merge main

.coveragerc

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

.gitattributes

@@ -0,0 +1,2 @@
+*.ipynb linguist-language=Python
+libpysal/_version.py export-subst

.github/workflows/build_docs.yml

@@ -0,0 +1,60 @@
+
+ name: Build Docs
+ 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 Doc Build Reason
+         default: test
+         required: false
+
+ jobs:
+   docs:
+     name: Build & Push Docs
+     runs-on: ${{ matrix.os }}
+     timeout-minutes: 90
+     strategy:
+       matrix:
+         os: ['ubuntu-latest']
+         environment-file: [ci/310.yaml]
+         experimental: [false]
+     defaults:
+       run:
+         shell: bash -l {0}
+
+     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: 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
+           cp -r docs/_build/html/* gh-pages/
+           cd gh-pages
+           git config --local user.email "[email protected]"
+           git config --local user.name "GitHub Action"
+           git add .
+           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
+         uses: ad-m/github-push-action@master
+         with:
+            branch: gh-pages
+            directory: gh-pages
+            github_token: ${{ secrets.GITHUB_TOKEN }}
+            force: true

.github/workflows/release_and_publish.yml

@@ -7,66 +7,59 @@
  # under the user's name, not the organzation.
 
  #--------------------------------------------------
- name: release_and_publish
-
+ 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
-
+       - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+ 
  jobs:
    build:
+     name: Create release & publish to PyPI
      runs-on: ubuntu-latest
      steps:
-     - uses: actions/checkout@v2
-     - name: Set up Python
-       uses: actions/setup-python@v2
-       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: Create Release
-       id: create_release
-       uses: actions/create-release@v1
-       env:
-         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # token is provided by GHA, DO NOT create
-       with:
-         tag_name: ${{ github.ref }}
-         release_name: Release ${{ github.ref }}
-         body: ${{ steps.changetxt.outputs.text }}
-         draft: false
-         prerelease: false
-     - name: Get Asset name
-       run: |
-         export PKG=$(ls dist/)
-         set -- $PKG
-         echo "name=$1" >> $GITHUB_ENV
-     - name: Upload Release Asset
-       id: upload-release-asset
-       uses: actions/upload-release-asset@v1
-       env:
-         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-       with:
-         upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-         asset_path: dist/${{ env.name }}
-         asset_name: ${{ env.name }}
-         asset_content_type: application/zip
-     - name: Publish distribution 📦 to PyPI
-       uses: pypa/gh-action-pypi-publish@master
-       with:
-         user: __token__
-         password: ${{ secrets.PYPI_PASSWORD }}
+       - name: Checkout repo
+         uses: actions/checkout@v3
+
+       - name: Set up python
+         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
+         with:
+           body: ${{ steps.changetxt.outputs.text }}
+           body_path: ${{ steps.changetxt.outputs.path }}
+           name: Release ${{ env.TAG }}
+         env:
+           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+       - name: Publish distribution 📦 to PyPI
+         uses: pypa/gh-action-pypi-publish@master
+         with:
+           user: __token__
+           password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/unittests.yml

@@ -10,46 +10,56 @@
 
  jobs:
    unittests:
-     name: conda (${{ matrix.os }}, ${{ matrix.environment-file }})
+     name: ${{ matrix.os }}, ${{ matrix.environment-file }}
      runs-on: ${{ matrix.os }}
-    #  timeout-minutes: 25
+     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: ['macos-latest', 'ubuntu-latest', 'windows-latest']
-         environment-file: [ci/36.yaml, ci/37.yaml, ci/38.yaml]
-         exclude:
-           - environment-file: ci/36.yaml
+         os: ['ubuntu-latest']
+         environment-file: [
+            ci/38-minimal.yaml,
+            ci/39.yaml,
+            ci/310.yaml,
+            ci/311.yaml,
+            ci/311-dev.yaml
+         ]
+         include:
+           - environment-file: ci/311.yaml
+             os: macos-latest
+           - environment-file: ci/311.yaml
              os: windows-latest
-     defaults:
-       run:
-         shell: bash -l {0}
+       fail-fast: false
+
      steps:
-       - uses: actions/checkout@v2
-       - uses: actions/cache@v2
-         env:
-           CACHE_NUMBER: 0
-         with:
-           path: ~/conda_pkgs_dir
-           key: ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(matrix.environment-file) }}
-       - uses: conda-incubator/setup-miniconda@v2
+       - name: checkout repo
+         uses: actions/checkout@v3
+
+       - name: setup micromamba
+         uses: mamba-org/provision-with-micromamba@main
          with:
-            miniconda-version: 'latest'
-            mamba-version: '*'
-            channels: conda-forge
-            channel-priority: true
-            auto-update-conda: false
-            auto-activate-base: false
-            environment-file: ${{ matrix.environment-file }}
-            activate-environment: test
-            use-only-tar-bz2: true
-       - run: mamba info --all
-       - run: mamba list
-       - run: conda config --show-sources
-       - run: conda config --show
-       - run: python -c 'import libpysal; libpysal.examples.fetch_all()'
-       - run: py.test -v libpysal --cov=libpysal --cov-report=xml
-       - name: codecov (${{ matrix.os }}, ${{ matrix.environment-file }})
-         uses: codecov/codecov-action@v1
+           environment-file: ${{ matrix.environment-file }}
+           micromamba-version: 'latest'
+           channel-priority: 'flexible'
+
+       - 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

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos: 
--   repo: https://github.com/ambv/black
-    rev: stable
-    hooks: 
-    - id: black
-      language_version: python3.8
+- repo: https://github.com/psf/black
+  rev: 22.10.0
+  hooks:
+  - id: black
+    language_version: python3

MANIFEST.in

@@ -1,2 +1,4 @@
 include authors.txt LICENSE.txt THANKS.txt CHANGELOG.md MANIFEST.in pysal/COPYING requirements_dev.txt requirements_plus.txt requirements.txt requirements_plus_conda.txt requirements_plus_pip.txt requirements_docs.txt
 
+include versioneer.py
+include libpysal/_version.py

ci/310.yaml

@@ -0,0 +1,30 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - platformdirs
+  - beautifulsoup4
+  - jinja2
+  - pandas
+  - scipy
+  - xarray
+  # testing
+  - codecov
+  - matplotlib
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  # optional
+  - geopandas
+  - joblib
+  - networkx
+  - numba
+  - packaging
+  - zstd
+  # for docs build action (this env only)
+  - nbsphinx
+  - numpydoc
+  - sphinx
+  - sphinxcontrib-bibtex
+  - sphinx_bootstrap_theme

ci/311-dev.yaml

@@ -0,0 +1,33 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - platformdirs
+  - beautifulsoup4
+  - jinja2
+  - pandas
+  - scipy
+  - xarray
+  # testing
+  - codecov
+  - matplotlib
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  # optional
+  - geopandas
+  - joblib
+  - networkx
+  - packaging
+  - zstd
+  - Cython
+  - pip
+  - pip:
+    # dev versions of packages
+    - --pre --extra-index https://pypi.anaconda.org/scipy-wheels-nightly/simple
+    - scipy
+    - pandas
+    - git+https://github.com/shapely/shapely.git@main
+    - git+https://github.com/geopandas/geopandas.git@main
+    - git+https://github.com/pydata/xarray.git@main

ci/311.yaml

@@ -0,0 +1,25 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - platformdirs
+  - beautifulsoup4
+  - jinja2
+  - pandas
+  - scipy
+  - xarray
+  # testing
+  - codecov
+  - matplotlib
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  # optional
+  - geopandas>=0.12.0
+  - joblib
+  - networkx
+  - packaging
+  - shapely>=2.0b1
+  - xarray
+  - zstd