Adding pysal to Docker

Dockerfile

@@ -0,0 +1,187 @@
+# PostgreSQL GIS stack
+#
+# This image includes the following tools
+# - PostgreSQL 9.5
+# - PostGIS 2.2 with raster, topology and sfcgal support
+# - OGR Foreign Data Wrapper
+# - PgRouting
+# - PDAL master
+# - PostgreSQL PointCloud version master
+#
+# Version 1.7
+
+FROM phusion/baseimage
+MAINTAINER Vincent Picavet, vincent.picavet@oslandia.com
+
+# Set correct environment variables.
+ENV HOME /root
+
+# Regenerate SSH host keys. baseimage-docker does not contain any, so you
+# have to do that yourself. You may also comment out this instruction; the
+# init system will auto-generate one during boot.
+RUN /etc/my_init.d/00_regen_ssh_host_keys.sh
+
+# Use baseimage-docker's init system.
+CMD ["/sbin/my_init"]
+
+
+RUN apt-get update && apt-get install -y wget ca-certificates
+
+# Use APT postgresql repositories for 9.5 version
+RUN echo "deb http://apt.postgresql.org/pub/repos/apt/ wheezy-pgdg main 9.5" > /etc/apt/sources.list.d/pgdg.list && wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
+
+# packages needed for compilation
+RUN apt-get update
+
+RUN apt-get install -y autoconf build-essential cmake docbook-mathml docbook-xsl libboost-dev libboost-thread-dev libboost-filesystem-dev libboost-system-dev libboost-iostreams-dev libboost-program-options-dev libboost-timer-dev libcunit1-dev libgdal-dev libgeos++-dev libgeotiff-dev libgmp-dev libjson0-dev libjson-c-dev liblas-dev libmpfr-dev libopenscenegraph-dev libpq-dev libproj-dev libxml2-dev postgresql-server-dev-9.5 xsltproc git build-essential wget
+
+RUN add-apt-repository ppa:fkrull/deadsnakes &&\
+    apt-get update &&\
+    apt-get install -y python3.2
+
+
+
+
+# application packages
+RUN apt-get install -y postgresql-9.5 postgresql-plpython-9.5
+
+
+# Download and compile CGAL
+RUN wget https://gforge.inria.fr/frs/download.php/file/32994/CGAL-4.3.tar.gz &&\
+    tar -xzf CGAL-4.3.tar.gz &&\
+    cd CGAL-4.3 &&\
+    mkdir build && cd build &&\
+    cmake .. &&\
+    make -j3 && make install
+
+# orig sfcgal method
+# download and compile SFCGAL
+# RUN git clone https://github.com/Oslandia/SFCGAL.git
+# RUN cd SFCGAL && cmake . && make -j3 && make install
+# # cleanup
+# RUN rm -Rf SFCGAL
+
+# andrewxhill fix for stable sfcgal version
+RUN wget https://github.com/Oslandia/SFCGAL/archive/v1.2.0.tar.gz
+RUN tar -xzf v1.2.0.tar.gz
+RUN cd SFCGAL-1.2.0 && cmake . && make -j 1 && make install
+RUN rm -Rf v1.2.0.tar.gz SFCGAL-1.2.0
+
+# download and install GEOS 3.5
+RUN wget http://download.osgeo.org/geos/geos-3.5.0.tar.bz2 &&\
+    tar -xjf geos-3.5.0.tar.bz2 &&\
+    cd geos-3.5.0 &&\
+    ./configure && make && make install &&\
+    cd .. && rm -Rf geos-3.5.0 geos-3.5.0.tar.bz2
+
+# Download and compile PostGIS
+RUN wget http://download.osgeo.org/postgis/source/postgis-2.2.0.tar.gz
+RUN tar -xzf postgis-2.2.0.tar.gz
+RUN cd postgis-2.2.0 && ./configure --with-sfcgal=/usr/local/bin/sfcgal-config --with-geos=/usr/local/bin/geos-config
+RUN cd postgis-2.2.0 && make && make install
+# cleanup
+RUN rm -Rf postgis-2.2.0.tar.gz postgis-2.2.0
+
+# Download and compile pgrouting
+RUN git clone https://github.com/pgRouting/pgrouting.git &&\
+    cd pgrouting &&\
+    mkdir build && cd build &&\
+    cmake -DWITH_DOC=OFF -DWITH_DD=ON .. &&\
+    make -j3 && make install
+# cleanup
+RUN rm -Rf pgrouting
+
+
+
+# Download and compile ogr_fdw
+RUN git clone https://github.com/pramsey/pgsql-ogr-fdw.git &&\
+    cd pgsql-ogr-fdw &&\
+    make && make install &&\
+    cd .. && rm -Rf pgsql-ogr-fdw
+
+# Compile PDAL
+RUN git clone https://github.com/PDAL/PDAL.git pdal
+RUN mkdir PDAL-build && \
+    cd PDAL-build && \
+    cmake ../pdal && \
+    make -j3 && \
+    make install
+# cleanup
+RUN rm -Rf pdal && rm -Rf PDAL-build
+
+# Compile PointCloud
+RUN git clone https://github.com/pramsey/pointcloud.git
+RUN cd pointcloud && ./autogen.sh && ./configure && make -j3 && make install
+# cleanup
+RUN rm -Rf pointcloud
+
+
+RUN git clone https://github.com/CartoDB/cartodb-postgresql.git &&\
+    cd cartodb-postgresql &&\
+    make all install &&\
+    cd .. && rm -Rf cartodb-postgresql
+
+# install pip
+
+RUN apt-get -y  install python-dev python-pip  liblapack-dev gfortran libyaml-dev
+
+RUN pip install numpy pandas scipy theano keras sklearn
+RUN pip install pysal
+
+# get compiled libraries recognized
+RUN ldconfig
+
+# clean packages
+
+# all -dev packages
+# RUN apt-get remove -y --purge autotools-dev libgeos-dev libgif-dev libgl1-mesa-dev libglu1-mesa-dev libgnutls-dev libgpg-error-dev libhdf4-alt-dev libhdf5-dev libicu-dev libidn11-dev libjasper-dev libjbig-dev libjpeg8-dev libjpeg-dev libjpeg-turbo8-dev libkrb5-dev libldap2-dev libltdl-dev liblzma-dev libmysqlclient-dev libnetcdf-dev libopenthreads-dev libp11-kit-dev libpng12-dev libpthread-stubs0-dev librtmp-dev libspatialite-dev libsqlite3-dev libssl-dev libstdc++-4.8-dev libtasn1-6-dev libtiff5-dev libwebp-dev libx11-dev libx11-xcb-dev libxau-dev libxcb1-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-present-dev libxcb-randr0-dev libxcb-render0-dev libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxdamage-dev libxdmcp-dev libxerces-c-dev libxext-dev libxfixes-dev libxshmfence-dev libxxf86vm-dev linux-libc-dev manpages-dev mesa-common-dev libgcrypt11-dev unixodbc-dev uuid-dev x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev x11proto-xf86vidmode-dev xtrans-dev zlib1g-dev
+
+# installed packages
+# RUN apt-get remove -y --purge autoconf build-essential cmake docbook-mathml docbook-xsl libboost-dev libboost-filesystem-dev libboost-timer-dev libcgal-dev libcunit1-dev libgdal-dev libgeos++-dev libgeotiff-dev libgmp-dev libjson0-dev libjson-c-dev liblas-dev libmpfr-dev libopenscenegraph-dev libpq-dev libproj-dev libxml2-dev postgresql-server-dev-9.5 xsltproc git build-essential wget
+
+# additional compilation packages
+# RUN apt-get remove -y --purge automake m4 make
+
+
+
+
+# ---------- SETUP --------------
+
+# add a baseimage PostgreSQL init script
+RUN mkdir /etc/service/postgresql
+ADD postgresql.sh /etc/service/postgresql/run
+
+# Adjust PostgreSQL configuration so that remote connections to the
+# database are possible.
+RUN echo "host all  all    0.0.0.0/0  md5" >> /etc/postgresql/9.5/main/pg_hba.conf
+
+# And add ``listen_addresses`` to ``/etc/postgresql/9.5/main/postgresql.conf``
+RUN echo "listen_addresses='*'" >> /etc/postgresql/9.5/main/postgresql.conf
+
+# Expose PostgreSQL
+EXPOSE 5432
+
+# Add VOLUMEs to allow backup of config, logs and databases
+VOLUME  ["/data", "/etc/postgresql", "/var/log/postgresql", "/var/lib/postgresql"]
+
+# Add pip
+
+
+# http://bugs.python.org/issue19846
+# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
+ENV LANG C.UTF-8
+
+
+# add database setup upon image start
+ADD pgpass /root/.pgpass
+RUN chmod 700 /root/.pgpass
+RUN mkdir -p /etc/my_init.d
+ADD init_db_script.sh /etc/my_init.d/init_db_script.sh
+ADD init_db.sh /root/init_db.sh
+ADD run_tests.sh /root/run_tests.sh
+ADD run_tests.sh /root/run_server.sh
+
+# ---------- Final cleanup --------------
+#
+# Clean up APT when done.
+# RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

Makefile

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

README.md

@@ -4,87 +4,37 @@ CartoDB Spatial Analysis extension for PostgreSQL.
 
 ## Code organization
 
-* *doc* documentation
-* *src* source code
-* - *src/pg* contains the PostgreSQL extension source code
-* - *src/py* Python module source code
-* *release* reselesed versions
+* *pg* contains the PostgreSQL extension source code
+* *python* Python module
+
+## Running with Docker
+
+Crankshaft comes with a Dockerfile to build and run a sandboxed machine for testing
+and development.
+
+First you have to build the docker container
+
+    docker build -t crankshaft .
+
+To run the pg tests run
+
+    docker run -it --rm -v $(pwd):/crankshaft  crankshaft /root/run_tests.sh
+
+if there are failures it will dump the reasion to the screen.
+
+To run a server you can develop on run
+
+    docker run -it --rm -v $(pwd):/crankshaft -p $(docker-machine ip default):5432:5432 /root/run_server.sh
+
+and connect from you host using
+
+    psql -U pggis -h $(docker-machine ip default) -p 5432 -W
+
+the password is pggis
+
+
+
 
 ## Requirements
 
-* 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...
+* pip

init_db.sh

@@ -0,0 +1,77 @@
+#!/bin/bash
+
+# wait for pg server to be ready
+echo "Waiting for PostgreSQL to run..."
+sleep 1
+while ! /usr/bin/pg_isready -q
+do
+    sleep 1
+    echo -n "."
+done
+
+# PostgreSQL running
+echo "PostgreSQL running, initializing database."
+
+# PostgreSQL user
+#
+# create postgresql user pggis
+
+/sbin/setuser postgres /usr/bin/psql -c "CREATE USER pggis with SUPERUSER PASSWORD 'pggis';"
+/sbin/setuser postgres /usr/bin/psql -c "CREATE role publicuser;"
+# == Auto restore dumps ==
+#
+# If we find some postgresql dumps in /data/restore, then we load it
+# in new databases
+shopt -s nullglob
+for f in /data/restore/*.backup
+do
+	echo "Found database dump to restore : $f"
+    DBNAME=$(basename -s ".backup" "$f")
+    echo "Creating a new database $DBNAME.."
+    /usr/bin/psql -U pggis -h localhost -c "CREATE DATABASE $DBNAME WITH OWNER = pggis     ENCODING = 'UTF8'     TEMPLATE = template0    CONNECTION LIMIT = -1;" postgres
+    /usr/bin/psql -U pggis -h localhost -w -c "CREATE EXTENSION citext; CREATE EXTENSION pg_trgm; CREATE EXTENSION btree_gist; CREATE EXTENSION hstore; CREATE EXTENSION fuzzystrmatch; CREATE EXTENSION unaccent; CREATE EXTENSION postgres_fdw; CREATE EXTENSION pgcrypto; CREATE EXTENSION plpythonu; CREATE EXTENSION postgis; CREATE EXTENSION postgis_topology; CREATE EXTENSION pgrouting; CREATE EXTENSION pointcloud; CREATE EXTENSION pointcloud_postgis; CREATE EXTENSION postgis_sfcgal; drop type if exists texture; create type texture as (url text,uv float[][]);CREATE ROLE publicuser;" $DBNAME
+
+#    /usr/bin/psql -U pggis -h localhost -w -f /usr/share/postgresql/9.5/contrib/postgis-2.1/sfcgal.sql -d $DBNAME
+
+
+    echo "Restoring database $DBNAME.."
+    /usr/bin/pg_restore -U pggis -h localhost -d $DBNAME -w "$f"
+
+    echo "creating public user"
+    /usr/bin/psql -U pggis -h localhost -w -c "CREATE ROLE publicuser;"
+
+    echo "Restore done."
+
+done
+
+# == Auto restore SQL backups ==
+#
+# If we find some postgresql sql scripts /data/restore, then we load it
+# in new databases
+shopt -s nullglob
+for f in /data/restore/*.sql
+do
+	echo "Found database SQL dump to restore : $f"
+    DBNAME=$(basename -s ".sql" "$f")
+    echo "Creating a new database $DBNAME.."
+    /usr/bin/psql -U pggis -h localhost -c "CREATE DATABASE $DBNAME WITH OWNER = pggis     ENCODING = 'UTF8'     TEMPLATE = template0    CONNECTION LIMIT = -1;" postgres
+    /usr/bin/psql -U pggis -h localhost -w -c "CREATE EXTENSION citext; CREATE EXTENSION pg_trgm; CREATE EXTENSION btree_gist; CREATE EXTENSION hstore; CREATE EXTENSION fuzzystrmatch; CREATE EXTENSION unaccent; CREATE EXTENSION postgres_fdw; CREATE EXTENSION pgcrypto; CREATE EXTENSION plpythonu; CREATE EXTENSION postgis; CREATE EXTENSION postgis_topology; CREATE EXTENSION postgis_sfcgal; CREATE EXTENSION pgrouting; CREATE EXTENSION pointcloud; CREATE EXTENSION pointcloud_postgis; drop type if exists texture; create type texture as (url text,uv float[][]);" $DBNAME
+#    /usr/bin/psql -U pggis -h localhost -w -f /usr/share/postgresql/9.5/contrib/postgis-2.1/sfcgal.sql -d $DBNAME
+    echo "Restoring database $DBNAME.."
+    /usr/bin/psql -U pggis -h localhost -d $DBNAME -w -f "$f"
+    echo "Restore done."
+done
+
+# == create new database pggis ==
+echo "Creating a new empty database..."
+# create user and main database
+/usr/bin/psql -U pggis -h localhost -c "CREATE DATABASE pggis WITH OWNER = pggis     ENCODING = 'UTF8'     TEMPLATE = template0    CONNECTION LIMIT = -1;" postgres
+
+# activate all needed extension in pggis database
+/usr/bin/psql -U pggis -h localhost -w -c "CREATE EXTENSION citext; CREATE EXTENSION pg_trgm; CREATE EXTENSION btree_gist; CREATE EXTENSION hstore; CREATE EXTENSION fuzzystrmatch; CREATE EXTENSION unaccent; CREATE EXTENSION postgres_fdw; CREATE EXTENSION pgcrypto; CREATE EXTENSION plpythonu; CREATE EXTENSION postgis; CREATE EXTENSION postgis_topology; CREATE EXTENSION postgis_sfcgal; CREATE EXTENSION pgrouting; CREATE EXTENSION pointcloud; CREATE EXTENSION pointcloud_postgis; drop type if exists texture;
+create type texture as (url text,uv float[][]);" pggis
+#/usr/bin/psql -U pggis -h localhost -w -f /usr/share/postgresql/9.5/contrib/postgis-2.1/sfcgal.sql -d pggis
+
+echo "Database initialized. Connect from host with :"
+echo "psql -h localhost -p <PORT> -U pggis -W pggis"
+echo "Get <PORT> value with 'docker ps'"

init_db_script.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+# Script for my_init.d, so as to run database init without blocking
+/root/init_db.sh &

pg/.gitignore

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

pg/Makefile

@@ -0,0 +1,33 @@
+# 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

@@ -0,0 +1,148 @@
+--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;
+-- 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/0.0.1/01_random_seeds.sql

@@ -4,7 +4,6 @@
 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;

pg/sql/0.0.1/02_moran.sql

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

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

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

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

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

pg/test/0.0.1/sql/01_install_test.sql

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

pgpass

@@ -0,0 +1 @@
+localhost:5432:*:pggis:pggis

postgresql.sh

@@ -0,0 +1,5 @@
+#!/bin/sh
+# `/sbin/setuser postgres` runs the given command as the user `postgres`.
+# If you omit that part, the command will be run as root.
+rm -rf /etc/ssl/private-copy; mkdir /etc/ssl/private-copy; mv /etc/ssl/private/* /etc/ssl/private-copy/; rm -r /etc/ssl/private; mv /etc/ssl/private-copy /etc/ssl/private; chmod -R 0700 /etc/ssl/private; chown -R postgres /etc/ssl/private
+exec /sbin/setuser postgres /usr/lib/postgresql/9.5/bin/postgres -D /var/lib/postgresql/9.5/main -c config_file=/etc/postgresql/9.5/main/postgresql.conf >> /var/log/postgresql.log 2>&1

python/.gitignore

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

python/Makefile

@@ -0,0 +1,11 @@
+# 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/

run_server.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+/sbin/my_init &
+
+echo "Waiting for PostgreSQL to run..."
+sleep 1
+while ! /usr/bin/pg_isready -q
+do
+    sleep 1
+    echo -n "."
+done
+
+cd /crankshaft/pg
+make install
+fg

run_tests.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+/sbin/my_init &
+
+echo "Waiting for PostgreSQL to run..."
+sleep 1
+while ! /usr/bin/pg_isready -q
+do
+    sleep 1
+    echo -n "."
+done
+
+cd /crankshaft/pg
+make install
+PGUSER=pggis PGPASSOWRD=pggis PGHOST=localhost make installcheck
+
+
+
+if [ "$?" -eq "0" ]
+then
+  echo "PASSED"
+else
+  cat /crankshaft/pg/test/0.0.1/regression.diffs
+fi

src/pg/.gitignore

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

src/pg/Makefile

@@ -1,41 +0,0 @@
-# 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

@@ -1,18 +0,0 @@
--- 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/py/Makefile

@@ -1,9 +0,0 @@
-# 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/