Modify sql code to user the python virtualenv

Makefile

@@ -1,5 +1,5 @@
-EXT_DIR = pg
-PYP_DIR = python
+EXT_DIR = src/pg
+PYP_DIR = src/py
 
 .PHONY: install
 .PHONY: run_tests

README.md

@@ -4,9 +4,87 @@ CartoDB Spatial Analysis extension for PostgreSQL.
 
 ## Code organization
 
-* *pg* contains the PostgreSQL extension source code
-* *python* Python module
+* *doc* documentation
+* *src* source code
+* - *src/pg* contains the PostgreSQL extension source code
+* - *src/py* Python module source code
+* *release* reselesed versions
 
 ## Requirements
 
-* pip
+* pip, virtualenv, PostgreSQL
+
+# Working Process
+
+## Development
+
+Work in `src/pg/sql`, `src/py/crankshaft`;
+use topic branch.
+
+Update local installation with `sudo make install`
+(this will update the 'dev' version of the extension in 'src/pg/')
+
+Run the tests with `PGUSER=postgres make test`
+
+Update extension in working database with
+
+* `ALTER EXTENSION crankshaft VERSION TO 'current';`
+  `ALTER EXTENSION crankshaft VERSION TO 'dev';`
+
+Note: we keep the current development version install as 'dev' always;
+we update through the 'current' alias to allow changing the extension
+contents but not the version identifier. This will fail if the
+changes involve incompatible function changes such as a different
+return type; in that case the offending function (or the whole extension)
+should be dropped manually before the update.
+
+If the extension has not previously been installed in a database
+we can:
+
+Add tests...
+
+* `CREATE EXTENSION crankshaft WITH VERSION 'dev';`
+
+Test
+
+Commit, push, create PR, wait for CI tests, CR, ...
+
+## Release
+
+To release current development version
+(working directory should be clean in dev branch)
+
+(process to be gradually automated)
+
+For backwards compatible changes (no return value, num of arguments, etc. changes...)
+new version number increasing either patch level (no new functionality)
+or minor level (new functionality) => 'X.Y.Z'.
+Update version in src/pg/crankshaft.control
+Copy release/crankshaft--current.sql to release/crankshaft--X.Y.Z.sql
+Prepare incremental downgrade, upgrade scripts....
+
+Python: ...
+
+Install the new release
+
+`make install-release`
+
+Test the new release
+
+`make test-release`
+
+Push the release
+
+Wait for CI tests
+
+Merge into master
+
+Deploy: install extension and python to production hosts,
+update extension in databases (limited to team users, data observatory, ...)
+
+Release manager role: ...
+
+.sql release scripts
+commit
+tests: staging....
+merge, tag, deploy...

pg/.gitignore

@@ -1,3 +0,0 @@
-regression.diffs
-regression.out
-results/

pg/Makefile

@@ -1,33 +0,0 @@
-# Makefile to generate the extension out of separate sql source files.
-# Once a version is released, it is not meant to be changed. E.g: once version 0.0.1 is out, it SHALL NOT be changed.
-
-EXTENSION    = crankshaft
-EXTVERSION   = $(shell grep default_version $(EXTENSION).control | sed -e "s/default_version[[:space:]]*=[[:space:]]*'\([^']*\)'/\1/")
-
-# The new version to be generated from templates
-NEW_EXTENSION_ARTIFACT = $(EXTENSION)--$(EXTVERSION).sql
-
-# DATA is a special variable used by postgres build infrastructure
-# These are the files to be installed in the server shared dir,
-# for installation from scratch, upgrades and downgrades.
-# @see http://www.postgresql.org/docs/current/static/extend-pgxs.html
-DATA =  $(NEW_EXTENSION_ARTIFACT)
-
-SOURCES_DATA_DIR = sql/$(EXTVERSION)
-SOURCES_DATA = $(wildcard sql/$(EXTVERSION)/*.sql)
-
-# The extension installation artifacts are stored in the base subdirectory
-$(NEW_EXTENSION_ARTIFACT): $(SOURCES_DATA)
-	rm -f $@
-	cat $(SOURCES_DATA_DIR)/*.sql >> $@
-
-REGRESS = $(notdir $(basename $(wildcard test/$(EXTVERSION)/sql/*test.sql)))
-TEST_DIR = test/$(EXTVERSION)
-REGRESS_OPTS = --inputdir='$(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

@@ -1,195 +0,0 @@
---DO NOT MODIFY THIS FILE, IT IS GENERATED AUTOMATICALLY FROM SOURCES
--- Complain if script is sourced in psql, rather than via CREATE EXTENSION
-\echo Use "CREATE EXTENSION crankshaft" to load this file. \quit
--- Internal function.
--- Set the seeds of the RNGs (Random Number Generators)
--- used internally.
-CREATE OR REPLACE FUNCTION
-_cdb_random_seeds (seed_value INTEGER) RETURNS VOID
-AS $$
-  from crankshaft import random_seeds
-  random_seeds.set_random_seeds(seed_value)
-$$ LANGUAGE plpythonu;
--- Moran's I
-CREATE OR REPLACE FUNCTION
-  cdb_moran_local (
-      t TEXT,
-  	  attr TEXT,
-  	  significance float DEFAULT 0.05,
-  	  num_ngbrs INT DEFAULT 5,
-  	  permutations INT DEFAULT 99,
-  	  geom_column TEXT DEFAULT 'the_geom',
-  	  id_col TEXT DEFAULT 'cartodb_id',
-      w_type TEXT DEFAULT 'knn')
-RETURNS TABLE (moran FLOAT, quads TEXT, significance FLOAT, ids INT)
-AS $$
-  from crankshaft.clustering import moran_local
-  # TODO: use named parameters or a dictionary
-  return moran_local(t, attr, significance, num_ngbrs, permutations, geom_column, id_col, w_type)
-$$ LANGUAGE plpythonu;
-
--- Moran's I Local Rate
-CREATE OR REPLACE FUNCTION
-  cdb_moran_local_rate(t TEXT,
-		 numerator TEXT,
-		 denominator TEXT,
-		 significance FLOAT DEFAULT 0.05,
-		 num_ngbrs INT DEFAULT 5,
-		 permutations INT DEFAULT 99,
-		 geom_column TEXT DEFAULT 'the_geom',
-		 id_col TEXT DEFAULT 'cartodb_id',
-		 w_type TEXT DEFAULT 'knn')
-RETURNS TABLE(moran FLOAT, quads TEXT, significance FLOAT, ids INT, y numeric)
-AS $$
-  from crankshaft.clustering import moran_local_rate
-  # TODO: use named parameters or a dictionary
-  return moran_local_rate(t, numerator, denominator, significance, num_ngbrs, permutations, geom_column, id_col, w_type)
-$$ LANGUAGE plpythonu;
--- Function by Stuart Lynn for a simple interpolation of a value
--- from a polygon table over an arbitrary polygon
--- (weighted by the area proportion overlapped)
--- Aereal weighting is a very simple form of aereal interpolation.
---
--- Parameters:
---   * geom a Polygon geometry which defines the area where a value will be
---     estimated as the area-weighted sum of a given table/column
---   * target_table_name table name of the table that provides the values
---   * target_column column name of the column that provides the values
---   * schema_name optional parameter to defina the schema the target table
---     belongs to, which is necessary if its not in the search_path.
---     Note that target_table_name should never include the schema in it.
--- Return value:
---   Aereal-weighted interpolation of the column values over the geometry
-CREATE OR REPLACE
-FUNCTION cdb_overlap_sum(geom geometry, target_table_name text, target_column text, schema_name text DEFAULT NULL)
-  RETURNS numeric AS
-$$
-DECLARE
-	result numeric;
-  qualified_name text;
-BEGIN
-  IF schema_name IS NULL THEN
-    qualified_name := Format('%I', target_table_name);
-  ELSE
-    qualified_name := Format('%I.%s', schema_name, target_table_name);
-  END IF;
-  EXECUTE Format('
-    SELECT sum(%I*ST_Area(St_Intersection($1, a.the_geom))/ST_Area(a.the_geom))
-    FROM %s AS a
-    WHERE $1 && a.the_geom
-  ', target_column, qualified_name)
-  USING geom
-  INTO result;
-  RETURN result;
-END;
-$$ LANGUAGE plpgsql;
---
--- Creates N points randomly distributed arround the polygon
---
--- @param g - the geometry to be turned in to points
---
--- @param no_points - the number of points to generate
---
--- @params max_iter_per_point - the function generates points in the polygon's bounding box
--- and discards points which don't lie in the polygon. max_iter_per_point specifies how many
--- misses per point the funciton accepts before giving up.
---
--- Returns: Multipoint with the requested points
-CREATE OR REPLACE FUNCTION cdb_dot_density(geom geometry , no_points Integer, max_iter_per_point Integer DEFAULT 1000)
-RETURNS GEOMETRY AS $$
-DECLARE
-  extent GEOMETRY;
-  test_point Geometry;
-  width                NUMERIC;
-  height               NUMERIC;
-  x0                   NUMERIC;
-  y0                   NUMERIC;
-  xp                   NUMERIC;
-  yp                   NUMERIC;
-  no_left              INTEGER;
-  remaining_iterations INTEGER;
-  points               GEOMETRY[];
-  bbox_line            GEOMETRY;
-  intersection_line    GEOMETRY;
-BEGIN
-  extent  := ST_Envelope(geom);
-  width   := ST_XMax(extent) - ST_XMIN(extent);
-  height  := ST_YMax(extent) - ST_YMIN(extent);
-  x0 	  := ST_XMin(extent);
-  y0 	  := ST_YMin(extent);
-  no_left := no_points;
-
-  LOOP
-    if(no_left=0) THEN
-      EXIT;
-    END IF;
-    yp = y0 + height*random();
-    bbox_line  = ST_MakeLine(
-      ST_SetSRID(ST_MakePoint(yp, x0),4326),
-      ST_SetSRID(ST_MakePoint(yp, x0+width),4326)
-    );
-    intersection_line = ST_Intersection(bbox_line,geom);
-  	test_point = ST_LineInterpolatePoint(st_makeline(st_linemerge(intersection_line)),random());
-	  points := points || test_point;
-	  no_left = no_left - 1 ;
-  END LOOP;
-  RETURN ST_Collect(points);
-END;
-$$
-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;
-
--- Grant permissions on the schema to publicuser (but just the schema)
-GRANT USAGE ON SCHEMA cdb_crankshaft TO publicuser;
-
--- Revoke execute permissions on all functions in the schema by default
--- REVOKE EXECUTE ON ALL FUNCTIONS IN SCHEMA cdb_crankshaft FROM PUBLIC, publicuser;

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;

pg/test/0.0.1/results/01_install_test.out

@@ -1,6 +0,0 @@
--- Install dependencies
-CREATE EXTENSION plpythonu;
-CREATE EXTENSION postgis;
-CREATE EXTENSION cartodb;
--- Install the extension
-CREATE EXTENSION crankshaft;

python/Makefile

@@ -1,11 +0,0 @@
-# Install the package (needs root privileges)
-install:
-	pip install ./crankshaft --upgrade
-
-# Test from source code
-test:
-	(cd crankshaft && nosetests test/)
-
-# Test currently installed package
-testinstalled:
-	nosetests crankshaft/test/

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]

src/pg/.gitignore

@@ -0,0 +1,6 @@
+regression.diffs
+regression.out
+results/
+crankshaft--dev.sql
+crankshaft--dev--current.sql
+crankshaft--current--dev.sql

src/pg/Makefile

@@ -0,0 +1,41 @@
+# Generation of a new development version 'dev' (with an alias 'current' for
+# updating easily by upgrading to 'current', then 'dev')
+
+# sudo make install -- generate the 'dev' version from current source
+#                      and make it available to PostgreSQL
+# PGUSER=postgres make installcheck -- test the 'dev' extension
+
+EXTENSION    = crankshaft
+
+DATA         = $(EXTENSION)--dev.sql \
+	             $(EXTENSION)--current--dev.sql \
+	             $(EXTENSION)--dev--current.sql
+
+SOURCES_DATA_DIR = sql
+SOURCES_DATA = $(wildcard $(SOURCES_DATA_DIR)/*.sql)
+
+$(DATA): $(SOURCES_DATA)
+	cat $(SOURCES_DATA_DIR)/*.sql > $@
+
+TEST_DIR = test
+REGRESS = $(notdir $(basename $(wildcard $(TEST_DIR)/sql/*test.sql)))
+REGRESS_OPTS = --inputdir='$(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)
+
+# WIP: goals for releasing the extension...
+
+EXTVERSION   = $(shell grep default_version $(EXTENSION).control | sed -e "s/default_version[[:space:]]*=[[:space:]]*'\([^']*\)'/\1/")
+
+../release/$(EXTENSION).control: $(EXTENSION).control
+	cp $< $@
+
+release: ../release/$(EXTENSION).control
+	cp $(EXTENSION)--dev.sql $(EXTENSION)--$(EXTVERSION).sql
+	# pending: create upgrade/downgrade scripts,
+	#          commit, push, tag....

src/pg/sql/01_py.sql

@@ -0,0 +1,18 @@
+-- Use the crankshaft python module
+CREATE OR REPLACE FUNCTION _cdb_crankshaft_activate_py()
+RETURNS VOID
+AS $$
+    # activate virtualenv
+    # TODO: parameterize with environment variables or something
+    venv_path = '/home/ubuntu/crankshaft/src/py/dev'
+    activate_path = venv_path + '/bin/activate_this.py'
+    exec(open(activate_path).read(),
+         dict(__file__=activate_path))
+
+    # import something from virtualenv
+    # from crankshaft import random_seeds
+
+    # do some stuff
+    # random_seeds.set_random_seeds(123)
+    # plpy.notice('here we are')
+$$ LANGUAGE plpythonu;

src/pg/sql/02_random_seeds.sql

@@ -4,6 +4,7 @@
 CREATE OR REPLACE FUNCTION
 _cdb_random_seeds (seed_value INTEGER) RETURNS VOID
 AS $$
+  plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_activate_py()')
   from crankshaft import random_seeds
   random_seeds.set_random_seeds(seed_value)
 $$ LANGUAGE plpythonu;

src/pg/sql/10_moran.sql

@@ -11,6 +11,7 @@ CREATE OR REPLACE FUNCTION
       w_type TEXT DEFAULT 'knn')
 RETURNS TABLE (moran FLOAT, quads TEXT, significance FLOAT, ids INT)
 AS $$
+  plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_activate_py()')
   from crankshaft.clustering import moran_local
   # TODO: use named parameters or a dictionary
   return moran_local(t, attr, significance, num_ngbrs, permutations, geom_column, id_col, w_type)
@@ -29,6 +30,7 @@ CREATE OR REPLACE FUNCTION
 		 w_type TEXT DEFAULT 'knn')
 RETURNS TABLE(moran FLOAT, quads TEXT, significance FLOAT, ids INT, y numeric)
 AS $$
+  plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_activate_py()')
   from crankshaft.clustering import moran_local_rate
   # TODO: use named parameters or a dictionary
   return moran_local_rate(t, numerator, denominator, significance, num_ngbrs, permutations, geom_column, id_col, w_type)

src/pg/test/expected/01_install_test.out

@@ -3,4 +3,4 @@ CREATE EXTENSION plpythonu;
 CREATE EXTENSION postgis;
 CREATE EXTENSION cartodb;
 -- Install the extension
-CREATE EXTENSION crankshaft;
+CREATE EXTENSION crankshaft VERSION 'dev';

src/pg/test/sql/01_install_test.sql

@@ -4,4 +4,4 @@ CREATE EXTENSION postgis;
 CREATE EXTENSION cartodb;
 
 -- Install the extension
-CREATE EXTENSION crankshaft;
+CREATE EXTENSION crankshaft VERSION 'dev';

src/py/.gitignore

@@ -1 +1,2 @@
 *.pyc
+dev/

src/py/Makefile

@@ -0,0 +1,9 @@
+# Install the package locally for development
+install:
+	virtualenv dev
+	./dev/bin/pip install ./crankshaft --upgrade
+	./dev/bin/pip install nose
+
+# Test develpment install
+testinstalled:
+	./dev/bin/nosetests crankshaft/test/

src/py/crankshaft/crankshaft/__init__.py

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

src/py/crankshaft/setup.py

@@ -40,7 +40,7 @@ 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==1.6.1','scipy==0.17.0'],
 
     requires=['pysal', 'numpy'],