Merge pull request #46 from ljwolf/tests

[WIP] add model csvs rather than pickles
pysal · Jan 5, 2019 · f77e334 · f77e334
2 parents 02337c6 + d3e626d
commit f77e334
Showing 25 changed files with 706 additions and 2,175 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -4,8 +4,8 @@ branches:
 only:
   - master
 python:
-  - "3.5"
-  - "3.6"
+  - 3.5
+  - 3.6
 
 env:
   - PYSAL_PLUS=false
@@ -19,7 +19,7 @@ matrix:
           env: PYSAL_PYPI=false
 
 before_install:
-  - wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b -p ./miniconda
   - export PATH=`pwd`/miniconda/bin:$PATH
@@ -49,6 +49,7 @@ notifications:
     email:
         recipients:
             - tayoshan@gmail.com
+            - jgaboardi@gmail.com
         on_change: change
         on_failure: always
 

diff --git a/mgwr/tests/georgia/.DS_Store b/mgwr/tests/georgia/.DS_Store
diff --git a/mgwr/tests/georgia/GData_utm.csv b/mgwr/tests/georgia/GData_utm.csv
diff --git a/mgwr/tests/georgia/G_utm.dbf b/mgwr/tests/georgia/G_utm.dbf
diff --git a/mgwr/tests/georgia/G_utm.sbn b/mgwr/tests/georgia/G_utm.sbn
diff --git a/mgwr/tests/georgia/G_utm.sbx b/mgwr/tests/georgia/G_utm.sbx
diff --git a/mgwr/tests/georgia/G_utm.shp b/mgwr/tests/georgia/G_utm.shp
diff --git a/mgwr/tests/georgia/G_utm.shx b/mgwr/tests/georgia/G_utm.shx
diff --git a/mgwr/tests/georgia/georgia_BS_F.ctl b/mgwr/tests/georgia/georgia_BS_F.ctl
diff --git a/mgwr/tests/georgia/georgia_BS_F_listwise.csv b/mgwr/tests/georgia/georgia_BS_F_listwise.csv
diff --git a/mgwr/tests/georgia/georgia_BS_F_summary.txt b/mgwr/tests/georgia/georgia_BS_F_summary.txt
diff --git a/mgwr/tests/georgia/georgia_BS_NN.ctl b/mgwr/tests/georgia/georgia_BS_NN.ctl
diff --git a/mgwr/tests/georgia/georgia_BS_NN_listwise.csv b/mgwr/tests/georgia/georgia_BS_NN_listwise.csv
diff --git a/mgwr/tests/georgia/georgia_BS_NN_summary.txt b/mgwr/tests/georgia/georgia_BS_NN_summary.txt
diff --git a/mgwr/tests/georgia/georgia_GS_F.ctl b/mgwr/tests/georgia/georgia_GS_F.ctl
diff --git a/mgwr/tests/georgia/georgia_GS_F_listwise.csv b/mgwr/tests/georgia/georgia_GS_F_listwise.csv
diff --git a/mgwr/tests/georgia/georgia_GS_F_summary.txt b/mgwr/tests/georgia/georgia_GS_F_summary.txt
diff --git a/mgwr/tests/georgia/georgia_GS_NN.ctl b/mgwr/tests/georgia/georgia_GS_NN.ctl
diff --git a/mgwr/tests/georgia/georgia_GS_NN_listwise.csv b/mgwr/tests/georgia/georgia_GS_NN_listwise.csv
diff --git a/mgwr/tests/georgia/georgia_GS_NN_summary.txt b/mgwr/tests/georgia/georgia_GS_NN_summary.txt
diff --git a/mgwr/tests/georgia_mgwr_results.csv b/mgwr/tests/georgia_mgwr_results.csv
diff --git a/mgwr/tests/test_gwr.py b/mgwr/tests/test_gwr.py
diff --git a/mgwr/tests/test_sel_bw.py b/mgwr/tests/test_sel_bw.py
@@ -5,15 +5,15 @@
 import os
 import numpy as np
 from libpysal import io
+import libpysal as ps
 import unittest
 from spglm.family import Gaussian, Poisson, Binomial
 from ..sel_bw import Sel_BW
 from numpy.testing import assert_allclose
 
 class TestSelBW(unittest.TestCase):
     def setUp(self):
-        data_path = os.path.join(os.path.dirname(__file__),'georgia/GData_utm.csv')
-        #data = libpysal.open(data_path)
+        data_path = ps.examples.get_path("GData_utm.csv")
         data = io.open(data_path)
         self.coords = list(zip(data.by_col('X'), data.by_col('Y')))
         self.y = np.array(data.by_col('PctBach')).reshape((-1,1))

diff --git a/notebooks/GWR_MGWR_example.ipynb b/notebooks/GWR_MGWR_example.ipynb
@@ -2,28 +2,24 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 1,
+   "metadata": {},
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import scipy as sp\n",
+    "# import scipy as sp\n",
     "from mgwr.sel_bw import Sel_BW\n",
-    "from mgwr.gwr import GWR, MGWR\n",
+    "# from mgwr.gwr import GWR, MGWR\n",
     "import pandas as pd\n",
     "import libpysal as ps\n",
-    "import pickle as pk\n",
-    "import os"
+    "# import pickle as pk\n",
+    "# import os"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 2,
+   "metadata": {},
    "outputs": [],
    "source": [
     "data = ps.io.open(ps.examples.get_path('GData_utm.csv'))\n",
@@ -41,17 +37,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "bw: 117.0\n",
-      "aicc: 299.0508086830288\n",
-      "ENP: 11.804769716730096\n",
-      "sigma2: 0.34774354749782793\n"
+      "bw: 117.0\n"
+     ]
+    },
+    {
+     "ename": "NameError",
+     "evalue": "name 'GWR' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-3-2da488ac544f>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      9\u001b[0m \u001b[0mbw\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msearch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     10\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'bw:'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0mgwr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mGWR\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcoords\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0my\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mX\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     12\u001b[0m \u001b[0mgwr_results\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgwr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     13\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'aicc:'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgwr_results\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maicc\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'GWR' is not defined"
      ]
     }
    ],
@@ -75,44 +79,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "  4%|▍         | 9/200 [00:01<00:37,  5.10it/s]\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "bw(intercept): 92.0\n",
-      "bw(foreign): 101.0\n",
-      "bw(african_amer): 136.0\n",
-      "bw(rural): 158.0\n",
-      "aicc: 297.12013812258783\n",
-      "sigma2: 0.34477258292171475\n",
-      "ENP(model): 11.36825087269831\n",
-      "adj_alpha(model): 0.017592855949398047\n",
-      "critical_t(model): 2.399257840857394\n",
-      "ENP(intercept): 3.844671080264143\n",
-      "adj_alpha(intercept): 0.013005013681577365\n",
-      "critical_t(intercept): 2.512107491068591\n",
-      "ENP(foreign): 3.513770805151652\n",
-      "adj_alpha(foreign): 0.014229727199820033\n",
-      "critical_t(foreign): 2.4788879239423856\n",
-      "ENP(african_amer): 2.2580525278898254\n",
-      "adj_alpha(african_amer): 0.022142974701622884\n",
-      "critical_t(african_amer): 2.3106911297007184\n",
-      "ENP(rural): 1.7517564593926893\n",
-      "adj_alpha(rural): 0.028542780437261432\n",
-      "critical_t(rural): 2.210001836555586\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "X = (X - X.mean(axis=0)) / X.std(axis=0)\n",
     "\n",
@@ -152,9 +121,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": []
   }
@@ -176,7 +143,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.4"
+   "version": "3.6.6"
   }
  },
  "nbformat": 4,

diff --git a/requirements_tests.txt b/requirements_tests.txt
@@ -2,4 +2,5 @@ nose
 nose-progressive
 nose-exclude
 coverage
-coveralls
+coveralls
+pandas