Add Python 3.14 support

.github/workflows/ci.yml

@@ -1,61 +1,160 @@
 name: CI
+
 on:
   push:
-  schedule:
-    - cron: '0 0 1 * *'
   pull_request:
   workflow_dispatch:
+  schedule:
+    - cron: "0 0 1 * *"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  ci:
+  lint:
+    name: Ruff
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - name: Checkout
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.12.2"
+          python-version: "3.14"
+          enable-cache: true
+
+      - name: Ruff
+        run: uvx ruff@0.7.1 check
+
+  test:
+    name: Test (${{ matrix.os }}, Python ${{ matrix.python-version }})
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-2022, macos-13, macos-14]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-2022, macos-15-intel, macos-15]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+    env:
+      UV_PYTHON: ${{ matrix.python-version }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+
+      - name: Install uv and Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.12.2"
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-suffix: ${{ matrix.os }}-${{ matrix.python-version }}
+
+      - name: Install core test dependencies
+        run: uv sync --frozen --extra dev
+
+      - name: Run the canonical core suite
+        run: uv run --frozen --no-sync python tests/test.py
+
+      - name: Install optional dependencies
+        run: uv sync --frozen --all-extras
+
+      - name: Run the optional BGEN suite
+        run: uv run --frozen --no-sync pytest pysnptools/distreader/test_bgen2.py
+
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
     steps:
-    - name: Checkout
-      uses: actions/checkout@v4
-
-    - name: Install the latest version of uv
-      uses: astral-sh/setup-uv@v3
-    - name: Install Python ${{ matrix.python-version }}
-      run: uv python install ${{ matrix.python-version }}
-
-
-    - name: Pinned Ruff
-      run:  uvx ruff@0.7.1 check
-    - name: Lastest Ruff (just to check for warnings)
-      run: uvx ruff@latest check || echo "Ignoring warnings from the latest version of ruff"
-    - name: Install minimal dependencies
-      run: uv sync --extra dev
-    - name: Run min test
-      shell: bash
-      run: |
-        if [[ "$RUNNER_OS" != "Windows" ]]; then
-          source .venv/bin/activate
-        else
-          source .venv/Scripts/activate
-        fi
-        python tests/test.py
-    - name: Install all dependencies
-      run: uv sync --all-extras
-    - name: Run all tests
-      shell: bash
-      run: |
-        if [[ "$RUNNER_OS" != "Windows" ]]; then
-          source .venv/bin/activate
-        else
-          source .venv/Scripts/activate
-        fi
-        pytest pysnptools/distreader/test_bgen2.py
-
-    - name: Build
-      run: uv build        
-    - name: Save SDist
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13'
-      uses: actions/upload-artifact@v4
-      with:
-        name: wheels
-        path: dist/*.tar.gz
+      - name: Checkout
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.12.2"
+          python-version: "3.14"
+          enable-cache: true
+
+      - name: Build wheel and source distribution
+        run: uv build --no-sources
+
+      - name: Build wheel directly from the checkout
+        run: uv build --wheel --no-sources --out-dir direct-dist
+
+      - name: Compare direct and sdist-derived wheels
+        shell: bash
+        run: cmp dist/*.whl direct-dist/*.whl
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: distributions
+          path: |
+            dist/*.whl
+            dist/*.tar.gz
+          if-no-files-found: error
+          retention-days: 7
+
+  artifact-test:
+    name: Artifact test (${{ matrix.kind }}, Python ${{ matrix.python-version }})
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - kind: wheel
+            python-version: "3.10"
+            package: dist/*.whl
+          - kind: sdist
+            python-version: "3.10"
+            package: dist/*.tar.gz
+          - kind: wheel
+            python-version: "3.14"
+            package: dist/*.whl
+          - kind: sdist
+            python-version: "3.14"
+            package: dist/*.tar.gz
+    steps:
+      - name: Install uv and Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.12.2"
+          python-version: ${{ matrix.python-version }}
+          no-project: true
+          enable-cache: false
+
+      - name: Download distributions
+        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
+        with:
+          name: distributions
+          path: dist
+
+      - name: Create clean environment
+        run: uv venv --python ${{ matrix.python-version }} .artifact-venv
+
+      - name: Install exact ${{ matrix.kind }} artifact
+        run: uv pip install --python .artifact-venv/bin/python ${{ matrix.package }}
+
+      - name: Smoke-test installed package
+        run: >-
+          .artifact-venv/bin/python -c
+          "from importlib.resources import files;
+          import numpy as np;
+          import pysnptools;
+          from pysnptools.snpreader import SnpData;
+          data = SnpData(iid=[['a','a'],['b','b']], sid=['s1','s2'], val=np.array([[0.0,1.0],[2.0,1.0]]));
+          assert data.standardize().read().val.shape == (2,2);
+          manifests = ['pysnptools.hashdown.json','bgen.hashdown.json','synth.hashdown.json'];
+          assert all(files('pysnptools.util').joinpath(name).is_file() for name in manifests);
+          assert '.artifact-venv' in pysnptools.__file__;
+          print(pysnptools.__file__)"

.github/workflows/release.yml

@@ -0,0 +1,150 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build and test distributions
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - name: Checkout tagged source
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+
+      - name: Install uv and Python
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.12.2"
+          python-version: "3.14"
+          enable-cache: true
+
+      - name: Verify tag and package version
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: >-
+          python -c
+          "import os, pathlib, tomllib;
+          version = tomllib.loads(pathlib.Path('pyproject.toml').read_text())['project']['version'];
+          expected = f'v{version}';
+          assert os.environ['RELEASE_TAG'] == expected,
+          f'tag {os.environ[\"RELEASE_TAG\"]!r} does not match package version {version!r}'"
+
+      - name: Verify the lockfile
+        run: uv lock --check
+
+      - name: Install all test dependencies
+        run: uv sync --frozen --all-extras
+
+      - name: Run the canonical core suite
+        run: uv run --frozen --no-sync python tests/test.py
+
+      - name: Run the optional BGEN suite
+        run: uv run --frozen --no-sync pytest pysnptools/distreader/test_bgen2.py
+
+      - name: Build wheel and source distribution
+        run: uv build --no-sources
+
+      - name: Build wheel directly from the checkout
+        run: uv build --wheel --no-sources --out-dir direct-dist
+
+      - name: Compare direct and sdist-derived wheels
+        run: cmp dist/*.whl direct-dist/*.whl
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: release-distributions
+          path: |
+            dist/*.whl
+            dist/*.tar.gz
+          if-no-files-found: error
+          retention-days: 14
+
+  artifact-test:
+    name: Test ${{ matrix.kind }} on Python ${{ matrix.python-version }}
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - kind: wheel
+            python-version: "3.10"
+            package: dist/*.whl
+          - kind: sdist
+            python-version: "3.10"
+            package: dist/*.tar.gz
+          - kind: wheel
+            python-version: "3.14"
+            package: dist/*.whl
+          - kind: sdist
+            python-version: "3.14"
+            package: dist/*.tar.gz
+    steps:
+      - name: Install uv and Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        with:
+          version: "0.12.2"
+          python-version: ${{ matrix.python-version }}
+          no-project: true
+          enable-cache: false
+
+      - name: Download distributions
+        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
+        with:
+          name: release-distributions
+          path: dist
+
+      - name: Create clean environment
+        run: uv venv --python ${{ matrix.python-version }} .artifact-venv
+
+      - name: Install exact ${{ matrix.kind }} artifact
+        run: uv pip install --python .artifact-venv/bin/python ${{ matrix.package }}
+
+      - name: Smoke-test installed package
+        run: >-
+          .artifact-venv/bin/python -c
+          "from importlib.resources import files;
+          import numpy as np;
+          import pysnptools;
+          from pysnptools.snpreader import SnpData;
+          data = SnpData(iid=[['a','a'],['b','b']], sid=['s1','s2'], val=np.array([[0.0,1.0],[2.0,1.0]]));
+          assert data.standardize().read().val.shape == (2,2);
+          manifests = ['pysnptools.hashdown.json','bgen.hashdown.json','synth.hashdown.json'];
+          assert all(files('pysnptools.util').joinpath(name).is_file() for name in manifests);
+          assert '.artifact-venv' in pysnptools.__file__;
+          print(pysnptools.__file__)"
+
+  publish:
+    name: Publish to PyPI
+    needs: artifact-test
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pysnptools
+    permissions:
+      id-token: write
+    steps:
+      - name: Download tested distributions
+        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
+        with:
+          name: release-distributions
+          path: dist
+
+      - name: Publish distributions with Trusted Publishing
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2
+        with:
+          packages-dir: dist/
+          attestations: true

.gitignore

@@ -36,4 +36,3 @@ doc/ipynb/example2.dist.memmap
 doc/ipynb/.ipynb_checkpoints/*
 localcache*/*
 peertopeer*/*
-uv.lock

.python-version

@@ -0,0 +1 @@
+3.14