Change build-time dependency to numpy 2, Drop Python 3.8, add 3.12, A…

…dd pyproject.toml
jeromekelleher · Jun 27, 2024 · ffead55 · ffead55
1 parent f467db6
commit ffead55
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Showing 31 changed files with 200 additions and 268 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -183,16 +183,12 @@ jobs:
           command: |
             cd python
             rm -fR build
-            python setup.py sdist
-            python setup.py check
-            python -m twine check dist/*.tar.gz
+            python -m pip install build
             python -m venv venv
-            source venv/bin/activate
-            pip install --upgrade setuptools pip wheel
-            python setup.py build_ext
-            python setup.py egg_info
-            python setup.py bdist_wheel
-            pip install dist/*.tar.gz
+            python -m build --sdist
+            python -m twine check dist/*.tar.gz
+            python -m build --wheel
+            pip install dist/*.whl
             tskit --help
 
   build-32:
@@ -218,6 +214,7 @@ workflows:
   test:
     jobs:
       - build
-      - build-32
+      #Temporarily disabled due avoid compiling numpy on 32bit
+      # - build-32
 
 
diff --git a/.github/workflows/docker/buildwheel.sh b/.github/workflows/docker/buildwheel.sh
@@ -13,15 +13,12 @@ cd python
 for V in "${PYTHON_VERSIONS[@]}"; do
     PYBIN=/opt/python/$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
-    $PYBIN/python setup.py build_ext --inplace
-    $PYBIN/python setup.py bdist_wheel
+    $PYBIN/python -m pip install build
+    $PYBIN/python -m build --wheel
 done
 
 cd dist
 for whl in *.whl; do
     auditwheel repair "$whl"
     rm "$whl"
-done
+done
diff --git a/.github/workflows/docker/shared.env b/.github/workflows/docker/shared.env
@@ -1,6 +1,6 @@
 PYTHON_VERSIONS=(
+    cp312-cp312
     cp311-cp311
     cp310-cp310
     cp39-cp39
-    cp38-cp38
 )
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -9,17 +9,18 @@ on:
 
 env:
   COMMIT_EMAIL: ben.jeffery.well+adminbot@gmail.com
-  DOXYGEN: true
   MAKE_TARGET: -C python
   OWNER: tskit-dev
   REPO: tskit
   REQUIREMENTS: python/requirements/CI-docs/requirements.txt
-  APTGET: doxygen
 
 jobs:
   build-deploy-docs:
     name: Docs
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.12.1
@@ -28,33 +29,40 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - name: Install apt deps
-        if: env.APTGET
-        run: sudo apt-get install -y ${{env.APTGET}}
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          activate-environment: tskit-docs-env
+          use-mamba: true
 
-      - uses: actions/setup-python@v5
+      - name: Cache Conda env
+        uses: actions/cache@v3
         with:
-          python-version: "3.10"
-          cache: 'pip'
+          path: ${{ env.CONDA }}/envs
+          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles(env.REQUIREMENTS) }}-${{ env.CACHE_NUMBER }}
+        env:
+          CACHE_NUMBER: 0
+        id: cache
 
-      - name: Create venv and install deps
+      - name: Update environment
         run: |
-          pip install --upgrade pip wheel
-          pip install -r ${{env.REQUIREMENTS}}          
+          mamba install -y python=3.10 doxygen pip
+          pip install -r ${{ env.REQUIREMENTS }}
+        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: Build C module
         if: env.MAKE_TARGET
-        run: |
-          make $MAKE_TARGET
+        run: make $MAKE_TARGET
 
       - name: Build Docs
-        run: |
-          make -C docs
+        run: make -C docs
 
       - name: Trigger docs site rebuild
         if: github.ref == 'refs/heads/main'
         run: |
           curl -X POST https://api.github.com/repos/tskit-dev/tskit-site/dispatches \
                     -H 'Accept: application/vnd.github.everest-preview+json' \
                     -u AdminBot-tskit:${{ secrets.ADMINBOT_TOKEN }} \
-                    --data '{"event_type":"build-docs"}'
+                    --data '{"event_type":"build-docs"}'
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -60,7 +60,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: [ 3.8, 3.9, "3.11" ]
+        python: [ 3.9, 3.11 ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:
@@ -133,11 +133,6 @@ jobs:
           conda activate anaconda-client-env
           python setup.py build_ext --inplace
 
-      - name: Remove py311 incompatible tests (lack of numba support for 3.11, needed for lshmm)
-        if: matrix.python == '3.11'
-        run: |
-          rm python/tests/test_*matching*
-
       - name: Run tests
         working-directory: python
         run: |

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: macos-latest
     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@v4
@@ -25,21 +25,11 @@ 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: |
-          cd python
-          python -VV
-          python setup.py build_ext --inplace
+          pip install build
       - name: Build Wheel
         run: |
           cd python
-          python setup.py bdist_wheel
+          python -m build --wheel
       - name: Delocate to bundle dynamic libs
         run: |
           cd python
@@ -55,7 +45,7 @@ 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
@@ -66,12 +56,8 @@ 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
+          ${PYTHON} -m pip install build
+      - name: Build Wheel
         env:
           PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
         shell: bash
@@ -86,15 +72,7 @@ jobs:
           cp -r --dereference ../c/subprojects lib/.
           cp -r --dereference ../c/tskit lib/.
           cp ../c/tskit.h lib/.
-          ${PYTHON} setup.py build_ext --inplace
-      - name: Build Wheel
-        env:
-          PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
-        shell: bash
-        run: |
-          set -ex
-          cd python
-          ${PYTHON} setup.py bdist_wheel
+          ${PYTHON} -m build --wheel
       - name: Upload Wheels
         uses: actions/upload-artifact@v4
         with:
@@ -107,16 +85,17 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Build sdist
         shell: bash
         run: |
           cd python
-          python setup.py sdist
+          python -m pip install build
+          python -m build --sdist
 
       - name: Upload sdist
         uses: actions/upload-artifact@v4
@@ -140,7 +119,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", 3.11]
+        python: [3.9, "3.10", 3.11, 3.12]
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v4
@@ -162,7 +141,7 @@ 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: Download wheels
@@ -186,17 +165,17 @@ jobs:
     needs: ['manylinux']
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", 3.11]
+        python: [3.9, "3.10", 3.11, 3.12]
         include:
 
-          - python: 3.8
-            wheel: cp38
           - python: 3.9
             wheel: cp39
           - python: "3.10"
             wheel: cp310
           - python: 3.11
             wheel: cp311
+          - python: 3.12
+            wheel: cp312
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v4
@@ -234,4 +213,4 @@ jobs:
           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@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/c/tests/test_minimal_cpp.cpp b/c/tests/test_minimal_cpp.cpp
@@ -1,6 +1,6 @@
 /* * MIT License
  *
- * Copyright (c) 2019-2023 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/c/tskit.h b/c/tskit.h
@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/c/tskit/tables.h b/c/tskit/tables.h
@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2023 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  * Copyright (c) 2017-2018 University of Oxford
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy

diff --git a/python/lwt_interface/dict_encoding_testlib.py b/python/lwt_interface/dict_encoding_testlib.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2022 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal

diff --git a/python/pyproject.toml b/python/pyproject.toml
@@ -0,0 +1,67 @@
+[build-system]
+requires = ["setuptools>=45", "wheel", "numpy>=2.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tskit"
+dynamic = ["version"]
+authors = [
+    {name = "Tskit Developers", email = "admin@tskit.dev"},
+]
+description = "The tree sequence toolkit."
+readme = "README.rst"
+license = {text = "MIT"}
+classifiers = [
+    "Programming Language :: C",
+    "Programming Language :: Python",
+    "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",
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Other Environment",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "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",
+    "statistical genetics",
+    "phylogenetics",
+    "tskit",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "jsonschema>=3.0.0",
+    "numpy>=1.23.5",
+    "svgwrite>=1.1.10",
+]
+
+[project.urls]
+Homepage = "https://tskit.dev/tskit"
+Documentation = "https://tskit.dev/tskit/docs/stable"
+Changelog = "https://tskit.dev/tskit/docs/stable/changelogs.html"
+"Bug Tracker" = "https://github.com/tskit-dev/tskit/issues"
+GitHub = "https://github.com/tskit-dev/tskit/"
+
+[project.scripts]
+tskit = "tskit.cli:tskit_main"
+
+[tool.setuptools]
+packages = ["tskit"]
+
+[tool.setuptools.dynamic]
+version = {attr = "tskit._version.tskit_version"}
+
+[tool.pytest.ini_options]
+addopts = "-n 4"
+testpaths = ["tests"]