Merge pull request #314 from benjeffery/packaging-update

Update packaging

.circleci/config.yml

@@ -6,7 +6,7 @@ orbs:
 jobs:
   build:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.10.13
     steps:
       - checkout
       - run:
@@ -17,10 +17,6 @@ jobs:
               sudo apt-get install libgsl-dev
               # way to set path persistently https://circleci.com/docs/2.0/env-vars/#setting-path
               echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
-      - run:
-          name: Compile Python
-          command: |
-              python setup.py build_ext --inplace      
       - run:
           name: install dependencies
           command: |
@@ -44,6 +40,13 @@ jobs:
               python -m pytest -vv -n0 --cov=tsdate  --cov-report=xml --cov-branch tests
           environment:
             NUMBA_DISABLE_JIT: 1
-
       - codecov/upload:
           token: CODECOV_TOKEN
+      - run:
+          name: Build the distribution tarball.
+          command: |
+            python -m build
+
+
+
+

.github/workflows/wheels.yml

@@ -15,33 +15,29 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
             submodules: true
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: "3.10"
 
       - name: Build sdist
         shell: bash
         run: |
-          python setup.py sdist
+          python -m pip install --upgrade build
+          python -m build
 
       - name: Upload sdist
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: sdist
           path: dist
 
-      - name: Build wheels in docker
-        shell: bash
-        run: |
-          docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2010_x86_64 bash .github/workflows/docker/buildwheel.sh
-
       - name: Upload Wheels
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: wheels
           path: dist
@@ -54,11 +50,11 @@ jobs:
         python: [3.7, 3.8, 3.9, "3.10"]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: wheels
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -80,11 +76,11 @@ jobs:
         wordsize: [64]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: wheels
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -105,11 +101,11 @@ jobs:
         python: [3.7, 3.8, 3.9, "3.10"]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: wheels
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -126,21 +122,22 @@ jobs:
   PyPI_Upload:
     runs-on: ubuntu-latest
     needs: ['windows-test', 'OSX-test', 'manylinux-test']
+    environment: release
+    permissions:
+      id-token: write
     steps:
       - name: Download all
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
       - name: Move to dist
         run: |
           mkdir dist
           cp */*.{whl,gz} dist/.
       - name: Publish distribution to Test PyPI
         if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          password: ${{ secrets.test_pypi_password }}
           repository_url: https://test.pypi.org/legacy/
       - name: Publish distribution to PRODUCTION PyPI
         if: github.event_name == 'release'
-        uses: pypa/gh-action-pypi-publish@master
-        with:
-          password: ${{ secrets.pypi_password }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+

.pre-commit-config.yaml

@@ -1,29 +1,29 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.4.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
       - id: mixed-line-ending
       - id: check-case-conflict
       - id: check-yaml
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.0.1
+    rev: v3.10.0
     hooks:
       - id: reorder-python-imports
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.1
+    rev: v3.10.1
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py37-plus]
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.7.0
     hooks:
       - id: black
         language_version: python3
   - repo: https://github.com/pycqa/flake8
-    rev: 3.9.2
+    rev: 6.1.0
     hooks:
       - id: flake8
         args: [--config=.flake8]
-        additional_dependencies: ["flake8-bugbear==22.3.23", "flake8-builtins==1.5.3"]
+        additional_dependencies: ["flake8-bugbear==23.7.10", "flake8-builtins==2.1.0"]

pyproject.toml

@@ -0,0 +1,12 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "setuptools_scm",
+    "wheel",
+    "oldest-supported-numpy"
+]
+
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "tsdate/_version.py"

requirements.txt

@@ -14,3 +14,6 @@ pytest-xdist
 pytest-cov
 mpmath
 numdifftools
+setuptools>=45
+twine
+build

setup.cfg

@@ -0,0 +1,63 @@
+[metadata]
+name = tsdate
+author = Tskit Developers
+author_email = admin@tskit.dev
+license = MIT
+description = Infer node ages from a tree sequence topology.
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = http://pypi.python.org/pypi/tsdate
+project_urls =
+    Documentation = https://tsdate.readthedocs.io/en/latest/
+    Changelog = https://github.com/tskit-dev/tsdate/blob/main/CHANGELOG.rst
+    Bug Tracker = https://github.com/tskit-dev/tsdate/issues
+    GitHub = https://github.com/tskit-dev/tsdate
+classifiers =
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3 :: Only
+    License :: OSI Approved :: MIT License
+    Development Status :: 3 - Alpha
+    Environment :: Other Environment
+    Intended Audience :: Science/Research
+    Operating System :: POSIX
+    Operating System :: MacOS :: MacOS X
+    Operating System :: Microsoft :: Windows
+    Topic :: Scientific/Engineering
+    Topic :: Scientific/Engineering :: Bio-Informatics
+keywords =
+    population genetics
+    tree sequence
+    ancestral recombination graph
+    evolutionary tree
+    inference
+    dating
+    tsdate
+platforms =
+    POSIX
+    Windows
+    MacOS X
+
+[options]
+packages = tsdate
+python_requires = >=3.7
+include_package_data = True
+install_requires =
+    numpy
+    tskit>=0.2.3
+    scipy>1.2.3
+    numba>=0.46.0
+    tqdm
+    appdirs
+
+[options.entry_points]
+console_scripts =
+    tsdate=tsdate.__main__:main
+
+[tool:pytest]
+testpaths =
+    tests

setup.py

@@ -1,41 +1,8 @@
 from setuptools import setup
 
-with open("README.md") as fh:
-    long_description = fh.read()
-
 setup(
+    # The package name along with all the other metadata is specified in setup.cfg
+    # However, GitHub's dependency graph can't see the package unless we put this here.
     name="tsdate",
-    author="Anthony Wilder Wohns and Yan Wong",
-    author_email="awohns@gmail.com",
-    description="Infer node ages from a tree sequence topology",
-    long_description=long_description,
     packages=["tsdate"],
-    long_description_content_type="text/markdown",
-    url="http://pypi.python.org/pypi/tsdate",
-    python_requires=">=3.7",
-    entry_points={
-        "console_scripts": [
-            "tsdate=tsdate.__main__:main",
-        ]
-    },
-    setup_requires=["setuptools_scm"],
-    install_requires=[
-        "numpy",
-        "tskit>=0.2.3",
-        "scipy>1.2.3",
-        "numba>=0.46.0",
-        "tqdm",
-        "appdirs",
-    ],
-    project_urls={
-        "Source": "https://github.com/awohns/tsdate",
-        "Bug Reports": "https://github.com/awohns/tsdate/issues",
-    },
-    classifiers=[
-        "Programming Language :: Python :: 3.7",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: MacOS :: MacOS X",
-        "Operating System :: POSIX",
-    ],
-    use_scm_version={"write_to": "tsdate/_version.py"},
 )

tests/test_accuracy.py

@@ -122,7 +122,7 @@ def test_basic(
         }
 
         expected = ts.nodes_time[nonsamples]
-        for (observed, src) in [
+        for observed, src in [
             (dts.nodes_time[nonsamples], "ts"),
             ([dts.node(i).metadata["mn"] for i in np.where(nonsamples)[0]], "unconstr"),
         ]:

tsdate/prior.py

@@ -1044,7 +1044,6 @@ def __init__(
         allow_unary=False,
         progress=False,
     ):
-
         if approximate_priors:
             if not approx_prior_size:
                 approx_prior_size = 1000