diff --git a/.circleci/config.yml b/.circleci/config.yml
deleted file mode 100644
index 4247d7946..000000000
--- a/.circleci/config.yml
+++ /dev/null
@@ -1,126 +0,0 @@
-version: 2.1
-orbs:
-  codecov: codecov/codecov@3.2.4
-
-jobs:
-  build:
-    docker:
-      - image: cimg/python:3.10
-    working_directory: /home/circleci/msprime
-    steps:
-      - checkout
-      - run: sudo chown -R circleci:circleci *
-      - restore_cache:
-          # Note: we put a v{x} suffix at the end of the cache key so that
-          # we can invalidate the cache when we need to. Note that we need
-          # to update the key in the ``save_cache`` block below also when
-          # doing that.
-          key: msprime-{{ .Branch }}-v5
-      - run:
-          name: Checkout submodules
-          command: |
-            git submodule update --init --recursive
-            # Write out the status for debugging purposes. Are we checked out at tags?
-            git submodule status --recursive
-      - run:
-          name: Install dependencies and set path
-          command: |
-            sudo apt-get update
-            sudo apt-get install libgsl0-dev libcunit1-dev libconfig-dev ninja-build valgrind clang
-            pip install uv
-            uv venv
-            uv pip install -r pyproject.toml --extra test
-            # way to set path persistently https://circleci.com/docs/2.0/env-vars/#setting-path
-            echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
-      - save_cache:
-          key: msprime-{{ .Branch }}-v5
-          paths:
-            - "/home/circleci/.local"
-
-      - run:
-          name: Compile Python
-          command: |
-            source .venv/bin/activate
-            make allchecks
-
-      - run:
-          name: Run highlevel tests
-          # Run tests without background threads
-          command: |
-            source .venv/bin/activate
-            pytest --cov=msprime --cov-report=xml --cov-branch -n 0 tests
-
-      - codecov/upload:
-          flags: python
-          token: CODECOV_TOKEN
-
-      - run:
-            name: Delete coverage
-            command: |
-              rm .coverage
-
-      - run:
-          name: Compile C with gcc
-          command: |
-            source .venv/bin/activate
-            CFLAGS=--coverage meson lib/ build-gcc && ninja -C build-gcc
-
-      - run:
-          name: Run the low-level tests.
-          command: |
-            source .venv/bin/activate
-            ninja -C build-gcc test
-
-      - run:
-          name: Run gcov manually, as the one used in codecov doesn't work here.
-          command: |
-            gcov -pb -o ./build/temp.linux*/msprime msprime/_msprimemodule.c
-            cd build-gcc
-            # TODO should be able to do this with 'find', but it's tricky and opaque.
-            gcov -pb ./libmsprime.a.p/fenwick.c.gcno ../lib/fenwick.c
-            gcov -pb ./libmsprime.a.p/msprime.c.gcno ../lib/msprime.c
-            gcov -pb ./libmsprime.a.p/mutgen.c.gcno ../lib/mutgen.c
-            gcov -pb ./libmsprime.a.p/object_heap.c.gcno ../lib/object_heap.c
-            gcov -pb ./libmsprime.a.p/interval_map.c.gcno ../lib/interval_map.c
-            gcov -pb ./libmsprime.a.p/util.c.gcno ../lib/util.c
-            gcov -pb ./libmsprime.a.p/likelihood.c.gcno ../lib/likelihood.c
-            gcov -pb ./libmsprime.a.p/rate_map.c.gcno ../lib/rate_map.c
-            cd ..
-
-      - codecov/upload:
-          flags: C
-          token: CODECOV_TOKEN
-
-      - run:
-          name: Valgrind for C tests.
-          command: |
-            valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_core
-            valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_ancestry
-            valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_fenwick
-            valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_likelihood
-            valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_mutations
-            valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_rate_map
-            valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_sweeps
-
-      - run:
-          name: Make sure we can build a distribution.
-          command: |
-            source .venv/bin/activate
-            python -m build --sdist
-            python -m build --wheel
-            python -m twine check dist/*.tar.gz --strict
-
-      - run:
-          name: Install from the distribution tarball
-          command: |
-            mkdir installtest
-            cd installtest
-            python -m venv venv
-            source venv/bin/activate
-            pip install --upgrade setuptools pip
-            pip install ../dist/*.whl
-            python -c 'import msprime; print(msprime.__version__)'
-
-            # We should still be able to import without the newick module
-            python -m pip uninstall -y newick
-            python -c 'import msprime; print(msprime.__version__)'
diff --git a/.github/workflows/debug-windows.yml b/.github/workflows/debug-windows.yml
new file mode 100644
index 000000000..67f5a57de
--- /dev/null
+++ b/.github/workflows/debug-windows.yml
@@ -0,0 +1,53 @@
+name: Debug Windows
+
+on:
+  pull_request:
+
+jobs:
+  debug-windows:
+    name: Debug Windows Python 3.13
+    runs-on: windows-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.12.1
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Checkout
+        uses: actions/checkout@v4.2.2
+        with:
+          submodules: true
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5.4.0
+        with:
+          python-version: "3.13"
+
+      - name: Fix windows symlinks
+        run: |
+          rm lwt_interface
+          cp -r --dereference git-submodules/tskit/python/lwt_interface ./lwt_interface
+
+      - name: Install GSL (Windows)
+        run: |
+          vcpkg install gsl:x64-windows
+          # Add GSL DLL directory to PATH for runtime
+          $vcpkgRoot = $env:VCPKG_INSTALLATION_ROOT
+          if (-not $vcpkgRoot) { $vcpkgRoot = "C:\vcpkg" }
+          $gslBinPath = Join-Path $vcpkgRoot "installed\x64-windows\bin"
+          echo "$gslBinPath" >> $env:GITHUB_PATH
+          Write-Output "Added to PATH: $gslBinPath"
+        shell: powershell
+
+      - name: Install pip deps
+        run: | 
+          pip install uv
+          uv pip install --system -r pyproject.toml --extra test
+
+      - name: Setup tmate session
+        uses: mxschmitt/action-tmate@v3
+        with:
+          limit-access-to-actor: true
\ No newline at end of file
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
deleted file mode 100644
index 56b086330..000000000
--- a/.github/workflows/docs.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-name: Docs
-on:
-  pull_request:
-  push:
-    branches: [main]
-    tags:
-      - '*'
-  merge_group:
-jobs:
-  Docs:
-    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
-    with:
-      additional-setup: sudo apt-get install -y libgsl0-dev
-      make-command: make cmodule
\ No newline at end of file
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
deleted file mode 100644
index 3ca3ea03d..000000000
--- a/.github/workflows/tests.yml
+++ /dev/null
@@ -1,104 +0,0 @@
-name: Tests
-
-on:
-  pull_request:
-  push:
-    branches: [main, test]
-  merge_group:
-
-jobs:
-  pre-commit:
-    name: Lint
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v2
-
-  test:
-    name: Python
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        python: [ "3.10", 3.13 ]
-        os:  [ macos-latest, ubuntu-24.04, windows-latest ]
-    defaults:
-      run:
-        shell: bash
-    steps:
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.12.1
-        with:
-          access_token: ${{ github.token }}
-
-      - name: Checkout
-        uses: actions/checkout@v4.2.2
-        with:
-          submodules: true
-
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: "${{ matrix.python }}"
-
-      - name: Fix windows symlinks
-        # This is horrible, but the "git config core.symlinks true" didn't work.
-        if: matrix.os == 'windows-latest'
-        run: |
-          rm lwt_interface
-          cp -r --dereference git-submodules/tskit/python/lwt_interface ./lwt_interface
-
-      - name: Install GSL (macOS)
-        if: matrix.os == 'macos-latest'
-        run: brew install gsl
-        
-      - name: Install GSL (Windows)
-        if: matrix.os == 'windows-latest'
-        run: |
-          vcpkg install gsl:x64-windows
-          # Add GSL DLL directory to PATH for runtime
-          $vcpkgRoot = $env:VCPKG_INSTALLATION_ROOT
-          if (-not $vcpkgRoot) { $vcpkgRoot = "C:\vcpkg" }
-          $gslBinPath = Join-Path $vcpkgRoot "installed\x64-windows\bin"
-          echo "$gslBinPath" >> $env:GITHUB_PATH
-          Write-Output "Added to PATH: $gslBinPath"
-        shell: powershell
-
-      - name: Install GSL (Ubuntu)
-        if: matrix.os == 'ubuntu-24.04'
-        run: sudo apt-get update && sudo apt-get install -y libgsl-dev
-      
-      - name: Install pip deps
-        run: | 
-          pip install uv
-          uv pip install --system -r pyproject.toml --extra test
-
-      - name: Build module and run tests
-        if: matrix.os != 'windows-latest'
-        run: |
-          python setup.py build_ext --inplace
-          pytest -xvs -n0
-
-      - name: Build wheel and run tests
-        if: matrix.os == 'windows-latest'
-        shell: powershell
-        run: |
-          uv pip install --system build delvewheel
-          python -m build --wheel
-          $vcpkgRoot = $env:VCPKG_INSTALLATION_ROOT
-          if (-not $vcpkgRoot) { $vcpkgRoot = 'C:\vcpkg' }
-          $gslBinPath = Join-Path $vcpkgRoot 'installed\x64-windows\bin'
-          # Ensure GSL bin is on PATH for this session
-          $env:PATH = "$gslBinPath;$env:PATH"
-          # Repair wheel(s) to bundle DLLs
-          $whls = Get-ChildItem -Path dist -Filter '*.whl'
-          if ($whls) {
-            foreach ($w in $whls) {
-              delvewheel repair $w.FullName -w dist --add-path $gslBinPath
-            }
-          } else {
-            Write-Error 'No wheel files found in dist/'
-            exit 1
-          }
-          # Remove source package directory to ensure pip installs wheel
-          if (Test-Path msprime) { Remove-Item -Recurse -Force msprime }
-          # Install repaired wheel(s)
-          Get-ChildItem -Path dist -Filter '*.whl' | ForEach-Object { pip install $_.FullName }
-          pytest -xvs -n0
\ No newline at end of file
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
deleted file mode 100644
index 40d3ebbea..000000000
--- a/.github/workflows/wheels.yml
+++ /dev/null
@@ -1,254 +0,0 @@
-name: Binary wheels
-
-on:
-  push:
-    branches:
-      - main
-      - test
-    tags:
-      - '*'
-  release:
-    types: [published]
-
-jobs:
-  OSX:
-    name: Build ${{ matrix.os }} - ${{ matrix.python }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [macos-13, macos-14, macos-15]
-        python: ["3.10", 3.11, 3.12, 3.13]
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4.2.2
-        with:
-            submodules: true
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install deps
-        run: |
-          brew install gsl
-          pip install --upgrade pip build
-      - name: Build Wheel (arm64)
-        if: matrix.os == 'macos-14' || matrix.os == 'macos-15'
-        run: |
-          export PLAT="arm64"
-          export _PYTHON_HOST_PLATFORM="macosx-11.0-arm64"
-          export CFLAGS+=" -arch arm64"
-          export CXXFLAGS+=" -arch arm64"
-          export ARCHFLAGS=$OLDARCHFLAGS
-          export ARCHFLAGS+=" -arch arm64"
-          export CPPFLAGS+=" -arch arm64"
-          export LDFLAGS+=" -arch arm64"
-          python -m build --wheel
-      - name: Build Wheel (x86_64)
-        if: matrix.os == 'macos-13'
-        run: |
-          export PLAT="x86_64"
-          export _PYTHON_HOST_PLATFORM="macosx-11.0-x86_64"
-          export CFLAGS+=" -arch x86_64"
-          export CXXFLAGS+=" -arch x86_64"
-          export ARCHFLAGS=$OLDARCHFLAGS
-          export ARCHFLAGS+=" -arch x86_64"
-          export CPPFLAGS+=" -arch x86_64"
-          export LDFLAGS+=" -arch x86_64"
-          python -m build --wheel
-      - name: Delocate to bundle dynamic libs
-        run: |
-          pip install delocate
-          delocate-wheel -v dist/*.whl
-      - name: Upload Wheels
-        uses: actions/upload-artifact@v4.6.1
-        with:
-          name: osx-wheel-${{ matrix.os }}-${{ matrix.python }}
-          path: dist
-
-  Windows:
-    name: Build Windows - ${{ matrix.python }}
-    runs-on: windows-latest
-    strategy:
-      matrix:
-        python: ["3.10", 3.11, 3.12, 3.13]
-        arch: [x64]
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4.2.2
-        with:
-          submodules: true
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: ${{ matrix.python }}
-          architecture: ${{ matrix.arch }}
-      - name: Install GSL via vcpkg
-        run: |
-          vcpkg install gsl:${{ matrix.arch }}-windows
-        shell: cmd
-      - name: Install deps
-        run: |
-          pip install --upgrade pip build delvewheel
-      - name: Fix windows symlinks
-        run: |
-          if (Test-Path "lwt_interface") { Remove-Item -Recurse -Force "lwt_interface" }
-          Copy-Item -Recurse "git-submodules/tskit/python/lwt_interface" "./lwt_interface"
-        shell: powershell
-      - name: Build Wheel
-        run: |
-          # The symlink fix above confuses setuptools_scm
-          $tag = git describe --tags --exact-match HEAD 2>$null
-          if ($tag) {
-            $env:SETUPTOOLS_SCM_PRETEND_VERSION_FOR_MSPRIME = $tag
-          }
-          python -m build --wheel
-      - name: Bundle dynamic libs
-        run: |
-          $vcpkgRoot = $env:VCPKG_INSTALLATION_ROOT
-          if (-not $vcpkgRoot) { $vcpkgRoot = "C:\vcpkg" }
-          $gslBinPath = Join-Path $vcpkgRoot "installed\x64-windows\bin"
-          $env:PATH = "$gslBinPath;$env:PATH"
-          delvewheel repair dist/*.whl -w dist/ --add-path "$gslBinPath"
-        shell: powershell
-      - name: Upload Wheels
-        uses: actions/upload-artifact@v4.6.1
-        with:
-          name: win-wheel-${{ matrix.python }}
-          path: dist
-
-  manylinux:
-    runs-on: ubuntu-24.04
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4.2.2
-        with:
-            submodules: true
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: "3.10"
-      - name: Build sdist
-        shell: bash
-        run: |
-          pip install --upgrade pip build
-          python -m build --sdist
-      - name: Upload sdist
-        uses: actions/upload-artifact@v4.6.1
-        with:
-          name: sdist
-          path: dist
-      - name: Build wheels in docker
-        shell: bash
-        run: |
-          docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2014_x86_64 bash .github/workflows/docker/buildwheel.sh
-
-      - name: Upload Wheels
-        uses: actions/upload-artifact@v4.6.1
-        with:
-          name: linux-wheels
-          path: dist/wheelhouse
-
-  OSX-test:
-    name: Test ${{ matrix.os }} - ${{ matrix.python }}
-    needs: ['OSX']
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [macos-13, macos-14, macos-15]
-        python: ["3.10", 3.11, 3.12, 3.13]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.2.0
-        with:
-          name: osx-wheel-${{ matrix.os }}-${{ matrix.python }} 
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          # Install the local wheel
-          pip install numpy newick>=1.3.0 tskit>=0.5.2 demes>=0.2
-          pip install msprime --no-index --only-binary msprime -f .
-          python -c "import msprime"
-          msp simulate 10 tmp.trees
-          tskit info tmp.trees
-          tskit provenances tmp.trees
-
-  manylinux-test:
-    runs-on: ubuntu-24.04
-    needs: ['manylinux']
-    strategy:
-      matrix:
-        python: ["3.10", 3.11, 3.12, 3.13]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.2.0
-        with:
-          name: linux-wheels
-      - name: Set up Python
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          # Install the local wheel
-          pip install numpy newick demes
-          pip install --no-dependencies msprime --no-index --only-binary msprime -f .
-          pip install tskit
-          python -c "import msprime"
-          msp simulate 10 tmp.trees
-          tskit info tmp.trees
-          tskit provenances tmp.trees
-
-
-  Windows-test:
-    runs-on: windows-latest
-    needs: ['Windows']
-    strategy:
-      matrix:
-        python: ["3.10", 3.11, 3.12, 3.13]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.2.0
-        with:
-          name: win-wheel-${{ matrix.python }}
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          pip install numpy newick>=1.3.0 tskit>=0.5.2 demes>=0.2
-          pip install msprime --no-index --only-binary msprime -f .
-          python -c "import msprime"
-          msp simulate 10 tmp.trees
-          tskit info tmp.trees
-          tskit provenances tmp.trees
-
-  PyPI_Upload:
-    runs-on: ubuntu-24.04
-    environment: release
-    needs: ['OSX-test', 'manylinux-test', 'Windows-test']
-    permissions:
-      id-token: write
-    steps:
-      - name: Download all
-        uses: actions/download-artifact@v4.2.0
-      - name: Move to dist
-        run: |
-          mkdir dist
-          cp */*.{whl,gz} dist/.
-          # Windows wheels have different naming pattern
-          if [ -d "win-wheel"* ]; then cp win-wheel*/*.whl dist/. || true; fi
-      - name: Publish distribution to Test PyPI
-        if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@v1.12.4
-        with:
-          repository_url: https://test.pypi.org/legacy/
-      - name: Publish distribution to PRODUCTION PyPI
-        if: github.event_name == 'release'
-        uses: pypa/gh-action-pypi-publish@v1.12.4