Update setup.py

adding scikit-image to list of desired python modules

CONTRIBUTING.md

@@ -12,7 +12,7 @@ name must be created.
 ### Version numbers
 
 The version of both the SQL extension and the Python package shall
-follow the [Semantic Versioning 2.0](http://semver.org/) guidelines:
+follow the[Semantic Versioning 2.0](http://semver.org/) guidelines:
 
 * When backwards incompatibility is introduced the major number is incremented
 * When functionally is added (in a backwards-compatible manner) the minor number

pg/Makefile

@@ -28,6 +28,3 @@ REGRESS_OPTS = --inputdir='$(TEST_DIR)' --outputdir='$(TEST_DIR)'
 PG_CONFIG = pg_config
 PGXS := $(shell $(PG_CONFIG) --pgxs)
 include $(PGXS)
-
-# This seems to be needed at least for PG 9.3.11
-all: $(DATA)

pg/crankshaft--0.0.1.sql

@@ -137,53 +137,6 @@ BEGIN
 END;
 $$
 LANGUAGE plpgsql VOLATILE;
-CREATE OR REPLACE FUNCTION
-  cdb_create_segment (
-      segment_name TEXT,
-      table_name TEXT,
-  	  column_name TEXT,
-      geoid_column TEXT DEFAULT 'geoid',
-      census_table TEXT DEFAULT 'block_groups'
-  )
-RETURNS NUMERIC
-AS $$
-  from crankshaft.segmentation import create_segemnt
-  # TODO: use named parameters or a dictionary
-  return create_segment('table')
-$$ LANGUAGE plpythonu;
-
-CREATE OR REPLACE FUNCTION
-  cdb_predict_segment (
-      segment_name TEXT,
-      geoid_column TEXT DEFAULT 'geoid',
-      census_table TEXT DEFAULT 'block_groups'
-  )
-RETURNS TABLE(geoid TEXT, prediction NUMERIC)
-AS $$
-  from crankshaft.segmentation import create_segemnt
-  # TODO: use named parameters or a dictionary
-  return create_segment('table')
-$$ LANGUAGE plpythonu;
-CREATE OR REPLACE FUNCTION
-  cdb_adaptive_histogram (
-      table_name  TEXT,
-      column_name TEXT
-  )
-RETURNS TABLE (bin_start numeric,bin_end numeric,value numeric)
-
-AS $$
-  from crankshaft.bayesian_blocks import adaptive_histogram
-  return adaptive_histogram(table_name,column_name)
-$$ LANGUAGE plpythonu;
-
-CREATE OR REPLACE FUNCTION
-  cdb_simple_test (
-  )
-RETURNS NUMERIC
-
-AS $$
-  return 5
-$$ LANGUAGE plpythonu;
 -- Make sure by default there are no permissions for publicuser
 -- NOTE: this happens at extension creation time, as part of an implicit transaction.
 -- REVOKE ALL PRIVILEGES ON SCHEMA cdb_crankshaft FROM PUBLIC, publicuser CASCADE;

pg/sql/0.0.1/06_bayesian_blocks.sql

@@ -1,11 +0,0 @@
-CREATE OR REPLACE FUNCTION
-  cdb_adaptive_histogram (
-      table_name  TEXT,
-      column_name TEXT
-  )
-RETURNS TABLE (bin_start numeric,bin_end numeric,value numeric)
-
-AS $$
-  from crankshaft.bayesian_blocks import adaptive_histogram
-  return adaptive_histogram(table_name,column_name)
-$$ LANGUAGE plpythonu;

python/crankshaft/crankshaft/__init__.py

@@ -1,3 +1,2 @@
 import random_seeds
 import clustering
-import bayesian_blocks

python/crankshaft/crankshaft/bayesian_blocks/__init__.py

@@ -1 +0,0 @@
-from bayesian_blocks import *

python/crankshaft/crankshaft/bayesian_blocks/bayesian_blocks.py

@@ -1,84 +0,0 @@
-import plpy
-import numpy as np
-
-
-def adaptive_histogram(table_name,column_name):
-    data = plpy.execute("select {column_name} from {table_name}".format(**locals()))
-
-    data = [float(d['count']) for d in data]
-    plpy.notice(data)
-    vals, bins = np.histogram( data, bins=_bayesian_blocks(data))
-    return zip(vals,bins, bins[1:])
-
-
-def _bayesian_blocks(t):
-    """Bayesian Blocks Implementation
-
-    By Jake Vanderplas.  License: BSD
-    Based on algorithm outlined in http://adsabs.harvard.edu/abs/2012arXiv1207.5578S
-
-    Parameters
-    ----------
-    t : ndarray, length N
-        data to be histogrammed
-
-    Returns
-    -------
-    bins : ndarray
-        array containing the (N+1) bin edges
-
-    Notes
-    -----
-    This is an incomplete implementation: it may fail for some
-    datasets.  Alternate fitness functions and prior forms can
-    be found in the paper listed above.
-    """
-    # copy and sort the array
-    t = np.sort(t)
-    N = t.size
-
-    # create length-(N + 1) array of cell edges
-    edges = np.concatenate([t[:1],
-                            0.5 * (t[1:] + t[:-1]),
-                            t[-1:]])
-    block_length = t[-1] - edges
-
-    # arrays needed for the iteration
-    nn_vec = np.ones(N)
-    best = np.zeros(N, dtype=float)
-    last = np.zeros(N, dtype=int)
-
-    #-----------------------------------------------------------------
-    # Start with first data cell; add one cell at each iteration
-    #-----------------------------------------------------------------
-    for K in range(N):
-        # Compute the width and count of the final bin for all possible
-        # locations of the K^th changepoint
-        width = block_length[:K + 1] - block_length[K + 1]
-        count_vec = np.cumsum(nn_vec[:K + 1][::-1])[::-1]
-
-        # evaluate fitness function for these possibilities
-        fit_vec = count_vec * (np.log(count_vec) - np.log(width))
-        fit_vec -= 4  # 4 comes from the prior on the number of changepoints
-        fit_vec[1:] += best[:K]
-
-        # find the max of the fitness: this is the K^th changepoint
-        i_max = np.argmax(fit_vec)
-        last[K] = i_max
-        best[K] = fit_vec[i_max]
-
-    #-----------------------------------------------------------------
-    # Recover changepoints by iteratively peeling off the last block
-    #-----------------------------------------------------------------
-    change_points =  np.zeros(N, dtype=int)
-    i_cp = N
-    ind = N
-    while True:
-        i_cp -= 1
-        change_points[i_cp] = ind
-        if ind == 0:
-            break
-        ind = last[ind - 1]
-    change_points = change_points[i_cp:]
-
-    return edges[change_points]

python/crankshaft/setup.py

@@ -10,7 +10,7 @@ from setuptools import setup, find_packages
 setup(
     name='crankshaft',
 
-    version='0.0.1',
+    version='0.0.01',
 
     description='CartoDB Spatial Analysis Python Library',
 
@@ -40,9 +40,9 @@ setup(
 
     # The choice of component versions is dictated by what's
     # provisioned in the production servers.
-    install_requires=['pysal==1.11.0','numpy==1.10.1','scipy==0.17.0'],
+    install_requires=['pysal==1.11.0', 'numpy==1.10.4', 'scipy==0.17.0', 'pandas==0.17.1', 'scikit-learn==0.17.0', 'statsmodels==0.6.1', 'keras==0.3.2', 'shapely==1.5.3', 'osgeo==2.0.2','scikit-image==0.12.3'],
 
-    requires=['pysal', 'numpy'],
+    requires=['pysal', 'numpy', 'scipy', 'pandas', 'scikit-learn', 'statsmodels', 'keras', 'shapely', 'osgeo','skimage'],
 
     test_suite='test'
 )