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Geographs #563

Merged
merged 230 commits into from
Sep 7, 2023
Merged

Geographs #563

merged 230 commits into from
Sep 7, 2023

Commits on Apr 4, 2021

  1. start geographs

    @ljwolf
    ljwolf committed Apr 4, 2021
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  2. Add start of workbench notebook

    @darribas
    darribas committed Apr 4, 2021
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  3. Merge pull request #392 from pysal/upstream/geographs 

    Add start of workbench notebook
    @darribas
    darribas committed Apr 4, 2021
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  4. finish skeleton of an xarray weights impl

    @ljwolf
    ljwolf committed Apr 4, 2021
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  5. Merge pull request #395 from ljwolf/geographs 

    xarray geograph implementation
    @sjsrey
    sjsrey committed Apr 4, 2021
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  6. Draft of adjacency table as df

    @sjsrey
    sjsrey committed Apr 4, 2021
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Commits on Apr 6, 2021

  1. Update w_workbench.ipynb

    @martinfleis
    martinfleis committed Apr 6, 2021
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Commits on Apr 8, 2021

  1. Merge pull request #398 from martinfleis/workbench 

    Expand weights benchmark
    @ljwolf
    ljwolf committed Apr 8, 2021
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  2. handle directed links in adjlist

    @ljwolf
    ljwolf committed Apr 8, 2021
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  3. add convenience from_w method

    @ljwolf
    ljwolf committed Apr 8, 2021
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  4. Merge pull request #397 from sjsrey/geographs 

    Draft of adjacency table as df
    @ljwolf
    ljwolf committed Apr 8, 2021
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Commits on May 25, 2023

  1. Merge branch 'main' of github.com:pysal/libpysal into geographs

    @ljwolf
    ljwolf committed May 25, 2023
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  2. move graphs to weights/experimental

    @ljwolf
    ljwolf committed May 25, 2023
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  3. consolidate on simple wdf

    @ljwolf
    ljwolf committed May 25, 2023
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  4. update roadmap

    @ljwolf
    ljwolf committed May 25, 2023
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  5. Update ROADMAP.md

    @martinfleis
    martinfleis committed May 25, 2023
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  6. start stubs for four builder classes

    @ljwolf
    ljwolf committed May 25, 2023
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  7. rewrite as multi-indexed series

    @martinfleis
    martinfleis committed May 25, 2023
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  8. transform

    @martinfleis
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  9. docs

    @martinfleis
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  10. dict output and components

    @martinfleis
    martinfleis committed May 25, 2023
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  11. add contiguity builders with simplified methods for new shapely

    @ljwolf
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  12. defunct higher order

    @martinfleis
    martinfleis committed May 25, 2023
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  13. SQUASHME: stashing temporarily to write sparse.linalg.matrix_power

    @ljwolf
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  14. from sparse, cardinalities

    @martinfleis
    martinfleis committed May 25, 2023
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  15. from_arrays

    @martinfleis
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  16. from_weights_dict

    @martinfleis
    martinfleis committed May 25, 2023
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  17. get vertex set back to a working state and fix rook misamtch

    @ljwolf
    ljwolf committed May 25, 2023
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  18. nnz, cardinalities

    @martinfleis
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  19. continuity pipe in

    @martinfleis
    martinfleis committed May 25, 2023
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  20. ensure numeric dtype on weight

    @martinfleis
    martinfleis committed May 25, 2023
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  21. add ids to from_sparse

    @martinfleis
    martinfleis committed May 25, 2023
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Commits on May 26, 2023

  1. finalise implementations of constructors

    @ljwolf
    ljwolf committed May 26, 2023
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  2. use dataframe

    @martinfleis
    martinfleis committed May 26, 2023
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  3. fixup for a new structure

    @martinfleis
    martinfleis committed May 26, 2023
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  4. lag

    @martinfleis
    martinfleis committed May 26, 2023
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  5. typo

    @martinfleis
    martinfleis committed May 26, 2023
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  6. remove cache

    @martinfleis
    martinfleis committed May 26, 2023
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  7. add kernel options to triangulation weights

    @ljwolf
    ljwolf committed May 26, 2023
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  8. use _validate_geometry_input() throughout

    @ljwolf
    ljwolf committed May 26, 2023
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  9. asymmetry

    @martinfleis
    martinfleis committed May 26, 2023
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  10. Merge branch 'geographs' of https://github.com/pysal/libpysal into ge… 

    …ographs
    @martinfleis
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  11. asymmetry as a series

    @martinfleis
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  12. cannot assign to none in dict constructor

    @ljwolf
    ljwolf committed May 26, 2023
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  13. make private

    @martinfleis
    martinfleis committed May 26, 2023
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  14. contiguity

    @martinfleis
    martinfleis committed May 26, 2023
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  15. fix import after refactor

    @martinfleis
    martinfleis committed May 26, 2023
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  16. todo

    @martinfleis
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  17. initialise base tests

    @ljwolf
    ljwolf committed May 26, 2023
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  18. rename function to kernel

    @ljwolf
    ljwolf committed May 26, 2023
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  19. move test of validation out of base into utils

    @ljwolf
    ljwolf committed May 26, 2023
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  20. todo islands

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  21. Merge branch 'geographs' of https://github.com/pysal/libpysal into ge… 

    …ographs
    @martinfleis
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  22. include geodatasets in the env

    @martinfleis
    martinfleis committed May 26, 2023
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  23. bump shapely

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    martinfleis committed May 26, 2023
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  24. specific pin

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Commits on May 27, 2023

  1. todo

    @martinfleis
    martinfleis committed May 27, 2023
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  2. start on testing contiguity

    @ljwolf
    ljwolf committed May 27, 2023
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  3. add full start to tests in contiguity and stubs for others

    @ljwolf
    ljwolf committed May 27, 2023
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  4. finalise most tests

    @ljwolf
    ljwolf committed May 27, 2023
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  5. add final contiguity test

    @ljwolf
    ljwolf committed May 27, 2023
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  6. add docs

    @ljwolf
    ljwolf committed May 27, 2023
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  7. add docstrings

    @ljwolf
    ljwolf committed May 27, 2023
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  8. fix docstrings

    @ljwolf
    ljwolf committed May 27, 2023
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  9. finish testing matrix with explicit id checks

    @ljwolf
    ljwolf committed May 27, 2023
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  10. add start of set ops mixin to make comparisons more rigorous

    @ljwolf
    ljwolf committed May 27, 2023
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  11. rename equality to be more evocative

    @ljwolf
    ljwolf committed May 27, 2023
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Commits on May 30, 2023

  1. finalize api for _set_ops.py

    @ljwolf
    ljwolf committed May 30, 2023
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  2. make _identical private

    @ljwolf
    ljwolf committed May 30, 2023
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Commits on Jun 15, 2023

  1. minor housekeeping

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    martinfleis committed Jun 15, 2023
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Commits on Jun 16, 2023

  1. add testbench for the triangulation and kernel weights

    @ljwolf
    ljwolf committed Jun 16, 2023
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  2. update docstring for voronoi function

    @ljwolf
    ljwolf committed Jun 16, 2023
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Commits on Jul 18, 2023

  1. ensure contiguity weghts are int

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    martinfleis committed Jul 18, 2023
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  2. handle islands properly

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    martinfleis committed Jul 18, 2023
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  3. furher island handling

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    martinfleis committed Jul 18, 2023
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  4. higher order as not implemented

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    martinfleis committed Jul 18, 2023
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  5. Merge remote-tracking branch 'upstream/main' into geographs

    @martinfleis
    martinfleis committed Jul 18, 2023
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  6. comment out unused WIP tests

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    martinfleis committed Jul 18, 2023
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Commits on Jul 26, 2023

  1. add dummy constructors

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Commits on Jul 28, 2023

  1. from to build

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  2. rename to Graph and move namespace

    @martinfleis
    martinfleis committed Jul 28, 2023
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  3. test init

    @martinfleis
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  4. add todo

    @martinfleis
    martinfleis committed Jul 28, 2023
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  5. update graph namespace

    @sjsrey
    sjsrey committed Jul 28, 2023
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  6. rename from_kernel to build_kernel

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    sjsrey committed Jul 28, 2023
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Commits on Jul 29, 2023

  1. to_W and from_W

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  2. handle diagonals and islands

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  3. bump pandas min to 1.5

    @martinfleis
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  4. revert pandas bump (the issue is in test setup)

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  5. test from_sparse

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Commits on Jul 30, 2023

  1. input data validation

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  2. test from_arrays

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  3. test from dicts

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  4. islands to isolates

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  5. neighbors, weights

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  6. fix __eq__ and use in tests, add copy, fix sparse

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  7. remove imoprt

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  8. copy

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  9. more property tests

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  10. test and fix transform

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  11. test asymmetry

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  12. possible fix for old pandas

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Commits on Jul 31, 2023

  1. resolve review comments

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  2. Merge remote-tracking branch 'upstream/main' into geographs

    @martinfleis
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  3. Merge branch 'geographs' into test_graph_class

    @martinfleis
    martinfleis committed Jul 31, 2023
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  4. uncomment test

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    martinfleis committed Jul 31, 2023
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  5. old numpy compat fix

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    martinfleis committed Jul 31, 2023
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Commits on Aug 3, 2023

  1. Merge pull request #536 from martinfleis/test_graph_class 

    Test graph class
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  2. Merge branch 'geographs' into pr/sjsrey/537

    @martinfleis
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  3. avoid pytest-xdist

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  4. compat pandas<1.5

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  5. loosen dtype checks to accodomate win default

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  6. try fixing windows again

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  7. i hate windows

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  8. fix that fix of a fix

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  9. one more

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  10. bring back -n

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Commits on Aug 4, 2023

  1. Merge pull request #541 from martinfleis/graph_tests_fix

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Commits on Aug 6, 2023

  1. Merge remote-tracking branch 'upstream/geographs' into pr/sjsrey/537

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  2. Merge pull request #537 from sjsrey/geographs 

    Geographs _triangulation weights
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  3. expose triangulation in build_triangulation

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  4. fix scipy imports

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  5. support string ids

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  6. fix sparse

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  7. fix unique_ids to preserve order of sparse

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  8. expose kernel and knn

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  9. fix from_sparse to ensure proper sorting

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  10. incorporate review comments

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  11. add geodatasets to test reqs

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  12. _VALID_GEOMETRY_TYPES as lists

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  13. add docstrings

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Commits on Aug 7, 2023

  1. Merge pull request #542 from martinfleis/constructors 

    graph.Graph build_* constructors
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  2. Merge remote-tracking branch 'upstream/main' into geographs

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  3. add distance_band

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  4. channel distance band through kernel

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  5. fix isolates in distance band

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Commits on Aug 8, 2023

  1. clarify Graph.asymmetry() docstring

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  2. Merge pull request #546 from jGaboardi/graph_asymm_docstring 

    clarify `Graph.asymmetry()` docstring
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Commits on Aug 10, 2023

  1. lag, parquet IO, __getitem__, block placeholder

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  2. docstrings, optional pyarrow

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  3. fix test

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  4. [WIP] start intercepting coincidence, probably should use a decorator… 

    … instead
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  5. block contiguity

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  6. add tests

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  7. to-dos

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  8. Apply suggestions from code review 

    Co-authored-by: James Gaboardi <[email protected]>
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  9. test block_contiguity

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  10. test parquet without meta

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  11. test lag

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Commits on Aug 11, 2023

  1. haversine todo note

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  2. comment on diag

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  3. finalize decorator implementation for _triangulation

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  4. finish jitter implementation

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  5. propagate coincident to build_triangulation

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  6. add reasons to assert clauses

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  7. voronoi should still admit kernels

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  8. move to None for defaults, not boxcar/inf

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  9. Merge pull request #544 from martinfleis/more_constructors 

    expand graph.Graph constructors and other functionality
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  10. add distance_band

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  11. channel distance band through kernel

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  12. fix isolates in distance band

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  13. lag, parquet IO, __getitem__, block placeholder

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  14. docstrings, optional pyarrow

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  15. fix test

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  16. block contiguity

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  17. add tests

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  18. to-dos

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  19. Apply suggestions from code review 

    Co-authored-by: James Gaboardi <[email protected]>
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  20. test block_contiguity

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  21. test parquet without meta

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  22. test lag

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  23. haversine todo note

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  24. comment on diag

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  25. [WIP] work through integrations of kernel and triangulation in prep t… 

    …o rebase
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  26. move back to upstream kernel

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  27. migrate checks for arrays, complete test battery

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  28. Merge remote-tracking branch 'upstream/geographs' into geographs

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  29. fix docstrings

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  30. Update libpysal/graph/_triangulation.py 

    Co-authored-by: James Gaboardi <[email protected]>
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Commits on Aug 22, 2023

  1. fix to_W

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  2. Merge pull request #551 from martinfleis/geog_cont 

    BUG: fix Graph.to_W
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Commits on Aug 23, 2023

  1. pass id_order as a list

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Commits on Aug 25, 2023

  1. remove unused import

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  2. document coincident option for graph

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  3. add coincidence checks to knn

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  4. Merge pull request #2 from sjsrey/ljwgeographs 

    document coincident option for graph
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  5. Update libpysal/graph/_utils.py 

    Co-authored-by: James Gaboardi <[email protected]>
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  6. Update libpysal/graph/_utils.py 

    Co-authored-by: James Gaboardi <[email protected]>
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  7. Update libpysal/graph/_utils.py 

    Co-authored-by: James Gaboardi <[email protected]>
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  8. finalize coincident checks in knn

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  9. add the reorder table function to base, prepare for sorting inputs to… 

    … weights
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  10. handle ids is none

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  11. Merge pull request #548 from ljwolf/geographs 

    Intercept Coincident points
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  12. tests for clique policy in triangulation weights

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  13. fix piping of constructors to Graph after #548 (#553) 

    * piping

* fix stuff
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  14. Merge remote-tracking branch 'upstream/geographs' into pr/sjsrey/552

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  15. lint

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  16. numpy 1.25 compat

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  17. Merge pull request #552 from sjsrey/geographs 

    tests for clique policy in triangulation weights
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  18. reformat and comment decorator

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Commits on Aug 26, 2023

  1. authors

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Commits on Aug 28, 2023

  1. fix distance band

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  2. triangulation sorting and tests

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  3. enforce sorting along both focal and neighbor

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Commits on Sep 1, 2023

  1. Merge pull request #554 from martinfleis/coindicent_tests

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  2. reorder

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  3. pivot to sparse

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  4. sort labels

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  5. from adjacency

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  6. formatting

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Commits on Sep 2, 2023

  1. from_adjacency tests

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  2. tweak adj test

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Commits on Sep 4, 2023

  1. rm unnecessary sort, ruff imports

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Commits on Sep 5, 2023

  1. adjacency as mutliindex series

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Commits on Sep 6, 2023

  1. bump min pandas to 1.4

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  2. Merge pull request #557 from martinfleis/adj_series 

    adjacency as mutliindex series
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  3. minor cleanups

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Commits on Sep 7, 2023

  1. Merge pull request #559 from martinfleis/cleanup

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  2. Merge remote-tracking branch 'upstream/main' into geographs

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  3. fix scipy query compat

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  4. perimeter weights in contiguity

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  5. remove lat2Graph

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  6. fix kernel (was weirdly sorted)

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  7. set ops

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  8. raise not implemented for set ops apart from ==

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  9. try setting precision on perimeter weights

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    martinfleis committed Sep 7, 2023
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  10. fix perimeter weights

    @martinfleis
    martinfleis committed Sep 7, 2023
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  11. enable issubraph and issupergraph

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    martinfleis committed Sep 7, 2023
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  12. Merge pull request #561 from martinfleis/gg_cont 

    perimeter weights, fix kernel, set_ops
    @ljwolf
    ljwolf committed Sep 7, 2023
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  13. remove roadmap and workbench

    @martinfleis
    martinfleis committed Sep 7, 2023
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