Merge branch 'main' into vi_dev

.github/workflows/benchmark.yml

@@ -0,0 +1,28 @@
+name: Benchmarks
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  benchmark:
+    name: Run benchmarks
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.10' ]
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up benchmark environment
+        run: |
+          python -m pip install -U pip
+          pip install .
+          less requirements.txt | grep 'pytest\|chex' | xargs -i -t pip install {}
+      - name: Run benchmarks
+        run: |
+          pytest -vv -m benchmark

.github/workflows/nightly.yml

@@ -1,28 +1,48 @@
 name: Nightly
+
 on:
-  schedule:
-    - cron: "0 0 * * *"
+  push:
+    branches: [main]
 
 jobs:
   build_and_publish:
-    name: Build source distribution
+    name: Build and publish on PyPi
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
-      - uses: actions/setup-python@v2
-        with:
-          python-version: "3.7"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade build
-      - name: Build the sdist
-        run: python -m build
-        env:
-          BUILD_BLACKJAX_NIGHTLY: true
-      - uses: pypa/gh-action-pypi-publish@v1.4.2
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_NIGHTLY_TOKEN }}
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Update pyproject.toml
+      # Taken from /~https://github.com/aesara-devs/aesara/pull/1375
+      run: |
+        curl -sSLf /~https://github.com/TomWright/dasel/releases/download/v2.0.2/dasel_linux_amd64 \
+          -L -o /tmp/dasel && chmod +x /tmp/dasel
+        /tmp/dasel put -f pyproject.toml project.name -v blackjax-nightly
+        /tmp/dasel put -f pyproject.toml tool.setuptools_scm.version_scheme -v post-release
+        /tmp/dasel put -f pyproject.toml tool.setuptools_scm.local_scheme -v no-local-version
+    - name: Build the sdist and wheel
+      run: |
+        python -m pip install -U pip
+        python -m pip install build
+        python -m build
+    - name: Check sdist install and imports
+      run: |
+        mkdir -p test-sdist
+        cd test-sdist
+        python -m venv venv-sdist
+        venv-sdist/bin/python -m pip install ../dist/blackjax-nightly-*.tar.gz
+        venv-sdist/bin/python -c "import blackjax"
+    - name: Check wheel install and imports
+      run: |
+        mkdir -p test-wheel
+        cd test-wheel
+        python -m venv venv-wheel
+        venv-wheel/bin/python -m pip install ../dist/blackjax_nightly-*.whl
+    - name: Publish to PyPi
+      uses: pypa/gh-action-pypi-publish@v1.4.2
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_NIGHTLY_TOKEN }}

.github/workflows/release.yml

@@ -7,32 +7,42 @@ on:
 
 jobs:
   release-job:
-    name: Release on PyPi
+    name: Build and publish on PyPi
     runs-on: ubuntu-latest
-    env:
-      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
-        python-version: 3.7
-    - name: Install release tooling
+        python-version: 3.9
+    - name: Build sdist and wheel
       run: |
-        pip install twine wheel
-    - name: Build package
+        python -m pip install -U pip
+        python -m pip install build
+        python -m build
+    - name: Check that the package version matches the Release name
       run: |
-        python setup.py sdist bdist_wheel
-    - name: Check that `blackjax.__version__` matches the Release name
-      run: |
-        echo "GITHUB_REF: ${GITHUB_REF}"
-        # The GITHUB_REF should be something like "refs/tags/v3.x.x"
-        # Make sure the package version is the same as the tag
         grep -Rq "^Version: ${GITHUB_REF:10}$" blackjax.egg-info/PKG-INFO
-    - name: Publish to PyPi
+    - name: Check sdist install and imports
       run: |
-        twine check dist/*
-        twine upload --repository pypi --username __token__ --password ${PYPI_TOKEN} dist/*
+        mkdir -p test-sdist
+        cd test-sdist
+        python -m venv venv-sdist
+        venv-sdist/bin/python -m pip install ../dist/blackjax-*.tar.gz
+        venv-sdist/bin/python -c "import blackjax"
+    - name: Check wheel install and imports
+      run: |
+        mkdir -p test-wheel
+        cd test-wheel
+        python -m venv venv-wheel
+        venv-wheel/bin/python -m pip install ../dist/blackjax-*.whl
+        venv-wheel/bin/python -c "import blackjax"
+    - name: Publish to PyPi
+      uses: pypa/gh-action-pypi-publish@v1.4.2
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}
+
   test-install-job:
     name: Test install from PyPi
     needs: release-job

.github/workflows/test.yml

@@ -13,6 +13,8 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
     - uses: pre-commit/action@v2.0.0
 
   test:
@@ -24,44 +26,22 @@ jobs:
       matrix:
         python-version: [ '3.7', '3.10']
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dev environment & blackjax
-        run: |
-          python -m pip install --upgrade pip
-          pip install .
-          less requirements.txt | grep 'pytest\|chex' | xargs -i -t pip install {}
-      - name: Run the tests with pytest
-        run: |
-          pytest -n 4 -vv -m "not benchmark" --cov=blackjax --cov-report=xml --cov-report=term tests
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
-        with:
-          env_vars: OS,PYTHON
-          name: codecov-umbrella
-          fail_ci_if_error: false
-
-  benchmark:
-    name: Run benchmarks
-    needs: [test]
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [ '3.10' ]
-    steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dev environment & blackjax
-        run: |
-          python -m pip install --upgrade pip
-          pip install .
-          less requirements.txt | grep 'pytest\|chex' | xargs -i -t pip install {}
-      - name: Run the benchmarks with pytest-benchmark
-        run: |
-          pytest -n 4 -vv -m benchmark --cov=blackjax --cov-report=xml --cov-report=term tests
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Set up test environment
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+        less requirements.txt | grep 'pytest\|chex' | xargs -i -t pip install {}
+    - name: Run tests
+      run: |
+        pytest -n auto -vv -m "not benchmark" --cov=blackjax --cov-report=xml --cov-report=term tests
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        env_vars: OS,PYTHON
+        name: codecov-umbrella
+        fail_ci_if_error: false

.gitignore

@@ -30,6 +30,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+_version.py
 
 # Installer logs
 pip-log.txt

.gitlint

@@ -0,0 +1,20 @@
+[title-max-length]
+line-length=120
+
+[title-min-length]
+min-length=15
+
+[title-match-regex]
+# python-style regex that the commit-msg title must match
+# Note that the regex can contradict with other rules if not used correctly
+# (e.g. title-must-not-contain-word).
+regex=^[A-Z].*$
+
+[title-must-not-contain-word]
+# Comma-separated list of words that should not occur in the title. Matching is case
+# insensitive. It's fine if the keyword occurs as part of a larger word (so "WIPING"
+# will not cause a violation, but "WIP: my title" will.
+words=wip
+
+[body-max-line-length]
+line-length=72

.pre-commit-config.yaml

@@ -1,6 +1,5 @@
 exclude: |
     (?x)^(
-        versioneer\.py|
         blackjax/_version\.py|
     )$
 repos:
@@ -46,3 +45,8 @@ repos:
       args: ['--profile=black']
     - id: nbqa-flake8
       args: ['--ignore=E501,E203,E302,E402,E731,W503']
+- repo: /~https://github.com/jorisroovers/gitlint
+  rev: v0.18.0
+  hooks:
+    - id: gitlint
+    - id: gitlint-ci

blackjax/__init__.py

@@ -1,3 +1,5 @@
+from blackjax._version import __version__
+
 from .diagnostics import effective_sample_size as ess
 from .diagnostics import potential_scale_reduction as rhat
 from .kernels import (
@@ -22,6 +24,7 @@
 from .optimizers import dual_averaging, lbfgs
 
 __all__ = [
+    "__version__",
     "dual_averaging",  # optimizers
     "lbfgs",
     "hmc",  # mcmc
@@ -44,7 +47,3 @@
     "ess",  # diagnostics
     "rhat",
 ]
-
-from . import _version
-
-__version__ = _version.get_versions()["version"]