Project setup stuff

.github/release.yml

@@ -0,0 +1,24 @@
+# This file contains configuration for the automatic generation of release notes in GitHub.
+# It's not perfect, but it makes it a little less laborious to write informative release notes.
+# Also see https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes
+changelog:
+  exclude:
+    labels:
+      - no releasenotes
+  categories:
+    - title: Major Changes 🛠
+      labels:
+        - major
+    - title: New Features 🎉
+      labels:
+        - enhancements
+        - feature request
+    - title: Bugfixes 🪲
+      labels:
+        - bug
+    - title: Documentation 📖
+      labels:
+        - docs
+    - title: Maintenance 🔧
+      labels:
+        - "*"

.github/workflows/pypi.yml

@@ -0,0 +1,46 @@
+name: PyPI
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4.3.1
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
+        with:
+          python-version: "3.12"
+      - name: Build the sdist and the wheel
+        run: |
+          pip install build
+          python3 -m build
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+        with:
+          name: artifact
+          path: dist/*
+
+  publish:
+    name: upload release to PyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'bwengals' && github.event_name == 'release' && github.event.action == 'published'
+    # Use the `release` GitHub environment to protect the Trusted Publishing (OIDC)
+    # workflow by requiring signoff from a maintainer.
+    environment: release
+    permissions:
+      # write id-token is necessary for trusted publishing (OIDC)
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0

.github/workflows/test.yml

@@ -0,0 +1,53 @@
+name: pytest
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+    paths:
+      - ".github/workflows/*"
+      - "ptgp/**"
+      - "tests/**"
+      - "pyproject.toml"
+      - "conda_envs/**"
+
+# Cancels all previous workflow runs for pull requests that have not completed.
+concurrency:
+  # The concurrency group contains the workflow name and the branch name for pull requests
+  # or the commit hash for any other events.
+  group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python-version: "3.13"
+            shell: bash -leo pipefail {0}
+          - os: windows-latest
+            python-version: "3.12"
+            shell: cmd /C call {0}
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: ${{ matrix.shell }}
+    steps:
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4.3.1
+      - uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        with:
+          environment-file: conda_envs/environment-test.yaml
+          create-args: >-
+            python=${{ matrix.python-version }}
+          environment-name: ptgp-test
+          init-shell: ${{ matrix.os == 'windows-latest' && 'cmd.exe' || 'bash' }}
+          cache-environment: true
+      - name: Install ptgp
+        run: |
+          pip install -e .
+          python --version
+      - name: Run tests
+        run: |
+          python -m pytest --color=yes -vv --durations=50 tests/

.gitignore

@@ -1,3 +1,7 @@
+# Don't check in hatch-vcs generated version file
+ptgp/_version.py
+
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -174,3 +178,4 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+ci:
+  autofix_prs: false
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+    -   id: check-merge-conflict
+    -   id: check-toml
+    -   id: check-yaml
+    -   id: debug-statements
+    -   id: end-of-file-fixer
+    -   id: no-commit-to-branch
+        args: [--branch, main]
+    -   id: trailing-whitespace
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.5
+  hooks:
+    - id: ruff
+      args: [ --fix, --unsafe-fixes, --exit-non-zero-on-fix ]
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]
+
+- repo: https://github.com/MarcoGorelli/madforhooks
+  rev: 0.4.1
+  hooks:
+    - id: no-print-statements
+      files: ^ptgp/

README.md

@@ -72,4 +72,4 @@ Requires the `assumption-system` branch of PyTensor:
 
 ```bash
 pip install git+https://github.com/jessegrabowski/pytensor@assumption-system
-```
+```

conda_envs/environment-test.yaml

@@ -0,0 +1,15 @@
+name: ptgp-test
+channels:
+    - conda-forge
+dependencies:
+    - python>=3.12
+    - jax
+    - jaxlib
+    - optax
+    - numpy
+    - pytest
+    - gpjax
+    - pip
+    - pip:
+        - git+https://github.com/jessegrabowski/pytensor@assumption-system
+        - git+https://github.com/pymc-devs/pymc@v6

environment.yaml → conda_envs/environment.yaml

@@ -2,7 +2,7 @@ name: ptgp
 channels:
     - conda-forge
 dependencies:
-    - python>=3.11
+    - python>=3.12
     #- pymc  # installed from v6 branch via pip
     - jax
     - jaxlib
@@ -19,7 +19,10 @@ dependencies:
     - seaborn
     - pandas
     - scikit-learn
+    - pre-commit
+    - pytest
     #- arviz  # installed via pip (arviz 1.x + arviz-base + arviz-plots)
+    - pymc
     - pip
     - pip:
         - git+https://github.com/jessegrabowski/pytensor@assumption-system

notebooks/demo.md

@@ -125,7 +125,7 @@ with pm.Model() as vfe_model:
 
 train_step_vfe, shared_params_vfe, shared_extras_vfe = pg.compile_training_step(
     pg.collapsed_elbo, vfe, X_var, y_var,
-    pm_model=vfe_model, 
+    pm_model=vfe_model,
     extra_vars=[Z_var],
     extra_init=[Z_init],
     learning_rate=1e-2,