Merge remote-tracking branch 'upstream/main' into centroid

.coveragerc

@@ -4,6 +4,7 @@ omit =
     */contrib/*
     */test/*
 include=libpysal/*
+disable_warnings=include-ignored
 [report]
 omit = 
     __init__.py 

.github/release.yml

@@ -0,0 +1,19 @@
+changelog:
+  exclude:
+    labels:
+      - ignore-for-release
+    authors:
+      - dependabot
+  categories:
+    - title: Bug Fixes
+      labels:
+        - bug
+    - title: Enhancements
+      labels:
+        - enhancement
+    - title: Maintenance
+      labels:
+        - maintenance
+    - title: Other Changes
+      labels:
+        - "*"

.github/workflows/build_docs.yml

@@ -20,25 +20,30 @@
      strategy:
        matrix:
          os: ['ubuntu-latest']
-         environment-file: [ci/310.yaml]
+         environment-file: [ci/312.yaml]
          experimental: [false]
      defaults:
        run:
          shell: bash -l {0}
-     
+
      steps:
        - name: Checkout repo
-         uses: actions/checkout@v3
-
+         uses: actions/checkout@v4
+         with:
+           fetch-depth: 0 # Fetch all history for all branches and tags.
+
        - name: Setup micromamba
-         uses: mamba-org/provision-with-micromamba@main
+         uses: mamba-org/setup-micromamba@v1
          with:
            environment-file: ${{ matrix.environment-file }}
            micromamba-version: 'latest'
-
+
+       - name: Install
+         run: pip install -e . --no-deps --force-reinstall
+
        - name: Make Docs
          run: cd docs; make html
-       
+
        - name: Commit Docs
          run: |
            git clone https://github.com/ammaraskar/sphinx-action-test.git --branch gh-pages --single-branch gh-pages
@@ -50,8 +55,8 @@
            git commit -m "Update documentation" -a || true
            # 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

@@ -1,65 +1,60 @@
  # Release package on GitHub and publish to PyPI
- 
+
  # Important: In order to trigger this workflow for the organization
  # repo (organzation-name/repo-name vs. user-name/repo-name), a tagged
  # commit must be made to *organzation-name/repo-name*. If the tagged
  # commit is made to *user-name/repo-name*, a release will be published
  # under the user's name, not the organzation.
- 
+
  #--------------------------------------------------
  name: Release & Publish
- 
+
  on:
    push:
      # Sequence of patterns matched against refs/tags
      tags:
        - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
-
+   workflow_dispatch:
+     inputs:
+       version:
+         description: Manual Release
+         default: test
+         required: false
+
  jobs:
    build:
      name: Create release & publish to PyPI
      runs-on: ubuntu-latest
+
      steps:
        - name: Checkout repo
-         uses: actions/checkout@v3
-
+         uses: actions/checkout@v4
+         with:
+           fetch-depth: 0 # Fetch all history for all branches and tags.
+
        - name: Set up python
-         uses: actions/setup-python@v3
+         uses: actions/setup-python@v4
          with:
            python-version: "3.x"
- 
+
        - name: Install Dependencies
          run: |
-           python -m pip install --upgrade pip
-           pip install setuptools wheel twine jupyter urllib3 pandas pyyaml
-           python setup.py sdist bdist_wheel
- 
-       - name: run Changelog
-         run: |
-           jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=-1  --ExecutePreprocessor.kernel_name=python3 tools/gitcount.ipynb
- 
-       - name: cat Changelog
-         uses: pCYSl5EDgo/cat@master
-         id: changetxt
-         with:
-           path: ./tools/changelog.md
-         env:
-           TEXT: ${{ steps.changetxt.outputs.text }}
-
-       - name: Get the tag name
-         run: echo "TAG=${GITHUB_REF/refs\/tags\//}" >> $GITHUB_ENV
-
-       - name: Release
-         uses: softprops/action-gh-release@v1
+           python -m pip install --upgrade pip build twine
+           python -m build
+           twine check --strict dist/*
+
+       - name: Create Release Notes
+         uses: actions/github-script@v6
          with:
-           body: ${{ steps.changetxt.outputs.text }}
-           body_path: ${{ steps.changetxt.outputs.path }}
-           name: Release ${{ env.TAG }}
-         env:
-           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
+           github-token: ${{secrets.GITHUB_TOKEN}}
+           script: |
+             await github.request(`POST /repos/${{ github.repository }}/releases`, {
+                tag_name: "${{ github.ref }}",
+                generate_release_notes: true
+              });
+
        - name: Publish distribution 📦 to PyPI
-         uses: pypa/gh-action-pypi-publish@master
+         uses: pypa/gh-action-pypi-publish@release/v1
          with:
            user: __token__
            password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/unittests.yml

@@ -1,58 +1,72 @@
- on:
-   push:
-     branches:
-     - '*'
-   pull_request:
-     branches:
-     - '*'
-   schedule:
-     - cron: '59 21 * * *'
-
- jobs:
-   unittests:
-     name: ${{ matrix.os }}, ${{ matrix.environment-file }}
-     runs-on: ${{ matrix.os }}
-     env:
-       FETCH_EXAMPLES: python -c 'import libpysal; libpysal.examples.fetch_all()'
-       RUN_TEST: pytest -v -n auto libpysal --cov libpysal --cov-config .coveragerc --cov-report xml --color yes --cov-append --cov-report term-missing
-     #timeout-minutes: 25
-     strategy:
-       matrix:
-         os: ['ubuntu-latest']
-         environment-file: [ci/37-minimal.yaml, ci/37.yaml, ci/38.yaml, ci/39.yaml, ci/310.yaml]
-         include:
-           - environment-file: ci/310.yaml
-             os: macos-latest
-           - environment-file: ci/310.yaml
-             os: windows-latest
-
-     steps:
-       - name: checkout repo
-         uses: actions/checkout@v3
-
-       - name: setup micromamba
-         uses: mamba-org/provision-with-micromamba@main
-         with:
-           environment-file: ${{ matrix.environment-file }}
-           micromamba-version: 'latest'
-
-       - name: run tests - bash
-         shell: bash -l {0}
-         run: |
-           ${{ env.FETCH_EXAMPLES }}
-           ${{ env.RUN_TEST }}
-         if: matrix.os != 'windows-latest'
-
-       - name: run tests - powershell
-         shell: powershell
-         run: |
-           ${{ env.FETCH_EXAMPLES }}
-           ${{ env.RUN_TEST }}
-         if: matrix.os == 'windows-latest'
-
-       - name: codecov
-         uses: codecov/codecov-action@v3
-         with:
-           token: ${{ secrets.CODECOV_TOKEN }}
-           file: ./coverage.xml
-           name: libpysal-codecov
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches:
+      - "*"
+  schedule:
+    - cron: "0 0 * * 1,4"
+  workflow_dispatch:
+    inputs:
+      version:
+        description: Manual Unittest Run
+        default: test
+        required: false
+
+jobs:
+  Test:
+    name: ${{ matrix.os }}, ${{ matrix.environment-file }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        environment-file:
+          - ci/310-oldest.yaml
+          - ci/310.yaml
+          - ci/311.yaml
+          - ci/312.yaml
+          - ci/312-dev.yaml
+          - ci/312-no-optional.yaml
+        include:
+          - environment-file: ci/312.yaml
+            os: macos-latest
+          - environment-file: ci/312.yaml
+            os: windows-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    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:
+          environment-file: ${{ matrix.environment-file }}
+          micromamba-version: "latest"
+
+      - name: Install libpysal
+        run: pip install .; python -c 'import libpysal; libpysal.examples.fetch_all()'
+
+      - name: Test libpysal
+        run: |
+          pytest -v --color yes --cov libpysal --cov-append --cov-report term-missing --cov-report xml .
+
+      - name: Codecov
+        uses: codecov/codecov-action@v3
+
+      - name: Generate and publish the report
+        if: |
+          failure()
+          && steps.status.outcome == 'failure'
+          && github.event_name == 'schedule'
+          && github.repository_owner == 'pysal'
+        uses: xarray-contrib/issue-from-pytest-log@v1
+        with:
+          log-path: pytest-log.jsonl

.pre-commit-config.yaml

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