pysal/pysal: PySAL 2.0.0

Release Notes for PySAL 2.0 This release represents over 15 months of hard work on PySAL. It brings major transitions in the project together with many new enhancements, improved documentation, along with many bug fixes and optimizations. **Table of Contents** - [Release Notes for PySAL 2.0](#release-notes-for-pysal-20) - [Major Changes](#major-changes) - [Entirely New Packages](#entirely-new-packages) - [Significant Enhancements to Existing Packages](#significant-enhancements-to-existing-packages) - [Changes by Package](#changes-by-package) - [libpysal](#libpysal) - [esda](#esda) - [giddy](#giddy) - [inequality](#inequality) - [pointpats](#pointpats) - [spaghetti](#spaghetti) - [mapclassify](#mapclassify) - [splot](#splot) - [spreg](#spreg) - [spglm](#spglm) - [spint](#spint) - [mgwr](#mgwr) - [spvcm](#spvcm) - [Summary Statistics](#summary-statistics) - [Package Activity](#package-activity) - [Contributor Activity](#contributor-activity) - [Contributor by Package Activity](#contributor-by-package-activity) Major Changes This release, we've had a ton of activity in PySAL, but it has all been conducted in our subpackages, the independently-released components of our library. Because it is too onerous to list all the changes to the API here, please consult the Migrating to PySAL 2.0 page for a detailed discussion of all reorganization-related changes. This document will focus only on improvements to functionality, enhancements, and additional modules added to 2.0, over and above the last stable release of the 1.0 series, PySAL 1.14.4. Entirely New Packages For starters, we've added some entirely-new subpackages to this release candidate: mgwr, the multi-scale Geographically-weighted regression package for Python. Don't worry, mgwr fits single-scale geographically-weighted regressions, too. Geographically-weighted regression is a kind of generalized additive model that uses kernel functions in the geographic area around each observation to predict outcomes at that area more accuratly, kind of like Gaussian Process regression for geographic data. spvcm, for spatially-correlated multilevel models. Spatially-correlated multilevel models are models that allow for random effects of nearby areas, regions, or groups to be correlated with one another. This is a Gibbs sampling framework plus diagnostics & plotting tools for general Bayesian analysis of Gibbs samplers. The package also contains simple tools to implement new samplers on top of the infrastructure provided, which is fast, parallel, serializable, iterative-write, and interruptible. spint, for estimating spatial interaction models, such as the production-constrained or consumption-constrained gravity models. spglm, a package for fitting sparse GLMs, focused on performance over sparse categorical data. splot, for spatial vizualization in Python, built on top of the excellent geopandas. This is headed by our Google Summer of Code (2018) student, Stefanie Lumnitz, and will be ongoing throughout the release candidate maturation cycle. pointpats, a package for the statistical analysis of point patterns, geographical colocation, and dispersion. Significant Enhancements to Existing Packages We've also had a ton of activity adding new features in our submodules: alpha shapes, a generalization of convex hulls to allow for non-convex hulls Contiguity weights from voronoi tesselations/delaunay triangulation graphs for point patterns Fuzzy contiguity weights, for polygonal data where planarity is not strictly enforced (provided in part by geopandas) A family of spatially explicit indicators of mobility association including the inter- and intra-regional indicators as well as the local indicators. The former provide a meso-level view on the exchange mobility pattern, shedding light on specific regions hosting frequent rank exchanges while the latter examine the concordance relationship between a focal spatial unit and its neighbors for revealing the role of space in shaping the exchange mobility pattern over time. Categorical Spatial Markov, a generalization of the Spatial_Markov class previously implemented to interrogate the role of space in shaping regional income distribution dynamics to incorporate directe variables. Here, the categorical spatial lag is adopted for formalizing the neighborhood. Connected Components checks for our spatial graph matrices Pandas Adjacency list constructors and NetworkX adapters for PySAL graph objects Attach islands, tooling to merge isolated observations into existing spatial graphs Construct Contiguity graphs from linestrings, allowing for easy and fast access to road network data in PySAL Changes by Package Overall, there were 1636 commits that closed 368 issues, together with 236 pull requests since our last release on 2017-11-03. libpysal weights.distance.KNN.from_dataframe ignoring radius (#116) Always make spherical KDTrees if radius is passed (#117) [ENH] should weights.util.get_ids() also accept a geodataframe? (#97) enh: add doctests to travis (#2) (#112) sphinx docs need updating (#49) Add notebooks for subpackage contract (#108) Api docs complete (#110) Doctests and start of documentation for libpysal (#109) Add dependencies to requirements_plus.txt for test_db (#107) Weights/util/get ids gdf (#101) missing adjustments to lower case module names (#106) Rel.4.0.0 (#105) REL: 3.0.8 (#104) error importing v3.0.7 (#100) Lower case module names (#98) remove function regime_weights (#96) depreciating regime_weights in the new release? (#94) inconsistency in api? (#93) Ensure consistency in from .module import * in components of libpysal (#95) [WIP] cleanup (#88) docstrings for attributes are defined in properties (#87) docstrings in W class need editing (#64) version name as version (#92) remove del statements and modify alphashape all (#89) libpysal/libpysal/cg/init.py not importing rtree (#90) including rtree in imports (#91) BUG: test_weights_IO.py is using pysal and hard-coded paths (#85) fix hardcoded swm test (#86) check for spatial index if nonplanar neighbors (#84) nonplanar_neighbors fails when sindex is not constructed. (#63) increment version number and add bugfixes, api changes (#79) Spherebug (#82) only warn once for islands/disconnected components (#83) only warn on disconnected components if there are no islands (#81) LEP: Stuff/use pysal/network stuff to provide queen weights on linestring dataframes (#59) swm fix not ported forward from pysal. (#66) import scipy syntax typo in the new issue template (#68) deletion of extra spaces in warning message (#78) Nightli.es build permissions (#77) name of geometry column is hardcoded in nonplanar_neighbors (#75) changed geometry column name from a str to an attribute (#76) Missing example file (#71) if numba isn't present, libpysal warns every time imported (#73) add check for disconnected components (#65) clean up for release (#74) update for new examples (#72) Swm (#70) Remaining concerns left unfixed in #61 (#62) [WIP] Alpha shapes (2D) code (#58) [WIP]: add linestring/multilinestring functionality (#61) Fuzzy contiguity (#57) add berlin example (#56) force UTF8 encoding for the long description read (#55) add guerry example dataset (#45) update georgia shapefile (#53) fix typo add non_planar_joins instead of non_planar_neighbor attr… (#54) add voronoi to the API (#46) ENH: Neighbor detection for nonplanar enforced polygon collections. (#51) Missing example used by gwr tests (#43) Wplot (#50) close the door on 2 for libpysal (#44) To networkx argument name changed (#40) bump micro version (#42) fix networkx adapters (#41) minor version bump for release (#39) Plot weights (#38) forward port of legacy fix #1028 (#37) Adding Voronoi generator for cg as well as Voronoi weights from 2-d points (#36) bump version for release (#34) attach_islands correction: incorporate pr #32 (#33) change data type of contiguity W.neighbors value from set to list (consistent with other weights) (#32) add a function to attach the nearest neighbor to island (#30) fix id2i lookup for string names and make better names (#31) two modules "Wsets.py" and "util.py" depend on each other (#26) add unittest for Wset.w_clip (#29) resolve circular import in Wsets and util (#28) update doctests in weights module to use libpysal instead of pysal (#27) bump stable date (#25) bump version for point release of lag cat fix (#24) esda enh: updating travis build and rtd (#40) BUG: missing rtd file (#39) REL: 2.0.1 (#38) Prepping for a doc release (#37) docstrings are using pysal legacy (#4) add zenodo doi badge (#36) REL: 2.0.0 (#34) Changing esda setup to handle version programatically (#33) port legacy esda fix for 1013 (#12) notebook links broken (#29) include /tests in release (#32) Add tests to release (#27) Accounting for incoming API changes to libpysal and adding testing against libpysal's master branch (#26) no varnames in Moran_BV_matrix (#22) add .varnames attribute to Moran_BV objects in Moran_BV_Matrix results (#23) Inconsistent metadata in setup.py (#28) Update license (#30) esda has no readme (#14) Readme added (#25) move api into init and remove api (#24) .z attribute divided by standard deviation (#21) offer standardised and non-standardised .z, .x and .y attributes (#20) get sjsrey's changes into a release (#16) esda's namespace is broken (#17) update api.py (#18) Update docstrings to use libpysal not pysal (#13) esda needs an api.py module (#9) chore: Update setup for 3+ (#15) Master (#10) giddy remove giddy.api in README.rst (#66) chore: update for libpysal lower case module name changes (#65) remove api.py (#62) set up travis dual testing against mapclassify and esda (#63) replace libpysal.api imports with new imports in markov.py and `d… (#61) Remove api.py and account for changes in (incoming) API of mapclassify, esda, and libpysal (#64) version giddy only in giddy/ini.py (#60) remove duplicate makefile for sphinx build (#59) add zenodo doi badge to README (#58) add changelog for the release 1.2.0 (#57) prepare for release 1.2.0 (#56) set up dual travis tests for libpysal (pip and github) (#55) ENH: Allow for more flexible specification of Spatial Markov (#54) Update notebooks to rely on geopandas for mapping (#52) ENH to docs (#51) include /tests in the release and correct for the directional doctests (#50) add doc building badge to README (#49) Tests and documentation for rose.plot() and rose.plot_vectors() (#47) A tentative version of giddy documentation website with sphinx (#48) encoding issue in README.rst (#45) force utf8 for the install description read (#46) implement rose.plot() and rose.plot_vectors() method using splot (#43) More on building doc webpages using sphinx (#44) Gallery (#42) new features for sphinx documentation website (#41) typo - email notifications (#40) fix for python 3 (#38) first draft of sphinx gallery (#39) add docstring for categorical spatial Markov (#37) add changelog for the release 1.1.0 (#36) prepare for release (#35) code 2to3 (#34) chore: update for python 3+ only (#33) How to use the 'development' version (#31) KeyError: 1 in spatial_lag.py (#30) giddy needs an api.py module (#26) add inequality to api (#28) adding discretized Spatial_Markov (#29) inequality Change setup to handle version pragmatically (#6) accounting for libpysal api changes in unittests (#5) missing parenthesis in call to print (#2) setting up dual testing (#4) 2to3 for _indices.py (#3) Initial setup (#1) pointpats add changelog for release 2.0.0 (#21) remove api.py & adjust notebooks and doctests for changes in libpysal (#19) version pointpats only in pointpats/ini.py (#18) include /tests in the release (#17) configure dual testing (#16) install stable released libpysal for travis testing (#15) force UTF8 encoding for the long description read (#14) Prepare for the release (#13) chore: libpysal is 3 only now so removing travis tests on python 2 (#12) try removing conversion and see if this passes (#11) spaghetti refreshing documentation (#124) option to add distance from point to snapped location (#75) attempting pyproj_fix (#122) [WIP] Add snap dist (#123) travis CI build failing with KeyError: 'PROJ_LIB' (#121) resolving obs_to_node question (#120) why convert obs_to_node from defaultdict to list? (#93) network.PointPatterns condense code chunk (#74) condensing idvariable code chunk (#119) Network Cross Nearest Neighbor (#102) refreshing docs (#117) shortest path look up from allneighborsdistances? (#115) adding shortest path traceback for point patterns (#116) ImportError: No module named 'boto3' (#113) adding boto3 test req for current fiona bug (#114) [WIP] cleanup_nearest_neighbor (#112) duplicate neighbor distance functions? (#91) network.allneighbordistances documentation not accurate (#111) [WIP] General package maintenance (#109) new badges (#96) tools/ (#99) updating thumbnails in docs (#108) [WIP] updating docs, badges, tools, etc. (#107) initializing new sphinx docs based on submodule_template (#98) new labels for issues (#105) populating sphinx docs (#37) tests for analysis and util (#44) NetworkF (#94) rename functions to be more pythonic (#104) add poisson distribution to tests (#106) initial sphix docs attempt (#67) bumping version to 1.1.0 (#97) adding in new tests for utils.py (#95) add flag for util.generatetree() (#92) [completed atm] - docstrings cleanup (#89) clean docstrings (#77) adding MANIFEST.in (#88) clearing Facility_Location.ipynb (#87) removing typo in Facility_Location (#86) clearing Facility_Location.ipynb (#85) updating Facility_Location.ipynb for typos (#84) adding Facility_Location.ipynb (#83) new notebook ideas (#48) adding windows functionality for 'last updated' (#82) ensure nearest nodes are returned as np.array() (#73) snapping trouble when the initial node in KDtree is the nearest (#72) add Github version badge (#80) add open issues badge (#79) update notebooks as per pysal/pysal#1057 (#81) [Complete/Needs Review] updating in_shp parameter in spaghetti.Network (#69) [ENH] geopandas.GeoDataFrame for PointPattern (#28) update in_shp kwarg in spaghetti.Network (#68) removing undeclared edge_time attribute (#65) update README.txt (#33) [ENH] Add badges (#31) Publish on Zenodo (#36) Some errors in node_distance_matrix() (#64) declare SMALL as np.finfo(float).eps (#63) smallest numpy epsilon float? (#61) [WIP] Prep for next pypi (#60) mimic other pysal submodules for api removal (#50) PEP8 compliant (#38) update notebooks (#43) api testing (#59) DRY version documentation (#53) configure travis dual testing for "Allowed Failures" to work (#58) adding geopandas for dual travis testing (#56) New tests required for new in_shp parameter option (#30) fix or remove code_health badge (#54) add .landscape.yml for code health (#51) removing code health badge from README (#55) adding .landscape.yml for code health (#52) adding additional pip install instructions/options (#35) dual testing (#45) change libpysal imports in tests (#46) change weights variable name (#47) update notebooks for reorg (#1) spaghetti/analysis.py:182: RuntimeWarning (#42) change xrange to range (#40) summation error in computeobserved() of spaghetti.analysis.py (#41) TypeError: can't pickle dict_keys objects (#39) add CHANGELOG (#34) update import scheme for new package name (#5) Prepare a release of spaghetti for pypi (#26) pip (#32) preparing for pypi release (#25) api.py tests (#19) trailing comma not allowed with surrounding parenthesis (#29) Necessity of future? (#27) spaghetti currently only python 2.7.x compatible (#21) Geopandas read (#22) Py2topy3 (#23) Spaghetti/update travis (#24) Generalize the Network input API for libpysal/#59 (#20) mapclassify fix doctests (interactive examples in inline docstrings) (#19) complete readthedocs configuration & add Slocum 2009 reference (#17) prepping for a doc based release (#15) new release on pypi (#10) prepare for release 2.0.0 (#13) Clean up for next pypi release (#12) move notebooks outside of the package (#11) ENH: move classifiers up into init (#9) Moving to python 3+ (#8) splot merge Sprint with master branch (#39) Change documentation style (#38) add travis build badge to README.md (#37) fix current documentation for sprint (#36) value_by_alpha prototype (#28) Clean up of current code base (#30) Value By Alpha specification (#24) nonplanar example update (#33) add README.md (#29) issues in some docstrings for giddy (#26) debug splot documentation (#25) collection of cleanups forsplot.giddy (#23) created esda.moran.Moran_Local_BV visualisations (#20) add esda.moran.Moran_BV visualizations to splot.esda (#18) add seaborn and matplotlib to install_requirements in setup.py (#19) prototype moran_scatterplot(), plot_moran_simulation() and plot_moran() for esda (#17) include utility functions shift_colormap and truncate_colormap (#15) fix setup.py so files are installed with "pip install ." (#16) plot_spatial_weights including network joins for non_planar_joins (#14) adapting existing esda functionality to splot.esda namespace and allow .plot() method (#13) adding license (#4) add giddy dynamic LISA functionality under splot.giddy (#11) start sphinx html documentation (#12) add visualization option with significance to mplot (#7) Visualising Local Autocorrelation (#8) Copy new changes made to viz module into split (#5) run 2to3 for splot (#6) spreg update docstrings for libpysal API changes (#9) Merging in spanel & spreg2 code necessary for new spatial panel & GeoDaSpace (#10) move to silence_warnings from current libpysal (#7) add init to ensure tests are shipped (#6) weights typechecking will only accept things from pysal. (#3) relax error checking in check_weights (#4) simplify testing (#5) Convert spreg to common subset 2,3 code (#2) spglm fix docstrings (as well as some within interactive examples) (#14) Fix docs (#17) Submodule (#16) submodule_contract (#13) Inconsistent metadata in setup.py (#10) adapting spglm to new libpysal (#12) move to using libpysal.io.open rather than just libpysal.open (#11) Freeze (#8) add tr_S attribute for use in GWR (#7) remove pysal requirements (#6) remove v 2.x tests from CI (#5) houskeeping of new basefiles needed as a submodule (#4) spint add changelog (#15) pypi files do not include tests (#9) Submodule (#14) adapting spint to newest version of libpysal (#13) Reorg (#12) spint has pysal as a dependency, should be libpysal (#2) api.py syntax error (#10) removed trailing api comma (#11) Freeze (#8) update dependencies (#7) remove v 2.x test from CI (#6) version bump (#5) Common subset (#4) houskeeping of basefiles needed for submodule (#3) mgwr add solve from scipy instead of inv (#45) bool variables and singular matrix error (#42) update travis.yml for matrix testing (#44) add changelog (#43) fix compare_surfaces docstrings (#40) add docs for viz function compare_surfaces (#39) add compare_surfaces docstring and bump version (#38) add viz functions to docs (#37) add_map_func (#36) add badges to README (#35) (ENH) prepare online docs (#33) Revert "move notebooks outside of the package folder and fix notebooks" (#34) move notebooks outside of the package folder and fix notebooks (#32) Georgia main example patch (#31) format gwr.py following PEP 8 style and fix docstrings (#30) use libpysal in docstrings and adapt to python 3 syntax (#29) Inconsistent metadata info on setup.py (#25) rebuild rights access? (#28) swap to libpysal.io.open (#26) adapting mgwr to newest libpysal (#27) change spreg import pattern (#24) change imports from spreg (#22) rework pickles in the tests (#21) Swap to use more portable types than pickles (#23) Output summary (#17) Adding summary output (#18) Freeze (#20) Allow user-set BW's for MGWR (#7) Set mgwr bw (#15) adds py27 to ci (#16) Gwr to mgwr (#14) Standard errors and t-vals (#8) Redundant calculation of Aj (#10) question about final fit in MGWR class? (#1) change main directory from gwr to mgwr (#13) Update mgwr (#12) clean up MGWR (#11) Consolidate MGWR (#5) hat matrices (#2) spvcm change the API to reflect up-to-date libpysal api (#7) Test failures in effective size & geweke diagnostics (#2) update plotting and diagnostics for pandas deprecation (#3) Summary Statistics Package Activity package commits total issues pulls spaghetti 282 94 34 libpysal 276 79 57 splot 247 27 21 mgwr 245 39 24 giddy 137 38 31 esda 80 29 1