pysal/pysal: PySAL v2.2.0

PySAL v, 2020-02-13 PySAL 2.2.0 represents 6 months of enhancements, bug-fixes, widening of test coverage, and improved documentation. All users are encouraged to upgrade to this version as there are numerous optimizations as well as new features (see below) that have been implemented. Overall, there were 1122 commits that closed 307 issues, together with 192 pull requests since our last release on 2019-07-29. Major Highlights of PySAL 2.2.0 Meta-package loses some serious weight PySAL is no longer a source release meta-package, but instead specifies the packages in the PySAL ecosystem as dependencies. This means that installing the pysal meta-package will ensure that all the ecosystem packages are installed. Entirely New Packages In this release, the PySAL family has expanded to include: tobler Areal interpolation and dasymetric mapping. Enhancements to Existing Packages Refactoring of pysal/libpysal to use remote example data sets which reduces the footprint of the source install from 25mb to under 3mb. Remote examples can now be examined with interactive maps if being run in Jupyter Notebooks. pysal/mapclassify: Choropleth legend formatting has been enhanced to permit more granular control of class labels. pysal/spaghetti: This release includes a major overhaul to the API documentation and notebooks/tutorials. and here pysal/splot: This release includes additional documentation, in-depth tutorials and pointers how to solve common installation issues. splot has been submitted and will soon be available as an article in the journal of open source software. pysal/giddy: Two enhancements: (1) a new sequence module consisting of several alignment-based sequence analysis methods (example notebook) (2) extend Markov methods to deal with non-ergodic Markov chains. This release also includes a bug fix for the estimation of kendall's Tau and its spatial extension when ties are present. Changes by Package libpysal #176: Fetch #238: REL: version bump for bug fix release #236: test_map breakage due to pandas 1.0 deprecation of ufunc.outer #237: BUG: ufunc.outer deprecated #230: raise warning when islands are used in to_adjlist #113: Some example datasets are missing documentation #229: DOC: Cleaning up docs and docsr for tutorial #165: to_adjlist(remove_symmetric=True) fails on string-indexed weights. #204: AttributeError: 'Queen' object has no attribute 'silent_island_warning' #226: 4.2.1 #228: Revert "4.2.1" #227: 4.2.1 #225: DOC: images for notebooks #224: 4.2.1 #223: 4.2.1 #221: duplicate pypi package badge #222: 4.2.1 #220: REL: 4.2.1 #214: libpysal 4.2.0 won't import on Windows #215: libpysal 4.2.0 Windows import issue #212: Constructing contiguity spatial weights using from_dataframe and from_shapefile could give different results #213: fix bug 212 #216: alpha_shapes docs not rendering #217: corrected docstrings in cg.alpha_shapes.py #211: Updating requirements #174: Big tarball #209: DOC: math rendering in sphinx, and members included for W #125: metadata for examples #210: (docs) automatically generate docstrings for class members #207: (docs) keep file .nojekyll in docs when syncing between docs/ and docsrc/_build/html/ #206: (bug) replace silent_island_warning with silence_warnings for weights #205: Documentation does not work #203: updating cg.standalone.distance_matrix docs #195: error message in cg.standalone.distance_matrix() #202: improved docs in io.util.shapefile #201: [ENH] moving jit import to common.py / improve documentation #199: rearrange shapely import in cg.alpha_shapes #200: fix quasi-redundant import of shapely #196: Remove more relics (from pre-reorg PySAL) #198: [BUG] correcting shapely import bug #197: [BUG] alpha_shapes/shapely import error #129: decorating functions with requires() #192: removing iteritems decorator #193: [WIP] removing unused relics #194: README.txt refers to pre-reorg PySAL #147: remove distribute_setup.py? #128: requires() decorator for libpysal.cg.alpha_shapes #191: necessity of libpysal.common.iteritems()? #189: Voronoi results in weights of different shape than input points #190: BUG: alpha_shape_auto can fail to contain all points in the set. #186: Cast arrays as lists (Issue 185) #185: WSP(sparse).to_W() has arrays in weights,neighbors dictionaries, rather than lists. #188: BUG: Update for geopandas use of GeometryArray #187: Updated documentation error (link incorrectly specified) in README.rst #182: Docs: badges for pypi #178: development guidelines link failure #181: DOCS: moving off rtd #180: REL 4.1.1 bf release #179: BUG: Updating manifest for additional requirements files #169: libpysal 4.1.0 is not released on pypi or conda-forge #131: addressing DeprecationWarning: fromstring() #132: addressing DeprecationWarning: fromstring() #175: ENH: fromstring has been deprecated #172: Ci esda #102: REL: 2.2.1 bf release #101: Fixes for pandas deprecation and 3.8 verbosity #98: ENH: adjust tests for new libpysal.examples #97: update docs #96: DOC: changelog update #95: ENH: bumping version and handle array creation error in join counts #87: development guidelines link in README.md and README.rst #92: PYSAL_PYPI is not defined in .travis.yml #93: addressing #92 -- .travis.yml issue #88: resolving dev guidelines link #80: Update officially supported Python versions #74: ENH - Join count tails #83: DOC: Have notebooks show output in the src #82: no output in documentation notebooks giddy #107: Extend functions for Markov classes to deal with non-ergodic Markov chains #127: prepare for releasing V2.3.0 #109: (ENH) Extend functions for Markov classes to deal with non-ergodic Markov chains #126: travis CI: pip install from git clone #125: rewrite utility function "get_lower" using numpy's more efficient functionality #121: Release version 2.2.2 for bug fix #123: prepare for new release: version 2.2.2 #122: remove the parameter in plt.show() due to the API change in Matplotlib (deprecation) #119: development guidelines link in README.md #118: BUG: Fix for correct handling of ties in Tau #120: resolving broken dev link #117: initialization of ECount parameter in Kendall's Tau #116: (bug) debug travis-ci inequality pointpats segregation #146: Merge pull request #146 from knaaptime/warnings #144: move import down #141: addressing pysal/pysal#1145 #137: tweaks readme #140: Fix ReadMe #139: resolving broken link #138: development guidelines link broken #136: improve inference wrappers docstring #135: Strange non-corresponding legend on output (Out)when running indexes #130: [WIP] NA handling #132: Update link for instruction of LTDB_Std_All_fullcount.zip #105: handling nans/missing values #131: Raise an informative error when input data have NAs (also update geosnap links) #129: ModuleNotFoundError: No module named 'segregation.spatial' #127: haversine_distance relies on newer version of scikit-learn #128: update scikit-learn requirements #126: fix bug of compute_all tests #123: Swap to more robust tests that rely on numpy seeds #121: Adds MinMax and SpatialMinMax to documentations/notebooks and compute_all and tweak notebooks #125: Change precision of simulated-based tests. #124: Increase the precision of simulated-based tests. #86: [ENH] extend inference framework to multigroup indices #122: Adds inference wrappers for multigroup indexes (Single and Two) spaghetti #401: Version bump to v1.4.1 #399: Binder is broken for network-analysis #400: Some tutorial links giving 404 #398: Fix links 2 #397: Fix links for notebooks #396: [DOC] Reorg for tutorials page #110: Traveling Salesperson Notebook #100: create new TSP notebook with pulp #386: [WIP] TSP notebook #394: [DOC] paths docstring missing #395: correcting routes doc #393: [ENH] add back build badge #387: [BUG] Stale links on pysal.org/spaghetti #391: Rebuild docs #390: force read-add conn-comp notebook #389: repushing missing notebooks #388: Stale links #343: tarball jobs failing on Travis #380: [ENH] shortest-path extraction #385: [ENH] regular lattice generator #382: [WIP][ENH] addressing shortest path extract #384: mention the pysal/notebook project #383: point pattern --> network error message #381: [ENH] connected components demo notebook #217: spaghetti should handle native cg.Point/Chain objects #377: Native geometries #379: updating README.md #378: data type testing #376: adding CoC link to README.md #375: update CHANGELOG.md format #346: all reqs found in requirements*.txt necessary? #320: [ENH] explore overlapping "nearest point" calculation — DRY #372: altering reference format in docs #369: Clear instructions for black/pre-commit for contributing #371: Contrib precommit #351: alldistances vs. distancematrix? #370: distance matrix and tree storage #367: update readme #366: Adding citations for facility location notebook #340: v1.4 release checklist #364: updating README.md #333: add pre-commit black for PRs? #363: trying out the black pre-commit hook #362: adding descartes to environment.yml #361: Attempt binder3 #360: need readthedocs.yml? #359: need all tarball tests? #358: Attempt binder2 #357: using environment.yml for binder #354: Add blob/master/ to notebooks link #356: addressing #354 #355: Citation review #78: launch binder #353: version 1.3.1 --> 1.4 bump #352: updating version and docs #332: improve spaghetti homepage and notebooks? #338: Review docs for links, etc. #341: Spelling and default value of n_processes #342: [ENH][WIP]extension of #339: Rahul799 docs/bugfix #330: [WIP] TSP notebook #350: Revert "order analysis.py classes/functions alphabetically" #349: order analysis.py classes/functions alphabetically #347: updating requirement_dev.txt #348: update README.md #339: links in the docs,reviewed #344: updating README.md #336: automatically generate docstrings for class members #337: Update docs #335: Updating .travis.yml #334: fix indentation in .travis.yml #331: update README.md badges #327: Citation stipulation for notebooks #329: Notebooks update part 2 #328: Notebooks update #326: Updating Notebooks #324: update email address in notebooks #325: Plotting error in Facility_Location.ipynb #323: module 'pysal.explore.spaghetti' has no attribute 'element_as_gdf' #319: swapping out distance calculation function #318: [ENH] util.compute_length() — DRY #317: adjusting snapping image in README.md #315: inaccurate documentation — Network.split_arcs() #316: Split arcs update #313: streamline badges in README.md #314: streaming badges on README.md #312: adding +travis to notification recipients #308: Update travis CI for new testing schema #309: broken "development guidelines" link #311: updating broken dev link #299: Update Travis CI schema #310: adding static docs badge #288: mock c modules for doc dependencies #306: doi missing from citation #307: adding Zenodo DOI to README.md and website #305: blackify setup.py #301: Change Read the Docs to GitHub? #304: updating README to reflect GitHub docs #303: switching to github docs as per #301 #302: get_versions() function #293: code formatting with black #300: blackifying code (#293) mgwr spglm spint spreg spvcm #14: ENH: bump version and retool setup for pysal-meta integration #10: addressing pysal #1139 & new libpysal.examples schema tobler #45: MNT: release tooling #44: add pysal integration/import test #43: update docs #40: return dfs #42: Move example data to remotes #41: revisit regression approach #36: generalize regression approach #38: License? #34: wrapper for regression approach #39: update docs #9: sphinx docs #37: remove shap and xgboost as hard deps #35: cosmetic upgrades #33: reorg and add masked_area_interpolate func #31: Move data into data direcotry for examples #32: Environment #8: decide on working notebooks #30: Reorg #29: fix for quilt dep clash #28: quilt3 breakage #26: raise ioerror #24: raise IOError if rasters are missing #25: Rel01 #23: add xgboost approach in tests #22: update readme image from harmonize notebook #21: Add raster regression tests (also small tweak in a notebook) #20: handle "file://" in raster path #19: add quilt dependency #18: extra reqs files #17: update travis #16: turn on travis #15: swap to pytest tests #14: fix url and keywords from setup.py #13: tweak badge link #12: add build and coverage badges in readme #7: remove local paths #5: Drop scanlines (and harmonize) and improve notebooks and include tobler examples notebook (also adds tests and create travis file) #1: put NLCD as default for raster data #4: default to nlcd data from quilt #3: keep input crs mapclassify #43: Remove doc badge #55: REL: update changelog for release. #54: 2.2 #53: 2.2 #52: conda-forge UnsatisfiableError on windows and python 3.7 #49: [MAINT] updating supported Python versions in setup.py #46: BUG: RecursiveError in HeadTailBreaks #45: BUG: HeadTailBreaks raise RecursionError #47: BUG: UserDefined accepts only list if max not in bins #44: BUG: avoid deprecation warning in HeadTailBreaks #42: remove docs badge #41: Docs: moving to project pages on github and off rtd splot #98: Release prep for 1.1.2 #88: Installation instructions; pip install fails on macOS #90: Usage in readme is a fragment #92: JOSS: missing figure captions #96: [DOC] update installation instruction #97: [DOC] add example links to README.md & figure captions in joss article #83: [BUG] vba_choropleth failure #95: BUG: Fix breakage due to mapclassify deprecation #93: addressing pysal/pysal#1145 & adapting testing examples #89: Fix docstring for plot_spatial_weights #59: JOSS paper submission #87: Fix format for multiple citations in JOSS paper #86: Joss paper, finalise title #62: [JOSS] work on paper.md #85: [ENH] change doc badge to latest doc #84: [BUG] require geopandas>=0.4.0,<=0.6.0rc1 for vba_choropleth testing #82: plot_moran_simulation weird dimensions pysal #1157: DOC: update build instructions #1156: Frozen #1152: Metalite #1148: Meta-package not building for 3.6 #1151: Update issue templates #1145: testing submodules' master in .travis.yml #1144: [ENH] Contribute A-DBSCAN #1098: doc typos in pysal.lib.weights.W #1143: Voronoi results in weights of different shape than input points #966: Preserving more than one underscore if present in the original column name. Currently if a column name has more than one underscore, they are smashed into one. #1140: local_moran #889: Approximate spatial weights for barely-touching polygons #1126: Bumping spaghetti version #1135: DOC: update links to repositories feeding into the meta project #1136: Numpy 1.17 #1134: Rtdmove #1131: Use markdown README #1118: Release Notes for PySAL 2.1.0 #1120: Spatial autoregressive processes #1130: Don't use conda-env files with Travis-CI #1129: Updating for docs on RTD Summary Statistics Package Activity package commits total issues pulls spaghetti 348 101 61 libpysal 204 64 37 tobler 187 40 31 pysal 82 21 10 esda 51 14 10 spreg 44 0 0 splot 42 17 11 giddy 42 13 9 segregation 38 23 12 mapclassify 32 12 9 pointpats 25 0 0 spvcm 12 2 2 spint 7 0 0 mgwr 5 0 0 spglm 2 0 0 inequality 1 0 0 Contributor Activity commits Eli Knaap 123 Filipe Fernandes 3 James Gaboardi 385 Leonardo Uieda 1 Levi John Wolf 12 Martin Fleischmann 4 Rahul799 2 Renan Xavier Cortes 60 Serge Rey 308 Siddharths8212376 2 Stefanie Lumnitz 28 Wei Kang 38 Contributor by Package Activity Serge Rey Levi John Wolf James Gaboardi Wei Kang Siddharths8212376 Eli Knaap Renan Xavier Cortes Rahul799 Martin Fleischmann Stefanie Lumnitz Leonardo Uieda Filipe Fernandes libpysal 145 6 43 6 2 0 0 0 0 0 0 0 esda 30 3 6 1 0 2 0 0 0 0 0 0 giddy 2 0 3 26 0 0 0 0 0 0 0 0 inequality 0 0 0 0 0 0 0 0 0 0 0 0 pointpats 0 0 0 0 0 0 0 0 0 0 0 0 segregation 0 0 2 0 0 17 19 0 0 0 0 0 spaghetti 0 0 305 0 0 0 0 2 0 0 0 0 mgwr 0 0 0 0 0 0 0 0 0 0 0 0 spglm 0 0 0 0 0 0 0 0 0 0 0 0 spint 0 0 0 0 0 0 0 0 0 0 0 0 spreg 0 0 0 0 0 0 0 0 0 0 0 0 spvcm 1 2 9 0 0 0 0 0 0 0 0 0 tobler<