packaging changes

.github/workflows/coverage.yml

@@ -13,11 +13,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.11" ]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: "pip: Python ${{ matrix.python-version }} coverage"
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/pypi-release.yml

@@ -11,7 +11,7 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'Bump version')"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         persist-credentials: false
     - name: current_version
@@ -22,11 +22,11 @@ jobs:
         current_version: "${{ env.current_version }}"
         files: DESCRIPTION
         commit_name: Version autobump
-        commit_email: andrew@friarswood.net
-        login: virgesmith
+        commit_email: devops@friarswood.net
+        login: "${{ secrets.REPO_LOGIN }}"
         token: "${{ secrets.REPO_PAT }}"
         # part defaults to patch
-        part: minor
+        # part: minor
     - name: Create dist
       run: |
         pip install pybind11

.github/workflows/python-test.yml

@@ -19,12 +19,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: "pip: Python ${{ matrix.python-version }} / ${{ matrix.os }}"
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -44,30 +44,3 @@ jobs:
       run: |
         python -m pytest
 
-  # package:
-  #   needs: build
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #   - uses: actions/checkout@v3
-  #   - name: "pip: Python 3.11 / ubuntu-latest"
-  #     uses: actions/setup-python@v4
-  #     with:
-  #       python-version: "3.11"
-  #   - name: Bump version
-  #     run: |
-  #       python -m pip install bump2version pybind11
-  #       bump2version patch
-  #   - name: Create dist
-  #     run: |
-  #       python setup.py sdist
-  #   - name: artifacts
-  #     uses: actions/upload-artifact@v3
-  #     with:
-  #       name: dt_utils_${{ matrix.python-version }}
-  #       path: |
-  #         dist
-  #   - name: Publish
-  #     uses: pypa/gh-action-pypi-publish@release/v1
-  #     with:
-  #       password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-  #       repository-url: https://test.pypi.org/legacy/

.github/workflows/r-cmd-check.yml

@@ -1,5 +1,7 @@
 on:
   push:
+    branches:
+      - main
   pull_request:
     branches:
       - main
@@ -29,7 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
@@ -46,6 +48,6 @@ jobs:
           check-dir: '"check"'
       - name: artifacts
         if: ${{ matrix.config.r == 'release' && matrix.config.os == 'ubuntu-latest' }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           path: check

.gitignore

@@ -3,12 +3,11 @@
 .RData
 .Ruserdata
 build/
-node_modules/
 stubs/
 *.o
 *.d
-src/*.so
-src/*.dll
+*.so
+*.dll
 *.log
 
 dist/

R/humanleague.R

@@ -54,7 +54,7 @@
 #'
 #' @docType package
 #' @name humanleague
-NULL
+"_PACKAGE"
 
 #' @useDynLib humanleague
 #' @importFrom Rcpp sourceCpp

README.md

@@ -2,14 +2,14 @@
 
 [![License](https://img.shields.io/github/license/mashape/apistatus.svg)](https://opensource.org/licenses/MIT)
 
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/humanleague)](https://pypi.org/project/humanleague/)
 [![PyPI version](https://badge.fury.io/py/humanleague.svg)](https://badge.fury.io/py/humanleague)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/humanleague)](https://CRAN.R-project.org/package=humanleague)
-[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/grand-total/humanleague?color=black)](https://cran.r-project.org/package=humanleague)
 
 [![DOI](https://zenodo.org/badge/95961787.svg)](https://zenodo.org/badge/latestdoi/95961787)
 [![status](https://joss.theoj.org/papers/d5aaf6e1c2efed431c506762622473b4/status.svg)](https://joss.theoj.org/papers/d5aaf6e1c2efed431c506762622473b4)
 
-[![python (pip) build](https://github.com/virgesmith/humanleague/actions/workflows/pip-package.yml/badge.svg)](https://github.com/virgesmith/humanleague/actions/workflows/pip-package.yml/badge.svg)
+[![python (pip) build](https://github.com/virgesmith/humanleague/actions/workflows/python-test.yml/badge.svg)](https://github.com/virgesmith/humanleague/actions/workflows/python-test.yml/badge.svg)
 [![r-cmd-check](https://github.com/virgesmith/humanleague/actions/workflows/r-cmd-check.yml/badge.svg)](https://github.com/virgesmith/humanleague/actions/workflows/r-cmd-check/badge.svg)
 
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/430da36db15f46978bfccd1ad3243ae9)](https://www.codacy.com/gh/virgesmith/humanleague/dashboard?utm_source=github.com&utm_medium=referral&utm_content=virgesmith/humanleague&utm_campaign=Badge_Grade)
@@ -57,10 +57,12 @@ Requires Python 3.9 or newer. The package can be installed using `pip`, e.g.
 python -m pip install humanleague --user
 ```
 
-### Build, install and test (from cloned repo)
+#### Development
+
+Fork or clone the repo, then
 
 ```bash
-pip install -e .
+pip install -e .[dev]
 pytest
 ```
 

humanleague/__init__.py

@@ -1 +1,5 @@
-from _humanleague import flatten, integerise, ipf, qis, qisi, SobolSequence, __version__
+import importlib.metadata
+
+__version__ = importlib.metadata.version("humanleague")
+
+from _humanleague import flatten, integerise, ipf, qis, qisi, SobolSequence

pyproject.toml

@@ -2,14 +2,52 @@
 requires = [
   "setuptools>=42",
   "wheel",
-  "pybind11>=2.6.0",
+  "pybind11>=2.10.3",
   "pytest"
 ]
 
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "humanleague"
+version = "2.3.0"
+authors = [
+  { name="Andrew Smith", email="[email protected]" },
+]
+license = {file = "LICENSE.md"}
+description = "Microsynthesis using quasirandom sampling and/or IPF"
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy>=1.19.1"
+]
+
+[project.optional-dependencies]
+dev = [
+  "pybind11>=2.10.3",
+  "pytest>=7.1.3",
+  "mypy>=1.5.0",
+  "mypy-extensions>=1.0.0",
+  "ruff>=0.0.286",
+  "build>=0.10.0"
+]
+
 [tool.pytest.ini_options]
 minversion = "6.0"
 testpaths = [
   "tests"
 ]
+
+[tool.ruff]
+select = ["E", "F"]
+ignore = ["E501"]
+
+[tool.ruff.per-file-ignores]
+"**/__init__.py" = ["F401", "F403"]

setup.cfg

@@ -1,6 +1,14 @@
 [bumpversion]
 current_version = 2.3.0
 
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:DESCRIPTION]
+search = Version: "{current_version}"
+replace = version: "{new_version}"
+
 [aliases]
 test = pytest
 

setup.py

@@ -5,20 +5,6 @@
 from pybind11.setup_helpers import Pybind11Extension, ParallelCompile
 
 
-def readme():
-  with open('README.md') as f:
-    return f.read()
-
-
-def version():
-  """ The R file DESCRIPTION in the project root is now the single source of version info """
-  with open("DESCRIPTION") as fd:
-    lines = fd.readlines()
-    for line in lines:
-      if line.startswith("Version:"):
-        return line.rstrip().split(":")[1].lstrip()
-
-
 def source_files():
   sources = glob.glob("src/*.cpp")
   # can't use compile skips as some files are auto-generated
@@ -35,7 +21,6 @@ def header_files():
 
 def defines():
   return [
-    ("HUMANLEAGUE_VERSION", version()),
     ("PYTHON_MODULE", None)
   ]
 
@@ -46,7 +31,7 @@ def defines():
     sources=source_files(),
     include_dirs=["src"],
     define_macros=defines(),
-    depends=["setup.py", "DESCRIPTION", "src/docstr.inl"] + header_files(),
+    depends=["setup.py", "src/docstr.inl"] + header_files(),
     cxx_std=20,
   )
 ]
@@ -56,23 +41,8 @@ def defines():
 
 setup(
   name='humanleague',
-  version=version(),
-  description='Microsynthesis using quasirandom sampling and/or IPF',
-  author='Andrew P Smith',
-  author_email='[email protected]',
-  url='http://github.com/virgesmith/humanleague',
-  long_description=readme(),
-  long_description_content_type="text/markdown",
   packages=["humanleague"],
   package_data={"humanleague": ["py.typed", "*.pyi"]},
   ext_modules=ext_modules,
-  install_requires=['numpy>=1.19.1'],
-  setup_requires=['pybind11>=2.5.0', 'pytest-runner'],
-  tests_require=['pytest'],
-  classifiers=[
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
-  ],
   zip_safe=False,
 )

src/NDArray.h

@@ -8,6 +8,7 @@
 #if __cplusplus <= 201703l
 #include <cstddef>
 #endif
+#include <cstdint>
 #include <cassert>
 
 // The array storage

src/module.cpp

@@ -15,9 +15,6 @@
 
 namespace py = pybind11;
 
-#define STR2(x) #x
-#define STR(x) STR2(x)
-
 using namespace py::literals;
 
 
@@ -298,8 +295,6 @@ PYBIND11_MODULE(_humanleague, m) {
 
   m.doc() = module_docstr;
 
-  m.attr("__version__") = STR(HUMANLEAGUE_VERSION);
-
   m.def("flatten",
         hl::flatten,
         flatten_docstr,