Merge pull request #45 from mattwigway/automated-tests

Automated tests

.github/workflows/test.yml

@@ -0,0 +1,38 @@
+# run the linter and tests
+# copied and lightly edited from https://docs.github.com/en/actions/guides/building-and-testing-python
+
+name: eqsormo
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # only supporting py 3.7/3.8
+        python-version: [3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        pip install -r requirements.txt
+    - name: Install package
+      run: |
+          python setup.py install
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

environment.yml

@@ -6,4 +6,8 @@ dependencies:
   - numpy>=1.0
   - pandas>=1.0
   - dill>=0.3
-  - scipy>=1.5
+  - scipy>=1.5
+  - python>=3.7
+  # figure out how to mark these as dev dependencies
+  - flake8>=3.7
+  - pytest>=6

requirements.txt

@@ -0,0 +1,7 @@
+statsmodels>=0.11
+tqdm>=4.0
+numba>=0.51
+numpy>=1.0
+pandas>=1.0
+dill>=0.3
+scipy>=1.5

setup.cfg

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 120

setup.py

@@ -3,7 +3,8 @@
 setup(
     name='eqsormo',
     version='0.2.3',
-    packages=find_packages(),
+    packages=find_packages('src'),
+    package_dir={'': 'src'},
     requirements=['statsmodels>=0.11', 'tqdm>=4.0', 'numba>=0.51', 'numpy>=1.0', 'pandas>=1.0', 'dill>=0.3', 'scipy>=1.5'],
     author='Matthew Wigginton Conway',
     author_email='[email protected]',

eqsormo/tra/price_income.py → src/eqsormo/tra/price_income.py

@@ -68,10 +68,12 @@ def __repr__ (self):
 # box-cox transform of income - price
 # Box and Cox (1964)
 # NB any price > income should be taken care of by a max_rent_to_income parameter
+# TODO can we remove the max rent to income param here?
 boxcoxdiff = FunctionalForm(lambda income, price, lmbda: scipy.stats.boxcox(np.maximum(income - price, 1), lmbda=lmbda), 'boxcox(income - price)',
      n_params=1, param_names=['boxcox_lambda'])
 
 # Form suggested by Stephane Hess in his advanced discrete choice modelling class, London, UK, July 2019
 # Note that this will not behave right if called on a subset of the data, since it uses the mean of income
-hess = FunctionalForm(lambda income, price, hess_lambda: ((income / np.mean(income)) ** hess_lambda) * price,
-    'Hess: (income / mean(income)) ^ lambda * price', n_params=1, param_names=['hess_lambda'], starting_values=[-1])
+# Removed because these functions are now always called on subsets
+# hess = FunctionalForm(lambda income, price, hess_lambda: ((income / np.mean(income)) ** hess_lambda) * price,
+#     'Hess: (income / mean(income)) ^ lambda * price', n_params=1, param_names=['hess_lambda'], starting_values=[-1])

tests/tra/test_price_income_transformation.py

@@ -0,0 +1,49 @@
+#    Copyright 2020 Matthew Wigginton Conway
+
+#    Licensed under the Apache License, Version 2.0 (the "License");
+#    you may not use this file except in compliance with the License.
+#    You may obtain a copy of the License at
+
+#        http://www.apache.org/licenses/LICENSE-2.0
+
+#    Unless required by applicable law or agreed to in writing, software
+#    distributed under the License is distributed on an "AS IS" BASIS,
+#    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#    See the License for the specific language governing permissions and
+#    limitations under the License.
+
+# Author: Matthew Wigginton Conway <[email protected]>, School of Geographical Sciences and Urban Planning, Arizona State University
+
+from eqsormo.tra import price_income
+import numpy as np
+import scipy.stats
+import pandas as pd
+
+income = np.array([100, 150, 30, 20, 70])
+price = np.array([8, 12, 14, 9, 10])
+
+def test_logdiff ():
+    assert np.allclose(price_income.logdiff.apply(income, price), np.log(income - price))
+
+def test_sqrtdiff ():
+    assert np.allclose(price_income.sqrtdiff.apply(income, price), np.sqrt(income - price))
+
+def test_normdiff ():
+    assert np.allclose(price_income.normdiff.apply(income, price, 200), scipy.stats.norm.cdf(income - price, scale=200))
+    assert np.allclose(price_income.normdiff.apply(income, price, 300), scipy.stats.norm.cdf(income - price, scale=300))
+    # make sure the scale param has an effect
+    assert not np.allclose(price_income.normdiff.apply(income, price, 300), price_income.normdiff.apply(income, price, 200))
+    # make sure it works with price > income - this transformation can handle this, unlike the other transformations
+    bigprice = np.array([8, 12, 14, 30, 10])
+    assert np.any(bigprice > income)
+    assert not pd.isnull(price_income.normdiff.apply(income, bigprice, 200)).any()
+
+def test_boxcox ():
+    assert np.allclose(price_income.boxcoxdiff.apply(income, price, 1), scipy.stats.boxcox(income - price, lmbda=1))
+    assert np.allclose(price_income.boxcoxdiff.apply(income, price, 3), scipy.stats.boxcox(income - price, lmbda=3))
+    assert not np.allclose(price_income.boxcoxdiff.apply(income, price, 1), price_income.boxcoxdiff.apply(income, price, 3))
+    # TODO test behavior when price >= income
+
+
+
+