[pysal] 01/08: New upstream version 1.14.3
Bas Couwenberg
sebastic at debian.org
Mon Nov 6 19:01:38 UTC 2017
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sebastic pushed a commit to branch master
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commit 7e03f07a0310deced36f01a8e95154c462750e2d
Author: Bas Couwenberg <sebastic at xs4all.nl>
Date: Mon Nov 6 07:52:58 2017 +0100
New upstream version 1.14.3
---
.github/PULL_REQUEST_TEMPLATE.md | 2 +-
.travis.yml | 1 +
CHANGELOG.txt | 49 +
README.rst | 1 -
THANKS.txt | 1 +
doc/source/conf.py | 4 +-
doc/source/developers/release.rst | 64 +-
doc/source/index.rst | 2 +-
doc/source/users/tutorials/smoothing.rst | 4 +-
pysal/cg/tests/test_sphere.py | 5 +-
pysal/common.py | 20 +-
pysal/contrib/glm/iwls.py | 10 +-
pysal/contrib/viz/color.py | 18 +-
pysal/contrib/viz/folium_mapping.ipynb | 471 +---
pysal/contrib/viz/folium_mapping.py | 36 +-
pysal/contrib/viz/mapping.py | 2 +-
pysal/core/util/shapefile.py | 5 +-
pysal/esda/moran.py | 120 +-
pysal/esda/smoothing.py | 29 +-
pysal/examples/10740/10740.dbf | Bin
pysal/examples/10740/10740.shp | Bin
pysal/examples/10740/10740.shx | Bin
pysal/examples/10740/10740_queen.gal | 0
pysal/examples/10740/10740_rook.gal | 0
pysal/examples/10740/README.md | 16 +-
pysal/examples/Line/Line.dbf | Bin
pysal/examples/Line/Line.prj | 0
pysal/examples/Line/Line.shp | Bin
pysal/examples/Line/Line.shx | Bin
pysal/examples/Line/README.md | 11 +-
pysal/examples/Point/Point.dbf | Bin
pysal/examples/Point/Point.prj | 0
pysal/examples/Point/Point.shp | Bin
pysal/examples/Point/Point.shx | Bin
pysal/examples/Point/README.md | 12 +
pysal/examples/Polygon/Polygon.dbf | Bin
pysal/examples/Polygon/Polygon.prj | 0
pysal/examples/Polygon/Polygon.shp | Bin
pysal/examples/Polygon/Polygon.shx | Bin
pysal/examples/Polygon/README.md | 7 +-
pysal/examples/Polygon_Holes/Polygon_Holes.cpg | 0
pysal/examples/Polygon_Holes/Polygon_Holes.dbf | Bin
pysal/examples/Polygon_Holes/Polygon_Holes.prj | 0
pysal/examples/Polygon_Holes/Polygon_Holes.qpj | 0
pysal/examples/Polygon_Holes/Polygon_Holes.shp | Bin
pysal/examples/Polygon_Holes/Polygon_Holes.shx | Bin
pysal/examples/README.txt | 2 +-
pysal/examples/__init__.py | 0
pysal/examples/arcgis/README.md | 5 +-
pysal/examples/arcgis/arcgis_ohio.dbf | Bin
pysal/examples/arcgis/arcgis_txt.txt | 0
pysal/examples/baltim/README.md | 20 +-
pysal/examples/baltim/baltim.dbf | Bin
pysal/examples/baltim/baltim.shp | Bin
pysal/examples/baltim/baltim.shx | Bin
pysal/examples/baltim/baltim.tri.k12.kwt | 0
pysal/examples/baltim/baltim_k4.gwt | 0
pysal/examples/baltim/baltim_q.gal | 0
pysal/examples/baltim/baltimore.geojson | 0
pysal/examples/book/README.md | 8 +-
pysal/examples/book/book.gal | 0
pysal/examples/book/book.txt | 0
pysal/examples/burkitt/README.md | 8 +-
pysal/examples/burkitt/burkitt.dbf | Bin
pysal/examples/burkitt/burkitt.shp | Bin
pysal/examples/burkitt/burkitt.shx | Bin
pysal/examples/calemp/README.md | 4 +-
pysal/examples/calemp/calempdensity.csv | 0
pysal/examples/chicago/Chicago77.dbf | Bin
pysal/examples/chicago/Chicago77.shp | Bin
pysal/examples/chicago/Chicago77.shx | Bin
pysal/examples/chicago/README.md | 8 +-
pysal/examples/columbus/README.md | 14 +
pysal/examples/columbus/columbus.dbf | Bin
pysal/examples/columbus/columbus.gal | 0
pysal/examples/columbus/columbus.html | 0
pysal/examples/columbus/columbus.json | 0
pysal/examples/columbus/columbus.shp | Bin
pysal/examples/columbus/columbus.shx | Bin
pysal/examples/desmith/README.md | 9 +-
pysal/examples/desmith/desmith.gal | 0
pysal/examples/desmith/desmith.txt | 0
pysal/examples/examples.txt | 475 +++-
pysal/examples/geodanet/README.md | 40 +-
pysal/examples/geodanet/crimes.dbf | Bin
pysal/examples/geodanet/crimes.prj | 0
pysal/examples/geodanet/crimes.sbn | Bin
pysal/examples/geodanet/crimes.sbx | Bin
pysal/examples/geodanet/crimes.shp | Bin
pysal/examples/geodanet/crimes.shp.xml | 0
pysal/examples/geodanet/crimes.shx | Bin
pysal/examples/geodanet/schools.dbf | Bin
pysal/examples/geodanet/schools.prj | 0
pysal/examples/geodanet/schools.sbn | Bin
pysal/examples/geodanet/schools.sbx | Bin
pysal/examples/geodanet/schools.shp | Bin
pysal/examples/geodanet/schools.shp.xml | 0
pysal/examples/geodanet/schools.shx | Bin
pysal/examples/geodanet/streets.dbf | Bin
pysal/examples/geodanet/streets.prj | 0
pysal/examples/geodanet/streets.sbn | Bin
pysal/examples/geodanet/streets.sbx | Bin
pysal/examples/geodanet/streets.shp | Bin
pysal/examples/geodanet/streets.shx | Bin
pysal/examples/georgia/FB.p | 0
pysal/examples/georgia/XB.p | 0
pysal/examples/georgia/err.p | 0
pysal/examples/juvenile/README.md | 12 +-
pysal/examples/juvenile/juvenile.dbf | Bin
pysal/examples/juvenile/juvenile.gwt | 0
pysal/examples/juvenile/juvenile.shp | Bin
pysal/examples/juvenile/juvenile.shx | Bin
pysal/examples/londonhp/londonhp.dbf | Bin
pysal/examples/londonhp/londonhp.shp | Bin
pysal/examples/londonhp/londonhp.shx | Bin
pysal/examples/mexico/README.md | 11 +-
pysal/examples/mexico/mexico.csv | 0
pysal/examples/mexico/mexico.gal | 0
pysal/examples/nat/NAT.dbf | Bin
pysal/examples/nat/NAT.shp | Bin
pysal/examples/nat/NAT.shx | Bin
pysal/examples/nat/README.md | 16 +
pysal/examples/nat/nat.geojson | 0
pysal/examples/nat/nat_queen.gal | 0
pysal/examples/nat/nat_queen_old.gal | 0
pysal/examples/nat/nat_trian_k20.kwt | 0
pysal/examples/nat/natregimes.dbf | Bin
pysal/examples/nat/natregimes.shp | Bin
pysal/examples/nat/natregimes.shx | Bin
pysal/examples/networks/README.md | 20 +
pysal/examples/networks/eberly_net.dbf | Bin
pysal/examples/networks/eberly_net.shp | Bin
pysal/examples/networks/eberly_net.shx | Bin
.../networks/eberly_net_pts_offnetwork.dbf | Bin
.../networks/eberly_net_pts_offnetwork.shp | Bin
.../networks/eberly_net_pts_offnetwork.shx | Bin
.../examples/networks/eberly_net_pts_onnetwork.dbf | Bin
.../examples/networks/eberly_net_pts_onnetwork.shp | Bin
.../examples/networks/eberly_net_pts_onnetwork.shx | Bin
pysal/examples/networks/nonplanarsegments.dbf | Bin
pysal/examples/networks/nonplanarsegments.prj | 0
pysal/examples/networks/nonplanarsegments.qpj | 0
pysal/examples/networks/nonplanarsegments.shp | Bin
pysal/examples/networks/nonplanarsegments.shx | Bin
pysal/examples/newHaven/README.md | 14 +
pysal/examples/newHaven/new_haven_merged.dbf | Bin
pysal/examples/newHaven/new_haven_merged.shp | Bin
pysal/examples/newHaven/new_haven_merged.shx | Bin
pysal/examples/newHaven/newhaven_nework.dbf | Bin
pysal/examples/newHaven/newhaven_nework.prj | 0
pysal/examples/newHaven/newhaven_nework.qpj | 0
pysal/examples/newHaven/newhaven_nework.shp | Bin
pysal/examples/newHaven/newhaven_nework.shx | Bin
pysal/examples/nyc_bikes/nyc_bikes_ct.csv | 0
pysal/examples/nyc_bikes/nyct2010.dbf | Bin
pysal/examples/nyc_bikes/nyct2010.prj | 0
pysal/examples/nyc_bikes/nyct2010.shp | Bin
pysal/examples/nyc_bikes/nyct2010.shp.xml | 0
pysal/examples/nyc_bikes/nyct2010.shx | Bin
pysal/examples/sacramento2/README.md | 14 +
pysal/examples/sacramento2/sacramentot2.dbf | Bin
pysal/examples/sacramento2/sacramentot2.gal | 0
pysal/examples/sacramento2/sacramentot2.sbn | Bin
pysal/examples/sacramento2/sacramentot2.sbx | Bin
pysal/examples/sacramento2/sacramentot2.shp | Bin
pysal/examples/sacramento2/sacramentot2.shx | Bin
pysal/examples/sids2/README.md | 17 +-
pysal/examples/sids2/sids2.dbf | Bin
pysal/examples/sids2/sids2.gal | 0
pysal/examples/sids2/sids2.html | 0
pysal/examples/sids2/sids2.shp | Bin
pysal/examples/sids2/sids2.shx | Bin
pysal/examples/sids2/sids2.swm | Bin
pysal/examples/snow_maps/README.md | 24 +
pysal/examples/snow_maps/SohoPeople.dbf | Bin
pysal/examples/snow_maps/SohoPeople.prj | 0
pysal/examples/snow_maps/SohoPeople.sbn | Bin
pysal/examples/snow_maps/SohoPeople.sbx | Bin
pysal/examples/snow_maps/SohoPeople.shp | Bin
pysal/examples/snow_maps/SohoPeople.shx | Bin
pysal/examples/snow_maps/SohoWater.dbf | Bin
pysal/examples/snow_maps/SohoWater.prj | 0
pysal/examples/snow_maps/SohoWater.sbn | Bin
pysal/examples/snow_maps/SohoWater.sbx | Bin
pysal/examples/snow_maps/SohoWater.shp | Bin
pysal/examples/snow_maps/SohoWater.shx | Bin
pysal/examples/snow_maps/Soho_Network.dbf | Bin
pysal/examples/snow_maps/Soho_Network.prj | 0
pysal/examples/snow_maps/Soho_Network.sbn | Bin
pysal/examples/snow_maps/Soho_Network.sbx | Bin
pysal/examples/snow_maps/Soho_Network.shp | Bin
pysal/examples/snow_maps/Soho_Network.shx | Bin
pysal/examples/south/README.md | 11 +
pysal/examples/south/south.dbf | Bin
pysal/examples/south/south.shp | Bin
pysal/examples/south/south.shx | Bin
pysal/examples/south/south_q.gal | 0
pysal/examples/south/south_queen.gal | 0
pysal/examples/stl/README.md | 17 +
pysal/examples/stl/stl.gal | 0
pysal/examples/stl/stl_hom.csv | 0
pysal/examples/stl/stl_hom.dbf | Bin
pysal/examples/stl/stl_hom.html | 0
pysal/examples/stl/stl_hom.shp | Bin
pysal/examples/stl/stl_hom.shx | Bin
pysal/examples/stl/stl_hom.txt | 0
pysal/examples/stl/stl_hom.wkt | 0
pysal/examples/stl/stl_hom_rook.gal | 0
pysal/examples/street_net_pts/README.md | 11 +
pysal/examples/street_net_pts/street_net_pts.dbf | Bin
pysal/examples/street_net_pts/street_net_pts.prj | 0
pysal/examples/street_net_pts/street_net_pts.qpj | 0
pysal/examples/street_net_pts/street_net_pts.shp | Bin
pysal/examples/street_net_pts/street_net_pts.shx | Bin
pysal/examples/taz/README.md | 9 +
pysal/examples/taz/taz.dbf | Bin
pysal/examples/taz/taz.shp | Bin
pysal/examples/taz/taz.shx | Bin
pysal/examples/test_examples.py | 7 +-
pysal/examples/tmpIvIYa5.gwt | 2803 ++++++++++++++++++++
pysal/examples/tokyo/Tokyomortality.csv | 0
pysal/examples/tokyo/tokyo_BS_NN_OFF.ctl | 0
pysal/examples/tokyo/tokyo_BS_NN_OFF_listwise.csv | 0
pysal/examples/tokyo/tokyo_BS_NN_OFF_summary.txt | 0
pysal/examples/us_income/README.md | 13 +-
pysal/examples/us_income/spi_download.csv | 0
pysal/examples/us_income/states48.gal | 0
pysal/examples/us_income/us48.dbf | Bin
pysal/examples/us_income/us48.shp | Bin
pysal/examples/us_income/us48.shx | Bin
pysal/examples/us_income/usjoin.csv | 0
pysal/examples/virginia/README.md | 19 +-
pysal/examples/virginia/virginia.dbf | Bin
pysal/examples/virginia/virginia.gal | 0
pysal/examples/virginia/virginia.json | 0
pysal/examples/virginia/virginia.prj | 0
pysal/examples/virginia/virginia.shp | Bin
pysal/examples/virginia/virginia.shx | Bin
pysal/examples/virginia/virginia_queen.dat | 0
pysal/examples/virginia/virginia_queen.dbf | Bin
pysal/examples/virginia/virginia_queen.gal | 0
pysal/examples/virginia/virginia_queen.mat | Bin
pysal/examples/virginia/virginia_queen.mtx | 0
pysal/examples/virginia/virginia_queen.swm | Bin
pysal/examples/virginia/virginia_queen.txt | 0
pysal/examples/virginia/virginia_queen.wk1 | Bin
pysal/examples/virginia/virginia_rook.gal | 0
pysal/examples/wmat/README.md | 21 +
pysal/examples/wmat/geobugs_scot | 0
pysal/examples/wmat/ohio.swm | Bin
pysal/examples/wmat/rook31.dbf | Bin
pysal/examples/wmat/rook31.gal | 0
pysal/examples/wmat/rook31.shp | Bin
pysal/examples/wmat/rook31.shx | Bin
pysal/examples/wmat/spat-sym-us.mat | Bin
pysal/examples/wmat/spat-sym-us.wk1 | Bin
pysal/examples/wmat/spdep_listw2WB_columbus | 0
pysal/examples/wmat/stata_full.txt | 0
pysal/examples/wmat/stata_sparse.txt | 0
pysal/examples/wmat/us48_CONTIGUITY_EDGES_ONLY.swm | Bin
pysal/examples/wmat/us48_INVERSE_DISTANCE.swm | Bin
pysal/examples/wmat/wmat.dat | 0
pysal/examples/wmat/wmat.mtx | 0
pysal/spreg/diagnostics.py | 11 +-
pysal/spreg/diagnostics_sp.py | 3 +-
pysal/spreg/probit.py | 3 +-
pysal/spreg/regimes.py | 3 +-
pysal/spreg/sur_error.py | 7 +-
pysal/version.py | 4 +-
pysal/weights/Contiguity.py | 13 +-
requirements_plus.txt | 1 +
setup.py | 2 +-
tools/bump.py | 4 +-
tools/github_stats.py | 8 +-
274 files changed, 3799 insertions(+), 782 deletions(-)
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index d5173f9..d1c0760 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -3,7 +3,7 @@ Hello! Please make sure to check all these boxes before submitting a Pull Reques
justification in point 5.
1. [ ] You have run tests on this submission, either by using [Travis Continuous Integration testing](https://github.com/pysal/pysal/wiki/GitHub-Standard-Operating-Procedures#automated-testing-w-travis-ci) testing or running `nosetests` on your changes?
-2. [ ] This pull request is directed to the `pysal/dev` branch.
+2. [ ] This pull request is directed to the `pysal/master` branch. **This is important, as any PRs submitted against any other branches will be delayed.**
3. [ ] This pull introduces new functionality covered by
[docstrings](https://en.wikipedia.org/wiki/Docstring#Python) and
[unittests](https://docs.python.org/2/library/unittest.html)?
diff --git a/.travis.yml b/.travis.yml
index dac6dd6..c8accf3 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,6 +7,7 @@ python:
- "2.7"
- "3.4"
- "3.5"
+ - "3.6"
env:
- PYSAL_PLUS=false
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 4635e57..db06423 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,52 @@
+v<1.14.3>, 2017-11-2
+
+
+GitHub stats for 2017/09/23 - 2017/11/02
+
+These lists are automatically generated, and may be incomplete or contain duplicates.
+
+
+We closed a total of 31 issues, 8 pull requests and 23 regular issues;
+this is the full list (generated with the script
+:file:`tools/github_stats.py`):
+
+Pull Requests (8):
+
+* :ghpull:`997`: b'edit README.md for example datasets'
+* :ghpull:`999`: b'Raise ImportError on missing palettable and PEP8'
+* :ghpull:`983`: b'Fix inconsistent use of tabs and spaces in indentation.'
+* :ghpull:`995`: b'Foliumfix'
+* :ghpull:`993`: b'B991'
+* :ghpull:`988`: b'Resolve issue of "False" "id_order_set" when building contiguity weights from shapefile even if `idVariable` is given in initialization'
+* :ghpull:`982`: b'update release instructions for new test.pypi'
+* :ghpull:`979`: b'Rel 1.14.2'
+
+Issues (23):
+
+* :ghissue:`997`: b'edit README.md for example datasets'
+* :ghissue:`970`: b'Odd pysal.Moran() randomisation VI'
+* :ghissue:`999`: b'Raise ImportError on missing palettable and PEP8'
+* :ghissue:`998`: b'Should missing palettable be a warning or error? '
+* :ghissue:`981`: b'mixed indentation in `iwls`'
+* :ghissue:`987`: b"discrepancy in EB Local Moran's I with PySAL vs. GeoDa results"
+* :ghissue:`992`: b'Scipy 1.0.0 Compat issues'
+* :ghissue:`991`: b'Chisqprob is deprecated'
+* :ghissue:`983`: b'Fix inconsistent use of tabs and spaces in indentation.'
+* :ghissue:`996`: b'edit README for example datasets'
+* :ghissue:`989`: b"resolve discrepancy of estimating Moran's I corrected for rates between GeoDa and pysal"
+* :ghissue:`995`: b'Foliumfix'
+* :ghissue:`994`: b'folium breakage'
+* :ghissue:`971`: b'base_lisa_cluster function call does not pass p_thresh'
+* :ghissue:`993`: b'B991'
+* :ghissue:`984`: b'Level dev & master, incorporate 983'
+* :ghissue:`990`: b'problem with open shp file'
+* :ghissue:`988`: b'Resolve issue of "False" "id_order_set" when building contiguity weights from shapefile even if `idVariable` is given in initialization'
+* :ghissue:`980`: b'release documentation test pypi is out of date'
+* :ghissue:`982`: b'update release instructions for new test.pypi'
+* :ghissue:`978`: b'Coordinate releases on pypi and github'
+* :ghissue:`976`: b'bump pysal/pysal/version.py please'
+* :ghissue:`979`: b'Rel 1.14.2'
+
v<1.14.2>, 2017-09-23
This is a bug fix release for the 1.14 Python 2.x. series of PySAL.
diff --git a/README.rst b/README.rst
index ef5c32d..8091f69 100644
--- a/README.rst
+++ b/README.rst
@@ -28,7 +28,6 @@ applications for spatial analysis.
Counties 1990.*
-
PySAL modules
=============
diff --git a/THANKS.txt b/THANKS.txt
index 6b2b267..d3752cf 100644
--- a/THANKS.txt
+++ b/THANKS.txt
@@ -42,6 +42,7 @@ fnorf
mylons-tcc
dnadai2
MridulS
+thequackdaddy
Funding from the following sources has supported PySAL development:
diff --git a/doc/source/conf.py b/doc/source/conf.py
index e051b80..35ddbe6 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -47,9 +47,9 @@ copyright = u'2014-, PySAL Developers; 2009-13 Sergio Rey'
# built documents.
#
# The short X.Y version.
-version = '1.14.2'
+version = '1.14.3'
# The full version, including alpha/beta/rc tags.
-release = '1.14.2'
+release = '1.14.3'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/doc/source/developers/release.rst b/doc/source/developers/release.rst
index bee0cbf..bd5d67a 100644
--- a/doc/source/developers/release.rst
+++ b/doc/source/developers/release.rst
@@ -9,7 +9,6 @@ PySAL Release Management
Prepare the release
-------------------
-- Create a branch_ out of the `dev` branch
- Check all tests pass. See :doc:`testing`.
- Update CHANGELOG::
@@ -29,46 +28,36 @@ Prepare the release
Add a comment that this is for release.
-Tag
----
-
-With version 1.10 we changed the way the tags are created to reflect our
-policy_ of not pushing directly to upstream.
-
-After you have issued a pull request, the project maintainer can `create the release`_ on GitHub.
-
Make docs
---------
As of version 1.6, docs are automatically compiled and hosted_.
-Make and Upload and Test Distributions
---------------------------------------
-
-On each build machine, clone and checkout the newly created tag (assuming that
-is `v1.10` in what follows)::
-
- $ git clone http://github.com/pysal/pysal.git
- $ cd pysal
- $ git fetch --tags
- $ git checkout v1.10
-
-- Make and upload_ to the **Testing** Python Package Index::
-
- $ python setup.py sdist upload -r https://testpypi.python.org/pypi
+Make a source dist and test locally (Python 3)
+----------------------------------------------
-- Test that your package can install correctly::
+On each build machine
- $ pip install --extra-index-url https://testpypi.python.org/pypi pysal
+ $ git clone http://github.com/pysal/pysal.git
+ $ cd pysal
+ $ python setup.py sdist
+ $ cp dist/PySAL-1.14.2.tar.gz ../junk/.
+ $ cd ../junk
+ $ conda create -n pysaltest3 python=3 pip
+ $ source activate pysaltest3
+ $ pip install PySAL-1.14.2.tar.gz
+ $ rm -r /home/serge/anaconda3/envs/pysaltest3/lib/python3.6/site-packages/pysal/contrib
+ $ nosetests /home/serge/anaconda3/envs/pysaltest3/lib/python3.6/site-packages/pysal/
+You can modify the above to test for Python 2 environments.
-If all is good, proceed, otherwise fix, and repeat.
+Upload release to pypi
+----------------------
- Make and upload_ to the Python Package Index in one shot!::
- $ python setup.py sdist (to test it)
$ python setup.py sdist upload
- if not registered_, do so. Follow the prompts. You can save the
@@ -79,25 +68,20 @@ If all is good, proceed, otherwise fix, and repeat.
$ python setup.py bdist_wininst
-Announce
---------
+Create a release on github
+--------------------------
-- Draft and distribute press release on geodacenter.asu.edu, openspace-list, and pysal.org
+https://help.github.com/articles/creating-releases/
- - On GeoDa center website, do this:
- - Login and expand the wrench icon to reveal the Admin menu
- - Click "Administer", "Content Management", "Content"
- - Next, click "List", filter by type, and select "Featured Project".
- - Click "Filter"
+Announce
+--------
- Now you will see the list of Featured Projects. Find "PySAL".
+- Draft and distribute press release on openspace-list, pysal.org, spatial.ucr.edu
- - Choose to 'edit' PySAL and modify the short text there. This changes the text users see on the homepage slider.
- - Clicking on the name "PySAL" allows you to edit the content of the PySAL project page, which is also the "About PySAL" page linked to from the homepage slider.
-Put master back to dev
-----------------------
+Bump master version
+-------------------
- Change MAJOR, MINOR version in setup script.
- Change pysal/version.py to dev number
diff --git a/doc/source/index.rst b/doc/source/index.rst
index de9c263..2e29a51 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -20,7 +20,7 @@ PySAL
.. sidebar:: Releases
- - `Stable 1.14.2 (Released 2017-9-23) <users/installation.html>`_
+ - `Stable 1.14.3 (Released 2017-11-2) <users/installation.html>`_
- `Development <http://github.com/pysal/pysal/tree/dev>`_
PySAL is an open source library of spatial analysis functions written in
diff --git a/doc/source/users/tutorials/smoothing.rst b/doc/source/users/tutorials/smoothing.rst
index 1a52e45..f5c4cbc 100644
--- a/doc/source/users/tutorials/smoothing.rst
+++ b/doc/source/users/tutorials/smoothing.rst
@@ -141,7 +141,7 @@ and total population (the 13th column):
.. doctest::
>>> import pysal
- >>> stl = pysal.open('../pysal/examples/stl_hom.csv', 'r')
+ >>> stl = pysal.open(pysal.examples.get_path('stl_hom.csv'), 'r')
>>> e, b = np.array(stl[:,10]), np.array(stl[:,13])
We then read the spatial weights file defining neighborhood relationships among the counties
@@ -149,7 +149,7 @@ and ensure that the :ref:`order <id_order>` of observations in the weights objec
.. doctest::
- >>> w = pysal.open('../pysal/examples/stl.gal', 'r').read()
+ >>> w = pysal.open(pysal.examples.get_path("stl.gal"),"r").read()
>>> if not w.id_order_set: w.id_order = range(1,len(stl) + 1)
Now we calculate locally weighted averages of the homicide rates.
diff --git a/pysal/cg/tests/test_sphere.py b/pysal/cg/tests/test_sphere.py
index 8139ada..7f1b41d 100644
--- a/pysal/cg/tests/test_sphere.py
+++ b/pysal/cg/tests/test_sphere.py
@@ -2,7 +2,8 @@ from pysal.cg import sphere
import pysal
import math
import unittest
-
+import numpy as np
+from pysal.common import (RTOL, ATOL)
class Sphere(unittest.TestCase):
@@ -70,7 +71,7 @@ class Sphere(unittest.TestCase):
pup = (42.023768, -87.946389) # Arlington Heights IL
pdown = (41.644415, -87.524102) # Hammond, IN
grid1 = sphere.geogrid(pup, pdown, 3, lonx=False)
- self.assertAlmostEqual(grid, grid1)
+ np.testing.assert_allclose(grid, grid1, rtol=RTOL, atol=ATOL)
def test_toXYZ(self):
w2 = {0: [2, 5, 6, 10], 1: [4, 7, 9, 14], 2: [6, 0, 3, 8],
diff --git a/pysal/common.py b/pysal/common.py
index 513db5a..4311a4f 100644
--- a/pysal/common.py
+++ b/pysal/common.py
@@ -1,20 +1,12 @@
# external imports
-try:
- import numpy as np
- import numpy.linalg as la
-except:
- print('numpy 1.3 is required')
- raise
-try:
- import scipy as sp
- import scipy.stats as stats
- from cg.kdtree import KDTree
- from scipy.spatial.distance import pdist, cdist
-except:
- print('scipy 0.7+ is required')
- raise
+import numpy as np
+import numpy.linalg as la
+import scipy as sp
+import scipy.stats as stats
+from cg.kdtree import KDTree
+from scipy.spatial.distance import pdist, cdist
RTOL = .00001
ATOL = 1e-7
diff --git a/pysal/contrib/glm/iwls.py b/pysal/contrib/glm/iwls.py
index 082fd05..2b832bf 100644
--- a/pysal/contrib/glm/iwls.py
+++ b/pysal/contrib/glm/iwls.py
@@ -45,7 +45,7 @@ def iwls(y, x, family, offset, y_fix,
diff = 1.0e6
if ini_betas is None:
- betas = np.zeros((x.shape[1], 1), np.float)
+ betas = np.zeros((x.shape[1], 1), np.float)
else:
betas = ini_betas
@@ -53,9 +53,9 @@ def iwls(y, x, family, offset, y_fix,
y = family.link._clean(y)
if isinstance(family, Poisson):
y_off = y/offset
- y_off = family.starting_mu(y_off)
- v = family.predict(y_off)
- mu = family.starting_mu(y)
+ y_off = family.starting_mu(y_off)
+ v = family.predict(y_off)
+ mu = family.starting_mu(y)
else:
mu = family.starting_mu(y)
v = family.predict(mu)
@@ -78,7 +78,7 @@ def iwls(y, x, family, offset, y_fix,
mu = family.fitted(v)
if isinstance(family, Poisson):
- mu = mu * offset
+ mu = mu * offset
diff = min(abs(n_betas-betas))
betas = n_betas
diff --git a/pysal/contrib/viz/color.py b/pysal/contrib/viz/color.py
index e69b5d3..bca31ae 100644
--- a/pysal/contrib/viz/color.py
+++ b/pysal/contrib/viz/color.py
@@ -2,13 +2,8 @@
color handling for mapping and geovisualization
"""
-from warnings import warn
-try:
- import palettable as pltt
- from palettable.colorbrewer import qualitative, sequential, diverging
-except:
- warn('palettable not installed. Functionality '
- 'related to it will not work')
+import palettable as pltt
+
def get_color_map(palette=None, name='BuGn', cmtype='sequential', k=5,
color_encoding='hex'):
@@ -50,20 +45,21 @@ def get_color_map(palette=None, name='BuGn', cmtype='sequential', k=5,
cmtype = pltt2type[name.lower()]
if name[-2:] == '_r':
palette = pltt.colorbrewer.get_map(name[:-2], cmtype,
- k, reverse=True)
+ k, reverse=True)
else:
palette = pltt.colorbrewer.get_map(name, cmtype, k)
colors = getattr(palette, encs[color_encoding.lower()])
return colors
+
def _build_pltt2type():
types = ['sequential', 'diverging', 'qualitative']
pltt2type = {}
for t in types:
pals = list(set([
p.split('_')[0] for p in dir(getattr(pltt.colorbrewer, t))
- if p[0]!='_'
- ]))
+ if p[0] != '_'
+ ]))
pals = pals + [p+'_r' for p in pals]
for p in pals:
pltt2type[p.lower()] = t
@@ -71,7 +67,7 @@ def _build_pltt2type():
pltt2type = _build_pltt2type()
+
def get_maps_by_type(data_type):
names = [name for name in dir(data_type) if not name.startswith('_')]
return names
-
diff --git a/pysal/contrib/viz/folium_mapping.ipynb b/pysal/contrib/viz/folium_mapping.ipynb
index 8aad55a..25a0019 100644
--- a/pysal/contrib/viz/folium_mapping.ipynb
+++ b/pysal/contrib/viz/folium_mapping.ipynb
@@ -4,316 +4,97 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Mapping using Pysal and Folium: Example"
+ "# Mapping using Pysal and Folium: Texas"
]
},
{
"cell_type": "code",
- "execution_count": 1,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 12,
+ "metadata": {},
"outputs": [],
"source": [
"import pysal as ps\n",
- "import geojson as gj\n",
- "import folium_mapping as fm"
+ "import geopandas as gpd\n",
+ "import folium_mapping as fm\n",
+ "%matplotlib inline"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "First, we need to convert the data into a JSON format. JSON, short for \"Javascript Serialized Object Notation,\" is a simple and effective way to represent objects in a digital environment. For geographic information, the [GeoJSON](https://geojson.org) standard defines how to represent geographic information in JSON format. Python programmers may be more comfortable thinking of JSON data as something akin to a standard Python dictionary. "
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "filepath = ps.examples.get_path('south.shp')[:-4]"
+ "Let's look at the columns that we're going to map."
]
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 9,
"metadata": {
- "collapsed": false
+ "collapsed": true
},
"outputs": [],
"source": [
- "shp = ps.open(filepath + '.shp')\n",
- "dbf = ps.open(filepath + '.dbf')"
+ "df = gpd.read_file('./example.json')"
]
},
{
"cell_type": "code",
- "execution_count": 4,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "js = fm.build_features(shp, dbf)"
- ]
- },
- {
- "cell_type": "markdown",
+ "execution_count": 13,
"metadata": {},
- "source": [
- "Just to show, this constructs a dictionary with the following keys:"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "metadata": {
- "collapsed": false
- },
"outputs": [
{
"data": {
"text/plain": [
- "dict_keys(['bbox', 'features', 'type'])"
+ "<matplotlib.axes._subplots.AxesSubplot at 0x7f03fd71bba8>"
]
},
- "execution_count": 5,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "js.keys()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "'FeatureCollection'"
- ]
- },
- "execution_count": 6,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "js.type"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "[-106.6495132446289, 24.95596694946289, -75.0459976196289, 40.63713836669922]"
- ]
- },
- "execution_count": 7,
+ "execution_count": 13,
"metadata": {},
"output_type": "execute_result"
- }
- ],
- "source": [
- "js.bbox"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 8,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
+ },
{
"data": {
+ "image/png": "iVBORw0KGgoAAAANSUhEUgAAAXcAAAEACAYAAABI5zaHAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAEThJREFUeJzt3XuM5WV9x/H3Z91FWMZigGXRWF0lKNJVSZkgat3O1DZS\nTYvxiiki8semphYjGjFWQ4BaaU0s4qXbxYK0jV2qTQRvpSZ1tNTLyhqtyMV6KUFEXYWiwyLL5ds/\nfmfrcTnLnJk9O2fmmfcrmczM8/wuD1/OfM5vn/Oc30lVIUlqy6pxD0CSNHqGuyQ1yHCXpAYZ7pLU\nIMNdkhpkuEtSgwx3SWqQ4S5JDTLcJalBq8d14iOPPLI2bNiwoH3vvvtuDj300NEOqAHWZTDrMph1\nGWyp12XHjh0/qap1c203tnDfsGED11133YL2nZmZYWpqarQDaoB1Gcy6DGZdBlvqdUlyyzDbOS0j\nSQ0y [...]
"text/plain": [
- "{\"bbox\": [-80.6688232421875, 40.39815902709961, -80.52220916748047, 40.63713836669922], \"geometry\": {\"coordinates\": [[[-80.6280517578125, 40.39815902709961], [-80.60203552246094, 40.480472564697266], [-80.62545776367188, 40.504398345947266], [-80.6336441040039, 40.53913879394531], [-80.6688232421875, 40.568214416503906], [-80.66793060302734, 40.58207321166992], [-80.63754272460938, 40.61391830444336], [-80.61175537109375, 40.619998931884766], [-80.57462310791016, 40.6159095 [...]
+ "<matplotlib.figure.Figure at 0x7f03ff4caf98>"
]
},
- "execution_count": 8,
"metadata": {},
- "output_type": "execute_result"
+ "output_type": "display_data"
}
],
"source": [
- "js.features[0]"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Then, we write the json to a file. "
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 9,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "with open('./example.json', 'w') as out:\n",
- " gj.dump(js, out)"
+ "df.HR90.hist()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Mapping"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Let's look at the columns that we're going to map."
+ "To use the folium mapper, you pass the the geodataframe, a unique key for the geometries, & the attribute to be mapped: "
]
},
{
"cell_type": "code",
- "execution_count": 10,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "['POL80', 'PO70', 'UE70', 'PO80', 'BLK80']"
- ]
- },
- "execution_count": 10,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "#js.features[0].properties.keys()[0:5]\n",
- "list(js.features[0].properties.keys())[:5]"
- ]
- },
- {
- "cell_type": "markdown",
+ "execution_count": 15,
"metadata": {},
- "source": [
- "We can map these attributes by calling them as commands to the choropleth mapping function. \n",
- "\n",
- "Here's the simplest mapping command:"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 11,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "import folium as fol"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 12,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "fol.Map.choropleth?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 13,
- "metadata": {
- "collapsed": false
- },
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/home/ljw/.local/lib/python3.5/site-packages/folium/folium.py:504: UserWarning: This method is deprecated. Please use Map.choropleth instead.\n",
- " warnings.warn('This method is deprecated. '\n"
- ]
- },
- {
"data": {
"text/html": [
- "<div style=\"width:100%;\"><div style=\"position:relative;width:100%;height:0;padding-bottom:60%;\"><iframe src=\"data:text/html;base64,CiAgICAgICAgPCFET0NUWVBFIGh0bWw+CiAgICAgICAgPGhlYWQ+CiAgICAgICAgICAgIAogICAgICAgIAogICAgICAgICAgICA8bWV0YSBodHRwLWVxdWl2PSJjb250ZW50LXR5cGUiIGNvbnRlbnQ9InRleHQvaHRtbDsgY2hhcnNldD1VVEYtOCIgLz4KICAgICAgICAKICAgICAgICAgICAgCiAgICAgICAgCiAgICAgICAgICAgIDxzY3JpcHQgc3JjPSJodHRwczovL2NkbmpzLmNsb3VkZmxhcmUuY29tL2FqYXgvbGlicy9sZWFmbGV0LzAuNy4zL2xlYWZsZXQu [...]
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- "<folium.folium.Map at 0x7fdb350ff198>"
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- "execution_count": 13,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "fm.choropleth_map('./example.json', 'FIPS', 'HR90')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 14,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/home/ljw/.local/lib/python3.5/site-packages/folium/folium.py:504: UserWarning: This method is deprecated. Please use Map.choropleth instead.\n",
- " warnings.warn('This method is deprecated. '\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "<div style=\"width:100%;\"><div style=\"position:relative;width:100%;height:0;padding-bottom:60%;\"><iframe src=\"data:text/html;base64,CiAgICAgICAgPCFET0NUWVBFIGh0bWw+CiAgICAgICAgPGhlYWQ+CiAgICAgICAgICAgIAogICAgICAgIAogICAgICAgICAgICA8bWV0YSBodHRwLWVxdWl2PSJjb250ZW50LXR5cGUiIGNvbnRlbnQ9InRleHQvaHRtbDsgY2hhcnNldD1VVEYtOCIgLz4KICAgICAgICAKICAgICAgICAgICAgCiAgICAgICAgCiAgICAgICAgICAgIDxzY3JpcHQgc3JjPSJodHRwczovL2NkbmpzLmNsb3VkZmxhcmUuY29tL2FqYXgvbGlicy9sZWFmbGV0LzAuNy4zL2xlYWZsZXQu [...]
- ],
- "text/plain": [
- "<folium.folium.Map at 0x7fdb33932c50>"
- ]
- },
- "execution_count": 14,
+ "execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "fm.choropleth_map('./example.json', 'FIPS', 'HR90')"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This produces a map using default classifications and color schemes and saves it to an html file. We set the function to have sane defaults. However, if the user wants to have more control, we have many options available. "
+ "fm.choropleth_map(df, key='FIPS', attribute='HR90')"
]
},
{
@@ -325,35 +106,25 @@
},
{
"cell_type": "code",
- "execution_count": 15,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 18,
+ "metadata": {},
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/home/ljw/.local/lib/python3.5/site-packages/folium/folium.py:504: UserWarning: This method is deprecated. Please use Map.choropleth instead.\n",
- " warnings.warn('This method is deprecated. '\n"
- ]
- },
- {
"data": {
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],
"text/plain": [
- "<folium.folium.Map at 0x7fdb31931c88>"
+ "<folium.folium.Map at 0x7f03f46a2438>"
]
},
- "execution_count": 15,
+ "execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "fm.choropleth_map('./example.json', 'FIPS', 'HR90', classification = 'Quantiles')"
+ "fm.choropleth_map(ex, 'FIPS', 'HR90', classification = 'Equal Interval')"
]
},
{
@@ -372,35 +143,27 @@
},
{
"cell_type": "code",
- "execution_count": 16,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 19,
+ "metadata": {},
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/home/ljw/.local/lib/python3.5/site-packages/folium/folium.py:504: UserWarning: This method is deprecated. Please use Map.choropleth instead.\n",
- " warnings.warn('This method is deprecated. '\n"
- ]
- },
- {
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+ "<folium.folium.Map at 0x7f03f448afd0>"
]
},
- "execution_count": 16,
+ "execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "fm.choropleth_map('./example.json', 'FIPS', 'HR90', classification = 'Jenks Caspall', tiles='Stamen Toner', save=True) "
+ "fm.choropleth_map(ex, 'FIPS', 'HR90', \n",
+ " classification = 'Jenks Caspall', \n",
+ " tiles='Stamen Toner', save=True) "
]
},
{
@@ -419,35 +182,27 @@
},
{
"cell_type": "code",
- "execution_count": 17,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 20,
+ "metadata": {},
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/home/ljw/.local/lib/python3.5/site-packages/folium/folium.py:504: UserWarning: This method is deprecated. Please use Map.choropleth instead.\n",
- " warnings.warn('This method is deprecated. '\n"
- ]
- },
- {
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- "<folium.folium.Map at 0x7fdb3421c9b0>"
+ "<folium.folium.Map at 0x7f03f42d4fd0>"
]
},
- "execution_count": 17,
+ "execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "fm.choropleth_map('./example.json', 'FIPS', 'HR80', classification = 'Jenks Caspall', tiles='Stamen Toner', fill_color = 'PuBuGn', save=True) "
+ "fm.choropleth_map(ex, 'FIPS', 'HR80', \n",
+ " classification = 'Jenks Caspall', \n",
+ " tiles='Stamen Toner', fill_color = 'PuBuGn', save=True) "
]
},
{
@@ -466,42 +221,28 @@
},
{
"cell_type": "code",
- "execution_count": 18,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 25,
+ "metadata": {},
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/home/ljw/.local/lib/python3.5/site-packages/folium/folium.py:504: UserWarning: This method is deprecated. Please use Map.choropleth instead.\n",
- " warnings.warn('This method is deprecated. '\n"
- ]
- },
- {
"data": {
"text/html": [
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- "<folium.folium.Map at 0x7fdb34200ac8>"
+ "<folium.folium.Map at 0x7f03ea94a0f0>"
]
},
- "execution_count": 18,
+ "execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "fm.choropleth_map('./example.json', 'FIPS', 'HR80', classification = 'Equal Interval', classes=6, tiles='Stamen Toner', fill_color='PuBuGn',save=True) "
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Folium supports up to 6 classes."
+ "fm.choropleth_map('./example.json', 'FIPS', 'HR80', \n",
+ " classification = 'Jenks Caspall', \n",
+ " classes=3, tiles='Stamen Toner', \n",
+ " fill_color='PuBuGn',save=True) "
]
},
{
@@ -513,114 +254,48 @@
},
{
"cell_type": "code",
- "execution_count": 19,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/home/ljw/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:3142: RuntimeWarning: Invalid value encountered in median\n",
- " RuntimeWarning)\n",
- "/home/ljw/.local/lib/python3.5/site-packages/folium/folium.py:504: UserWarning: This method is deprecated. Please use Map.choropleth instead.\n",
- " warnings.warn('This method is deprecated. '\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "<div style=\"width:100%;\"><div style=\"position:relative;width:100%;height:0;padding-bottom:60%;\"><iframe src=\"data:text/html;base64,CiAgICAgICAgPCFET0NUWVBFIGh0bWw+CiAgICAgICAgPGhlYWQ+CiAgICAgICAgICAgIAogICAgICAgIAogICAgICAgICAgICA8bWV0YSBodHRwLWVxdWl2PSJjb250ZW50LXR5cGUiIGNvbnRlbnQ9InRleHQvaHRtbDsgY2hhcnNldD1VVEYtOCIgLz4KICAgICAgICAKICAgICAgICAgICAgCiAgICAgICAgCiAgICAgICAgICAgIDxzY3JpcHQgc3JjPSJodHRwczovL2NkbmpzLmNsb3VkZmxhcmUuY29tL2FqYXgvbGlicy9sZWFmbGV0LzAuNy4zL2xlYWZsZXQu [...]
- ],
- "text/plain": [
- "<folium.folium.Map at 0x7fdb2b922470>"
- ]
- },
- "execution_count": 19,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "fm.choropleth_map('./example.json', 'FIPS', 'HR90', classification = 'Quantiles', std='HR80' , tiles='Stamen Toner', fill_color='PuBuGn',save=True) "
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The goal of the `std` argument was to implement a very flexible transformation argument that could take functions, fields, and static items. As of now, it only supports float/int scaling and division by another field, which would support the mapping of spatial rates or population rates."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Conclusion"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Overall, the function neatly encapsulates three components:\n",
- "\n",
- "- plumbing large lists of arguments together to simplify mapping from JSON files\n",
- "- searching for sane defaults (bounding box & zoom level)\n",
- "- implementing classification and standardization useful for choropleth mapping"
- ]
- },
- {
- "cell_type": "markdown",
+ "execution_count": 27,
"metadata": {},
- "source": [
- "Due to some pretty strong limitations in `Folium` itself, its usefulness for rich, dynamic, and interactive visualizations built from small, atomic functions is probably limited. It would need to be extended quite significantly (or linked with even more packages with more fickle APIs) to usefully generate mixed-mode scientific visualizations. With `Folium`'s natural linkages to `Pandas`, mapping derived quantites is also possible.\n",
- "\n",
- "But, it's really simple to map quickly from PySAL:"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 20,
- "metadata": {
- "collapsed": false
- },
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
- "/home/ljw/.local/lib/python3.5/site-packages/folium/folium.py:504: UserWarning: This method is deprecated. Please use Map.choropleth instead.\n",
- " warnings.warn('This method is deprecated. '\n"
+ "/home/ljw/anaconda3/envs/ana/lib/python3.6/site-packages/pysal/esda/mapclassify.py:267: RuntimeWarning: invalid value encountered in greater\n",
+ " binIds += (x > l) * (x <= r) * k\n",
+ "/home/ljw/anaconda3/envs/ana/lib/python3.6/site-packages/pysal/esda/mapclassify.py:267: RuntimeWarning: invalid value encountered in less_equal\n",
+ " binIds += (x > l) * (x <= r) * k\n",
+ "/home/ljw/anaconda3/envs/ana/lib/python3.6/site-packages/numpy/lib/function_base.py:4016: RuntimeWarning: Invalid value encountered in median\n",
+ " r = func(a, **kwargs)\n"
]
},
{
"data": {
"text/html": [
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+ "<div style=\"width:100%;\"><div style=\"position:relative;width:100%;height:0;padding-bottom:60%;\"><iframe src=\"data:text/html;charset=utf-8;base64,PCFET0NUWVBFIGh0bWw+CjxoZWFkPiAgICAKICAgIDxtZXRhIGh0dHAtZXF1aXY9ImNvbnRlbnQtdHlwZSIgY29udGVudD0idGV4dC9odG1sOyBjaGFyc2V0PVVURi04IiAvPgogICAgPHNjcmlwdD5MX1BSRUZFUl9DQU5WQVMgPSBmYWxzZTsgTF9OT19UT1VDSCA9IGZhbHNlOyBMX0RJU0FCTEVfM0QgPSBmYWxzZTs8L3NjcmlwdD4KICAgIDxzY3JpcHQgc3JjPSJodHRwczovL2Nkbi5qc2RlbGl2ci5uZXQvbnBtL2xlYWZsZXRAMS4yLjAvZG [...]
],
"text/plain": [
- "<folium.folium.Map at 0x7fdb3433d1d0>"
+ "<folium.folium.Map at 0x7f03ea94ae48>"
]
},
- "execution_count": 20,
+ "execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "with open('example2.json', 'w') as out:\n",
- " gj.dump(fm.build_features(ps.open(filepath + '.shp'), ps.open(filepath + '.dbf')), out)\n",
- "fm.choropleth_map('example2.json', 'FIPS', 'HR70')"
+ "fm.choropleth_map(ex, 'FIPS', 'HR90', \n",
+ " classification = 'Quantiles', \n",
+ " std='HR80' , tiles='Stamen Toner', \n",
+ " fill_color='PuBuGn',save=True) "
]
}
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python [conda env:ana]",
"language": "python",
- "name": "python3"
+ "name": "conda-env-ana-py"
},
"language_info": {
"codemirror_mode": {
@@ -632,9 +307,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.5.1"
+ "version": "3.6.2"
}
},
"nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
}
diff --git a/pysal/contrib/viz/folium_mapping.py b/pysal/contrib/viz/folium_mapping.py
index 1fef65a..808d3d7 100644
--- a/pysal/contrib/viz/folium_mapping.py
+++ b/pysal/contrib/viz/folium_mapping.py
@@ -142,14 +142,7 @@ def choropleth_map(jsonpath, key, attribute, df = None,
sjson = gj.load(open(jsonpath))
else:
raise IOError('File not found')
-
- if isinstance(jsonpath, dict):
- raise NotImplementedError('Direct mapping from dictionary not yet supported')
- #with open('tmp.json', 'w') as out:
- # gj.dump(jsonpath, out)
- # sjson = gj.load(open('tmp.json'))
-
- if isinstance(jsonpath, tuple):
+ elif isinstance(jsonpath, tuple):
if 'ShpWrapper' in str(type(jsonpath[0])) and 'DBF' in str(type(jsonpath[1])):
flip('tmp.json', jsonpath[0], jsonpath[1])
sjson = gj.load(open('tmp.json'))
@@ -162,6 +155,14 @@ def choropleth_map(jsonpath, key, attribute, df = None,
else:
raise IOError('Inputs must be GeoJSON filepath, GeoJSON dictionary in memory, or shp-dbf tuple')
+ else:
+ import geopandas
+ if isinstance(jsonpath, geopandas.GeoDataFrame):
+ jsonpath = jsonpath
+ df = jsonpath
+ geom_col = df._geometry_column_name
+ centroid = tuple(reversed(np.hstack(df[geom_col].centroid.cascaded_union.centroid.xy)))
+ bbox = df.total_bounds
#key construction
if df is None:
@@ -169,7 +170,7 @@ def choropleth_map(jsonpath, key, attribute, df = None,
dfkey = [key, attribute]
#centroid search
- if centroid == None:
+ if centroid is None:
if 'bbox' in sjson.keys():
bbox = sjson.bbox
bbox = bboxsearch(sjson)
@@ -194,15 +195,13 @@ def choropleth_map(jsonpath, key, attribute, df = None,
y = np.array(df[attribute].tolist())
#For people who don't read documentation...
- if isinstance(classes, list):
- bins = classes
- classes = len(bins)
- elif isinstance(classes, float):
+ if isinstance(classes, float):
try:
classes = int(classes)
except:
raise ValueError('Classes must be coercable to integers')
+ classes += 1
#classification passing
if classification != None:
if classification == "Maximum Breaks": #there is probably a better way to do this, but it's a start.
@@ -248,14 +247,19 @@ def choropleth_map(jsonpath, key, attribute, df = None,
mapclass = ps.Quantiles(y, k=classes).bins.tolist()
#folium call, try abstracting to a "mapper" function, passing list of args
- choromap.geo_json(geo_path=jsonpath, key_on = jsonkey,
+ if len(mapclass) > 6:
+ raise ValueError('Folium only supports a maximum of'
+ ' six classes on threshold scales')
+ #return dict(geo_data = jsonpath, key_on = jsonkey, data = df, columns=dfkey, fill_color=fill_color,
+ # fill_opacity=fill_opacity, line_opacity=line_opacity, threshold_scale=mapclass, legend_name=legend_name)
+ choromap.choropleth(geo_data=jsonpath, key_on = jsonkey,
data = df, columns = dfkey,
fill_color = fill_color, fill_opacity = fill_opacity,
- line_opacity = line_opacity, threshold_scale = mapclass[:-1] , legend_name = legend_name
+ line_opacity = line_opacity, threshold_scale = mapclass, legend_name = legend_name
)
if save:
- fname = jsonpath.rstrip('.json') + '_' + attribute + '.html'
+ fname = '_'.join((key,attribute))+'.html'
choromap.save(fname)
return choromap
diff --git a/pysal/contrib/viz/mapping.py b/pysal/contrib/viz/mapping.py
index 3f857d4..0346b89 100644
--- a/pysal/contrib/viz/mapping.py
+++ b/pysal/contrib/viz/mapping.py
@@ -1097,7 +1097,7 @@ def plot_lisa_cluster(shp_link, lisa, p_thres=0.01, shp_type='poly',
shp = ps.open(shp_link)
# Lisa layer
lisa_obj = map_poly_shp(shp)
- lisa_obj = base_lisa_cluster(lisa_obj, lisa)
+ lisa_obj = base_lisa_cluster(lisa_obj, lisa, p_thres=p_thres)
lisa_obj.set_alpha(alpha)
# Figure
fig = plt.figure(figsize=figsize)
diff --git a/pysal/core/util/shapefile.py b/pysal/core/util/shapefile.py
index 98a020a..58f95be 100644
--- a/pysal/core/util/shapefile.py
+++ b/pysal/core/util/shapefile.py
@@ -149,7 +149,10 @@ def _unpackDict2(d, structure, fileObj):
for name, dtype, order in structure:
dtype, n = dtype
result = array.array(dtype)
- result.fromstring(fileObj.read(result.itemsize * n))
+ try:
+ result.frombytes(fileObj.read(result.itemsize * n))
+ except AttributeError:
+ result.fromstring(fileObj.read(result.itemsize * n))
if order != SYS_BYTE_ORDER:
result.byteswap()
d[name] = result.tolist()
diff --git a/pysal/esda/moran.py b/pysal/esda/moran.py
index 6f356a6..b6d76f0 100644
--- a/pysal/esda/moran.py
+++ b/pysal/esda/moran.py
@@ -726,10 +726,10 @@ class Moran_Local(object):
Parameters
----------
- y : array
- (n,1), attribute array
- w : W
- weight instance assumed to be aligned with y
+ y : array
+ (n,1), attribute array
+ w : W
+ weight instance assumed to be aligned with y
transformation : {'R', 'B', 'D', 'U', 'V'}
weights transformation, default is row-standardized "r".
Other options include
@@ -952,12 +952,12 @@ class Moran_Local_BV(object):
Parameters
----------
- x : array
- x-axis variable
- y : array
- (n,1), wy will be on y axis
- w : W
- weight instance assumed to be aligned with y
+ x : array
+ x-axis variable
+ y : array
+ (n,1), wy will be on y axis
+ w : W
+ weight instance assumed to be aligned with y
transformation : {'R', 'B', 'D', 'U', 'V'}
weights transformation, default is row-standardized "r".
Other options include
@@ -1197,15 +1197,15 @@ class Moran_Local_Rate(Moran_Local):
Parameters
----------
- e : array
- (n,1), an event variable across n spatial units
- b : array
- (n,1), a population-at-risk variable across n spatial units
- w : W
- weight instance assumed to be aligned with y
- adjusted : boolean
- whether or not local Moran statistics need to be adjusted for
- rate variable
+ e : array
+ (n,1), an event variable across n spatial units
+ b : array
+ (n,1), a population-at-risk variable across n spatial units
+ w : W
+ weight instance assumed to be aligned with y
+ adjusted : boolean
+ whether or not local Moran statistics need to be adjusted for
+ rate variable
transformation : {'R', 'B', 'D', 'U', 'V'}
weights transformation, default is row-standardized "r".
Other options include
@@ -1222,47 +1222,47 @@ class Moran_Local_Rate(Moran_Local):
If False use PySAL Scheme: HH=1, LH=2, LL=3, HL=4
Attributes
----------
- y : array
- rate variables computed from parameters e and b
- if adjusted is True, y is standardized rates
- otherwise, y is raw rates
- w : W
- original w object
- permutations : int
- number of random permutations for calculation of pseudo
- p_values
- I : float
- value of Moran's I
- q : array
- (if permutations>0)
- values indicate quandrant location 1 HH, 2 LH, 3 LL, 4 HL
- sim : array
- (if permutations>0)
- vector of I values for permuted samples
- p_sim : array
- (if permutations>0)
- p-value based on permutations (one-sided)
- null: spatial randomness
- alternative: the observed Ii is further away or extreme
- from the median of simulated Iis. It is either extremely
- high or extremely low in the distribution of simulated Is
- EI_sim : float
- (if permutations>0)
- average value of I from permutations
- VI_sim : float
- (if permutations>0)
- variance of I from permutations
- seI_sim : float
- (if permutations>0)
- standard deviation of I under permutations.
- z_sim : float
- (if permutations>0)
- standardized I based on permutations
- p_z_sim : float
- (if permutations>0)
- p-value based on standard normal approximation from
- permutations (one-sided)
- for two-sided tests, these values should be multiplied by 2
+ y : array
+ rate variables computed from parameters e and b
+ if adjusted is True, y is standardized rates
+ otherwise, y is raw rates
+ w : W
+ original w object
+ permutations : int
+ number of random permutations for calculation of pseudo
+ p_values
+ Is : float
+ local Moran's I values for rates or Empirical Bayes Index
+ q : array
+ (if permutations>0)
+ values indicate quandrant location 1 HH, 2 LH, 3 LL, 4 HL
+ sim : array
+ (if permutations>0)
+ vector of I values for permuted samples
+ p_sim : array
+ (if permutations>0)
+ p-values based on permutations (one-sided)
+ null: spatial randomness
+ alternative: the observed Ii is further away or extreme
+ from the median of simulated values. It is either extremelyi
+ high or extremely low in the distribution of simulated Is.
+ EI_sim : array
+ (if permutations>0)
+ average values of local Is from permutations
+ VI_sim : array
+ (if permutations>0)
+ variance of Is from permutations
+ seI_sim : array
+ (if permutations>0)
+ standard deviations of Is under permutations.
+ z_sim : arrray
+ (if permutations>0)
+ standardized Is based on permutations
+ p_z_sim : array
+ (if permutations>0)
+ p-values based on standard normal approximation from
+ permutations (one-sided)
+ for two-sided tests, these values should be multiplied by 2
Examples
--------
diff --git a/pysal/esda/smoothing.py b/pysal/esda/smoothing.py
index 7a27966..5c709c2 100644
--- a/pysal/esda/smoothing.py
+++ b/pysal/esda/smoothing.py
@@ -510,10 +510,10 @@ def assuncao_rate(e, b):
Parameters
----------
- e : array(n, 1)
- event variable measured at n spatial units
- b : array(n, 1)
- population at risk variable measured at n spatial units
+ e : array
+ (n, 1), event variable measured at n spatial units
+ b : array
+ (n, 1), population at risk variable measured at n spatial units
Notes
-----
@@ -521,7 +521,8 @@ def assuncao_rate(e, b):
Returns
-------
- : array (nx1)
+ : array
+ (n,1)
Examples
--------
@@ -540,7 +541,7 @@ def assuncao_rate(e, b):
Computing the rates
>>> print assuncao_rate(e, b)[:4]
- [ 1.04319254 -0.04117865 -0.56539054 -1.73762547]
+ [ 1.03843594 -0.04099089 -0.56250375 -1.73061861]
"""
@@ -667,15 +668,15 @@ class Empirical_Bayes(_Smoother):
Parameters
----------
- e : array (n, 1)
- event variable measured across n spatial units
- b : array (n, 1)
- population at risk variable measured across n spatial units
+ e : array
+ (n, 1), event variable measured across n spatial units
+ b : array
+ (n, 1), population at risk variable measured across n spatial units
Attributes
----------
- r : array (n, 1)
- rate values from Empirical Bayes Smoothing
+ r : array
+ (n, 1), rate values from Empirical Bayes Smoothing
Examples
--------
@@ -1665,7 +1666,7 @@ class Headbanging_Triples(object):
(0.33753, 0.302707)
"""
def __init__(self, data, w, k=5, t=3, angle=135.0, edgecor=False):
- raise DepricationWarning('Depricated')
+ raise DeprecationWarning('Deprecated. This function is no longer supported.')
if k < 3:
raise ValueError("w should be NeareastNeighbors instance & the number of neighbors should be more than 3.")
if not w.id_order_set:
@@ -1811,7 +1812,7 @@ class Headbanging_Median_Rate(object):
array([ 0.00091659, 0. , 0.00156838, 0.0018315 , 0.00498891])
"""
def __init__(self, e, b, t, aw=None, iteration=1):
- warnings.warn("Deprecated", DepricationWarning)
+ raise DeprecationWarning('Deprecated. This function is no longer supported.')
self.r = e * 1.0 / b
self.tr, self.aw = t.triples, aw
if hasattr(t, 'extra'):
diff --git a/pysal/examples/10740/10740.dbf b/pysal/examples/10740/10740.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/10740/10740.shp b/pysal/examples/10740/10740.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/10740/10740.shx b/pysal/examples/10740/10740.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/10740/10740_queen.gal b/pysal/examples/10740/10740_queen.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/10740/10740_rook.gal b/pysal/examples/10740/10740_rook.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/10740/README.md b/pysal/examples/10740/README.md
index ef6eccc..282613e 100644
--- a/pysal/examples/10740/README.md
+++ b/pysal/examples/10740/README.md
@@ -1,13 +1,11 @@
10740
=====
-Albuquerque Census 2000 Tract Data
-----------------------------------
+Albuquerque, New Mexico, Census 2000 Tract Data
+-----------------------------------------------
-Albuquerque, New Mexico, 2000 Census Tracts (n = 141)
-
-* 10740.dbf: attribute database file
-* 10740.shp: shapefile
-* 10740.shx: spatial index
-* 10740_queen.gal: queen contiguity GAL format
-* 10740_rook.gal: rook contiguity GAL format
+* 10740.dbf: attribute data. (k=5)
+* 10740.shp: shapefile. (n=195)
+* 10740.shx: spatial index.
+* 10740_queen.gal: queen contiguity weights in GAL format.
+* 10740_rook.gal: rook contiguity weights in GAL format.
diff --git a/pysal/examples/Line/Line.dbf b/pysal/examples/Line/Line.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/Line/Line.prj b/pysal/examples/Line/Line.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/Line/Line.shp b/pysal/examples/Line/Line.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/Line/Line.shx b/pysal/examples/Line/Line.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/Line/README.md b/pysal/examples/Line/README.md
index ea83d38..9ce20bf 100644
--- a/pysal/examples/Line/README.md
+++ b/pysal/examples/Line/README.md
@@ -1,7 +1,12 @@
-Point
+Line
=====
-Point Shapefile
+Line Shapefile
---------------
-Used for testing
+* Line.dbf: attribute data. (k=3)
+* Line.prj: ESRI projection file.
+* Line.shp: Line shapefile. (n=4)
+* Line.shx: spatial index.
+
+Used for testing.
diff --git a/pysal/examples/Point/Point.dbf b/pysal/examples/Point/Point.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/Point/Point.prj b/pysal/examples/Point/Point.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/Point/Point.shp b/pysal/examples/Point/Point.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/Point/Point.shx b/pysal/examples/Point/Point.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/Point/README.md b/pysal/examples/Point/README.md
new file mode 100644
index 0000000..2595b6b
--- /dev/null
+++ b/pysal/examples/Point/README.md
@@ -0,0 +1,12 @@
+Point
+=====
+
+Point Shapefile
+---------------
+
+* Point.dbf: attribute data. (k=3)
+* Point.prj: ESRI projection file.
+* Point.shp: Point shapefile. (n=9)
+* Point.shx: spatial index.
+
+Used for testing
diff --git a/pysal/examples/Polygon/Polygon.dbf b/pysal/examples/Polygon/Polygon.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon/Polygon.prj b/pysal/examples/Polygon/Polygon.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon/Polygon.shp b/pysal/examples/Polygon/Polygon.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon/Polygon.shx b/pysal/examples/Polygon/Polygon.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon/README.md b/pysal/examples/Polygon/README.md
index 3f3a53b..13b7f5b 100644
--- a/pysal/examples/Polygon/README.md
+++ b/pysal/examples/Polygon/README.md
@@ -4,4 +4,9 @@ Polygon
Polygon Shapefile
-----------------
-Used for testing
+* Polygon.dbf: attribute data. (k=3)
+* Polygon.prj: ESRI projection file.
+* Polygon.shp: Polygon shapefile. (n=3)
+* Polygon.shx: spatial index.
+
+Used for testing.
diff --git a/pysal/examples/Polygon_Holes/Polygon_Holes.cpg b/pysal/examples/Polygon_Holes/Polygon_Holes.cpg
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon_Holes/Polygon_Holes.dbf b/pysal/examples/Polygon_Holes/Polygon_Holes.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon_Holes/Polygon_Holes.prj b/pysal/examples/Polygon_Holes/Polygon_Holes.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon_Holes/Polygon_Holes.qpj b/pysal/examples/Polygon_Holes/Polygon_Holes.qpj
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon_Holes/Polygon_Holes.shp b/pysal/examples/Polygon_Holes/Polygon_Holes.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/Polygon_Holes/Polygon_Holes.shx b/pysal/examples/Polygon_Holes/Polygon_Holes.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/README.txt b/pysal/examples/README.txt
index 11d7482..4ca70d9 100644
--- a/pysal/examples/README.txt
+++ b/pysal/examples/README.txt
@@ -1,5 +1,5 @@
Documentation for all example data sets for PySAL can be found at
-http://pysal.org/users/tutorials/examples.html
+http://pysal.readthedocs.io/en/latest/users/tutorials/examples.html
If you obtained this example data by downloading it as a separate zip file, it should be unzipped in the pysal directory, so that the path to the data herein would be like pysal/examples/rook31.dbf, for example.
diff --git a/pysal/examples/__init__.py b/pysal/examples/__init__.py
old mode 100644
new mode 100755
diff --git a/pysal/examples/arcgis/README.md b/pysal/examples/arcgis/README.md
index 8204b83..5fdf379 100644
--- a/pysal/examples/arcgis/README.md
+++ b/pysal/examples/arcgis/README.md
@@ -4,4 +4,7 @@ arcgis
arcgis testing files
--------------------
-Files used for internal testing
+* arcgis_ohio.dbf: spatial weights in ArcGIS DBF format.
+* arcgis_txt.txt: spatial weights in ArcGIS TXT format.
+
+Files used for internal testing.
diff --git a/pysal/examples/arcgis/arcgis_ohio.dbf b/pysal/examples/arcgis/arcgis_ohio.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/arcgis/arcgis_txt.txt b/pysal/examples/arcgis/arcgis_txt.txt
old mode 100644
new mode 100755
diff --git a/pysal/examples/baltim/README.md b/pysal/examples/baltim/README.md
index 00949c5..82817b4 100644
--- a/pysal/examples/baltim/README.md
+++ b/pysal/examples/baltim/README.md
@@ -1,16 +1,14 @@
baltim
======
-Baltimore house sales prices and hedonics
------------------------------------------
+Baltimore house sales prices and hedonics 1978
+----------------------------------------------------------------
-* baltim.dbf attribute data
-* baltim.shp shape file
-* baltim.shx spatial index file
-* baltim.tri.k12.kwt Kernel weights using a triangular kernel with 12 neares
- neighbors
-* baltim_k4.gwt Nearest neighbor weights (4nn)
-* baltim_q.gal Queen contiguity file
-* baltimore.geojson
+* baltim.dbf: attribute data. (k=17)
+* baltim.shp: Point shapefile. (n=211)
+* baltim.shx: spatial index.
+* baltim.tri.k12.kwt: kernel weights using a triangular kernel with 12 nearest neighbors in KWT format.
+* baltim_k4.gwt: nearest neighbor weights (4nn) in GWT format.
+* baltim_q.gal: queen contiguity weights in GAL format.
+* baltimore.geojson: spatial weights in geojson format.
-Point data, n=211, k= 17.
diff --git a/pysal/examples/baltim/baltim.dbf b/pysal/examples/baltim/baltim.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/baltim/baltim.shp b/pysal/examples/baltim/baltim.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/baltim/baltim.shx b/pysal/examples/baltim/baltim.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/baltim/baltim.tri.k12.kwt b/pysal/examples/baltim/baltim.tri.k12.kwt
old mode 100644
new mode 100755
diff --git a/pysal/examples/baltim/baltim_k4.gwt b/pysal/examples/baltim/baltim_k4.gwt
old mode 100644
new mode 100755
diff --git a/pysal/examples/baltim/baltim_q.gal b/pysal/examples/baltim/baltim_q.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/baltim/baltimore.geojson b/pysal/examples/baltim/baltimore.geojson
old mode 100644
new mode 100755
diff --git a/pysal/examples/book/README.md b/pysal/examples/book/README.md
index b9dc8b9..18a255d 100644
--- a/pysal/examples/book/README.md
+++ b/pysal/examples/book/README.md
@@ -1,10 +1,8 @@
book
====
-Synthetic data to illustrate spatial weights
+Synthetic data to illustrate spatial weights
--------------------------------------------
-* book.gal: rook contiguity for regular lattice
-* book.txt: attribute data for regular lattice
-
-Source: Anselin, L. and S.J. Rey (in progress) Spatial Econometrics: Foundations.
+* book.gal: rook contiguity weights in GAL format for regular lattice.
+* book.txt: attribute data for regular lattice.
diff --git a/pysal/examples/book/book.gal b/pysal/examples/book/book.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/book/book.txt b/pysal/examples/book/book.txt
old mode 100644
new mode 100755
diff --git a/pysal/examples/burkitt/README.md b/pysal/examples/burkitt/README.md
index de37cf8..4ba9a5f 100644
--- a/pysal/examples/burkitt/README.md
+++ b/pysal/examples/burkitt/README.md
@@ -4,8 +4,6 @@ burkitt
Burkitt's lymphoma in the Western Nile district of Uganda
---------------------------------------------------------
- * burkitt.dbf attribute file
- * burkitt.shp shapefile
- * burkitt.shx spatial index
-
- Point data, n=188, k=6
+* burkitt.dbf: attribute data. (k=6)
+* burkitt.shp: Point shapefile. (n=188)
+* burkitt.shx: spatial index.
diff --git a/pysal/examples/burkitt/burkitt.dbf b/pysal/examples/burkitt/burkitt.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/burkitt/burkitt.shp b/pysal/examples/burkitt/burkitt.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/burkitt/burkitt.shx b/pysal/examples/burkitt/burkitt.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/calemp/README.md b/pysal/examples/calemp/README.md
index 76c0e9c..78232e4 100644
--- a/pysal/examples/calemp/README.md
+++ b/pysal/examples/calemp/README.md
@@ -5,9 +5,7 @@ Employment density for California counties
------------------------------------------
* calempdensity.csv: data on employment and employment density in California
- counties.
-
-Polygon data, n=58, k=11.
+ counties. (n=58, k=11)
Source: Anselin, L. and S.J. Rey (in progress) Spatial Econometrics: Foundations.
diff --git a/pysal/examples/calemp/calempdensity.csv b/pysal/examples/calemp/calempdensity.csv
old mode 100644
new mode 100755
diff --git a/pysal/examples/chicago/Chicago77.dbf b/pysal/examples/chicago/Chicago77.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/chicago/Chicago77.shp b/pysal/examples/chicago/Chicago77.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/chicago/Chicago77.shx b/pysal/examples/chicago/Chicago77.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/chicago/README.md b/pysal/examples/chicago/README.md
index 2184228..379c24d 100644
--- a/pysal/examples/chicago/README.md
+++ b/pysal/examples/chicago/README.md
@@ -4,8 +4,6 @@ chicago
Chicago neighborhoods
--------------------
- * Chicago77.dbf attribute file
- * Chicago77.shp shapefile
- * Chicago77.shx spatial index
-
-Polygons, n=77, k=11
+* Chicago77.dbf: attribute data. (k=11)
+* Chicago77.shp: Polygon shapefile. (n=77)
+* Chicago77.shx: spatial index.
diff --git a/pysal/examples/columbus/README.md b/pysal/examples/columbus/README.md
new file mode 100644
index 0000000..87df42e
--- /dev/null
+++ b/pysal/examples/columbus/README.md
@@ -0,0 +1,14 @@
+columbus
+========
+
+Columbus neighborhood crime data 1980
+-------------------------------------
+
+* columbus.dbf: attribute data. (k=20)
+* columbus.gal: queen contiguity file in GAL format.
+* columbus.html: metadata.
+* columbus.json: shape and attribute data file in JSON format.
+* columbus.shp: Polygon shapefile. (n=49)
+* columbus.shx: spatial index.
+
+Anselin, Luc (1988). Spatial Econometrics. Boston, Kluwer Academic, Table 12.1, p. 189.
\ No newline at end of file
diff --git a/pysal/examples/columbus/columbus.dbf b/pysal/examples/columbus/columbus.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/columbus/columbus.gal b/pysal/examples/columbus/columbus.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/columbus/columbus.html b/pysal/examples/columbus/columbus.html
old mode 100644
new mode 100755
diff --git a/pysal/examples/columbus/columbus.json b/pysal/examples/columbus/columbus.json
old mode 100644
new mode 100755
diff --git a/pysal/examples/columbus/columbus.shp b/pysal/examples/columbus/columbus.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/columbus/columbus.shx b/pysal/examples/columbus/columbus.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/desmith/README.md b/pysal/examples/desmith/README.md
index 2ffd8ef..e697978 100644
--- a/pysal/examples/desmith/README.md
+++ b/pysal/examples/desmith/README.md
@@ -1,12 +1,13 @@
desmith
=======
-Small data set to illustrate Moran's I statistic
-------------------------------------------------
+Small dataset to illustrate Moran's I statistic
+-----------------------------------------------
-Figure 5-31 of de Smith, Goodchild and Longley (2015)
+* desmith.gal: spatial weights in GAL format.
+* desmith.txt: attribute data. (n=10, k=2)
-Polygons, n=12, k=1
+Figure 5-31 of de Smith, Goodchild and Longley (2015)
Source: <http://www.spatialanalysisonline.com/>
diff --git a/pysal/examples/desmith/desmith.gal b/pysal/examples/desmith/desmith.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/desmith/desmith.txt b/pysal/examples/desmith/desmith.txt
old mode 100644
new mode 100755
diff --git a/pysal/examples/examples.txt b/pysal/examples/examples.txt
index 68640e3..b512363 100644
--- a/pysal/examples/examples.txt
+++ b/pysal/examples/examples.txt
@@ -8,134 +8,437 @@ found in the **examples** directory.
10740
=====
-Polygon shapefile for Albuquerque New Mexico.
-* 10740.dbf: attribute database file
-* 10740.shp: shapefile
-* 10740.shx: spatial index
-* 10740_queen.gal: queen contiguity GAL format
-* 10740_rook.gal: rook contiguity GAL format
+Albuquerque, New Mexico, Census 2000 Tract Data
+-----------------------------------------------
+
+* 10740.dbf: attribute data. (k=5)
+* 10740.shp: shapefile. (n=195)
+* 10740.shx: spatial index.
+* 10740_queen.gal: queen contiguity weights in GAL format.
+* 10740_rook.gal: rook contiguity weights in GAL format.
+
+
+Line
+=====
+
+Line Shapefile
+---------------
+
+* Line.dbf: attribute data. (k=3)
+* Line.prj: ESRI projection file.
+* Line.shp: Line shapefile. (n=4)
+* Line.shx: spatial index.
+
+Used for testing.
+
+
+Point
+=====
+
+Point Shapefile
+---------------
+
+* Point.dbf: attribute data. (k=3)
+* Point.prj: ESRI projection file.
+* Point.shp: Point shapefile. (n=9)
+* Point.shx: spatial index.
+
+Used for testing
+
+
+Polygon
+=======
+
+Polygon Shapefile
+-----------------
+
+* Polygon.dbf: attribute data. (k=3)
+* Polygon.prj: ESRI projection file.
+* Polygon.shp: Polygon shapefile. (n=3)
+* Polygon.shx: spatial index.
+
+Used for testing.
+
+
+arcgis
+======
+
+arcgis testing files
+--------------------
+
+* arcgis_ohio.dbf: spatial weights in ArcGIS DBF format.
+* arcgis_txt.txt: spatial weights in ArcGIS TXT format.
+
+Files used for internal testing.
+
+
+baltim
+======
+
+Baltimore house sales prices and hedonics 1978
+----------------------------------------------------------------
+
+* baltim.dbf: attribute data. (k=17)
+* baltim.shp: Point shapefile. (n=211)
+* baltim.shx: spatial index.
+* baltim.tri.k12.kwt: kernel weights using a triangular kernel with 12 nearest neighbors in KWT format.
+* baltim_k4.gwt: nearest neighbor weights (4nn) in GWT format.
+* baltim_q.gal: queen contiguity weights in GAL format.
+* baltimore.geojson: spatial weights in geojson format.
book
====
-Synthetic data to illustrate spatial weights. Source: Anselin, L. and S.J. Rey (in
-progress) Spatial Econometrics: Foundations.
-* book.gal: rook contiguity for regular lattice
-* book.txt: attribute data for regular lattice
+Synthetic data to illustrate spatial weights
+--------------------------------------------
+
+* book.gal: rook contiguity weights in GAL format for regular lattice.
+* book.txt: attribute data for regular lattice.
+
+
+burkitt
+=======
+
+Burkitt's lymphoma in the Western Nile district of Uganda
+---------------------------------------------------------
+
+* burkitt.dbf: attribute data. (k=6)
+* burkitt.shp: Point shapefile. (n=188)
+* burkitt.shx: spatial index.
+
+
+calemp
+======
-calempdensity
-=============
-Employment density for California counties. Source: Anselin, L. and S.J. Rey (in
-progress) Spatial Econometrics: Foundations.
+Employment density for California counties
+------------------------------------------
* calempdensity.csv: data on employment and employment density in California
- counties.
+ counties. (n=58, k=11)
+
+
+chicago
+=======
+
+Chicago neighborhoods
+--------------------
+
+* Chicago77.dbf: attribute data. (k=11)
+* Chicago77.shp: Polygon shapefile. (n=77)
+* Chicago77.shx: spatial index.
-chicago77
-=========
-Chicago Community Areas (n=77). Source: Anselin, L. and S.J. Rey (in
-progress) Spatial Econometrics: Foundations.
-* Chicago77.dbf: attribute data
-* Chicago77.shp: shapefile
-* Chicago77.shx: spatial index
+columbus
+========
+
+Columbus neighborhood crime data 1980
+-------------------------------------
+
+* columbus.dbf: attribute data. (k=20)
+* columbus.gal: queen contiguity file in GAL format.
+* columbus.html: metadata.
+* columbus.json: shape and attribute data file in JSON format.
+* columbus.shp: Polygon shapefile. (n=49)
+* columbus.shx: spatial index.
+
+Anselin, Luc (1988). Spatial Econometrics. Boston, Kluwer Academic, Table 12.1, p. 189.
desmith
=======
-Example data for autocorrelation analysis. Source: de Smith et al (2009)
-`Geospatial Analysis
-<http://www.spatialanalysisonline.com/output/html/MoranIandGearyC.html>`_ (Used
-with permission)
-* desmith.txt: attribute data for 10 spatial units
-* desmith.gal: spatial weights in GAL format
+Small dataset to illustrate Moran's I statistic
+-----------------------------------------------
+
+* desmith.gal: spatial weights in GAL format.
+* desmith.txt: attribute data. (n=10, k=2)
+
+Figure 5-31 of de Smith, Goodchild and Longley (2015)
+
+Source: <http://www.spatialanalysisonline.com/>
+
+Used with permission.
+
+
+geodanet
+========
+
+Datasets from geodanet for network analysis
+-------------------------------------------
+
+* crimes.dbf: attribute data for crime point set. (k=2)
+* crimes.prj: ESRI projection file.
+* crimes.sbn: spatial index.
+* crimes.sbx: spatial index.
+* crimes.shp: Point shapefile for crime data. (n=287)
+* crimes.shp.xml: metadata.
+* crimes.shx: spatial index.
+* schools.dbf: attribute data for schools point set. (k=1)
+* schools.prj: ESRI projection file.
+* schools.sbn: spatial index.
+* schools.sbx: spatial index.
+* schools.shp: Point shapefile for schools data. (n=8)
+* schools.shp.xml: metadata.
+* schools.shx: spatial index.
+* streets.dbf: attribute data for street polyline set. (k=2)
+* streets.prj: ESRI projection file.
+* streets.sbn: spatial index.
+* streets.sbx: spatial index.
+* streets.shp: Line shapefile data for street data. (n=293)
+* streets.shx: spatial index.
+
juvenile
========
-Cardiff juvenile delinquent residences.
-* juvenile.dbf: attribute data
-* juvenile.html: documentation
-* juvenile.shp: shapefile
-* juvenile.shx: spatial index
+Residences of juvenile offenders in Cardiff, UK
+-----------------------------------------------
+
+* juvenile.dbf: attribute data. (k=3)
+* juvenile.gwt: spatial weights in GWT format.
+* juvenile.shp: Point shapefile. (n=168)
+* juvenile.shx: spatial index.
+
+Source: https://s3.amazonaws.com/geoda/data/juvenile.zip
+
mexico
======
-State regional income Mexican states 1940-2000. Source: Rey, S.J. and M.L.
-Sastre Gutierrez. "Interregional inequality dynamics in Mexico." Spatial
-Economic Analysis. Forthcoming.
-* mexico.csv: attribute data
-* mexico.gal: spatial weights in GAL format
+Mexican states regional income 1940-2000
+----------------------------------------
+
+* mexico.csv: attribute data. (n=32, k=13)
+* mexico.gal: spatial weights in GAL format.
+
+Data used in Rey, S.J. and M.L. Sastre Gutierrez. (2010) "Interregional inequality dynamics in Mexico." Spatial Economic Analysis, 5: 277-298.
-rook31
-======
-Small test shapefile
-* rook31.dbf: attribute data
-* rook31.gal: spatia weights in GAL format
-* rook31.shp: shapefile
-* rook31.shx: spatial index
+nat
+===
+
+US county homicides 1960-1990
+-----------------------------
+
+* NAT.dbf: attribute data for US county homicides. (k=69)
+* NAT.shp: Polygon shapefile for US counties. (n=3085)
+* NAT.shx: spatial index.
+* nat.geojson: shape and attribute data in GeoJSON format.
+* nat_queen.gal: queen contiguity weights in GAL format.
+* nat_queen_old.gal: queen contiguity weights in GAL format using old polygon index.
+* nat_trian_k20.kwt: kernel weights in KWT format.
+* natregimes.dbf: attribute data for US county homicides with regimes assigned. (k=73)
+* natregimes.shp: Polygon shapefile for US counties. (n=3085)
+* natregimes.shx: spatial index.
+
+
+networks
+========
+
+Datasets used for network testing
+---------------------------------
+
+* eberly_net.dbf: attribute data. (k=3)
+* eberly_net.shp: Line shapefile. (n=29)
+* eberly_net.shx: spatial index.
+* eberly_net_pts_offnetwork.dbf: attribute data for points off network. (k=2)
+* eberly_net_pts_offnetwork.shp: Point shapefile. (n=100)
+* eberly_net_pts_offnetwork.shx: spatial index。
+* eberly_net_pts_onnetwork.dbf: attribute data for points on network. (k=1)
+* eberly_net_pts_onnetwork.shp: Point shapefile. (n=110)
+* eberly_net_pts_onnetwork.shx: spatial index.
+* nonplanarsegments.dbf: attribute data. (k=1)
+* nonplanarsegments.prj: ESRI projection file.
+* nonplanarsegments.qpj: QGIS projection file.
+* nonplanarsegments.shp: Line shapefile. (n=2)
+* nonplanarsegments.shx: spatial index.
+
+
+newHaven
+========
+
+New Haven crime dataset Sept 2014
+---------------------------------
+
+* new_haven_merged.dbf: attribute data for New Haven crimes. (k=5)
+* new_haven_merged.shp: Point shapefile. (n=3293)
+* new_haven_merged.shx: spatial index.
+* newhaven_nework.dbf: attribute data for New Haven street network. (k=6)
+* newhaven_nework.prj: ESRI projection file.
+* newhaven_nework.qpj: QGIS projection file.
+* newhaven_nework.shp: Line shapefile. (n=1537)
+* newhaven_nework.shx: spatial index.
sacramento2
===========
-1998 and 2001 Zip Code Business Patterns (Census Bureau) for Sacramento MSA
- * sacramento2.dbf
- * sacramento2.sbn
- * sacramento2.sbx
- * sacramento2.shp
- * sacramento2.shx
+2000 Census Tract Data for Sacramento MSA
+-----------------------------------------
-shp_test
-========
-Sample Shapefiles used only for testing purposes. Each example include a ".shp" Shapefile, ".shx" Shapefile Index, ".dbf" DBase file, and a ".prj" ESRI Projection file.
+* sacramentot2.dbf: attribute data. (k=31)
+* sacramentot2.gal: queen contiguity weights in GAL format.
+* sacramentot2.sbn: spatial index.
+* sacramentot2.sbx: spatial index.
+* sacramentot2.shp: Polygon shapefile. (n=403)
+* sacramentot2.shx: spatial index.
-Examples include:
+Source: US Census Bureau, 2000 Census (Summary File 3). Extracted from http://factfinder.census.gov in April 2004.
- * Point: Example of an ESRI Shapefile of Type 1 (Point).
- * Line: Example of an ESRI Shapefile of Type 3 (Line).
- * Polygon: Example of an ESRI Shapefile of Type 5 (Polygon).
sids2
=====
-North Carolina county SIDS death counts and rates
+
+North Carolina county Sudden Infant Death Syndrome (SIDS) death counts and rates
+--------------------------------------------------------------------------------
- * sids2.dbf: attribute data
- * sids2.html: documentation
- * sids2.shp: shapefile
- * sids2.shx: spatial index
- * sids2.gal: GAL file for spatial weights
+* sids2.dbf: attribute data. (k=18)
+* sids2.html: metadata.
+* sids2.shp: Polygon shapefile. (n=100)
+* sids2.shx: spatial index.
+* sids2.gal: spatial weights in GAL format.
-stl_hom
-=======
-Homicides and selected socio-economic characteristics for counties surrounding St Louis, MO. Data aggregated for three time periods: 1979-84 (steady decline in homicides), 1984-88 (stable period), and 1988-93 (steady increase in homicides). Source: S. Messner, L. Anselin, D. Hawkins, G. Deane, S. Tolnay, R. Baller (2000). An Atlas of the Spatial Patterning of County-Level Homicide, 1960-1990. Pittsburgh, PA, National Consortium on Violence Research (NCOVR).
+Source: https://s3.amazonaws.com/geoda/data/sids2.zip
- * stl_hom.html: Metadata
- * stl_hom.txt: txt file with attribute data
- * stl_hom.wkt: A Well-Known-Text representation of the geometry.
- * stl_hom.csv: attribute data and WKT geometry.
- * stl.hom.gal: GAL file for spatial weights
-
-US Regional Incomes
-===================
-Per capita income for the lower 48 US states, 1929-2010
+snow_maps
+=========
+
+Public water pumps and Cholera deaths in London 1954 (Snow's Map)
+-----------------------------------------------------------------
+
+* SohoPeople.dbf: attribute data for Cholera deaths. (k=2)
+* SohoPeople.prj: ESRI projection file.
+* SohoPeople.sbn: spatial index.
+* SohoPeople.sbx: spatial index.
+* SohoPeople.shp: Point shapefile for Cholera deaths. (n=324)
+* SohoPeople.shx: spatial index.
+* SohoWater.dbf: attribute data for public water pumps. (k=1)
+* SohoWater.prj: ESRI projection file.
+* SohoWater.sbn: spatial index.
+* SohoWater.sbx: spatial index.
+* SohoWater.shp: Point shapefile for public water pumps. (n=13)
+* SohoWater.shx: spatial index.
+* Soho_Network.dbf: attribute data for street network. (k=1)
+* Soho_Network.prj: ESRI projection file.
+* Soho_Network.sbn: spatial index.
+* Soho_Network.sbx: spatial index.
+* Soho_Network.shp: Line shapefile for street network. (n=118)
+* Soho_Network.shx: spatial index.
+
+
+south
+=====
+
+Homicides and selected socio-economic characteristics for Southern U.S. counties (subset of NCOVR national data set). Data for four decennial census years: 1960, 1970, 1980, 1990
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+* south.dbf: attribute data. (k=69)
+* south.shp: Polygon shapefile. (n=1412)
+* south.shx: spatial index.
+* south_q.gal: queen contiguity weights in GAL format.
+* south_queen.gal: queen contiguity weights in GAL format.
+
+
+stl
+===
+
+Homicides and selected socio-economic characteristics for counties surrounding St Louis, MO. Data aggregated for three time periods: 1979-84 (steady decline in homicides), 1984-88 (stable period), and 1988-93 (steady increase in homicides).
+---------------------------------------------------------------------------
+
+* stl.gal: queen contiguity weights in GAL format.
+* stl_hom.csv: attribute data and WKT geometry.
+* stl_hom.dbf: attribute data. (k=22)
+* stl_hom.html: metadata.
+* stl_hom.shp: Polygon shapefile. (n=78)
+* stl_hom.shx: spatial index.
+* stl_hom.txt: selected attribute data.
+* stl_hom.wkt: a Well-Known-Text representation of the geometry.
+* stl_hom_rook.gal: rook contiguity weights in GAL format.
+
+Source: S. Messner, L. Anselin, D. Hawkins, G. Deane, S. Tolnay, R. Baller (2000). An Atlas of the Spatial Patterning of County-Level Homicide, 1960-1990. Pittsburgh, PA, [National Consortium on Violence Research (NCOVR)](http://www.ncovr.heinz.cmu.edu).
+
+
+street_net_pts
+==============
+
+Street network points
+---------------------
- * us48.shp: shapefile
- * us48.dbf: dbf for shapefile
- * us48.shx: index for shapefile
- * usjoin.csv: attribute data (comma delimited file)
+* street_net_pts.dbf: attribute data. (k=1)
+* street_net_pts.prj: ESRI projection file.
+* street_net_pts.qpj: QGIS projection file.
+* street_net_pts.shp: Point shapefile. (n=303)
+* street_net_pts.shx: spatial index.
-Virginia
+
+taz
+===
+
+Dataset used for regionalization
+--------------------------------
+
+* taz.dbf: attribute data. (k=14)
+* taz.shp: Polygon shapefile. (n=4109)
+* taz.shx: spatial index.
+
+
+us_income
+=========
+
+Nominal per capita income for the lower 48 US states 1929-2009
+——————————————————————————————————————————————————————————————
+
+* states48.gal: queen contiguity weights in GAL format.
+* us48.dbf: attribute data. (k=8)
+* us48.shp: Polygon shapefile. (n=48)
+* us48.shx: spatial index.
+* usjoin.csv: 48 US states nominal per capita income time series 1929-2009.
+
+
+virginia
========
-Virginia Counties Shapefile.
- * virginia.shp: Shapefile
- * virginia.shx: shapefile index
- * virginia.dbf: attributes
- * virginia.prj: shapefile projection
+Virginia counties shapefile
+---------------------------
+
+* virginia.dbf: attribute data. (k=7)
+* virginia.gal: rook contiguity weights in GAL format.
+* virginia.json: attribute and shape data in JSON format.
+* virginia.prj: ESRI projection file.
+* virginia.shp: Polygon shapefile. (n=136)
+* virginia.shx: spatial index.
+* virginia_queen.dat: queen contiguity weights in DAT format.
+* virginia_queen.dbf: queen contiguity weights in DBF format.
+* virginia_queen.gal: queen contiguity weights in GAL format.
+* virginia_queen.mat: queen contiguity weights in MATLAB MAT format.
+* virginia_queen.mtx: queen contiguity weights in Matrix Market MTX format.
+* virginia_queen.swm: queen contiguity weight in ArcGIS SWM format.
+* virginia_queen.txt: queen contiguity weights in TXT format.
+* virginia_queen.wk1: queen contiguity weights in Lotus Wk1 format.
+* virginia_rook.gal: rook contiguity weights in GAL format.
+
+
+wmat
+====
+
+Datasets used for spatial weights testing
+-----------------------------------------
+
+* geobugs_scot: spatial weights in GeoBUGS text format.
+* lattice10x10.shp: Polygon shapefile for 10 * 10 regular lattices. (n=100)
+* lattice10x10.shx: spatial index.
+* ohio.swm: spatial weights in ArcGIS SWM format.
+* rook31.dbf: attribute data. (k=2)
+* rook31.gal: rook contiguity weights in GAL format.
+* rook31.shp: Polygon shapefile. (n=3)
+* rook31.shx: spatial index.
+* spat-sym-us.mat: spatial weights in MATLAB MAT format.
+* spat-sym-us.wk1: spatial weights in Lotus Wk1 format.
+* spdep_listw2WB_columbus: spatial weights in GeoBUGS text format.
+* stata_full.txt: full spatial weights matrix.
+* stata_sparse.txt: sparse spatial weights matrix.
+* wmat.dat: spatial weights in DAT format.
+* wmat.mtx: spatial weights in Matrix Market MTX format.
diff --git a/pysal/examples/geodanet/README.md b/pysal/examples/geodanet/README.md
index f8b53da..3c4f212 100644
--- a/pysal/examples/geodanet/README.md
+++ b/pysal/examples/geodanet/README.md
@@ -4,23 +4,23 @@ geodanet
Datasets from geodanet for network analysis
-------------------------------------------
-* crimes.dbf attribute data for crime point set
-* crimes.prj projection
-* crimes.sbn spatial index
-* crimes.sbx spatial index
-* crimes.shp shapefile for crime point data
-* crimes.shp.xml metadata
-* crimes.shx shape index
-* schools.dbf attribute data for schools point set
-* schools.prj projection
-* schools.sbn spatial index
-* schools.sbx spatial index
-* schools.shp spatial index
-* schools.shp.xml metadata
-* schools.shx shape index
-* streets.dbf attribute data for street polyline
-* streets.prj projection
-* streets.sbn spatial index
-* streets.sbx spatial index
-* streets.shp shapefile
-* streets.shx shape index
+* crimes.dbf: attribute data for crime point set. (k=2)
+* crimes.prj: ESRI projection file.
+* crimes.sbn: spatial index.
+* crimes.sbx: spatial index.
+* crimes.shp: Point shapefile for crime data. (n=287)
+* crimes.shp.xml: metadata.
+* crimes.shx: spatial index.
+* schools.dbf: attribute data for schools point set. (k=1)
+* schools.prj: ESRI projection file.
+* schools.sbn: spatial index.
+* schools.sbx: spatial index.
+* schools.shp: Point shapefile for schools data. (n=8)
+* schools.shp.xml: metadata.
+* schools.shx: spatial index.
+* streets.dbf: attribute data for street polyline set. (k=2)
+* streets.prj: ESRI projection file.
+* streets.sbn: spatial index.
+* streets.sbx: spatial index.
+* streets.shp: Line shapefile data for street data. (n=293)
+* streets.shx: spatial index.
diff --git a/pysal/examples/geodanet/crimes.dbf b/pysal/examples/geodanet/crimes.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/crimes.prj b/pysal/examples/geodanet/crimes.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/crimes.sbn b/pysal/examples/geodanet/crimes.sbn
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/crimes.sbx b/pysal/examples/geodanet/crimes.sbx
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/crimes.shp b/pysal/examples/geodanet/crimes.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/crimes.shp.xml b/pysal/examples/geodanet/crimes.shp.xml
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/crimes.shx b/pysal/examples/geodanet/crimes.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/schools.dbf b/pysal/examples/geodanet/schools.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/schools.prj b/pysal/examples/geodanet/schools.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/schools.sbn b/pysal/examples/geodanet/schools.sbn
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/schools.sbx b/pysal/examples/geodanet/schools.sbx
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/schools.shp b/pysal/examples/geodanet/schools.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/schools.shp.xml b/pysal/examples/geodanet/schools.shp.xml
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/schools.shx b/pysal/examples/geodanet/schools.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/streets.dbf b/pysal/examples/geodanet/streets.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/streets.prj b/pysal/examples/geodanet/streets.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/streets.sbn b/pysal/examples/geodanet/streets.sbn
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/streets.sbx b/pysal/examples/geodanet/streets.sbx
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/streets.shp b/pysal/examples/geodanet/streets.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/geodanet/streets.shx b/pysal/examples/geodanet/streets.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/georgia/FB.p b/pysal/examples/georgia/FB.p
old mode 100644
new mode 100755
diff --git a/pysal/examples/georgia/XB.p b/pysal/examples/georgia/XB.p
old mode 100644
new mode 100755
diff --git a/pysal/examples/georgia/err.p b/pysal/examples/georgia/err.p
old mode 100644
new mode 100755
diff --git a/pysal/examples/juvenile/README.md b/pysal/examples/juvenile/README.md
index a9e1066..0587f6c 100644
--- a/pysal/examples/juvenile/README.md
+++ b/pysal/examples/juvenile/README.md
@@ -4,11 +4,9 @@ juvenile
Residences of juvenile offenders in Cardiff, UK
-----------------------------------------------
- * juvenile.dbf attribute file
- * juvenile.gwt spatial weights
- * juvenile.shp shapefile
- * juvenile.shx spatial index
+* juvenile.dbf: attribute data. (k=3)
+* juvenile.gwt: spatial weights in GWT format.
+* juvenile.shp: Point shapefile. (n=168)
+* juvenile.shx: spatial index.
-Point data, unknown coordinates, n=168, k=3.
-
-Source: http://geodacenter.org/downloads/data-files/juvenile.zip
+Source: https://s3.amazonaws.com/geoda/data/juvenile.zip
\ No newline at end of file
diff --git a/pysal/examples/juvenile/juvenile.dbf b/pysal/examples/juvenile/juvenile.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/juvenile/juvenile.gwt b/pysal/examples/juvenile/juvenile.gwt
old mode 100644
new mode 100755
diff --git a/pysal/examples/juvenile/juvenile.shp b/pysal/examples/juvenile/juvenile.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/juvenile/juvenile.shx b/pysal/examples/juvenile/juvenile.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/londonhp/londonhp.dbf b/pysal/examples/londonhp/londonhp.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/londonhp/londonhp.shp b/pysal/examples/londonhp/londonhp.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/londonhp/londonhp.shx b/pysal/examples/londonhp/londonhp.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/mexico/README.md b/pysal/examples/mexico/README.md
index 5fab293..aa128f6 100644
--- a/pysal/examples/mexico/README.md
+++ b/pysal/examples/mexico/README.md
@@ -4,12 +4,7 @@ mexico
Mexican states regional income 1940-2000
----------------------------------------
-Data used in Rey, S.J. and M.L. Sastre Gutierrez. (2010) "Interregional inequality
-dynamics in Mexico." Spatial Economic Analysis, 5: 277-298
-
-* mexico.csv: attribute data
-* mexico.gal: spatial weights in GAL format
-
-Polygon data, n=32, k=13
-
+* mexico.csv: attribute data. (n=32, k=13)
+* mexico.gal: spatial weights in GAL format.
+Data used in Rey, S.J. and M.L. Sastre Gutierrez. (2010) "Interregional inequality dynamics in Mexico." Spatial Economic Analysis, 5: 277-298.
diff --git a/pysal/examples/mexico/mexico.csv b/pysal/examples/mexico/mexico.csv
old mode 100644
new mode 100755
diff --git a/pysal/examples/mexico/mexico.gal b/pysal/examples/mexico/mexico.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/nat/NAT.dbf b/pysal/examples/nat/NAT.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/nat/NAT.shp b/pysal/examples/nat/NAT.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/nat/NAT.shx b/pysal/examples/nat/NAT.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/nat/README.md b/pysal/examples/nat/README.md
new file mode 100644
index 0000000..ab747db
--- /dev/null
+++ b/pysal/examples/nat/README.md
@@ -0,0 +1,16 @@
+nat
+===
+
+US county homicides 1960-1990
+-----------------------------
+
+* NAT.dbf: attribute data for US county homicides. (k=69)
+* NAT.shp: Polygon shapefile for US counties. (n=3085)
+* NAT.shx: spatial index.
+* nat.geojson: shape and attribute data in GeoJSON format.
+* nat_queen.gal: queen contiguity weights in GAL format.
+* nat_queen_old.gal: queen contiguity weights in GAL format using old polygon index.
+* nat_trian_k20.kwt: kernel weights in KWT format.
+* natregimes.dbf: attribute data for US county homicides with regimes assigned. (k=73)
+* natregimes.shp: Polygon shapefile for US counties. (n=3085)
+* natregimes.shx: spatial index.
diff --git a/pysal/examples/nat/nat.geojson b/pysal/examples/nat/nat.geojson
old mode 100644
new mode 100755
diff --git a/pysal/examples/nat/nat_queen.gal b/pysal/examples/nat/nat_queen.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/nat/nat_queen_old.gal b/pysal/examples/nat/nat_queen_old.gal
old mode 100644
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diff --git a/pysal/examples/nat/nat_trian_k20.kwt b/pysal/examples/nat/nat_trian_k20.kwt
old mode 100644
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diff --git a/pysal/examples/nat/natregimes.dbf b/pysal/examples/nat/natregimes.dbf
old mode 100644
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diff --git a/pysal/examples/nat/natregimes.shp b/pysal/examples/nat/natregimes.shp
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diff --git a/pysal/examples/nat/natregimes.shx b/pysal/examples/nat/natregimes.shx
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diff --git a/pysal/examples/networks/README.md b/pysal/examples/networks/README.md
new file mode 100644
index 0000000..1f97a78
--- /dev/null
+++ b/pysal/examples/networks/README.md
@@ -0,0 +1,20 @@
+networks
+========
+
+Datasets used for network testing
+---------------------------------
+
+* eberly_net.dbf: attribute data. (k=3)
+* eberly_net.shp: Line shapefile. (n=29)
+* eberly_net.shx: spatial index.
+* eberly_net_pts_offnetwork.dbf: attribute data for points off network. (k=2)
+* eberly_net_pts_offnetwork.shp: Point shapefile. (n=100)
+* eberly_net_pts_offnetwork.shx: spatial index。
+* eberly_net_pts_onnetwork.dbf: attribute data for points on network. (k=1)
+* eberly_net_pts_onnetwork.shp: Point shapefile. (n=110)
+* eberly_net_pts_onnetwork.shx: spatial index.
+* nonplanarsegments.dbf: attribute data. (k=1)
+* nonplanarsegments.prj: ESRI projection file.
+* nonplanarsegments.qpj: QGIS projection file.
+* nonplanarsegments.shp: Line shapefile. (n=2)
+* nonplanarsegments.shx: spatial index.
diff --git a/pysal/examples/networks/eberly_net.dbf b/pysal/examples/networks/eberly_net.dbf
old mode 100644
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diff --git a/pysal/examples/networks/eberly_net.shp b/pysal/examples/networks/eberly_net.shp
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diff --git a/pysal/examples/networks/eberly_net.shx b/pysal/examples/networks/eberly_net.shx
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diff --git a/pysal/examples/networks/eberly_net_pts_offnetwork.dbf b/pysal/examples/networks/eberly_net_pts_offnetwork.dbf
old mode 100644
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diff --git a/pysal/examples/networks/eberly_net_pts_offnetwork.shp b/pysal/examples/networks/eberly_net_pts_offnetwork.shp
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diff --git a/pysal/examples/networks/eberly_net_pts_offnetwork.shx b/pysal/examples/networks/eberly_net_pts_offnetwork.shx
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diff --git a/pysal/examples/networks/eberly_net_pts_onnetwork.dbf b/pysal/examples/networks/eberly_net_pts_onnetwork.dbf
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diff --git a/pysal/examples/networks/eberly_net_pts_onnetwork.shp b/pysal/examples/networks/eberly_net_pts_onnetwork.shp
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diff --git a/pysal/examples/networks/eberly_net_pts_onnetwork.shx b/pysal/examples/networks/eberly_net_pts_onnetwork.shx
old mode 100644
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diff --git a/pysal/examples/networks/nonplanarsegments.dbf b/pysal/examples/networks/nonplanarsegments.dbf
old mode 100644
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diff --git a/pysal/examples/networks/nonplanarsegments.prj b/pysal/examples/networks/nonplanarsegments.prj
old mode 100644
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diff --git a/pysal/examples/networks/nonplanarsegments.qpj b/pysal/examples/networks/nonplanarsegments.qpj
old mode 100644
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diff --git a/pysal/examples/networks/nonplanarsegments.shp b/pysal/examples/networks/nonplanarsegments.shp
old mode 100644
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diff --git a/pysal/examples/networks/nonplanarsegments.shx b/pysal/examples/networks/nonplanarsegments.shx
old mode 100644
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diff --git a/pysal/examples/newHaven/README.md b/pysal/examples/newHaven/README.md
new file mode 100644
index 0000000..00f1885
--- /dev/null
+++ b/pysal/examples/newHaven/README.md
@@ -0,0 +1,14 @@
+newHaven
+========
+
+New Haven crime dataset Sept 2014
+---------------------------------
+
+* new_haven_merged.dbf: attribute data for New Haven crimes. (k=5)
+* new_haven_merged.shp: Point shapefile. (n=3293)
+* new_haven_merged.shx: spatial index.
+* newhaven_nework.dbf: attribute data for New Haven street network. (k=6)
+* newhaven_nework.prj: ESRI projection file.
+* newhaven_nework.qpj: QGIS projection file.
+* newhaven_nework.shp: Line shapefile. (n=1537)
+* newhaven_nework.shx: spatial index.
diff --git a/pysal/examples/newHaven/new_haven_merged.dbf b/pysal/examples/newHaven/new_haven_merged.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/newHaven/new_haven_merged.shp b/pysal/examples/newHaven/new_haven_merged.shp
old mode 100644
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diff --git a/pysal/examples/newHaven/new_haven_merged.shx b/pysal/examples/newHaven/new_haven_merged.shx
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diff --git a/pysal/examples/newHaven/newhaven_nework.dbf b/pysal/examples/newHaven/newhaven_nework.dbf
old mode 100644
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diff --git a/pysal/examples/newHaven/newhaven_nework.prj b/pysal/examples/newHaven/newhaven_nework.prj
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diff --git a/pysal/examples/newHaven/newhaven_nework.qpj b/pysal/examples/newHaven/newhaven_nework.qpj
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diff --git a/pysal/examples/newHaven/newhaven_nework.shp b/pysal/examples/newHaven/newhaven_nework.shp
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diff --git a/pysal/examples/newHaven/newhaven_nework.shx b/pysal/examples/newHaven/newhaven_nework.shx
old mode 100644
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diff --git a/pysal/examples/nyc_bikes/nyc_bikes_ct.csv b/pysal/examples/nyc_bikes/nyc_bikes_ct.csv
old mode 100644
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diff --git a/pysal/examples/nyc_bikes/nyct2010.dbf b/pysal/examples/nyc_bikes/nyct2010.dbf
old mode 100644
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diff --git a/pysal/examples/nyc_bikes/nyct2010.prj b/pysal/examples/nyc_bikes/nyct2010.prj
old mode 100644
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diff --git a/pysal/examples/nyc_bikes/nyct2010.shp b/pysal/examples/nyc_bikes/nyct2010.shp
old mode 100644
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diff --git a/pysal/examples/nyc_bikes/nyct2010.shp.xml b/pysal/examples/nyc_bikes/nyct2010.shp.xml
old mode 100644
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diff --git a/pysal/examples/nyc_bikes/nyct2010.shx b/pysal/examples/nyc_bikes/nyct2010.shx
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diff --git a/pysal/examples/sacramento2/README.md b/pysal/examples/sacramento2/README.md
new file mode 100644
index 0000000..8287245
--- /dev/null
+++ b/pysal/examples/sacramento2/README.md
@@ -0,0 +1,14 @@
+sacramento2
+===========
+
+2000 Census Tract Data for Sacramento MSA
+-----------------------------------------
+
+* sacramentot2.dbf: attribute data. (k=31)
+* sacramentot2.gal: queen contiguity weights in GAL format.
+* sacramentot2.sbn: spatial index.
+* sacramentot2.sbx: spatial index.
+* sacramentot2.shp: Polygon shapefile. (n=403)
+* sacramentot2.shx: spatial index.
+
+Source: US Census Bureau, 2000 Census (Summary File 3). Extracted from http://factfinder.census.gov in April 2004.
\ No newline at end of file
diff --git a/pysal/examples/sacramento2/sacramentot2.dbf b/pysal/examples/sacramento2/sacramentot2.dbf
old mode 100644
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diff --git a/pysal/examples/sacramento2/sacramentot2.gal b/pysal/examples/sacramento2/sacramentot2.gal
old mode 100644
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diff --git a/pysal/examples/sacramento2/sacramentot2.sbn b/pysal/examples/sacramento2/sacramentot2.sbn
old mode 100644
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diff --git a/pysal/examples/sacramento2/sacramentot2.sbx b/pysal/examples/sacramento2/sacramentot2.sbx
old mode 100644
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diff --git a/pysal/examples/sacramento2/sacramentot2.shp b/pysal/examples/sacramento2/sacramentot2.shp
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diff --git a/pysal/examples/sacramento2/sacramentot2.shx b/pysal/examples/sacramento2/sacramentot2.shx
old mode 100644
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diff --git a/pysal/examples/sids2/README.md b/pysal/examples/sids2/README.md
index bacdf3c..7674392 100644
--- a/pysal/examples/sids2/README.md
+++ b/pysal/examples/sids2/README.md
@@ -1,14 +1,13 @@
sids2
=====
-North Carolina county SIDS death counts and rates
--------------------------------------------------
-
- * sids2.dbf: attribute data
- * sids2.html: documentation
- * sids2.shp: shapefile
- * sids2.shx: spatial index
- * sids2.gal: GAL file for spatial weights
+North Carolina county Sudden Infant Death Syndrome (SIDS) death counts and rates
+--------------------------------------------------------------------------------
+* sids2.dbf: attribute data. (k=18)
+* sids2.html: metadata.
+* sids2.shp: Polygon shapefile. (n=100)
+* sids2.shx: spatial index.
+* sids2.gal: spatial weights in GAL format.
-Source: http://geodacenter.org/downloads/data-files/sids2.zip
+Source: https://s3.amazonaws.com/geoda/data/sids2.zip
diff --git a/pysal/examples/sids2/sids2.dbf b/pysal/examples/sids2/sids2.dbf
old mode 100644
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diff --git a/pysal/examples/sids2/sids2.gal b/pysal/examples/sids2/sids2.gal
old mode 100644
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diff --git a/pysal/examples/sids2/sids2.html b/pysal/examples/sids2/sids2.html
old mode 100644
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diff --git a/pysal/examples/sids2/sids2.shp b/pysal/examples/sids2/sids2.shp
old mode 100644
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diff --git a/pysal/examples/sids2/sids2.shx b/pysal/examples/sids2/sids2.shx
old mode 100644
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diff --git a/pysal/examples/sids2/sids2.swm b/pysal/examples/sids2/sids2.swm
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diff --git a/pysal/examples/snow_maps/README.md b/pysal/examples/snow_maps/README.md
new file mode 100644
index 0000000..1b2f86f
--- /dev/null
+++ b/pysal/examples/snow_maps/README.md
@@ -0,0 +1,24 @@
+snow_maps
+=========
+
+Public water pumps and Cholera deaths in London 1954 (Snow's Map)
+-----------------------------------------------------------------
+
+* SohoPeople.dbf: attribute data for Cholera deaths. (k=2)
+* SohoPeople.prj: ESRI projection file.
+* SohoPeople.sbn: spatial index.
+* SohoPeople.sbx: spatial index.
+* SohoPeople.shp: Point shapefile for Cholera deaths. (n=324)
+* SohoPeople.shx: spatial index.
+* SohoWater.dbf: attribute data for public water pumps. (k=1)
+* SohoWater.prj: ESRI projection file.
+* SohoWater.sbn: spatial index.
+* SohoWater.sbx: spatial index.
+* SohoWater.shp: Point shapefile for public water pumps. (n=13)
+* SohoWater.shx: spatial index.
+* Soho_Network.dbf: attribute data for street network. (k=1)
+* Soho_Network.prj: ESRI projection file.
+* Soho_Network.sbn: spatial index.
+* Soho_Network.sbx: spatial index.
+* Soho_Network.shp: Line shapefile for street network. (n=118)
+* Soho_Network.shx: spatial index.
diff --git a/pysal/examples/snow_maps/SohoPeople.dbf b/pysal/examples/snow_maps/SohoPeople.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/snow_maps/SohoPeople.prj b/pysal/examples/snow_maps/SohoPeople.prj
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diff --git a/pysal/examples/snow_maps/SohoPeople.sbn b/pysal/examples/snow_maps/SohoPeople.sbn
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diff --git a/pysal/examples/snow_maps/SohoPeople.sbx b/pysal/examples/snow_maps/SohoPeople.sbx
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diff --git a/pysal/examples/snow_maps/SohoPeople.shp b/pysal/examples/snow_maps/SohoPeople.shp
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diff --git a/pysal/examples/snow_maps/SohoPeople.shx b/pysal/examples/snow_maps/SohoPeople.shx
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diff --git a/pysal/examples/snow_maps/SohoWater.dbf b/pysal/examples/snow_maps/SohoWater.dbf
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diff --git a/pysal/examples/snow_maps/SohoWater.prj b/pysal/examples/snow_maps/SohoWater.prj
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diff --git a/pysal/examples/snow_maps/SohoWater.sbn b/pysal/examples/snow_maps/SohoWater.sbn
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diff --git a/pysal/examples/snow_maps/SohoWater.sbx b/pysal/examples/snow_maps/SohoWater.sbx
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diff --git a/pysal/examples/snow_maps/SohoWater.shp b/pysal/examples/snow_maps/SohoWater.shp
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diff --git a/pysal/examples/snow_maps/SohoWater.shx b/pysal/examples/snow_maps/SohoWater.shx
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diff --git a/pysal/examples/snow_maps/Soho_Network.dbf b/pysal/examples/snow_maps/Soho_Network.dbf
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diff --git a/pysal/examples/snow_maps/Soho_Network.prj b/pysal/examples/snow_maps/Soho_Network.prj
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diff --git a/pysal/examples/snow_maps/Soho_Network.sbn b/pysal/examples/snow_maps/Soho_Network.sbn
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diff --git a/pysal/examples/snow_maps/Soho_Network.sbx b/pysal/examples/snow_maps/Soho_Network.sbx
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diff --git a/pysal/examples/snow_maps/Soho_Network.shp b/pysal/examples/snow_maps/Soho_Network.shp
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diff --git a/pysal/examples/snow_maps/Soho_Network.shx b/pysal/examples/snow_maps/Soho_Network.shx
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diff --git a/pysal/examples/south/README.md b/pysal/examples/south/README.md
new file mode 100644
index 0000000..d028201
--- /dev/null
+++ b/pysal/examples/south/README.md
@@ -0,0 +1,11 @@
+south
+=====
+
+Homicides and selected socio-economic characteristics for Southern U.S. counties (subset of NCOVR national data set). Data for four decennial census years: 1960, 1970, 1980, 1990.
+----------------------------------------------------------------------
+
+* south.dbf: attribute data. (k=69)
+* south.shp: Polygon shapefile. (n=1412)
+* south.shx: spatial index.
+* south_q.gal: queen contiguity weights in GAL format.
+* south_queen.gal: queen contiguity weights in GAL format.
diff --git a/pysal/examples/south/south.dbf b/pysal/examples/south/south.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/south/south.shp b/pysal/examples/south/south.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/south/south.shx b/pysal/examples/south/south.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/south/south_q.gal b/pysal/examples/south/south_q.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/south/south_queen.gal b/pysal/examples/south/south_queen.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/stl/README.md b/pysal/examples/stl/README.md
new file mode 100644
index 0000000..a18c091
--- /dev/null
+++ b/pysal/examples/stl/README.md
@@ -0,0 +1,17 @@
+stl
+===
+
+Homicides and selected socio-economic characteristics for counties surrounding St Louis, MO. Data aggregated for three time periods: 1979-84 (steady decline in homicides), 1984-88 (stable period), and 1988-93 (steady increase in homicides).
+---------------------------------------------------------------------------
+
+* stl.gal: queen contiguity weights in GAL format.
+* stl_hom.csv: attribute data and WKT geometry.
+* stl_hom.dbf: attribute data. (k=22)
+* stl_hom.html: metadata.
+* stl_hom.shp: Polygon shapefile. (n=78)
+* stl_hom.shx: spatial index.
+* stl_hom.txt: selected attribute data.
+* stl_hom.wkt: a Well-Known-Text representation of the geometry.
+* stl_hom_rook.gal: rook contiguity weights in GAL format.
+
+Source: S. Messner, L. Anselin, D. Hawkins, G. Deane, S. Tolnay, R. Baller (2000). An Atlas of the Spatial Patterning of County-Level Homicide, 1960-1990. Pittsburgh, PA, [National Consortium on Violence Research (NCOVR)](http://www.ncovr.heinz.cmu.edu).
diff --git a/pysal/examples/stl/stl.gal b/pysal/examples/stl/stl.gal
old mode 100644
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diff --git a/pysal/examples/stl/stl_hom.csv b/pysal/examples/stl/stl_hom.csv
old mode 100644
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diff --git a/pysal/examples/stl/stl_hom.dbf b/pysal/examples/stl/stl_hom.dbf
old mode 100644
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diff --git a/pysal/examples/stl/stl_hom.html b/pysal/examples/stl/stl_hom.html
old mode 100644
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diff --git a/pysal/examples/stl/stl_hom.shp b/pysal/examples/stl/stl_hom.shp
old mode 100644
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diff --git a/pysal/examples/stl/stl_hom.shx b/pysal/examples/stl/stl_hom.shx
old mode 100644
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diff --git a/pysal/examples/stl/stl_hom.txt b/pysal/examples/stl/stl_hom.txt
old mode 100644
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diff --git a/pysal/examples/stl/stl_hom.wkt b/pysal/examples/stl/stl_hom.wkt
old mode 100644
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diff --git a/pysal/examples/stl/stl_hom_rook.gal b/pysal/examples/stl/stl_hom_rook.gal
old mode 100644
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diff --git a/pysal/examples/street_net_pts/README.md b/pysal/examples/street_net_pts/README.md
new file mode 100644
index 0000000..0e7317a
--- /dev/null
+++ b/pysal/examples/street_net_pts/README.md
@@ -0,0 +1,11 @@
+street_net_pts
+==============
+
+Street network points
+---------------------
+
+* street_net_pts.dbf: attribute data. (k=1)
+* street_net_pts.prj: ESRI projection file.
+* street_net_pts.qpj: QGIS projection file.
+* street_net_pts.shp: Point shapefile. (n=303)
+* street_net_pts.shx: spatial index.
diff --git a/pysal/examples/street_net_pts/street_net_pts.dbf b/pysal/examples/street_net_pts/street_net_pts.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/street_net_pts/street_net_pts.prj b/pysal/examples/street_net_pts/street_net_pts.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/street_net_pts/street_net_pts.qpj b/pysal/examples/street_net_pts/street_net_pts.qpj
old mode 100644
new mode 100755
diff --git a/pysal/examples/street_net_pts/street_net_pts.shp b/pysal/examples/street_net_pts/street_net_pts.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/street_net_pts/street_net_pts.shx b/pysal/examples/street_net_pts/street_net_pts.shx
old mode 100644
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diff --git a/pysal/examples/taz/README.md b/pysal/examples/taz/README.md
new file mode 100644
index 0000000..94ffc16
--- /dev/null
+++ b/pysal/examples/taz/README.md
@@ -0,0 +1,9 @@
+taz
+===
+
+Dataset used for regionalization
+--------------------------------
+
+* taz.dbf: attribute data. (k=14)
+* taz.shp: Polygon shapefile. (n=4109)
+* taz.shx: spatial index.
diff --git a/pysal/examples/taz/taz.dbf b/pysal/examples/taz/taz.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/taz/taz.shp b/pysal/examples/taz/taz.shp
old mode 100644
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diff --git a/pysal/examples/taz/taz.shx b/pysal/examples/taz/taz.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/test_examples.py b/pysal/examples/test_examples.py
old mode 100644
new mode 100755
index c5e44f3..04e9dce
--- a/pysal/examples/test_examples.py
+++ b/pysal/examples/test_examples.py
@@ -1,12 +1,13 @@
import unittest
import pysal.examples as ex
+import os
class Example_Tester(unittest.TestCase):
def test_get_path(self):
- pathparts = ex.get_path('').split('/')
- self.localpath = '/'.join(pathparts[-3:])
- self.assertEquals(self.localpath, 'pysal/examples/')
+ pathparts = os.path.normpath(ex.get_path('')).split(os.path.sep)
+ self.localpath = os.path.join(*pathparts[-2:])
+ self.assertEquals(self.localpath, os.path.normpath('pysal/examples/'))
def test_parser(self):
for example in ex.available():
diff --git a/pysal/examples/tmpIvIYa5.gwt b/pysal/examples/tmpIvIYa5.gwt
new file mode 100755
index 0000000..157ec16
--- /dev/null
+++ b/pysal/examples/tmpIvIYa5.gwt
@@ -0,0 +1,2803 @@
+0 168 juvenile ID
+1 2 14.1421
+2 1 14.1421
+2 3 5.09902
+2 4 3.60555
+2 5 5
+2 6 14.1421
+2 57 7.61577
+2 58 7
+3 2 5.09902
+3 4 2.23607
+3 5 3.60555
+3 6 13.3417
+3 52 14.1421
+3 53 11.3137
+3 54 11.4018
+3 55 9.43398
+3 56 9.84886
+3 57 2.82843
+3 58 2.23607
+3 59 13.3417
+4 2 3.60555
+4 3 2.23607
+4 5 2
+4 6 12.0416
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diff --git a/pysal/examples/tokyo/Tokyomortality.csv b/pysal/examples/tokyo/Tokyomortality.csv
old mode 100644
new mode 100755
diff --git a/pysal/examples/tokyo/tokyo_BS_NN_OFF.ctl b/pysal/examples/tokyo/tokyo_BS_NN_OFF.ctl
old mode 100644
new mode 100755
diff --git a/pysal/examples/tokyo/tokyo_BS_NN_OFF_listwise.csv b/pysal/examples/tokyo/tokyo_BS_NN_OFF_listwise.csv
old mode 100644
new mode 100755
diff --git a/pysal/examples/tokyo/tokyo_BS_NN_OFF_summary.txt b/pysal/examples/tokyo/tokyo_BS_NN_OFF_summary.txt
old mode 100644
new mode 100755
diff --git a/pysal/examples/us_income/README.md b/pysal/examples/us_income/README.md
index d076762..ec845b8 100644
--- a/pysal/examples/us_income/README.md
+++ b/pysal/examples/us_income/README.md
@@ -1,10 +1,11 @@
us_income
=========
-Per-capita income for the lower 47 US states 1929-2010
-------------------------------------------------------
+Nominal per capita income for the lower 48 US states 1929-2009
+--------------------------------------------------------------
- * us48.shp: shapefile
- * us48.dbf: dbf for shapefile
- * us48.shx: index for shapefile
- * usjoin.csv: attribute data (comma delimited file)
+* states48.gal: queen contiguity weights in GAL format.
+* us48.dbf: attribute data. (k=8)
+* us48.shp: Polygon shapefile. (n=48)
+* us48.shx: spatial index.
+* usjoin.csv: 48 US states nominal per capita income time series 1929-2009.
diff --git a/pysal/examples/us_income/spi_download.csv b/pysal/examples/us_income/spi_download.csv
old mode 100644
new mode 100755
diff --git a/pysal/examples/us_income/states48.gal b/pysal/examples/us_income/states48.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/us_income/us48.dbf b/pysal/examples/us_income/us48.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/us_income/us48.shp b/pysal/examples/us_income/us48.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/us_income/us48.shx b/pysal/examples/us_income/us48.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/us_income/usjoin.csv b/pysal/examples/us_income/usjoin.csv
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/README.md b/pysal/examples/virginia/README.md
index 5703feb..843e3c9 100644
--- a/pysal/examples/virginia/README.md
+++ b/pysal/examples/virginia/README.md
@@ -4,7 +4,18 @@ virginia
Virginia counties shapefile
---------------------------
- * virginia.shp: Shapefile
- * virginia.shx: shapefile index
- * virginia.dbf: attributes
- * virginia.prj: shapefile projection
+* virginia.dbf: attribute data. (k=7)
+* virginia.gal: rook contiguity weights in GAL format.
+* virginia.json: attribute and shape data in JSON format.
+* virginia.prj: ESRI projection file.
+* virginia.shp: Polygon shapefile. (n=136)
+* virginia.shx: spatial index.
+* virginia_queen.dat: queen contiguity weights in DAT format.
+* virginia_queen.dbf: queen contiguity weights in DBF format.
+* virginia_queen.gal: queen contiguity weights in GAL format.
+* virginia_queen.mat: queen contiguity weights in MATLAB MAT format.
+* virginia_queen.mtx: queen contiguity weights in Matrix Market MTX format.
+* virginia_queen.swm: queen contiguity weight in ArcGIS SWM format.
+* virginia_queen.txt: queen contiguity weights in TXT format.
+* virginia_queen.wk1: queen contiguity weights in Lotus Wk1 format.
+* virginia_rook.gal: rook contiguity weights in GAL format.
diff --git a/pysal/examples/virginia/virginia.dbf b/pysal/examples/virginia/virginia.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia.gal b/pysal/examples/virginia/virginia.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia.json b/pysal/examples/virginia/virginia.json
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia.prj b/pysal/examples/virginia/virginia.prj
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia.shp b/pysal/examples/virginia/virginia.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia.shx b/pysal/examples/virginia/virginia.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_queen.dat b/pysal/examples/virginia/virginia_queen.dat
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_queen.dbf b/pysal/examples/virginia/virginia_queen.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_queen.gal b/pysal/examples/virginia/virginia_queen.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_queen.mat b/pysal/examples/virginia/virginia_queen.mat
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_queen.mtx b/pysal/examples/virginia/virginia_queen.mtx
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_queen.swm b/pysal/examples/virginia/virginia_queen.swm
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_queen.txt b/pysal/examples/virginia/virginia_queen.txt
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_queen.wk1 b/pysal/examples/virginia/virginia_queen.wk1
old mode 100644
new mode 100755
diff --git a/pysal/examples/virginia/virginia_rook.gal b/pysal/examples/virginia/virginia_rook.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/README.md b/pysal/examples/wmat/README.md
new file mode 100644
index 0000000..8021a5a
--- /dev/null
+++ b/pysal/examples/wmat/README.md
@@ -0,0 +1,21 @@
+wmat
+====
+
+Datasets used for spatial weights testing
+-----------------------------------------
+
+* geobugs_scot: spatial weights in GeoBUGS text format.
+* lattice10x10.shp: Polygon shapefile for 10 * 10 regular lattices. (n=100)
+* lattice10x10.shx: spatial index.
+* ohio.swm: spatial weights in ArcGIS SWM format.
+* rook31.dbf: attribute data. (k=2)
+* rook31.gal: rook contiguity weights in GAL format.
+* rook31.shp: Polygon shapefile. (n=3)
+* rook31.shx: spatial index.
+* spat-sym-us.mat: spatial weights in MATLAB MAT format.
+* spat-sym-us.wk1: spatial weights in Lotus Wk1 format.
+* spdep_listw2WB_columbus: spatial weights in GeoBUGS text format.
+* stata_full.txt: full spatial weights matrix.
+* stata_sparse.txt: sparse spatial weights matrix.
+* wmat.dat: spatial weights in DAT format.
+* wmat.mtx: spatial weights in Matrix Market MTX format.
diff --git a/pysal/examples/wmat/geobugs_scot b/pysal/examples/wmat/geobugs_scot
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/ohio.swm b/pysal/examples/wmat/ohio.swm
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/rook31.dbf b/pysal/examples/wmat/rook31.dbf
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/rook31.gal b/pysal/examples/wmat/rook31.gal
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/rook31.shp b/pysal/examples/wmat/rook31.shp
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/rook31.shx b/pysal/examples/wmat/rook31.shx
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/spat-sym-us.mat b/pysal/examples/wmat/spat-sym-us.mat
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/spat-sym-us.wk1 b/pysal/examples/wmat/spat-sym-us.wk1
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/spdep_listw2WB_columbus b/pysal/examples/wmat/spdep_listw2WB_columbus
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/stata_full.txt b/pysal/examples/wmat/stata_full.txt
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/stata_sparse.txt b/pysal/examples/wmat/stata_sparse.txt
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/us48_CONTIGUITY_EDGES_ONLY.swm b/pysal/examples/wmat/us48_CONTIGUITY_EDGES_ONLY.swm
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/us48_INVERSE_DISTANCE.swm b/pysal/examples/wmat/us48_INVERSE_DISTANCE.swm
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/wmat.dat b/pysal/examples/wmat/wmat.dat
old mode 100644
new mode 100755
diff --git a/pysal/examples/wmat/wmat.mtx b/pysal/examples/wmat/wmat.mtx
old mode 100644
new mode 100755
diff --git a/pysal/spreg/diagnostics.py b/pysal/spreg/diagnostics.py
index 45f6e1d..77e950c 100644
--- a/pysal/spreg/diagnostics.py
+++ b/pysal/spreg/diagnostics.py
@@ -6,6 +6,7 @@ __author__ = "Luc Anselin luc.anselin at asu.edu, Nicholas Malizia nicholas.malizia
import pysal
from pysal.common import *
+chisqprob = stats.chi2.sf
import scipy.sparse as SP
from math import sqrt
from utils import spmultiply, sphstack, spmin, spmax
@@ -657,7 +658,7 @@ def jarque_bera(reg):
S = mu3 / (mu2 ** (1.5)) # skewness measure
K = (mu4 / (mu2 ** 2)) # kurtosis measure
jb = n * (((S ** 2) / 6) + ((K - 3) ** 2) / 24)
- pvalue = stats.chisqprob(jb, 2)
+ pvalue = chisqprob(jb, 2)
jb_result = {"df": 2, "jb": jb, 'pvalue': pvalue}
return jb_result
@@ -807,7 +808,7 @@ def breusch_pagan(reg, z=None):
bp_array = 0.5 * part2
bp = bp_array[0, 0]
- pvalue = stats.chisqprob(bp, df)
+ pvalue = chisqprob(bp, df)
bp_result = {'df': df, 'bp': bp, 'pvalue': pvalue}
return bp_result
@@ -961,7 +962,7 @@ def white(reg):
aux_r2 = r2(aux_reg)
wh = aux_r2 * n
df = k - 1
- pvalue = stats.chisqprob(wh, df)
+ pvalue = chisqprob(wh, df)
white_result = {'df': df, 'wh': wh, 'pvalue': pvalue}
return white_result
@@ -1116,7 +1117,7 @@ def koenker_bassett(reg, z=None):
kb_array = (1.0 / v) * part2
kb = kb_array[0, 0]
- pvalue = stats.chisqprob(kb, df)
+ pvalue = chisqprob(kb, df)
kb_result = {'kb': kb, 'df': df, 'pvalue': pvalue}
return kb_result
@@ -1330,7 +1331,7 @@ def likratiotest(reg0, reg1):
raise Exception, "Missing or improper log-likelihoods in regression objects"
if likr < 0.0: # always enforces positive likelihood ratio
likr = -likr
- pvalue = stats.chisqprob(likr, 1)
+ pvalue = chisqprob(likr, 1)
likratio = {"likr": likr, "df": 1, "p-value": pvalue}
return likratio
diff --git a/pysal/spreg/diagnostics_sp.py b/pysal/spreg/diagnostics_sp.py
index 806e394..4a71166 100644
--- a/pysal/spreg/diagnostics_sp.py
+++ b/pysal/spreg/diagnostics_sp.py
@@ -4,7 +4,8 @@ Spatial diagnostics module
__author__ = "Luc Anselin luc.anselin at asu.edu, Daniel Arribas-Bel darribas at asu.edu"
from utils import spdot
-from scipy.stats.stats import chisqprob
+from scipy.stats import chi2
+chisqprob = chi2.sf
from scipy.stats import norm
import numpy as np
import numpy.linalg as la
diff --git a/pysal/spreg/probit.py b/pysal/spreg/probit.py
index e1a7ad5..e00701d 100644
--- a/pysal/spreg/probit.py
+++ b/pysal/spreg/probit.py
@@ -5,7 +5,8 @@ __author__ = "Luc Anselin luc.anselin at asu.edu, Pedro V. Amaral pedro.amaral at asu.
import numpy as np
import numpy.linalg as la
import scipy.optimize as op
-from scipy.stats import norm, chisqprob
+from scipy.stats import norm, chi2
+chisqprob = chi2.sf
import scipy.sparse as SP
import user_output as USER
import summary_output as SUMMARY
diff --git a/pysal/spreg/regimes.py b/pysal/spreg/regimes.py
index 1896a2b..0eb6086 100644
--- a/pysal/spreg/regimes.py
+++ b/pysal/spreg/regimes.py
@@ -2,7 +2,8 @@ import numpy as np
import pysal
import scipy.sparse as SP
import itertools as iter
-from scipy.stats import f, chisqprob
+from scipy.stats import f, chi2
+chisqprob = chi2.sf
import numpy.linalg as la
from utils import spbroadcast
diff --git a/pysal/spreg/sur_error.py b/pysal/spreg/sur_error.py
index 94adb3e..338bc84 100644
--- a/pysal/spreg/sur_error.py
+++ b/pysal/spreg/sur_error.py
@@ -9,7 +9,8 @@ __author__= "Luc Anselin lanselin at gmail.com, \
import numpy as np
import pysal
import numpy.linalg as la
-import scipy.stats as stats
+from scipy.stats import chi2
+chisqprob = chi2.sf
import summary_output as SUMMARY
import user_output as USER
from scipy.sparse.linalg import splu as SuperLU
@@ -320,7 +321,7 @@ class SURerrorML(BaseSURerrorML):
if nonspat_diag:
M = self.n_eq * (self.n_eq - 1)/2.0
likrodiag = 2.0 * (self.surerrllik - self.errllik)
- plik1 = stats.chisqprob(likrodiag, M)
+ plik1 = chisqprob(likrodiag, M)
self.lrtest = (likrodiag,int(M),plik1)
else:
self.lrtest = None
@@ -328,7 +329,7 @@ class SURerrorML(BaseSURerrorML):
# LR test on spatial autoregressive coefficients
if spat_diag:
liklambda = 2.0 * (self.surerrllik - self.llik)
- plik2 = stats.chisqprob(liklambda, self.n_eq)
+ plik2 = chisqprob(liklambda, self.n_eq)
self.likrlambda = (liklambda,self.n_eq,plik2)
else:
self.likrlambda = None
diff --git a/pysal/version.py b/pysal/version.py
index a2665ea..78de2d4 100644
--- a/pysal/version.py
+++ b/pysal/version.py
@@ -1,3 +1,3 @@
import datetime
-version = "1.14.2"
-stable_release_date = datetime.date(2017, 9, 23)
+version = "1.14.3"
+stable_release_date = datetime.date(2017, 11, 2)
diff --git a/pysal/weights/Contiguity.py b/pysal/weights/Contiguity.py
index 346aa9a..687a9a8 100644
--- a/pysal/weights/Contiguity.py
+++ b/pysal/weights/Contiguity.py
@@ -79,11 +79,13 @@ class Rook(W):
"""
sparse = kwargs.pop('sparse', False)
if idVariable is not None:
- ids = get_ids(filepath, idVariable)
+ ids = get_ids(filepath, idVariable)
+ id_order = ids
else:
ids = None
+ id_order = None
iterable = FileIO(filepath)
- w = cls(FileIO(filepath), ids=ids, **kwargs)
+ w = cls(iterable, ids=ids, id_order=id_order, **kwargs)
w.set_shapefile(filepath, idVariable=idVariable, full=full)
if sparse:
w = w.to_WSP()
@@ -243,11 +245,14 @@ class Queen(W):
"""
sparse = kwargs.pop('sparse', False)
if idVariable is not None:
- ids = get_ids(filepath, idVariable)
+ ids = get_ids(filepath, idVariable)
+ id_order = ids
else:
ids = None
+ id_order = None
+
iterable = FileIO(filepath)
- w = cls(FileIO(filepath), ids=ids, **kwargs)
+ w = cls(iterable, ids=ids, id_order=id_order, **kwargs)
w.set_shapefile(filepath, idVariable=idVariable, full=full)
if sparse:
w = w.to_WSP()
diff --git a/requirements_plus.txt b/requirements_plus.txt
index 2a57755..e74b5e0 100644
--- a/requirements_plus.txt
+++ b/requirements_plus.txt
@@ -9,3 +9,4 @@ mplleaflet>=0.0.5
statsmodels>=0.6.1
numba
numexpr
+palettable
diff --git a/setup.py b/setup.py
index 343be39..07eaaf4 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,7 @@ with open('README.rst') as file:
MAJOR = 1
MINOR = 14
-MICRO = 2
+MICRO = 3
ISRELEASED = False
VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)
diff --git a/tools/bump.py b/tools/bump.py
index f96609a..cf22b61 100644
--- a/tools/bump.py
+++ b/tools/bump.py
@@ -60,10 +60,10 @@ with open("../doc/source/conf.py") as c_file:
tok = line[:9]
if tok == 'version =':
lines[i] = "version = '{}'\n".format(version)
- print lines[i]
+ print(lines[i])
elif tok == 'release =':
lines[i] = "release = '{}'\n".format(version)
- print lines[i]
+ print(lines[i])
with open("../doc/source/conf.py", 'w') as c_file:
c_file.write("".join(lines))
diff --git a/tools/github_stats.py b/tools/github_stats.py
index 92913de..db622ac 100644
--- a/tools/github_stats.py
+++ b/tools/github_stats.py
@@ -15,7 +15,11 @@ import sys
from datetime import datetime, timedelta
from subprocess import check_output
-from urllib2 import urlopen
+try:
+ from urllib import urlopen
+except:
+ from urllib.request import urlopen
+
import ssl
context = ssl._create_unverified_context()
@@ -48,7 +52,7 @@ def get_paged_request(url):
results = []
while url:
print("fetching %s" % url, file=sys.stderr)
- f = urlopen(url, context=context)
+ f = urlopen(url)
results.extend(json.load(f))
links = parse_link_header(f.headers)
url = links.get('next')
--
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