more cleaning

Makefile

@@ -152,7 +152,7 @@ testdata:
 	@echo "Updating inasafe_data - public test and demo data repository"
 	@echo "You should update the hash to check out a specific data version"
 	@echo "-----------------------------------------------------------"
-	@scripts/update-test-data.sh 1ba76b17cb9f5d5bf521bdfac0a03f9929cacef3 2>&1 | tee tmp_warnings.txt; [ $${PIPESTATUS[0]} -eq 0 ] && rm -f tmp_warnings.txt || echo "Stored update warnings in tmp_warnings.txt";
+	@scripts/update-test-data.sh e550ec0edae9e6cb6bc3653e76a357dd0af559af 2>&1 | tee tmp_warnings.txt; [ $${PIPESTATUS[0]} -eq 0 ] && rm -f tmp_warnings.txt || echo "Stored update warnings in tmp_warnings.txt";
 
 #check and show if there was an error retrieving the test data
 testdata_errorcheck:
@@ -291,4 +291,4 @@ jenkins-pep8:
 	@echo "-----------------------------"
 	@echo "PEP8 issue check for Jenkins"
 	@echo "-----------------------------"
-	@pep8 --repeat --ignore=E203 --exclude docs,odict.py,keywords_dialog_base.py,dock_base.py,options_dialog_base.py,resources.py,resources_rc.py,help_base.py,xml_tools.py,system_tools.py,data_audit.py,data_audit_wrapper.py,impact_functions_doc_base.py . > pep8.log || :
+	@pep8 --repeat --ignore=E203 --exclude docs,odict.py,keywords_dialog_base.py,dock_base.py,options_dialog_base.py,resources.py,resources_rc.py,help_base.py,xml_tools.py,system_tools.py,data_audit.py,data_audit_wrapper.py,impact_functions_doc_base.py,configurable_impact_functions_dialog_base.py . > pep8.log || :

docs/make.bat

@@ -5,7 +5,7 @@ REM Command file for Sphinx documentation
 path %PATH%;"%OSGEO4W_ROOT%\apps\Python25\Scripts\"
 set PYTHONPATH=%PYTHONPATH%;%OSGEO4W_ROOT%\\apps\\qgis\\python;
 set PYTHONPATH=%PYTHONPATH%;%OSGEO4W_ROOT%\\apps\\Python25\\Lib\\site-packages
-set QGISPATH=%OSGEO4W_ROOT%\apps\qgis
+set QGIS_PREFIX_PATH=%OSGEO4W_ROOT%\apps\qgis
 
 echo %PYTHONPATH%
 

docs/source/api-docs/safe.rst

@@ -5,9 +5,9 @@ Package::safe
    :maxdepth: 2
 
    safe/api
-   safe/test
    safe/storage
-   safe/i18n
    safe/engine
    safe/impact_functions
+   safe/i18n
+   safe/test
    safe/common

docs/source/api-docs/safe/common.rst

@@ -4,17 +4,19 @@ Package::safe.common
 .. toctree::
    :maxdepth: 2
 
-   common/utilities
-   common/interpolation1d
-   common/test_polygon
-   common/dynamic_translations
-   common/interpolation2d
-   common/test_numerics
+   common/geodesy
+   common/tables
    common/exceptions
-   common/polygon
+   common/numerics
    common/testing
+   common/polygon
    common/test_tables
-   common/numerics
-   common/tables
-   common/test_interpolate
+   common/interpolation2d
+   common/utilities
+   common/test_polygon
    common/version
+   common/test_interpolate
+   common/dynamic_translations
+   common/test_numerics
+   common/interpolation1d
+   common/test_geodesy

docs/source/api-docs/safe/common/geodesy.rst

@@ -0,0 +1,7 @@
+Module:  safe.common.geodesy
+============================
+
+.. automodule:: safe.common.geodesy
+      :members:
+
+This module forms part of the `InaSAFE <http://inasafe.org>`_ tool.

docs/source/api-docs/safe/common/test_geodesy.rst

@@ -0,0 +1,7 @@
+Module:  safe.common.test_geodesy
+=================================
+
+.. automodule:: safe.common.test_geodesy
+      :members:
+
+This module forms part of the `InaSAFE <http://inasafe.org>`_ tool.

docs/source/api-docs/safe/engine.rst

@@ -4,8 +4,8 @@ Package::safe.engine
 .. toctree::
    :maxdepth: 2
 
-   engine/utilities
-   engine/interpolation
    engine/test_engine
+   engine/interpolation
+   engine/utilities
    engine/core
    engine/impact_functions_for_testing

docs/source/api-docs/safe/engine/impact_functions_for_testing.rst

@@ -4,11 +4,11 @@ Package::safe.engine.impact_functions_for_testing
 .. toctree::
    :maxdepth: 2
 
-   impact_functions_for_testing/NEXIS_building_impact_model
+   impact_functions_for_testing/BNPB_earthquake_guidelines
+   impact_functions_for_testing/unspecific_building_impact_model
    impact_functions_for_testing/flood_road_impact
    impact_functions_for_testing/allen_fatality_model
-   impact_functions_for_testing/unspecific_building_impact_model
-   impact_functions_for_testing/empirical_fatality_model
    impact_functions_for_testing/general_ashload_impact
-   impact_functions_for_testing/BNPB_earthquake_guidelines
+   impact_functions_for_testing/empirical_fatality_model
    impact_functions_for_testing/HKV_flood_study
+   impact_functions_for_testing/NEXIS_building_impact_model

docs/source/api-docs/safe/impact_functions.rst

@@ -4,16 +4,16 @@ Package::safe.impact_functions
 .. toctree::
    :maxdepth: 2
 
-   impact_functions/utilities
-   impact_functions/mappings
+   impact_functions/test_plugin_core
+   impact_functions/test_real_impact_functions
    impact_functions/test_mappings
-   impact_functions/test_plugins
+   impact_functions/mappings
    impact_functions/styles
+   impact_functions/utilities
+   impact_functions/test_plugins
    impact_functions/core
-   impact_functions/test_plugin_core
-   impact_functions/test_real_impact_functions
+   impact_functions/tephra
    impact_functions/generic
    impact_functions/inundation
-   impact_functions/earthquake
-   impact_functions/tephra
    impact_functions/volcanic
+   impact_functions/earthquake

docs/source/api-docs/safe/impact_functions/earthquake.rst

@@ -4,7 +4,7 @@ Package::safe.impact_functions.earthquake
 .. toctree::
    :maxdepth: 2
 
-   earthquake/padang_building_impact_model
-   earthquake/itb_building_impact_model
    earthquake/earthquake_impact_on_women
+   earthquake/itb_building_impact_model
    earthquake/itb_earthquake_fatality_model
+   earthquake/padang_building_impact_model

docs/source/api-docs/safe/impact_functions/generic.rst

@@ -4,5 +4,5 @@ Package::safe.impact_functions.generic
 .. toctree::
    :maxdepth: 2
 
-   generic/categorised_hazard_population
    generic/categorised_hazard_building_impact
+   generic/categorised_hazard_population

docs/source/api-docs/safe/impact_functions/inundation.rst

@@ -4,6 +4,6 @@ Package::safe.impact_functions.inundation
 .. toctree::
    :maxdepth: 2
 
-   inundation/flood_population_evacuation_polygon_hazard
    inundation/flood_population_evacuation
    inundation/flood_OSM_building_impact
+   inundation/flood_population_evacuation_polygon_hazard

docs/source/api-docs/safe/storage.rst

@@ -4,15 +4,15 @@ Package::safe.storage
 .. toctree::
    :maxdepth: 2
 
-   storage/vector
-   storage/utilities
-   storage/raster
-   storage/test_clipping
    storage/projection
+   storage/test_io
+   storage/test_clipping
+   storage/utilities_test
    storage/clipping
+   storage/layer
+   storage/test_vector
    storage/test_utilities
+   storage/raster
+   storage/utilities
+   storage/vector
    storage/core
-   storage/test_vector
-   storage/layer
-   storage/test_io
-   storage/utilities_test

docs/source/api-docs/safe_qgis.rst

@@ -4,27 +4,28 @@ Package::safe_qgis
 .. toctree::
    :maxdepth: 2
 
-   safe_qgis/keywords_dialog
-   safe_qgis/impact_functions_doc_base
-   safe_qgis/utilities
    safe_qgis/options_dialog_base
-   safe_qgis/impact_calculator_thread
-   safe_qgis/options_dialog
-   safe_qgis/map
-   safe_qgis/resources
    safe_qgis/clipper
-   safe_qgis/dock_base
-   safe_qgis/exceptions
-   safe_qgis/dock
-   safe_qgis/keyword_io
-   safe_qgis/resources_rc
-   safe_qgis/keywords_dialog_base
-   safe_qgis/help_base
    safe_qgis/impact_calculator
-   safe_qgis/help
+   safe_qgis/keywords_dialog_base
+   safe_qgis/resources_rc
+   safe_qgis/dock
    safe_qgis/odict
-   safe_qgis/qgis_interface
+   safe_qgis/help
    safe_qgis/impact_functions_doc
+   safe_qgis/impact_calculator_thread
+   safe_qgis/exceptions
+   safe_qgis/dock_base
+   safe_qgis/keywords_dialog
+   safe_qgis/resources
+   safe_qgis/keyword_io
    safe_qgis/utilities_test
-   safe_qgis/safe_interface
+   safe_qgis/help_base
    safe_qgis/plugin
+   safe_qgis/aggregation_attribute_dialog_base
+   safe_qgis/safe_interface
+   safe_qgis/impact_functions_doc_base
+   safe_qgis/options_dialog
+   safe_qgis/utilities
+   safe_qgis/qgis_interface
+   safe_qgis/map

docs/source/api-docs/safe_qgis/aggregation_attribute_dialog_base.rst

@@ -0,0 +1,7 @@
+Module:  safe_qgis.aggregation_attribute_dialog_base
+====================================================
+
+.. automodule:: safe_qgis.aggregation_attribute_dialog_base
+      :members:
+
+This module forms part of the `InaSAFE <http://inasafe.org>`_ tool.

docs/source/api-docs/safe_qgis_tests.rst

@@ -4,15 +4,15 @@ Package::safe_qgis_tests
 .. toctree::
    :maxdepth: 2
 
-   safe_qgis_tests/test_qgis_environment
-   safe_qgis_tests/test_map
-   safe_qgis_tests/test_utilities
-   safe_qgis_tests/test_impact_calculator
    safe_qgis_tests/test_clipper
-   safe_qgis_tests/test_dock
+   safe_qgis_tests/test_qgis_environment
    safe_qgis_tests/test_keyword_io
    safe_qgis_tests/test_plugin
-   safe_qgis_tests/test_safe_interface
    safe_qgis_tests/test_keywords_dialog
+   safe_qgis_tests/test_map
+   safe_qgis_tests/test_impact_calculator
+   safe_qgis_tests/test_dock
    safe_qgis_tests/test_impact_functions_doc
+   safe_qgis_tests/test_utilities
+   safe_qgis_tests/test_safe_interface
    safe_qgis_tests/test_help

docs/source/developer-docs/jenkins_ci.rst

@@ -168,7 +168,7 @@ Here is a log of the options we set for the Jenkins job:
 
        export PYTHONPATH=/usr/local/qgis1.8/share/qgis/python/
        export LD_LIBRARY_PATH=/usr/local/qgis1.8/lib
-       export QGISPATH=/usr/local/qgis1.8/
+       export QGIS_PREFIX_PATH=/usr/local/qgis1.8/
 
        # Make sure data dir is current and synced it its git clone
        scripts/update-test-data.sh

docs/source/developer-docs/platform_linux.rst

@@ -84,11 +84,11 @@ QGIS installed in a non-standard location
 .........................................
 
 For running unit tests that need QGIS, you may need to adjust *PYTHONPATH* and
-*QGISPATH* if QGIS is running in a non standard location. For example with
+*QGIS_PREFIX_PATH* if QGIS is running in a non standard location. For example with
 QGIS built from source into /usr/local (and python bindings global install
 option disabled), you could run these commands (or add them to your ~/.bashrc)::
 
-   export QGISPATH=/usr/local
+   export QGIS_PREFIX_PATH=/usr/local
    export PYTHONPATH=$PYTHONPATH:/usr/local/share/qgis/python/
 
 .. note:: The above can be set within Eclipse's project properties if you are

docs/source/developer-docs/platform_windows.rst

@@ -187,11 +187,11 @@ following listing in <QGIS Install Dir>/bin/python-shell.bat::
    
    set PYTHONPATH=%PYTHONPATH%;%OSGEO4W_ROOT%\apps\qgis\python;
    set PYTHONPATH=%PYTHONPATH%;%OSGEO4W_ROOT%\apps\Python27\Lib\site-packages
-   set QGISPATH=%OSGEO4W_ROOT%\apps\qgis
+   set QGIS_PREFIX_PATH=%OSGEO4W_ROOT%\apps\qgis
    cd "%HOMEPATH%\.qgis\python\plugins\inasafe-dev"
    start "Quantum GIS Shell" /B "cmd.exe" %*
 
-.. note:: The QGISPATH environment variable should be unquoted!.
+.. note:: The QGIS_PREFIX_PATH environment variable should be unquoted!.
 
 .. note:: You may need to replace PROGRA~1 above with PROGRA~2 if you are
    on 64bit windows.
@@ -408,7 +408,7 @@ environment has been imported. Here are the typical contexts of the file::
    path %PATH%;%OSGEO4W_ROOT%\apps\qgis\bin;%OSGEO4W_ROOT%\apps\grass\grass-6.4.2\lib
    set PYTHONPATH=%PYTHONPATH%;%OSGEO4W_ROOT%\apps\qgis\python;
    set PYTHONPATH=%PYTHONPATH%;%OSGEO4W_ROOT%\apps\Python27\Lib\site-packages
-   set QGISPATH=%OSGEO4W_ROOT%\apps\qgis
+   set QGIS_PREFIX_PATH=%OSGEO4W_ROOT%\apps\qgis
    "C:\Progra~2\eclipse\eclipse.exe"
 
 .. note:: Use the path where your eclipse was extracted. Also note that PROGRA~2 may 
@@ -484,7 +484,7 @@ You will be returned to the Python Interpreters list and should see an entry for
 
 In the dialog that appears 
 
-:guilabel:`Name` : :kbd:`QGISPATH`
+:guilabel:`Name` : :kbd:`QGIS_PREFIX_PATH`
 :guilabel:`Value` : :kbd:`C:\\PROGRA~1\\QUANTU~1\\apps\\qgis`
 
 Then click ok to close the environment variable editor.

docs/source/user-docs/options.rst

@@ -37,9 +37,12 @@ The following options are available on the :guilabel:`Options Dialog`:
   option will cause QGIS to turn off the exposure layer used when InaSAFE
   completes the current analysis. You can re-enable the layer visibility
   again by checking its checkbox in the legend.
-* :guilabel:`Hide exposure layer on scenario estimate completion` : This
+* :guilabel:`Clip datasets to visible extent before analysis` : This
   option will cause QGIS to clip hazard and exposure layers to the currently
   visible extent on the map canvas.
+* :guilabel:`Show intermediate layers generated by postprocessing` : This
+  option will cause QGIS to show the intermediate files generated by the
+  postprocessing steps in the map canvas.
 * :guilabel:`Keyword cache for remote datasources` : This option is used to
   determine where keywords are stored for datasets where it is not possible
   to write them into a .keywords file. See :doc:`keywords` for more information

pylintrc

@@ -35,7 +35,7 @@ profile=no
 
 # Add files or directories to the blacklist. They should be base names, not
 # paths.
-ignore=odict.py,help_base.py,keywords_dialog_base.py,options_dialog_base.py,dock_base.py,resources.py,resources_rc.py,impact_functions_doc_base.py
+ignore=odict.py,help_base.py,keywords_dialog_base.py,options_dialog_base.py,dock_base.py,resources.py,resources_rc.py,impact_functions_doc_base.py,configurable_impact_functions_dialog_base.py
 
 # Pickle collected data for later comparisons.
 persistent=yes

runguitests.bat

@@ -1 +1 @@
-nosetests -v --with-id --with-coverage --cover-package=gui gui
+nosetests -v --with-id --with-coverage --cover-package=gui

safe/common/polygon.py

@@ -133,7 +133,8 @@ def separate_points_by_polygon(points, polygon,
             raise PolygonInputError(msg)
 
     # Get polygon extents to rule out segments that
-    # are outside its bounding box
+    # are outside its bounding box. This is a very important
+    # optimisation
     if polygon_bbox is None:
         minpx = min(polygon[:, 0])
         maxpx = max(polygon[:, 0])

safe/i18n/af/LC_MESSAGES/inasafe.po

@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2012-09-28 15:41+0700\n"
+"POT-Creation-Date: 2012-10-03 10:25+0700\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"