Merge branch 'main' of github.com:pysal/esda into corrfix

.github/workflows/build_docs.yml

@@ -19,7 +19,7 @@
      strategy:
        matrix:
          os: ['ubuntu-latest']
-         environment-file: [ci/311.yaml]
+         environment-file: [ci/312-latest.yaml]
          experimental: [false]
      defaults:
        run:

.github/workflows/testing.yml

@@ -19,35 +19,30 @@
  jobs:
    unittests:
      env:
-       FETCH_DATA: python -c 'from libpysal.examples import load_example as ex; [ex(e) for e in ["columbus", "desmith", "sids2", "stl"]]'
-       RUN_TEST: pytest esda -v -r a -n auto --cov esda --cov-config .coveragerc --cov-report xml --color yes --cov-append --cov-report term-missing
+       FETCH_DATA: python -c 'from libpysal.examples import load_example as ex; [ex(e) for e in ["columbus", "desmith", "sids2", "stl", "Sacramento1"]]'
+       RUN_TEST: pytest esda -v -r a -n auto --cov esda --cov-report xml --color yes --cov-append --cov-report term-missing
      name: CI (${{ matrix.os }}, ${{ matrix.environment-file }})
      runs-on: ${{ matrix.os }}
      timeout-minutes: 25
      strategy:
        matrix:
          os: [ubuntu-latest]
          environment-file:
-           - ci/38-minimal.yaml
-           - ci/38-minimal-numba.yaml
-           - ci/39.yaml
-           - ci/39-numba.yaml
-           - ci/310.yaml
-           - ci/310-numba.yaml
-           - ci/310-DEV.yaml
-           - ci/310-numba-DEV.yaml
-           - ci/311.yaml
-           - ci/311-numba.yaml
-           - ci/311-DEV.yaml
-           - ci/311-numba-DEV.yaml
+           - ci/310-oldest.yaml
+           - ci/310-numba-oldest.yaml
+           - ci/311-latest.yaml
+           - ci/311-numba-latest.yaml
+           - ci/312-min.yaml
+           - ci/312-latest.yaml
+           - ci/312-dev.yaml
+           - ci/312-numba-latest.yaml
+           - ci/312-numba-dev.yaml
          include:
-           - environment-file: ci/310-numba.yaml
-             os: macos-latest
-           - environment-file: ci/311.yaml
-             os: macos-latest
-           - environment-file: ci/310-numba.yaml
-             os: windows-latest
-           - environment-file: ci/311.yaml
+           - environment-file: ci/312-numba-latest.yaml
+             os: macos-13 # Intel
+           - environment-file: ci/312-numba-latest.yaml
+             os: macos-14 # Apple Silicon
+           - environment-file: ci/312-numba-latest.yaml
              os: windows-latest
        fail-fast: false
      defaults:
@@ -63,11 +58,6 @@
             micromamba-version: 'latest'
             environment-file: ${{ matrix.environment-file }}
 
-       - name: install bleeding edge libpysal (Ubuntu / Python 3.10)
-         run: |
-           pip install git+https://github.com/pysal/libpysal.git@main
-         if: matrix.os == 'ubuntu-latest' && contains(matrix.environment-file, 'DEV')
-
        - name: environment info
          run: |
            micromamba info
@@ -82,7 +72,7 @@
            ${{ env.RUN_TEST }}
 
        - name: ${{ matrix.os }}, ${{ matrix.environment-file }}
-         uses: codecov/codecov-action@v3
+         uses: codecov/codecov-action@v4
          with:
            token: ${{ secrets.CODECOV_TOKEN }}
            file: ./coverage.xml

.github/workflows/upload_package.yml

@@ -18,7 +18,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 
@@ -29,7 +29,7 @@ jobs:
         twine check --strict dist/*
 
     - name: Create Release Notes
-      uses: actions/github-script@v6
+      uses: actions/github-script@v7
       with:
         github-token: ${{secrets.GITHUB_TOKEN}}
         script: |

.gitignore

@@ -10,7 +10,7 @@ dist
 .bash_history
 .cache/
 .conda/
-.coverage
+*.coverage*
 .coverage.snuc.30509.410533
 .eggs/
 .ipython/

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+files: "esda\/"
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.5.3"
+    hooks:
+      - id: ruff
+      - id: ruff-format
+
+ci:
+  autofix_prs: false
+  autoupdate_schedule: quarterly

README.md

@@ -1,7 +1,8 @@
 # Exploratory Spatial Data Analysis in PySAL
 
+![tag](https://img.shields.io/github/v/release/pysal/esda?include_prereleases&sort=semver)
 [![Continuous Integration](https://github.com/pysal/esda/actions/workflows/testing.yml/badge.svg)](https://github.com/pysal/esda/actions/workflows/testing.yml) 
-[![codecov](https://codecov.io/gh/pysal/esda/branch/master/graph/badge.svg)](https://codecov.io/gh/pysal/esda)
+[![codecov](https://codecov.io/gh/pysal/esda/branch/main/graph/badge.svg)](https://codecov.io/gh/pysal/esda)
 [![DOI](https://zenodo.org/badge/81873636.svg)](https://zenodo.org/badge/latestdoi/81873636)
 
 Methods for testing for global and local autocorrelation in areal unit data.
@@ -11,41 +12,60 @@ Methods for testing for global and local autocorrelation in areal unit data.
 - [Tutorial](https://pysal.org/esda/tutorial.html)
 - [API](https://pysal.org/esda/api.html)
 
-
 ## Installation
 
-Install esda by running:
+Install `esda` by running:
+
+### conda-forge
+
+*preferred*
+
+```
+$ conda install -c conda-forge esda
+```
+
+### PyPI
 
 ```
 $ pip install esda
 ```
 
+### GitHub
+
+```
+$ pip install git+https://github.com/pysal/esda@main
+```
 
 ## Requirements
 
-- libpysal
+- `geopandas>=0.12`
+- `libpysal>=4.12`
+- `numpy>=1.24`
+- `pandas>1.5`
+- `scikit-learn>=1.2`
+- `scipy>=1.9`
+- `shapely>=2.0`
 
 ### Optional dependencies
 
-- `numba`, version `0.50.1` or greater, is used to accelerate computational geometry and permutation-based statistical inference. Unfortunately, versions before `0.50.1` may cause some local statistical functions to break, so please ensure you have `numba>=0.50.1` installed. 
+- `numba>=0.57` - used to accelerate computational geometry and permutation-based statistical inference.
+- `rtree>=1.0` - required for `esda.topo.isolation()`
+- `matplotlib` - required for `esda.moran.explore()`
 
 ## Contribute
 
 PySAL-esda is under active development and contributors are welcome.
 
 If you have any suggestion, feature request, or bug report, please open a new [issue](https://github.com/pysal/esda/issues) on GitHub. To submit patches, please follow the PySAL development [guidelines](https://github.com/pysal/pysal/wiki) and open a [pull request](https://github.com/pysal/esda). Once your changes get merged, you’ll automatically be added to the [Contributors List](https://github.com/pysal/esda/graphs/contributors).
 
-
 ## Support
 
-If you are having issues, please talk to us in the [gitter room](https://gitter.im/pysal/pysal).
-
-
-## License
+If you are having issues, please talk to us in the [`esda` Discord channel](https://discord.gg/Re46DjyB9U).
 
-The project is licensed under the [BSD 3-Clause license](https://github.com/pysal/esda/blob/master/LICENSE).
+## License
 
+The project is licensed under the [BSD 3-Clause license](https://github.com/pysal/esda/blob/main/LICENSE).
 
 ## Funding
 
-[<img align="middle" src="/Users/the-gaboardi/esda/docs/_static/images/nsf_logo.jpg" width="100">](https://www.nsf.gov/index.jsp) National Science Foundation Award #1421935: [New Approaches to Spatial Distribution Dynamics](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1421935)
+[<img align="middle" src="https://github.com/pysal/esda/blob/main/docs/_static/images/nsf_logo.jpg" width="100">](https://www.nsf.gov/index.jsp) National Science Foundation Award #1421935: [New Approaches to Spatial Distribution Dynamics](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1421935)

ci/310-numba-oldest.yaml

@@ -0,0 +1,24 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  # required
+  - libpysal=4.12
+  - geopandas=0.12
+  - numpy=1.24
+  - pandas<1.6
+  - scikit-learn=1.2
+  - scipy=1.9
+  - shapely=2.0
+  # optional
+  - numba=0.57
+  - rtree=1.0
+  # testing
+  - codecov
+  - folium
+  - mapclassify
+  - matplotlib
+  - pytest
+  - pytest-cov
+  - pytest-xdist

ci/310-numba.yaml → ci/310-oldest.yaml

@@ -4,17 +4,20 @@ channels:
 dependencies:
   - python=3.10
   # required
-  - libpysal
-  - numba
-  - pandas>=1.0
-  - scikit-learn
-  - scipy>=1.0
+  - libpysal=4.12
+  - geopandas=0.12
+  - numpy=1.24
+  - pandas<1.6
+  - scikit-learn=1.2
+  - scipy=1.9
+  - shapely=2.0
+  # optional
+  - rtree=1.0
   # testing
   - codecov
+  - folium
+  - mapclassify
   - matplotlib
   - pytest
   - pytest-cov
   - pytest-xdist
-  # optional
-  - geopandas>=0.7.0
-  - shapely>=2

ci/39-numba.yaml → ci/311-latest.yaml

@@ -2,20 +2,21 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.11
   # required
-  - libpysal
-  - numba
-  - pandas>=1.0
+  - geopandas
+  - libpysal>=4.12
+  - pandas
   - scikit-learn
-  - scipy>=1.0
+  - scipy
+  - shapely
   # testing
   - codecov
+  - folium
+  - mapclassify
   - matplotlib
   - pytest
   - pytest-cov
   - pytest-xdist
-  - rtree
   # optional
-  - geopandas>=0.7.0
-  - shapely>=2
+  - rtree

ci/310-numba-DEV.yaml → ci/311-numba-latest.yaml

@@ -2,19 +2,23 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.11
   # required
-  - numba
-  - pandas>=1.0
+  - geopandas
+  - libpysal>=4.12
+  - numpy
+  - pandas
   - scikit-learn
-  - scipy>=1.0
+  - scipy
+  - shapely
   # testing
   - codecov
+  - folium
+  - mapclassify
   - matplotlib
   - pytest
   - pytest-cov
   - pytest-xdist
-  - rtree
   # optional
-  - geopandas>=0.12.0
-  - shapely>=2
+  - numba
+  - rtree

ci/311-DEV.yaml → ci/312-dev.yaml

@@ -2,23 +2,19 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.11
+  - python=3.12
   # required
   - geos
+  # optional
+  - rtree
   # testing
   - codecov
+  - folium
+  - mapclassify
   - matplotlib
   - pytest
   - pytest-cov
   - pytest-xdist
-  - rtree
-  # doc build
-  - nbsphinx
-  - numpydoc
-  - sphinx
-  - sphinxcontrib-bibtex
-  - sphinxcontrib-napoleon
-  - sphinx_bootstrap_theme
   - pip:
       - --pre --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --extra-index-url https://pypi.org/simple
       - scikit-learn