Upgrade actions infrastructure, numpy2 support, osx ARM wheels.

tskit-dev · Jun 25, 2024 · dc776a3 · dc776a3
1 parent dd693ed
commit dc776a3
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Showing 11 changed files with 124 additions and 135 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,7 +6,7 @@ orbs:
 jobs:
   build:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.9
     steps:
       - checkout
       - run:
@@ -16,7 +16,6 @@ jobs:
             sudo apt-get install -y ninja-build libcunit1-dev valgrind clang doxygen python3-pip
             # Install meson as root so we can install to the system below.
             sudo pip install meson
-            pip install numpy==1.18.5
             pip install --user -r python/requirements/development.txt
             echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
       - run:

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Install dependencies and set path
         run: |
             sudo apt-get update

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
       - uses: actions/checkout@v3
@@ -27,21 +27,21 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.8, 3.11 ]
+        python: [ 3.9, 3.12 ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:
         shell: bash
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{matrix.python}}
 
@@ -51,9 +51,15 @@ jobs:
       - name: Build module
         working-directory: python
         run: |
-          python setup.py build_ext --inplace
+          python -m build
+          python -m pip install dist/*.whl
 
       - name: Run tests
-        working-directory: python
         run: |
-          python -m pytest tests
+          python -m pytest python/tests
+          
+      - name: Run tests (numpy < 2)
+        run: |
+          pip install setuptools
+          pip install "numpy<2"
+          python -m pytest python/tests
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -15,11 +15,11 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", 3.11]
+        python: [3.9, "3.10", 3.11, 3.12]
         wordsize: [64]
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Build wheel
         env:
           PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
@@ -49,21 +49,21 @@ jobs:
           rm -rf python/kastore python/*.pyd
           ${PYTHON} -m pytest -v python
       - name: Upload Wheels
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }}
           path: python/dist
 
-  OSX:
-    runs-on: macos-latest
+  OSX-ARM:
+    runs-on: macos-14
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", 3.11]
+        python: [3.9, "3.10", 3.11, 3.12]
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
       - name: Build Wheel
@@ -82,21 +82,22 @@ jobs:
           rm -rf python/kastore python/*.so
           python -m pytest -v python
       - name: Upload Wheels
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
-          name: osx-wheel-${{ matrix.python }}
+          name: osxarm-wheel-${{ matrix.python }}
           path: python/dist
 
+
   manylinux:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Build sdist
         shell: bash
@@ -106,7 +107,7 @@ jobs:
           python setup.py sdist
 
       - name: Upload sdist
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: sdist
           path: python/dist
@@ -116,12 +117,12 @@ jobs:
         run: |
           docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2014_x86_64 bash docker/buildwheel.sh
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
 
-      - name: Run tests (3.11)
+      - name: Run tests (3.12)
         run: |
           python -VV
           # We install in this odd way to make sure we get both deps and a local kastore
@@ -132,12 +133,12 @@ jobs:
           pip install -r python/requirements/CI/tests/requirements.txt
           python -m pytest -v python
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: 3.12
 
-      - name: Run tests (3.10)
+      - name: Run tests (3.11)
         run: |
           python -VV
           # We install in this odd way to make sure we get both deps and a local kastore
@@ -148,12 +149,12 @@ jobs:
           pip install -r python/requirements/CI/tests/requirements.txt
           python -m pytest -v python
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
-      - name: Run tests (3.9)
+      - name: Run tests (3.10)
         run: |
           python -VV
           # We install in this odd way to make sure we get both deps and a local kastore
@@ -164,12 +165,12 @@ jobs:
           pip install -r python/requirements/CI/tests/requirements.txt
           python -m pytest -v python
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - name: Run tests (3.8)
+      - name: Run tests (3.9)
         run: |
           python -VV
           # We install in this odd way to make sure we get both deps and a local kastore
@@ -181,30 +182,30 @@ jobs:
           python -m pytest -v python
 
       - name: Upload Wheels
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: linux-wheels
           path: python/dist/wheelhouse
 
 
   PyPI_Upload:
     runs-on: ubuntu-latest
-    needs: ['windows', 'OSX', 'manylinux']
+    environment: release
+    needs: ['windows', 'OSX-ARM', 'manylinux']
+    permissions:
+      id-token: write
     steps:
       - name: Download all
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
       - 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') && !contains(github.event.ref, 'C_')
-        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' && !startsWith(github.event.release.tag_name, 'C_')
-        uses: pypa/gh-action-pypi-publish@master
-        with:
-          password: ${{ secrets.pypi_password }}
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.mergify.yml b/.mergify.yml
@@ -4,12 +4,12 @@ queue_rules:
       - "#approved-reviews-by>=1"
       - "#changes-requested-reviews-by=0"
       - status-success=Lint
-      - status-success=Python (3.8, macos-latest)
-      - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.8, ubuntu-latest)
-      - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.8, windows-latest)
-      - status-success=Python (3.11, windows-latest)
+      - status-success=Python (3.9, macos-latest)
+      - status-success=Python (3.12, macos-latest)
+      - status-success=Python (3.9, ubuntu-latest)
+      - status-success=Python (3.12, ubuntu-latest)
+      - status-success=Python (3.9, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
 
 pull_request_rules:
@@ -21,12 +21,12 @@ pull_request_rules:
       - base=main
       - label=AUTOMERGE-REQUESTED
       - status-success=Lint
-      - status-success=Python (3.8, macos-latest)
-      - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.8, ubuntu-latest)
-      - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.8, windows-latest)
-      - status-success=Python (3.11, windows-latest)
+      - status-success=Python (3.9, macos-latest)
+      - status-success=Python (3.12, macos-latest)
+      - status-success=Python (3.9, ubuntu-latest)
+      - status-success=Python (3.12, ubuntu-latest)
+      - status-success=Python (3.9, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
     actions:
       queue:

diff --git a/docker/shared.env b/docker/shared.env
@@ -1,7 +1,6 @@
 PYTHON_VERSIONS=(
+    cp312-cp312
     cp311-cp311
     cp310-cp310
     cp39-cp39
-    cp38-cp38
-    cp37-cp37m
 )
diff --git a/python/CHANGELOG.rst b/python/CHANGELOG.rst
@@ -1,8 +1,11 @@
 --------------------
-[0.3.X] - 202X-XX-XX
+[0.3.3] - 202X-XX-XX
 --------------------
 
-kastore now requires Python 3.8 or later.
+Maintenance release:
+
+- Support for numpy 1.x and 2.x
+- Require Python >= 3.9
 
 
 --------------------

diff --git a/python/pyproject.toml b/python/pyproject.toml
@@ -1,7 +1,50 @@
 [build-system]
-requires = [
-    "setuptools>=42",
-    "wheel",
-    "oldest-supported-numpy"
+requires = ["setuptools>=45", "wheel", "numpy>=2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "kastore"
+dynamic = ["version"]
+authors = [
+    {name = "Tskit Developers", email = "[email protected]"},
 ]
-build-backend = "setuptools.build_meta"
+description = "A write-once-read-many store for simple numerical data"
+readme = "README.md"
+license = {text = "MIT"}
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3 :: Only",
+]
+keywords = ["binary store", "numerical", "arrays"]
+dependencies = [
+    "numpy>=1.23.5",
+    "humanize",
+]
+requires-python = ">=3.9"
+
+[project.urls]
+Homepage = "https://github.com/tskit-dev/kastore"
+Documentation = "https://kastore.readthedocs.io/en/latest/"
+Changelog = "https://kastore.readthedocs.io/en/latest/changelogs.html"
+"Bug Tracker" = "https://github.com/tskit-dev/kastore/issues"
+GitHub = "https://github.com/tskit-dev/kastore"
+
+[project.scripts]
+kastore = "kastore.__main__:main"
+
+[tool.setuptools]
+packages = ["kastore"]
+
+[tool.setuptools.dynamic]
+version = {attr = "kastore._version.kastore_version"}
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
diff --git a/python/requirements/CI/tests/requirements.txt b/python/requirements/CI/tests/requirements.txt
@@ -1,7 +1,9 @@
 attrs
+build
 hypothesis
 humanize
 pytest
 pytest-cov
 numpy
 mock
+setuptools