodels
+    import numpy as np
+    import pandas as pd
+    from collections import OrderedDict
+    endog = np.random.randint(2, size=50)
+    exog = np.random.rand(50, 5)
+    m = choicemodels.Logit(endog, exog)
+    results = m.fit()
+    results.summary()

choicemodels/tools/tests/test_interaction.py → tests/test_interaction.py

@@ -3,7 +3,7 @@
 import pandas as pd
 import pytest
 
-from .. import interaction as inter
+from choicemodels.tools import interaction as inter
 
 
 @pytest.fixture

choicemodels/tools/tests/test_mnl.py → tests/test_mnl.py

@@ -13,7 +13,7 @@
 import pytest
 from patsy import dmatrix
 
-from .. import mnl
+from choicemodels import mnl
 
 
 @pytest.fixture