Update documentation

Also, version the virtualenv

CONTRIBUTING.md

@@ -1,84 +0,0 @@
-# Contributing guide
-
-## How to add new functions
-
-Try to put as little logic in the SQL extension as possible and
-just use it as a wrapper to the Python module functionality.
-
-Once a function is defined it should never change its signature in subsequent
-versions. To change a function's signature a new function with a different
-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:
-
-* When backwards incompatibility is introduced the major number is incremented
-* When functionally is added (in a backwards-compatible manner) the minor number
-  is incremented
-* When only fixes are introduced (backwards-compatible) the patch number is
-  incremented
-
-### Python Package
-
-...
-
-### SQL Extension
-
-* Generate a **new subfolder version** for `sql` and `test` folders to define
-  the new functions and tests
-  - Use symlinks to avoid file duplication between versions that don't update them
-  - Add new files or modify copies of the old files to add new functions or
-    modify existing functions (remember to rename a function if the signature
-    changes)
-  - Add or modify the corresponding documentation files in the `doc` folder.
-    Since we expect to have highly technical functions here, an extense
-    background explanation would be of great help to users of this extension.
-  - Create tests for the new functions/behaviour
-
-* Generate the **upgrade and downgrade files** for the extension
-
-* Update the control file and the Makefile to generate the complete SQL
-  file for the new created version. After running `make` a new
-  file `crankshaft--X.Y.Z.sql` will be created for the current version.
-  Additional files for migrating to/from the previous version A.B.Z should be
-  created:
-  - `crankshaft--X.Y.Z--A.B.C.sql`
-  - `crankshaft--A.B.C--X.Y.Z.sql`
-  All these new files must be added to git and pushed.
-
-* Update the public docs! ;-)
-
-## Conventions
-
-# SQL
-
-Use snake case (i.e. `snake_case` and not `CamelCase`) for all
-functions. Prefix functions intended for public use with `cdb_`
-and private functions (to be used only internally inside
-the extension)  with `_cdb_`.
-
-# Python
-
-...
-
-## Testing
-
-Running just the Python tests:
-
-```
-(cd python && make test)
-```
-
-Installing the Extension and running just the PostgreSQL tests:
-
-```
-(cd pg && sudo make install && PGUSER=postgres make installcheck)
-```
-
-Installing and testing everything:
-
-```
-sudo make install && PGUSER=postgres make testinstalled
-```

Dockerfile

@@ -1,187 +0,0 @@
-# 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 = pg
+EXT_DIR = src/pg
-PYP_DIR = python
+PYP_DIR = src/py
 
 .PHONY: install
 .PHONY: run_tests

README.md

@@ -4,37 +4,99 @@ CartoDB Spatial Analysis extension for PostgreSQL.
 
 ## Code organization
 
-* *pg* contains the PostgreSQL extension source code
+* *doc* documentation
-* *python* Python module
+* *src* source code
-
+* - *src/pg* contains the PostgreSQL extension source code
-## Running with Docker
+* - *src/py* Python module source code
-
+* *release* reseleased versions
-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
+* pip, virtualenv, PostgreSQL
+* python-scipy system package (see src/py/README.md)
+
+# Working Process
+
+## Development
+
+Work in `src/pg/sql`, `src/py/crankshaft`;
+use a topic branch. See src/py/README.md
+for the procedure to work with the Python local environment.
+
+Take into account:
+
+*  Always remember to add tests for any new functionality
+   documentation.
+*  Add or modify the corresponding documentation files in the `doc` folder.
+   Since we expect to have highly technical functions here, an extense
+   background explanation would be of great help to users of this extension.
+*  Convention: Use snake case (i.e. `snake_case` and not `CamelCase`) for all
+   functions. Prefix functions intended for public use with `cdb_`
+   and private functions (to be used only internally inside
+   the extension)  with `_cdb_`.
+
+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:
+
+* `CREATE EXTENSION crankshaft WITH VERSION 'dev';`
+
+Once the tests are succeeding a new Pull-Request can be created.
+CI-tests must be checked to be successfull.
+
+Before merging a topic branch peer code reviewing of the code is a must.
+
+
+## Release
+
+The release process of a new version of the extension
+shall by performed by the designated *Release Manager*.
+
+Note that we expect to gradually automate this process.
+
+Having checkout the topic branch of the PR to be released:
+
+The version number in `pg/cranckshaft.control` must first be updated.
+To do so [Semantic Versioning 2.0](http://semver.org/) is in order.
+
+We now will explain the process for the case of backwards-compatible
+releases (updating the minor or patch version numbers).
+
+TODO: document the complex case of major releases.
+
+The next command must be executed to produce the main installation
+script for the new release, `release/cranckshaft--X.Y.Z.sql`.
+
+```
+make release
+```
+
+Then, the release manager shall produce upgrade and downgrade scripts
+to migrate to/from the previous release. In the case of minor/patch
+releases this simply consist in extracting the functions that have changed
+and placing them in the proper `release/cranckshaft--X.Y.Z--A.B.C.sql`
+file.
+
+TODO: configure the local enviroment to be used by the release;
+currently should be directory `src/py/X.Y.Z`, but this must be fixed;
+a possibility to explore is to use the `cdb_conf` table.
+
+TODO: testing procedure for the new release
+
+TODO: push, merge, tag, deploy procedures.

init_db.sh

@@ -1,77 +0,0 @@
-#!/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

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

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

@@ -1,148 +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;
--- 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/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;

pgpass

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

postgresql.sh

@@ -1,5 +0,0 @@
-#!/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/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/README.md

@@ -1,9 +0,0 @@
-# Crankshaft Python Package
-
-...
-### Run the tests
-
-```bash
-cd crankshaft
-nosetests test/
-```

run_server.sh

@@ -1,14 +0,0 @@
-#!/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

@@ -1,23 +0,0 @@
-#!/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

@@ -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 +1,48 @@
+# 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
+
+SED = sed
+
+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)
+
+VIRTUALENV_PATH = $(realpath ../py/)
+ESC_VIRVIRTUALENV_PATH = $(subst /,\/,$(VIRTUALENV_PATH))
+
+REPLACEMENTS = -e 's/@@VERSION@@/$(EXTVERSION)/g' \
+               -e 's/@@VIRTUALENV_PATH@@/$(ESC_VIRVIRTUALENV_PATH)/g'
+
+$(DATA): $(SOURCES_DATA)
+	$(SED) $(REPLACEMENTS) $(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

src/pg/sql/01_version.sql

@@ -0,0 +1,12 @@
+-- Version number of the extension release
+CREATE OR REPLACE FUNCTION cdb_crankshaft_version()
+RETURNS text AS $$
+  SELECT '@@VERSION@@'::text;
+$$ language 'sql' IMMUTABLE STRICT;
+
+-- Internal identifier of the installed extension instence
+-- e.g. 'dev' for current development version
+CREATE OR REPLACE FUNCTION cdb_crankshaft_internal_version()
+RETURNS text AS $$
+  SELECT installed_version FROM pg_available_extensions where name='crankshaft' and pg_available_extensions IS NOT NULL;
+$$ language 'sql' IMMUTABLE STRICT;

src/pg/sql/02_py.sql

@@ -0,0 +1,23 @@
+CREATE OR REPLACE FUNCTION _cdb_crankshaft_virtualenvs_path()
+RETURNS text
+AS $$
+  BEGIN
+    -- RETURN '/opt/virtualenvs/crankshaft';
+    RETURN '@@VIRTUALENV_PATH@@';
+  END;
+$$ language plpgsql IMMUTABLE STRICT;
+
+-- Use the crankshaft python module
+CREATE OR REPLACE FUNCTION _cdb_crankshaft_activate_py()
+RETURNS VOID
+AS $$
+    import os
+    # plpy.notice('%',str(os.environ))
+    # activate virtualenv
+    crankshaft_version = plpy.execute('SELECT cdb_crankshaft.cdb_crankshaft_internal_version()')[0]['cdb_crankshaft_internal_version']
+    base_path = plpy.execute('SELECT cdb_crankshaft._cdb_crankshaft_virtualenvs_path()')[0]['_cdb_crankshaft_virtualenvs_path']
+    default_venv_path = os.path.join(base_path, crankshaft_version)
+    venv_path =  os.environ.get('CRANKSHAFT_VENV', default_venv_path)
+    activate_path = venv_path + '/bin/activate_this.py'
+    exec(open(activate_path).read(), dict(__file__=activate_path))
+$$ LANGUAGE plpythonu;

src/pg/sql/03_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 --system-site-packages dev
+	./dev/bin/pip install -I ./crankshaft
+	./dev/bin/pip install -I nose
+
+# Test develpment install
+testinstalled:
+	./dev/bin/nosetests crankshaft/test/

src/py/README.md

@@ -0,0 +1,130 @@
+# Crankshaft Python Package
+
+...
+### Run the tests
+
+```bash
+cd crankshaft
+nosetests test/
+```
+
+## Notes about python dependencies
+* This extension is targeted at production databases. Therefore certain restrictions must be assumed about the production environment vs other experimental environments.
+* We're using `pip` and `virtualenv` to generate a suitable isolated environment for python code that has  all the dependencies
+* Every dependency should be:
+  - Added to the `setup.py` file
+  - Installed through it
+  - Tested, when they have a test suite.
+  - Fixed in the `requirements.txt`
+* At present we use Python version 2.7.3
+
+---
+
+We have two possible approaches being considered as to how manage
+the Python virtual environment: using a pure virtual enviroment
+or combine it with some system packages that include depencencies
+for the *hard-to-compile* packages (and pin them in somewhat old versions).
+
+### Alternative A: pure virtual environment
+
+In this case we will install all the packages needed in the
+virtual environment.
+This will involve, specially for the numerical packages compiling
+and linking code that uses a number of third party libraries,
+and requires having theses depencencies solved for the production
+environments.
+
+#### Create and use a virtual env
+
+We'll use a virtual enviroment directory `dev`
+under the `src/pg` directory.
+
+    # Create the virtual environment for python
+    $ virtualenv dev
+
+    # Activate the virtualenv
+    $ source dev/bin/activate
+
+    # Install all the requirements
+    # expect this to take a while, as it will trigger a few compilations
+    (dev) $ pip install -r requirements.txt
+
+    # Add a new pip to the party
+    (dev) $ pip install pandas
+
+#### Test the libraries with that virtual env
+
+##### Test numpy library dependency:
+
+    import numpy
+    numpy.test('full')
+
+##### Run scipy tests
+
+    import scipy
+    scipy.test('full')
+
+##### Testing pysal
+
+See [http://pysal.readthedocs.org/en/latest/developers/testing.html]
+
+This will require putting this into `dev/lib/python2.7/site-packages/setup.cfg`:
+
+```
+[nosetests]
+ignore-files=collection
+exclude-dir=pysal/contrib
+
+[wheel]
+universal=1
+```
+
+And copying some files before executing the tests:
+(we'll use a temporary directory from where the tests will be executed because
+some tests expect some files in the current directory). Next must be executed
+from
+
+```
+cp dev/lib/python2.7/site-packages/pysal/examples/geodanet/* dev/local/lib/python2.7/site-packages/pysal/examples
+mkdir -p test_tmp && cd test_tmp && cp ../dev/lib/python2.7/site-packages/pysal/examples/geodanet/* ./
+```
+
+Then, execute the tests with:
+
+    import pysal
+    import nose
+    nose.runmodule('pysal')
+
+
+### Alternative B: using some packaged modules
+
+This option avoids troublesome compilations/linkings, at the cost
+of freezing some module versions as available in system packages,
+namely numpy 1.6.1 and scipy 0.9.0. (in turn, this implies
+the most recent version of PySAL we can use is 1.9.1)
+
+
+TODO: to use this alternative the python-scipy package must be
+installed (this will have to be included in server provisioning)
+
+```
+apt-get install -y python-scipy
+```
+
+#### Create and use a virtual env
+
+We'll use a `dev` enviroment as before, but will configure it to
+use also system modules.
+
+
+    # Create the virtual environment for python
+    $ virtualenv --system-site-packages dev
+
+    # Activate the virtualenv
+    $ source dev/bin/activate
+
+    # Install all the requirements
+    # expect this to take a while, as it will trigger a few compilations
+    (dev) $ pip install -I ./crankshaft
+
+Then we can proceed to testing as in Alternative A.

src/py/crankshaft/setup.py

@@ -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==1.6.1','scipy==0.17.0'],
+    install_requires=['pysal==1.9.1'],
 
-    requires=['pysal', 'numpy'],
+    requires=['pysal', 'numpy' ],
 
     test_suite='test'
 )