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‎.gitattributes‎

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*.ipynb linguist-language=Python
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libpysal/_version.py export-subst

‎.github/CONTRIBUTING.md‎

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Thank you for your interest in contributing! We work primarily on Github. Please
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review the [contributing procedures](https://github.com/pysal/pysal/wiki/GitHub-Standard-Operating-Procedures) so that we can accept your contributions! Alternatively, contact someone in the [development chat channel](https://gitter.im/pysal.pysal).
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## Style and format
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1. Python 3.6, 3.7, and 3.8 are the officially supported versions.
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2. This project follows the formatting conventions of [`black`](https://black.readthedocs.io/en/stable/) and utilizes [`pre-commit`](https://pre-commit.com) to format commits prior to pull requests being made.
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* LJ Miranda provides an [excellent, concise guide](https://ljvmiranda921.github.io/notebook/2018/06/21/precommits-using-black-and-flake8/) on setting up and implementing a `pre-commit` hook for `black`.

‎.github/PULL_REQUEST_TEMPLATE.md‎

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@@ -2,7 +2,7 @@ Hello! Please make sure to check all these boxes before submitting a Pull Reques
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(PR). Once you have checked the boxes, feel free to remove all text except the
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justification in point 5.
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1. [ ] You have run tests on this submission, either by using [Travis Continuous Integration testing](https://github.com/pysal/pysal/wiki/GitHub-Standard-Operating-Procedures#automated-testing-w-travis-ci) testing or running `nosetests` on your changes?
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1. [ ] You have run tests on this submission locally using `pytest` on your changes. Continuous integration will be run on all PRs with [GitHub Actions](https://github.com/pysal/libpysal/blob/master/.github/workflows/unittests.yml), but it is good practice to test changes locally prior to a making a PR.
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2. [ ] This pull request is directed to the `pysal/master` branch.
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3. [ ] This pull introduces new functionality covered by
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[docstrings](https://en.wikipedia.org/wiki/Docstring#Python) and

‎.github/dependabot.yml‎

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# To get started with Dependabot version updates, you'll need to specify which
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# package ecosystems to update and where the package manifests are located.
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# Please see the documentation for all configuration options:
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# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "daily"
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reviewers:
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- "sjsrey"
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- "jGaboardi"
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- package-ecosystem: "pip"
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directory: "/"
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schedule:
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interval: "daily"
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reviewers:
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- "sjsrey"
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- "jGaboardi"

‎.github/workflows/build_docs.yml‎

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name: Build Docs
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on:
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push:
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# Sequence of patterns matched against refs/tags
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tags:
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- 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
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workflow_dispatch:
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inputs:
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version:
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description: Manual Doc Build Reason
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default: test
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required: false
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jobs:
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docs:
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name: Build & Push Docs
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runs-on: ${{ matrix.os }}
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timeout-minutes: 90
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strategy:
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matrix:
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os: ['ubuntu-latest']
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environment-file: [ci/39.yaml]
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experimental: [false]
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v2
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- name: Setup micromamba
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uses: mamba-org/provision-with-micromamba@main
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with:
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environment-file: ${{ matrix.environment-file }}
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micromamba-version: 'latest'
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- name: Make Docs
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run: cd docs; make html
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- name: Commit Docs
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run: |
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git clone https://github.com/ammaraskar/sphinx-action-test.git --branch gh-pages --single-branch gh-pages
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cp -r docs/_build/html/* gh-pages/
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cd gh-pages
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git config --local user.email "action@github.com"
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git config --local user.name "GitHub Action"
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git add .
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git commit -m "Update documentation" -a || true
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# The above command will fail if no changes were present,
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# so we ignore the return code.
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- name: push to gh-pages
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uses: ad-m/github-push-action@master
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with:
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branch: gh-pages
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directory: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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force: true

‎.github/workflows/release_and_publish.yml‎

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# Release package on GitHub and publish to PyPI
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# Important: In order to trigger this workflow for the organization
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# repo (organzation-name/repo-name vs. user-name/repo-name), a tagged
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# commit must be made to *organzation-name/repo-name*. If the tagged
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# commit is made to *user-name/repo-name*, a release will be published
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# under the user's name, not the organzation.
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#--------------------------------------------------
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name: Release & Publish
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on:
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push:
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# Sequence of patterns matched against refs/tags
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tags:
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- "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
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jobs:
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build:
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name: Create release & publish to PyPI
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v2
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- name: Set up python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install setuptools wheel twine jupyter urllib3 pandas pyyaml
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python setup.py sdist bdist_wheel
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- name: run Changelog
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run: |
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jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=-1 --ExecutePreprocessor.kernel_name=python3 tools/gitcount.ipynb
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- name: cat Changelog
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uses: pCYSl5EDgo/cat@master
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id: changetxt
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with:
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path: ./tools/changelog.md
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env:
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TEXT: ${{ steps.changetxt.outputs.text }}
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- name: Get the tag name
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run: echo "TAG=${GITHUB_REF/refs\/tags\//}" >> $GITHUB_ENV
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- name: Release
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uses: softprops/action-gh-release@v1
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with:
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body: ${{ steps.changetxt.outputs.text }}
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body_path: ${{ steps.changetxt.outputs.path }}
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name: Release ${{ env.TAG }}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Publish distribution 📦 to PyPI
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uses: pypa/gh-action-pypi-publish@master
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with:
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user: __token__
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password: ${{ secrets.PYPI_PASSWORD }}

‎.github/workflows/unittests.yml‎

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jobs:
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unittests:
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name: conda (${{ matrix.os }}, ${{ matrix.environment-file }})
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name: ${{ matrix.os }}, ${{ matrix.environment-file }}
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runs-on: ${{ matrix.os }}
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timeout-minutes: 15
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#timeout-minutes: 25
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strategy:
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matrix:
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os: ['macos-latest', 'ubuntu-latest', 'windows-latest']
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environment-file: [ci/36.yaml, ci/37.yaml, ci/38.yaml]
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environment-file: [ci/37.yaml, ci/38.yaml, ci/39.yaml]
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steps:
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- uses: actions/checkout@v2
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- uses: goanpeca/setup-miniconda@v1
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- name: checkout repo
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uses: actions/checkout@v2
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- name: setup micromamba
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uses: mamba-org/provision-with-micromamba@main
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with:
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miniconda-version: 'latest'
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auto-update-conda: true
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auto-activate-base: false
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environment-file: ${{ matrix.environment-file }}
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activate-environment: test
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- shell: bash -l {0}
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run: conda info --all
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- shell: bash -l {0}
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run: conda list
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- shell: bash -l {0}
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run: conda config --show-sources
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- shell: bash -l {0}
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run: conda config --show
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- shell: bash -l {0}
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run: python -c 'import libpysal; libpysal.examples.fetch_all()'
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- shell: bash -l {0}
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run: py.test -v libpysal --cov=libpysal --cov-report=xml
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- name: codecov (${{ matrix.os }}, ${{ matrix.environment-file }})
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uses: codecov/codecov-action@v1
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environment-file: ${{ matrix.environment-file }}
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micromamba-version: 'latest'
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- name: run tests - bash
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shell: bash -l {0}
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run: |
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python -c 'import libpysal; libpysal.examples.fetch_all()'
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pytest -v libpysal --cov=libpysal --cov-report=xml
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if: matrix.os != 'windows-latest'
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- name: run tests - powershell
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shell: powershell
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run: |
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python -c 'import libpysal; libpysal.examples.fetch_all()'
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pytest -v libpysal --cov=libpysal --cov-report=xml
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if: matrix.os == 'windows-latest'
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- name: ${{ matrix.os }}, ${{ matrix.environment-file }}
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uses: codecov/codecov-action@v2
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: ./coverage.xml

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/ambv/black
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rev: stable
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hooks:
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- id: black
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language_version: python3.8

‎CHANGELOG.md‎

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# Version 4.3.0 (2020-06-28)
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We closed a total of 85 issues (enhancements and bug fixes) through 27 pull requests, since our last release on 2020-02-01.
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## Issues Closed
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- Standardize libpysal/examples/*.py docstrings (#294)
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- Fetch (#295)
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- Mac builds seem to take longer — bump up timeout (#273)
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- Voronoi_frames function causes jupyter notebook kernel to die (#281)
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- ENH: allow specific buffer in fuzzy_contiguity (#280)
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- Return alpha option & use pygeos for alphashaping if available (#278)
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- add weights writing as a method on weights. (#276)
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- Docs ci badge (#277)
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- [rough edge] libpysal.examples w/o internet? (#259)
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- removing six from ci (#275)
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- Handle connection errors for remote datasets (#274)
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- examples directory prevents installing with pyInstaller (#263)
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- GH-263: Don't implicitly import examples when importing base library (#264)
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- Error in the internal hack for the Arc_KDTree class inheritance and the KDTree function (#254)
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- GitHub Actions failures (#271)
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- Bugfix (#255)
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- dropping nose in ci/36.yml (#270)
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- Follow-up To Do for GH Actions (#268)
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- Polish up GitHub Action residuals (#269)
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- TEST: turning off 3.6 on github actions (#266)
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- Initializing complete Github Actions CI (#267)
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- fix for issue #153 (#256)
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- DOC: Udpdating citations, minor description editing (#265)
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- Cleaning up weights/weights.py docs (#262)
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- Unused code in weights.from_networkx()? (#261)
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- redirect pysal/#934 to libpysal (#9)
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- defaulting to using the dataframe index as the id set (#35)
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- Handling coincident points in KNN (#23)
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- MGWR_Georgia_example.ipynb fails due to different sample data shapes (#67)
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- Kernel docstring does not mention unique Gaussian kernel behavior (#47)
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- MGWR_Georgia_example.ipynb missing pickle import statement (#69)
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- weights.Voronoi is a function, not a class. (#99)
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- some weights util functions are lost in __ini__.py (#121)
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- Current weight plot method is time consuming for a large data set (#123)
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- [ENH][WIP] Adding a `rasterW` to extract `W` from raster and align values (#150)
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- network kernel weights (#151)
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- Add `from_sparse` and `from_numpy` methods, to match the other `from_` methods (#173)
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- Weight Object Question (#208)
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- ENH: setting up github actions (#258)
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- deprecate or test shapely_ext (#114)
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- Tests failures under Python 3.8 (#177)
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- Update reqs for tests (#250)
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- Nbdocs (#253)
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- test_fiiter fails on 3.8 but passes on < 3.8 (#249)
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- 3.8 (#251)
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- rebuild docs; (#235)
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- DOC: Fix invalid section headings. (#243)
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- Fix syntax errors (#242)
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- Remove calls to deprecated/removed time.clock. (#240)
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- Fix and simplify filter_adjlist. (#244)
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- set up appveyor or circle ci for multiplatform testing (#219)
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- Nose is unmaintained (#241)
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- Add appveyor badge (#248)
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- Appveyor (#247)
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- correct name for beautifulsoup4 (#239)
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- REL: version bump for bug fix release (#238)
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- test_map breakage due to pandas 1.0 deprecation of ufunc.outer (#236)
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- BUG: ufunc.outer deprecated (#237)
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## Pull Requests
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- Standardize libpysal/examples/*.py docstrings (#294)
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- Fetch (#295)
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- Mac builds seem to take longer — bump up timeout (#273)
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- ENH: allow specific buffer in fuzzy_contiguity (#280)
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- Return alpha option & use pygeos for alphashaping if available (#278)
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- add weights writing as a method on weights. (#276)
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- Docs ci badge (#277)
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- removing six from ci (#275)
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- Handle connection errors for remote datasets (#274)
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- GH-263: Don't implicitly import examples when importing base library (#264)
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- Bugfix (#255)
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- dropping nose in ci/36.yml (#270)
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- Polish up GitHub Action residuals (#269)
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- Initializing complete Github Actions CI (#267)
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- DOC: Udpdating citations, minor description editing (#265)
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- Cleaning up weights/weights.py docs (#262)
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- ENH: setting up github actions (#258)
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- Update reqs for tests (#250)
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- Nbdocs (#253)
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- 3.8 (#251)
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- DOC: Fix invalid section headings. (#243)
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- Fix syntax errors (#242)
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- Fix and simplify filter_adjlist. (#244)
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- Appveyor (#247)
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- correct name for beautifulsoup4 (#239)
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- REL: version bump for bug fix release (#238)
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- BUG: ufunc.outer deprecated (#237)
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The following individuals contributed to this release:
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- Serge Rey
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- James Gaboardi
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- Martin Fleischmann
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- Dani Arribas-Bel
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- Levi John Wolf
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- Bryan Bennett
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- Jeffery Sauer
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- Elliott Sales De Andrade
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- Joshua Wagner
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# Version 4.2.2 (2020-02-01)
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This is a bug fix release.

‎MANIFEST.in‎

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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
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include versioneer.py
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include libpysal/_version.py

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