Clean up Namespaces

[GoogleCodeExporter]

knnW can be found in at least 3 different places, pysal.knnW, 
pysal.weights.knnW and 
pysal.weights.Distance.knnW.  Along with many other modules and methods.

Remove unnecessary imports and make sure the published API reflects the 
structure we want to 
continue using in the future.

Original issue reported on code.google.com by schmi...@gmail.com on 14 May 2010 at 9:56

[GoogleCodeExporter]

should we keep the packages and have imports be required:

import pysal.weights

versus having from pysal import * 
work?

i think packages is cleaner and less error prone. before we finalize the import 
scheme we should decide on 
packages or?

Original comment by sjsrey on 31 May 2010 at 7:54

[GoogleCodeExporter]

The attached GraphViz files show the dependancy structure within PySAL.  The 
structure seems overly complicated and trying to simplify the import structure 
for a 1.0 release doesn't seem very realistic at this point.

As this relates to maintainability let make sure this get high-priority for 1.1.

Original comment by schmi...@gmail.com on 31 Jul 2010 at 4:08

• Added labels: Priority-High, Milestone-1.1
• Removed labels: Priority-Medium, Milestone-1.0

Attachments:

• pysal_only.dot
• pysal_only_no_common.dot

[GoogleCodeExporter]

PySAL NameSpace Cleanup.

Version 1.0:
['Box_Plot', 'DistanceBand', 'Equal_Interval', 'Fisher_Jenks', 'Geary', 
'Jenks_Caspall', 'Jenks_Caspall_Forced', 'Jenks_Caspall_Sampled', 
'Join_Counts', 'KDTree', 'K_classifiers', 'Kernel', 'LISA_Markov', 'Markov', 
'Max_P_Classifier', 'Maximum_Breaks', 'Maxp', 'Maxp_LISA', 'Moran', 'Moran_BV', 
'Moran_BV_matrix', 'Moran_Local', 'Natural_Breaks', 'Percentiles', 'Quantiles', 
'ROD', 'SpatialTau', 'Spatial_Markov', 'Std_Mean', 'Theil', 'TheilD', 
'TheilDSim', 'Theta', 'User_Defined', 'W', '__all__', '__builtins__', 
'__doc__', '__file__', '__name__', '__package__', '__path__', 
'adaptive_kernelW', 'adaptive_kernelW_from_shapefile', 'bin', 'bin1d', 'binC', 
'buildContiguity', 'cdist', 'cg', 'comb', 'common', 'copy', 'core', 
'directional', 'distance_matrix', 'ergodic', 'esda', 'full', 'gadf', 'get_ids', 
'get_points_array_from_shapefile', 'higher_order', 'inequality', 'kernelW', 
'kernelW_from_shapefile', 'knnW', 'knnW_from_array', 'knnW_from_shapefile', 
'la', 'lag_spatial', 'lat2W', 'math', 'min_threshold_dist_from_shapefile', 
'min_threshold_distance', 'np', 'open', 'order', 'os', 'pdist', 'pysal', 
'quantile', 'queen_from_shapefile', 'random', 'regime_weights', 'region', 
'remap_ids', 'rook_from_shapefile', 'shimbel', 'sp', 'spatial_dynamics', 
'stats', 'sys', 'threshold_binaryW_from_array', 
'threshold_binaryW_from_shapefile', 'threshold_continuousW_from_array', 
'threshold_continuousW_from_shapefile', 'time', 'unittest', 'version', 
'w_difference', 'w_intersection', 'w_subset', 'w_symmetric_difference', 
'w_union', 'weights']

Removed "from common import*"
['Box_Plot', 'DistanceBand', 'Equal_Interval', 'Fisher_Jenks', 'Geary', 
'Jenks_Caspall', 'Jenks_Caspall_Forced', 'Jenks_Caspall_Sampled', 
'Join_Counts', 'K_classifiers', 'Kernel', 'LISA_Markov', 'Markov', 
'Max_P_Classifier', 'Maximum_Breaks', 'Maxp', 'Maxp_LISA', 'Moran', 'Moran_BV', 
'Moran_BV_matrix', 'Moran_Local', 'Natural_Breaks', 'Percentiles', 'Quantiles', 
'SpatialTau', 'Spatial_Markov', 'Std_Mean', 'Theil', 'TheilD', 'TheilDSim', 
'Theta', 'User_Defined', 'W', '__all__', '__builtins__', '__doc__', '__file__', 
'__name__', '__package__', '__path__', 'adaptive_kernelW', 
'adaptive_kernelW_from_shapefile', 'bin', 'bin1d', 'binC', 'buildContiguity', 
'cg', 'comb', 'common', 'core', 'directional', 'ergodic', 'esda', 'full', 
'gadf', 'get_ids', 'get_points_array_from_shapefile', 'higher_order', 
'inequality', 'kernelW', 'kernelW_from_shapefile', 'knnW', 'knnW_from_array', 
'knnW_from_shapefile', 'lag_spatial', 'lat2W', 
'min_threshold_dist_from_shapefile', 'min_threshold_distance', 'np', 'open', 
'order', 'os', 'pysal', 'quantile', 'queen_from_shapefile', 'regime_weights', 
'region', 'remap_ids', 'rook_from_shapefile', 'shimbel', 'spatial_dynamics', 
'threshold_binaryW_from_array', 'threshold_binaryW_from_shapefile', 
'threshold_continuousW_from_array', 'threshold_continuousW_from_shapefile', 
'version', 'w_difference', 'w_intersection', 'w_subset', 
'w_symmetric_difference', 'w_union', 'weights']

Added __all__ to weights.user,
['Box_Plot', 'DistanceBand', 'Equal_Interval', 'Fisher_Jenks', 'Geary', 
'Jenks_Caspall', 'Jenks_Caspall_Forced', 'Jenks_Caspall_Sampled', 
'Join_Counts', 'K_classifiers', 'Kernel', 'LISA_Markov', 'Markov', 
'Max_P_Classifier', 'Maximum_Breaks', 'Maxp', 'Maxp_LISA', 'Moran', 'Moran_BV', 
'Moran_BV_matrix', 'Moran_Local', 'Natural_Breaks', 'Percentiles', 'Quantiles', 
'SpatialTau', 'Spatial_Markov', 'Std_Mean', 'Theil', 'TheilD', 'TheilDSim', 
'Theta', 'User_Defined', 'W', '__all__', '__builtins__', '__doc__', '__file__', 
'__name__', '__package__', '__path__', 'adaptive_kernelW', 
'adaptive_kernelW_from_shapefile', 'bin', 'bin1d', 'binC', 'buildContiguity', 
'cg', 'comb', 'common', 'core', 'directional', 'ergodic', 'esda', 'full', 
'gadf', 'higher_order', 'inequality', 'kernelW', 'kernelW_from_shapefile', 
'knnW', 'knnW_from_array', 'knnW_from_shapefile', 'lag_spatial', 'lat2W', 
'min_threshold_dist_from_shapefile', 'open', 'order', 'quantile', 
'queen_from_shapefile', 'regime_weights', 'region', 'remap_ids', 
'rook_from_shapefile', 'shimbel', 'spatial_dynamics', 
'threshold_binaryW_from_array', 'threshold_binaryW_from_shapefile', 
'threshold_continuousW_from_array', 'threshold_continuousW_from_shapefile', 
'version', 'w_difference', 'w_intersection', 'w_subset', 
'w_symmetric_difference', 'w_union', 'weights']

Original comment by schmi...@gmail.com on 7 Jan 2011 at 9:15

• Changed state: Started

[GoogleCodeExporter]

define __all__ in all modules.
module.__all__ = ['X','Y','Z']
move "code" from module/__init__.py to module/module.py
__init__.py should include from module import *

Original comment by schmi...@gmail.com on 7 Jan 2011 at 9:16

• Changed state: Fixed

[GoogleCodeExporter]

i opened this back up as i'm not sure the final changes to the toplevel 
pysal.__init__ file were made. It looks like we still have explicit imports in 
there and not the scheme from module import *

do we keep the explicit imports (i.e., from Markov import Spatial_Markov)?

Original comment by sjsrey on 18 Jan 2011 at 3:24

• Changed state: Started

[GoogleCodeExporter]

The "from module import *" scheme is only for sub-packages. The top level 
__init__.py needs to remain explicit.  

This allows us to maintain the 2 level structure where pysal.X is a flat 
sub-package of pysal.  In the long run the pysal namespace should contain only 
the half dozen or so sub-packages and optionally objects that at common to all 
sub-packages.

Original comment by schmi...@gmail.com on 18 Jan 2011 at 7:30

[GoogleCodeExporter]

Pysal's top level __init__.py will keep explicit imports.

I think this issue is resolved.  tests.py is reporting all modules that still 
need work.  Re-open if this issues needs more clarification.

Original comment by schmi...@gmail.com on 19 Jan 2011 at 7:27

• Changed state: Fixed