diff --git a/.circleci/config.yml b/.circleci/config.yml
index 69dd2472ae..67b37f7187 100644
--- 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
index ad0cd14b03..3e9e6e324b 100644
--- 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
\ No newline at end of file
+done
diff --git a/.github/workflows/docker/shared.env b/.github/workflows/docker/shared.env
index 3f299243a5..c10e471e72 100644
--- 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
index f45258e3a9..4cf4e454fd 100644
--- 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
@@ -28,28 +29,35 @@ 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'
@@ -57,4 +65,4 @@ jobs:
           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"}'
\ No newline at end of file
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ab6a496eeb..c1498cb242 100644
--- 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, 3.12 ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:
@@ -121,7 +121,6 @@ jobs:
         if: steps.cache.outputs.cache-hit != 'true'
         shell: bash -l {0}
         run: |
-          pip install setuptools==57.5.0 #v58 broke some deps https://setuptools.pypa.io/en/latest/history.html#v58-0-0
           pip install -r python/requirements/CI-tests-pip/requirements.txt
           # Remove tskit installed by conda
           pip uninstall -y tskit
@@ -133,11 +132,6 @@ 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
index 110d02bb98..50f430619e 100644
--- 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
\ No newline at end of file
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.mergify.yml b/.mergify.yml
index 48d34a24a3..d51c1a62a7 100644
--- a/.mergify.yml
+++ b/.mergify.yml
@@ -5,15 +5,12 @@ queue_rules:
       - "#changes-requested-reviews-by=0"
       - status-success=Docs
       - status-success=Lint
-      - status-success=Python (3.8, macos-latest)
       - status-success=Python (3.9, macos-latest)
-      - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.8, ubuntu-latest)
+      - status-success=Python (3.12, macos-latest)
       - status-success=Python (3.9, ubuntu-latest)
-      - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.8, windows-latest)
+      - status-success=Python (3.12, ubuntu-latest)
       - status-success=Python (3.9, windows-latest)
-      - status-success=Python (3.11, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
 pull_request_rules:
   - name: Automatic rebase, CI and merge
@@ -25,15 +22,12 @@ pull_request_rules:
       - label=AUTOMERGE-REQUESTED
       - status-success=Docs
       - status-success=Lint
-      - status-success=Python (3.8, macos-latest)
       - status-success=Python (3.9, macos-latest)
-      - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.8, ubuntu-latest)
+      - status-success=Python (3.12, macos-latest)
       - status-success=Python (3.9, ubuntu-latest)
-      - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.8, windows-latest)
+      - status-success=Python (3.12, ubuntu-latest)
       - status-success=Python (3.9, windows-latest)
-      - status-success=Python (3.11, windows-latest)
+      - status-success=Python (3.12, windows-latest)
       - "status-success=ci/circleci: build"
       #- status-success=codecov/patch
       #- status-success=codecov/project/c-tests
diff --git a/c/tests/test_minimal_cpp.cpp b/c/tests/test_minimal_cpp.cpp
index 8754f4f636..8e9296f410 100644
--- 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
index e55ffc664a..e8f1b69f60 100644
--- 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
index 38f3096c9d..204e39e2db 100644
--- 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
index 72acea4dce..01ed9a865c 100644
--- 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
new file mode 100644
index 0000000000..f4d2a8bda7
--- /dev/null
+++ 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"]
diff --git a/python/pytest.ini b/python/pytest.ini
deleted file mode 100644
index 50b8418b9c..0000000000
--- a/python/pytest.ini
+++ /dev/null
@@ -1,4 +0,0 @@
-[pytest]
-addopts = -n 4
-testpaths =
-    tests
diff --git a/python/requirements/CI-complete/requirements.txt b/python/requirements/CI-complete/requirements.txt
index 62e2d3d365..257b08c4ce 100644
--- a/python/requirements/CI-complete/requirements.txt
+++ b/python/requirements/CI-complete/requirements.txt
@@ -1,16 +1,15 @@
-biopython==1.81
-coverage==7.2.7
-dendropy==4.6.1
+biopython==1.83
+coverage==7.5.4
+dendropy==5.0.1
 h5py==3.9.0
-kastore==0.3.2
+kastore==0.3.3
 lshmm==0.0.8
-msgpack==1.0.5
-msprime==1.2.0
-networkx==3.1
-portion==2.4.1
-pytest==7.4.0
-pytest-cov==4.1.0
-pytest-xdist==3.3.1
-tszip==0.2.2
+msgpack==1.0.8
+msprime==1.3.1
+networkx==3.3
+portion==2.4.2
+pytest==8.2.2
+pytest-cov==5.0.0
+pytest-xdist==3.6.1
+tszip==0.2.3
 xmlunittest==0.5.0
-llvmlite==0.39.1
diff --git a/python/requirements/CI-docs/requirements.txt b/python/requirements/CI-docs/requirements.txt
index 8ba78c7aa4..3b5a3118ea 100644
--- a/python/requirements/CI-docs/requirements.txt
+++ b/python/requirements/CI-docs/requirements.txt
@@ -1,9 +1,8 @@
-jupyter-book==0.15.1
+jupyter-book==1.0.0
 breathe==4.35.0
-sphinx-autodoc-typehints==1.19.1
-sphinx-issues==3.0.1
+sphinx-autodoc-typehints==2.2.2
+sphinx-issues==4.1.0
 sphinx-argparse==0.4.0
-numpy==1.25.1
 svgwrite==1.4.3
-msprime==1.2.0
+msprime==1.3.1
 sphinx-book-theme
\ No newline at end of file
diff --git a/python/requirements/CI-tests-conda/requirements.txt b/python/requirements/CI-tests-conda/requirements.txt
index 66e5f62b37..3c58381b9e 100644
--- a/python/requirements/CI-tests-conda/requirements.txt
+++ b/python/requirements/CI-tests-conda/requirements.txt
@@ -1,2 +1,3 @@
-msprime==1.2.0
-h5py==3.7.0
+msprime==1.3.1
+tszip==0.2.3
+h5py==3.11.0
diff --git a/python/requirements/CI-tests-pip/requirements.txt b/python/requirements/CI-tests-pip/requirements.txt
index d713bbdea0..96010f3958 100644
--- a/python/requirements/CI-tests-pip/requirements.txt
+++ b/python/requirements/CI-tests-pip/requirements.txt
@@ -1,17 +1,14 @@
 lshmm==0.0.8
-numpy==1.24.1
-pytest==7.1.3
-pytest-cov==4.0.0
-pytest-xdist==2.5.0
+pytest==8.2.2
+pytest-cov==5.0.0
+pytest-xdist==3.6.1
 svgwrite==1.4.3
-portion==2.3.0
+portion==2.4.2
 xmlunittest==0.5.0
-biopython==1.79
-dendropy==4.5.2
-networkx==3.1
-msgpack==1.0.4
-newick==1.3.2
-tszip==0.2.2
-kastore==0.3.2
-lxml==4.9.2
-numba<=0.59.1 #Pinned directly as 0.60.0 fails
+biopython==1.83
+dendropy==5.0.1
+networkx==3.2.1
+msgpack==1.0.8
+newick==1.9.0
+kastore==0.3.3
+jsonschema==4.22.0
\ No newline at end of file
diff --git a/python/setup.cfg b/python/setup.cfg
deleted file mode 100644
index 350d3c1d0b..0000000000
--- a/python/setup.cfg
+++ /dev/null
@@ -1,72 +0,0 @@
-[metadata]
-name = tskit
-author= Tskit Developers
-author_email = admin@tskit.dev
-license = MIT
-description= The tree sequence toolkit.
-long_description_content_type = text/x-rst
-long_description = file: README.rst
-url = https://tskit.dev/tskit
-project_urls =
-    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/
-classifiers =
-    Programming Language :: C
-    Programming Language :: Python
-    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.11
-    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
-platforms =
-    POSIX
-    Windows
-    MacOS X
-
-[options]
-packages = tskit
-python_requires = >=3.8
-include_package_data = True
-install_requires =
-    jsonschema>=3.0.0
-    numpy>=1.7,<2
-    svgwrite>=1.1.10
-setup_requires =
-    numpy>=1.7
-    setuptools
-
-[options.entry_points]
-console_scripts =
-    tskit = tskit.cli:tskit_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/python/setup.py b/python/setup.py
index 44e15b9869..0f8e77abdb 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -1,28 +1,13 @@
-import os.path
+import os
 import platform
 
+import numpy
 from setuptools import Extension
 from setuptools import setup
-from setuptools.command.build_ext import build_ext
-
 
 IS_WINDOWS = platform.system() == "Windows"
 
 
-# Obscure magic required to allow numpy be used as a 'setup_requires'.
-# Based on https://stackoverflow.com/questions/19919905
-class local_build_ext(build_ext):
-    def finalize_options(self):
-        build_ext.finalize_options(self)
-        import builtins
-
-        # Prevent numpy from thinking it is still in its setup process:
-        builtins.__NUMPY_SETUP__ = False
-        import numpy
-
-        self.include_dirs.append(numpy.get_include())
-
-
 libdir = "lib"
 kastore_dir = os.path.join(libdir, "subprojects", "kastore")
 tsk_source_files = [
@@ -43,7 +28,6 @@ def finalize_options(self):
 defines = []
 libraries = []
 if IS_WINDOWS:
-    # Needed for generating UUIDs
     libraries.append("Advapi32")
     defines.append(("WIN32", None))
 
@@ -53,21 +37,9 @@ def finalize_options(self):
     extra_compile_args=["-std=c99"],
     libraries=libraries,
     define_macros=defines,
-    include_dirs=["lwt_interface", libdir, kastore_dir],
+    include_dirs=["lwt_interface", libdir, kastore_dir, numpy.get_include()],
 )
 
-
-# After exec'ing this file we have tskit_version defined.
-tskit_version = None  # Keep PEP8 happy.
-version_file = os.path.join("tskit", "_version.py")
-with open(version_file) as f:
-    exec(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="tskit",
-    version=tskit_version,
     ext_modules=[_tskit_module],
-    cmdclass={"build_ext": local_build_ext},
 )
diff --git a/python/tests/ibd.py b/python/tests/ibd.py
index 53e28cc5c0..64f1e8be63 100644
--- a/python/tests/ibd.py
+++ b/python/tests/ibd.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2020-2022 Tskit Developers
+# Copyright (c) 2020-2024 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/tests/simplify.py b/python/tests/simplify.py
index 1e62c9d11b..9e416c3e78 100644
--- a/python/tests/simplify.py
+++ b/python/tests/simplify.py
@@ -157,7 +157,9 @@ def __init__(
             if self.update_sample_flags:
                 flags = self.tables.nodes.flags
                 # Zero out other sample flags
-                flags = np.bitwise_and(flags, ~tskit.NODE_IS_SAMPLE)
+                flags = np.bitwise_and(
+                    flags, np.uint32(~tskit.NODE_IS_SAMPLE & 0xFFFFFFFF)
+                )
                 flags[sample] |= tskit.NODE_IS_SAMPLE
                 self.tables.nodes.flags = flags.astype(np.uint32)
 
diff --git a/python/tests/test_avl_tree.py b/python/tests/test_avl_tree.py
index 999b09b528..2afaa0615e 100644
--- a/python/tests/test_avl_tree.py
+++ b/python/tests/test_avl_tree.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2021 Tskit Developers
+# Copyright (c) 2021-2024 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/tests/test_coalrate.py b/python/tests/test_coalrate.py
index dcfcfc8d66..471f63ff1d 100644
--- a/python/tests/test_coalrate.py
+++ b/python/tests/test_coalrate.py
@@ -464,7 +464,7 @@ def test_missing_leaves(self):
         """
         t = self.example_ts().dump_tables()
         ss0 = np.flatnonzero(t.nodes.population == 0)
-        remove = np.in1d(t.edges.child, ss0)
+        remove = np.isin(t.edges.child, ss0)
         assert np.any(remove)
         t.edges.set_columns(
             left=t.edges.left[~remove],
diff --git a/python/tests/test_haplotype_matching.py b/python/tests/test_haplotype_matching.py
index dc01e8370d..4c7d5fc18a 100644
--- a/python/tests/test_haplotype_matching.py
+++ b/python/tests/test_haplotype_matching.py
@@ -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/python/tests/test_ld_matrix.py b/python/tests/test_ld_matrix.py
index 1733ea140f..761658224e 100644
--- a/python/tests/test_ld_matrix.py
+++ b/python/tests/test_ld_matrix.py
@@ -46,8 +46,8 @@
 
 
 @contextlib.contextmanager
-def suppress_division_by_zero_warning():
-    with np.errstate(invalid="ignore", divide="ignore"):
+def suppress_overflow_div0_warning():
+    with np.errstate(over="ignore", invalid="ignore", divide="ignore"):
         yield
 
 
@@ -901,7 +901,7 @@ def r2_summary_func(
         D = p_AB - (p_A * p_B)
         denom = p_A * p_B * (1 - p_A) * (1 - p_B)
 
-        with suppress_division_by_zero_warning():
+        with suppress_overflow_div0_warning():
             result[k] = (D * D) / denom
 
 
@@ -952,7 +952,7 @@ def D_prime_summary_func(
         p_B = p_AB + p_aB
 
         D = p_AB - (p_A * p_B)
-        with suppress_division_by_zero_warning():
+        with suppress_overflow_div0_warning():
             if D >= 0:
                 result[k] = D / min(p_A * (1 - p_B), (1 - p_A) * p_B)
             else:
@@ -975,7 +975,7 @@ def r_summary_func(
         D = p_AB - (p_A * p_B)
         denom = p_A * p_B * (1 - p_A) * (1 - p_B)
 
-        with suppress_division_by_zero_warning():
+        with suppress_overflow_div0_warning():
             result[k] = D / np.sqrt(denom)
 
 
@@ -1034,7 +1034,7 @@ def pi2_unbiased(
         w_Ab = state[1, k]
         w_aB = state[2, k]
         w_ab = n - (w_AB + w_Ab + w_aB)
-        with suppress_division_by_zero_warning():
+        with suppress_overflow_div0_warning():
             result[k] = (1 / (n * (n - 1) * (n - 2) * (n - 3))) * (
                 ((w_AB + w_Ab) * (w_aB + w_ab) * (w_AB + w_aB) * (w_Ab + w_ab))
                 - ((w_AB * w_ab) * (w_AB + w_ab + (3 * w_Ab) + (3 * w_aB) - 1))
@@ -1052,7 +1052,7 @@ def dz_unbiased(
         w_Ab = state[1, k]
         w_aB = state[2, k]
         w_ab = n - (w_AB + w_Ab + w_aB)
-        with suppress_division_by_zero_warning():
+        with suppress_overflow_div0_warning():
             result[k] = (1 / (n * (n - 1) * (n - 2) * (n - 3))) * (
                 (
                     ((w_AB * w_ab) - (w_Ab * w_aB))
@@ -1074,7 +1074,7 @@ def d2_unbiased(
         w_Ab = state[1, k]
         w_aB = state[2, k]
         w_ab = n - (w_AB + w_Ab + w_aB)
-        with suppress_division_by_zero_warning():
+        with suppress_overflow_div0_warning():
             result[k] = (1 / (n * (n - 1) * (n - 2) * (n - 3))) * (
                 ((w_aB**2) * (w_Ab - 1) * w_Ab)
                 + ((w_ab - 1) * w_ab * (w_AB - 1) * w_AB)
diff --git a/python/tests/test_lowlevel.py b/python/tests/test_lowlevel.py
index 54b19b1d6f..0fd20b3442 100644
--- a/python/tests/test_lowlevel.py
+++ b/python/tests/test_lowlevel.py
@@ -1671,7 +1671,7 @@ def test_divergence_matrix(self):
                 ts.divergence_matrix(windows, [1, 1], [0, bad_node])
         with pytest.raises(ValueError, match="Sum of sample_set_sizes"):
             ts.divergence_matrix(windows, [1, 2], [0, 1])
-        with pytest.raises(ValueError, match="Overflow"):
+        with pytest.raises((ValueError, OverflowError), match="Overflow|out of bounds"):
             ts.divergence_matrix(windows, [-1, 2], [0])
 
         with pytest.raises(TypeError, match="str"):
@@ -3321,23 +3321,19 @@ def test_bad_tracked_samples(self):
                 )
         for bad_sample in [10**6, -1e6]:
             with pytest.raises(ValueError):
-                # Implicit conversion to integers using __int__ is deprecated
-                with pytest.deprecated_call():
-                    _tskit.Tree(
-                        ts,
-                        options=options,
-                        tracked_samples=[bad_sample],
-                    )
+                _tskit.Tree(
+                    ts,
+                    options=options,
+                    tracked_samples=[bad_sample],
+                )
             with pytest.raises(ValueError):
-                with pytest.deprecated_call():
-                    _tskit.Tree(
-                        ts,
-                        options=options,
-                        tracked_samples=[1, bad_sample],
-                    )
+                _tskit.Tree(
+                    ts,
+                    options=options,
+                    tracked_samples=[1, bad_sample],
+                )
             with pytest.raises(ValueError):
-                with pytest.deprecated_call():
-                    _tskit.Tree(ts, tracked_samples=[1, bad_sample, 1])
+                _tskit.Tree(ts, tracked_samples=[1, bad_sample, 1])
 
     def test_while_loop_semantics(self):
         for ts in self.get_example_tree_sequences():
diff --git a/python/tests/test_metadata.py b/python/tests/test_metadata.py
index d57e6ea9d3..b6c2ed664b 100644
--- a/python/tests/test_metadata.py
+++ b/python/tests/test_metadata.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2022 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 # Copyright (c) 2017 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
diff --git a/python/tests/test_tables.py b/python/tests/test_tables.py
index 51852a2c79..7551f3250c 100644
--- a/python/tests/test_tables.py
+++ b/python/tests/test_tables.py
@@ -1254,7 +1254,7 @@ def verify_metadata_vector(self, table, key, dtype, default_value=9999):
                 else:
                     md = default_value
                     break
-            assert np.all(np.cast[dtype](md) == x)
+            assert np.all(np.asarray(md, dtype=dtype) == x)
 
     def test_metadata_vector_errors(self):
         table = self.table_class()
@@ -1396,9 +1396,7 @@ def test_metadata_schema(self, table_5row):
             table2.metadata_schema = tskit.MetadataSchema({"codec": "json"})
             with pytest.raises(
                 AssertionError,
-                match=f"{type(table_5row).__name__} metadata schemas differ: self=None "
-                f"other=OrderedDict([('codec', "
-                "'json')])",
+                match=f"{type(table_5row).__name__} metadata schemas differ:",
             ):
                 table_5row.assert_equals(table2)
             table_5row.assert_equals(table2, ignore_metadata=True)
@@ -4091,10 +4089,7 @@ def test_metadata_schema(self, t1, t2):
         t2.metadata_schema = tskit.MetadataSchema(None)
         with pytest.raises(
             AssertionError,
-            match=re.escape(
-                "Metadata schemas differ: self=OrderedDict([('codec', 'json')]) "
-                "other=None"
-            ),
+            match=re.escape("Metadata schemas differ"),
         ):
             t1.assert_equals(t2)
         t1.assert_equals(t2, ignore_metadata=True)
@@ -4140,10 +4135,7 @@ def test_ignore_metadata(self, t1, t2, table_name):
             table.metadata_schema = tskit.MetadataSchema(None)
             with pytest.raises(
                 AssertionError,
-                match=re.escape(
-                    f"{type(table).__name__} metadata schemas differ: "
-                    f"self=OrderedDict([('codec', 'json')]) other=None"
-                ),
+                match=re.escape(f"{type(table).__name__} metadata schemas differ:"),
             ):
                 t1.assert_equals(t2)
             t1.assert_equals(t2, ignore_metadata=True)
@@ -4201,10 +4193,7 @@ def test_ignore_reference_sequence(self, t1, t2):
         t2.reference_sequence.clear()
         with pytest.raises(
             AssertionError,
-            match=re.escape(
-                "Metadata schemas differ: "
-                "self=OrderedDict([('codec', 'json')]) other=None"
-            ),
+            match=re.escape("Metadata schemas differ"),
         ):
             t1.assert_equals(t2)
         t1.assert_equals(t2, ignore_reference_sequence=True)
diff --git a/python/tests/test_tree_stats.py b/python/tests/test_tree_stats.py
index a272c4f8cf..4b608b5d75 100644
--- a/python/tests/test_tree_stats.py
+++ b/python/tests/test_tree_stats.py
@@ -1280,7 +1280,7 @@ def site_segregating_sites(ts, sample_sets, windows=None, span_normalise=True):
         haps = ts.genotype_matrix(isolated_as_missing=False)
         site_positions = [x.position for x in ts.sites()]
         for i, X in enumerate(sample_sets):
-            X_index = np.where(np.in1d(samples, X))[0]
+            X_index = np.where(np.isin(samples, X))[0]
             for k in range(ts.num_sites):
                 if (site_positions[k] >= begin) and (site_positions[k] < end):
                     num_alleles = len(set(haps[k, X_index]))
@@ -1428,7 +1428,7 @@ def site_tajimas_d(ts, sample_sets, windows=None):
             nn = n[i]
             S = 0
             T = 0
-            X_index = np.where(np.in1d(samples, X))[0]
+            X_index = np.where(np.isin(samples, X))[0]
             for k in range(ts.num_sites):
                 if (site_positions[k] >= begin) and (site_positions[k] < end):
                     hX = haps[k, X_index]
@@ -4571,7 +4571,7 @@ def branch_trait_covariance(ts, W, windows=None, span_normalise=True):
                     has_trees = True
                 SS = 0
                 for u in range(ts.num_nodes):
-                    below = np.in1d(samples, list(tr.samples(u)))
+                    below = np.isin(samples, list(tr.samples(u)))
                     branch_length = tr.branch_length(u)
                     SS += covsq(w, below) * branch_length
                 S += SS * (min(end, tr.interval.right) - max(begin, tr.interval.left))
@@ -4606,7 +4606,7 @@ def node_trait_covariance(ts, W, windows=None, span_normalise=True):
                     break
                 SS = np.zeros(ts.num_nodes)
                 for u in range(ts.num_nodes):
-                    below = np.in1d(samples, list(tr.samples(u)))
+                    below = np.isin(samples, list(tr.samples(u)))
                     SS[u] += covsq(w, below)
                 S += SS * (min(end, tr.interval.right) - max(begin, tr.interval.left))
             out[j, :, i] = S
@@ -4782,7 +4782,7 @@ def branch_trait_correlation(ts, W, windows=None, span_normalise=True):
                     has_trees = True
                 SS = 0
                 for u in range(ts.num_nodes):
-                    below = np.in1d(samples, list(tr.samples(u)))
+                    below = np.isin(samples, list(tr.samples(u)))
                     p = np.mean(below)
                     if p > 0 and p < 1:
                         branch_length = tr.branch_length(u)
@@ -4823,7 +4823,7 @@ def node_trait_correlation(ts, W, windows=None, span_normalise=True):
                     break
                 SS = np.zeros(ts.num_nodes)
                 for u in range(ts.num_nodes):
-                    below = np.in1d(samples, list(tr.samples(u)))
+                    below = np.isin(samples, list(tr.samples(u)))
                     p = np.mean(below)
                     if p > 0 and p < 1:
                         # SS[u] += sum(w[below])**2 / 2
@@ -5046,7 +5046,7 @@ def branch_trait_linear_model(ts, W, Z, windows=None, span_normalise=True):
                     has_trees = True
                 SS = 0
                 for u in range(ts.num_nodes):
-                    below = np.in1d(samples, list(tr.samples(u)))
+                    below = np.isin(samples, list(tr.samples(u)))
                     branch_length = tr.branch_length(u)
                     SS += linear_model(w, below, Z) * branch_length
                 S += SS * (min(end, tr.interval.right) - max(begin, tr.interval.left))
@@ -5081,7 +5081,7 @@ def node_trait_linear_model(ts, W, Z, windows=None, span_normalise=True):
                     break
                 SS = np.zeros(ts.num_nodes)
                 for u in range(ts.num_nodes):
-                    below = np.in1d(samples, list(tr.samples(u)))
+                    below = np.isin(samples, list(tr.samples(u)))
                     SS[u] += linear_model(w, below, Z)
                 S += SS * (min(end, tr.interval.right) - max(begin, tr.interval.left))
             out[j, :, i] = S
diff --git a/python/tests/test_util.py b/python/tests/test_util.py
index eaed4d07e3..4a124619fa 100644
--- a/python/tests/test_util.py
+++ b/python/tests/test_util.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2023 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
@@ -196,8 +196,7 @@ def test_nonrectangular_input(self):
                 # On some platforms and Python / numpy versions, a ValueError
                 # occurs instead
                 with pytest.raises((TypeError, ValueError)):
-                    with pytest.deprecated_call():
-                        util.safe_np_int_cast(bad_input, dtype)
+                    util.safe_np_int_cast(bad_input, dtype)
 
 
 class TestIntervalOps:
diff --git a/python/tests/test_version.py b/python/tests/test_version.py
index 19cd2bc5dc..65a8ab5b13 100644
--- a/python/tests/test_version.py
+++ b/python/tests/test_version.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2020-2022 Tskit Developers
+# Copyright (c) 2020-2024 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/tskit/formats.py b/python/tskit/formats.py
index ac466ce1a8..76d0ad7376 100644
--- a/python/tskit/formats.py
+++ b/python/tskit/formats.py
@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2023 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 # Copyright (c) 2016-2017 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -150,9 +150,9 @@ def _load_legacy_hdf5_v2(root, remove_duplicate_positions):
     population[cr_node] = cr_population
     if "samples" in root:
         samples_group = root["samples"]
-        population[:sample_size] = samples_group["population"]
+        population[:sample_size] = np.array(samples_group["population"], copy=True)
         if "time" in samples_group:
-            time[:sample_size] = samples_group["time"]
+            time[:sample_size] = np.array(samples_group["time"], copy=True)
     tables.nodes.set_columns(flags=flags, population=population, time=time)
     _set_populations(tables)