Upgrade project, testing with nox, replace VisibleDeprecationWarning (#…

…106)

.github/workflows/deploy.yml

@@ -0,0 +1,35 @@
+name: Deploy
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+  pull_request:
+    paths:
+      - .github/workflows/deploy.yml
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/numba-stats
+    permissions:
+      id-token: write
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+          fetch-depth: 0  # needed by setuptools_scm
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+
+    - run: python -m pip install --upgrade pip build
+    - run: python -m build
+    - run: python -m pip install --prefer-binary $(echo dist/*.whl)'[test]'
+    - run: python -m pytest
+
+    - uses: pypa/gh-action-pypi-publish@release/v1
+      if: github.event_name == 'push' && contains(github.event.ref, '/tags/')

.github/workflows/ci.yml → .github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: CI
+name: Test
 
 on:
   push:
@@ -8,19 +8,25 @@ on:
     paths-ignore:
       - '*.md'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+env:
+  PIP_ONLY_BINARY: ":all:"
+
 jobs:
-  build:
+  test:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.12"]
+        python-version: ["3.9", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - run: python -m pip install --upgrade pip
-    - run: python -m pip install --prefer-binary -e .[test]
-    - run: python -m pytest
+    - run: python -m pip install --upgrade pip nox
+    - run: nox -s test

.gitignore

@@ -15,3 +15,4 @@ venv
 *.egg-info
 .vscode
 bench/*.svg
+.nox

.pre-commit-config.yaml

@@ -40,6 +40,6 @@ repos:
 
 # Python formatting
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 24.4.2
+  rev: 24.8.0
   hooks:
   - id: black

README.md

@@ -1,8 +1,10 @@
 # numba-stats
 
 ![](https://img.shields.io/pypi/v/numba-stats.svg)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13236518.svg)](https://doi.org/10.5281/zenodo.13236518)
 
-We provide `numba`-accelerated implementations of statistical distributions for common probability distributions
+
+We provide `numba`-accelerated implementations of common probability distributions.
 
 * Uniform
 * (Truncated) Normal
@@ -83,6 +85,16 @@ You won't get these errors when you call the numba-stats PDFs outside of a compi
 but
 `norm_pdf(1, 2, 3)` (as implemented above) will fail.
 
+## Documentation
+
+To get documentation, please use `help()` in the Python interpreter.
+
+Functions with equivalents in `scipy.stats` follow the `scipy` calling conventions exactly, except for distributions starting with `trunc...`, which follow a different convention, since the `scipy` behavior is very impractical. Even so, note that the `scipy` conventions are sometimes a bit unusual, particular in case of the exponential, the log-normal, and the uniform distribution. See the `scipy` docs for details.
+
+## Citation
+
+If you use this package in a scientific work, please cite us. You can generate citations in your preferred format on the [Zenodo website](https://doi.org/10.5281/zenodo.13236518).
+
 ## Benchmarks
 
 The following benchmarks were produced on an Intel(R) Core(TM) i7-8569U CPU @ 2.80GHz against SciPy-1.10.1. The dotted line on the right-hand figure shows the expected speedup (4x) from parallelization on a CPU with four physical cores.
@@ -113,15 +125,9 @@ The `bernstein.density` does not profit from auto-parallelization, on the contra
 ![](docs/_static/bernstein.density.svg)
 ![](docs/_static/truncexpon.pdf.plus.norm.pdf.svg)
 
-## Documentation
-
-To get documentation, please use `help()` in the Python interpreter.
-
-Functions with equivalents in `scipy.stats` follow the `scipy` calling conventions exactly, except for distributions starting with `trunc...`, which follow a different convention, since the `scipy` behavior is very impractical. Even so, note that the `scipy` conventions are sometimes a bit unusual, particular in case of the exponential, the log-normal, and the uniform distribution. See the `scipy` docs for details.
-
 ## Contributions
 
-**You can help with adding more distributions, patches are very welcome.** Implementing a probability distribution is easy. You need to write it in simple Python that `numba` can understand. Special functions from `scipy.special` can be used after some wrapping, see submodule `numba_stats._special.py` how it is done.
+**You can help with adding more distributions, patches are welcome.** Implementing a probability distribution is easy. You need to write it in simple Python that `numba` can understand. Special functions from `scipy.special` can be used after some wrapping, see submodule `numba_stats._special.py` how it is done.
 
 ## numba-stats and numba-scipy
 

noxfile.py

@@ -0,0 +1,50 @@
+"""
+Noxfile to orchestrate tests and computing coverage.
+
+Pass extra arguments to pytest after --
+"""
+
+import nox
+import sys
+
+sys.path.append(".")
+import python_releases
+
+nox.needs_version = ">=2024.3.2"
+nox.options.default_venv_backend = "uv|virtualenv"
+
+ENV = {
+    "COVERAGE_CORE": "sysmon",  # faster coverage on Python 3.12
+}
+
+PYPROJECT = nox.project.load_toml("pyproject.toml")
+MINIMUM_PYTHON = PYPROJECT["project"]["requires-python"].strip(">=")
+LATEST_PYTHON = str(python_releases.latest())
+
+nox.options.sessions = ["test", "maxtest"]
+
+# running in parallel with pytest-xdist does not make the tests faster
+
+
+@nox.session(reuse_venv=True)
+def test(session: nox.Session) -> None:
+    """Run all tests."""
+    session.install("-e.[test]")
+    session.run("pytest", *session.posargs)
+
+
+@nox.session(python=LATEST_PYTHON, reuse_venv=True)
+def maxtest(session: nox.Session) -> None:
+    """Run the unit and regular tests."""
+    session.install("-e.[test]")
+    session.run("pytest", *session.posargs, env=ENV)
+
+
+# Python-3.12 provides coverage info faster
+@nox.session(python="3.12", reuse_venv=True)
+def cov(session: nox.Session) -> None:
+    """Run covage and place in 'htmlcov' directory."""
+    session.install("-e.[test]")
+    session.run("coverage", "run", "-m", "pytest", env=ENV)
+    session.run("coverage", "html", "-d", "htmlcov")
+    session.run("coverage", "report", "-m")

pyproject.toml

@@ -2,8 +2,47 @@
 requires = ["setuptools>=42", "setuptools_scm[toml]>=3.4"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "numba-stats"
+dynamic = ["version"]
+requires-python = ">=3.9"
+dependencies = ["numba>=0.53", "numpy>=1.20", "scipy>=1.5"]
+authors = [{ name = "Hans Dembinski", email = "[email protected]" }]
+readme = "README.md"
+description = "Numba-accelerated implementations of scipy probability distributions and others used in particle physics"
+license = { text = "MIT" }
+classifiers = [
+    # complete classifier list: http://pypi.python.org/pypi?%3Aaction=list_classifiers
+    'Development Status :: 5 - Production/Stable',
+    'Intended Audience :: Science/Research',
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3 :: Only',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+    'Programming Language :: Python :: Implementation :: CPython',
+]
+
+[project.urls]
+repository = "https://github.com/hdembinski/numba-stats"
+
+[project.optional-dependencies]
+test = [
+    "pytest>=6",
+    "pytest-cov>=5",
+    "pytest-benchmark>=4",
+    "pydocstyle>=6",
+    "coverage>=6",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
 [tool.setuptools_scm]
-write_to = "src/numba_stats/_version.py"
 
 [tool.pytest.ini_options]
 minversion = "6.0"

python_releases.py

@@ -0,0 +1,64 @@
+"""Get the latest Python release which is online."""
+
+import urllib.request
+import re
+from html.parser import HTMLParser
+import gzip
+from packaging.version import Version
+
+
+class PythonVersionParser(HTMLParser):
+    """Specialized HTMLParser to get Python version number."""
+
+    def __init__(self):
+        """Initialize parser state."""
+        super().__init__()
+        self.versions = set()
+        self.found_version = False
+
+    def handle_starttag(self, tag, attrs):
+        """Look for the right tag and store result in an attribute."""
+        if tag == "a":
+            for attr in attrs:
+                if attr[0] == "href" and "/downloads/release/python-" in attr[1]:
+                    self.found_version = True
+                    return
+
+    def handle_data(self, data):
+        """Extract Python version from entry."""
+        if self.found_version:
+            self.found_version = False
+            match = re.search(r"Python (\d+\.\d+)", data)
+            if match:
+                self.versions.add(Version(match.group(1)))
+
+
+def versions():
+    """Get all Python release versions."""
+    req = urllib.request.Request("https://www.python.org/downloads/")
+    req.add_header("Accept-Encoding", "gzip")
+
+    with urllib.request.urlopen(req) as response:
+        raw = response.read()
+        if response.info().get("Content-Encoding") == "gzip":
+            raw = gzip.decompress(raw)
+        html = raw.decode("utf-8")
+
+    parser = PythonVersionParser()
+    parser.feed(html)
+
+    return parser.versions
+
+
+def latest():
+    """Return version of latest Python release."""
+    return max(versions())
+
+
+def main():
+    """Print all discovered release versions."""
+    print(" ".join(str(x) for x in sorted(versions())))
+
+
+if __name__ == "__main__":
+    main()