Tooling

.github/workflows/release.yml

@@ -0,0 +1,47 @@
+name: Release
+
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: build release distributions
+        run: |
+          python -m pip install pdm
+          pdm build
+
+      - name: upload windows dists
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+

.github/workflows/run_tests.yml

@@ -0,0 +1,43 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+      - '**'
+    tags-ignore:
+      - '**'
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+        matrix:
+            os: [ubuntu-latest, windows-latest]
+            python-version: [3.12]
+
+    steps:
+
+    - name: checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install pdm
+      run: pip install pdm
+
+    - name: pre-commit checks
+      uses: pre-commit/action@v2.0.3
+
+    - name: Run tests
+      run: |
+        pdm install --dev
+        pdm run pytest tests --cov=src
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.0
+  hooks:
+    # Run the linter.
+    - id: ruff
+    # Run the formatter.
+    - id: ruff-format
+

README.md

@@ -1,8 +1,8 @@
 # grapevine
 
-JAX/Blackjax implementation of the grapevine method for reusing the solutions of guessing problems embedded in Hamiltonian trajectories. 
+JAX/Blackjax implementation of the grapevine method for reusing the solutions of guessing problems embedded in Hamiltonian trajectories.
 
-The grapevine method can dramatically speed up MCMC for statistical with embedded equation solving problems. 
+The grapevine method can dramatically speed up MCMC for statistical with embedded equation solving problems.
 
 ## Installation
 

benchmarks/optimistix_example.py

@@ -1,6 +1,6 @@
 """An example comparing GrapeNUTS and NUTS on a representative problem.
 
-This is supposed to be a complete example, mirroring how the grapevine method is used in practice.  
+This is supposed to be a complete example, mirroring how the grapevine method is used in practice.
 
 
 """

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "grapevine"
+name = "grapevine-mcmc"
 version = "0.1.0"
 description = "Faster Hamiltonian trajectories for problems with guesses, using Blackjax"
 authors = [
@@ -33,3 +33,6 @@ dev = [
 ]
 [tool.hatch.metadata]
 allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/grapevine"]

tests/simple_example_problem.py

@@ -1,4 +1,5 @@
 """Simple example problems for other tests to use."""
+
 from functools import partial
 
 from jax.scipy.special import expit