Merge pull request #288 from jGaboardi/rerun_notebooks

Update/cleanup/standardize notebooks

Author: jGaboardi

.ci/310-DEV_shapely20b1.yaml

@@ -0,0 +1,23 @@
+name: test
+channels:
+  - conda-forge
+  - conda-forge/label/shapely_dev
+dependencies:
+  - python=3.10
+  - geopandas>=0.12.0
+  - matplotlib
+  - networkx
+  - numpy>=1.3
+  - pandas>=1
+  - pip
+  - scikit-learn>=0.22
+  - scipy>=1.0
+  - shapely==2.0b1
+  - spenc
+  - spaghetti
+  # testing
+  - codecov
+  - coverage
+  - pytest
+  - pytest-cov
+  - pytest-xdist

.github/workflows/unittests.yml

@@ -18,12 +18,13 @@
      strategy:
        matrix:
          os: [ubuntu-latest]
-         environment-file: [.ci/37.yaml, .ci/38.yaml, .ci/39.yaml, .ci/310.yaml, .ci/310-DEV.yaml]
+         environment-file: [.ci/37.yaml, .ci/38.yaml, .ci/39.yaml, .ci/310.yaml, .ci/310-DEV.yaml, .ci/310-DEV_shapely20b1.yaml]
          include:
            - environment-file: .ci/310.yaml
              os: macos-latest
            - environment-file: .ci/310.yaml
              os: windows-latest
+       fail-fast: false
 
      steps:
        - name: checkout repo
@@ -34,6 +35,8 @@
          with:
            environment-file: ${{ matrix.environment-file }}
            micromamba-version: 'latest'
+           channel-priority: 'flexible'
+
        - name: install pulp via pip
          shell: bash -l {0}
          run: pip install pulp 

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
-repos: 
--   repo: https://github.com/ambv/black
-    rev: 21.12b0
-    hooks: 
+repos:
+-   repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
     - id: black
-      language_version: python3.9
+      language_version: python3

README.md

@@ -113,6 +113,15 @@ You may also install the latest stable spopt via conda-forge channel by running:
 $ conda install --channel conda-forge spopt
 ```
 
+## Related packages
+
+* Region
+* Locate
+  * [`allagash`](https://github.com/apulverizer/allagash)
+  * [`maximum-coverage-location`](https://github.com/cyang-kth/maximum-coverage-location)
+  * [`p-center`](https://github.com/antoniomedrano/p-center)
+  * [`pyspatialopt`](https://github.com/apulverizer/pyspatialopt)
+
 ## Contribute
 
 PySAL-spopt is under active development and contributors are welcome.

docs/_static/references.bib

@@ -2,16 +2,63 @@
 %% Saved with string encoding Unicode (UTF-8) 
 
 
-@article{wei2020efficient,
-  title={Efficient Regionalization for Spatially Explicit Neighborhood Delineation},
-  author={Wei, R and Rey, SJ and Knaap, E},
-  journal={International Journal of Geographical Information Science},
-  pages={1--17},
-  year={2020},
-  publisher={Taylor \& Francis},
-  doi={10.1080/13658816.2020.1759806},
+@article{assunccao2006efficient,
+  title={Efficient Regionalization Techniques for Socio-economic Geographical Units Using Minimum Spanning Trees},
+  author={Assunção, RM and Neves, MC and Câmara, G and da Costa Freitas, C},
+  journal={IJGIS},
+  volume={20},
+  number={7},
+  pages={797--811},
+  year={2006},
+  doi={10.1080/13658810600665111},
+  publisher={Taylor \& Francis}
+}
+
+
+@article{calik_labbé_yaman_2015, 
+  author={Calik, Hatice and Labbé, Martine and Yaman, Hande},
+  title={p-Center Problems}, 
+  journal={Location Science},
+  pages={79–92},
+  year={2015},
+  doi={10.1007/978-3-319-13111-5_4},
+}
+
+
+@article{chen_murray_jiang_2021,
+  author={Chen, Huanfa and Murray, Alan T. and Jiang, Rui},
+  title={Open-source approaches for location cover models: capabilities and efficiency},
+  journal={Journal of Geographical Systems},
+  doi={10.1007/s10109-021-00350-w},
+  year={2021}
+}
+
+
+@book{church_murray_2018, 
+  author={Church, Richard L. and Murray, Alan T.},
+  title={Location covering models: history, applications and advancements}, 
+  publisher={Springer},  
+  year={2018},
+}
+
+
+@article{daskin_stern_edmund_1981,
+author = {Daskin, Mark S. and Stern, Edmund H.},
+title = {A Hierarchical Objective Set Covering Model for Emergency Medical Service Vehicle Deployment},
+journal = {Transportation Science},
+doi = {10.1287/trsc.15.2.137},
+year = {1981}
+}
+
+
+@book{daskin_2013, 
+  author={Daskin, Mark S.},
+  title={Network and discrete location: models, algorithms, and applications}, 
+  publisher={John Wiley & Sons, Inc.}, 
+  year={2013},
 }
 
+
 @article{duque2011p,
   title={The p-Regions Problem},
   author={Duque, JC and Church, RL and Middleton, RS},
@@ -24,27 +71,6 @@ @article{duque2011p
   doi={10.1111/j.1538-4632.2010.00810.x},
 }
 
-@article{assunccao2006efficient,
-  title={Efficient Regionalization Techniques for Socio-economic Geographical Units Using Minimum Spanning Trees},
-  author={Assunção, RM and Neves, MC and Câmara, G and da Costa Freitas, C},
-  journal={IJGIS},
-  volume={20},
-  number={7},
-  pages={797--811},
-  year={2006},
-  doi={10.1080/13658810600665111},
-  publisher={Taylor \& Francis}
-}
-
-@article{openshaw1977geographical,
-  title={A Geographical Solution to Scale and Aggregation Problems in Region-building, Partitioning and Spatial Modelling},
-  author={Openshaw, S},
-  journal={Transactions of the Institute of British Geographers},
-  pages={459--472},
-  year={1977},
-  publisher={JSTOR},
-  doi={doi.org/10.2307/622300},
-}
 
 @article{duque2012max,
   author={Duque, JC and Anselin, L and Rey, SJ},
@@ -57,35 +83,6 @@ @article{duque2012max
   year={2012}
 }
 
-@article{openshaw1995algorithms,
-  title={Algorithms for Reengineering 1991 Census Geography},
-  author={Openshaw, S and Rao, L},
-  journal={Environment and Planning A},
-  volume={27},
-  number={3},
-  pages={425--446},
-  year={1995},
-  doi={10.1068/a270425},
-  publisher={SAGE Publications Sage UK: London, England}
-}
-
-@misc{wolf2018,
-  title={{ljwolf/spenc: GISRUK}},
-  author={Wolf, LJ},
-  year={2018},
-  doi={10.5281/zenodo.1219904},
-}
-
-@article{wolf2021,
-  author={Wolf, LJ},
-  title={Spatially–encouraged spectral clustering: a technique for blending map typologies and regionalization},
-  journal={International Journal of Geographical Information Science},
-  volume={0},
-  number={0},
-  pages={1-18},
-  year={2021},
-  doi={10.1080/13658816.2021.1934475},
-}
 
 @article{hakimi_1964, 
   author={Hakimi, S. L.},
@@ -109,6 +106,49 @@ @article{hakimi_1965
   doi={10.1287/opre.13.3.462},
 }
 
+
+@article{kuby_1987,
+author = {Kuby, Michael J.},
+title = {Programming Models for Facility Dispersion: The p-Dispersion and Maxisum Dispersion Problems},
+journal = {Geographical Analysis},
+doi = {10.1111/j.1538-4632.1987.tb00133.x},
+year = {1987}
+}
+
+
+@article{MALISZEWSKI2012331,
+author = {Paul J. Maliszewski and Michael J. Kuby and Mark W. Horner},
+title = {A comparison of multi-objective spatial dispersion models for managing critical assets in urban areas},
+journal = {Computers, Environment and Urban Systems},
+doi = {10.1016/j.compenvurbsys.2011.12.006},
+year = {2012}
+}
+
+
+@article{openshaw1977geographical,
+  title={A Geographical Solution to Scale and Aggregation Problems in Region-building, Partitioning and Spatial Modelling},
+  author={Openshaw, S},
+  journal={Transactions of the Institute of British Geographers},
+  pages={459--472},
+  year={1977},
+  publisher={JSTOR},
+  doi={doi.org/10.2307/622300},
+}
+
+
+@article{openshaw1995algorithms,
+  title={Algorithms for Reengineering 1991 Census Geography},
+  author={Openshaw, S and Rao, L},
+  journal={Environment and Planning A},
+  volume={27},
+  number={3},
+  pages={425--446},
+  year={1995},
+  doi={10.1068/a270425},
+  publisher={SAGE Publications Sage UK: London, England}
+}
+
+
 @article{toregas_swain_revelle_bergman_1971, 
   author={Toregas, Constantine and Swain, Ralph and Revelle, Charles and Bergman, Lawrence}, 
   title={The Location of Emergency Service Facilities}, 
@@ -120,59 +160,36 @@ @article{toregas_swain_revelle_bergman_1971
   doi={10.1287/opre.19.6.1363},
 }
 
-@article{calik_labbé_yaman_2015, 
-  author={Calik, Hatice and Labbé, Martine and Yaman, Hande},
-  title={p-Center Problems}, 
-  journal={Location Science},
-  pages={79–92},
-  year={2015},
-  doi={10.1007/978-3-319-13111-5_4},  
-}
 
-@article{chen_murray_jiang_2021,
-  author={Chen, Huanfa and Murray, Alan T. and Jiang, Rui},
-  title={Open-source approaches for location cover models: capabilities and efficiency},
-  journal={Journal of Geographical Systems},
-  doi={10.1007/s10109-021-00350-w},
-  year={2021}
+@article{wei2020efficient,
+  title={Efficient Regionalization for Spatially Explicit Neighborhood Delineation},
+  author={Wei, R and Rey, SJ and Knaap, E},
+  journal={International Journal of Geographical Information Science},
+  pages={1--17},
+  year={2020},
+  publisher={Taylor \& Francis},
+  doi={10.1080/13658816.2020.1759806},
 }
 
-@book{daskin_2013, 
-  author={Daskin, Mark S.},
-  title={Network and discrete location: models, algorithms, and applications}, 
-  publisher={John Wiley & Sons, Inc.}, 
-  year={2013},
-}
 
-@book{church_murray_2018, 
-  author={Church, Richard L. and Murray, Alan T.},
-  title={Location covering models: history, applications and advancements}, 
-  publisher={Springer},  
+@misc{wolf2018,
+  title={{ljwolf/spenc: GISRUK}},
+  author={Wolf, LJ},
   year={2018},
+  doi={10.5281/zenodo.1219904},
 }
 
-@article{MALISZEWSKI2012331,
-author = {Paul J. Maliszewski and Michael J. Kuby and Mark W. Horner},
-title = {A comparison of multi-objective spatial dispersion models for managing critical assets in urban areas},
-journal = {Computers, Environment and Urban Systems},
-doi = {10.1016/j.compenvurbsys.2011.12.006},
-year = {2012}
-}
 
-@article{kuby_1987,
-author = {Kuby, Michael J.},
-title = {Programming Models for Facility Dispersion: The p-Dispersion and Maxisum Dispersion Problems},
-journal = {Geographical Analysis},
-doi = {10.1111/j.1538-4632.1987.tb00133.x},
-year = {1987}
+@article{wolf2021,
+  author={Wolf, LJ},
+  title={Spatially–encouraged spectral clustering: a technique for blending map typologies and regionalization},
+  journal={International Journal of Geographical Information Science},
+  volume={0},
+  number={0},
+  pages={1-18},
+  year={2021},
+  doi={10.1080/13658816.2021.1934475},
 }
 
-@article{daskin_stern_edmund_1981,
-author = {Daskin, Mark S. and Stern, Edmund H.},
-title = {A Hierarchical Objective Set Covering Model for Emergency Medical Service Vehicle Deployment},
-journal = {Transportation Science},
-doi = {10.1287/trsc.15.2.137},
-year = {1981}
-}
 
 %======

docs/api.rst

@@ -8,7 +8,7 @@ API reference
 .. _data_api:
 
 Region Methods
------------------------
+--------------
 Model based approaches for aggregating a large set of geographic units (with small footprints) into a smaller number of regions (with large footprints).
 
 
@@ -27,6 +27,8 @@ Model based approaches for aggregating a large set of geographic units (with sma
 Locate Methods
 --------------
 
+Exact solution approaches to facility location modeling problems.
+
 .. autosummary::
    :toctree: generated/