Modernize infrastructure

.github/CONTRIBUTING.md

@@ -0,0 +1,11 @@
+# Contributing Guidelines for `spglm`
+
+Thank you for your interest in contributing! We work primarily on Github. Please review the contributing procedures [here](http://pysal.org/getting_started#for-developers) and [here](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).
+
+
+## Style and format
+
+This project utilizes:
+* [`black`](https://black.readthedocs.io/en/stable/) for formatting;
+* [`ruff`](https://docs.astral.sh/ruff/) for linting; and
+* [`pre-commit`](https://pre-commit.com) to check format and lint on commits prior to pull requests being made. 

.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

@@ -0,0 +1,62 @@
+ 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/311.yaml]
+         experimental: [false]
+     defaults:
+       run:
+         shell: bash -l {0}
+
+     steps:
+       - name: checkout repo
+         uses: actions/checkout@v4
+
+       - name: setup micromamba
+         uses: mamba-org/setup-micromamba@v1
+         with:
+           environment-file: ${{ matrix.environment-file }}
+           micromamba-version: 'latest'
+
+       - name: Install package
+         run: pip install .
+
+       - 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

@@ -0,0 +1,48 @@
+name: Release Package
+
+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:
+    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 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 }}

.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+files: "spglm\/"
+repos:
+  - repo: https://github.com/psf/black
+    rev: "23.9.1"
+    hooks:
+      - id: black
+        language_version: python3
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.2"
+    hooks:
+      - id: ruff
+
+ci:
+  autofix_prs: false
+  autoupdate_schedule: quarterly

codecov.yml

@@ -0,0 +1,22 @@
+codecov:
+  notify:
+    after_n_builds: 5
+coverage:
+  range: 50..95
+  round: nearest
+  precision: 1
+  status:
+    project:
+      default:
+        threshold: 2%
+    patch:
+      default:
+        threshold: 2%
+        target: 80%
+  ignore:
+    - "tests/*"
+comment:
+  layout: "reach, diff, files"
+  behavior: once
+  after_n_builds: 5
+  require_changes: true

docs/Makefile

@@ -17,8 +17,18 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
+	@rsync -r --exclude '.ipynb_checkpoints/' ../notebooks/ ./notebooks/
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
+github:
+	@make html
+
+sync:
+	@rsync -avh _build/html/ ../docs/ --delete
+	@make clean
+	touch .nojekyll
+
 clean:
 	rm -rf $(BUILDDIR)/*
 	rm -rf auto_examples/
+	rm -rf generated/