Update packaging

tskit-dev · Oct 13, 2022 · de277cf · de277cf
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -91,12 +91,23 @@ jobs:
 
       - run:
           name: Build the distribution tarball.
-          command: python setup.py sdist
+          command: |
+            python setup.py sdist
+            python setup.py check
+            python -m twine check dist/*.tar.gz --strict
+            rm dist/*
+            python -m build
 
       - run:
           name: Install from the distribution tarball
           command: |
-               python -m venv venv
-               source venv/bin/activate
-               pip install --upgrade setuptools pip
-               pip install dist/*.tar.gz
+            python -m venv venv
+            source venv/bin/activate
+            pip install dist/*.tar.gz
+            python -c 'import tsinfer; print(tsinfer.__version__)'
+            
+            #Also check the wheel
+            pip uninstall --yes tsinfer
+            pip install dist/*.whl
+            python -c 'import tsinfer; print(tsinfer.__version__)'
+            
diff --git a/.github/workflows/docker/buildwheel.sh b/.github/workflows/docker/buildwheel.sh
@@ -6,21 +6,23 @@ set -e -x
 
 ARCH=`uname -p`
 echo "arch=$ARCH"
-#yum -y install gsl-devel #For msprime
 
 # We're running as root in the docker container so git commands issued by
 # setuptools_scm will fail without this:
 git config --global --add safe.directory /project
 # Fetch the full history as we'll be missing tags otherwise.
 git fetch --unshallow
 for V in "${PYTHON_VERSIONS[@]}"; do
+    git reset --hard
+    git clean -fd
     PYBIN=/opt/python/$V/bin
     rm -rf build/       # Avoid lib build by narrow Python is used by wide python
     # Instead of letting setup.py install a newer numpy we install it here
     # using the oldest supported version for ABI compatibility
-    $PYBIN/pip install oldest-supported-numpy
-    SETUPTOOLS_SCM_DEBUG=1 $PYBIN/python setup.py build_ext --inplace
-    SETUPTOOLS_SCM_DEBUG=1 $PYBIN/python setup.py bdist_wheel
+    $PYBIN/python -m venv env
+    source env/bin/activate
+    $PYBIN/python -m pip install --upgrade build
+    SETUPTOOLS_SCM_DEBUG=1 $PYBIN/python -m build
 done
 
 cd dist

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -27,22 +27,12 @@ jobs:
           python-version: ${{ matrix.python }}
       - name: Install deps
         run: |
-          # Upgrade pip to get bdist_wheel
-          pip install --upgrade pip
-          pip install setuptools wheel
-          # Instead of letting setup.py install a newer numpy we install it here
-          # using the oldest supported version for ABI compatibility
-          pip install oldest-supported-numpy
-      - name: Build C extension
-        run: |
-          python -VV
-          python setup.py build_ext --inplace
+          pip install --upgrade pip build delocate
       - name: Build Wheel
         run: |
-          python setup.py bdist_wheel
+          python -m build --wheel
       - name: Delocate to bundle dynamic libs
         run: |
-          pip install delocate
           delocate-wheel -v dist/*.whl
       - name: Upload Wheels
         uses: actions/upload-artifact@v3
@@ -67,27 +57,14 @@ jobs:
         shell: bash
         run: |
           set -ex
-          ${PYTHON} -m pip install --upgrade pip
-          ${PYTHON} -m pip install setuptools wheel
-          # Instead of letting setup.py install a newer numpy we install it here
-          # using the oldest supported version for ABI compatibility
-          ${PYTHON} -m pip install oldest-supported-numpy
-      - name: Build C Extension
-        env:
-          PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
-        shell: bash
-        run: |
-          set -ex
-          git reset --hard
-          ${PYTHON} -VV
-          ${PYTHON} setup.py build_ext --inplace
+          ${PYTHON} -m pip install --upgrade pip build
       - name: Build Wheel
         env:
           PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
         shell: bash
         run: |
           set -ex
-          ${PYTHON} setup.py bdist_wheel
+          ${PYTHON} -m build --wheel
       - name: Upload Wheels
         uses: actions/upload-artifact@v3
         with:
@@ -110,7 +87,8 @@ jobs:
       - name: Build sdist
         shell: bash
         run: |
-          python setup.py sdist
+          pip install --upgrade pip build
+          python -m build --sdist
 
       - name: Upload sdist
         uses: actions/upload-artifact@v3
@@ -137,7 +115,7 @@ 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: osx-wheel-${{ matrix.python }}
       - name: Set up Python ${{ matrix.python }}
@@ -160,7 +138,7 @@ jobs:
         wordsize: [64]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }}
       - name: Set up Python ${{ matrix.python }}
@@ -184,7 +162,7 @@ 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: linux-wheels
       - name: Set up Python
@@ -204,7 +182,7 @@ jobs:
     needs: ['windows-test', 'OSX-test', 'manylinux-test']
     steps:
       - name: Download all
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
       - name: Move to dist
         run: |
           mkdir dist

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@ The [documentation](https://tskit.dev/tsinfer/docs/stable) contains details of h
 
 The algorithm, its rationale, and results from testing on simulated and real data are described in the following [Nature Genetics paper](https://doi.org/10.1038/s41588-019-0483-y):
 
-> Jerome Kelleher, Yan Wong, Anthony W Wohns, Chaimaa Fadil, Patrick K Albers and Gil McVean (2019) _Inferring whole-genome histories in large population datasets_. Nature Genetics **51**: 1330-1338
+> Jerome Kelleher, Yan Wong, Anthony W Wohns, Chaimaa Fadil, Patrick K Albers and Gil McVean (2019) *Inferring whole-genome histories in large population datasets*. Nature Genetics **51**: 1330-1338
 
 Please cite this if you use ``tsinfer`` in your work. Code to reproduce the results in the paper is present in a [separate GitHub repository](https://github.com/mcveanlab/treeseq-inference).
 

diff --git a/pyproject.toml b/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 = "tsinfer/_version.py"
diff --git a/pytest.ini b/pytest.ini
diff --git a/requirements/CI-tests-complete/requirements.txt b/requirements/CI-tests-complete/requirements.txt
@@ -1,4 +1,5 @@
 attrs==21.4.0
+build==0.8.0
 codecov==2.1.12
 colorama==0.4.4
 daiquiri==3.0.1
@@ -14,7 +15,9 @@ pytest==7.1.2
 pytest-cov==3.0.0
 pytest-xdist==2.5.0
 seaborn==0.11.2
+setuptools==65.4.1
 sortedcontainers==2.4.0
 tqdm==4.64.0
 tskit==0.5.3
+twine==4.0.1
 zarr==2.11.3
diff --git a/requirements/development.txt b/requirements/development.txt
@@ -25,6 +25,7 @@ numa; sys_platform == 'linux'
 sphinx
 sphinx-argparse
 sphinx_rtd_theme
+setuptools>=45
 setuptools_scm
 # Needed for evaluation script.
 pandas

diff --git a/setup.cfg b/setup.cfg
@@ -0,0 +1,77 @@
+[metadata]
+name = tsinfer
+author= Tskit Developers
+author_email = admin@tskit.dev
+license = GNU GPLv3+
+description= Infer tree sequences from genetic variation data.
+long_description_content_type = text/x-markdown
+long_description = file: README.md
+url = https://tskit.dev/tsinfer
+project_urls =
+    Documentation = https://tskit.dev/tsinfer/docs/stable
+    Changelog = https://tskit.dev/tsinfer/docs/stable/CHANGELOG.html
+    Bug Tracker = https://github.com/tskit-dev/tsinfer/issues
+    GitHub = https://github.com/tskit-dev/tsinfer/
+classifiers =
+    Programming Language :: C
+    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 :: GNU General Public License v3 or later (GPLv3+)
+    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
+    tsinfer
+platforms =
+    POSIX
+    Windows
+    MacOS X
+
+[options]
+packages = tsinfer
+python_requires = >=3.7
+include_package_data = True
+install_requires =
+    numpy
+    six
+    tqdm
+    humanize
+    daiquiri
+    tskit>=0.5.3
+    numcodecs>=0.6
+    # issues 965 and 967 at zarr-python prevent usage of 2.11.0 and 2.11.1
+    zarr>=2.2!=2.11.0!=2.11.1!=2.11.2
+    lmdb
+    sortedcontainers
+    attrs>=19.2.0
+
+[options.entry_points]
+console_scripts =
+    tsinfer = tsinfer.__main__:main
+
+[tool:pytest]
+addopts = -n 4
+testpaths =
+    tests
+
+[bdist_wheel]
+# This flag says to generate wheels that support both Python 2 and Python
+# 3. If your code will not run unchanged on both Python 2 and 3, you will
+# need to generate separate wheels for each Python version that you
+# support.
+universal=0
diff --git a/setup.py b/setup.py
@@ -1,26 +1,15 @@
 import os
 import platform
 
+import numpy
 from setuptools import Extension
 from setuptools import setup
-from setuptools.command.build_ext import build_ext as _build_ext
 
-IS_WINDOWS = platform.system() == "Windows"
-
-
-# Obscure magic required to allow numpy be used as an 'setup_requires'.
-class build_ext(_build_ext):
-    def finalize_options(self):
-        super().finalize_options()
-        # Prevent numpy from thinking it is still in its setup process:
-        __builtins__.__NUMPY_SETUP__ = False
-        import numpy
-
-        self.include_dirs.append(numpy.get_include())
 
+IS_WINDOWS = platform.system() == "Windows"
 
 libdir = "lib"
-tskroot = os.path.join("lib", "subprojects", "tskit")
+tskroot = os.path.join(libdir, "subprojects", "tskit")
 tskdir = os.path.join(tskroot, "tskit")
 kasdir = os.path.join(tskroot, "subprojects", "kastore")
 includes = [libdir, tskroot, tskdir, kasdir]
@@ -53,59 +42,16 @@ def finalize_options(self):
 _tsinfer_module = Extension(
     "_tsinfer",
     sources=sources,
-    # Enable asserts by default.
-    undef_macros=["NDEBUG"],
     extra_compile_args=["-std=c99"],
-    include_dirs=includes,
     libraries=libraries,
+    # Enable asserts by default.
+    undef_macros=["NDEBUG"],
+    include_dirs=includes + [numpy.get_include()],
 )
 
-with open("README.md") as f:
-    long_description = f.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="tsinfer",
-    description="Infer tree sequences from genetic variation data.",
-    long_description=long_description,
-    packages=["tsinfer"],
-    author="Jerome Kelleher",
-    author_email="jerome.kelleher@bdi.ox.ac.uk",
-    url="http://pypi.python.org/pypi/tsinfer",
-    python_requires=">=3.7",
-    entry_points={"console_scripts": ["tsinfer=tsinfer.__main__:main"]},
-    setup_requires=["setuptools_scm", "numpy"],
-    cmdclass={"build_ext": build_ext},
-    install_requires=[
-        "numpy",
-        "six",
-        "tqdm",
-        "humanize",
-        "daiquiri",
-        "tskit>=0.5.3",
-        "numcodecs>=0.6",
-        # issues 965 and 967 at zarr-python prevent usage of 2.11.0 and 2.11.1
-        "zarr>=2.2,!=2.11.0,!=2.11.1,!=2.11.2",
-        "lmdb",
-        "sortedcontainers",
-        "attrs>=19.2.0",
-    ],
     ext_modules=[_tsinfer_module],
-    keywords=[],
-    license="GNU GPLv3+",
-    classifiers=[
-        "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 :: GNU General Public License v3 or later (GPLv3+)",
-        "Development Status :: 3 - Alpha",
-        "Environment :: Other Environment",
-        "Intended Audience :: Science/Research",
-        "Operating System :: POSIX",
-        "Topic :: Scientific/Engineering",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-    ],
-    use_scm_version={"write_to": "tsinfer/_version.py"},
 )