Accounting for incoming API changes to libpysal and adding testing against libpysal's master branch

.travis.yml

@@ -3,13 +3,26 @@ sudo: false
 branches:
 only:
   - master
-python:
-  - "3.5"
-  - "3.6"
 
-env:
-  - PYSAL_PLUS=false
-  - PYSAL_PLUS=true
+python:
+    - 3.5
+    - 3.6
+env: 
+    - PYSAL_PYPI=true PYSAL_PLUS=true
+    - PYSAL_PYPI=true PYSAL_PLUS=false
+    - PYSAL_PYPI=false PYSAL_PLUS=true
+    - PYSAL_PYPI=false PYSAL_PLUS=false
+
+matrix:
+  allow_failures:
+      - python: 3.5
+        env: PYSAL_PYPI=false PYSAL_PLUS=false
+      - python: 3.5
+        env: PYSAL_PYPI=false PYSAL_PLUS=true
+      - python: 3.6
+        env: PYSAL_PYPI=false PYSAL_PLUS=false
+      - python: 3.6
+        env: PYSAL_PYPI=false PYSAL_PLUS=true
 
 before_install:
   - wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
@@ -23,9 +36,12 @@ before_install:
 install:
   - conda install --yes pip nose
   - which pip
+  - if "$PYSAL_PYPI"; then
+        echo 'testing pypi libpysal' && pip install libpysal;
+        else echo 'testing git libpysal'; git clone https://github.com/pysal/libpysal.git; cd libpysal; pip install .; cd ../;
+    fi;
   - conda install --yes --file requirements.txt;
-  - pip install libpysal
-  - if [[ PYSAL_PLUS ]]; then conda install --yes numba; fi
+  - if "$PYSAL_PLUS"; then conda install --yes numba; fi
 
 script:
   - pwd
@@ -38,8 +54,8 @@ notifications:
         recipients:
             - [email protected]
             - [email protected]
-        on_change: always
-        on_failure: always
+        on_success: change
+        on_failure: change
 
 after_success:
   - coveralls

esda/gamma.py

@@ -75,9 +75,9 @@ class Gamma(object):
 
     use same example as for join counts to show similarity
 
-    >>> import libpysal.api as lps, numpy as np
+    >>> import libpysal, numpy as np
     >>> from esda.gamma import Gamma
-    >>> w = lps.lat2W(4,4)
+    >>> w = libpysal.weights.lat2W(4,4)
     >>> y=np.ones(16)
     >>> y[0:8]=0
     >>> np.random.seed(12345)

esda/geary.py

@@ -80,10 +80,10 @@ class Geary(object):
 
     Examples
     --------
-    >>> import libpysal.api as lps
+    >>> import libpysal
     >>> from esda.geary import Geary
-    >>> w = lps.open(lps.get_path("book.gal")).read()
-    >>> f = lps.open(lps.get_path("book.txt"))
+    >>> w = libpysal.io.open(libpysal.examples.get_path("book.gal")).read()
+    >>> f = libpysal.io.open(libpysal.examples.get_path("book.txt"))
     >>> y = np.array(f.by_col['y'])
     >>> c = Geary(y,w,permutations=0)
     >>> round(c.C,7)

esda/getisord.py

@@ -4,7 +4,7 @@
 __author__ = "Sergio J. Rey <[email protected]>, Myunghwa Hwang <[email protected]> "
 __all__ = ['G', 'G_Local']
 
-from libpysal.common import np, stats, math
+from libpysal.common import np, stats 
 from libpysal.weights.spatial_lag import lag_spatial as slag
 from .tabular import _univariate_handler
 
@@ -67,15 +67,15 @@ class G(object):
 
     Examples
     --------
-    >>> import libpysal.api as lps
+    >>> import libpysal
     >>> import numpy
     >>> numpy.random.seed(10)
 
     Preparing a point data set
     >>> points = [(10, 10), (20, 10), (40, 10), (15, 20), (30, 20), (30, 30)]
 
     Creating a weights object from points
-    >>> w = lps.DistanceBand(points,threshold=15)
+    >>> w = libpysal.weights.DistanceBand(points,threshold=15)
     >>> w.transform = "B"
 
     Preparing a variable
@@ -106,7 +106,7 @@ def __init__(self, y, w, permutations=PERMUTATIONS):
         y = y.reshape(len(y), 1)  # Ensure that y is an n by 1 vector, otherwise y*y.T == y*y
         self.den_sum = (y * y.T).sum() - (y * y).sum()
         self.G = self.__calc(self.y)
-        self.z_norm = (self.G - self.EG) / math.sqrt(self.VG)
+        self.z_norm = (self.G - self.EG) / np.sqrt(self.VG)
         self.p_norm = 1.0 - stats.norm.cdf(np.abs(self.z_norm))
 
         if permutations:
@@ -278,7 +278,7 @@ class G_Local(object):
 
     Examples
     --------
-    >>> import libpysal.api as lps
+    >>> import libpysal
     >>> import numpy
     >>> numpy.random.seed(10)
 
@@ -288,7 +288,7 @@ class G_Local(object):
 
     Creating a weights object from points
 
-    >>> w = lps.DistanceBand(points,threshold=15)
+    >>> w = libpysal.weights.DistanceBand(points,threshold=15)
 
     Prepareing a variable
 

esda/join_counts.py

@@ -79,8 +79,8 @@ class Join_Counts(object):
     Replicate example from anselin and rey
 
     >>> import numpy as np
-    >>> import libpysal.api as lps
-    >>> w = lps.lat2W(4, 4)
+    >>> import libpysal
+    >>> w = libpysal.weights.lat2W(4, 4)
     >>> y = np.ones(16)
     >>> y[0:8] = 0
     >>> np.random.seed(12345)

esda/moran.py

@@ -98,9 +98,9 @@ class Moran(object):
 
     Examples
     --------
-    >>> import libpysal.api as lps
-    >>> w = lps.open(lps.get_path("stl.gal")).read()
-    >>> f = lps.open(lps.get_path("stl_hom.txt"))
+    >>> import libpysal
+    >>> w = libpysal.io.open(libpysal.examples.get_path("stl.gal")).read()
+    >>> f = libpysal.io.open(libpysal.examples.get_path("stl_hom.txt"))
     >>> y = np.array(f.by_col['HR8893'])
     >>> from esda.moran import Moran
     >>> mi = Moran(y,  w)
@@ -112,8 +112,8 @@ class Moran(object):
     0.00027147862770937614
 
     SIDS example replicating OpenGeoda
-    >>> w = lps.open(lps.get_path("sids2.gal")).read()
-    >>> f = lps.open(lps.get_path("sids2.dbf"))
+    >>> w = libpysal.io.open(libpysal.examples.get_path("sids2.gal")).read()
+    >>> f = libpysal.io.open(libpysal.examples.get_path("sids2.dbf"))
     >>> SIDR = np.array(f.by_col("SIDR74"))
     >>> mi = Moran(SIDR,  w)
     >>> round(mi.I, 3)
@@ -327,7 +327,7 @@ class Moran_BV(object):
 
     Examples
     --------
-    >>> import libpysal.api as lps
+    >>> import libpysal
     >>> import numpy as np
 
     Set random number generator seed so we can replicate the example
@@ -337,13 +337,13 @@ class Moran_BV(object):
     Open the sudden infant death dbf file and read in rates for 74 and 79
     converting each to a numpy array
 
-    >>> f = lps.open(lps.get_path("sids2.dbf"))
+    >>> f = libpysal.io.open(libpysal.examples.get_path("sids2.dbf"))
     >>> SIDR74 = np.array(f.by_col['SIDR74'])
     >>> SIDR79 = np.array(f.by_col['SIDR79'])
 
     Read a GAL file and construct our spatial weights object
 
-    >>> w = lps.open(lps.get_path("sids2.gal")).read()
+    >>> w = libpysal.io.open(libpysal.examples.get_path("sids2.gal")).read()
 
     Create an instance of Moran_BV
     >>> from esda.moran import Moran_BV
@@ -481,8 +481,8 @@ def Moran_BV_matrix(variables, w, permutations=0, varnames=None):
 
     open dbf
 
-    >>> import libpysal.api as lps
-    >>> f = lps.open(lps.get_path("sids2.dbf"))
+    >>> import libpysal
+    >>> f = libpysal.io.open(libpysal.examples.get_path("sids2.dbf"))
 
     pull of selected variables from dbf and create numpy arrays for each
 
@@ -491,7 +491,7 @@ def Moran_BV_matrix(variables, w, permutations=0, varnames=None):
 
     create a contiguity matrix from an external gal file
 
-    >>> w = lps.open(lps.get_path("sids2.gal")).read()
+    >>> w = libpysal.io.open(libpysal.examples.get_path("sids2.gal")).read()
 
     create an instance of Moran_BV_matrix
 
@@ -612,9 +612,9 @@ class Moran_Rate(Moran):
 
     Examples
     --------
-    >>> import libpysal.api as lps
-    >>> w = lps.open(lps.get_path("sids2.gal")).read()
-    >>> f = lps.open(lps.get_path("sids2.dbf"))
+    >>> import libpysal
+    >>> w = libpysal.io.open(libpysal.examples.get_path("sids2.gal")).read()
+    >>> f = libpysal.io.open(libpysal.examples.get_path("sids2.dbf"))
     >>> e = np.array(f.by_col('SID79'))
     >>> b = np.array(f.by_col('BIR79'))
     >>> from esda.moran import Moran_Rate
@@ -788,11 +788,11 @@ class Moran_Local(object):
 
     Examples
     --------
-    >>> import libpysal.api as lps
+    >>> import libpysal
     >>> import numpy as np
     >>> np.random.seed(10)
-    >>> w = lps.open(lps.get_path("desmith.gal")).read()
-    >>> f = lps.open(lps.get_path("desmith.txt"))
+    >>> w = libpysal.io.open(libpysal.examples.get_path("desmith.gal")).read()
+    >>> f = libpysal.io.open(libpysal.examples.get_path("desmith.txt"))
     >>> y = np.array(f.by_col['z'])
     >>> from esda.moran import Moran_Local
     >>> lm = Moran_Local(y, w, transformation = "r", permutations = 99)
@@ -1020,11 +1020,11 @@ class Moran_Local_BV(object):
 
     Examples
     --------
-    >>> import libpysal.api as lps
+    >>> import libpysal
     >>> import numpy as np
     >>> np.random.seed(10)
-    >>> w = lps.open(lps.get_path("sids2.gal")).read()
-    >>> f = lps.open(lps.get_path("sids2.dbf"))
+    >>> w = libpysal.io.open(libpysal.examples.get_path("sids2.gal")).read()
+    >>> f = libpysal.io.open(libpysal.examples.get_path("sids2.dbf"))
     >>> x = np.array(f.by_col['SIDR79'])
     >>> y = np.array(f.by_col['SIDR74'])
     >>> from esda.moran import Moran_Local_BV
@@ -1265,11 +1265,11 @@ class Moran_Local_Rate(Moran_Local):
 
     Examples
     --------
-    >>> import libpysal.api as lps
+    >>> import libpysal
     >>> import numpy as np
     >>> np.random.seed(10)
-    >>> w = lps.open(lps.get_path("sids2.gal")).read()
-    >>> f = lps.open(lps.get_path("sids2.dbf"))
+    >>> w = libpysal.io.open(libpysal.examples.get_path("sids2.gal")).read()
+    >>> f = libpysal.io.open(libpysal.examples.get_path("sids2.dbf"))
     >>> e = np.array(f.by_col('SID79'))
     >>> b = np.array(f.by_col('BIR79'))
     >>> from esda.moran import Moran_Local_Rate