Libpysal

We closed a total of 21 issues (enhancements and bug fixes) through 8 pull requests, since our last release on 2018-08-22.

Issues Closed
- 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)

Pull Requests
- Always make spherical KDTrees if radius is passed (117)
- enh: add doctests to travis (2) (112)
- 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)

The following individuals contributed to this release:

- Serge Rey
- Levi John Wolf
- Wei Kang

We closed a total of 52 issues (enhancements and bug fixes) through 18 pull requests, since our last release on 2018-07-15.

Issues Closed
- 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)
- fix hardcoded swm test (86)
- BUG: test_weights_IO.py is using pysal and hard-coded paths (85)
- 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)

Pull Requests
- Lower case module names (98)
- remove function regime_weights (96)
- Ensure consistency in `from .module import *` in components of libpysal (95)
- [WIP] cleanup (88)
- docstrings for attributes are defined in properties (87)
- version name as __version__ (92)
- remove `del` statements and modify alphashape __all__ (89)
- including rtree in imports (91)
- fix hardcoded swm test (86)
- check for spatial index if nonplanar neighbors (84)
- increment version number and add bugfixes, api changes (79)
- Spherebug (82)
- only warn once for islands/disconnected components (83)
- deletion of extra spaces in warning message (78)
- changed geometry column name from a str to an attribute (76)
- add check for disconnected components (65)
- clean up for release (74)
- update for new examples (72)

The following individuals contributed to this release:

- Serge Rey
- Levi John Wolf
- Wei Kang
- James Gaboardi
- Eli Knaap

We closed a total of 38 issues, 7 pull requests and 31 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (7):

* :ghpull:`844`: Geotable plot
* :ghpull:`875`: Spint constant
* :ghpull:`874`: Use standard python facilites for warning
* :ghpull:`873`: updating release schedule
* :ghpull:`871`: Put requirements into setup.py so they are installed if missing
* :ghpull:`870`: Doc/release
* :ghpull:`869`: Dev

Issues (31):

* :ghissue:`844`: Geotable plot
* :ghissue:`877`: documentation links to numpy and scipy are broken
* :ghissue:`875`: Spint constant
* :ghissue:`874`: Use standard python facilites for warning
* :ghissue:`873`: updating release schedule
* :ghissue:`871`: Put requirements into setup.py so they are installed if missing
* :ghissue:`591`: check pysal version and report if a more recent stable version is available
* :ghissue:`410`: prototype LISA cluster map
* :ghissue:`333`: Add k functions
* :ghissue:`274`: Implement LISA in network module
* :ghissue:`746`: Network data structures
* :ghissue:`751`: A method to get a list of example-files by type
* :ghissue:`219`: inconsistent treatment of centroids in arc distance calculations in weights/user.py
* :ghissue:`173`: implement cross sectional and space-time scan statistics
* :ghissue:`170`: centralize all kernel based calculations
* :ghissue:`134`: Complete cg.locators
* :ghissue:`94`: Smoothing: add another module based on model-based smoothing
* :ghissue:`91`: Smoothing: Develop simulations for comparing different smoothers
* :ghissue:`90`: Overhaul Polygon class
* :ghissue:`89`: Optimize shapefile reader
* :ghissue:`88`: Optimize Clockwise test
* :ghissue:`86`: Spatial_Dynamics: LISA Time paths
* :ghissue:`85`: Spatial_Dynamics: modified knox statistic
* :ghissue:`84`: Spatial_Dynamics: Optimize Theta
* :ghissue:`652`: Use cKDtree for Arc_KDTree
* :ghissue:`697`: Update Release Management to Support Rolling Releases
* :ghissue:`761`: Object-oriented design for viz module
* :ghissue:`767`: ZeroDivisonError when calculating certain centroids
* :ghissue:`849`: dbf2df can not read dbf files within which there are Chinese characters
* :ghissue:`870`: Doc/release
* :ghissue:`869`: Dev

We closed a total of 100 issues, 33 pull requests and 67 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (33):

* :ghpull:`864`: addressing issue 845 and adding tests
* :ghpull:`862`: Memory efficient Gini and tests
* :ghpull:`865`: fix space/tab inconsistency
* :ghpull:`861`: GSOC -SpInt
* :ghpull:`847`: spatial interaction weights
* :ghpull:`863`: B859
* :ghpull:`860`: Incoprate updates to db driver and unittests
* :ghpull:`858`: Dev mltest
* :ghpull:`857`: Fix TabErrors, replace tabs with spaces
* :ghpull:`856`: Make the output and build reproducible
* :ghpull:`851`: fixed typo in test_network.py
* :ghpull:`850`: [REBASE] Distance band speed ups
* :ghpull:`843`: update and clean aesthetic of Network_Usage.ipynb
* :ghpull:`842`: typo correction in network.py
* :ghpull:`841`: [REBASE & REDIRECT] Conditional Database Imports & Docos, 692
* :ghpull:`840`: minor bugfix to 816
* :ghpull:`839`: documentation cleanup on network.analysis.py
* :ghpull:`838`: network.util.py documentation cleanup
* :ghpull:`836`: re: network.py documentation cleanup
* :ghpull:`768`: Modified the way area of a ring is calculated to allow for more precision
* :ghpull:`829`: numba autojit _fisher_jenks_means if numba is available
* :ghpull:`832`: Handling a deprecation warning, and latex errors corrected.
* :ghpull:`834`: Travis testing matrix
* :ghpull:`831`: Refactoring Markov classes for efficiency
* :ghpull:`827`: ESDA Tabular Functions
* :ghpull:`823`: typo and format of docstring of user.py in weights module
* :ghpull:`821`: Pdio
* :ghpull:`817`: D/sur
* :ghpull:`818`: Documentation fix + some PEP8 standardization
* :ghpull:`811`: DistanceBand should correctly handle named weights
* :ghpull:`808`: Dev
* :ghpull:`807`: Updating contrib docs and bumping version for dev
* :ghpull:`797`: working moran plot func

Issues (67):

* :ghissue:`855`: Inefficient Gini Coefficient calculation?
* :ghissue:`864`: addressing issue 845 and adding tests
* :ghissue:`862`: Memory efficient Gini and tests
* :ghissue:`865`: fix space/tab inconsistency
* :ghissue:`861`: GSOC -SpInt
* :ghissue:`847`: spatial interaction weights
* :ghissue:`859`: Wrong there is one disconnected observation (no neighbors)
* :ghissue:`863`: B859
* :ghissue:`860`: Incoprate updates to db driver and unittests
* :ghissue:`858`: Dev mltest
* :ghissue:`857`: Fix TabErrors, replace tabs with spaces
* :ghissue:`854`: handle verication context for githubstats
* :ghissue:`856`: Make the output and build reproducible
* :ghissue:`851`: fixed typo in test_network.py
* :ghissue:`850`: [REBASE] Distance band speed ups
* :ghissue:`846`: DistanceBand speed ups
* :ghissue:`843`: update and clean aesthetic of Network_Usage.ipynb
* :ghissue:`842`: typo correction in network.py
* :ghissue:`692`: Conditional Database Import / Docos
* :ghissue:`841`: [REBASE & REDIRECT] Conditional Database Imports & Docos, 692
* :ghissue:`769`: Windows 7, 64 bit installation issue with visual C++ for python
* :ghissue:`816`: Exception TypeError in geoda_txt.py
* :ghissue:`840`: minor bugfix to 816
* :ghissue:`839`: documentation cleanup on network.analysis.py
* :ghissue:`397`: integrate optimized contiguity builder
* :ghissue:`531`: add user space function to generate numpy arrays
* :ghissue:`654`: meta update for 2-3 conversion
* :ghissue:`676`: Meta not importable from pysal
* :ghissue:`838`: network.util.py documentation cleanup
* :ghissue:`753`: Fix the network ring bug
* :ghissue:`836`: re: network.py documentation cleanup
* :ghissue:`768`: Modified the way area of a ring is calculated to allow for more precision
* :ghissue:`837`: re: network.allneighbordistances() diagonal fill
* :ghissue:`822`: two issues about function choropleth_map in viz module
* :ghissue:`835`: fix deprecation warnings noted in 822
* :ghissue:`829`: numba autojit _fisher_jenks_means if numba is available
* :ghissue:`832`: Handling a deprecation warning, and latex errors corrected.
* :ghissue:`834`: Travis testing matrix
* :ghissue:`825`: Headbanging Median Rate ignores edge correction
* :ghissue:`826`: Spatial Filtering grid definition
* :ghissue:`824`: Direct Age Standardization fails for empty regions
* :ghissue:`833`: PySAL+ optional testing matrix
* :ghissue:`830`: [REBASED] PySAL+ optional testing matrix
* :ghissue:`831`: Refactoring Markov classes for efficiency
* :ghissue:`827`: ESDA Tabular Functions
* :ghissue:`815`: rook case not working in ContiguityWeightsPolygons
* :ghissue:`828`: Fisher_Jenks pure python implementation is too slow
* :ghissue:`814`: Explore Classmethods for alternative constructors
* :ghissue:`795`: switch to scipy.linalg instead of numpy.linalg
* :ghissue:`799`: w_subset(weights:W, ids:np.ndarray) constructs faulty weights object
* :ghissue:`823`: typo and format of docstring of user.py in weights module
* :ghissue:`821`: Pdio
* :ghissue:`794`: spreg ML_lag doesn't always set W in __init__
* :ghissue:`754`: Update README
* :ghissue:`819`: add LIMAs
* :ghissue:`817`: D/sur
* :ghissue:`818`: Documentation fix + some PEP8 standardization
* :ghissue:`809`: Fixed documentation
* :ghissue:`813`: w.remap_ids(ids) never sets w.id_order_set
* :ghissue:`775`: Added a prototype for constructing weights from a list of shapely Polygons
* :ghissue:`810`: DistanceBand fails to accept custom ids
* :ghissue:`811`: DistanceBand should correctly handle named weights
* :ghissue:`780`: Doctests failing on travis
* :ghissue:`801`: ImportError: No module named scipy.spatial
* :ghissue:`808`: Dev
* :ghissue:`807`: Updating contrib docs and bumping version for dev
* :ghissue:`797`: working moran plot func

We closed a total of 20 issues, 6 pull requests and 14 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (6):

* :ghpull:`805`: pre Rel1.11.2 and 840
* :ghpull:`802`: fixed issues with model handler failing to correctly discover models
* :ghpull:`798`: fix for css problem on rtd 790
* :ghpull:`793`: Getting weights doctests to pass
* :ghpull:`791`: Doc/rolling
* :ghpull:`792`: Local Moran was using the incorrect moments in z_sim and p_z_sim

Issues (14):

* :ghissue:`805`: pre Rel1.11.2 and 840
* :ghissue:`803`: check_contiguity error..
* :ghissue:`802`: fixed issues with model handler failing to correctly discover models
* :ghissue:`800`: `ps.threshold_continuousW_from_shapefile` returning inf along diagonal
* :ghissue:`771`: KDtree type mismatch in knnW
* :ghissue:`798`: fix for css problem on rtd 790
* :ghissue:`796`: working moran plot func
* :ghissue:`787`: Update docs to reflect Python-3 compatibility
* :ghissue:`587`: ML Lag indexing error on optimization result
* :ghissue:`793`: Getting weights doctests to pass
* :ghissue:`791`: Doc/rolling
* :ghissue:`792`: Local Moran was using the incorrect moments in z_sim and p_z_sim
* :ghissue:`674`: Have PySAL included on OSGeo Live 9
* :ghissue:`779`: DistanceBand include the point itself as neighbor

We closed a total of 62 issues, 20 pull requests and 42 regular issues;
this is the full list (generated with the script
:file:`tools/github_stats.py`):

Pull Requests (20):

* :ghpull:`777`: fix minor issues with using stdlib warnings in mapclassify.py
* :ghpull:`766`: Constant check
* :ghpull:`781`: Dev
* :ghpull:`778`: Wkb
* :ghpull:`776`: Updating & find-bin-as-call for Map_Classifiers
* :ghpull:`770`: adding github chrome to make project contributions easier to handle
* :ghpull:`764`: add folium changes needed for notebook to run
* :ghpull:`760`: Update docs for 697
* :ghpull:`763`: docs fix: incorrect array dimensions listed for spatial interaction SpaceTimeEvents
* :ghpull:`756`: B726
* :ghpull:`749`: remove cruft in git root and add gitter badge to the readme
* :ghpull:`748`: Replace deprecated np.rank with np.ndim
* :ghpull:`745`: Lag Categorical & Find Bins
* :ghpull:`741`: fix for 740
* :ghpull:`739`: Dev
* :ghpull:`738`: fixing master version
* :ghpull:`737`: Bumping dev
* :ghpull:`736`: Merge pull request 734 from sjsrey/master
* :ghpull:`735`: Dev in sync with master for 1.11