modernize infrastructure

.github/release.yml

@@ -0,0 +1,16 @@
+changelog:
+ exclude:
+ labels:
+ - ignore-for-release
+ authors:
+ - dependabot
+ categories:
+ - title: Bug Fixes
+ labels:
+ - bug
+ - title: Enhancements
+ labels:
+ - enhancement
+ - title: Other Changes
+ labels:
+ - "*"

.github/workflows/build_docs.yml

@@ -1,44 +1,48 @@
  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
+ branches:
+ - master
+ - main
  jobs:
  docs:
- name: build & push docs
+ name: CI (${{ matrix.os }}-${{ matrix.environment-file }})
  runs-on: ${{ matrix.os }}
- timeout-minutes: 90
+ continue-on-error: ${{ matrix.experimental }}
+ timeout-minutes: 20
  strategy:
  matrix:
  os: ['ubuntu-latest']
- environment-file: [ci/310.yaml]
+ environment-file: [.ci/39.yml]
  experimental: [false]
  defaults:
  run:
  shell: bash -l {0}
-
  steps:
- - name: checkout repo
- uses: actions/checkout@v4
-
- - name: setup micromamba
- uses: mamba-org/provision-with-micromamba@main
+ - uses: actions/checkout@v2
+ - uses: actions/cache@v2
+ env:
+ CACHE_NUMBER: 0
  with:
- environment-file: ${{ matrix.environment-file }}
- micromamba-version: 'latest'
-
- - name: make docs
- run: cd docs; make html
-
- - name: commit docs
+ path: ~/conda_pkgs_dir
+ key: ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(matrix.environment-file) }}
+ - uses: conda-incubator/setup-miniconda@v2
+ with:
+ miniconda-version: 'latest'
+ channels: conda-forge
+ channel-priority: true
+ auto-update-conda: true
+ auto-activate-base: false
+ environment-file: ${{ matrix.environment-file }}
+ activate-environment: test
+ use-only-tar-bz2: true
+ - run: conda info --all
+ - run: conda list
+ - run: conda config --show-sources
+ - run: conda config --show
+ - run: pip install -e . --no-deps --force-reinstall
+ - run: cd docs; make html
+ - name: Commit documentation changes
  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/
@@ -47,10 +51,9 @@
  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
+ # The above command will fail if no changes were present, so we ignore
+ # the return code.
+ - name: Push changes
  uses: ad-m/github-push-action@master
  with:
  branch: gh-pages

.github/workflows/release_and_publish.yml

@@ -7,59 +7,52 @@
  # under the user's name, not the organzation.
 
  #--------------------------------------------------
- name: Release & 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
-
- jobs:
- build:
- name: Create release & publish to PyPI
- runs-on: ubuntu-latest
- steps:
- - name: Checkout repo
- uses: actions/checkout@v4
-
- - 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 versioneer
- 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 }}
+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
+
+ - name: Set up python
+ uses: actions/setup-python@v4
+ with:
+ python-version: "3.x"
+
+ - name: Install Dependencies
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install --upgrade build twine
+ python -m build
+ twine check --strict dist/*
+ 
+ - name: Create Release Notes
+ uses: actions/github-script@v6
+ with:
+ 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@release/v1
+ with:
+ user: __token__
+ password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/unittests.yml

@@ -24,11 +24,11 @@
  matrix:
  os: [ubuntu-latest]
  environment-file:
- - ci/38.yaml
  - ci/39.yaml
  - ci/310.yaml
  - ci/310-BASE.yaml
  - ci/310-DEV.yaml
+ - ci/311.yaml
  include:
  - environment-file: ci/310.yaml
  os: macos-latest

ci/38.yaml → ci/311.yaml

@@ -2,7 +2,7 @@ name: test
 channels:
  - conda-forge
 dependencies:
- - python=3.8
+ - python=3.11
  # required
  - libpysal
  - numpy>=1.3

docs/conf.py

@@ -16,12 +16,8 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import sys, os
 import sphinx_bootstrap_theme
 
-
-sys.path.insert(0, os.path.abspath("../"))
-
 # import your package to obtain the version info to display on the docs website
 import spreg
 

environment.yml

@@ -1,8 +1,8 @@
-name: notebooks-environment
+name: spreg
 channels:
  - conda-forge
 dependencies:
- - python=3.10
+ - python>=3.10
  - bokeh
  - folium
  - geojson

pyproject.toml

@@ -0,0 +1,105 @@
+[build-system]
+requires = ["setuptools>=61.0", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+
+[project]
+name = "spreg"
+dynamic = ["version"]
+authors = [
+ { name = "Luc Anselin", email = "[email protected]" },
+ { name = "Serge Rey", email = "[email protected]" },
+ { name = "Pedo Amaral", email = "[email protected]" },
+]
+maintainers = [{ name = "pysal contributors" }]
+license = { text = "BSD 3-Clause" }
+description = "PySAL Spatial Econometric Regression in Python"
+keywords = [
+ "spatial econometrics, regression, statistics, spatial modeling"
+]
+readme = { text = """\
+Spatial Econometric Regression in Python"
+
+""", content-type = "text/x-rst" }
+classifiers = [
+ "Programming Language :: Python :: 3",
+ "License :: OSI Approved :: BSD License",
+ "Operating System :: OS Independent",
+ "Intended Audience :: Science/Research",
+ "Topic :: Scientific/Engineering :: GIS",
+]
+requires-python = ">=3.8"
+dependencies = [
+"scipy>=0.11",
+"numpy>=1.3",
+"pandas",
+"libpysal>=4.0.0",
+"scikit-learn>=0.22",
+]
+
+[project.urls]
+Home = "https://github.com/pysal/spreg/"
+Repository = "https://github.com/pysal/spreg"
+
+[project.optional-dependencies]
+dev = ["pre-commit"]
+docs = [
+ "nbsphinx",
+ "numpydoc",
+ "pandoc",
+ "sphinx",
+ "sphinxcontrib-bibtex",
+ "sphinx_bootstrap_theme",
+ "mkdocs-jupyter",
+ "myst-parser"
+]
+tests = [
+ "codecov",
+ "coverage",
+ "pytest",
+ "pytest-mpl",
+ "pytest-cov",
+ "watermark",
+
+]
+
+[tool.setuptools.packages.find]
+include = ["spreg", "spreg.*"]
+
+[tool.black]
+line-length = 88
+
+[tool.ruff]
+line-length = 88
+select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
+target-version = "py39"
+ignore = [
+ "B006",
+ "B008",
+ "B009",
+ "B010",
+ "C408",
+ "E731",
+ "F401",
+ "F403",
+ "N803",
+ "N806",
+ "N999",
+ "UP007"
+]
+exclude = ["spreg/tests/*", "docs/*"]
+
+[tool.coverage.run]
+source = ["./spreg"]
+
+[tool.coverage.report]
+exclude_lines = [
+ "if self.debug:",
+ "pragma: no cover",
+ "raise NotImplementedError",
+ "except ModuleNotFoundError:",
+ "except ImportError",
+]
+ignore_errors = true
+omit = ["spreg/tests/*", "docs/conf.py"]