PySAL 23.01, 2023-01-30

Overall, there were 479 commits that closed 205 issues, together with 19 pull requests since our last release on 2022-07-31.

Highlights

Version numbering has switched to YR.MO for the pysal meta-package release.
The spopt package added a LSCP-B formulation and the P-Dispersion model through the excellent GSoC project by Erin Olson

Changes by Package

libpysal

#488: type vs. geom_type with shapely
#487: address ShapelyDeprecationWarning The 'type' attribute is...
#485: allow for individual downloads and access to remote urls in examples
#486: ENH: more granularity in example handling
#482: test against shapely prerelease
#479: Creating Weights from dataframe: IndexError: index 0 is out of bounds for axis 0 with size 0
#483: Networkx3.0
#481: Platformdirs
#478: Updates warnings, etc.
#391: Test failures with GEOS 3.9.0

access

esda

giddy

inequality

pointpats

segregation

spaghetti

#701: another release_and_publish.yml failures (due to pyproject.toml)
#703: Update Versioneer
#700: Update Versioneer
#702: add formatting exclusions properly in toml
#699: Update Versioneer
#698: Update Versioneer
#697: try versioneer action
#696: remove pygeos from environments
#680: remove pygeos
#695: supplement setup.py with a name kwarg for dep graph
#694: add name keyword in setup.py
#693: [pre-commit.ci] pre-commit autoupdate
#692: [pre-commit.ci] pre-commit autoupdate
#690: try pyproject.toml; remove setup.cfg
#691: [pre-commit.ci] pre-commit autoupdate
#689: [pre-commit.ci] pre-commit autoupdate
#688: adjust css for doc references
#687: esda master -> main
#686: update sphinx tooling, etc.
#685: 1st attempt for Python 3.11 testing
#684: [pre-commit.ci] pre-commit autoupdate
#683: Bump actions/setup-python from 3 to 4
#682: add linting in CI
#681: Try out pre-commit.ci
#679: Test against shapely pre-release
#678: test against shapely==2.0b1
#677: rerun notebooks
#676: Update warnings, etc.

mgwr

momepy

#422: RLS: add 0.5.4 changelog
#420: Add pyproject.toml file
#415: add a project.toml?
#419: proof README.md
#416: Scour docs for consistency, grammar, etc.
#414: scour docstrings (grammar, punctuation, etc.)
#418: GHA: update PyPI release action
#413: add flake8 and isort to CI
#412: enhance CI with flake8 & isort
#409: BUG: get_network_ratio non-interescting joins fix
#408: BUG: get_network_ratio returns wrong ID for non-intersecting join
#410: minor spelling and punctuation update
#392: ENH: roundabout_simplification() notebook example
#407: CI: test preprocessing part of user guide
#405: Run user guide tests with Python 3.10
#403: remove pygeos duplicate
#400: standardize pytest.approx() in testing files
#404: bump copyright year
#402: pygeos occurs twice in asv.conf.json - matrix
#401: test user guide against Python 3.10?
#399: both pytest.approx() and approx() used in testing
#398: Fix various warnings
#397: Fix thrown warnings in dimension, elements, diversity
#395: handle All NaN slice warning
#394: Handle All-NaN slice encountered warning in diversity.Percentiles()
#390: limit numpy version evaluations in diversity.Percentiles
#393: DOC: create preprocessing section
#388: suppress warnings in dimensions.StreetProfile()
#389: handle scenarios leading to dimensions.StreetProfile() warnings
#391: Rabs geom
#386: numpy. nanpercentile() has a renamed keyword
#383: update .append method for dataframes
#382: REF: remove deprecated pandas append
#384: REF: replace append with concat
#387: address numpy.nanpercentile warning
#385: DOC: temporarily pin theme
#371: ENH: geometry-based simplification of roundabouts
#379: Added warning for gdp_to_nx if geometries are not LineStrings
#378: BUG: make coins independent of gdf index
#373: DOC: compat with latest sphinx pydata theme
#362: DOC: broken colours with new pydata_sphinx_theme

spglm

spint

spreg

#108: update gitcount and conf.py
#107: update workflows/ci
#100: update tools/gitcount notebook
#105: Fixing failed tests for new release
#104: Version update

spvcm

tobler

mapclassify

#165: Update Versioneer
#167: Try skipping certain files with isort
#166: update master/main link issue
#164: Update Versioneer
#163: Update infrastructure (actions)
#162: GHA for updating versioneer
#161: update branch of gh-action-pypi-publish
#37: Add VBA functionality
#159: [pre-commit.ci] pre-commit autoupdate
#158: [pre-commit.ci] pre-commit autoupdate
#157: [pre-commit.ci] pre-commit autoupdate
#156: [pre-commit.ci] pre-commit autoupdate
#142: MaxP.update() – bins used by not defined
#155: Remove update method from MaxP
#154: Use libpysal.fuzzy_contiguity() in greedy
#148: swap greedy. _geos_sw() for libpysal.fuzzy_contiguity
#135: Thorough scouring of docs + doc build infrastructure
#141: love and care for docstrings, etc.
#152: ENH: addressing #145
#153: remove spaces after table string title
#145: remove spaces from title of classifier table string
#150: Switch to pytest
#146: convert from unittest to pytest
#147: improve warnings and exceptions
#140: warn or raise vs. print statements for unexpected behavior
#151: [pre-commit.ci] pre-commit autoupdate
#149: silence warnings option when k classes not possible?
#144: update GHA for CI
#143: remove _table_string() method
#139: remove old/redundant MapClassifier._table_string() method
#138: Bump actions/checkout from 2 to 3
#137: Bump codecov/codecov-action from 2 to 3
#136: update release action, etc.
#105: Fix changelog builder to give proper attribution
#134: updating branch in badges on README
#133: resolves #132
#132: update binder environment
#129: RuntimeWarning: invalid value encountered in double_scalars
#131: ENH: handle invariant arrays
#112: plot doesn't work for pooled classifications
#130: change default branch from master to main
#128: [MAINT] lint & format repo; update CI; handle DeprWarns, etc.

splot

spopt

#276: P-Median Problem Tutorial Binder example
#344: Add requirements_notebooks.txt to MANIFEST
#343: The requirementes notebook is missing from the MANIFEST.in
#342: Update Versioneer
#340: add versioneer action
#339: add a GHA for updating versioneer
#338: Update release_and_publish.yml
#337: update branch of gh-action-pypi-publish
#336: [BUG] bounds for client assignment variables
#328: [BUG] client assignment variable bounds for CLSCP-SO
#329: Clean up the implementation of the capacitated LSCP
#320: clean up CLSCP-SO implementation
#335: polish up docstrings, etc. in skater.py
#333: [BUG] affinity in Skater spanning forest
#332: customize tqdm progress bar in Skater
#321: [BUG] using affinity in skater.SpanningForest
#334: doc build env correction
#330: Update sphinx requirement from <=4.5.0 to <6.2.0
#309: workaround for cascading references in docs
#327: Update sphinx requirement from <=4.5.0 to <6.1.0
#324: individual locate test, tqdm, & bare minimal testing env
#323: test against a minimal / bare bones environment
#322: add tqdm as on optional req
#318: break out test_locate.py
#234: Factoring in Facility Capacities
#319: Streamline redundant parameter passing in constraint constructors
#317: streamline variable and constraint creation
#7: input is not sanitised before it is used
#316: Fix CLSCP-SO bugs and add tests
#315: raise if demand > capacity in CLSCP-SO
#314: [BUG] service radius threshold not respected in CLSCP-SO
#273: Facility capacity for LSCP
#313: [pre-commit.ci] pre-commit autoupdate
#307: doc work and formatting continued (random_region, util, ward)
#312: expose SPENC kwargs
#310: remove external spenc from CI envs
#172: Allow passing all keywords into Spenc
#305: utilize BaseSpOptExactSolver
#306: Update sphinx requirement from <=4.5.0 to <5.4.0
#302: start of doc work – focusing on locate docs
#304: update locate images & add tutorial links
#300: doc work and cleanup -- add locate formulations to docstrings
#296: New attributes & functionality for locate models
#287: calculate get_percentage() within MCLP.solve(results=True)
#286: calculate get_mean_distance() within PMedian.solve(results=True)
#285: remove BaseOutputMixin from PDispersion
#283: get_backup_percentage method for LSCP-B
#282: maybe set solver as attribute in LSCPB?
#267: pre-defined facilities for all location models?
#301: [pre-commit.ci] pre-commit autoupdate
#294: Region-k-means seed
#213: K means heuristic test failure
#297: keep or remove RegionMixin
#215: maximum-coverage-location package
#293: remove pip install in notebooks
#290: more issues with binder for locate notebooks
#292: Drop Py37, update binders, & test future shapely dev
#291: update shapely_dev testing
#284: drop testing/support for Python 3.7
#288: Update/cleanup/standardize notebooks
#289: test spopt against the shapely==2.0b1
#269: update docs for new location models
#57: Throws an error when silhoutte coefficients for two clusters are the same
#187: The dissimilarity parameter should be able to accept a distance/dissimilarity matrix as an alternative to a callable distance function
#188: [WIP] allow for precomputed distance matrices
#263: LSCP Notebook Plots
#21: differentiating spatial clusterers
#281: comparing the LSCP and LSCP-B results
#278: AttributeError: type object 'FacilityModelBuilder' has no attribute 'add_maximized_min_variable'
#279: testing overhaul, etc
#260: GSoC 2022 Interfaces for Consistent API Design
#277: .coverage in .gitignore
#265: Add .coverage to .gitignore
#268: P dispersion
#275: Update typo in p-median example
#259: LSCP-B
#271: Lscpb formulation
#270: LSCP-B formulation?
#272: Rewrite LSCPB formulation

Contributors

Many thanks to all of the following individuals who contributed to this release:

Andres Morfin Veytia
Erin Olson
Germano Barcelos
Greg Maya
James Gaboardi
Levi John Wolf
Martin Fleischmann
Nick Bearman
Pedro Amaral
Serge Rey

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Release v23.01