Modernize development infraestructure (#925)

* Progress towards more modern repo

* Start migration to pixi based dev

* Use all 3 python versions

* Run all tests, upload pixi.lock for caching

* Update pixi.lock

* Compare sets instead of lists

* Finalize CI file, which is now called ci.yml

* Update more workflows

* Compare sets instead of lists

* Final touches

* Remove pixi.lock

Author: tomicapretto

.github/workflows/ci.yml

@@ -0,0 +1,52 @@
+name: Run CI
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "bambi/**"
+      - "tests/**"
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths:
+      - "bambi/**"
+      - "tests/**"
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        pixi-env: ["py311", "py312", "py313"]
+
+    name: CI on ${{ matrix.pixi-env }}
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.48.0
+          environments: ${{ matrix.pixi-env }}
+
+      - name: Run pre-commit checks
+        run: pixi run -e ${{ matrix.pixi-env }} pre-commit run --all
+
+      - name: Run pylint
+        run: pixi run -e ${{ matrix.pixi-env }} pylint bambi
+
+      - name: Run tests with Coverage
+        run: pixi run -e ${{ matrix.pixi-env }} pytest -vv --cov=bambi --cov-report=term --cov-report=xml tests
+
+      - name: Check Coverage Report
+        run: pixi run -e ${{ matrix.pixi-env }} coverage report -m
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false

.github/workflows/post-release.yml

@@ -9,11 +9,13 @@ jobs:
     name: Update changelog
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           ref: main
+          fetch-depth: 0
+
       - uses: rhysd/changelog-from-release/action@v3
         with:
           file: CHANGELOG.md
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          commit_summary_template: 'update changelog for %s changes'
+          commit_summary_template: 'update changelog for %s changes'

.github/workflows/publish-docs.yml

@@ -11,45 +11,51 @@ on:
       - synchronize
 
 jobs:
-  build:
+  build-dics:
+    if: github.repository == 'bambinos/bambi'
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
-      - name: Install quartodoc and griffe
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install quartodoc==0.11.1
+      - name: Install quartodoc
+        run: python -m pip install quartodoc==0.11.1
 
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
         with:
           version: 1.7.32 # since this is my local version, we could change it
 
-      - name: Build docs
+      - name: Build documentation
         shell: bash
         run: |
           python -m quartodoc build --config docs/_quarto.yml
           quarto render docs
           touch docs/_site/.nojekyll
 
       - name: Publish to GitHub
-        if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags') # Only from main or a tag
+        if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags')
         uses: quarto-dev/quarto-actions/publish@v2
         with:
           target: gh-pages
           render: false
           path: docs/_site
 
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+
+# NOTES
+# 1. The job runs only in the bambinos/bambi repository. It does not make sense to do it elsewhere.
+# 2. The rendered webpage is published ONLY when the job was triggered by:
+#   - A commit to main
+#   - A tagged release

.github/workflows/publish-pypi.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -42,7 +42,7 @@ jobs:
           path: dist
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -55,7 +55,7 @@ jobs:
           TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
         run: python3 -m twine upload --skip-existing --repository testpypi dist/*
 
-      - name: Test pip install from test.pypi
+      - name: Test pip install from Test PyPI and verify version number
         run: |
           python -m venv venv-test-pypi
           venv-test-pypi/bin/python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple bambi
@@ -73,7 +73,7 @@ jobs:
           path: dist
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -87,6 +87,6 @@ jobs:
         run: python3 -m twine upload dist/*
 
 # See documentation on accesing the tag from the release
-# Look for 'github.ref' and 'github.ref_name' in https://docs.github.com/en/actions/learn-github-actions/contexts 
+# Look for 'github.ref' and 'github.ref_name' in https://docs.github.com/en/actions/learn-github-actions/contexts
 # On October, 2023 it says "For workflows triggered by release, this is the release tag created"
-# So 'github.ref_name' should be the version number of the release we're making.
+# So 'github.ref_name' should be the version number of the release we're making.

.github/workflows/test.yml

@@ -1,24 +1,17 @@
-*.pyc
-*.so
-*~
-.#*
-.DS_Store
-build
-*.egg-info/
-dist/
+.cache
 .coverage
-tags
-*.zip
-*.nt.bz2
-*.tar.gz
-*.tgz
+.DS_Store
 .ipynb_checkpoints
-*.orig
-.cache
-docs/_build
+.pixi
+.pytest_cache
+.Rproj.user
 .vscode/
-pytest.ini
+*.egg-info/
+*.ipynb
+*.pyc
 /.quarto/
-.Rproj.user
-# Git ignore all the notebook files in the root
-*.ipynb
+build
+dist/
+docs/_build
+tags
+pixi.lock

.gitignore

@@ -1,18 +1,20 @@
 fail_fast: true
 
 repos:
-  - repo: https://github.com/ambv/black
-    rev: 22.3.0
+  - repo: https://github.com/psf/black
+    rev: 25.9.0
     hooks:
       - id: black
-        args: [--diff, --check]
+        args: [--diff, --check, --color]
 
-  - repo: https://github.com/PyCQA/pylint
-    rev: v2.10.2
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
     hooks:
-      - id: pylint
-        args: [--rcfile=.pylintrc]
-  - repo: https://github.com/MarcoGorelli/madforhooks
-    rev: 0.3.0
-    hooks:
-      - id: no-print-statements
+      - id: check-toml
+        types: [toml]
+      - id: check-yaml
+        types: [yaml]
+      - id: end-of-file-fixer
+        types: [text]
+      - id: check-added-large-files
+        args: ["--maxkb=2048"]