CI against Python 3.12

.github/workflows/build_docs.yml

@@ -20,7 +20,7 @@
      strategy:
        matrix:
          os: ['ubuntu-latest']
-         environment-file: [ci/310.yaml]
+         environment-file: [ci/312.yaml]
          experimental: [false]
      defaults:
        run:
@@ -29,7 +29,9 @@
      steps:
        - name: Checkout repo
          uses: actions/checkout@v4
-
+         with:
+           fetch-depth: 0 # Fetch all history for all branches and tags.
+
        - name: Setup micromamba
          uses: mamba-org/setup-micromamba@v1
          with:
@@ -54,7 +56,7 @@
            # The above command will fail if no changes were present,
            # so we ignore the return code.
 
-       - name: push to gh-pages
+       - name: Push to gh-pages
          uses: ad-m/github-push-action@master
          with:
             branch: gh-pages

.github/workflows/release_and_publish.yml

@@ -25,9 +25,12 @@
    build:
      name: Create release & publish to PyPI
      runs-on: ubuntu-latest
+
      steps:
        - name: Checkout repo
          uses: actions/checkout@v4
+         with:
+           fetch-depth: 0 # Fetch all history for all branches and tags.
 
        - name: Set up python
          uses: actions/setup-python@v4

.github/workflows/unittests.yml

@@ -24,25 +24,28 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         environment-file:
-          - ci/38-minimal.yaml
-          - ci/39.yaml
+          - ci/310-oldest.yaml
           - ci/310.yaml
           - ci/311.yaml
-          - ci/311-dev.yaml
-          - ci/311-no-optional.yaml
+          - ci/312.yaml
+          - ci/312-dev.yaml
+          - ci/312-no-optional.yaml
         include:
-          - environment-file: ci/310.yaml
+          - environment-file: ci/312.yaml
             os: macos-latest
-          - environment-file: ci/310.yaml
+          - environment-file: ci/312.yaml
             os: windows-latest
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
 
-      - name: setup micromamba
+      - name: Setup micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ matrix.environment-file }}
@@ -55,7 +58,8 @@ jobs:
         run: |
           pytest -v --color yes --cov libpysal --cov-append --cov-report term-missing --cov-report xml .
 
-      - uses: codecov/codecov-action@v3
+      - name: Codecov
+        uses: codecov/codecov-action@v3
 
       - name: Generate and publish the report
         if: |

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos: 
 - repo: https://github.com/psf/black
-  rev: 23.9.1
+  rev: "23.10.0"
   hooks:
   - id: black
     language_version: python3

README.rst

@@ -5,7 +5,7 @@ Python Spatial Analysis Library Core
 .. image:: https://github.com/pysal/libpysal/workflows/.github/workflows/unittests.yml/badge.svg
     :target: https://github.com/pysal/libpysal/actions?query=workflow%3A.github%2Fworkflows%2Funittests.yml
 
-.. image:: https://codecov.io/gh/pysal/libpysal/branch/master/graph/badge.svg
+.. image:: https://codecov.io/gh/pysal/libpysal/branch/main/graph/badge.svg
     :target: https://codecov.io/gh/pysal/libpysal
 
 .. image:: https://badge.fury.io/py/libpysal.svg
@@ -59,7 +59,7 @@ If you have any suggestions, feature requests, or bug reports,
 please open new `issues <https://github.com/pysal/libpysal/issues>`_ on GitHub. 
 To submit patches, please review `PySAL's documentation for developers <https://pysal.org/docs/devs/>`_, 
 the PySAL `development guidelines <https://github.com/pysal/pysal/wiki>`_, 
-the `libpysal contributing guidelines <https://github.com/pysal/libpysal/blob/master/.github/CONTRIBUTING.md>`_
+the `libpysal contributing guidelines <https://github.com/pysal/libpysal/blob/main/.github/CONTRIBUTING.md>`_
 before  opening a `pull request <https://github.com/pysal/libpysal/pulls>`_. 
 Once your changes get merged, you’ll automatically be added to 
 the `Contributors List <https://github.com/pysal/libpysal/graphs/contributors>`_.
@@ -76,6 +76,6 @@ To search for or report bugs, please see `libpysal's issues <https://github.com/
 License information
 *******************
 
-See the `LICENSE <https://github.com/pysal/libpysal/blob/master/LICENSE.txt>`_
+See the `LICENSE <https://github.com/pysal/libpysal/blob/main/LICENSE.txt>`_
 for information on the history of this software, terms & conditions for usage,
 and a DISCLAIMER OF ALL WARRANTIES.

ci/38-minimal.yaml → ci/310-oldest.yaml

@@ -2,27 +2,32 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.10
   - beautifulsoup4=4.10
+  - geopandas=0.10.0
   - jinja2=3.0
+  - numpy=1.22
+  - packaging=22
   - pandas=1.4
+  - requests=2.27
   - scipy=1.8
-  - xarray=0.18
+  - shapely=2.0.1
+  - xarray=2022.3
   # testing
   - codecov
-  - matplotlib
+  - matplotlib>=3.6
   - pytest
   - pytest-cov
+  - pytest-mpl
   - pytest-xdist
   # optional
-  - geopandas>=0.10.0,<0.13
-  - shapely==2.0.1
-  - joblib
+  - geodatasets=2023.3.0
+  - joblib>=1.2
   - networkx=2.7
-  - numba=0.54
-  - packaging
+  - numba=0.55
+  - pyarrow>=7.0
+  - scikit-learn=1.1
   - zstd
-  - geodatasets
   - pip
   - pip:
       - platformdirs==2.0.2

ci/310.yaml

@@ -3,30 +3,28 @@ channels:
   - conda-forge
 dependencies:
   - python=3.10
-  - platformdirs
   - beautifulsoup4
+  - geopandas
   - jinja2
+  - packaging
   - pandas
+  - platformdirs
+  - requests
   - scipy
+  - shapely
   - xarray
   # testing
   - codecov
   - matplotlib
   - pytest
   - pytest-cov
+  - pytest-mpl
   - pytest-xdist
   # optional
-  - geopandas
+  - geodatasets
   - joblib
   - networkx
   - numba
-  - packaging
-  - zstd
-  - geodatasets
   - pyarrow
-  # for docs build action (this env only)
-  - nbsphinx
-  - numpydoc
-  - sphinx
-  - sphinxcontrib-bibtex
-  - sphinx_bootstrap_theme
+  - scikit-learn
+  - zstd

ci/311.yaml

@@ -3,25 +3,28 @@ channels:
   - conda-forge
 dependencies:
   - python=3.11
-  - platformdirs
   - beautifulsoup4
+  - geopandas
   - jinja2
+  - packaging
   - pandas
+  - platformdirs
+  - requests
   - scipy
+  - shapely
   - xarray
   # testing
   - codecov
   - matplotlib
   - pytest
   - pytest-cov
+  - pytest-mpl
   - pytest-xdist
   # optional
-  - geopandas>=0.12.0
+  - geodatasets
   - joblib
   - networkx
-  - packaging
-  - shapely>=2.0b1
-  - xarray
-  - zstd
-  - geodatasets
+  - numba
   - pyarrow
+  - scikit-learn
+  - zstd

ci/311-dev.yaml → ci/312-dev.yaml

@@ -2,34 +2,37 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.11
-  - platformdirs
+  - python=3.12
   - beautifulsoup4
   - jinja2
+  - platformdirs
+  - requests
   # testing
   - codecov
   - matplotlib
   - pytest
   - pytest-cov
+  - pytest-mpl
   - pytest-xdist
   # optional
-  - geos
-  - pyproj
+  - Cython
   - fiona
+  - geodatasets
+  - geos
   - joblib
   - networkx
+  # - numba # follow up when numba is ready for 3.12
   - packaging
-  - zstd
-  - Cython
-  - geodatasets
   - pyarrow
+  - pyproj
+  - zstd
   - pip
   - pip:
       # dev versions of packages
       - --pre --index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --extra-index-url https://pypi.org/simple
-      - scipy
       - pandas
-      - xarray
       - scikit-learn
-      - git+https://github.com/shapely/shapely.git@main
+      - scipy
+      - xarray
       - git+https://github.com/geopandas/geopandas.git@main
+      - git+https://github.com/shapely/shapely.git@main

ci/311-no-optional.yaml → ci/312-no-optional.yaml

@@ -2,20 +2,22 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.11
-  - platformdirs
+  - python=3.12
   - beautifulsoup4
+  - fiona
+  - geopandas-base>=0.12.0  # base to avoid pulling sklearn
   - jinja2
   - pandas
+  - platformdirs
+  - requests
   - scipy
   - xarray
   # testing
   - codecov
   - matplotlib
   - pytest
   - pytest-cov
+  - pytest-mpl
   - pytest-xdist
   # optional used in ci
-  - geopandas-base>=0.12.0  # base to avoid pulling sklearn
-  - fiona
   - geodatasets

ci/39.yaml → ci/312.yaml

@@ -2,25 +2,38 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
-  - platformdirs
+  - python=3.12
   - beautifulsoup4
+  - geopandas
   - jinja2
+  - packaging
   - pandas
+  - platformdirs
+  - requests
   - scipy
+  - shapely
   - xarray
   # testing
   - codecov
   - matplotlib
   - pytest
   - pytest-cov
+  - pytest-mpl
   - pytest-xdist
   # optional
-  - geopandas
+  - geodatasets
   - joblib
   - networkx
-  - numba
-  - packaging
-  - zstd
-  - geodatasets
+  # - numba # follow up when numba is ready for 3.12
   - pyarrow
+  - scikit-learn
+  - zstd
+  # for docs build action (this env only)
+  - mkdocs-jupyter
+  - myst-parser
+  - nbsphinx
+  - numpydoc
+  - pandoc
+  - sphinx
+  - sphinxcontrib-bibtex
+  - sphinx_bootstrap_theme

docs/conf.py

@@ -279,7 +279,7 @@ def setup(app):
     "networkx": ("https://networkx.org/documentation/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
-    "python": ("https://docs.python.org/3.11/", None),
+    "python": ("https://docs.python.org/3.12/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
 }
 

docs/index.rst

@@ -19,7 +19,7 @@ libpysal: Python Spatial Analysis Library Core
         <div class="col-sm-1 col-xs-hidden">
         </div>
         <div class="col-sm-10 col-xs-12">
-            <a href="http://nbviewer.jupyter.org/github/pysal/libpysal/blob/master/notebooks/weights.ipynb" class="thumbnail">
+            <a href="http://nbviewer.jupyter.org/github/pysal/libpysal/blob/main/notebooks/weights.ipynb" class="thumbnail">
                 <img src="_static/images/npweights.png" class="img-responsive center-block">
                 <div class="caption text-center">
                 <h6>Weights for nonplanar enforced geometries</h6>
@@ -38,10 +38,10 @@ Introduction
 
 **libpysal** offers four modules that form the building blocks in many upstream packages in the `PySAL family <https://pysal.org>`_:
 
-- Spatial Weights: libpysal.weights 
-- Input-and output: libpysal.io 
-- Computational geometry: libpysal.cg  
-- Built-in example datasets libpysal.examples  
+- Spatial Weights: libpysal.weights
+- Input-and output: libpysal.io
+- Computational geometry: libpysal.cg
+- Built-in example datasets libpysal.examples
 
 
 Examples demonstrating some of **libpysal** functionality are available in the `tutorial <tutorial.html>`_.